From b5871fa07605da01186c86783c0b56748961108b Mon Sep 17 00:00:00 2001 From: Marty Pradere Date: Fri, 10 Jul 2026 14:23:52 -0600 Subject: [PATCH 1/3] Create nbri_ehr module as a renamed copy of nirc_ehr MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Seeds the new nbriEHRModules repository from the nircEHRModules module tree, with every occurrence of nirc replaced by nbri (casing-matched: NIRC→NBRI, Nirc→Nbri, nirc→nbri) in file contents, file names, and directory names. Also carries over the nircEHRModules versions of the GitHub workflow files (adding permissions blocks) and .gitignore (ignoring referenceStudy ETL logs). --- .github/workflows/branch_release.yml | 6 +- .github/workflows/merge_release.yml | 6 +- .github/workflows/validate_pr.yml | 5 +- .gitignore | 6 +- build.gradle | 27 + gradle.properties | 1 + nbri_ehr/build.gradle | 32 + nbri_ehr/module.properties | 2 + .../resources/data/abdominal_obs_types.tsv | 8 + .../data/abnormal_behavior_types.tsv | 7 + nbri_ehr/resources/data/acquisition_type.tsv | 6 + nbri_ehr/resources/data/activity.tsv | 7 + nbri_ehr/resources/data/ageclass.tsv | 79 + nbri_ehr/resources/data/alias_category.tsv | 5 + nbri_ehr/resources/data/alopecia_regrowth.tsv | 4 + nbri_ehr/resources/data/alopecia_score.tsv | 6 + nbri_ehr/resources/data/alopecia_type.tsv | 10 + nbri_ehr/resources/data/amount_units.tsv | 14 + nbri_ehr/resources/data/app_score.tsv | 6 + nbri_ehr/resources/data/arrival_type.tsv | 3 + nbri_ehr/resources/data/att_score.tsv | 6 + .../resources/data/bandage_observations.tsv | 4 + nbri_ehr/resources/data/bcs_score.tsv | 10 + .../resources/data/behavior_abnormality.tsv | 7 + .../resources/data/behavior_mgmt_codes.tsv | 4 + nbri_ehr/resources/data/behavior_types.tsv | 6 + nbri_ehr/resources/data/blood_draw_reason.tsv | 3 + .../resources/data/blood_draw_tube_type.tsv | 5 + nbri_ehr/resources/data/blood_sample_type.tsv | 3 + .../resources/data/blood_tube_volumes.tsv | 8 + nbri_ehr/resources/data/cage_type.tsv | 8 + .../data/calculated_status_codes.tsv | 7 + .../resources/data/capillary_refill_time.tsv | 3 + nbri_ehr/resources/data/card_format.tsv | 4 + .../resources/data/census_activity_status.tsv | 4 + nbri_ehr/resources/data/conc_units.tsv | 18 + nbri_ehr/resources/data/cost_type.tsv | 3 + nbri_ehr/resources/data/country.tsv | 9 + nbri_ehr/resources/data/country_category.tsv | 3 + .../resources/data/daily_enrich_codes.tsv | 13 + nbri_ehr/resources/data/data_category.tsv | 5 + nbri_ehr/resources/data/death_reason.tsv | 6 + nbri_ehr/resources/data/delivery_state.tsv | 5 + nbri_ehr/resources/data/dental_obs.tsv | 7 + nbri_ehr/resources/data/derm_obs.tsv | 6 + nbri_ehr/resources/data/divider_types.tsv | 6 + nbri_ehr/resources/data/dosage_units.tsv | 14 + nbri_ehr/resources/data/editable_lookups.tsv | 140 ++ nbri_ehr/resources/data/esig_events.tsv | 16 + nbri_ehr/resources/data/euthanasia_type.tsv | 5 + nbri_ehr/resources/data/exam_findings.tsv | 3 + .../resources/data/exemption_category.tsv | 9 + nbri_ehr/resources/data/expense_class.tsv | 32 + nbri_ehr/resources/data/fecal_smear_score.tsv | 6 + nbri_ehr/resources/data/feed_assess_types.tsv | 4 + nbri_ehr/resources/data/gender_codes.tsv | 4 + nbri_ehr/resources/data/general_obs.tsv | 7 + nbri_ehr/resources/data/genitourinary_obs.tsv | 7 + .../resources/data/geographic_origins.tsv | 32 + nbri_ehr/resources/data/hernia_types.tsv | 5 + nbri_ehr/resources/data/housing_reason.tsv | 25 + nbri_ehr/resources/data/hyd_score.tsv | 7 + nbri_ehr/resources/data/id_history_type.tsv | 6 + nbri_ehr/resources/data/incision_score.tsv | 8 + nbri_ehr/resources/data/indoor_outdoor.tsv | 4 + nbri_ehr/resources/data/lameness.tsv | 5 + nbri_ehr/resources/data/lookup_sets.tsv | 118 ++ nbri_ehr/resources/data/lookupsManifest.tsv | 131 ++ .../resources/data/lookupsManifestTest.tsv | 133 ++ nbri_ehr/resources/data/mens_score.tsv | 4 + nbri_ehr/resources/data/mucous_membranes.tsv | 7 + .../data/musculoskeletal_observations.tsv | 8 + .../data/necropsy_disposition_codes.tsv | 7 + .../resources/data/necropsy_exam_reason.tsv | 4 + .../data/necropsy_organ_appearance.tsv | 3 + .../resources/data/necropsy_organ_systems.tsv | 10 + .../data/necropsy_physical_condition.tsv | 4 + .../data/necropsy_specimen_condition.tsv | 4 + nbri_ehr/resources/data/necropsy_tissue.tsv | 17 + .../data/neurologic_observations.tsv | 8 + .../resources/data/nhp_training_reason.tsv | 6 + .../resources/data/nhp_training_result.tsv | 4 + nbri_ehr/resources/data/nhp_training_type.tsv | 5 + nbri_ehr/resources/data/normal_abnormal.tsv | 4 + .../resources/data/normal_abnormal_only.tsv | 3 + nbri_ehr/resources/data/numeric_unit.tsv | 91 + nbri_ehr/resources/data/observation_areas.tsv | 34 + nbri_ehr/resources/data/observation_types.tsv | 55 + .../resources/data/obstetric_observations.tsv | 9 + .../resources/data/ocular_observations.tsv | 8 + .../data/pairing_formation_types.tsv | 7 + nbri_ehr/resources/data/pairing_goal.tsv | 5 + .../resources/data/pairing_observation.tsv | 4 + nbri_ehr/resources/data/pairing_reason.tsv | 9 + .../data/pairing_separation_reason.tsv | 8 + nbri_ehr/resources/data/preferences.tsv | 4 + nbri_ehr/resources/data/pregnancy_result.tsv | 3 + .../resources/data/problem_list_category.tsv | 14 + .../data/problem_list_subcategory.tsv | 75 + .../resources/data/procedure_category.tsv | 5 + nbri_ehr/resources/data/procedures.tsv | 130 ++ nbri_ehr/resources/data/protocol_category.tsv | 3 + nbri_ehr/resources/data/protocol_state.tsv | 7 + nbri_ehr/resources/data/protocol_type.tsv | 6 + nbri_ehr/resources/data/qualifier.tsv | 54 + nbri_ehr/resources/data/questionnaire.tsv | 4 + nbri_ehr/resources/data/rectal_prolapse.tsv | 3 + .../data/regulatory_stress_levels.tsv | 6 + nbri_ehr/resources/data/req_order_state.tsv | 6 + nbri_ehr/resources/data/req_order_type.tsv | 5 + .../data/respiratory_observations.tsv | 9 + nbri_ehr/resources/data/routes.tsv | 17 + nbri_ehr/resources/data/sib_score.tsv | 8 + nbri_ehr/resources/data/snomed.tsv | 357 ++++ nbri_ehr/resources/data/source.tsv | 108 ++ nbri_ehr/resources/data/species.tsv | 7 + nbri_ehr/resources/data/species_codes.tsv | 7 + nbri_ehr/resources/data/stool_score.tsv | 7 + nbri_ehr/resources/data/stool_types.tsv | 10 + nbri_ehr/resources/data/temperament.tsv | 5 + nbri_ehr/resources/data/testicular_volume.tsv | 13 + .../resources/data/treatment_frequency.tsv | 12 + .../data/treatment_frequency_times.tsv | 18 + .../data/vaginal_uterine_prolapse.tsv | 3 + .../resources/data/vendor_approval_code.tsv | 4 + .../data/vendor_production_location.tsv | 47 + nbri_ehr/resources/data/volume_units.tsv | 16 + nbri_ehr/resources/data/weight_ranges.tsv | 3 + nbri_ehr/resources/data/wound_severity.tsv | 6 + .../resources/data/wound_status_behavior.tsv | 5 + .../resources/data/wound_status_clinical.tsv | 11 + nbri_ehr/resources/data/yes_no_only.tsv | 3 + nbri_ehr/resources/data/yes_no_order.tsv | 4 + .../domain-templates/ehr.template.xml | 125 ++ .../domain-templates/ehr_lookups.template.xml | 52 + .../resources/etls/ProjectAndAssignment.xml | 31 + .../resources/etls/ProtocolAndAssignment.xml | 50 + nbri_ehr/resources/etls/account.xml | 17 + nbri_ehr/resources/etls/animalDelivery.xml | 32 + nbri_ehr/resources/etls/animalReqOrder.xml | 36 + nbri_ehr/resources/etls/animalShipment.xml | 21 + nbri_ehr/resources/etls/animalVendor.xml | 17 + nbri_ehr/resources/etls/arrival.xml | 30 + nbri_ehr/resources/etls/biopsy.xml | 30 + nbri_ehr/resources/etls/birth.xml | 29 + nbri_ehr/resources/etls/blood.xml | 30 + nbri_ehr/resources/etls/breeder.xml | 30 + nbri_ehr/resources/etls/cageCard.xml | 33 + nbri_ehr/resources/etls/cases.xml | 28 + nbri_ehr/resources/etls/chemistryResults.xml | 30 + nbri_ehr/resources/etls/clinremarks.xml | 30 + nbri_ehr/resources/etls/deaths.xml | 26 + nbri_ehr/resources/etls/deletedRecord.xml | 21 + nbri_ehr/resources/etls/demographics.xml | 28 + nbri_ehr/resources/etls/department.xml | 21 + nbri_ehr/resources/etls/departure.xml | 26 + nbri_ehr/resources/etls/drug.xml | 30 + nbri_ehr/resources/etls/ehrRecords.xml | 45 + nbri_ehr/resources/etls/ehr_lookups.xml | 48 + nbri_ehr/resources/etls/exemptions.xml | 30 + nbri_ehr/resources/etls/flags.xml | 30 + nbri_ehr/resources/etls/foster.xml | 30 + nbri_ehr/resources/etls/histopathology.xml | 25 + nbri_ehr/resources/etls/historicalOther.xml | 25 + nbri_ehr/resources/etls/housing.xml | 26 + nbri_ehr/resources/etls/idHistory.xml | 17 + nbri_ehr/resources/etls/locations.xml | 42 + nbri_ehr/resources/etls/lotNumber.xml | 18 + nbri_ehr/resources/etls/necropsy.xml | 30 + nbri_ehr/resources/etls/notes.xml | 26 + nbri_ehr/resources/etls/obs.xml | 44 + nbri_ehr/resources/etls/pairings.xml | 30 + nbri_ehr/resources/etls/physicalExam.xml | 30 + nbri_ehr/resources/etls/prc.xml | 30 + nbri_ehr/resources/etls/pregnancy.xml | 30 + nbri_ehr/resources/etls/procedure.xml | 21 + nbri_ehr/resources/etls/protocolCounts.xml | 17 + .../resources/etls/protocolSupplement.xml | 35 + nbri_ehr/resources/etls/protocolUsage.xml | 17 + nbri_ehr/resources/etls/questionResponse.xml | 21 + nbri_ehr/resources/etls/serology.xml | 30 + nbri_ehr/resources/etls/shipTo.xml | 18 + nbri_ehr/resources/etls/staff.xml | 18 + nbri_ehr/resources/etls/stress.xml | 18 + nbri_ehr/resources/etls/vitals.xml | 30 + nbri_ehr/resources/etls/weight.xml | 30 + .../folderTypes/NBRI_EHR.folderType.xml | 70 + nbri_ehr/resources/module.xml | 17 + .../queries/dbo/auditDeleteEvent.sql | 23 + nbri_ehr/resources/queries/dbo/q_account.sql | 17 + nbri_ehr/resources/queries/dbo/q_alopecia.sql | 25 + .../queries/dbo/q_alopecia_delete.sql | 12 + .../queries/dbo/q_animal_delivery.sql | 31 + .../queries/dbo/q_animal_delivery_esig.sql | 13 + .../queries/dbo/q_animal_req_order.sql | 46 + .../queries/dbo/q_animal_req_order_esig.sql | 13 + .../queries/dbo/q_animal_shipment.sql | 33 + .../resources/queries/dbo/q_animal_vendor.sql | 23 + nbri_ehr/resources/queries/dbo/q_areas.sql | 9 + nbri_ehr/resources/queries/dbo/q_arrival.sql | 25 + .../queries/dbo/q_arrival_delete.sql | 12 + .../resources/queries/dbo/q_assignment.sql | 41 + .../queries/dbo/q_assignment_delete.sql | 11 + nbri_ehr/resources/queries/dbo/q_biopsy.sql | 48 + .../resources/queries/dbo/q_biopsy_delete.sql | 13 + nbri_ehr/resources/queries/dbo/q_births.sql | 26 + .../resources/queries/dbo/q_births_delete.sql | 11 + nbri_ehr/resources/queries/dbo/q_blood.sql | 28 + .../resources/queries/dbo/q_blood_delete.sql | 13 + nbri_ehr/resources/queries/dbo/q_breeder.sql | 28 + .../queries/dbo/q_breeder_delete.sql | 14 + .../resources/queries/dbo/q_buildings.sql | 12 + .../resources/queries/dbo/q_cage_card.sql | 38 + .../queries/dbo/q_cage_card_history.sql | 47 + nbri_ehr/resources/queries/dbo/q_cages.sql | 18 + nbri_ehr/resources/queries/dbo/q_cases.sql | 36 + .../resources/queries/dbo/q_cases_delete.sql | 29 + .../queries/dbo/q_chemistryResults.sql | 23 + .../queries/dbo/q_chemistryResults_delete.sql | 11 + .../resources/queries/dbo/q_clinremarks.sql | 27 + .../queries/dbo/q_clinremarks_delete.sql | 31 + nbri_ehr/resources/queries/dbo/q_deaths.sql | 26 + .../resources/queries/dbo/q_deaths_delete.sql | 11 + .../queries/dbo/q_deleted_record.sql | 17 + .../resources/queries/dbo/q_demographics.sql | 64 + .../queries/dbo/q_demographics_delete.sql | 11 + .../resources/queries/dbo/q_department.sql | 13 + .../resources/queries/dbo/q_departure.sql | 229 +++ .../queries/dbo/q_departure_delete.sql | 12 + nbri_ehr/resources/queries/dbo/q_drug.sql | 48 + .../resources/queries/dbo/q_drug_delete.sql | 28 + .../resources/queries/dbo/q_exemptions.sql | 24 + .../queries/dbo/q_exemptions_delete.sql | 13 + .../queries/dbo/q_finalDeparture.sql | 15 + .../queries/dbo/q_flag_categories.sql | 15 + .../resources/queries/dbo/q_flag_values.sql | 18 + nbri_ehr/resources/queries/dbo/q_flags.sql | 51 + .../resources/queries/dbo/q_flags_delete.sql | 14 + nbri_ehr/resources/queries/dbo/q_floors.sql | 14 + nbri_ehr/resources/queries/dbo/q_foster.sql | 22 + .../resources/queries/dbo/q_foster_delete.sql | 12 + .../queries/dbo/q_histopathology.sql | 26 + .../queries/dbo/q_historicalOther.sql | 19 + nbri_ehr/resources/queries/dbo/q_housing.sql | 24 + .../queries/dbo/q_housing_delete.sql | 12 + .../resources/queries/dbo/q_idHistory.sql | 12 + .../resources/queries/dbo/q_latestArrival.sql | 11 + .../queries/dbo/q_latestDeparture.sql | 11 + nbri_ehr/resources/queries/dbo/q_lookups.sql | 75 + .../resources/queries/dbo/q_lot_number.sql | 11 + .../queries/dbo/q_modified_event.sql | 15 + nbri_ehr/resources/queries/dbo/q_necropsy.sql | 26 + .../queries/dbo/q_necropsy_delete.sql | 15 + nbri_ehr/resources/queries/dbo/q_notes.sql | 29 + .../resources/queries/dbo/q_notes_delete.sql | 18 + .../resources/queries/dbo/q_observations.sql | 30 + .../queries/dbo/q_observations_delete.sql | 24 + nbri_ehr/resources/queries/dbo/q_pairings.sql | 23 + .../queries/dbo/q_pairings_delete.sql | 29 + .../resources/queries/dbo/q_physicalExam.sql | 42 + .../queries/dbo/q_physicalExam_delete.sql | 33 + nbri_ehr/resources/queries/dbo/q_prc.sql | 54 + .../resources/queries/dbo/q_prc_delete.sql | 78 + .../resources/queries/dbo/q_pregnancy.sql | 29 + .../queries/dbo/q_pregnancy_delete.sql | 13 + .../resources/queries/dbo/q_procedures.sql | 11 + nbri_ehr/resources/queries/dbo/q_project.sql | 20 + nbri_ehr/resources/queries/dbo/q_protocol.sql | 61 + .../queries/dbo/q_protocolAssignment.sql | 52 + .../queries/dbo/q_protocol_amendments.sql | 21 + .../queries/dbo/q_protocol_counts.sql | 33 + .../resources/queries/dbo/q_protocol_esig.sql | 13 + .../queries/dbo/q_protocol_procedures.sql | 10 + .../queries/dbo/q_protocol_stress.sql | 12 + .../queries/dbo/q_protocol_usage.sql | 25 + nbri_ehr/resources/queries/dbo/q_question.sql | 11 + .../queries/dbo/q_question_response.sql | 14 + nbri_ehr/resources/queries/dbo/q_rooms.sql | 16 + nbri_ehr/resources/queries/dbo/q_serology.sql | 22 + .../queries/dbo/q_serology_delete.sql | 83 + nbri_ehr/resources/queries/dbo/q_ship_to.sql | 16 + nbri_ehr/resources/queries/dbo/q_species.sql | 12 + .../resources/queries/dbo/q_species_codes.sql | 16 + nbri_ehr/resources/queries/dbo/q_staff.sql | 50 + nbri_ehr/resources/queries/dbo/q_status.sql | 14 + nbri_ehr/resources/queries/dbo/q_stress.sql | 13 + nbri_ehr/resources/queries/dbo/q_vitals.sql | 42 + .../resources/queries/dbo/q_vitals_delete.sql | 18 + nbri_ehr/resources/queries/dbo/q_weight.sql | 22 + .../resources/queries/dbo/q_weight_delete.sql | 11 + nbri_ehr/resources/queries/dbo/staffInfo.sql | 17 + .../resources/queries/ehr/activeProtocols.sql | 7 + .../resources/queries/ehr/my_tasks.query.xml | 65 + nbri_ehr/resources/queries/ehr/my_tasks.sql | 28 + .../resources/queries/ehr/my_tasks/.qview.xml | 15 + .../ehr/my_tasks/Active Tasks.qview.xml | 18 + .../ehr/my_tasks/Review Required.qview.xml | 18 + .../queries/ehr/observation_types.query.xml | 17 + nbri_ehr/resources/queries/ehr/project.js | 32 + .../resources/queries/ehr/project.query.xml | 75 + .../resources/queries/ehr/project/.qview.xml | 8 + nbri_ehr/resources/queries/ehr/protocol.js | 37 + .../resources/queries/ehr/protocol.query.xml | 91 + .../resources/queries/ehr/protocol/.qview.xml | 41 + .../ehr/protocolActiveAnimals.query.xml | 29 + .../queries/ehr/protocolActiveAnimals.sql | 21 + .../queries/ehr/protocolAnimals.query.xml | 43 + .../resources/queries/ehr/protocolAnimals.sql | 22 + .../queries/ehr/protocolHistoricAnimals.sql | 26 + .../protocolTotalAnimalsBySpecies.query.xml | 36 + .../ehr/protocolTotalAnimalsBySpecies.sql | 18 + .../queries/ehr/protocol_counts.query.xml | 30 + .../queries/ehr/protocol_counts/.qview.xml | 9 + .../resources/queries/ehr/tasks/.qview.xml | 19 + .../queries/ehr/tasks/Active Tasks.qview.xml | 8 + .../ehr/tasks/Review Required.qview.xml | 22 + .../queries/ehr_lookups/ageclass.query.xml | 45 + .../queries/ehr_lookups/areas/.qview.xml | 7 + .../queries/ehr_lookups/buildings.js | 53 + .../queries/ehr_lookups/buildings.query.xml | 31 + .../queries/ehr_lookups/buildings/.qview.xml | 6 + .../resources/queries/ehr_lookups/cage.js | 50 + .../queries/ehr_lookups/cage.query.xml | 29 + .../queries/ehr_lookups/cage/.qview.xml | 12 + .../queries/ehr_lookups/country.query.xml | 20 + .../resources/queries/ehr_lookups/floors.js | 53 + .../queries/ehr_lookups/floors.query.xml | 28 + .../queries/ehr_lookups/floors/.qview.xml | 6 + .../queries/ehr_lookups/procedures/.qview.xml | 7 + .../ehr_lookups/roomUtilization.query.xml | 22 + .../queries/ehr_lookups/roomUtilization.sql | 16 + .../roomUtilizationByBuilding.query.xml | 81 + .../ehr_lookups/roomUtilizationByBuilding.sql | 30 + .../resources/queries/ehr_lookups/rooms.js | 54 + .../queries/ehr_lookups/rooms.query.xml | 24 + .../queries/ehr_lookups/rooms/.qview.xml | 6 + .../queries/ehr_lookups/snomed.query.xml | 9 + .../ehr_lookups/species_codes.query.xml | 19 + .../vendor_production_location.query.xml | 19 + .../queries/nbri_ehr/Account.query.xml | 48 + .../queries/nbri_ehr/AnimalDelivery.query.xml | 86 + .../nbri_ehr/AnimalDeliveryEsig.query.xml | 36 + .../queries/nbri_ehr/AnimalReqOrder.query.xml | 135 ++ .../nbri_ehr/AnimalReqOrderEsig.query.xml | 36 + .../queries/nbri_ehr/AnimalShipment.query.xml | 42 + .../queries/nbri_ehr/AnimalVendor.query.xml | 29 + .../queries/nbri_ehr/AnimalVendor/.qview.xml | 20 + .../queries/nbri_ehr/CageCard.query.xml | 56 + .../nbri_ehr/CageCardHistory.query.xml | 65 + .../queries/nbri_ehr/DeletedRecord.query.xml | 24 + .../queries/nbri_ehr/Department.query.xml | 25 + .../queries/nbri_ehr/IdHistory.query.xml | 29 + .../resources/queries/nbri_ehr/Lot.query.xml | 20 + .../queries/nbri_ehr/ProtocolEsig.query.xml | 31 + .../nbri_ehr/ProtocolProcedures.query.xml | 21 + .../queries/nbri_ehr/ProtocolStress.query.xml | 21 + .../queries/nbri_ehr/QuestionResponse.js | 35 + .../nbri_ehr/QuestionResponse.query.xml | 38 + .../queries/nbri_ehr/casesSource.sql | 19 + .../resources/queries/nbri_ehr/casesTemp.js | 42 + .../resources/queries/nbri_ehr/dateRange.sql | 25 + .../queries/nbri_ehr/locationTypes/.qview.xml | 5 + .../queries/nbri_ehr/locations.query.xml | 19 + .../queries/nbri_ehr/locations/.qview.xml | 6 + .../nbri_ehr/locationsMapping.query.xml | 28 + .../nbri_ehr/locationsMapping/.qview.xml | 7 + .../queries/nbri_ehr/necropsyTasks.query.xml | 28 + .../queries/nbri_ehr/necropsyTasks.sql | 26 + .../queries/nbri_ehr/necropsyTasks/.qview.xml | 28 + .../queries/nbri_ehr/staff.query.xml | 128 ++ .../queries/nbri_ehr/stress.query.xml | 20 + .../queries/study/AcquisitionReport.sql | 14 + .../study/AcquisitionReportBySpecies.sql | 18 + .../queries/study/BehaviorClinRemarks.sql | 7 + .../study/BehaviorClinRemarks/.qview.xml | 16 + .../queries/study/ClinicalClinRemarks.sql | 7 + .../study/ClinicalClinRemarks/.qview.xml | 20 + .../study/CurrentProtocolProjectReport.sql | 17 + nbri_ehr/resources/queries/study/MHC.js | 7 + .../resources/queries/study/MHC.query.xml | 14 + nbri_ehr/resources/queries/study/Pedigree.sql | 31 + nbri_ehr/resources/queries/study/Weight.js | 91 + .../queries/study/activeAssignments.sql | 22 + .../queries/study/activeBehaviorCases.sql | 7 + .../study/activeBehaviorCases/.qview.xml | 28 + .../activeBehaviorCases/Area 11.qview.xml | 31 + .../activeBehaviorCases/Area 51.qview.xml | 31 + .../activeBehaviorCases/Building 10.qview.xml | 31 + .../Building 10C.qview.xml | 31 + .../activeBehaviorCases/Building 27.qview.xml | 31 + .../activeBehaviorCases/Building 28.qview.xml | 31 + .../activeBehaviorCases/Building 29.qview.xml | 31 + .../activeBehaviorCases/Building 30.qview.xml | 31 + .../activeBehaviorCases/Building 31.qview.xml | 31 + .../Building 31C.qview.xml | 31 + .../Building 31D.qview.xml | 31 + .../activeBehaviorCases/Building 32.qview.xml | 31 + .../activeBehaviorCases/Building 34.qview.xml | 31 + .../activeBehaviorCases/Building 37.qview.xml | 31 + .../activeBehaviorCases/Building 41.qview.xml | 31 + .../activeBehaviorCases/Building 42.qview.xml | 31 + .../activeBehaviorCases/Building 43.qview.xml | 31 + .../activeBehaviorCases/Building 44.qview.xml | 31 + .../activeBehaviorCases/Building 45.qview.xml | 31 + .../activeBehaviorCases/Building 46.qview.xml | 31 + .../activeBehaviorCases/Building 50.qview.xml | 31 + .../activeBehaviorCases/Building 52.qview.xml | 31 + .../activeBehaviorCases/Building 53.qview.xml | 31 + .../Building 54A.qview.xml | 31 + .../Building 54B.qview.xml | 31 + .../queries/study/activeClinicalCases.sql | 7 + .../study/activeClinicalCases/.qview.xml | 28 + .../activeClinicalCases/Area 11.qview.xml | 31 + .../activeClinicalCases/Area 51.qview.xml | 31 + .../activeClinicalCases/Building 10.qview.xml | 31 + .../Building 10C.qview.xml | 31 + .../activeClinicalCases/Building 27.qview.xml | 31 + .../activeClinicalCases/Building 28.qview.xml | 31 + .../activeClinicalCases/Building 29.qview.xml | 31 + .../activeClinicalCases/Building 30.qview.xml | 31 + .../activeClinicalCases/Building 31.qview.xml | 31 + .../Building 31C.qview.xml | 31 + .../Building 31D.qview.xml | 31 + .../activeClinicalCases/Building 32.qview.xml | 31 + .../activeClinicalCases/Building 34.qview.xml | 31 + .../activeClinicalCases/Building 37.qview.xml | 31 + .../activeClinicalCases/Building 41.qview.xml | 31 + .../activeClinicalCases/Building 42.qview.xml | 31 + .../activeClinicalCases/Building 43.qview.xml | 31 + .../activeClinicalCases/Building 44.qview.xml | 31 + .../activeClinicalCases/Building 45.qview.xml | 31 + .../activeClinicalCases/Building 46.qview.xml | 31 + .../activeClinicalCases/Building 50.qview.xml | 31 + .../activeClinicalCases/Building 52.qview.xml | 31 + .../activeClinicalCases/Building 53.qview.xml | 31 + .../Building 54A.qview.xml | 31 + .../Building 54B.qview.xml | 31 + .../study/activeProjectsFromHousing.sql | 10 + .../queries/study/activeTreatmentOrders.sql | 25 + nbri_ehr/resources/queries/study/alias.js | 6 + .../resources/queries/study/alias.query.xml | 29 + nbri_ehr/resources/queries/study/aliases.sql | 19 + .../queries/study/alopecia/.qview.xml | 18 + nbri_ehr/resources/queries/study/arrival.js | 176 ++ .../resources/queries/study/arrival.query.xml | 79 + .../queries/study/arrival/.qview.xml | 18 + .../resources/queries/study/assignment.js | 91 + .../queries/study/assignment.query.xml | 28 + .../resources/queries/study/behaviorCases.sql | 7 + .../queries/study/behaviorCases/.qview.xml | 28 + .../study/behaviorCases/Area 11.qview.xml | 31 + .../study/behaviorCases/Area 51.qview.xml | 31 + .../study/behaviorCases/Building 10.qview.xml | 31 + .../behaviorCases/Building 10C.qview.xml | 31 + .../study/behaviorCases/Building 27.qview.xml | 31 + .../study/behaviorCases/Building 28.qview.xml | 31 + .../study/behaviorCases/Building 29.qview.xml | 31 + .../study/behaviorCases/Building 30.qview.xml | 31 + .../study/behaviorCases/Building 31.qview.xml | 31 + .../behaviorCases/Building 31C.qview.xml | 31 + .../behaviorCases/Building 31D.qview.xml | 31 + .../study/behaviorCases/Building 32.qview.xml | 31 + .../study/behaviorCases/Building 34.qview.xml | 31 + .../study/behaviorCases/Building 37.qview.xml | 31 + .../study/behaviorCases/Building 41.qview.xml | 31 + .../study/behaviorCases/Building 42.qview.xml | 31 + .../study/behaviorCases/Building 43.qview.xml | 31 + .../study/behaviorCases/Building 44.qview.xml | 31 + .../study/behaviorCases/Building 45.qview.xml | 31 + .../study/behaviorCases/Building 46.qview.xml | 31 + .../study/behaviorCases/Building 50.qview.xml | 31 + .../study/behaviorCases/Building 52.qview.xml | 31 + .../study/behaviorCases/Building 53.qview.xml | 31 + .../behaviorCases/Building 54A.qview.xml | 31 + .../behaviorCases/Building 54B.qview.xml | 31 + .../queries/study/behaviorObservations.sql | 7 + .../study/behaviorObservations/.qview.xml | 18 + .../behaviorObservations/Area 11.qview.xml | 21 + .../behaviorObservations/Area 51.qview.xml | 21 + .../Building 10.qview.xml | 21 + .../Building 10C.qview.xml | 21 + .../Building 27.qview.xml | 21 + .../Building 28.qview.xml | 21 + .../Building 29.qview.xml | 21 + .../Building 30.qview.xml | 21 + .../Building 31.qview.xml | 21 + .../Building 31C.qview.xml | 21 + .../Building 31D.qview.xml | 21 + .../Building 32.qview.xml | 21 + .../Building 34.qview.xml | 21 + .../Building 37.qview.xml | 21 + .../Building 41.qview.xml | 21 + .../Building 42.qview.xml | 21 + .../Building 43.qview.xml | 21 + .../Building 44.qview.xml | 21 + .../Building 45.qview.xml | 21 + .../Building 46.qview.xml | 21 + .../Building 50.qview.xml | 21 + .../Building 52.qview.xml | 21 + .../Building 53.qview.xml | 21 + .../Building 54A.qview.xml | 21 + .../Building 54B.qview.xml | 21 + nbri_ehr/resources/queries/study/birth.js | 169 ++ .../resources/queries/study/birth.query.xml | 52 + .../resources/queries/study/blood/.qview.xml | 19 + .../queries/study/bloodDrawChanges.sql | 66 + .../queries/study/breeder/.qview.xml | 15 + nbri_ehr/resources/queries/study/cases.js | 71 + .../resources/queries/study/cases.query.xml | 71 + .../resources/queries/study/cases/.qview.xml | 28 + .../cases/Active Behavior Cases.qview.xml | 29 + .../cases/Active Clinical Cases.qview.xml | 32 + .../study/cases/All Behavior Cases.qview.xml | 28 + .../study/cases/All Clinical Cases.qview.xml | 31 + .../queries/study/chemistryResults.query.xml | 22 + .../queries/study/chemistryResults/.qview.xml | 18 + .../resources/queries/study/clinicalCases.sql | 7 + .../queries/study/clinicalCases/.qview.xml | 28 + .../study/clinicalCases/Area 11.qview.xml | 31 + .../study/clinicalCases/Area 51.qview.xml | 31 + .../study/clinicalCases/Building 10.qview.xml | 31 + .../clinicalCases/Building 10C.qview.xml | 31 + .../study/clinicalCases/Building 27.qview.xml | 31 + .../study/clinicalCases/Building 28.qview.xml | 31 + .../study/clinicalCases/Building 29.qview.xml | 31 + .../study/clinicalCases/Building 30.qview.xml | 31 + .../study/clinicalCases/Building 31.qview.xml | 31 + .../clinicalCases/Building 31C.qview.xml | 31 + .../clinicalCases/Building 31D.qview.xml | 31 + .../study/clinicalCases/Building 32.qview.xml | 31 + .../study/clinicalCases/Building 34.qview.xml | 31 + .../study/clinicalCases/Building 37.qview.xml | 31 + .../study/clinicalCases/Building 41.qview.xml | 31 + .../study/clinicalCases/Building 42.qview.xml | 31 + .../study/clinicalCases/Building 43.qview.xml | 31 + .../study/clinicalCases/Building 44.qview.xml | 31 + .../study/clinicalCases/Building 45.qview.xml | 31 + .../study/clinicalCases/Building 46.qview.xml | 31 + .../study/clinicalCases/Building 50.qview.xml | 31 + .../study/clinicalCases/Building 52.qview.xml | 31 + .../study/clinicalCases/Building 53.qview.xml | 31 + .../clinicalCases/Building 54A.qview.xml | 31 + .../clinicalCases/Building 54B.qview.xml | 31 + .../queries/study/clinicalObservations.sql | 7 + .../study/clinicalObservations/.qview.xml | 17 + .../clinicalObservations/Area 11.qview.xml | 20 + .../clinicalObservations/Area 51.qview.xml | 20 + .../Building 10.qview.xml | 20 + .../Building 10C.qview.xml | 20 + .../Building 27.qview.xml | 20 + .../Building 28.qview.xml | 20 + .../Building 29.qview.xml | 20 + .../Building 30.qview.xml | 20 + .../Building 31.qview.xml | 20 + .../Building 31C.qview.xml | 20 + .../Building 31D.qview.xml | 20 + .../Building 32.qview.xml | 20 + .../Building 34.qview.xml | 20 + .../Building 37.qview.xml | 20 + .../Building 41.qview.xml | 20 + .../Building 42.qview.xml | 20 + .../Building 43.qview.xml | 20 + .../Building 44.qview.xml | 20 + .../Building 45.qview.xml | 20 + .../Building 46.qview.xml | 20 + .../Building 50.qview.xml | 20 + .../Building 52.qview.xml | 20 + .../Building 53.qview.xml | 20 + .../Building 54A.qview.xml | 20 + .../Building 54B.qview.xml | 20 + .../queries/study/clinical_observations.js | 77 + .../study/clinical_observations.query.xml | 58 + .../study/clinical_observations/.qview.xml | 19 + .../Alopecia Scores.qview.xml | 21 + .../clinical_observations/Behavior.qview.xml | 21 + .../clinical_observations/Clinical.qview.xml | 21 + .../study/clinical_observationsSummary.sql | 29 + .../clinical_observationsSummary/.qview.xml | 18 + .../Area 11.qview.xml | 21 + .../Area 51.qview.xml | 21 + .../Building 10.qview.xml | 21 + .../Building 10C.qview.xml | 21 + .../Building 27.qview.xml | 21 + .../Building 28.qview.xml | 21 + .../Building 29.qview.xml | 21 + .../Building 30.qview.xml | 21 + .../Building 31.qview.xml | 21 + .../Building 31C.qview.xml | 21 + .../Building 31D.qview.xml | 21 + .../Building 32.qview.xml | 21 + .../Building 34.qview.xml | 21 + .../Building 37.qview.xml | 21 + .../Building 41.qview.xml | 21 + .../Building 42.qview.xml | 21 + .../Building 43.qview.xml | 21 + .../Building 44.qview.xml | 21 + .../Building 45.qview.xml | 21 + .../Building 46.qview.xml | 21 + .../Building 50.qview.xml | 21 + .../Building 52.qview.xml | 21 + .../Building 53.qview.xml | 21 + .../Building 54A.qview.xml | 21 + .../Building 54B.qview.xml | 21 + .../resources/queries/study/clinremarks.js | 31 + .../queries/study/clinremarks.query.xml | 63 + .../queries/study/clinremarks/.qview.xml | 21 + .../study/clinremarks/Behavior.qview.xml | 19 + .../study/clinremarks/Clinical.qview.xml | 24 + .../colonyPopulationByAgeClass.query.xml | 30 + .../queries/study/colonyPopulationChange.sql | 59 + .../study/colonyPopulationSummary.query.xml | 28 + .../queries/study/currentBloodDraws.sql | 84 + .../queries/study/currentproject.sql | 11 + .../queries/study/deathNotification.sql | 13 + nbri_ehr/resources/queries/study/deaths.js | 180 ++ .../resources/queries/study/deaths.query.xml | 34 + .../resources/queries/study/deaths/.qview.xml | 14 + .../resources/queries/study/demographics.js | 80 + .../queries/study/demographics.query.xml | 112 ++ .../queries/study/demographics/.qview.xml | 23 + .../queries/study/demographicsActiveFlags.sql | 24 + .../demographicsActiveProjectAssignment.sql | 10 + ...graphicsActiveProtocolAssignment.query.xml | 29 + .../demographicsActiveProtocolAssignment.sql | 18 + .../study/demographicsAliases.query.xml | 9 + .../queries/study/demographicsAliases.sql | 11 + .../study/demographicsCagemates.query.xml | 24 + .../queries/study/demographicsCagemates.sql | 33 + .../study/demographicsCurLocation.query.xml | 35 + .../queries/study/demographicsCurLocation.sql | 37 + .../study/demographicsLastProject.query.xml | 13 + .../queries/study/demographicsLastProject.sql | 15 + .../study/demographicsLastProtocol.query.xml | 13 + .../study/demographicsLastProtocol.sql | 15 + .../study/demographicsOffspring.query.xml | 20 + .../queries/study/demographicsOffspring.sql | 21 + .../study/demographicsParents.query.xml | 31 + .../queries/study/demographicsParents.sql | 30 + .../study/demographicsSiblings.query.xml | 44 + .../queries/study/demographicsSiblings.sql | 36 + .../study/demographicsSource.query.xml | 17 + .../queries/study/demographicsSource.sql | 35 + .../demographicsTotalOffspring.query.xml | 34 + .../study/demographicsTotalOffspring.sql | 42 + nbri_ehr/resources/queries/study/departure.js | 31 + .../queries/study/departure.query.xml | 23 + .../queries/study/departure/.qview.xml | 14 + nbri_ehr/resources/queries/study/drug.js | 28 + .../resources/queries/study/drug.query.xml | 111 ++ .../resources/queries/study/drug/.qview.xml | 26 + .../queries/study/drug/Behavior.qview.xml | 28 + .../resources/queries/study/exemptions.js | 6 + .../queries/study/exemptions.query.xml | 29 + .../queries/study/exemptions/.qview.xml | 14 + nbri_ehr/resources/queries/study/flags.js | 6 + .../resources/queries/study/flags.query.xml | 46 + .../resources/queries/study/flags/.qview.xml | 19 + .../resources/queries/study/grossPathology.js | 6 + .../queries/study/grossPathology.query.xml | 41 + .../queries/study/grossPathology/.qview.xml | 12 + .../queries/study/histopathology.query.xml | 16 + .../queries/study/historicalOther.query.xml | 13 + nbri_ehr/resources/queries/study/housing.js | 166 ++ .../resources/queries/study/housing.query.xml | 52 + .../queries/study/housing/.qview.xml | 15 + .../study/housing/Active Housing.qview.xml | 24 + nbri_ehr/resources/queries/study/necropsy.js | 59 + .../queries/study/necropsy.query.xml | 43 + .../queries/study/necropsy/.qview.xml | 18 + .../queries/study/necropsyStatus.sql | 10 + .../resources/queries/study/nhpTraining.js | 6 + .../queries/study/nhpTraining.query.xml | 46 + nbri_ehr/resources/queries/study/notes.js | 6 + .../resources/queries/study/notes.query.xml | 34 + .../resources/queries/study/notes/.qview.xml | 16 + .../study/notificationAnimalProject.sql | 13 + .../queries/study/observationOrdersByDate.sql | 59 + .../study/observationSchedule.query.xml | 20 + .../queries/study/observationSchedule.sql | 49 + .../study/observationSchedule/.qview.xml | 17 + .../observationSchedule/Area 11.qview.xml | 20 + .../observationSchedule/Area 51.qview.xml | 20 + .../observationSchedule/Building 10.qview.xml | 20 + .../Building 10C.qview.xml | 20 + .../observationSchedule/Building 27.qview.xml | 20 + .../observationSchedule/Building 28.qview.xml | 20 + .../observationSchedule/Building 29.qview.xml | 20 + .../observationSchedule/Building 30.qview.xml | 20 + .../observationSchedule/Building 31.qview.xml | 20 + .../Building 31C.qview.xml | 20 + .../Building 31D.qview.xml | 20 + .../observationSchedule/Building 32.qview.xml | 20 + .../observationSchedule/Building 34.qview.xml | 20 + .../observationSchedule/Building 37.qview.xml | 20 + .../observationSchedule/Building 41.qview.xml | 20 + .../observationSchedule/Building 42.qview.xml | 20 + .../observationSchedule/Building 43.qview.xml | 20 + .../observationSchedule/Building 44.qview.xml | 20 + .../observationSchedule/Building 45.qview.xml | 20 + .../observationSchedule/Building 46.qview.xml | 20 + .../observationSchedule/Building 50.qview.xml | 20 + .../observationSchedule/Building 52.qview.xml | 20 + .../observationSchedule/Building 53.qview.xml | 20 + .../Building 54A.qview.xml | 20 + .../Building 54B.qview.xml | 20 + .../queries/study/observation_order.js | 6 + .../queries/study/observation_order.query.xml | 45 + .../study/observation_order/.qview.xml | 20 + .../Active Behavior Orders.qview.xml | 24 + .../Active Clinical Orders.qview.xml | 24 + .../Behavior Orders.qview.xml | 23 + .../Clinical Orders.qview.xml | 23 + .../resources/queries/study/orchardData.sql | 18 + .../queries/study/orchardIdsForTaskid.sql | 17 + .../queries/study/pairingSummary.query.xml | 24 + .../queries/study/pairingSummary.sql | 25 + .../queries/study/pairingSummary/.qview.xml | 27 + .../pairingSummary/Active Pairing.qview.xml | 29 + .../pairingSummary/Pairing History.qview.xml | 25 + nbri_ehr/resources/queries/study/pairings.js | 15 + .../queries/study/pairings.query.xml | 90 + .../queries/study/pairings/.qview.xml | 25 + .../queries/study/parentageSummary.query.xml | 25 + .../queries/study/parentageSummary.sql | 36 + .../queries/study/physicalExam/.qview.xml | 16 + nbri_ehr/resources/queries/study/prc.js | 32 + .../resources/queries/study/prc.query.xml | 73 + .../resources/queries/study/prc/.qview.xml | 14 + .../queries/study/prcOverdue.query.xml | 154 ++ .../resources/queries/study/prcOverdue.sql | 20 + .../queries/study/prcOverdue/.qview.xml | 26 + .../queries/study/prcOverdueNotification.sql | 18 + .../study/prcOverdueNotification/.qview.xml | 5 + .../queries/study/prcSchedule.query.xml | 154 ++ .../resources/queries/study/prcSchedule.sql | 20 + .../queries/study/prcSchedule/.qview.xml | 23 + .../study/prcSchedule/Area 11.qview.xml | 22 + .../study/prcSchedule/Area 51.qview.xml | 22 + .../study/prcSchedule/Building 10.qview.xml | 22 + .../study/prcSchedule/Building 10C.qview.xml | 22 + .../study/prcSchedule/Building 27.qview.xml | 22 + .../study/prcSchedule/Building 28.qview.xml | 22 + .../study/prcSchedule/Building 29.qview.xml | 22 + .../study/prcSchedule/Building 30.qview.xml | 22 + .../study/prcSchedule/Building 31.qview.xml | 22 + .../study/prcSchedule/Building 31C.qview.xml | 22 + .../study/prcSchedule/Building 31D.qview.xml | 22 + .../study/prcSchedule/Building 32.qview.xml | 22 + .../study/prcSchedule/Building 34.qview.xml | 22 + .../study/prcSchedule/Building 37.qview.xml | 22 + .../study/prcSchedule/Building 41.qview.xml | 22 + .../study/prcSchedule/Building 42.qview.xml | 22 + .../study/prcSchedule/Building 43.qview.xml | 22 + .../study/prcSchedule/Building 44.qview.xml | 22 + .../study/prcSchedule/Building 45.qview.xml | 22 + .../study/prcSchedule/Building 46.qview.xml | 22 + .../study/prcSchedule/Building 50.qview.xml | 22 + .../study/prcSchedule/Building 52.qview.xml | 22 + .../study/prcSchedule/Building 53.qview.xml | 22 + .../study/prcSchedule/Building 54A.qview.xml | 22 + .../study/prcSchedule/Building 54B.qview.xml | 22 + nbri_ehr/resources/queries/study/prc_order.js | 14 + .../queries/study/prc_order.query.xml | 84 + .../queries/study/prc_order/.qview.xml | 17 + .../queries/study/prc_order_report.query.xml | 84 + .../queries/study/prc_order_report.sql | 6 + .../queries/study/prc_order_report/.qview.xml | 17 + nbri_ehr/resources/queries/study/pregnancy.js | 20 + .../queries/study/pregnancy.query.xml | 28 + .../queries/study/protocolAssignment.js | 153 ++ .../study/protocolAssignment.query.xml | 30 + .../Active Assignments.qview.xml | 8 + .../resources/queries/study/recentCases.sql | 11 + .../queries/study/serology.query.xml | 25 + .../queries/study/serology/.qview.xml | 11 + .../queries/study/tissueDisposition.js | 6 + .../queries/study/tissueDisposition.query.xml | 40 + .../study/tissueDisposition/.qview.xml | 12 + .../queries/study/treatmentSchedule.query.xml | 187 ++ .../queries/study/treatmentSchedule.sql | 79 + .../study/treatmentSchedule/.qview.xml | 28 + .../study/treatmentSchedule/Area 11.qview.xml | 30 + .../study/treatmentSchedule/Area 51.qview.xml | 30 + .../treatmentSchedule/Building 10.qview.xml | 30 + .../treatmentSchedule/Building 10C.qview.xml | 30 + .../treatmentSchedule/Building 27.qview.xml | 30 + .../treatmentSchedule/Building 28.qview.xml | 30 + .../treatmentSchedule/Building 29.qview.xml | 30 + .../treatmentSchedule/Building 30.qview.xml | 30 + .../treatmentSchedule/Building 31.qview.xml | 30 + .../treatmentSchedule/Building 31C.qview.xml | 30 + .../treatmentSchedule/Building 31D.qview.xml | 30 + .../treatmentSchedule/Building 32.qview.xml | 30 + .../treatmentSchedule/Building 34.qview.xml | 30 + .../treatmentSchedule/Building 37.qview.xml | 30 + .../treatmentSchedule/Building 41.qview.xml | 30 + .../treatmentSchedule/Building 42.qview.xml | 30 + .../treatmentSchedule/Building 43.qview.xml | 30 + .../treatmentSchedule/Building 44.qview.xml | 30 + .../treatmentSchedule/Building 45.qview.xml | 30 + .../treatmentSchedule/Building 46.qview.xml | 30 + .../treatmentSchedule/Building 50.qview.xml | 30 + .../treatmentSchedule/Building 52.qview.xml | 30 + .../treatmentSchedule/Building 53.qview.xml | 30 + .../treatmentSchedule/Building 54A.qview.xml | 30 + .../treatmentSchedule/Building 54B.qview.xml | 30 + .../Clinical Medications.qview.xml | 8 + .../queries/study/treatment_order.js | 23 + .../queries/study/treatment_order.query.xml | 170 ++ .../queries/study/treatment_order/.qview.xml | 31 + ...Behavior Active Treatment Orders.qview.xml | 6 + ...Clinical Active Treatment Orders.qview.xml | 6 + nbri_ehr/resources/queries/study/vitals.js | 7 + .../resources/queries/study/vitals.query.xml | 33 + .../resources/queries/study/vitals/.qview.xml | 19 + .../resources/queries/study/weight.query.xml | 36 + .../resources/queries/study/weight/.qview.xml | 14 + .../.labkey/protocols/kinship/default.xml | 3 + nbri_ehr/resources/referenceStudy/folder.xml | 4 + .../PrimateElectronicHealthRecord.dataset | 19 + .../study/datasets/datasets_manifest.xml | 44 + .../study/datasets/datasets_metadata.xml | 1514 +++++++++++++++ .../resources/referenceStudy/study/study.xml | 7 + .../resources/reports/additionalReports.tsv | 52 + .../postgresql/nbri_ehr-0.000-25.000.sql | 611 ++++++ .../postgresql/nbri_ehr-25.000-25.001.sql | 6 + nbri_ehr/resources/schemas/nbri_ehr.xml | 588 ++++++ nbri_ehr/resources/scripts/nbri_triggers.js | 150 ++ .../views/NBRI_amimalHistory.webpart.xml | 3 + .../resources/views/acquisitionReport.html | 217 +++ .../views/acquisitionReport.view.xml | 6 + nbri_ehr/resources/views/animalHistory.html | 107 ++ .../resources/views/animalHistory.view.xml | 13 + nbri_ehr/resources/views/begin.html | 251 +++ nbri_ehr/resources/views/begin.view.xml | 5 + nbri_ehr/resources/views/begin.webpart.xml | 7 + nbri_ehr/resources/views/cageDetails.html | 83 + nbri_ehr/resources/views/cageDetails.view.xml | 5 + .../views/clinicalHistoryExport.html | 87 + .../views/clinicalHistoryExport.view.xml | 5 + nbri_ehr/resources/views/datasets.html | 130 ++ nbri_ehr/resources/views/datasets.view.xml | 5 + nbri_ehr/resources/views/enterData.html | 43 + nbri_ehr/resources/views/enterData.view.xml | 9 + nbri_ehr/resources/views/nbri_login.html | 48 + nbri_ehr/resources/views/nbri_login.view.xml | 6 + nbri_ehr/resources/views/necropsy.html | 99 + nbri_ehr/resources/views/necropsy.view.xml | 3 + nbri_ehr/resources/views/participantView.html | 31 + .../resources/views/participantView.view.xml | 15 + .../resources/web/ehr/metadata/Default.js | 21 + .../buttons/ProcedureOrderCompleteButton.js | 112 ++ .../nbri_ehr/buttons/RecordProcedureButton.js | 149 ++ .../nbri_ehr/buttons/RecordTreatmentButton.js | 165 ++ .../web/nbri_ehr/buttons/SelectCaseButton.js | 95 + .../nbri_ehr/buttons/addClinicalObsButton.js | 85 + .../nbri_ehr/buttons/clinicalObsGridButton.js | 59 + .../nbri_ehr/buttons/deathNecropsyButtons.js | 144 ++ .../nbri_ehr/buttons/necropsyGridButtons.js | 37 + .../web/nbri_ehr/buttons/saveDraftButton.js | 20 + .../web/nbri_ehr/buttons/treatmentSubmit.js | 273 +++ .../data/AssignmentsAnyIdClientStore.js | 16 + .../nbri_ehr/data/AssignmentsClientStore.js | 60 + .../web/nbri_ehr/data/CaseClientStore.js | 47 + .../web/nbri_ehr/data/CaseStoreCollection.js | 240 +++ .../data/ClinicalObservationClientStore.js | 24 + .../DrugAdministrationRunsChildClientStore.js | 33 + .../data/DrugAdministrationRunsClientStore.js | 59 + .../nbri_ehr/data/ObsOrderChildClientStore.js | 33 + .../web/nbri_ehr/data/ObsOrdersClientStore.js | 45 + .../web/nbri_ehr/field/AnimalIdCases.js | 71 + .../web/nbri_ehr/field/DrugVolumeField.js | 61 + .../resources/web/nbri_ehr/field/EditCase.js | 115 ++ .../web/nbri_ehr/field/LocationField.js | 42 + .../nbri_ehr/images/ull-logo-main-subsite.png | Bin 0 -> 7359 bytes .../web/nbri_ehr/model/sources/Alias.js | 26 + .../web/nbri_ehr/model/sources/Arrival.js | 113 ++ .../web/nbri_ehr/model/sources/Assignment.js | 49 + .../model/sources/BehaviorDefaults.js | 107 ++ .../nbri_ehr/model/sources/BehaviorRounds.js | 131 ++ .../nbri_ehr/model/sources/BehavioralCase.js | 110 ++ .../web/nbri_ehr/model/sources/Birth.js | 77 + .../nbri_ehr/model/sources/BulkBehavior.js | 75 + .../nbri_ehr/model/sources/BulkClinical.js | 47 + .../nbri_ehr/model/sources/ClinicalCase.js | 158 ++ .../model/sources/ClinicalDefaults.js | 213 +++ .../nbri_ehr/model/sources/ClinicalRounds.js | 131 ++ .../nbri_ehr/model/sources/DeathNecropsy.js | 163 ++ .../model/sources/MedicationEndDate.js | 53 + .../web/nbri_ehr/model/sources/NBRIDefault.js | 353 ++++ .../web/nbri_ehr/model/sources/ObsDefaults.js | 25 + .../web/nbri_ehr/model/sources/ParentChild.js | 25 + .../web/nbri_ehr/model/sources/Pregnancy.js | 31 + .../web/nbri_ehr/model/sources/Rearrival.js | 62 + .../model/sources/TreatmentSchedule.js | 72 + nbri_ehr/resources/web/nbri_ehr/nbri.css | 7 + .../resources/web/nbri_ehr/nbriOverrides.js | 16 + .../resources/web/nbri_ehr/nbriReports.js | 287 +++ .../web/nbri_ehr/nbri_ehr_api.lib.xml | 9 + .../web/nbri_ehr/panel/AnimalDetailsPanel.js | 248 +++ .../panel/ArrivalInstructionsPanel.js | 22 + .../nbri_ehr/panel/BirthInstructionsPanel.js | 21 + .../web/nbri_ehr/panel/BloodSummaryPanel.js | 79 + .../web/nbri_ehr/panel/CaseHistoryPanel.js | 24 + .../web/nbri_ehr/panel/CaseTemplatePanel.js | 58 + .../nbri_ehr/panel/ClinicalHistoryPanel.js | 149 ++ .../web/nbri_ehr/panel/InstructionsPanel.js | 28 + .../panel/NBRIExamCasesDataEntryPanel.js | 44 + .../web/nbri_ehr/panel/NarrowSnapshotPanel.js | 42 + .../web/nbri_ehr/panel/SelectCasePanel.js | 188 ++ .../web/nbri_ehr/panel/SnapshotPanel.js | 394 ++++ .../web/nbri_ehr/plugin/RowEditor.js | 66 + nbri_ehr/resources/web/nbri_ehr/utils.js | 74 + .../web/nbri_ehr/window/AddAnimalsWindow.js | 112 ++ .../nbri_ehr/window/CopyFromSectionWindow.js | 181 ++ .../web/nbri_ehr/window/DrugAmountWindow.js | 326 ++++ .../web/nbri_ehr/window/FormBulkAddWindow.js | 24 + .../window/MarkTreatmentCompletedWindow.js | 188 ++ .../nbri_ehr/window/NBRICaseHistoryWindow.js | 53 + .../window/NBRIClinicalHistoryWindow.js | 74 + .../nbri_ehr/window/NBRIRecentCasesWindow.js | 108 ++ .../window/NBRIRecentRemarksWindow.js | 122 ++ .../web/nbri_ehr/window/SelectCaseWindow.js | 45 + .../nbri_ehr/NBRIOrchardFileGenerator.java | 204 +++ .../labkey/nbri_ehr/NBRI_EHRController.java | 30 + .../org/labkey/nbri_ehr/NBRI_EHRManager.java | 35 + .../org/labkey/nbri_ehr/NBRI_EHRModule.java | 266 +++ .../org/labkey/nbri_ehr/NBRI_EHRSchema.java | 46 + .../buttons/MarkTreatmentCompletedButton.java | 56 + .../NBRIUserCreateTransform.java | 205 +++ .../dataentry/form/NBRIAliasFormType.java | 49 + .../form/NBRIAnimalTrainingFormType.java | 39 + .../dataentry/form/NBRIArrivalFormType.java | 54 + .../form/NBRIAssignmentFormType.java | 50 + .../dataentry/form/NBRIBaseTaskFormType.java | 56 + .../form/NBRIBehaviorRoundsFormType.java | 119 ++ .../form/NBRIBehavioralCasesFormType.java | 123 ++ .../dataentry/form/NBRIBirthFormType.java | 75 + .../dataentry/form/NBRIBuildingFormType.java | 48 + .../form/NBRIBulkBehaviorFormType.java | 81 + .../form/NBRIBulkClinicalFormType.java | 93 + .../dataentry/form/NBRICageFormType.java | 48 + .../dataentry/form/NBRICasesFormType.java | 150 ++ .../form/NBRIChemistryImportFormType.java | 47 + .../NBRIClinicalObservationsFormType.java | 81 + .../form/NBRIClinicalRoundsFormType.java | 127 ++ .../form/NBRIDeathNecropsyFormType.java | 104 ++ .../dataentry/form/NBRIDepartureFormType.java | 39 + .../form/NBRIExemptionsFormType.java | 41 + .../dataentry/form/NBRIFlagsFormType.java | 41 + .../dataentry/form/NBRIFloorFormType.java | 48 + .../dataentry/form/NBRIHousingFormType.java | 48 + .../form/NBRIMedicationTreatmentFormType.java | 70 + .../dataentry/form/NBRINotesFormType.java | 41 + .../dataentry/form/NBRIPairingsFormType.java | 49 + .../dataentry/form/NBRIPregnancyFormType.java | 48 + .../dataentry/form/NBRIProjectFormType.java | 48 + .../dataentry/form/NBRIProtocolFormType.java | 48 + .../dataentry/form/NBRIRearrivalFormType.java | 58 + .../dataentry/form/NBRIRoomFormType.java | 48 + .../form/NBRISerologyImportFormType.java | 47 + .../dataentry/form/NBRIWeightFormType.java | 39 + .../dataentry/section/BaseFormSection.java | 139 ++ .../section/NBRIAliasFormSection.java | 24 + .../section/NBRIAnimalDetailsFormSection.java | 31 + .../section/NBRIArrivalFormSection.java | 54 + .../NBRIArrivalInstructionsFormSection.java | 41 + .../section/NBRIBirthFormSection.java | 82 + .../NBRIBirthInstructionsFormSection.java | 41 + .../section/NBRIBloodDrawFormSection.java | 95 + .../section/NBRICaseTemplateFormSection.java | 42 + .../section/NBRICasesFormPanelSection.java | 83 + .../NBRIClinicalObservationsFormSection.java | 71 + .../NBRIClinicalRemarksFormPanelSection.java | 89 + .../NBRIClinicalRemarksFormSection.java | 62 + .../section/NBRIDeathFormSection.java | 39 + .../section/NBRIDepartureFormSection.java | 24 + .../section/NBRIExemptionsFormSection.java | 24 + .../section/NBRIFlagsFormSection.java | 24 + .../NBRIGrossPathologyFormSection.java | 56 + .../section/NBRIHousingFormSection.java | 40 + .../section/NBRINecropsyFormSection.java | 51 + .../section/NBRINotesFormSection.java | 24 + .../NBRIObservationOrdersFormSection.java | 70 + .../section/NBRIPregnancyFormSection.java | 24 + .../section/NBRIProcedureFormSection.java | 42 + .../NBRIProcedureOrderFormSection.java | 56 + .../NBRIProjectAssignmentFormSection.java | 37 + .../NBRIProtocolAssignmentFormSection.java | 37 + .../section/NBRIRearrivalFormSection.java | 35 + .../section/NBRITaskFormSection.java | 33 + .../NBRITissueDispositionFormSection.java | 56 + .../NBRITreatmentGivenFormSection.java | 59 + .../NBRITreatmentOrderFormSection.java | 59 + .../section/NBRIVitalsFormSection.java | 42 + .../section/NBRIWeightFormSection.java | 40 + ...ActiveAssignmentsDemographicsProvider.java | 72 + .../ActiveCasesDemographicsProvider.java | 82 + .../ActiveFlagsDemographicsProvider.java | 79 + .../ActiveTreatmentsDemographicsProvider.java | 86 + .../CagematesDemographicsProvider.java | 105 ++ .../HousingDemographicsProvider.java | 58 + .../NecropsyStatusDemographicsProvider.java | 71 + ...rotocolAssignmentDemographicsProvider.java | 70 + .../nbri_ehr/history/ArrivalDataSource.java | 51 + .../nbri_ehr/history/BiopsyDataSource.java | 72 + .../nbri_ehr/history/BirthDataSource.java | 46 + .../nbri_ehr/history/BloodDrawDataSource.java | 51 + .../nbri_ehr/history/BreederDataSource.java | 42 + .../nbri_ehr/history/DeathDataSource.java | 61 + .../nbri_ehr/history/DepartureDataSource.java | 53 + .../nbri_ehr/history/DrugAdminDataSource.java | 82 + .../history/ExemptionsDataSource.java | 66 + .../nbri_ehr/history/FlagsDataSource.java | 66 + .../nbri_ehr/history/FosteringDataSource.java | 49 + .../history/HistopathologyDataSource.java | 49 + .../NBRIBehaviorObservationsDataSource.java | 27 + .../history/NBRICaseCloseDataSource.java | 74 + .../history/NBRICaseOpenDataSource.java | 74 + .../NBRIClinicalObservationsDataSource.java | 26 + .../NBRIClinicalRemarksDataSource.java | 96 + .../NBRIEndTreatmentOrderDataSource.java | 90 + .../history/NBRIHousingDataSource.java | 66 + .../NBRIObservationOrdersDataSource.java | 185 ++ .../history/NBRIObservationsDataSource.java | 198 ++ .../NBRIProcedureOrdersDataSource.java | 72 + .../history/NBRIVitalsDataSource.java | 87 + .../nbri_ehr/history/PairingsDataSource.java | 60 + .../history/PhysicalExamDataSource.java | 69 + .../nbri_ehr/history/PregnancyDataSource.java | 66 + .../history/ProceduresDataSource.java | 68 + .../history/ProjectAssignmentDataSource.java | 30 + .../nbri_ehr/history/ProtocolDataSource.java | 68 + .../nbri_ehr/history/SerologyDataSource.java | 67 + .../NBRIClinicalMoveNotification.java | 67 + .../notification/NBRIDeathNotification.java | 66 + .../NBRIPregnancyOutcomeNotification.java | 66 + .../NBRIProcedureOverdueNotification.java | 275 +++ .../notification/NotificationHelper.java | 75 + .../TriggerScriptNotification.java | 83 + .../nbri_ehr/query/NBRI_EHRTriggerHelper.java | 1159 ++++++++++++ .../nbri_ehr/query/NBRI_EHRUserSchema.java | 43 + .../security/NBRIEHRVetTechPermission.java | 26 + .../nbri_ehr/security/NBRIEHRVetTechRole.java | 36 + .../nbri_ehr/table/NBRI_EHRCustomizer.java | 1441 +++++++++++++++ .../table/NBRI_EHRSharedDatasetTrigger.java | 66 + .../table/NBRI_EHRTriggerScriptFactory.java | 36 + .../test/sampledata/nbriEHRStudyPolicy.xml | 188 ++ .../test/sampledata/nbri_ehr/study/folder.xml | 4 + .../PrimateElectronicHealthRecord.dataset | 19 + .../study/study/datasets/datasetArrival.tsv | 6 + .../study/datasets/datasetAssignment.tsv | 9 + .../study/study/datasets/datasetBirth.tsv | 9 + .../study/study/datasets/datasetBirth.tsv~ | 9 + .../study/study/datasets/datasetDeaths.tsv | 3 + .../study/datasets/datasetDemographics.tsv | 14 + .../study/study/datasets/datasetDeparture.tsv | 5 + .../study/study/datasets/datasetFlags.tsv | 11 + .../study/study/datasets/datasetHousing.tsv | 9 + .../datasets/datasetProtocolAssignment.tsv | 9 + .../study/study/datasets/datasetWeight.tsv | 811 ++++++++ .../sampledata/nbri_ehr/study/study/study.xml | 6 + .../tests.nbri_ehr/NBRI_EHRTest.java | 1630 +++++++++++++++++ 1063 files changed, 47314 insertions(+), 4 deletions(-) create mode 100644 build.gradle create mode 100644 gradle.properties create mode 100644 nbri_ehr/build.gradle create mode 100644 nbri_ehr/module.properties create mode 100644 nbri_ehr/resources/data/abdominal_obs_types.tsv create mode 100644 nbri_ehr/resources/data/abnormal_behavior_types.tsv create mode 100644 nbri_ehr/resources/data/acquisition_type.tsv create mode 100644 nbri_ehr/resources/data/activity.tsv create mode 100644 nbri_ehr/resources/data/ageclass.tsv create mode 100644 nbri_ehr/resources/data/alias_category.tsv create mode 100644 nbri_ehr/resources/data/alopecia_regrowth.tsv create mode 100644 nbri_ehr/resources/data/alopecia_score.tsv create mode 100644 nbri_ehr/resources/data/alopecia_type.tsv create mode 100644 nbri_ehr/resources/data/amount_units.tsv create mode 100644 nbri_ehr/resources/data/app_score.tsv create mode 100644 nbri_ehr/resources/data/arrival_type.tsv create mode 100644 nbri_ehr/resources/data/att_score.tsv create mode 100644 nbri_ehr/resources/data/bandage_observations.tsv create mode 100644 nbri_ehr/resources/data/bcs_score.tsv create mode 100644 nbri_ehr/resources/data/behavior_abnormality.tsv create mode 100644 nbri_ehr/resources/data/behavior_mgmt_codes.tsv create mode 100644 nbri_ehr/resources/data/behavior_types.tsv create mode 100644 nbri_ehr/resources/data/blood_draw_reason.tsv create mode 100644 nbri_ehr/resources/data/blood_draw_tube_type.tsv create mode 100644 nbri_ehr/resources/data/blood_sample_type.tsv create mode 100644 nbri_ehr/resources/data/blood_tube_volumes.tsv create mode 100644 nbri_ehr/resources/data/cage_type.tsv create mode 100644 nbri_ehr/resources/data/calculated_status_codes.tsv create mode 100644 nbri_ehr/resources/data/capillary_refill_time.tsv create mode 100644 nbri_ehr/resources/data/card_format.tsv create mode 100644 nbri_ehr/resources/data/census_activity_status.tsv create mode 100644 nbri_ehr/resources/data/conc_units.tsv create mode 100644 nbri_ehr/resources/data/cost_type.tsv create mode 100644 nbri_ehr/resources/data/country.tsv create mode 100644 nbri_ehr/resources/data/country_category.tsv create mode 100644 nbri_ehr/resources/data/daily_enrich_codes.tsv create mode 100644 nbri_ehr/resources/data/data_category.tsv create mode 100644 nbri_ehr/resources/data/death_reason.tsv create mode 100644 nbri_ehr/resources/data/delivery_state.tsv create mode 100644 nbri_ehr/resources/data/dental_obs.tsv create mode 100644 nbri_ehr/resources/data/derm_obs.tsv create mode 100644 nbri_ehr/resources/data/divider_types.tsv create mode 100644 nbri_ehr/resources/data/dosage_units.tsv create mode 100644 nbri_ehr/resources/data/editable_lookups.tsv create mode 100644 nbri_ehr/resources/data/esig_events.tsv create mode 100644 nbri_ehr/resources/data/euthanasia_type.tsv create mode 100644 nbri_ehr/resources/data/exam_findings.tsv create mode 100644 nbri_ehr/resources/data/exemption_category.tsv create mode 100644 nbri_ehr/resources/data/expense_class.tsv create mode 100644 nbri_ehr/resources/data/fecal_smear_score.tsv create mode 100644 nbri_ehr/resources/data/feed_assess_types.tsv create mode 100644 nbri_ehr/resources/data/gender_codes.tsv create mode 100644 nbri_ehr/resources/data/general_obs.tsv create mode 100644 nbri_ehr/resources/data/genitourinary_obs.tsv create mode 100644 nbri_ehr/resources/data/geographic_origins.tsv create mode 100644 nbri_ehr/resources/data/hernia_types.tsv create mode 100644 nbri_ehr/resources/data/housing_reason.tsv create mode 100644 nbri_ehr/resources/data/hyd_score.tsv create mode 100644 nbri_ehr/resources/data/id_history_type.tsv create mode 100644 nbri_ehr/resources/data/incision_score.tsv create mode 100644 nbri_ehr/resources/data/indoor_outdoor.tsv create mode 100644 nbri_ehr/resources/data/lameness.tsv create mode 100644 nbri_ehr/resources/data/lookup_sets.tsv create mode 100644 nbri_ehr/resources/data/lookupsManifest.tsv create mode 100644 nbri_ehr/resources/data/lookupsManifestTest.tsv create mode 100644 nbri_ehr/resources/data/mens_score.tsv create mode 100644 nbri_ehr/resources/data/mucous_membranes.tsv create mode 100644 nbri_ehr/resources/data/musculoskeletal_observations.tsv create mode 100644 nbri_ehr/resources/data/necropsy_disposition_codes.tsv create mode 100644 nbri_ehr/resources/data/necropsy_exam_reason.tsv create mode 100644 nbri_ehr/resources/data/necropsy_organ_appearance.tsv create mode 100644 nbri_ehr/resources/data/necropsy_organ_systems.tsv create mode 100644 nbri_ehr/resources/data/necropsy_physical_condition.tsv create mode 100644 nbri_ehr/resources/data/necropsy_specimen_condition.tsv create mode 100644 nbri_ehr/resources/data/necropsy_tissue.tsv create mode 100644 nbri_ehr/resources/data/neurologic_observations.tsv create mode 100644 nbri_ehr/resources/data/nhp_training_reason.tsv create mode 100644 nbri_ehr/resources/data/nhp_training_result.tsv create mode 100644 nbri_ehr/resources/data/nhp_training_type.tsv create mode 100644 nbri_ehr/resources/data/normal_abnormal.tsv create mode 100644 nbri_ehr/resources/data/normal_abnormal_only.tsv create mode 100644 nbri_ehr/resources/data/numeric_unit.tsv create mode 100644 nbri_ehr/resources/data/observation_areas.tsv create mode 100644 nbri_ehr/resources/data/observation_types.tsv create mode 100644 nbri_ehr/resources/data/obstetric_observations.tsv create mode 100644 nbri_ehr/resources/data/ocular_observations.tsv create mode 100644 nbri_ehr/resources/data/pairing_formation_types.tsv create mode 100644 nbri_ehr/resources/data/pairing_goal.tsv create mode 100644 nbri_ehr/resources/data/pairing_observation.tsv create mode 100644 nbri_ehr/resources/data/pairing_reason.tsv create mode 100644 nbri_ehr/resources/data/pairing_separation_reason.tsv create mode 100644 nbri_ehr/resources/data/preferences.tsv create mode 100644 nbri_ehr/resources/data/pregnancy_result.tsv create mode 100644 nbri_ehr/resources/data/problem_list_category.tsv create mode 100644 nbri_ehr/resources/data/problem_list_subcategory.tsv create mode 100644 nbri_ehr/resources/data/procedure_category.tsv create mode 100644 nbri_ehr/resources/data/procedures.tsv create mode 100644 nbri_ehr/resources/data/protocol_category.tsv create mode 100644 nbri_ehr/resources/data/protocol_state.tsv create mode 100644 nbri_ehr/resources/data/protocol_type.tsv create mode 100644 nbri_ehr/resources/data/qualifier.tsv create mode 100644 nbri_ehr/resources/data/questionnaire.tsv create mode 100644 nbri_ehr/resources/data/rectal_prolapse.tsv create mode 100644 nbri_ehr/resources/data/regulatory_stress_levels.tsv create mode 100644 nbri_ehr/resources/data/req_order_state.tsv create mode 100644 nbri_ehr/resources/data/req_order_type.tsv create mode 100644 nbri_ehr/resources/data/respiratory_observations.tsv create mode 100644 nbri_ehr/resources/data/routes.tsv create mode 100644 nbri_ehr/resources/data/sib_score.tsv create mode 100644 nbri_ehr/resources/data/snomed.tsv create mode 100644 nbri_ehr/resources/data/source.tsv create mode 100644 nbri_ehr/resources/data/species.tsv create mode 100644 nbri_ehr/resources/data/species_codes.tsv create mode 100644 nbri_ehr/resources/data/stool_score.tsv create mode 100644 nbri_ehr/resources/data/stool_types.tsv create mode 100644 nbri_ehr/resources/data/temperament.tsv create mode 100644 nbri_ehr/resources/data/testicular_volume.tsv create mode 100644 nbri_ehr/resources/data/treatment_frequency.tsv create mode 100644 nbri_ehr/resources/data/treatment_frequency_times.tsv create mode 100644 nbri_ehr/resources/data/vaginal_uterine_prolapse.tsv create mode 100644 nbri_ehr/resources/data/vendor_approval_code.tsv create mode 100644 nbri_ehr/resources/data/vendor_production_location.tsv create mode 100644 nbri_ehr/resources/data/volume_units.tsv create mode 100644 nbri_ehr/resources/data/weight_ranges.tsv create mode 100644 nbri_ehr/resources/data/wound_severity.tsv create mode 100644 nbri_ehr/resources/data/wound_status_behavior.tsv create mode 100644 nbri_ehr/resources/data/wound_status_clinical.tsv create mode 100644 nbri_ehr/resources/data/yes_no_only.tsv create mode 100644 nbri_ehr/resources/data/yes_no_order.tsv create mode 100644 nbri_ehr/resources/domain-templates/ehr.template.xml create mode 100644 nbri_ehr/resources/domain-templates/ehr_lookups.template.xml create mode 100644 nbri_ehr/resources/etls/ProjectAndAssignment.xml create mode 100644 nbri_ehr/resources/etls/ProtocolAndAssignment.xml create mode 100644 nbri_ehr/resources/etls/account.xml create mode 100644 nbri_ehr/resources/etls/animalDelivery.xml create mode 100644 nbri_ehr/resources/etls/animalReqOrder.xml create mode 100644 nbri_ehr/resources/etls/animalShipment.xml create mode 100644 nbri_ehr/resources/etls/animalVendor.xml create mode 100644 nbri_ehr/resources/etls/arrival.xml create mode 100644 nbri_ehr/resources/etls/biopsy.xml create mode 100644 nbri_ehr/resources/etls/birth.xml create mode 100644 nbri_ehr/resources/etls/blood.xml create mode 100644 nbri_ehr/resources/etls/breeder.xml create mode 100644 nbri_ehr/resources/etls/cageCard.xml create mode 100644 nbri_ehr/resources/etls/cases.xml create mode 100644 nbri_ehr/resources/etls/chemistryResults.xml create mode 100644 nbri_ehr/resources/etls/clinremarks.xml create mode 100644 nbri_ehr/resources/etls/deaths.xml create mode 100644 nbri_ehr/resources/etls/deletedRecord.xml create mode 100644 nbri_ehr/resources/etls/demographics.xml create mode 100644 nbri_ehr/resources/etls/department.xml create mode 100644 nbri_ehr/resources/etls/departure.xml create mode 100644 nbri_ehr/resources/etls/drug.xml create mode 100644 nbri_ehr/resources/etls/ehrRecords.xml create mode 100644 nbri_ehr/resources/etls/ehr_lookups.xml create mode 100644 nbri_ehr/resources/etls/exemptions.xml create mode 100644 nbri_ehr/resources/etls/flags.xml create mode 100644 nbri_ehr/resources/etls/foster.xml create mode 100644 nbri_ehr/resources/etls/histopathology.xml create mode 100644 nbri_ehr/resources/etls/historicalOther.xml create mode 100644 nbri_ehr/resources/etls/housing.xml create mode 100644 nbri_ehr/resources/etls/idHistory.xml create mode 100644 nbri_ehr/resources/etls/locations.xml create mode 100644 nbri_ehr/resources/etls/lotNumber.xml create mode 100644 nbri_ehr/resources/etls/necropsy.xml create mode 100644 nbri_ehr/resources/etls/notes.xml create mode 100644 nbri_ehr/resources/etls/obs.xml create mode 100644 nbri_ehr/resources/etls/pairings.xml create mode 100644 nbri_ehr/resources/etls/physicalExam.xml create mode 100644 nbri_ehr/resources/etls/prc.xml create mode 100644 nbri_ehr/resources/etls/pregnancy.xml create mode 100644 nbri_ehr/resources/etls/procedure.xml create mode 100644 nbri_ehr/resources/etls/protocolCounts.xml create mode 100644 nbri_ehr/resources/etls/protocolSupplement.xml create mode 100644 nbri_ehr/resources/etls/protocolUsage.xml create mode 100644 nbri_ehr/resources/etls/questionResponse.xml create mode 100644 nbri_ehr/resources/etls/serology.xml create mode 100644 nbri_ehr/resources/etls/shipTo.xml create mode 100644 nbri_ehr/resources/etls/staff.xml create mode 100644 nbri_ehr/resources/etls/stress.xml create mode 100644 nbri_ehr/resources/etls/vitals.xml create mode 100644 nbri_ehr/resources/etls/weight.xml create mode 100644 nbri_ehr/resources/folderTypes/NBRI_EHR.folderType.xml create mode 100644 nbri_ehr/resources/module.xml create mode 100644 nbri_ehr/resources/queries/dbo/auditDeleteEvent.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_account.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_alopecia.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_alopecia_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_animal_delivery.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_animal_delivery_esig.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_animal_req_order.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_animal_req_order_esig.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_animal_shipment.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_animal_vendor.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_areas.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_arrival.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_arrival_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_assignment.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_assignment_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_biopsy.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_biopsy_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_births.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_births_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_blood.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_blood_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_breeder.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_breeder_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_buildings.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_cage_card.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_cage_card_history.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_cages.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_cases.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_cases_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_chemistryResults.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_chemistryResults_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_clinremarks.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_clinremarks_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_deaths.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_deaths_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_deleted_record.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_demographics.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_demographics_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_department.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_departure.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_departure_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_drug.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_drug_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_exemptions.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_exemptions_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_finalDeparture.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_flag_categories.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_flag_values.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_flags.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_flags_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_floors.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_foster.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_foster_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_histopathology.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_historicalOther.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_housing.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_housing_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_idHistory.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_latestArrival.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_latestDeparture.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_lookups.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_lot_number.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_modified_event.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_necropsy.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_necropsy_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_notes.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_notes_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_observations.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_observations_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_pairings.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_pairings_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_physicalExam.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_physicalExam_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_prc.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_prc_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_pregnancy.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_pregnancy_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_procedures.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_project.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_protocol.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_protocolAssignment.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_protocol_amendments.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_protocol_counts.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_protocol_esig.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_protocol_procedures.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_protocol_stress.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_protocol_usage.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_question.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_question_response.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_rooms.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_serology.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_serology_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_ship_to.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_species.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_species_codes.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_staff.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_status.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_stress.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_vitals.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_vitals_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_weight.sql create mode 100644 nbri_ehr/resources/queries/dbo/q_weight_delete.sql create mode 100644 nbri_ehr/resources/queries/dbo/staffInfo.sql create mode 100644 nbri_ehr/resources/queries/ehr/activeProtocols.sql create mode 100644 nbri_ehr/resources/queries/ehr/my_tasks.query.xml create mode 100644 nbri_ehr/resources/queries/ehr/my_tasks.sql create mode 100644 nbri_ehr/resources/queries/ehr/my_tasks/.qview.xml create mode 100644 nbri_ehr/resources/queries/ehr/my_tasks/Active Tasks.qview.xml create mode 100644 nbri_ehr/resources/queries/ehr/my_tasks/Review Required.qview.xml create mode 100644 nbri_ehr/resources/queries/ehr/observation_types.query.xml create mode 100644 nbri_ehr/resources/queries/ehr/project.js create mode 100644 nbri_ehr/resources/queries/ehr/project.query.xml create mode 100644 nbri_ehr/resources/queries/ehr/project/.qview.xml create mode 100644 nbri_ehr/resources/queries/ehr/protocol.js create mode 100644 nbri_ehr/resources/queries/ehr/protocol.query.xml create mode 100644 nbri_ehr/resources/queries/ehr/protocol/.qview.xml create mode 100644 nbri_ehr/resources/queries/ehr/protocolActiveAnimals.query.xml create mode 100644 nbri_ehr/resources/queries/ehr/protocolActiveAnimals.sql create mode 100644 nbri_ehr/resources/queries/ehr/protocolAnimals.query.xml create mode 100644 nbri_ehr/resources/queries/ehr/protocolAnimals.sql create mode 100644 nbri_ehr/resources/queries/ehr/protocolHistoricAnimals.sql create mode 100644 nbri_ehr/resources/queries/ehr/protocolTotalAnimalsBySpecies.query.xml create mode 100644 nbri_ehr/resources/queries/ehr/protocolTotalAnimalsBySpecies.sql create mode 100644 nbri_ehr/resources/queries/ehr/protocol_counts.query.xml create mode 100644 nbri_ehr/resources/queries/ehr/protocol_counts/.qview.xml create mode 100644 nbri_ehr/resources/queries/ehr/tasks/.qview.xml create mode 100644 nbri_ehr/resources/queries/ehr/tasks/Active Tasks.qview.xml create mode 100644 nbri_ehr/resources/queries/ehr/tasks/Review Required.qview.xml create mode 100644 nbri_ehr/resources/queries/ehr_lookups/ageclass.query.xml create mode 100644 nbri_ehr/resources/queries/ehr_lookups/areas/.qview.xml create mode 100644 nbri_ehr/resources/queries/ehr_lookups/buildings.js create mode 100644 nbri_ehr/resources/queries/ehr_lookups/buildings.query.xml create mode 100644 nbri_ehr/resources/queries/ehr_lookups/buildings/.qview.xml create mode 100644 nbri_ehr/resources/queries/ehr_lookups/cage.js create mode 100644 nbri_ehr/resources/queries/ehr_lookups/cage.query.xml create mode 100644 nbri_ehr/resources/queries/ehr_lookups/cage/.qview.xml create mode 100644 nbri_ehr/resources/queries/ehr_lookups/country.query.xml create mode 100644 nbri_ehr/resources/queries/ehr_lookups/floors.js create mode 100644 nbri_ehr/resources/queries/ehr_lookups/floors.query.xml create mode 100644 nbri_ehr/resources/queries/ehr_lookups/floors/.qview.xml create mode 100644 nbri_ehr/resources/queries/ehr_lookups/procedures/.qview.xml create mode 100644 nbri_ehr/resources/queries/ehr_lookups/roomUtilization.query.xml create mode 100644 nbri_ehr/resources/queries/ehr_lookups/roomUtilization.sql create mode 100644 nbri_ehr/resources/queries/ehr_lookups/roomUtilizationByBuilding.query.xml create mode 100644 nbri_ehr/resources/queries/ehr_lookups/roomUtilizationByBuilding.sql create mode 100644 nbri_ehr/resources/queries/ehr_lookups/rooms.js create mode 100644 nbri_ehr/resources/queries/ehr_lookups/rooms.query.xml create mode 100644 nbri_ehr/resources/queries/ehr_lookups/rooms/.qview.xml create mode 100644 nbri_ehr/resources/queries/ehr_lookups/snomed.query.xml create mode 100644 nbri_ehr/resources/queries/ehr_lookups/species_codes.query.xml create mode 100644 nbri_ehr/resources/queries/ehr_lookups/vendor_production_location.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/Account.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/AnimalDelivery.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/AnimalDeliveryEsig.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/AnimalReqOrder.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/AnimalReqOrderEsig.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/AnimalShipment.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/AnimalVendor.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/AnimalVendor/.qview.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/CageCard.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/CageCardHistory.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/DeletedRecord.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/Department.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/IdHistory.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/Lot.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/ProtocolEsig.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/ProtocolProcedures.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/ProtocolStress.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/QuestionResponse.js create mode 100644 nbri_ehr/resources/queries/nbri_ehr/QuestionResponse.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/casesSource.sql create mode 100644 nbri_ehr/resources/queries/nbri_ehr/casesTemp.js create mode 100644 nbri_ehr/resources/queries/nbri_ehr/dateRange.sql create mode 100644 nbri_ehr/resources/queries/nbri_ehr/locationTypes/.qview.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/locations.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/locations/.qview.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/locationsMapping.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/locationsMapping/.qview.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/necropsyTasks.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/necropsyTasks.sql create mode 100644 nbri_ehr/resources/queries/nbri_ehr/necropsyTasks/.qview.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/staff.query.xml create mode 100644 nbri_ehr/resources/queries/nbri_ehr/stress.query.xml create mode 100644 nbri_ehr/resources/queries/study/AcquisitionReport.sql create mode 100644 nbri_ehr/resources/queries/study/AcquisitionReportBySpecies.sql create mode 100644 nbri_ehr/resources/queries/study/BehaviorClinRemarks.sql create mode 100644 nbri_ehr/resources/queries/study/BehaviorClinRemarks/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/ClinicalClinRemarks.sql create mode 100644 nbri_ehr/resources/queries/study/ClinicalClinRemarks/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/CurrentProtocolProjectReport.sql create mode 100644 nbri_ehr/resources/queries/study/MHC.js create mode 100644 nbri_ehr/resources/queries/study/MHC.query.xml create mode 100644 nbri_ehr/resources/queries/study/Pedigree.sql create mode 100644 nbri_ehr/resources/queries/study/Weight.js create mode 100644 nbri_ehr/resources/queries/study/activeAssignments.sql create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases.sql create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Area 11.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Area 51.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 10.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 10C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 27.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 28.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 29.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 30.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 31.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 31C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 31D.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 32.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 34.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 37.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 41.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 42.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 43.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 44.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 45.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 46.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 50.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 52.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 53.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 54A.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeBehaviorCases/Building 54B.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases.sql create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Area 11.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Area 51.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 10.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 10C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 27.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 28.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 29.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 30.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 31.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 31C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 31D.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 32.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 34.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 37.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 41.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 42.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 43.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 44.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 45.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 46.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 50.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 52.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 53.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 54A.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeClinicalCases/Building 54B.qview.xml create mode 100644 nbri_ehr/resources/queries/study/activeProjectsFromHousing.sql create mode 100644 nbri_ehr/resources/queries/study/activeTreatmentOrders.sql create mode 100644 nbri_ehr/resources/queries/study/alias.js create mode 100644 nbri_ehr/resources/queries/study/alias.query.xml create mode 100644 nbri_ehr/resources/queries/study/aliases.sql create mode 100644 nbri_ehr/resources/queries/study/alopecia/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/arrival.js create mode 100644 nbri_ehr/resources/queries/study/arrival.query.xml create mode 100644 nbri_ehr/resources/queries/study/arrival/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/assignment.js create mode 100644 nbri_ehr/resources/queries/study/assignment.query.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases.sql create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Area 11.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Area 51.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 10.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 10C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 27.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 28.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 29.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 30.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 31.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 31C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 31D.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 32.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 34.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 37.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 41.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 42.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 43.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 44.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 45.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 46.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 50.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 52.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 53.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 54A.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorCases/Building 54B.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations.sql create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Area 11.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Area 51.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 10.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 10C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 27.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 28.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 29.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 30.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 31.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 31C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 31D.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 32.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 34.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 37.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 41.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 42.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 43.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 44.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 45.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 46.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 50.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 52.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 53.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 54A.qview.xml create mode 100644 nbri_ehr/resources/queries/study/behaviorObservations/Building 54B.qview.xml create mode 100644 nbri_ehr/resources/queries/study/birth.js create mode 100644 nbri_ehr/resources/queries/study/birth.query.xml create mode 100644 nbri_ehr/resources/queries/study/blood/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/bloodDrawChanges.sql create mode 100644 nbri_ehr/resources/queries/study/breeder/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/cases.js create mode 100644 nbri_ehr/resources/queries/study/cases.query.xml create mode 100644 nbri_ehr/resources/queries/study/cases/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/cases/Active Behavior Cases.qview.xml create mode 100644 nbri_ehr/resources/queries/study/cases/Active Clinical Cases.qview.xml create mode 100644 nbri_ehr/resources/queries/study/cases/All Behavior Cases.qview.xml create mode 100644 nbri_ehr/resources/queries/study/cases/All Clinical Cases.qview.xml create mode 100644 nbri_ehr/resources/queries/study/chemistryResults.query.xml create mode 100644 nbri_ehr/resources/queries/study/chemistryResults/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases.sql create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Area 11.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Area 51.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 10.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 10C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 27.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 28.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 29.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 30.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 31.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 31C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 31D.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 32.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 34.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 37.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 41.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 42.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 43.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 44.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 45.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 46.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 50.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 52.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 53.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 54A.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalCases/Building 54B.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations.sql create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Area 11.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Area 51.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 10.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 10C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 27.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 28.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 29.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 30.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 31.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 31C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 31D.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 32.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 34.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 37.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 41.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 42.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 43.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 44.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 45.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 46.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 50.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 52.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 53.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 54A.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinicalObservations/Building 54B.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observations.js create mode 100644 nbri_ehr/resources/queries/study/clinical_observations.query.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observations/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observations/Alopecia Scores.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observations/Behavior.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observations/Clinical.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary.sql create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Area 11.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Area 51.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 10.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 10C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 27.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 28.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 29.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 30.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 31.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 31C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 31D.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 32.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 34.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 37.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 41.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 42.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 43.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 44.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 45.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 46.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 50.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 52.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 53.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 54A.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 54B.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinremarks.js create mode 100644 nbri_ehr/resources/queries/study/clinremarks.query.xml create mode 100644 nbri_ehr/resources/queries/study/clinremarks/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinremarks/Behavior.qview.xml create mode 100644 nbri_ehr/resources/queries/study/clinremarks/Clinical.qview.xml create mode 100644 nbri_ehr/resources/queries/study/colonyPopulationByAgeClass.query.xml create mode 100644 nbri_ehr/resources/queries/study/colonyPopulationChange.sql create mode 100644 nbri_ehr/resources/queries/study/colonyPopulationSummary.query.xml create mode 100644 nbri_ehr/resources/queries/study/currentBloodDraws.sql create mode 100644 nbri_ehr/resources/queries/study/currentproject.sql create mode 100644 nbri_ehr/resources/queries/study/deathNotification.sql create mode 100644 nbri_ehr/resources/queries/study/deaths.js create mode 100644 nbri_ehr/resources/queries/study/deaths.query.xml create mode 100644 nbri_ehr/resources/queries/study/deaths/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/demographics.js create mode 100644 nbri_ehr/resources/queries/study/demographics.query.xml create mode 100644 nbri_ehr/resources/queries/study/demographics/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/demographicsActiveFlags.sql create mode 100644 nbri_ehr/resources/queries/study/demographicsActiveProjectAssignment.sql create mode 100644 nbri_ehr/resources/queries/study/demographicsActiveProtocolAssignment.query.xml create mode 100644 nbri_ehr/resources/queries/study/demographicsActiveProtocolAssignment.sql create mode 100644 nbri_ehr/resources/queries/study/demographicsAliases.query.xml create mode 100644 nbri_ehr/resources/queries/study/demographicsAliases.sql create mode 100644 nbri_ehr/resources/queries/study/demographicsCagemates.query.xml create mode 100644 nbri_ehr/resources/queries/study/demographicsCagemates.sql create mode 100644 nbri_ehr/resources/queries/study/demographicsCurLocation.query.xml create mode 100644 nbri_ehr/resources/queries/study/demographicsCurLocation.sql create mode 100644 nbri_ehr/resources/queries/study/demographicsLastProject.query.xml create mode 100644 nbri_ehr/resources/queries/study/demographicsLastProject.sql create mode 100644 nbri_ehr/resources/queries/study/demographicsLastProtocol.query.xml create mode 100644 nbri_ehr/resources/queries/study/demographicsLastProtocol.sql create mode 100644 nbri_ehr/resources/queries/study/demographicsOffspring.query.xml create mode 100644 nbri_ehr/resources/queries/study/demographicsOffspring.sql create mode 100644 nbri_ehr/resources/queries/study/demographicsParents.query.xml create mode 100644 nbri_ehr/resources/queries/study/demographicsParents.sql create mode 100644 nbri_ehr/resources/queries/study/demographicsSiblings.query.xml create mode 100644 nbri_ehr/resources/queries/study/demographicsSiblings.sql create mode 100644 nbri_ehr/resources/queries/study/demographicsSource.query.xml create mode 100644 nbri_ehr/resources/queries/study/demographicsSource.sql create mode 100644 nbri_ehr/resources/queries/study/demographicsTotalOffspring.query.xml create mode 100644 nbri_ehr/resources/queries/study/demographicsTotalOffspring.sql create mode 100644 nbri_ehr/resources/queries/study/departure.js create mode 100644 nbri_ehr/resources/queries/study/departure.query.xml create mode 100644 nbri_ehr/resources/queries/study/departure/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/drug.js create mode 100644 nbri_ehr/resources/queries/study/drug.query.xml create mode 100644 nbri_ehr/resources/queries/study/drug/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/drug/Behavior.qview.xml create mode 100644 nbri_ehr/resources/queries/study/exemptions.js create mode 100644 nbri_ehr/resources/queries/study/exemptions.query.xml create mode 100644 nbri_ehr/resources/queries/study/exemptions/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/flags.js create mode 100644 nbri_ehr/resources/queries/study/flags.query.xml create mode 100644 nbri_ehr/resources/queries/study/flags/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/grossPathology.js create mode 100644 nbri_ehr/resources/queries/study/grossPathology.query.xml create mode 100644 nbri_ehr/resources/queries/study/grossPathology/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/histopathology.query.xml create mode 100644 nbri_ehr/resources/queries/study/historicalOther.query.xml create mode 100644 nbri_ehr/resources/queries/study/housing.js create mode 100644 nbri_ehr/resources/queries/study/housing.query.xml create mode 100644 nbri_ehr/resources/queries/study/housing/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/housing/Active Housing.qview.xml create mode 100644 nbri_ehr/resources/queries/study/necropsy.js create mode 100644 nbri_ehr/resources/queries/study/necropsy.query.xml create mode 100644 nbri_ehr/resources/queries/study/necropsy/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/necropsyStatus.sql create mode 100644 nbri_ehr/resources/queries/study/nhpTraining.js create mode 100644 nbri_ehr/resources/queries/study/nhpTraining.query.xml create mode 100644 nbri_ehr/resources/queries/study/notes.js create mode 100644 nbri_ehr/resources/queries/study/notes.query.xml create mode 100644 nbri_ehr/resources/queries/study/notes/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/notificationAnimalProject.sql create mode 100644 nbri_ehr/resources/queries/study/observationOrdersByDate.sql create mode 100644 nbri_ehr/resources/queries/study/observationSchedule.query.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule.sql create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Area 11.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Area 51.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 10.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 10C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 27.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 28.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 29.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 30.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 31.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 31C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 31D.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 32.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 34.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 37.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 41.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 42.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 43.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 44.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 45.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 46.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 50.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 52.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 53.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 54A.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observationSchedule/Building 54B.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observation_order.js create mode 100644 nbri_ehr/resources/queries/study/observation_order.query.xml create mode 100644 nbri_ehr/resources/queries/study/observation_order/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observation_order/Active Behavior Orders.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observation_order/Active Clinical Orders.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observation_order/Behavior Orders.qview.xml create mode 100644 nbri_ehr/resources/queries/study/observation_order/Clinical Orders.qview.xml create mode 100644 nbri_ehr/resources/queries/study/orchardData.sql create mode 100644 nbri_ehr/resources/queries/study/orchardIdsForTaskid.sql create mode 100644 nbri_ehr/resources/queries/study/pairingSummary.query.xml create mode 100644 nbri_ehr/resources/queries/study/pairingSummary.sql create mode 100644 nbri_ehr/resources/queries/study/pairingSummary/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/pairingSummary/Active Pairing.qview.xml create mode 100644 nbri_ehr/resources/queries/study/pairingSummary/Pairing History.qview.xml create mode 100644 nbri_ehr/resources/queries/study/pairings.js create mode 100644 nbri_ehr/resources/queries/study/pairings.query.xml create mode 100644 nbri_ehr/resources/queries/study/pairings/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/parentageSummary.query.xml create mode 100644 nbri_ehr/resources/queries/study/parentageSummary.sql create mode 100644 nbri_ehr/resources/queries/study/physicalExam/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prc.js create mode 100644 nbri_ehr/resources/queries/study/prc.query.xml create mode 100644 nbri_ehr/resources/queries/study/prc/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcOverdue.query.xml create mode 100644 nbri_ehr/resources/queries/study/prcOverdue.sql create mode 100644 nbri_ehr/resources/queries/study/prcOverdue/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcOverdueNotification.sql create mode 100644 nbri_ehr/resources/queries/study/prcOverdueNotification/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule.query.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule.sql create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Area 11.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Area 51.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 10.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 10C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 27.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 28.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 29.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 30.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 31.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 31C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 31D.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 32.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 34.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 37.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 41.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 42.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 43.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 44.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 45.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 46.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 50.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 52.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 53.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 54A.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prcSchedule/Building 54B.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prc_order.js create mode 100644 nbri_ehr/resources/queries/study/prc_order.query.xml create mode 100644 nbri_ehr/resources/queries/study/prc_order/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/prc_order_report.query.xml create mode 100644 nbri_ehr/resources/queries/study/prc_order_report.sql create mode 100644 nbri_ehr/resources/queries/study/prc_order_report/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/pregnancy.js create mode 100644 nbri_ehr/resources/queries/study/pregnancy.query.xml create mode 100644 nbri_ehr/resources/queries/study/protocolAssignment.js create mode 100644 nbri_ehr/resources/queries/study/protocolAssignment.query.xml create mode 100644 nbri_ehr/resources/queries/study/protocolAssignment/Active Assignments.qview.xml create mode 100644 nbri_ehr/resources/queries/study/recentCases.sql create mode 100644 nbri_ehr/resources/queries/study/serology.query.xml create mode 100644 nbri_ehr/resources/queries/study/serology/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/tissueDisposition.js create mode 100644 nbri_ehr/resources/queries/study/tissueDisposition.query.xml create mode 100644 nbri_ehr/resources/queries/study/tissueDisposition/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule.query.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule.sql create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Area 11.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Area 51.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 10.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 10C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 27.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 28.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 29.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 30.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 31.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 31C.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 31D.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 32.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 34.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 37.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 41.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 42.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 43.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 44.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 45.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 46.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 50.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 52.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 53.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 54A.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Building 54B.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatmentSchedule/Clinical Medications.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatment_order.js create mode 100644 nbri_ehr/resources/queries/study/treatment_order.query.xml create mode 100644 nbri_ehr/resources/queries/study/treatment_order/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatment_order/Behavior Active Treatment Orders.qview.xml create mode 100644 nbri_ehr/resources/queries/study/treatment_order/Clinical Active Treatment Orders.qview.xml create mode 100644 nbri_ehr/resources/queries/study/vitals.js create mode 100644 nbri_ehr/resources/queries/study/vitals.query.xml create mode 100644 nbri_ehr/resources/queries/study/vitals/.qview.xml create mode 100644 nbri_ehr/resources/queries/study/weight.query.xml create mode 100644 nbri_ehr/resources/queries/study/weight/.qview.xml create mode 100644 nbri_ehr/resources/referenceStudy/.labkey/protocols/kinship/default.xml create mode 100644 nbri_ehr/resources/referenceStudy/folder.xml create mode 100644 nbri_ehr/resources/referenceStudy/study/datasets/PrimateElectronicHealthRecord.dataset create mode 100644 nbri_ehr/resources/referenceStudy/study/datasets/datasets_manifest.xml create mode 100644 nbri_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml create mode 100644 nbri_ehr/resources/referenceStudy/study/study.xml create mode 100644 nbri_ehr/resources/reports/additionalReports.tsv create mode 100644 nbri_ehr/resources/schemas/dbscripts/postgresql/nbri_ehr-0.000-25.000.sql create mode 100644 nbri_ehr/resources/schemas/dbscripts/postgresql/nbri_ehr-25.000-25.001.sql create mode 100644 nbri_ehr/resources/schemas/nbri_ehr.xml create mode 100644 nbri_ehr/resources/scripts/nbri_triggers.js create mode 100644 nbri_ehr/resources/views/NBRI_amimalHistory.webpart.xml create mode 100644 nbri_ehr/resources/views/acquisitionReport.html create mode 100644 nbri_ehr/resources/views/acquisitionReport.view.xml create mode 100644 nbri_ehr/resources/views/animalHistory.html create mode 100644 nbri_ehr/resources/views/animalHistory.view.xml create mode 100644 nbri_ehr/resources/views/begin.html create mode 100644 nbri_ehr/resources/views/begin.view.xml create mode 100644 nbri_ehr/resources/views/begin.webpart.xml create mode 100644 nbri_ehr/resources/views/cageDetails.html create mode 100644 nbri_ehr/resources/views/cageDetails.view.xml create mode 100644 nbri_ehr/resources/views/clinicalHistoryExport.html create mode 100644 nbri_ehr/resources/views/clinicalHistoryExport.view.xml create mode 100644 nbri_ehr/resources/views/datasets.html create mode 100644 nbri_ehr/resources/views/datasets.view.xml create mode 100644 nbri_ehr/resources/views/enterData.html create mode 100644 nbri_ehr/resources/views/enterData.view.xml create mode 100644 nbri_ehr/resources/views/nbri_login.html create mode 100644 nbri_ehr/resources/views/nbri_login.view.xml create mode 100644 nbri_ehr/resources/views/necropsy.html create mode 100644 nbri_ehr/resources/views/necropsy.view.xml create mode 100644 nbri_ehr/resources/views/participantView.html create mode 100644 nbri_ehr/resources/views/participantView.view.xml create mode 100644 nbri_ehr/resources/web/ehr/metadata/Default.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/buttons/ProcedureOrderCompleteButton.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/buttons/RecordProcedureButton.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/buttons/RecordTreatmentButton.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/buttons/SelectCaseButton.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/buttons/addClinicalObsButton.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/buttons/clinicalObsGridButton.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/buttons/deathNecropsyButtons.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/buttons/necropsyGridButtons.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/buttons/saveDraftButton.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/buttons/treatmentSubmit.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/data/AssignmentsAnyIdClientStore.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/data/AssignmentsClientStore.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/data/CaseClientStore.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/data/CaseStoreCollection.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/data/ClinicalObservationClientStore.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/data/DrugAdministrationRunsChildClientStore.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/data/DrugAdministrationRunsClientStore.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/data/ObsOrderChildClientStore.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/data/ObsOrdersClientStore.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/field/AnimalIdCases.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/field/DrugVolumeField.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/field/EditCase.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/field/LocationField.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/images/ull-logo-main-subsite.png create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/Alias.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/Arrival.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/Assignment.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/BehaviorDefaults.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/BehaviorRounds.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/BehavioralCase.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/Birth.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/BulkBehavior.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/BulkClinical.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/ClinicalCase.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/ClinicalDefaults.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/ClinicalRounds.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/DeathNecropsy.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/MedicationEndDate.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/NBRIDefault.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/ObsDefaults.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/ParentChild.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/Pregnancy.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/Rearrival.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/model/sources/TreatmentSchedule.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/nbri.css create mode 100644 nbri_ehr/resources/web/nbri_ehr/nbriOverrides.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/nbriReports.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/nbri_ehr_api.lib.xml create mode 100644 nbri_ehr/resources/web/nbri_ehr/panel/AnimalDetailsPanel.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/panel/ArrivalInstructionsPanel.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/panel/BirthInstructionsPanel.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/panel/BloodSummaryPanel.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/panel/CaseHistoryPanel.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/panel/CaseTemplatePanel.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/panel/ClinicalHistoryPanel.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/panel/InstructionsPanel.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/panel/NBRIExamCasesDataEntryPanel.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/panel/NarrowSnapshotPanel.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/panel/SelectCasePanel.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/panel/SnapshotPanel.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/plugin/RowEditor.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/utils.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/window/AddAnimalsWindow.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/window/CopyFromSectionWindow.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/window/DrugAmountWindow.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/window/FormBulkAddWindow.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/window/MarkTreatmentCompletedWindow.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/window/NBRICaseHistoryWindow.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/window/NBRIClinicalHistoryWindow.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/window/NBRIRecentCasesWindow.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/window/NBRIRecentRemarksWindow.js create mode 100644 nbri_ehr/resources/web/nbri_ehr/window/SelectCaseWindow.js create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/NBRIOrchardFileGenerator.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/NBRI_EHRController.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/NBRI_EHRManager.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/NBRI_EHRModule.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/NBRI_EHRSchema.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/buttons/MarkTreatmentCompletedButton.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/columnTransform/NBRIUserCreateTransform.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIAliasFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIAnimalTrainingFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIArrivalFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIAssignmentFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIBaseTaskFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIBehaviorRoundsFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIBehavioralCasesFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIBirthFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIBuildingFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIBulkBehaviorFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIBulkClinicalFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRICageFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRICasesFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIChemistryImportFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIClinicalObservationsFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIClinicalRoundsFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIDeathNecropsyFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIDepartureFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIExemptionsFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIFlagsFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIFloorFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIHousingFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIMedicationTreatmentFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRINotesFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIPairingsFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIPregnancyFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIProjectFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIProtocolFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIRearrivalFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIRoomFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRISerologyImportFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIWeightFormType.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/BaseFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIAliasFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIAnimalDetailsFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIArrivalFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIArrivalInstructionsFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIBirthFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIBirthInstructionsFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIBloodDrawFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRICaseTemplateFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRICasesFormPanelSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIClinicalObservationsFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIClinicalRemarksFormPanelSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIClinicalRemarksFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIDeathFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIDepartureFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIExemptionsFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIFlagsFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIGrossPathologyFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIHousingFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRINecropsyFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRINotesFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIObservationOrdersFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIPregnancyFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIProcedureFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIProcedureOrderFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIProjectAssignmentFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIProtocolAssignmentFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIRearrivalFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRITaskFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRITissueDispositionFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRITreatmentGivenFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRITreatmentOrderFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIVitalsFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIWeightFormSection.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/demographics/ActiveAssignmentsDemographicsProvider.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/demographics/ActiveCasesDemographicsProvider.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/demographics/ActiveFlagsDemographicsProvider.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/demographics/ActiveTreatmentsDemographicsProvider.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/demographics/CagematesDemographicsProvider.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/demographics/HousingDemographicsProvider.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/demographics/NecropsyStatusDemographicsProvider.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/demographics/ProtocolAssignmentDemographicsProvider.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/ArrivalDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/BiopsyDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/BirthDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/BloodDrawDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/BreederDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/DeathDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/DepartureDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/DrugAdminDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/ExemptionsDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/FlagsDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/FosteringDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/HistopathologyDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/NBRIBehaviorObservationsDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/NBRICaseCloseDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/NBRICaseOpenDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/NBRIClinicalObservationsDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/NBRIClinicalRemarksDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/NBRIEndTreatmentOrderDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/NBRIHousingDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/NBRIObservationOrdersDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/NBRIObservationsDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/NBRIProcedureOrdersDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/NBRIVitalsDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/PairingsDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/PhysicalExamDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/PregnancyDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/ProceduresDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/ProjectAssignmentDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/ProtocolDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/history/SerologyDataSource.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/notification/NBRIClinicalMoveNotification.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/notification/NBRIDeathNotification.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/notification/NBRIPregnancyOutcomeNotification.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/notification/NBRIProcedureOverdueNotification.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/notification/NotificationHelper.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/notification/TriggerScriptNotification.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/query/NBRI_EHRTriggerHelper.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/query/NBRI_EHRUserSchema.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/security/NBRIEHRVetTechPermission.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/security/NBRIEHRVetTechRole.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/table/NBRI_EHRCustomizer.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/table/NBRI_EHRSharedDatasetTrigger.java create mode 100644 nbri_ehr/src/org/labkey/nbri_ehr/table/NBRI_EHRTriggerScriptFactory.java create mode 100644 nbri_ehr/test/sampledata/nbriEHRStudyPolicy.xml create mode 100644 nbri_ehr/test/sampledata/nbri_ehr/study/folder.xml create mode 100644 nbri_ehr/test/sampledata/nbri_ehr/study/study/datasets/PrimateElectronicHealthRecord.dataset create mode 100644 nbri_ehr/test/sampledata/nbri_ehr/study/study/datasets/datasetArrival.tsv create mode 100644 nbri_ehr/test/sampledata/nbri_ehr/study/study/datasets/datasetAssignment.tsv create mode 100644 nbri_ehr/test/sampledata/nbri_ehr/study/study/datasets/datasetBirth.tsv create mode 100644 nbri_ehr/test/sampledata/nbri_ehr/study/study/datasets/datasetBirth.tsv~ create mode 100644 nbri_ehr/test/sampledata/nbri_ehr/study/study/datasets/datasetDeaths.tsv create mode 100644 nbri_ehr/test/sampledata/nbri_ehr/study/study/datasets/datasetDemographics.tsv create mode 100644 nbri_ehr/test/sampledata/nbri_ehr/study/study/datasets/datasetDeparture.tsv create mode 100644 nbri_ehr/test/sampledata/nbri_ehr/study/study/datasets/datasetFlags.tsv create mode 100644 nbri_ehr/test/sampledata/nbri_ehr/study/study/datasets/datasetHousing.tsv create mode 100644 nbri_ehr/test/sampledata/nbri_ehr/study/study/datasets/datasetProtocolAssignment.tsv create mode 100644 nbri_ehr/test/sampledata/nbri_ehr/study/study/datasets/datasetWeight.tsv create mode 100644 nbri_ehr/test/sampledata/nbri_ehr/study/study/study.xml create mode 100644 nbri_ehr/test/src/org.labkey.test/tests.nbri_ehr/NBRI_EHRTest.java diff --git a/.github/workflows/branch_release.yml b/.github/workflows/branch_release.yml index c9583b2..e0b4cfc 100644 --- a/.github/workflows/branch_release.yml +++ b/.github/workflows/branch_release.yml @@ -8,6 +8,10 @@ on: tags: - '*' +permissions: + pull-requests: write + contents: write + jobs: branch_release: if: github.event.created && github.event.sender.login == 'labkey-teamcity' @@ -20,4 +24,4 @@ jobs: - name: Create branches and PRs uses: LabKey/gitHubActions/branch-release@develop with: - github_token: ${{ secrets.GITHUB_TOKEN }} \ No newline at end of file + github_token: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/merge_release.yml b/.github/workflows/merge_release.yml index 306d9e0..f6d8d6e 100644 --- a/.github/workflows/merge_release.yml +++ b/.github/workflows/merge_release.yml @@ -8,6 +8,10 @@ on: types: - submitted +permissions: + pull-requests: write + contents: write + jobs: merge_release: if: > @@ -25,4 +29,4 @@ jobs: target_branch: ${{ github.event.pull_request.base.ref }} merge_branch: ${{ github.event.pull_request.head.ref }} pr_number: ${{ github.event.pull_request.number }} - github_token: ${{ secrets.GITHUB_TOKEN }} \ No newline at end of file + github_token: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/validate_pr.yml b/.github/workflows/validate_pr.yml index 0af0396..69320ba 100644 --- a/.github/workflows/validate_pr.yml +++ b/.github/workflows/validate_pr.yml @@ -10,6 +10,9 @@ on: - reopened - ready_for_review +permissions: + pull-requests: write + jobs: validate_pr: if: github.event.pull_request.head.repo.owner.login == 'LabKey' @@ -23,4 +26,4 @@ jobs: pr_head: ${{ github.event.pull_request.head.ref }} pr_number: ${{ github.event.pull_request.number }} pr_title: ${{ github.event.pull_request.title }} - github_token: ${{ secrets.GITHUB_TOKEN }} \ No newline at end of file + github_token: ${{ secrets.GITHUB_TOKEN }} diff --git a/.gitignore b/.gitignore index 99c4bf4..6839374 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,10 @@ .gradle build/ +# Log Files +nbri_ehr/resources/referenceStudy/etlLogs/ +nbri_ehr/resources/referenceStudy/*.log + # Ignore Gradle GUI config gradle-app.setting @@ -21,4 +25,4 @@ gradle-app.setting *.ear # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml -hs_err_pid* \ No newline at end of file +hs_err_pid* diff --git a/build.gradle b/build.gradle new file mode 100644 index 0000000..bd63829 --- /dev/null +++ b/build.gradle @@ -0,0 +1,27 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +import org.labkey.gradle.util.BuildUtils +import org.labkey.gradle.util.ModuleFinder + +subprojects { + Project p -> + if (ModuleFinder.isPotentialModule(p)) + { + p.evaluationDependsOn(BuildUtils.getApiProjectPath(p.gradle)) + apply plugin: 'java' + apply plugin: 'org.labkey.build.module' + } +} diff --git a/gradle.properties b/gradle.properties new file mode 100644 index 0000000..f486eab --- /dev/null +++ b/gradle.properties @@ -0,0 +1 @@ +moduleContainer=:server:modules:nbriEHRModules \ No newline at end of file diff --git a/nbri_ehr/build.gradle b/nbri_ehr/build.gradle new file mode 100644 index 0000000..4d17f63 --- /dev/null +++ b/nbri_ehr/build.gradle @@ -0,0 +1,32 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +import org.labkey.gradle.util.BuildUtils + +dependencies + { + BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:ehrModules:ehr", depProjectConfig: "apiJarFile") + BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile") + BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:premiumModules:dataintegration", depProjectConfig: "apiJarFile") + BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:ehrModules:ehr", depProjectConfig: "published", depExtension: "module") + BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "published", depExtension: "module") + BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:premiumModules:dataintegration", depProjectConfig: "published", depExtension: "module") + BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:premiumModules:bigiron", depProjectConfig: "published", depExtension: "module") + BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:premiumModules:ldap", depProjectConfig: "published", depExtension: "module") + BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:premiumModules:premium", depProjectConfig: "published", depExtension: "module") + BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:premiumModules:professional", depProjectConfig: "published", depExtension: "module") + } + +tasks.named('module').configure { dependsOn(project(":server:modules:LabDevKitModules:LDK").tasks.module) } diff --git a/nbri_ehr/module.properties b/nbri_ehr/module.properties new file mode 100644 index 0000000..4260562 --- /dev/null +++ b/nbri_ehr/module.properties @@ -0,0 +1,2 @@ +ModuleClass: org.labkey.nbri_ehr.NBRI_EHRModule +ManageVersion: true diff --git a/nbri_ehr/resources/data/abdominal_obs_types.tsv b/nbri_ehr/resources/data/abdominal_obs_types.tsv new file mode 100644 index 0000000..2a02c74 --- /dev/null +++ b/nbri_ehr/resources/data/abdominal_obs_types.tsv @@ -0,0 +1,8 @@ +value sort_order +Abdominal Distension 1 +Normal Abdominal Palpation 2 +Abnormal Abdominal Palpation 3 +Hepatomegaly (enlarged liver) 4 +Firm or Tense Abdomen 5 +No Abdominal Abnormality Observed 6 +Other Abdominal Abnormality 7 \ No newline at end of file diff --git a/nbri_ehr/resources/data/abnormal_behavior_types.tsv b/nbri_ehr/resources/data/abnormal_behavior_types.tsv new file mode 100644 index 0000000..52daea9 --- /dev/null +++ b/nbri_ehr/resources/data/abnormal_behavior_types.tsv @@ -0,0 +1,7 @@ +value sort_order +SIB 1 +Hair Plucking 2 +Biting Without Injury 3 +Aggression 4 +Stereotypy 5 +Other Behavior Abnormality 6 \ No newline at end of file diff --git a/nbri_ehr/resources/data/acquisition_type.tsv b/nbri_ehr/resources/data/acquisition_type.tsv new file mode 100644 index 0000000..ba8ea9a --- /dev/null +++ b/nbri_ehr/resources/data/acquisition_type.tsv @@ -0,0 +1,6 @@ +value +Captive Bred Import +Feral Import +Lab Transfer (Wild Born) +Native Born (NBRI) +Native Born (US Born - Other colony) \ No newline at end of file diff --git a/nbri_ehr/resources/data/activity.tsv b/nbri_ehr/resources/data/activity.tsv new file mode 100644 index 0000000..b0487b9 --- /dev/null +++ b/nbri_ehr/resources/data/activity.tsv @@ -0,0 +1,7 @@ +value sort_order +0 Unresponsive 1 +0-1 Extremely Lethargic 2 +1 Lethargic 3 +1-2 Slightly Lethargic 4 +2 Normal 5 +Sedated 6 \ No newline at end of file diff --git a/nbri_ehr/resources/data/ageclass.tsv b/nbri_ehr/resources/data/ageclass.tsv new file mode 100644 index 0000000..d2cea5c --- /dev/null +++ b/nbri_ehr/resources/data/ageclass.tsv @@ -0,0 +1,79 @@ +label ageclass gender species min max +Infant 1 3 0 0.5 +Juvenile 2 3 0.5 5 +Adult 3 3 5 21 +Senior 4 3 21 + +Infant 1 4 0 0.5 +Juvenile 2 4 0.5 5 +Adult 3 4 5 21 +Senior 4 4 21 + +Infant 1 5 0 0.5 +Juvenile 2 5 0.5 5 +Adult 3 5 5 21 +Senior 4 5 21 + +Infant 1 18 0 0.25 +Juvenile 2 18 0.25 1.5 +Adult 3 18 1.5 8 +Senior 4 18 8 + +Infant 1 10 0 1 +Juvenile 2 1 10 1 4 +Juvenile 2 2 10 1 4 +Juvenile 2 3 10 1 5 +Adult 3 1 10 4 18 +Adult 3 2 10 4 18 +Adult 3 3 10 5 18 +Senior 4 10 18 + +Infant 1 13 0 1 +Juvenile 2 1 13 1 4 +Juvenile 2 2 13 1 4 +Juvenile 2 3 13 1 5 +Adult 3 1 13 4 18 +Adult 3 2 13 4 18 +Adult 3 3 13 5 18 +Senior 4 13 18 + +Infant 1 2 0 1 +Juvenile 2 1 2 1 4 +Juvenile 2 2 2 1 4 +Juvenile 2 3 2 1 5 +Adult 3 1 2 4 18 +Adult 3 2 2 4 18 +Adult 3 3 2 5 18 +Senior 4 2 18 + +Infant 1 7 0 1 +Juvenile 2 1 7 1 4 +Juvenile 2 2 7 1 4 +Juvenile 2 3 7 1 5 +Adult 3 1 7 4 18 +Adult 3 2 7 4 18 +Adult 3 3 7 5 18 +Senior 4 7 18 + +Infant 1 9 0 1 +Juvenile 2 1 9 1 4 +Juvenile 2 2 9 1 4 +Juvenile 2 3 9 1 5 +Adult 3 1 9 4 18 +Adult 3 2 9 4 18 +Adult 3 3 9 5 18 +Senior 4 9 18 + +Infant 1 6 0 5 +Juvenile 2 6 5 7 +Adult 3 6 7 34 +Senior 4 6 34 + +Infant 1 12 0 1 +Juvenile 2 12 1 3 +Adult 3 12 3 + +Infant 1 19 0 0.25 +Juvenile 2 19 0.25 1.5 +Adult 3 19 1.5 8 +Senior 4 19 8 \ No newline at end of file diff --git a/nbri_ehr/resources/data/alias_category.tsv b/nbri_ehr/resources/data/alias_category.tsv new file mode 100644 index 0000000..fcd8485 --- /dev/null +++ b/nbri_ehr/resources/data/alias_category.tsv @@ -0,0 +1,5 @@ +Value Title Category Description Sort Order Date Disabled +N Nickname +M Microchip +T Old Tattoo +I ISIS Stud Book Number \ No newline at end of file diff --git a/nbri_ehr/resources/data/alopecia_regrowth.tsv b/nbri_ehr/resources/data/alopecia_regrowth.tsv new file mode 100644 index 0000000..4a38100 --- /dev/null +++ b/nbri_ehr/resources/data/alopecia_regrowth.tsv @@ -0,0 +1,4 @@ +value sort_order +Yes 1 +No 2 +Not Evaluated 3 \ No newline at end of file diff --git a/nbri_ehr/resources/data/alopecia_score.tsv b/nbri_ehr/resources/data/alopecia_score.tsv new file mode 100644 index 0000000..2c4a408 --- /dev/null +++ b/nbri_ehr/resources/data/alopecia_score.tsv @@ -0,0 +1,6 @@ +value title sort_order description Date Disabled +Very good coat condition (1) Very good coat condition (1) 1 +1-25% hair loss (2) 1-25% hair loss (2) 2 +25-50% hair loss (3) 25-50% hair loss (3) 3 +More than 50% (4) More than 50% (4) 4 +Completely bald (5) Completely bald (5) 5 \ No newline at end of file diff --git a/nbri_ehr/resources/data/alopecia_type.tsv b/nbri_ehr/resources/data/alopecia_type.tsv new file mode 100644 index 0000000..42be6ed --- /dev/null +++ b/nbri_ehr/resources/data/alopecia_type.tsv @@ -0,0 +1,10 @@ +value sort_order +Thin 1 +Patchy 2 +Bald 3 +Thin and patchy 4 +Thin and bald 5 +Patchy and bald 6 +Thin, patchy and bald 7 +N/A 8 +Not Evaluated 9 \ No newline at end of file diff --git a/nbri_ehr/resources/data/amount_units.tsv b/nbri_ehr/resources/data/amount_units.tsv new file mode 100644 index 0000000..880b273 --- /dev/null +++ b/nbri_ehr/resources/data/amount_units.tsv @@ -0,0 +1,14 @@ +Unit +g +gummy +IU +mcg +mEq +mg +mL +no units +ounces +scoop +tablet +ug +units diff --git a/nbri_ehr/resources/data/app_score.tsv b/nbri_ehr/resources/data/app_score.tsv new file mode 100644 index 0000000..9847f19 --- /dev/null +++ b/nbri_ehr/resources/data/app_score.tsv @@ -0,0 +1,6 @@ +value +NPO +Normal +Normal to low +Low +Unknown \ No newline at end of file diff --git a/nbri_ehr/resources/data/arrival_type.tsv b/nbri_ehr/resources/data/arrival_type.tsv new file mode 100644 index 0000000..7a69edd --- /dev/null +++ b/nbri_ehr/resources/data/arrival_type.tsv @@ -0,0 +1,3 @@ +value +Non-quarantine Arrival +Quarantine Arrival \ No newline at end of file diff --git a/nbri_ehr/resources/data/att_score.tsv b/nbri_ehr/resources/data/att_score.tsv new file mode 100644 index 0000000..8c75361 --- /dev/null +++ b/nbri_ehr/resources/data/att_score.tsv @@ -0,0 +1,6 @@ +value +BAR +QAR +Lethargic +Sedated +Unknown \ No newline at end of file diff --git a/nbri_ehr/resources/data/bandage_observations.tsv b/nbri_ehr/resources/data/bandage_observations.tsv new file mode 100644 index 0000000..f206952 --- /dev/null +++ b/nbri_ehr/resources/data/bandage_observations.tsv @@ -0,0 +1,4 @@ +value sort_order +Intact 1 +Removed or partially removed 2 +Other 3 \ No newline at end of file diff --git a/nbri_ehr/resources/data/bcs_score.tsv b/nbri_ehr/resources/data/bcs_score.tsv new file mode 100644 index 0000000..4f02d84 --- /dev/null +++ b/nbri_ehr/resources/data/bcs_score.tsv @@ -0,0 +1,10 @@ +value title category description sort_order date_disabled +Emaciated (1) 1 +Very Thin (1.5) 2 +Thin (2) 3 +Lean (2.5) 4 +Optimum (3) 5 +Slightly Overweight (3.5) 6 +Heavy (4) 7 +Obese (4.5) 8 +Grossly Obese (5) 9 diff --git a/nbri_ehr/resources/data/behavior_abnormality.tsv b/nbri_ehr/resources/data/behavior_abnormality.tsv new file mode 100644 index 0000000..4daafa5 --- /dev/null +++ b/nbri_ehr/resources/data/behavior_abnormality.tsv @@ -0,0 +1,7 @@ +value sort_order +SIB 1 +Hair plucking 2 +Biting without injury 3 +Aggression 4 +Stereotypy 5 +Other behavior abnormality 6 \ No newline at end of file diff --git a/nbri_ehr/resources/data/behavior_mgmt_codes.tsv b/nbri_ehr/resources/data/behavior_mgmt_codes.tsv new file mode 100644 index 0000000..60efc6e --- /dev/null +++ b/nbri_ehr/resources/data/behavior_mgmt_codes.tsv @@ -0,0 +1,4 @@ +value title sort_order description Date Disabled +No Fleece Tube No Fleece Tube 1 +Fleece Tube Fleece Tube 2 +Wood Wood 3 \ No newline at end of file diff --git a/nbri_ehr/resources/data/behavior_types.tsv b/nbri_ehr/resources/data/behavior_types.tsv new file mode 100644 index 0000000..1162005 --- /dev/null +++ b/nbri_ehr/resources/data/behavior_types.tsv @@ -0,0 +1,6 @@ +value sort_order +Urine drinking 1 +Eye poke 2 +Copraphagy 3 +Stereotypy 4 +Other 5 \ No newline at end of file diff --git a/nbri_ehr/resources/data/blood_draw_reason.tsv b/nbri_ehr/resources/data/blood_draw_reason.tsv new file mode 100644 index 0000000..75a9424 --- /dev/null +++ b/nbri_ehr/resources/data/blood_draw_reason.tsv @@ -0,0 +1,3 @@ +value title +Clinical Clinical +Research Research \ No newline at end of file diff --git a/nbri_ehr/resources/data/blood_draw_tube_type.tsv b/nbri_ehr/resources/data/blood_draw_tube_type.tsv new file mode 100644 index 0000000..b0896aa --- /dev/null +++ b/nbri_ehr/resources/data/blood_draw_tube_type.tsv @@ -0,0 +1,5 @@ +type color +EDTA Purple +Heparin Green +No Additive Red +SST Striped diff --git a/nbri_ehr/resources/data/blood_sample_type.tsv b/nbri_ehr/resources/data/blood_sample_type.tsv new file mode 100644 index 0000000..ee6e939 --- /dev/null +++ b/nbri_ehr/resources/data/blood_sample_type.tsv @@ -0,0 +1,3 @@ +value +Whole Blood +Bone Marrow \ No newline at end of file diff --git a/nbri_ehr/resources/data/blood_tube_volumes.tsv b/nbri_ehr/resources/data/blood_tube_volumes.tsv new file mode 100644 index 0000000..7128a3e --- /dev/null +++ b/nbri_ehr/resources/data/blood_tube_volumes.tsv @@ -0,0 +1,8 @@ +tube_types volume +EDTA 0.5 +EDTA 2.0 +EDTA 3.0 +SST 3.5 +Heparin 4.0 +SST 5.0 +EDTA,Heparin 6.0 diff --git a/nbri_ehr/resources/data/cage_type.tsv b/nbri_ehr/resources/data/cage_type.tsv new file mode 100644 index 0000000..aaf6fb6 --- /dev/null +++ b/nbri_ehr/resources/data/cage_type.tsv @@ -0,0 +1,8 @@ +cagetype height sqft cageslots verticalSlots supportsTunnel +Double - 1 40 7 2 1 false +Double - 2 40 6 2 1 false +Quad - A 50 8 4 1 false +Quad - B 50 9 4 1 false +Quad - C 50 10 4 1 false +Tunnel - I 30 12 2 1 true +Tunnel - II 30 11 2 1 true \ No newline at end of file diff --git a/nbri_ehr/resources/data/calculated_status_codes.tsv b/nbri_ehr/resources/data/calculated_status_codes.tsv new file mode 100644 index 0000000..4989681 --- /dev/null +++ b/nbri_ehr/resources/data/calculated_status_codes.tsv @@ -0,0 +1,7 @@ +code +Alive +Alive - In Progress +Dead +ERROR +No Record +Shipped \ No newline at end of file diff --git a/nbri_ehr/resources/data/capillary_refill_time.tsv b/nbri_ehr/resources/data/capillary_refill_time.tsv new file mode 100644 index 0000000..c82fdd3 --- /dev/null +++ b/nbri_ehr/resources/data/capillary_refill_time.tsv @@ -0,0 +1,3 @@ +value sort_order +<2 sec (normal) 1 +Abnormal 2 \ No newline at end of file diff --git a/nbri_ehr/resources/data/card_format.tsv b/nbri_ehr/resources/data/card_format.tsv new file mode 100644 index 0000000..b786d2c --- /dev/null +++ b/nbri_ehr/resources/data/card_format.tsv @@ -0,0 +1,4 @@ +value title description +1 Default01 Initial Setup +2 Study Chimp Study Chimp Format +3 Study Monkey diff --git a/nbri_ehr/resources/data/census_activity_status.tsv b/nbri_ehr/resources/data/census_activity_status.tsv new file mode 100644 index 0000000..2fc4783 --- /dev/null +++ b/nbri_ehr/resources/data/census_activity_status.tsv @@ -0,0 +1,4 @@ +value title +I In +N New +O Out diff --git a/nbri_ehr/resources/data/conc_units.tsv b/nbri_ehr/resources/data/conc_units.tsv new file mode 100644 index 0000000..eb6660f --- /dev/null +++ b/nbri_ehr/resources/data/conc_units.tsv @@ -0,0 +1,18 @@ +Unit Denominator Numerator +g/gummy gummy g +g/mL mL g +g/tablet tablet g +g/tsp tsp g +IU/mL mL IU +mcg/mL mL mcg +mEq/mL mL mEq +mg/capsule capsule(s) mg +mg/implant implant mg +mg/kg kg mg +mg/mL mL mg +mg/piece piece(s) mg +mg/tablet tablet(s) mg +mg/tsp tsp mg +mL/kg kg mL +ug/mL mL ug +units/mL mL units diff --git a/nbri_ehr/resources/data/cost_type.tsv b/nbri_ehr/resources/data/cost_type.tsv new file mode 100644 index 0000000..e7db0fe --- /dev/null +++ b/nbri_ehr/resources/data/cost_type.tsv @@ -0,0 +1,3 @@ +value title +1 Indirect Cost +2 Direct Cost \ No newline at end of file diff --git a/nbri_ehr/resources/data/country.tsv b/nbri_ehr/resources/data/country.tsv new file mode 100644 index 0000000..97436ea --- /dev/null +++ b/nbri_ehr/resources/data/country.tsv @@ -0,0 +1,9 @@ +value title category +1 St. Kitts 2 +2 Italy 2 +3 Japan 2 +4 "U.S.A." 1 +5 Philippines 2 +6 Indonesia 2 +7 China 2 +8 Mauritius 2 \ No newline at end of file diff --git a/nbri_ehr/resources/data/country_category.tsv b/nbri_ehr/resources/data/country_category.tsv new file mode 100644 index 0000000..95b2d52 --- /dev/null +++ b/nbri_ehr/resources/data/country_category.tsv @@ -0,0 +1,3 @@ +value title +1 Domestic +2 Foreign diff --git a/nbri_ehr/resources/data/daily_enrich_codes.tsv b/nbri_ehr/resources/data/daily_enrich_codes.tsv new file mode 100644 index 0000000..8705eaf --- /dev/null +++ b/nbri_ehr/resources/data/daily_enrich_codes.tsv @@ -0,0 +1,13 @@ +value title sort_order description Date Disabled +Cone Cone 1 +Cap Feeder Cap Feeder 2 +Blind Forager Blind Forager 3 +Dried Fruit Dried Fruit 4 +Forage on Board Forage on Board 5 +Forage Tray Forage Tray 6 +Produce Produce 7 +Paper Burrito Paper Burrito 8 +Puzzle Feeder Puzzle Feeder 9 +Paper Paper 10 +Fleece Tube Replaced Fleece Tube Replaced 11 +Other Other 12 \ No newline at end of file diff --git a/nbri_ehr/resources/data/data_category.tsv b/nbri_ehr/resources/data/data_category.tsv new file mode 100644 index 0000000..102abe7 --- /dev/null +++ b/nbri_ehr/resources/data/data_category.tsv @@ -0,0 +1,5 @@ +value +Clinical +Surgical +Behavior +Research \ No newline at end of file diff --git a/nbri_ehr/resources/data/death_reason.tsv b/nbri_ehr/resources/data/death_reason.tsv new file mode 100644 index 0000000..0b39f78 --- /dev/null +++ b/nbri_ehr/resources/data/death_reason.tsv @@ -0,0 +1,6 @@ +value title +1 Euthanasia (clinical) +2 Euthaniasia (project) +3 Morbid +4 Natural Death +5 Program Management \ No newline at end of file diff --git a/nbri_ehr/resources/data/delivery_state.tsv b/nbri_ehr/resources/data/delivery_state.tsv new file mode 100644 index 0000000..5dc581f --- /dev/null +++ b/nbri_ehr/resources/data/delivery_state.tsv @@ -0,0 +1,5 @@ +value title +0 Template +1 Pending +2 Received +3 Cancelled \ No newline at end of file diff --git a/nbri_ehr/resources/data/dental_obs.tsv b/nbri_ehr/resources/data/dental_obs.tsv new file mode 100644 index 0000000..a4d1da6 --- /dev/null +++ b/nbri_ehr/resources/data/dental_obs.tsv @@ -0,0 +1,7 @@ +value sort_order +Fractured Tooth 1 +Gingival Hyperplasia 2 +Foreign Object in Cheek Pouch 3 +Tooth Abscess 4 +No Dental/Oral Abnormality Observed 5 +Other Dental/Oral Abnormality 6 \ No newline at end of file diff --git a/nbri_ehr/resources/data/derm_obs.tsv b/nbri_ehr/resources/data/derm_obs.tsv new file mode 100644 index 0000000..cfd9bb3 --- /dev/null +++ b/nbri_ehr/resources/data/derm_obs.tsv @@ -0,0 +1,6 @@ +value sort_order +Dermatitis 1 +Erythema (pink or red skin) 2 +Skin Ulceration 3 +No Dermatologic Abnormality Observed 4 +Other Dermatologic Abnormality 5 \ No newline at end of file diff --git a/nbri_ehr/resources/data/divider_types.tsv b/nbri_ehr/resources/data/divider_types.tsv new file mode 100644 index 0000000..8800fdb --- /dev/null +++ b/nbri_ehr/resources/data/divider_types.tsv @@ -0,0 +1,6 @@ +divider countAsSeparate countAsPaired countAsBoth isMoveable displaychar short_description bgcolor border_style +Mesh TRUE FALSE TRUE M MESH grey dotted +Solid TRUE FALSE TRUE S solid +Clear TRUE FALSE TRUE C CLEAR solid +No Slide TRUE TRUE TRUE NO yellow none +Pairing Divider TRUE FALSE TRUE P grey solid \ No newline at end of file diff --git a/nbri_ehr/resources/data/dosage_units.tsv b/nbri_ehr/resources/data/dosage_units.tsv new file mode 100644 index 0000000..66cb1ef --- /dev/null +++ b/nbri_ehr/resources/data/dosage_units.tsv @@ -0,0 +1,14 @@ +Unit Numerator Denominator +1/8 scoop/kg 1/8 scoop kg +g/kg g kg +IU/kg IU kg +mcg/kg mcg kg +mEq/kg mEq kg +mg +mg/animal mg animal +mg/kg mg kg +mL/kg ml kg +no units +ounces/kg ounces kg +ug/kg ug kg +units/kg units kg diff --git a/nbri_ehr/resources/data/editable_lookups.tsv b/nbri_ehr/resources/data/editable_lookups.tsv new file mode 100644 index 0000000..8e2bf6d --- /dev/null +++ b/nbri_ehr/resources/data/editable_lookups.tsv @@ -0,0 +1,140 @@ +sch query category title description +ehr_lookups abdominal_obs_types Clinical Abdominal Observation Types Used in clinical observations. +ehr_lookups abnormal_behavior_types Clinical Abnormal Behavior Observation Types Used in clinical observations. +ehr_lookups acquisition_type Colony Management Acquisition Type Types of acquisition for Arrivals. +ehr_lookups activity Behavior Activity Behavior observation fixed values. +ehr_lookups ageclass Colony Management Age Class "Categories of age, such as infant or adult, by species. Used in various reports grouping animals by age class." +ehr_lookups alias_category Colony Management Alias Category +ehr_lookups alopecia_score Behavior Alopecia Score Behavior observation fixed values. +ehr_lookups alopecia_type Behavior Alopecia Type Behavior observation fixed values. +ehr_lookups alopecia_regrowth Behavior Alopecia Regrowth Behavior observation fixed values. +ehr_lookups amount_units Clinical Amount Units "Used in drugs, treatments given and treatments ordered datasets." +ehr_lookups app_score Behavior Appetite Score Behavior observation fixed values. +ehr_lookups arrival_type Colony Management Arrival Type Types of arrivals. +ehr_lookups arthritis_types Clinical Arthritis Types Clinical observation fixed values. +ehr_lookups att_score Behavior Attitude Score Behavior observation fixed values. +ehr_lookups bandage_observations Clinical Bandage Observations Clinical observation fixed values. +ehr_lookups bcs_score Clinical Body Condition Score Clinical observation fixed values. +ehr_lookups behavior_abnormality Clinical Behavior Abnormality Clinical observation fixed values. +ehr_lookups behavior_mgmt_codes Behavior Behavior Management Codes Behavior observation fixed values. +ehr_lookups behavior_types Behavior Behavior Types Behavior observation fixed values. +ehr_lookups blood_draw_reason Clinical Blood Draw Reason Used in blood draw datasets. +ehr_lookups blood_draw_tube_type Clinical Blood Draw Tube Type Used in blood draw datasets. +ehr_lookups blood_sample_type Clinical Blood Sample Types Used in blood draw datasets. +ehr_lookups blood_tube_volumes Clinical Blood Tube Volumes Used in blood draw datasets. +ehr_lookups cage_type Colony Management Cage Type Used in cage details. +ehr_lookups calculated_status_codes Colony Management Calculated Status Animal status values. +ehr_lookups capillary_refill_time Clinical Capillary Refill Times Used clinical observations. +ehr_lookups card_format Colony Management Card Format +ehr_lookups census_activity_status Colony Management Census Activity Status +ehr_lookups clinremarks_category Clinical Clinical Remark Category Clinical remarks category. +ehr_lookups conc_units Clinical Concentration Units Used in drug and treatment datasets. +ehr_lookups congenital_abnormalities Clinical Congenital Abnormalities Clinical observation fixed values. +ehr_lookups cost_center Colony Management Cost Center +ehr_lookups cost_type Colony Management Cost Type +ehr_lookups country Colony Management Country +ehr_lookups country_category Colony Management Country Category +ehr_lookups daily_enrich_codes Behavior Daily enrichment codes. +ehr_lookups data_category Clinical Data Categories Used in datasets. +ehr_lookups death_reason Colony Management Death Reason +ehr_lookups delivery_state Colony Management Delivery State +ehr_lookups dental_obs Clinical Dental Observation Types Clinical observation values. +ehr_lookups derm_obs Clinical Dermatologic Observation Types Clinical observation values. +ehr_lookups digit_amputation Clinical Digit Amputation Clinical observation fixed values. +ehr_lookups divider_types Colony Management Divider Type Used in cage details. +ehr_lookups dosage_units Clinical Dosage Units Used in drug and treatment datasets. +ehr_lookups drug_defaults Clinical Formulary Default values in drug and treatment datasets. +ehr_lookups ear_types Clinical Ear Types Clinical observation fixed values. +ehr_lookups esig_events Colony Management Esig Events +ehr_lookups euthanasia_type Colony Management Euthanasia Type +ehr_lookups exam_findings Clinical Exam Findings Physical exam values. +ehr_lookups exemption_category Colony Management Exemption Category +ehr_lookups expense_class Colony Management Expense Class +ehr_lookups fecal_score Clinical Fecal Score Clinical observation fixed values. +ehr_lookups fecal_smear_score Clinical Fecal Smear Score Clinical observation fixed values. +ehr_lookups feed_assess_types Behavior Fecal Assessment Types Behavior observation fixed values. +ehr_lookups flag_categories Colony Management Flag Categories Used to specify flag behavior. +ehr_lookups flag_values Colony Management Flag Values Animal flag values. +ehr_lookups gastro_types Clinical Gastrointestinal Types Clinical observation fixed values. +ehr_lookups gender_codes Colony Management Sex Codes Used in demographics dataset. +ehr_lookups general_obs Clinical General Observation Types Clinical observation types. +ehr_lookups genital_types Colony Management Genital Types Clinical observation fixed values. +ehr_lookups genitourinary_obs Clinical Genitourinary Observation Types Clinical observation fixed values. +ehr_lookups geographic_origins Colony Management Geographic Origins Used in demographics dataset. +ehr_lookups hernia_types Clinical Hernia Types Clinical observation fixed values. +ehr_lookups housing_reason Housing Housing Move Reason Used in housing dataset for location transfers. +ehr_lookups hyd_score Clinical Hydration Score Clinical observation fixed values. +ehr_lookups id_history_type Colony Management Id History Type +ehr_lookups incision_score Clinical Incision Status Clinical observation fixed values. +ehr_lookups indoor_outdoor Colony Management Indoor/Outdoor Cage details +ehr_lookups keyword Clinical Keyword Clinical observation fixed values. +ehr_lookups lameness Clinical Lameness Clinical observation fixed values. +ehr_lookups mass_type Clinical Mass Type Clinical observation fixed values. +ehr_lookups mens_score Clinical Menses Types Clinical observation fixed values. +ehr_lookups mucous_membranes Clinical Mucous Membranes Used in clinical observations. +ehr_lookups musculoskeletal_observations Clinical Musculoskeletal Observations Used in clinical observations. +ehr_lookups necropsy_disposition_codes Colony Management Necropsy Disposition Codes +ehr_lookups necropsy_organ_appearance Colony Management Necropsy Organ Appearance +ehr_lookups necropsy_organ_systems Colony Management Necropsy Organ Systems +ehr_lookups necropsy_physical_condition Colony Management Necropsy Physical Condition +ehr_lookups necropsy_specimen_condition Colony Management Necropsy Specimen Condition +ehr_lookups necropsy_tissue Colony Management Necropsy Tissue +ehr_lookups neurologic_observations Clinical Neurologic Observations Used in clinical observations.. +ehr_lookups nhp_training_reason Behavior NHP Training Reason Behavior training reason values +ehr_lookups nhp_training_result Behavior NHP Training Result Behavior training result values +ehr_lookups nhp_training_type Behavior NHP Training Type Behavior training type values +ehr_lookups normal_abnormal_only Clinical Normal/Abnormal Values Clinical observation values. +ehr_lookups numeric_unit Colony Management Numeric Unit +ehr_lookups observation_areas Clinical Observation Areas Clinical observation areas. +ehr_lookups obstetric_observations Clinical Obstetric Observations Obstetric Observations Fixed Values. +ehr_lookups ocular_observations Clinical Ocular Observations Ocular Observations Fixed Values. +ehr_lookups ocular_problem Clinical Ocular Problem Clinical observation fixed values. +ehr_lookups pairing_formation_types Pairing Formation Type value +ehr_lookups pairing_goal Behavior Pairing Goal Used in pairing dataset. +ehr_lookups pairing_reason Behavior Introduction Reason Used in pairing dataset. +ehr_lookups pairing_observation Behavior Interaction Summary Used in pairing dataset. +ehr_lookups pairing_separation_reason Colony Management Pairing Status Change Reason Pairing Status Change Reason Fixed Values. +ehr_lookups preferences Behavior Preferences Behavior observation fixed values. +ehr_lookups pregnancy_result Colony Management Pregancy Result +ehr_lookups procedure_category Clinical Procedure Category Used in procedures to group procedures. +ehr_lookups procedures Clinical Procedures List of animal procedures.F +ehr_lookups problem_list_category Clinical Problem List Category Used in problem list dataset. Set when opening a case. +ehr_lookups problem_list_subcategory Clinical Problem List Subcategory Used in problem list to categorize problems. +ehr_lookups protocol_category Colony Management Protocol Category +ehr_lookups protocol_state Colony Management Protocol State +ehr_lookups protocol_type Colony Management Protocol Type +ehr_lookups qualifier Colony Management Qualifier +ehr_lookups questionnaire Colony Management Questionnaire +ehr_lookups rectal_prolapse Clinical Rectal Prolapse Used in clinical observations. +ehr_lookups regulatory_stress_levels Colony Management Regulatory Stress Levels +ehr_lookups req_order_state Colony Management Request Order State +ehr_lookups req_order_type Colony Management Request Order Type +ehr_lookups respiratory_observations Clinical Respiratory Observations Used in clinical observations. +ehr_lookups routes Clinical Treatment Routes Used in drug and treatment datasets. +ehr_lookups sib_score Behavior SIB Score Behavior observation fixed values. +ehr_lookups skin_problem Clinical Skin Problems Clinical observation fixed values. +ehr_lookups source Colony Management Source +ehr_lookups species Colony Management Species +ehr_lookups snomed Research Treatments List of animal treatments. +ehr_lookups species_codes Colony Management Species Codes +ehr_lookups stool_score Clinical Stool Score +ehr_lookups stool_types Clinical Stool Types +ehr_lookups tb_obs_score Clinical TB Observation Scores Clinical observation fixed values. +ehr_lookups temperament Behavior Temperament Behavior observation fixed values. +ehr_lookups testicular_volume Clinical Testicular Volume Testicular volume values. +ehr_lookups termination_reason_codes Clinical Termination Reason Codes Clinical observation fixed values. +ehr_lookups trauma_size Clinical Trauma Size Clinical observation fixed values. +ehr_lookups treatment_frequency Clinical Treatment Frequency Used in treatment and drug datasets. +ehr_lookups treatment_frequency_times Clinical Treatment Frequency Times "Used in treatment, drug and observation datasets." +ehr_lookups turgor_score Clinical Turgor Score Clinical observation fixed values. +ehr_lookups vaginal_uterine_prolapse Clinical Vaginal Uterine Prolapse Clinical observation fixed values. +ehr_lookups vendor_approval_code Colony Management Vendor Approval Code +ehr_lookups vendor_production_location Colony Management Vendor Production Location +ehr_lookups volume_units Clinical Volume Units Used in drug and treatment datasets. +ehr_lookups weight_ranges Clinical Weight Ranges Min/Max allowable weight per species. Used in various weight reports. +ehr_lookups wound_score Clinical Wound Score Clinical observation fixed values. +ehr_lookups wound_severity Clinical Wound Severity Clinical observation fixed values. +ehr_lookups wound_status_behavior Behavior Wound Status Behavioral observation fixed values. +ehr_lookups wound_status_clinical Clinical Wound Status Clinical observation fixed values. +ehr_lookups yes_no_order Clinical Yes/No Values in Order Used for yes/no values in various datasets. Includes sort order. +ehr_lookups yes_no_only Clinical Yes/No Forced Selection Must choose yes or no. diff --git a/nbri_ehr/resources/data/esig_events.tsv b/nbri_ehr/resources/data/esig_events.tsv new file mode 100644 index 0000000..5c099f6 --- /dev/null +++ b/nbri_ehr/resources/data/esig_events.tsv @@ -0,0 +1,16 @@ +value title description +1 Submit Protocol Request Submit Protocol Request +2 Question Answered Question Answered +3 Pre-Submission Pre-Submission +4 Designated Reviewer Approval Set Final Vote +5 Return for Modification Return for Modification +6 Assign Review Tier Assign Review Tier +7 Submit Opinion Render a Vote +8 Receive Animal Shipments Receive Animal Shipments +9 Transfer Animals Transfer Animals +10 Record Training Results Record Training Results +11 Submit Animal Order Request Submit Animal Order Request +12 Approve/Not Approve Animal Order Request Approve/Not Approve Animal Order Request +13 Global Protocol Deletion +14 Global Account Deletion +15 Unreceive Animal Shipment. Unreceive Animal Shipment \ No newline at end of file diff --git a/nbri_ehr/resources/data/euthanasia_type.tsv b/nbri_ehr/resources/data/euthanasia_type.tsv new file mode 100644 index 0000000..c021231 --- /dev/null +++ b/nbri_ehr/resources/data/euthanasia_type.tsv @@ -0,0 +1,5 @@ +value title +1 Sedate and exsanguinate +2 Gas anesthesia (isoflurane) +3 Lethal Injection (pentobarbital) + diff --git a/nbri_ehr/resources/data/exam_findings.tsv b/nbri_ehr/resources/data/exam_findings.tsv new file mode 100644 index 0000000..f2e67cc --- /dev/null +++ b/nbri_ehr/resources/data/exam_findings.tsv @@ -0,0 +1,3 @@ +value +No significant findings +See remarks diff --git a/nbri_ehr/resources/data/exemption_category.tsv b/nbri_ehr/resources/data/exemption_category.tsv new file mode 100644 index 0000000..50e3262 --- /dev/null +++ b/nbri_ehr/resources/data/exemption_category.tsv @@ -0,0 +1,9 @@ +value title +Food Exempt-Behavioral-Not Permanent Food Exempt-Behavioral-Not Permanent +Housing Exempt-Behavioral-Not Permanent Housing Exempt-Behavioral-Not Permanent +Housing Exempt-Behavioral-Permanent Housing Exempt-Behavioral-Permanent +Housing Exempt-Clinical-Not Permanent Housing Exempt-Clinical-Not Permanent +Housing Exempt-Clinical-Permanent Housing Exempt-Clinical-Permanent +Housing Exempt-Other-Not Permanent Housing Exempt-Other-Not Permanent +Housing Exempt-Released Housing Exempt-Released +Housing Exempt-Research Housing Exempt-Research \ No newline at end of file diff --git a/nbri_ehr/resources/data/expense_class.tsv b/nbri_ehr/resources/data/expense_class.tsv new file mode 100644 index 0000000..371ca83 --- /dev/null +++ b/nbri_ehr/resources/data/expense_class.tsv @@ -0,0 +1,32 @@ +value title description +1 1500 Labor +2 1998 Fringe +3 1999 Overhead +4 2000 Animals +5 2005 Feed +6 2006 Nutritional Supplements +7 2020 Animal Bedding +8 2021 Apparel +9 2022 Colony Supplies +10 2023 Clinical Supplies +11 2024 Laboratory Supplies +12 2025 Contract Laboratory +13 2026 Protective Disposables +14 2029 Other Operating Supplies +15 2040 Equipment Repair/Prototype +16 2041 Facilities/Safety Modifications +17 2042 Operating Services +18 2043 Utilities +19 2044 Professional Services +20 2050 Rentals +21 2060 Shipping/Receiving Animals +22 2061 Mail/Express +23 2065 Meetings +24 2066 Other Travel Expenses +25 2080 Office Supplies +26 2081 Computer Supplies +27 2082 Educational Materials/Memberships +28 2083 Medical Illustrations +29 2090 Telephone +30 4000 Fixed Equippment +31 9999 Fee \ No newline at end of file diff --git a/nbri_ehr/resources/data/fecal_smear_score.tsv b/nbri_ehr/resources/data/fecal_smear_score.tsv new file mode 100644 index 0000000..68e8207 --- /dev/null +++ b/nbri_ehr/resources/data/fecal_smear_score.tsv @@ -0,0 +1,6 @@ +value +0 +1 +2 +3 +4 \ No newline at end of file diff --git a/nbri_ehr/resources/data/feed_assess_types.tsv b/nbri_ehr/resources/data/feed_assess_types.tsv new file mode 100644 index 0000000..ad5f282 --- /dev/null +++ b/nbri_ehr/resources/data/feed_assess_types.tsv @@ -0,0 +1,4 @@ +Value Title Category Description Sort Order Date Disabled +Increase Feed +Decrease Feed +Maintain Feed \ No newline at end of file diff --git a/nbri_ehr/resources/data/gender_codes.tsv b/nbri_ehr/resources/data/gender_codes.tsv new file mode 100644 index 0000000..01c67fb --- /dev/null +++ b/nbri_ehr/resources/data/gender_codes.tsv @@ -0,0 +1,4 @@ +code meaning +1 unknown +2 female +3 male \ No newline at end of file diff --git a/nbri_ehr/resources/data/general_obs.tsv b/nbri_ehr/resources/data/general_obs.tsv new file mode 100644 index 0000000..3f77073 --- /dev/null +++ b/nbri_ehr/resources/data/general_obs.tsv @@ -0,0 +1,7 @@ +value sort_order +Edema 1 +Petechiae (pinpoint hemorrhages) 2 +Ecchymosis (bruising) 3 +Obtunded Demeanor (dull responses to stimuli) 4 +AV Fistula 5 +Other General Observations 6 \ No newline at end of file diff --git a/nbri_ehr/resources/data/genitourinary_obs.tsv b/nbri_ehr/resources/data/genitourinary_obs.tsv new file mode 100644 index 0000000..bd30f5b --- /dev/null +++ b/nbri_ehr/resources/data/genitourinary_obs.tsv @@ -0,0 +1,7 @@ +value sort_order +Blood Urine 1 +Dribbling Urine 2 +Distended Bladder 3 +Penile/Preputial Lesions 4 +No Genitourinary Abnormality Observed 5 +Other Genitourinary Abnormality 6 \ No newline at end of file diff --git a/nbri_ehr/resources/data/geographic_origins.tsv b/nbri_ehr/resources/data/geographic_origins.tsv new file mode 100644 index 0000000..aa32806 --- /dev/null +++ b/nbri_ehr/resources/data/geographic_origins.tsv @@ -0,0 +1,32 @@ +meaning +AFRICA +ARABIAN PENINSULA +ARGENTINA +BOLIVIA +BRAZIL +CAMBODIA +CARIBBEAN +CELEBES IS./INDONES +CENTRAL AFRICA +CENTRAL AMERICA +CHINA +COLUMBIA +CONGO +EAST AFRICA +EQUADOR +GHANA +INDIA +INDONESIA +JAPAN +KENYA +MALAGASY REPUBLIC +MAURITIUS, REPUBLIC OF +NIGERIA +ORIGIN UNKNOWN +PERU +PHILIPPINES +RUSSIA +SOUTH AMERICA +SPAIN +THIALAND +USA \ No newline at end of file diff --git a/nbri_ehr/resources/data/hernia_types.tsv b/nbri_ehr/resources/data/hernia_types.tsv new file mode 100644 index 0000000..499f45b --- /dev/null +++ b/nbri_ehr/resources/data/hernia_types.tsv @@ -0,0 +1,5 @@ +value sort_order +Inguinal Hernia on Right Side 1 +Inguinal Hernia on Left Side 2 +Umbilical Hernia 3 +Other 4 \ No newline at end of file diff --git a/nbri_ehr/resources/data/housing_reason.tsv b/nbri_ehr/resources/data/housing_reason.tsv new file mode 100644 index 0000000..356ba3f --- /dev/null +++ b/nbri_ehr/resources/data/housing_reason.tsv @@ -0,0 +1,25 @@ +Value Title Category Description Sort Order Date Disabled +Behavioral Behavioral +Breeding Breeding +Cage Configuration Change Cage Configuration Change +Construction Construction +Environmental conditions Environmental conditions +Husbandry Husbandry +New pair formation New pair formation +Pair formation Mother Surrogate Pair formation Mother Surrogate +Pair separation behavioral Pair separation behavioral +Pair separation clinical Pair separation clinical +Pair separation scientific Pair separation scientific +Quarantine Quarantine +Quarantine Arrival Quarantine Arrival +Non-quarantine Arrival Non-quarantine Arrival +Retirement Retirement +Return to Group Return to Group +Return to Social Partner Return to Social Partner +Room consolidation Room consolidation +Sale Sale +Scientific Scientific +Social group introduction breeding Social group introduction breeding +Social group introduction non-breeding Social group introduction non-breeding +Veterinary Treatment Veterinary Treatment +Weaning Weaning \ No newline at end of file diff --git a/nbri_ehr/resources/data/hyd_score.tsv b/nbri_ehr/resources/data/hyd_score.tsv new file mode 100644 index 0000000..fdac67e --- /dev/null +++ b/nbri_ehr/resources/data/hyd_score.tsv @@ -0,0 +1,7 @@ +value sort_order +0% 1 +0-5% 2 +5% 3 +5-10% 4 +10% 5 +>10% 6 \ No newline at end of file diff --git a/nbri_ehr/resources/data/id_history_type.tsv b/nbri_ehr/resources/data/id_history_type.tsv new file mode 100644 index 0000000..ba59b93 --- /dev/null +++ b/nbri_ehr/resources/data/id_history_type.tsv @@ -0,0 +1,6 @@ +value title +1 Old Tattoo Number +2 ISIS Stud Book Number +3 CITES Number +4 Name +5 Transponder Number \ No newline at end of file diff --git a/nbri_ehr/resources/data/incision_score.tsv b/nbri_ehr/resources/data/incision_score.tsv new file mode 100644 index 0000000..2dd205f --- /dev/null +++ b/nbri_ehr/resources/data/incision_score.tsv @@ -0,0 +1,8 @@ +value sort_order +Healing Well 1 +Seroma 2 +Infection 3 +Hernia 4 +Dehiscence (incision open) 5 +Erythema or Bruising at Incision Site 6 +Other 7 \ No newline at end of file diff --git a/nbri_ehr/resources/data/indoor_outdoor.tsv b/nbri_ehr/resources/data/indoor_outdoor.tsv new file mode 100644 index 0000000..7606761 --- /dev/null +++ b/nbri_ehr/resources/data/indoor_outdoor.tsv @@ -0,0 +1,4 @@ +value sort_order +Indoor 1 +Outdoor 2 +Indoor/Outdoor 3 \ No newline at end of file diff --git a/nbri_ehr/resources/data/lameness.tsv b/nbri_ehr/resources/data/lameness.tsv new file mode 100644 index 0000000..8a3ff33 --- /dev/null +++ b/nbri_ehr/resources/data/lameness.tsv @@ -0,0 +1,5 @@ +value sort_order +Lame on right leg 1 +Lame on left leg 2 +Not using legs 3 +No lameness observed 4 \ No newline at end of file diff --git a/nbri_ehr/resources/data/lookup_sets.tsv b/nbri_ehr/resources/data/lookup_sets.tsv new file mode 100644 index 0000000..613eb8e --- /dev/null +++ b/nbri_ehr/resources/data/lookup_sets.tsv @@ -0,0 +1,118 @@ +setname label keyfield titleColumn +abdominal_obs_types Abdominal Observation Types value +abnormal_behavior_types Abnormal Behavior Types value +acquisition_type Acquisition Type value +activity Activity value +alias_category Alias Category value title +alopecia_type Alopecia Type value +alopecia_score Alopecia Type value +alopecia_regrowth Alopecia Regrowth value +app_score Appetite Score value +arrival_type Arrival Type value +arthritis_types Arthritis Types value +att_score Attitude Score value +bandage_observations Bandage/splint Observations value +bcs_score BCS Store value title +behavior_abnormality Behavior Abnormality value +behavior_mgmt_codes Behavior Management Codes value +behavior_types Behavior Types value +blood_draw_reason Blood Draw Reason value +blood_sample_type Blood Sample Types value +cage_type Cage Type value title +capillary_refill_time Capillary Refill Time value +card_format Card Format value title +census_activity_status Census Activity Status value title +clinremarks_category Clinremarks Category value title +congenital_abnormalities Congenital Abnormalities value title +cost_center Cost Center value title +cost_type Cost Type value title +country Country value title +country_category Country Category value title +daily_enrich_codes Daily Enrichment Codes value +data_category Data Category Field Values value +death_reason Death Reason value +delivery_state Delivery State value title +dental_obs Dental Observations value +derm_obs Dermatologic Observations value +digit_amputation Digit Amputation value title +ear_types Ear Types value title +esig_events ESig Events value title +euthanasia_type Euthanasia Type value title +exam_findings Exam Findings value +exemption_category Exemption Category value title +expense_class Expense Class value description +fecal_score Fecal Score value description +fecal_smear_score Fecal Smear Scores value +feed_assess_types Feed Assessment Types value +gastro_types Gastrointestinal Types value +general_obs General Observations value +genital_types Genital Types value +genitourinary_obs Genitourinary Observations value +hernia_types Hernia Types value +housing_reason Housing Reason value +hyd_score Hyd Score value +id_history_type Id History Type value title +incision_score Incision Status value +indoor_outdoor Indoor/Outdoor value +keyword Keyword value title +lameness Lameness value title +mass_type Mass Type value title +mens_score Menses value +mucous_membranes Mucous Membranes value +musculoskeletal_observations Musculoskeletal Observations value +necropsy_disposition_codes Tissue Disposition Codes value title +necropsy_organ_appearance Appearance value title +necropsy_organ_systems Organ Systems value title +necropsy_physical_condition Physical Condition value title +necropsy_specimen_condition Specimen Condition value title +necropsy_tissue Tissues value title +neurologic_observations Neurologic Observations value +nhp_training_reason NHP Training Reason value +nhp_training_result NHP Training Result value +nhp_training_type NHP Training Type value +normal_abnormal_only Normal/Abnormal Type value +numeric_unit Numeric Units value title +obstetric_observations Obstetric Observations value +ocular_observations Ocular Observations value +observation_areas Observation Areas value +ocular_problem Ocular Problem value +pairing_goal Pairing Goal value +pairing_formation_types Pairing Formation Type value +pairing_reason Introduction Reason value +pairing_observation Interaction Summary value +pairing_separation_reason Pairing Status Change Reason value value +preferences Preferences value +pregnancy_result Pregnancy Results value +procedure_category Category of procedures value +problem_list_category Problem List Category value +problem_list_subcategory Problem List Sub-Category value +protocol_category Protocol Category value title +protocol_state Protocol State value title +protocol_type Protocol Type value title +qualifier Qualifier value title +questionnaire Questionnaire value title +rectal_prolapse Rectal Prolapse value +regulatory_stress_levels Regulatory Stress Levels value title +req_order_state Req Order State value title +req_order_type Req Order Type value title +respiratory_observations Respiratory Observations value title +sib_score SIB Score value +skin_problem Skin Problem value +stool_score Stool Score value +stool_types Stool Types value +tb_obs_score TB Obs Score value +temperament Temperament value title +testicular_volume Testicular Volume value title +trauma_size Trauma Size value +turgor_score Turgor Score value +termination_reason_codes Termination Reason Codes Codes value title +vendor_approval_code Vendor Approval Code value title +vaginal_uterine_prolapse Vaginal Uterine Prolapse value +vendor_production_location Vendor Production Location value title +weight_ranges Weight Ranges value +wound_score Wound Score value +wound_severity Wound Severity value +wound_status_behavior Wound Status Behavior value +wound_status_clinical Wound Status Clinical value +yes_no_order Yes/No Values in Order value +yes_no_only Yes/No Forced Selection value diff --git a/nbri_ehr/resources/data/lookupsManifest.tsv b/nbri_ehr/resources/data/lookupsManifest.tsv new file mode 100644 index 0000000..defb466 --- /dev/null +++ b/nbri_ehr/resources/data/lookupsManifest.tsv @@ -0,0 +1,131 @@ +name +abdominal_obs_types +abnormal_behavior_types +acquisition_type +activity +ageclass +alias_category +alopecia_type +alopecia_score +alopecia_regrowth +amount_units +app_score +arrival_type +arthritis_types +att_score +bandage_observations +bcs_score +behavior_abnormality +behavior_mgmt_codes +behavior_types +blood_draw_reason +blood_draw_tube_type +blood_sample_type +blood_tube_volumes +cage_type +calculated_status_codes +capillary_refill_time +card_format +census_activity_status +congenital_abnormalities +conc_units +cost_type +country +country_category +daily_enrich_codes +data_category +death_reason +delivery_state +dental_obs +derm_obs +digit_amputation +divider_types +dosage_units +ear_types +editable_lookups +esig_events +euthanasia_type +exam_findings +exemption_category +expense_class +fecal_score +fecal_smear_score +feed_assess_types +gastro_types +gender_codes +general_obs +genital_types +genitourinary_obs +geographic_origins +hernia_types +housing_reason +hyd_score +id_history_type +incision_score +indoor_outdoor +lameness +mass_type +mens_score +mucous_membranes +musculoskeletal_observations +necropsy_disposition_codes +necropsy_organ_appearance +necropsy_organ_systems +necropsy_physical_condition +necropsy_specimen_condition +necropsy_tissue +neurologic_observations +nhp_training_reason +nhp_training_result +nhp_training_type +normal_abnormal_only +numeric_unit +observation_areas +obstetric_observations +ocular_observations +ocular_problem +pairing_formation_types +pairing_goal +pairing_reason +pairing_observation +pairing_separation_reason +preferences +pregnancy_result +procedure_category +problem_list_category +problem_list_subcategory +protocol_category +protocol_state +protocol_type +qualifier +questionnaire +rectal_prolapse +regulatory_stress_levels +req_order_state +req_order_type +respiratory_observations +routes +sib_score +source +snomed +skin_problem +stool_score +stool_types +tb_obs_score +temperament +testicular_volume +trauma_size +treatment_frequency +treatment_frequency_times +turgor_score +vaginal_uterine_prolapse +vendor_approval_code +vendor_production_location +volume_units +weight_ranges +wound_score +wound_severity +wound_status_behavior +wound_status_clinical +yes_no_only +yes_no_order diff --git a/nbri_ehr/resources/data/lookupsManifestTest.tsv b/nbri_ehr/resources/data/lookupsManifestTest.tsv new file mode 100644 index 0000000..b2006c8 --- /dev/null +++ b/nbri_ehr/resources/data/lookupsManifestTest.tsv @@ -0,0 +1,133 @@ +name +abdominal_obs_types +abnormal_behavior_types +acquisition_type +activity +ageclass +alias_category +alopecia_type +alopecia_score +alopecia_regrowth +amount_units +app_score +arrival_type +arthritis_types +bandage_observations +bcs_score +behavior_abnormality +behavior_mgmt_codes +behavior_types +blood_draw_reason +blood_draw_tube_type +blood_sample_type +blood_tube_volumes +cage_type +calculated_status_codes +capillary_refill_time +card_format +census_activity_status +conc_units +congenital_abnormalities +cost_type +country +country_category +daily_enrich_codes +data_category +death_reason +delivery_state +dental_obs +derm_obs +divider_types +digit_amputation +dosage_units +ear_types +editable_lookups +esig_events +euthanasia_type +exam_findings +exemption_category +expense_class +fecal_score +fecal_smear_score +feed_assess_types +gastro_types +gender_codes +general_obs +genital_types +genitourinary_obs +geographic_origins +hernia_types +housing_reason +hyd_score +id_history_type +incision_score +indoor_outdoor +lameness +mass_type +mens_score +mucous_membranes +musculoskeletal_observations +necropsy_disposition_codes +necropsy_organ_appearance +necropsy_organ_systems +necropsy_physical_condition +necropsy_specimen_condition +necropsy_tissue +neurologic_observations +nhp_training_reason +nhp_training_result +nhp_training_type +normal_abnormal_only +numeric_unit +observation_areas +obstetric_observations +ocular_observations +ocular_problem +pairing_formation_types +pairing_goal +pairing_reason +pairing_observation +pairing_separation_reason +preferences +pregnancy_result +procedure_category +procedures +problem_list_category +problem_list_subcategory +protocol_category +protocol_state +protocol_type +qualifier +questionnaire +rectal_prolapse +regulatory_stress_levels +req_order_state +req_order_type +respiratory_observations +routes +sib_score +skin_problem +source +snomed +species +species_codes +stool_score +stool_types +tb_obs_score +temperament +testicular_volume +trauma_size +treatment_frequency +treatment_frequency_times +turgor_score +vaginal_uterine_prolapse +vendor_approval_code +vendor_production_location +volume_units +weight_ranges +wound_score +wound_severity +wound_status_behavior +wound_status_clinical +yes_no_only +yes_no_order \ No newline at end of file diff --git a/nbri_ehr/resources/data/mens_score.tsv b/nbri_ehr/resources/data/mens_score.tsv new file mode 100644 index 0000000..25e25fd --- /dev/null +++ b/nbri_ehr/resources/data/mens_score.tsv @@ -0,0 +1,4 @@ +value sort_order +Present 1 +Not present 2 +Heavy mense 3 \ No newline at end of file diff --git a/nbri_ehr/resources/data/mucous_membranes.tsv b/nbri_ehr/resources/data/mucous_membranes.tsv new file mode 100644 index 0000000..0e58c42 --- /dev/null +++ b/nbri_ehr/resources/data/mucous_membranes.tsv @@ -0,0 +1,7 @@ +value sort_order +Pink (normal) 1 +Pale 2 +Cyanosis (bluish discoloration) 3 +Icterus (jaundice; yellow discoloration) 4 +Cannot visualize 5 +Other 6 \ No newline at end of file diff --git a/nbri_ehr/resources/data/musculoskeletal_observations.tsv b/nbri_ehr/resources/data/musculoskeletal_observations.tsv new file mode 100644 index 0000000..b3c6d90 --- /dev/null +++ b/nbri_ehr/resources/data/musculoskeletal_observations.tsv @@ -0,0 +1,8 @@ +value sort_order +Muscle atrophy 1 +Fractured limb 2 +Decreased extension of knees 3 +Crepitus (crackling sensation upon palpation) 4 +Kyphosis (spinal curvature; hunchback) 5 +No musculoskeletal abnormality observed 6 +Other musculoskeletal abnormality 7 \ No newline at end of file diff --git a/nbri_ehr/resources/data/necropsy_disposition_codes.tsv b/nbri_ehr/resources/data/necropsy_disposition_codes.tsv new file mode 100644 index 0000000..958ee97 --- /dev/null +++ b/nbri_ehr/resources/data/necropsy_disposition_codes.tsv @@ -0,0 +1,7 @@ +value title +1 Formalin Fixed +2 Frozen +3 Tissue Culture +4 Bacteriology +5 Ship to Sponsor +6 Other \ No newline at end of file diff --git a/nbri_ehr/resources/data/necropsy_exam_reason.tsv b/nbri_ehr/resources/data/necropsy_exam_reason.tsv new file mode 100644 index 0000000..4b7c6ce --- /dev/null +++ b/nbri_ehr/resources/data/necropsy_exam_reason.tsv @@ -0,0 +1,4 @@ +value title +1 Natural Death +2 Euth.-moribund +3 Euth.-project \ No newline at end of file diff --git a/nbri_ehr/resources/data/necropsy_organ_appearance.tsv b/nbri_ehr/resources/data/necropsy_organ_appearance.tsv new file mode 100644 index 0000000..c530f3e --- /dev/null +++ b/nbri_ehr/resources/data/necropsy_organ_appearance.tsv @@ -0,0 +1,3 @@ +value title +1 Normal +2 Abnormal \ No newline at end of file diff --git a/nbri_ehr/resources/data/necropsy_organ_systems.tsv b/nbri_ehr/resources/data/necropsy_organ_systems.tsv new file mode 100644 index 0000000..7f0bc70 --- /dev/null +++ b/nbri_ehr/resources/data/necropsy_organ_systems.tsv @@ -0,0 +1,10 @@ +value title +1 Nervous system +2 Cardiovascular system +3 Respiratory system +4 Digestive system +5 Genitourinary system +6 Lymphatic system +7 Musculoskeletal system +8 Endocrine system +9 Integumentary system \ No newline at end of file diff --git a/nbri_ehr/resources/data/necropsy_physical_condition.tsv b/nbri_ehr/resources/data/necropsy_physical_condition.tsv new file mode 100644 index 0000000..b50cc92 --- /dev/null +++ b/nbri_ehr/resources/data/necropsy_physical_condition.tsv @@ -0,0 +1,4 @@ +value title +1 Excellent +2 Fair +3 Poor \ No newline at end of file diff --git a/nbri_ehr/resources/data/necropsy_specimen_condition.tsv b/nbri_ehr/resources/data/necropsy_specimen_condition.tsv new file mode 100644 index 0000000..6edff69 --- /dev/null +++ b/nbri_ehr/resources/data/necropsy_specimen_condition.tsv @@ -0,0 +1,4 @@ +value title +1 Fresh +2 Refrigerated +3 Autolysis \ No newline at end of file diff --git a/nbri_ehr/resources/data/necropsy_tissue.tsv b/nbri_ehr/resources/data/necropsy_tissue.tsv new file mode 100644 index 0000000..68fa361 --- /dev/null +++ b/nbri_ehr/resources/data/necropsy_tissue.tsv @@ -0,0 +1,17 @@ +value title +1 Blood +2 Brain +3 Cecum +4 Colon +5 Duodenum +6 Heart +7 Ileum +8 Jejunum +9 Pancreas +10 Kidney +11 Stomach +12 Liver +13 Lung +14 Spleen +15 Tracheobronchial l.n. +16 Other \ No newline at end of file diff --git a/nbri_ehr/resources/data/neurologic_observations.tsv b/nbri_ehr/resources/data/neurologic_observations.tsv new file mode 100644 index 0000000..c533b35 --- /dev/null +++ b/nbri_ehr/resources/data/neurologic_observations.tsv @@ -0,0 +1,8 @@ +value sort_order +No neurologic abnormality observed 1 +Seizures 2 +Ataxia (uncoordinated movements) 3 +Head tilt 4 +Intention tremors 5 +Paralysis/Paresis 6 +Other neurologic abnormality 7 \ No newline at end of file diff --git a/nbri_ehr/resources/data/nhp_training_reason.tsv b/nbri_ehr/resources/data/nhp_training_reason.tsv new file mode 100644 index 0000000..f1d9759 --- /dev/null +++ b/nbri_ehr/resources/data/nhp_training_reason.tsv @@ -0,0 +1,6 @@ +value +PI Request +Behavioral Initiated +Clinic +Husbandry +Other \ No newline at end of file diff --git a/nbri_ehr/resources/data/nhp_training_result.tsv b/nbri_ehr/resources/data/nhp_training_result.tsv new file mode 100644 index 0000000..7b240f2 --- /dev/null +++ b/nbri_ehr/resources/data/nhp_training_result.tsv @@ -0,0 +1,4 @@ +value +In-Progress +Successful +Unsuccessful \ No newline at end of file diff --git a/nbri_ehr/resources/data/nhp_training_type.tsv b/nbri_ehr/resources/data/nhp_training_type.tsv new file mode 100644 index 0000000..4398c3a --- /dev/null +++ b/nbri_ehr/resources/data/nhp_training_type.tsv @@ -0,0 +1,5 @@ +value +Chair +Present +Physical Therapy +Other \ No newline at end of file diff --git a/nbri_ehr/resources/data/normal_abnormal.tsv b/nbri_ehr/resources/data/normal_abnormal.tsv new file mode 100644 index 0000000..951bfe9 --- /dev/null +++ b/nbri_ehr/resources/data/normal_abnormal.tsv @@ -0,0 +1,4 @@ +state +Normal +Abnormal +Not Evaluated \ No newline at end of file diff --git a/nbri_ehr/resources/data/normal_abnormal_only.tsv b/nbri_ehr/resources/data/normal_abnormal_only.tsv new file mode 100644 index 0000000..1ea2e59 --- /dev/null +++ b/nbri_ehr/resources/data/normal_abnormal_only.tsv @@ -0,0 +1,3 @@ +value sort_order +Normal 1 +Abnormal 2 \ No newline at end of file diff --git a/nbri_ehr/resources/data/numeric_unit.tsv b/nbri_ehr/resources/data/numeric_unit.tsv new file mode 100644 index 0000000..909173d --- /dev/null +++ b/nbri_ehr/resources/data/numeric_unit.tsv @@ -0,0 +1,91 @@ +value title description +1 Kg Kilogram +2 mmol Millimole +3 mm Millimeter +4 mL/min Milliliters per minute +5 mL Milliliter +6 mg/L Milligrams per liter +7 mg/g Milligrams per gram +8 mg/dL Milligrams per deciliter +9 mg/d Milligrams per day +10 mg/24 hrs Milligrams per 24 hours +11 mg Milligram +12 mPOL Milli polarization unit +13 mIU/hr Milli international units per hour +14 mIU Milli international units +15 LIV Lyme index value +16 L Liter +17 IU/mL International units per milliliter +18 IU/L International units per liter +19 IU/g International units per gram +20 IU International unit +21 ISR Immune status ratio +22 MPL IgM phospholipid units +23 GPL IgG phospholipid units +24 h Hour +25 g/dL Grams per deciliter +26 g/d Grams per day +27 g/24 hrs Grams per 24 hours +28 g/5 hrs Grams per 5hours +29 g Gram +30 fL Femtoliter +31 EIU Enzyme immunoassay unit +32 EU/mL Ehrlich units per milliliter +33 EU/24 hrs Ehrlich units per 24 hours +34 EU Ehrlich unit +35 ETU/mL Endotoxin units per milliliter +36 dL Deciliter +37 d Day +38 cpy/mL Copies per milliliter +39 CMM Cubic milliliter +40 cP Centipoise unit +41 CFU/mL Colony forming units per milliliter +42 AU/mL Arbitrary units per milliliter +43 U/mL Units per milliliter +44 U/L Units per liter +45 U/hr Units per hour +46 U/g Units per gram +47 U/day Units per day +48 U Unit +49 TV Total volume +50 TIV Toxoplasma index value +51 SD Standard deviation +52 s Second +53 RIV Rubella index value +54 pmol/g Picomoles per gram +55 pmol Picomole +56 pg/mL Picograms per milliliter +57 pg Picogram +58 % Percent +59 ppm Parts per million +60 nmol/mL Nanomoles per milliliter +61 nmol/L Nanomoles per liter +62 nmol/g Nanomoles per gram +63 nmol/dL Nanomoles per deciliter +64 nmol/d Nanomoles per day +65 nmol Nanomole +66 nM/mM Nanomole per millimole +67 ng/mL/hr Nanograms per milliliter per hour +68 ng/mL Nanograms per milliliter +69 ng/L Nanograms per liter +70 ng/dL Nanograms per deciliter +71 ng Nanogram +72 mol Mole +73 min Minute +74 mU/mL Milliunits per milliliter +75 mU/L Milliunits per liter +76 mU/g Milliunits per gram +77 mU Milliunit +78 mOsm/kg Milliosmoles per kilogram +79 mOsm Milliosmole +80 mmol/L Millimoles per liter +81 mmol/d Millimoles per day +82 mmHg Millimeters of Mercury +83 p/m Pulses per minute +84 b/m Breaths per minute +85 hb/m Heartbeats per minute +86 °F Degree Fahrenheit +87 breaths/min Breaths per minute +88 heartbeats/min Heartbeats per minute +89 pulses/min Pulses per minute +90 BCS Body condition score diff --git a/nbri_ehr/resources/data/observation_areas.tsv b/nbri_ehr/resources/data/observation_areas.tsv new file mode 100644 index 0000000..d73b6b2 --- /dev/null +++ b/nbri_ehr/resources/data/observation_areas.tsv @@ -0,0 +1,34 @@ +value title sort_order +N/A N/A 1 +Whole Body Whole Body 2 +Thorax Thorax 4 +EENT EENT 5 +Integ Integ 6 +MS MS 7 +Oral Oral 8 +PLN PLN 9 +U/G U/G 10 +Incision: Main Incision: Main 12 +Incision: Scope Incision: Scope 13 +Incision: L-Port Incision: L-Port 14 +Incision: R-Port Incision: R-Port 15 +Incision: All Incision: All 16 +Right Eyelid Right Eyelid 17 +Left Eyelid Left Eyelid 18 +Left Hand Left Hand 19 +Right Hand Right Hand 20 +Left Foot Left Foot 21 +Right Foot Right Foot 22 +Head & Neck Head & Neck 23 +Right Forelimb Right Forelimb 24 +Left Forelimb Left Forelimb 25 +Chest Chest 26 +Abdomen Abdomen 27 +Upper Back Upper Back 28 +Lower Back Lower Back 29 +Right Upper Leg Right Upper Leg 30 +Left Upper Leg Left Upper Leg 31 +Right Lower Leg & Foot Right Lower Leg & Foot 32 +Left Lower Leg & Foot Left Lower Leg & Foot 33 +Tail Tail 34 +Other Other 35 \ No newline at end of file diff --git a/nbri_ehr/resources/data/observation_types.tsv b/nbri_ehr/resources/data/observation_types.tsv new file mode 100644 index 0000000..b59b7c2 --- /dev/null +++ b/nbri_ehr/resources/data/observation_types.tsv @@ -0,0 +1,55 @@ +value category editorconfig schemaName queryName valueColumn +Abdominal Observations {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"abdominal_obs_types","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups abdominal_obs_types value +Abnormal Behaviors Behavior {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"behavior_types","displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups behavior_types value +Activity {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"activity","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups activity value +Alopecia Regrowth Behavior {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"alopecia_regrowth","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups alopecia_regrowth value +Alopecia Score Behavior {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"alopecia_score","forceSelection":true,"displayField":"title","valueField":"value","sortFields":"sort_order"} ehr_lookups alopecia_score value +Alopecia Type Behavior {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"alopecia_type","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups alopecia_type value +Appetite {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"app_score","displayField":"value","sortFields":"sort_order","valueField":"value"} ehr_lookups app_score value +Attitude {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"att_score","displayField":"value","valueField":"value"} ehr_lookups att_score value +Auscultation {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"normal_abnormal_only","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups normal_abnormal_only value +Bandage/Splint Observations {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"bandage_observations","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups bandage_observations value +BCS {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"bcs_score","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups bcs_score value +Behavior Abnormality {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"behavior_abnormality","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups behavior_abnormality value +Behavior Management Behavior {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"behavior_mgmt_codes","forceSelection":true,"displayField":"title","valueField":"value","sortFields":"sort_order"} ehr_lookups behavior_mgmt_codes value +Capillary Refill Time {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"capillary_refill_time","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups capillary_refill_time value +Daily Enrichment Behavior {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"daily_enrich_codes","forceSelection":true,"displayField":"title","valueField":"value","sortFields":"sort_order"} ehr_lookups daily_enrich_codes value +Dental/Oral Observations {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"dental_obs","displayField":"value","sortFields":"sort_order","valueField":"value"} ehr_lookups dental_obs value +Dermatologic Observations {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"derm_obs","displayField":"value","sortFields":"sort_order","valueField":"value"} ehr_lookups derm_obs value +Environmental Change Behavior {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"yes_no_order","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups yes_no_order value +Feed Assessment {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"feed_assess_types","displayField":"value","valueField":"value"} ehr_lookups feed_assess_types value +General Behavior Observation Behavior {"xtype":"textfield"} +General Observations {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"general_obs","displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups general_obs value +Genitourinary Observations {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"genitourinary_obs","displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups genitourinary_obs value +Hernia {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"hernia_types","displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups hernia_types value +Hydration {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"hyd_score","displayField":"value","sortFields":"sort_order","valueField":"value"} ehr_lookups hyd_score value +Incision Status {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"incision_score","displayField":"value","sortFields":"sort_order","valueField":"value"} ehr_lookups incision_score value +Lameness {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"lameness","displayField":"value","valueField":"value"} ehr_lookups lameness value +Mass {"xtype":"textfield"} +Menses {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"mens_score","displayField":"value","sortFields":"sort_order","valueField":"value"} ehr_lookups mens_score value +Mucous Membranes {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"mucous_membranes","displayField":"value","sortFields":"sort_order","valueField":"value"} ehr_lookups mucous_membranes value +Musculoskeletal Observations {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"musculoskeletal_observations","displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups musculoskeletal_types value +Neurologic Observations {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"neurologic_observations","displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups neurologic_observations value +New Injury Observed Behavior {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"yes_no_order","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups yes_no_order value +Obstetric Observations {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"obstetric_observations","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups obstetric_observations value +Ocular Observations {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"ocular_observations","displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups ocular_problem value +Other Stereotopy Behavior {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"yes_no_order","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups yes_no_order value +Preferences Behavior {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"preferences","displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups preferences value +Rectal Prolapse {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"rectal_prolapse","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups rectal_prolapse value +Respiratory Observations {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"respiratory_observations","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups respiratory_observations value +Respiratory Rate {"xtype":"textfield"} +Self Biting Observed Behavior {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"yes_no_order","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups yes_no_order value +SIB Score Behavior {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"sib_score","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups sib_score value +Special Enrichment Behavior {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"yes_no_order","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups yes_no_order value +Stool {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"stool_types","displayField":"value","sortFields":"sort_order","valueField":"value"} ehr_lookups stool_types value +Temperament Behavior {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"temperament","displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups temperament value +Testicular volume-Left "{""xtype"":""ehr-simplecombo"",""schemaName"":""ehr_lookups"",""queryName"":""testicular_volume"",""displayField"":""value"",""valueField"":""value"",""sortFields"":""sort_order""}" ehr_lookups testicular_volume value +Testicular volume-Right "{""xtype"":""ehr-simplecombo"",""schemaName"":""ehr_lookups"",""queryName"":""testicular_volume"",""displayField"":""value"",""valueField"":""value"",""sortFields"":""sort_order""}" ehr_lookups testicular_volume value +Vaginal/Uterine Prolapse {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"vaginal_uterine_prolapse","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups vaginal_uterine_prolapse value +Verified Id? {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"yes_no_order","forceSelection":true,"displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups yes_no_order value +Wound Severity Behavior {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"wound_severity","displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups wound_severity value +Wound Status Behavior {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"wound_status_behavior","displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups wound_status_behavior value +Clinical Wound Status {"xtype":"ehr-simplecombo","schemaName":"ehr_lookups","queryName":"wound_status_clinical","displayField":"value","valueField":"value","sortFields":"sort_order"} ehr_lookups wound_status_clinical value +Annual Physical Exam "{""xtype"":""ehr-simplecombo"",""schemaName"":""ehr_lookups"",""queryName"":""exam_findings"",""displayField"":""value"",""valueField"":""value"",""sortFields"":""sort_order""}" ehr_lookups exam_findings value +Introductory Physical Exam "{""xtype"":""ehr-simplecombo"",""schemaName"":""ehr_lookups"",""queryName"":""exam_findings"",""displayField"":""value"",""valueField"":""value"",""sortFields"":""sort_order""}" ehr_lookups exam_findings value +Preshipment Physical Exam "{""xtype"":""ehr-simplecombo"",""schemaName"":""ehr_lookups"",""queryName"":""exam_findings"",""displayField"":""value"",""valueField"":""value"",""sortFields"":""sort_order""}" ehr_lookups exam_findings value \ No newline at end of file diff --git a/nbri_ehr/resources/data/obstetric_observations.tsv b/nbri_ehr/resources/data/obstetric_observations.tsv new file mode 100644 index 0000000..87fb182 --- /dev/null +++ b/nbri_ehr/resources/data/obstetric_observations.tsv @@ -0,0 +1,9 @@ +value sort_order +Pregnant 1 +No pregnancy detected 2 +Mammary gland abscess/mastitis 3 +Agalactia/low milk production 4 +Dystocia/difficult labor 5 +Retained placenta 6 +No abnormality observed 7 +Other 8 \ No newline at end of file diff --git a/nbri_ehr/resources/data/ocular_observations.tsv b/nbri_ehr/resources/data/ocular_observations.tsv new file mode 100644 index 0000000..41bd460 --- /dev/null +++ b/nbri_ehr/resources/data/ocular_observations.tsv @@ -0,0 +1,8 @@ +value sort_order +Blepharospasm/swollen eyelids 1 +Conjunctivitis 2 +Ocular discharge 3 +Phthisis bulbi (shrunken globe) 4 +Cataract(s) 5 +No ocular abnormality observed 6 +Other ocular abnormality 7 \ No newline at end of file diff --git a/nbri_ehr/resources/data/pairing_formation_types.tsv b/nbri_ehr/resources/data/pairing_formation_types.tsv new file mode 100644 index 0000000..64101aa --- /dev/null +++ b/nbri_ehr/resources/data/pairing_formation_types.tsv @@ -0,0 +1,7 @@ +value +Full Contact Pair +Group Formation +Introduction +Limited Contact Pair +Pair Formation +Other \ No newline at end of file diff --git a/nbri_ehr/resources/data/pairing_goal.tsv b/nbri_ehr/resources/data/pairing_goal.tsv new file mode 100644 index 0000000..0aa0edd --- /dev/null +++ b/nbri_ehr/resources/data/pairing_goal.tsv @@ -0,0 +1,5 @@ +value +Solid barrier +Mesh barrier +Full access +Clear barrier \ No newline at end of file diff --git a/nbri_ehr/resources/data/pairing_observation.tsv b/nbri_ehr/resources/data/pairing_observation.tsv new file mode 100644 index 0000000..796e9f1 --- /dev/null +++ b/nbri_ehr/resources/data/pairing_observation.tsv @@ -0,0 +1,4 @@ +value +Compatibility +Incompatible +Undetermined \ No newline at end of file diff --git a/nbri_ehr/resources/data/pairing_reason.tsv b/nbri_ehr/resources/data/pairing_reason.tsv new file mode 100644 index 0000000..92e62c5 --- /dev/null +++ b/nbri_ehr/resources/data/pairing_reason.tsv @@ -0,0 +1,9 @@ +value +Breeding +Buddy monkey +Predicted compatibility +Protocol +Other +Retirement +Re-pairing +Partner Availability \ No newline at end of file diff --git a/nbri_ehr/resources/data/pairing_separation_reason.tsv b/nbri_ehr/resources/data/pairing_separation_reason.tsv new file mode 100644 index 0000000..5290317 --- /dev/null +++ b/nbri_ehr/resources/data/pairing_separation_reason.tsv @@ -0,0 +1,8 @@ +value +Aggression +Sale +Move to social group +Clinical +Relocation +Other +None \ No newline at end of file diff --git a/nbri_ehr/resources/data/preferences.tsv b/nbri_ehr/resources/data/preferences.tsv new file mode 100644 index 0000000..ceff4a8 --- /dev/null +++ b/nbri_ehr/resources/data/preferences.tsv @@ -0,0 +1,4 @@ +Value Title Category Description Sort Order Date Disabled +Foods +Housing and Caging +Social Setting \ No newline at end of file diff --git a/nbri_ehr/resources/data/pregnancy_result.tsv b/nbri_ehr/resources/data/pregnancy_result.tsv new file mode 100644 index 0000000..1c615bc --- /dev/null +++ b/nbri_ehr/resources/data/pregnancy_result.tsv @@ -0,0 +1,3 @@ +value title +1 Stillborn +2 Abort \ No newline at end of file diff --git a/nbri_ehr/resources/data/problem_list_category.tsv b/nbri_ehr/resources/data/problem_list_category.tsv new file mode 100644 index 0000000..67fcf34 --- /dev/null +++ b/nbri_ehr/resources/data/problem_list_category.tsv @@ -0,0 +1,14 @@ +value description +Behavioral Behavioral issue or concern. Examples include SIB and fecal smearing. +Trauma Case opened for some type of trauma. +GI abnormality Abnormalities associated with the digestive system. +Neurologic abnormality Abnormalities associated with the neurologic system. +Dermatologic abnormality Abnormalities associated with the dermal system. +Genitourinary abnormality Abnormalities associated with the genitourinary system. +Circulatory abnormality Abnormalities associated with the circulatory system. +Ocular abnormality Abnormalities associated with the ocular system. +Respiratory abnormality Abnormalities associated with the respiratory system. +Oral abnormality Abnormalities associated with the oral cavity. +Musculoskeletal abnormality Abnormalities associated with the musculoskeletal system. +General abnormality Abnormalities that do not fit into any other category. +Study-related surgery Case opened for a surgery or activity supporting a research project. \ No newline at end of file diff --git a/nbri_ehr/resources/data/problem_list_subcategory.tsv b/nbri_ehr/resources/data/problem_list_subcategory.tsv new file mode 100644 index 0000000..fae2d42 --- /dev/null +++ b/nbri_ehr/resources/data/problem_list_subcategory.tsv @@ -0,0 +1,75 @@ +value category +Alopecia Behavioral +SIB Behavioral +Other behavioral Behavioral +Stereotypy Behavioral +Fecal smear Behavioral +Eye poking Behavioral +Urine drinking Behavioral +Copraphagy Behavioral +Skin laceration(s) Trauma +Muscle laceration(s) Trauma +Crushing wounds Trauma +Abrasions Trauma +Fracture(s) Trauma +Puncture wounds Trauma +Traumatic amputation(s) Trauma +SIB (self-injurious behavior) Trauma +Other trauma Trauma +Diarrhea GI abnormality +Undercondition General abnormality +Dehydration General abnormality +Bloody Stool GI abnormality +Anorexia GI abnormality +Rectal prolapse GI abnormality +Hepatomegaly GI abnormality +Other GI abnormality GI abnormality +Ataxia Neurologic abnormality +Paralysis/Paresis Neurologic abnormality +Head tilt Neurologic abnormality +Other neurologic abnormality Neurologic abnormality +Penile/preputial lesions Dermatologic abnormality +Dermatitis Dermatologic abnormality +Abscess Dermatologic abnormality +Incisional infection Dermatologic abnormality +Skin mass Dermatologic abnormality +Skin lesion(s) Dermatologic abnormality +Other dermatologic abnormality Dermatologic abnormality +Dystocia Genitourinary abnormality +Vaginal prolapse Genitourinary abnormality +Uterine enlargement Genitourinary abnormality +Endometriosis Genitourinary abnormality +Retained placenta Genitourinary abnormality +Hematuria (bloody urine) Genitourinary abnormality +Other genitourinary abnormality Genitourinary abnormality +AV fistula Circulatory abnormality +Heart murmur Circulatory abnormality +Other circulatory abnormality Circulatory abnormality +Conjunctivitis/ocular discharge Ocular abnormality +Blepharospasm Ocular abnormality +Corneal ulcer Ocular abnormality +Other ocular abnormality Ocular abnormality +Dyspnea/Labored breathing Respiratory abnormality +Purulent nasal discharge Respiratory abnormality +Epistaxis/bloody nasal discharge Respiratory abnormality +Other respiratory abnormality Respiratory abnormality +Tooth abscess Oral abnormality +Gingivitis/periodontal disease Oral abnormality +Foreign body in cheek pouch Oral abnormality +Oral mass Oral abnormality +Other oral abnormality Oral abnormality +Lameness Musculoskeletal abnormality +Other musculoskeletal abnormality Musculoskeletal abnormality +Weight loss General abnormality +Edema General abnormality +Abdominal mass General abnormality +Unresponsive/Down General abnormality +Lethargy General abnormality +Orphan/dam neglect General abnormality +Anemia General abnormality +Thrombocytopenia General abnormality +Other general abnormality General abnormality +Jejunal resection Study-related surgery +Liver biopsy Study-related surgery +Spleen biopsy Study-related surgery +Other study-related surgery Study-related surgery diff --git a/nbri_ehr/resources/data/procedure_category.tsv b/nbri_ehr/resources/data/procedure_category.tsv new file mode 100644 index 0000000..6a78807 --- /dev/null +++ b/nbri_ehr/resources/data/procedure_category.tsv @@ -0,0 +1,5 @@ +Value Title Category Description Sort Order Date Disabled +Pathology Pathology 4 +Procedure Procedure 1 +Research Research 3 +Surgery Surgery 2 \ No newline at end of file diff --git a/nbri_ehr/resources/data/procedures.tsv b/nbri_ehr/resources/data/procedures.tsv new file mode 100644 index 0000000..4560d70 --- /dev/null +++ b/nbri_ehr/resources/data/procedures.tsv @@ -0,0 +1,130 @@ +Name +Oral Dose Administration +Oral Dose Administration - Alert +Oral Dose Administration - Intubation +Sublingual Dose Administration +Intrarectal Dose Administration +Intramuscular Dose Administration +IM Dose Administration - Quadriceps +IM Dose Administration - Deltoid +Subcutaneous Dose Administration +Intravenous Dose Administration +Intravenous Dose Administration - Bolus +Intravenous Dose Admin - Infusion +Intraperitoneal Dose Administration +Topical Dose Administration +Inhalation Dose Administration +Intranasal Dose Administration +Intravaginal Dose Administration +Body Weight +Electrocardiogram +Temperature Monitoring +Heart Rate Monitoring +Blood Pressure Monitoring +WelshAllyn Vital Signs Montoring +Respiration Monitoring +Pulse Rate Monitoring +Sedative Administration +Ketamine Administration +Diazepam Administration +Telazol Administration +Xylazine Administration +Ketamine/Diazepam Administration +Ketamine/Xylazine Administration +Intramuscular Anesthesia +Venipuncture +Blood Collection +Blood Collection - SST for serum +Blood Collection - EDTA for plasma +BC - Sodium Heparin for plasma +Blood Collection - EDTA for PBMCs +BC - Sodium Heparin for PBMCs +Blood Collection - EDTA for Flow +Blood Collection - EDTA for CBC +Blood Collection - SST for Chemistry +B C - Sodium Citrate for Coag +B C - Sodium Citrate for plasma +Urine Collection +Urine Collection - Catheter +Urine Collection - Pan catch +Cervicovaginal Secretion Collection +Stool Collection +Rectal Swab Sample Collection +Nasal Wash Sample Collection +Saliva Sample Collection +Wound Specimen Collection +Tissue Collection +Tissue Collection - Necropsy +Bleeding Time Test +Radiography +Tuberculosis Skin Test +Intradermal Skin Test +Pole and Collar +Squeeze Cage +Primate Chair +Chemical Restraint +Hand Catch +Daily Observations +Apheresis +Endoscopy Assistance +Ultrasound Assistance +Lymph Node Biopsy +Liver Biopsy +Skin Biopsy +Behavioral Observations +Continuous Observations +30 - minute Observations +SID Observations +BID Observations +Interval Observations (IST) +Intravenous Anesthesia +BC - Sodium Citrate for Coag +BC - Sodium Citrate for plasma +Follow-up Physical Exam +Prestudy Physical Exam +Ophthalmic Exam - Direct +Ophthalmic Exam - Indirect +Oophorectomy +Wedge Liver Biopsy +Skin Boipsy +Liver Percutaneous Biopsy +Hepatic Biopsy - Tru Cut +Hepatic Biopsy - Menghini Technique +Skeletal Muscle Biopsy +Lung Biopsy +White fat Biopsy +Brown fat Biopsy +Renal Biopsy +Gastric Biopsy +Intestinal Biopsy +Cervical Biopsy +Rectal Biopsy +Urine Biopsy +Vaginal Biopsy +Testicular Biopsy +Bone Marrow Biopsy +Bone Marrow Aspirates +Splenectomy +Thoracocentesis +Abdominocentesis +Catheter/Canula Placement - Femoral +Catheter/Canula Placement - Saphenous +Cather/Canula Placement - Intestinal +Catheter/Canula Placement - Portal +Aspirate - Specify +Abdominal Ultrasound +Cardiac Ultrasound +Thoracic Ultrasound +Ultrasound - Specify +Skin-Biopsy +Embryo Transfer +Oocyte Collection +Electroejaculation +Cesarian section +Vasectomy +Pulpectomy +Pulpotomy +wfrfr3 +Thoracocentesiss +BC - Sodium Citrate for Coags +BC - Sodium Citrate for plasmas \ No newline at end of file diff --git a/nbri_ehr/resources/data/protocol_category.tsv b/nbri_ehr/resources/data/protocol_category.tsv new file mode 100644 index 0000000..6fb50d6 --- /dev/null +++ b/nbri_ehr/resources/data/protocol_category.tsv @@ -0,0 +1,3 @@ +value title +1 Stock/Breeder Protocol +2 Study Protocol \ No newline at end of file diff --git a/nbri_ehr/resources/data/protocol_state.tsv b/nbri_ehr/resources/data/protocol_state.tsv new file mode 100644 index 0000000..1420c93 --- /dev/null +++ b/nbri_ehr/resources/data/protocol_state.tsv @@ -0,0 +1,7 @@ +value title +0 Template +1 Unsubmitted +2 Submitted +3 Approved +4 Not Approved +5 Returned \ No newline at end of file diff --git a/nbri_ehr/resources/data/protocol_type.tsv b/nbri_ehr/resources/data/protocol_type.tsv new file mode 100644 index 0000000..2b0eb13 --- /dev/null +++ b/nbri_ehr/resources/data/protocol_type.tsv @@ -0,0 +1,6 @@ +value title +0 Template +1 Original +2 Amendment +3 Renewal +4 Renewal/Amendment \ No newline at end of file diff --git a/nbri_ehr/resources/data/qualifier.tsv b/nbri_ehr/resources/data/qualifier.tsv new file mode 100644 index 0000000..19fc27d --- /dev/null +++ b/nbri_ehr/resources/data/qualifier.tsv @@ -0,0 +1,54 @@ +value title description +1 Species Species +2 Sex Sex +3 Age Age +4 Naive Naive +5 No Exposure to MAB No Exposure to MAB +6 No Exposure to other No Exposure to other +7 No Exposure to 30ds No Exposure to 30ds +8 No Exposure to 60ds No Exposure to 60ds +9 No Exposure to 90ds No Exposure to 90ds +10 No exposure for other No exposure for other +11 Juvenile Juvenile +12 HCV negative HCV negative +13 HIV negative HIV negative +14 HBV negative HBV negative +15 Monoclonal negative Monoclonal negative +16 HCV HCV +17 Antigenemia positive Antigenemia positive +18 SPF SPF +19 Enteric pathogen negative Enteric pathogen negative +20 Accepts alert dosing Accepts alert dosing +21 Alert bleeding Alert bleeding +22 Chair trained Chair trained +23 Obesity Obesity +24 Diabetes Diabetes +25 Male Male +26 Female Female +27 Over 2 years old Over 2 years old +28 Oophorectomized Oophorectomized +29 Vasectomy Vasectomy +30 Castration Castration +31 Hysterectomy Hysterectomy +32 Canines blunted Canines blunted +33 Canines removed Canines removed +34 Limb amputation Limb amputation +35 Abdominal Surgery (in the past) Abdominal Surgery (in the past) +36 SIB (under current medication) Self Injurious Behavior (under current medication) +37 Chronic enteritis Chronic enteritis +38 Intermittent recurrent enteritis Intermittent recurrent enteritis +39 No experimental usage for 30days No experimental usage for 30days +40 Splenectomized Splenectomized +41 Partial hepatic lobectomy Partial hepatic lobectomy +42 Chronic disease Chronic disease (may be heart disease, anything other than enteritis or diabetes) +43 Alert bleeding trained Alert bleeding trained +44 Non-pregnant Non-pregnant +45 Lactating Lactating +46 Behavioral stereotypy (other than SIB) Behavioral stereotypy (other than SIB) +47 1 - 2 years old 1 - 2 years old +48 Less than 1 year old Less than 1 year old +49 Nursing infant Nursing infant +50 Pregnant Pregnant +51 No Exposure for 30ds No Exposure for 30ds +52 No Exposure for 60ds No Exposure for 60ds +53 No Exposure for 90ds No Exposure for 90ds diff --git a/nbri_ehr/resources/data/questionnaire.tsv b/nbri_ehr/resources/data/questionnaire.tsv new file mode 100644 index 0000000..08e8bad --- /dev/null +++ b/nbri_ehr/resources/data/questionnaire.tsv @@ -0,0 +1,4 @@ +value title +1 Short, ver 1 +3 Short, ver 2 +4 Complete, ver 1 \ No newline at end of file diff --git a/nbri_ehr/resources/data/rectal_prolapse.tsv b/nbri_ehr/resources/data/rectal_prolapse.tsv new file mode 100644 index 0000000..98f995c --- /dev/null +++ b/nbri_ehr/resources/data/rectal_prolapse.tsv @@ -0,0 +1,3 @@ +value sort_order +Present 1 +Not present 2 \ No newline at end of file diff --git a/nbri_ehr/resources/data/regulatory_stress_levels.tsv b/nbri_ehr/resources/data/regulatory_stress_levels.tsv new file mode 100644 index 0000000..40aed55 --- /dev/null +++ b/nbri_ehr/resources/data/regulatory_stress_levels.tsv @@ -0,0 +1,6 @@ +value title description +1 A USDA Stress Level A +2 B USDA Stress Level B +3 C USDA Stress Level C +4 D USDA Stress Level D +5 E USDA Stress Level E diff --git a/nbri_ehr/resources/data/req_order_state.tsv b/nbri_ehr/resources/data/req_order_state.tsv new file mode 100644 index 0000000..a30594d --- /dev/null +++ b/nbri_ehr/resources/data/req_order_state.tsv @@ -0,0 +1,6 @@ +value title +0 Template +1 In Progress +2 Submitted +4 Not Approved +5 Approved \ No newline at end of file diff --git a/nbri_ehr/resources/data/req_order_type.tsv b/nbri_ehr/resources/data/req_order_type.tsv new file mode 100644 index 0000000..1dd7d05 --- /dev/null +++ b/nbri_ehr/resources/data/req_order_type.tsv @@ -0,0 +1,5 @@ +value title +1 Single +2 Standing +3 Waiting List +4 Back \ No newline at end of file diff --git a/nbri_ehr/resources/data/respiratory_observations.tsv b/nbri_ehr/resources/data/respiratory_observations.tsv new file mode 100644 index 0000000..fdc5574 --- /dev/null +++ b/nbri_ehr/resources/data/respiratory_observations.tsv @@ -0,0 +1,9 @@ +value sort_order +Tachypnea (increased respiratory rate) 1 +Dyspnea (difficulty breathing) 2 +Epistaxis (bloody nasal discharge) 3 +Clear nasal discharge 4 +Purulent nasal discharge 5 +Wheezing or noisy breathing 6 +No respiratory abnormality observed 7 +Other respiratory abnormality 8 \ No newline at end of file diff --git a/nbri_ehr/resources/data/routes.tsv b/nbri_ehr/resources/data/routes.tsv new file mode 100644 index 0000000..8d83daf --- /dev/null +++ b/nbri_ehr/resources/data/routes.tsv @@ -0,0 +1,17 @@ +Route Meaning +IM +intracardiac +intracarotid +intracorneal Intracorneal +intracranial +IP intraperitoneal +IT +IV +IVAG +oral +PO +rectal +SQ +topical +topical (eye) +topical (skin) diff --git a/nbri_ehr/resources/data/sib_score.tsv b/nbri_ehr/resources/data/sib_score.tsv new file mode 100644 index 0000000..5998060 --- /dev/null +++ b/nbri_ehr/resources/data/sib_score.tsv @@ -0,0 +1,8 @@ +value sort_order +0 1 +1.1 2 +1.2 3 +1.3 4 +1 4 +2 5 +3 6 \ No newline at end of file diff --git a/nbri_ehr/resources/data/snomed.tsv b/nbri_ehr/resources/data/snomed.tsv new file mode 100644 index 0000000..9253d5d --- /dev/null +++ b/nbri_ehr/resources/data/snomed.tsv @@ -0,0 +1,357 @@ +Code Meaning +NBRI-001 Acepromazine +NBRI-002 Acetaminophen +NBRI-003 Adequan +NBRI-004 Albendazole +NBRI-005 Albon suspension +NBRI-006 Albuterol +NBRI-007 Alfaxalone +NBRI-008 Alfentanil +NBRI-009 Alprazolam +NBRI-010 Aluminum Hydroxide +NBRI-011 Amikacin Sulfate +NBRI-012 Aminophylline +NBRI-013 Amiodarone +NBRI-014 Amitriptyline +NBRI-015 Amoxicillin +NBRI-016 Amoxicillin / Clavulanic Acid +NBRI-017 Amoxi-Mast +NBRI-018 Ampicillin +NBRI-019 Ampicillin/Sulbactam +NBRI-020 Artemether +NBRI-021 Aspirin +NBRI-022 Atenolol Suspension +NBRI-023 Atipamezole HCl +NBRI-024 Atracurium +NBRI-025 Atropine Sulfate +NBRI-026 Azathioprine +NBRI-027 Azithromycin +NBRI-028 Barium Sulfate +NBRI-029 Belatacept +NBRI-030 Benzoyl Peroxide Shampoo +NBRI-031 Betamethasone Dipropionate +NBRI-032 Bethanechol +NBRI-033 Bio-Sponge +NBRI-034 Biozide Gel +NBRI-035 Bismuth Subsalicylate +NBRI-036 Budesonide +NBRI-037 Bupivacaine HCl +NBRI-038 Bupivacaine HCl And Epinephrine +NBRI-039 Bupivacaine SR (Nocita) +NBRI-040 Buprenorphine +NBRI-041 Buprenorphine SR +NBRI-042 Busulfan +NBRI-043 Butorphanol Tartrate +NBRI-044 Calcium citrate powder +NBRI-045 Calcium gluconate 23% +NBRI-046 Carprofen, injectable +NBRI-047 Carprofen, oral +NBRI-048 Carvedilol +NBRI-049 Cd3-Immunotoxin +NBRI-050 Cefazolin +NBRI-051 Cefdinir +NBRI-052 Cefovecin (Convenia) +NBRI-053 Cefpodoxime +NBRI-054 Ceftiofur crystalline free acid (CFFA) +NBRI-055 Ceftriaxone +NBRI-056 Cefuroxime +NBRI-057 Cephalexin +NBRI-058 Chloramphenicol +NBRI-059 Chlorhexidine spray (Duoxo®) +NBRI-060 Chloroquine +NBRI-061 Chlorpromazine +NBRI-062 Chlorthalidone +NBRI-063 Cimetidine +NBRI-064 Ciprofloxacin +NBRI-065 Cisapride +NBRI-066 Clay +NBRI-067 Clindamycin +NBRI-068 Clobetasol Propionate +NBRI-069 Clomipramine +NBRI-070 Clopidogrel +NBRI-071 Cloprostenol +NBRI-072 Colchicine +NBRI-073 Collodial Oatmeal +NBRI-074 Cyanocobalamin (Vitamin B12) +NBRI-075 Cyclomydril +NBRI-076 Cyclophosphamide +NBRI-077 Cyclosporine +NBRI-078 Cyproheptadine +NBRI-079 DA2PP Vaccine (Distemper, Adenovirus Type 2, Parvovirus, Parainfluenza) +NBRI-080 Definity +NBRI-081 Denv Vaccine +NBRI-082 Derma Caps +NBRI-083 Deslorelin +NBRI-084 Dexamethasone +NBRI-085 Dexamethasone SP +NBRI-086 Dexmedetomidine HCl +NBRI-087 Dextromethorphan +NBRI-088 Dextrose +NBRI-089 Diazepam +NBRI-090 Diclofenac Sodium Ophthalmic Solution +NBRI-091 Diet, Ensure Liquid Nutrition +NBRI-092 Diet, Ensure Soaked Biscuits +NBRI-093 Diet, Juice Soaked Biscuits +NBRI-094 Diet, Misc, Nos +NBRI-095 Diet, Water Soaked Biscuits +NBRI-096 Digoxin +NBRI-097 Dimethicone Barrier Cream +NBRI-098 Dinoprost (PGF2 alpha) +NBRI-099 Diphenhydramine, injectable +NBRI-100 Diphenhydramine, oral +NBRI-101 Diphenoxylate +NBRI-102 Dobutamine +NBRI-103 Docusate Sodium +NBRI-104 Dopamine +NBRI-105 Doxapram +NBRI-106 Doxipen +NBRI-107 Doxycycline +NBRI-108 Draxxin +NBRI-109 Dronabinol +NBRI-110 Drug, Nos +NBRI-111 Ear cleaning solution +NBRI-112 Enalapril +NBRI-113 Enrofloxacin, injectable +NBRI-114 Enrofloxacin, oral +NBRI-115 Enulose +NBRI-116 Epinephrine [1:1000, 1 mg/mL] +NBRI-117 Epoetin +NBRI-118 Epsom salt bag +NBRI-119 Erythromycin +NBRI-120 Essential 6 Spot On +NBRI-121 Famotidine, injectable +NBRI-122 Famotidine, oral +NBRI-123 Fenbendazole +NBRI-124 Fentanyl +NBRI-125 Fenugreek +NBRI-126 Finasteride +NBRI-127 Florfenicol +NBRI-128 Fluconazole +NBRI-129 Flumazenil +NBRI-130 Flunixin meglumine +NBRI-131 Fluoxetine +NBRI-132 Flurbiprofen +NBRI-133 Fosphenytoin +NBRI-134 FSH +NBRI-135 Furosemide +NBRI-136 FVRCP vaccine (Feline Viral Rhinotracheitis, Calicivirus, Panleukopenia) +NBRI-137 Gabapentin +NBRI-138 Gentamicin +NBRI-139 Gentamicin/ betamethasone spray +NBRI-140 Glipizide +NBRI-141 Glucosamine/Chondroitin Ds +NBRI-142 Glucosamine/Chondroitin/Msm +NBRI-143 Glycopyrrolate +NBRI-144 Golytely +NBRI-145 Granulex +NBRI-146 Griseofulvin +NBRI-147 Guanfacine +NBRI-148 Haloperidol decanoate (depot) +NBRI-149 Haloperidol lactate +NBRI-150 Heparin Sodium +NBRI-151 Hetastarch +NBRI-152 Human Chorionic Gonadotropin +NBRI-153 Humilac +NBRI-154 Hydrocortisone cream +NBRI-155 Hydrogel +NBRI-156 Hydromorphone +NBRI-157 Hydromorphone Injectable Hcl +NBRI-158 Hypertonic Saline +NBRI-159 Ibuprofen +NBRI-160 Indocyanine Green +NBRI-161 Influenza Vaccine +NBRI-162 Insulin +NBRI-163 Insulin (rapid, short, and intermediate acting) +NBRI-164 Insulin, Degludec +NBRI-165 Insulin, Glargine +NBRI-166 Iodoquinolol +NBRI-167 Iohexol (Omnipaque) +NBRI-168 Iron Dextran +NBRI-169 Isoflurane +NBRI-170 Isoniazid +NBRI-171 Isoproterenol +NBRI-172 Isovue-300 +NBRI-173 Isovue-370. T +NBRI-174 Itraconazole +NBRI-175 Ivermectin 1% Injectable +NBRI-176 Kaolin & Pectin +NBRI-177 Karo syrup +NBRI-178 Ketaloric Trimethamine Ophthalmic Solution +NBRI-179 Ketamine Injectable +NBRI-180 Ketoconazole +NBRI-181 Ketoprofen Injectable +NBRI-182 Ketorolac +NBRI-183 Lactated ringers solution +NBRI-184 Leuprolide +NBRI-185 Levetiracetam +NBRI-186 Lidocaine + epinephrine +NBRI-187 Lidocaine Hydrochloride +NBRI-188 Loperamide Hydrochloride +NBRI-189 Loratadine +NBRI-190 Lorazepam +NBRI-191 L-Tryptophan +NBRI-192 L-Lysine +NBRI-193 Magnesium hydroxide +NBRI-194 Mannitol +NBRI-195 Maropitant Citrate +NBRI-196 Mct Oil +NBRI-197 Measles, Mumps, Rubella Vaccine (MMR) +NBRI-198 Mebendazole +NBRI-199 Medetomidine Hcl +NBRI-200 Medihoney +NBRI-201 Medroxyprogesterone acetate (Depo-Provera) +NBRI-202 Mefloquine +NBRI-203 Megestrol Acetate +NBRI-204 Melengestrol Acetate +NBRI-205 Meloxicam, injectable +NBRI-206 Meloxicam, oral +NBRI-207 Meloxicam, sustained release +NBRI-208 Menotropins +NBRI-209 Mesalamine +NBRI-210 Metamucil Powder +NBRI-211 Metformin +NBRI-212 Methotrexate +NBRI-213 Methylene Blue +NBRI-214 Methylprednisolone acetate (Depo-Medrol) +NBRI-215 Methylprednisolone sodium succinate (Solu-medrol) +NBRI-216 Metoclopramide +NBRI-217 Metronidazole, injectable +NBRI-218 Metronidazole, oral +NBRI-219 Miconahex + Triz +NBRI-220 Midazolam +NBRI-221 Mifepristone +NBRI-222 Minocycline HCl +NBRI-223 Mirtazapine +NBRI-224 Misoprostol +NBRI-225 Morphine +NBRI-226 Moxidectin +NBRI-227 Moxifloxacin Opthalmic +NBRI-228 Multivitamin Preparation, Nos +NBRI-229 Mylanta +NBRI-230 Nalbuphine +NBRI-231 Naloxone +NBRI-232 Naltrexone +NBRI-233 Nembutal +NBRI-234 Neo/Poly/Bac W/Dexamethasone +NBRI-235 Neomycin Sulfate +NBRI-236 Neomycin/Bacitracin/Polymyxin +NBRI-237 Neostigmine +NBRI-238 Nitazoxanide +NBRI-239 Normasol +NBRI-240 Nystatin +NBRI-241 N-acetylcysteine +NBRI-242 Olanzapine +NBRI-243 Omeprazole +NBRI-244 Ondansetron +NBRI-245 Ophthalmic Eye Wash +NBRI-246 Oral rehydration salts (oral electrolytes) +NBRI-247 Oxacillin +NBRI-248 Oxycodone Hydrochloride +NBRI-249 Oxygen +NBRI-250 Oxymorphone Hydrochloride +NBRI-251 Oxytetracycline +NBRI-252 Oxytocin +NBRI-253 Packed red blood cells +NBRI-254 Pancuronium +NBRI-255 Pantoprazole (Protonix) +NBRI-256 Paromomycin +NBRI-257 Penicillin G Procaine +NBRI-258 Pentobarbital (euthanasia solution) +NBRI-259 Pentobarbitol Sodium +NBRI-260 Phenazopyridine +NBRI-261 Phenobarbital +NBRI-262 Phenylephrine +NBRI-263 Phenytoin +NBRI-264 Phytonadione (Vitamin K1) +NBRI-265 Pimobendan +NBRI-266 Pioglitazone +NBRI-267 Plasma +NBRI-268 Platelet rich plasma (PRP) +NBRI-269 Polymyxin B +NBRI-270 Polymyxin B Sulfate and Bacitracin ophthalmic ointment +NBRI-271 Potassium chloride 10%, injectable +NBRI-272 Potassium Gluconate +NBRI-273 Potassium, oral +NBRI-274 Prang +NBRI-275 Praziquantel +NBRI-276 Prazosin +NBRI-277 Prednisolone +NBRI-278 Prednisolone Sodium Succinate +NBRI-279 Prednisone +NBRI-280 Primaquine +NBRI-281 Probiotic, B. Infantis +NBRI-282 Probiotic, Capsule +NBRI-283 Probiotic, L. Reuteri +NBRI-284 Probiotic, Paste +NBRI-285 Probiotic, Visbiome +NBRI-286 Prochlorperazine +NBRI-287 Propofol +NBRI-288 Propranolol +NBRI-289 Psyllium Seed +NBRI-290 Putrescine +NBRI-291 Pyrantel pamoate +NBRI-292 Quinine +NBRI-293 Rabies Vaccine, Killed Virus, 1 year +NBRI-294 Rabies Vaccine, Killed Virus, 3 year +NBRI-295 Rabies Vaccine, Modified Live Virus +NBRI-296 Ranitidine +NBRI-297 Rapamycin +NBRI-298 Robenacoxib (Onsior) +NBRI-299 Rocuronium Bromide +NBRI-300 Ropivacaine +NBRI-301 S-adenosyl-L-methionine (SAMe) + milk thistle extract +NBRI-302 Sevoflurane +NBRI-303 Shampoo, Chlorhexidine +NBRI-304 Shampoo, Epi-Soothe +NBRI-305 Shampoo, medicated other +NBRI-306 Silver sulfadiazine (SSD) Cream +NBRI-307 Simethicone +NBRI-308 Sodium Bicarbonate +NBRI-309 Sodium Chloride +NBRI-310 Spironolactone +NBRI-311 Succinylcholine +NBRI-312 Sucralfate +NBRI-313 Sufentanil +NBRI-314 Sulfadimethoxine +NBRI-315 Sulfamethoxazole/Trimethoprim +NBRI-316 Sulfasalazine +NBRI-317 Tacrolimus +NBRI-318 Terbutaline +NBRI-319 Terbutaline Sulfate Injectable +NBRI-320 Tetanus Toxoid Vaccine +NBRI-321 Tetracaine ophthalmic solution +NBRI-322 Tetracycline +NBRI-323 Theophylline +NBRI-324 Thiabendazole +NBRI-325 Tiletamine/Zolazepam Injectable (Telazol) +NBRI-326 Tinidazole +NBRI-327 Tobramycin Opthalmic +NBRI-328 Tramadol +NBRI-329 Tranexamic acid (TEA) +NBRI-330 Trazadone +NBRI-331 Triamcinilone Acetate +NBRI-332 Trimethoprim/Sulfa +NBRI-333 Triple Antibiotic Ointment +NBRI-334 Tryptophan +NBRI-335 Tuberculin mammalian +NBRI-336 Tulathromycin +NBRI-337 Tylan Injectable +NBRI-338 Tylosin +NBRI-339 Ursodiol +NBRI-340 Valbazen +NBRI-341 Valganciclovir Hydrochloride +NBRI-342 Vancomycin +NBRI-343 Vanguard DM (Distemper-Measles vaccine) +NBRI-344 Vecuronium +NBRI-345 Venlafaxine +NBRI-346 Vetericyn Plus Spray +NBRI-347 Vitamin B Complex +NBRI-348 Vitamin C +NBRI-349 Vitamin D3 +NBRI-350 Vitamin K1 +NBRI-351 Water Soaked Chow +NBRI-352 Whole blood +NBRI-353 Xylazine Injectable +NBRI-354 Yohimbine +NBRI-355 Zenpep +NBRI-35p Post-Op Rounds \ No newline at end of file diff --git a/nbri_ehr/resources/data/source.tsv b/nbri_ehr/resources/data/source.tsv new file mode 100644 index 0000000..0d893c4 --- /dev/null +++ b/nbri_ehr/resources/data/source.tsv @@ -0,0 +1,108 @@ +code meaning +1 Adv Bioscience Labs +2 Alamogordo PrimateFaclty +3 Alpha Genesis, Inc. +4 Barton West End Farm +5 Battelle Memorial Inst +6 Baylor Research Inst +7 BIOCULTURE (MTIUS) LTD +8 Bioculture US LLC +9 BIOQUAL, Inc. +10 Boehringer Ingelheim +11 Boston University +12 Buckshire Corporation +13 Caribbean Primate Rsrch +14 CBNC +15 CDC +16 Charles River Laboratory +17 Charles River/Reno +18 Chimp Haven +19 China/Guangxi GF Sci Pri +20 Chiron Corp +21 CiToxLab North America +22 Covance Research Prod +23 CR Rsrch Models Houston +24 Ctr Captive Chimp Care +25 Cynologics Ltd +26 DHMRI +27 Duke Univ Medical Ctr +28 Durham Research Center +29 Emory University YPRC +30 Envigo Global Services +31 Guangdong Landau Biotech +32 Hainan, China +33 Harvard Medical School +34 Indonesia (Pt. W. Sat) +35 Johns Hopkins University +36 LC Preclinical Research +37 Lovelace Biomedical +38 LRRI +39 LSU Health Science BR +40 LSU Health Science NO +41 LSU Health Science Shv +42 Mannheimer Foundation +43 Mass. General Hospital +44 MD Anderson Cancer Ctr. +45 Merck & Co (Rahway) +46 Merck & Co (WP) +47 Merck Research Labs WP +48 Nationwide Children's +49 New England NPRC +50 New York University +51 NIAID (Bioqual) +52 NIAID Morgan Island +53 NIAID NIH Animal Ctr +54 NICHD/NIH +55 NIH +56 NIH Animal Center +57 NINDS NIH Animal Ctr +58 Novartis Pharm. Corp. +59 Novartis Vaccines Srl +60 NYU School of Medicine +61 Oregon NPRC +62 Pfizer +63 Pfizer-Andover +64 Pfizer-Pearl River +65 PreLabs +66 Primate Products +67 Primedica Labs +68 PrimGen +69 Primgen CSP +70 RainForest Adventures +71 Republic of Mauritius +72 Rocky Mountain Lab +73 Save the Chimps +74 Siconbrec Inc +75 Sierra Biomedical +76 SNBL-SRC +77 SRI International +78 St. Jude Childrens Rsrch +79 St. Kitts +80 Stanford Univ School Med +81 Stony Brook University +82 SUNY Downstate Medical +83 SW Found Biomed Rsrch +84 Texas Biomed +85 Three Springs Scientific +86 Tulane NPC (Covington) +87 Tulane Univ Medical Ctr +88 Univ Alabama Birmingham +89 Univ of Illinois +90 Univ of Kansas Med Ctr +91 Univ of Maryland +92 Univ of Nebraska Med Ctr +93 Univ of Pittsburgh +94 Univ of Texas at Austin +95 Univ of Washington NPRC +96 Univ of Wisconsin +97 Univ Tex MD Anderson CC +98 USAMRICD +99 USAMRIID +100 Virginia Commonwealth U +101 WakeForest School of Med +102 WaNPRC +103 Worldwide Primates, Inc. +104 WRAIR +105 Wyeth-Ayerst Rsrch (PR) +106 Yale Univ Sch Medicine +107 Yerkes Regional PRC \ No newline at end of file diff --git a/nbri_ehr/resources/data/species.tsv b/nbri_ehr/resources/data/species.tsv new file mode 100644 index 0000000..c95e4bd --- /dev/null +++ b/nbri_ehr/resources/data/species.tsv @@ -0,0 +1,7 @@ +Common Scientific Name Id Prefix Mhc Prefix Max Blood Draw (mL/kg) Max Percent Blood Drawn Blood Reconstitution Interval (Days) Cites Code Date Disabled USDA Gestation +African Green Monkey Chlorocebus aethiops AGM 3.0000 1.0000 7.0000 +Brown-Tufted Capuchin Cebus apella CAP 3.0000 1.0000 7.0000 +Cynomolgus Macaque Macaca fascicularis CYN 3.0000 1.0000 7.0000 +Marmoset 3.0000 1.0000 7.0000 +Pig-Tailed Macaque Macaca nemestrina PIG 3.0000 1.0000 7.0000 +Rhesus Macaque Macaca mulatta RHM 3.0000 1.0000 7.0000 \ No newline at end of file diff --git a/nbri_ehr/resources/data/species_codes.tsv b/nbri_ehr/resources/data/species_codes.tsv new file mode 100644 index 0000000..df698e7 --- /dev/null +++ b/nbri_ehr/resources/data/species_codes.tsv @@ -0,0 +1,7 @@ +Code Scientific Name Common Name Description Genus Species Date Disabled +1 Chlorocebus aethiops AGM African Green Monkey 3 +10 Macaca mulatta RHM Rhesus Macaque 3 +18 Marmoset 3 +4 Cebus apella CAP Brown-Tufted Capuchin 3 +7 Macaca fascicularis CYN Cynomolgus Macaque 3 +9 Macaca nemestrina PIG Pig-Tailed Macaque 3 \ No newline at end of file diff --git a/nbri_ehr/resources/data/stool_score.tsv b/nbri_ehr/resources/data/stool_score.tsv new file mode 100644 index 0000000..121feeb --- /dev/null +++ b/nbri_ehr/resources/data/stool_score.tsv @@ -0,0 +1,7 @@ +value sort_order +F 1 +F/M 2 +F/M/L 3 +M 4 +M/F 4 +M/F/L 5 \ No newline at end of file diff --git a/nbri_ehr/resources/data/stool_types.tsv b/nbri_ehr/resources/data/stool_types.tsv new file mode 100644 index 0000000..79aeb54 --- /dev/null +++ b/nbri_ehr/resources/data/stool_types.tsv @@ -0,0 +1,10 @@ +value +Formed (normal) +Formed to mounding +Formed with mounding/liquid components +Mounding (soft) +Mounding with liquid components +Liquid +Formed with bloody components +Mounding to liquid with bloody components +Primarily bloody \ No newline at end of file diff --git a/nbri_ehr/resources/data/temperament.tsv b/nbri_ehr/resources/data/temperament.tsv new file mode 100644 index 0000000..7acfc66 --- /dev/null +++ b/nbri_ehr/resources/data/temperament.tsv @@ -0,0 +1,5 @@ +Value Title Category Description Sort Order Date Disabled +Personality +Sociality +Study suitability +Breeding suitability \ No newline at end of file diff --git a/nbri_ehr/resources/data/testicular_volume.tsv b/nbri_ehr/resources/data/testicular_volume.tsv new file mode 100644 index 0000000..28aa0c2 --- /dev/null +++ b/nbri_ehr/resources/data/testicular_volume.tsv @@ -0,0 +1,13 @@ +value sort_order +1 mL 1 +2 mL 2 +3 mL 3 +4 mL 4 +5 mL 5 +6 mL 6 +8 mL 7 +10 mL 8 +12 mL 9 +15 mL 10 +20 mL 11 +25 mL 12 diff --git a/nbri_ehr/resources/data/treatment_frequency.tsv b/nbri_ehr/resources/data/treatment_frequency.tsv new file mode 100644 index 0000000..bbf36e0 --- /dev/null +++ b/nbri_ehr/resources/data/treatment_frequency.tsv @@ -0,0 +1,12 @@ +Meaning Sort Order Week of Month Day of Month Day of Week Interval in Days Short Name Active? Week Days +Monthly 30 true +Weekly 7 true +Alternating Days 2 true +SID 1 true +QID 1 true +TID 1 true +q7 days 7 true +q14 days 14 true +BID 1 true +Every 3 months 90 true +M-F (SID) 1 true 2,3,4,5,6 \ No newline at end of file diff --git a/nbri_ehr/resources/data/treatment_frequency_times.tsv b/nbri_ehr/resources/data/treatment_frequency_times.tsv new file mode 100644 index 0000000..61fd3d6 --- /dev/null +++ b/nbri_ehr/resources/data/treatment_frequency_times.tsv @@ -0,0 +1,18 @@ +Frequency Hour of Day Time Description +SID 800 AM +Monthly 800 AM +Weekly 800 AM +Alternating Days 800 AM +TID 800 AM +TID 1200 PM +TID 1600 PM +QID 800 AM +QID 1100 AM +QID 1400 PM +QID 1700 PM +BID 800 AM +BID 1600 PM +q7 days 800 AM +q14 days 800 AM +Every 3 months 800 AM +M-F (SID) 800 AM \ No newline at end of file diff --git a/nbri_ehr/resources/data/vaginal_uterine_prolapse.tsv b/nbri_ehr/resources/data/vaginal_uterine_prolapse.tsv new file mode 100644 index 0000000..98f995c --- /dev/null +++ b/nbri_ehr/resources/data/vaginal_uterine_prolapse.tsv @@ -0,0 +1,3 @@ +value sort_order +Present 1 +Not present 2 \ No newline at end of file diff --git a/nbri_ehr/resources/data/vendor_approval_code.tsv b/nbri_ehr/resources/data/vendor_approval_code.tsv new file mode 100644 index 0000000..863eb1a --- /dev/null +++ b/nbri_ehr/resources/data/vendor_approval_code.tsv @@ -0,0 +1,4 @@ +value title +1 Approved +2 Not Approved +3 Conditionally Approved \ No newline at end of file diff --git a/nbri_ehr/resources/data/vendor_production_location.tsv b/nbri_ehr/resources/data/vendor_production_location.tsv new file mode 100644 index 0000000..59a4ac9 --- /dev/null +++ b/nbri_ehr/resources/data/vendor_production_location.tsv @@ -0,0 +1,47 @@ +value title description +1 Andover MA 4 +2 Pearl River NY 4 +3 Alice TX 4 +4 West Point PA 4 +5 Bethesda MD 4 +6 Bastrop TX 4 +7 San Antonio TX 4 +8 Homestead FL 4 +9 Atlanta GA 4 +10 Emeryville CA 4 +11 Waltham MA 4 +12 Columbus OH 4 +13 Italy 2 +14 Dickerson MD 4 +15 Bethesda MD 4 +16 Basseterre 1 +17 Yemassee SC 4 +18 Bethesda MD 4 +19 Makati City 5 +20 UL Lafayette - NBRI 4 +21 NBRI +22 Columbus 4 +23 New York 4 +24 Yemassee 4 +25 Three Springs Scientific 4 +26 Sierra Biomedical 4 +27 NIH 4 +28 Lovelace Biomedical 4 +29 University of Washington NPRC 4 +30 "China/Guangxi Grand Forest Sci Primate " 4 +31 Charles River Laboratory 4 +33 Alamogordo Primate Facility 4 +34 Yale Univ Sch Medicine 4 +36 Cornell University Medical College 4 +37 Tulane NPC (Covington) 4 +38 CDC 4 +39 Covance, China 4 +42 St. Helena, SC 4 +44 MD Anderson Cancer Center 4 +45 University of Kentucky 4 +46 Wake Forest School of Medicine 4 +47 Hainan 7 +48 Cynologics Ltd 8 +49 Guangdong 7 +51 Mattawan, MI 4 +52 Phnom Penh 6 diff --git a/nbri_ehr/resources/data/volume_units.tsv b/nbri_ehr/resources/data/volume_units.tsv new file mode 100644 index 0000000..6f20a8c --- /dev/null +++ b/nbri_ehr/resources/data/volume_units.tsv @@ -0,0 +1,16 @@ +Unit +capsule +capsule(s) +cup +drop(s) +gummy +implant +mg +mL +no units +ounce(s) +piece(s) +scoop +tablet +tablet(s) +tsp diff --git a/nbri_ehr/resources/data/weight_ranges.tsv b/nbri_ehr/resources/data/weight_ranges.tsv new file mode 100644 index 0000000..bb2c94f --- /dev/null +++ b/nbri_ehr/resources/data/weight_ranges.tsv @@ -0,0 +1,3 @@ +Species Min Weight Max Weight +Cynomolgus 0.0 20.0 +Rhesus 0.0 35.0 \ No newline at end of file diff --git a/nbri_ehr/resources/data/wound_severity.tsv b/nbri_ehr/resources/data/wound_severity.tsv new file mode 100644 index 0000000..480eaab --- /dev/null +++ b/nbri_ehr/resources/data/wound_severity.tsv @@ -0,0 +1,6 @@ +value sort_order +N/A (0) 1 +Superficial (1) 2 +Partial Thickness (2) 3 +Full Thickness (3) 4 +Muscle Damage (4) 5 \ No newline at end of file diff --git a/nbri_ehr/resources/data/wound_status_behavior.tsv b/nbri_ehr/resources/data/wound_status_behavior.tsv new file mode 100644 index 0000000..c3dbc44 --- /dev/null +++ b/nbri_ehr/resources/data/wound_status_behavior.tsv @@ -0,0 +1,5 @@ +value sort_order +Completely healed 1 +Mostly healed 2 +Partially healed 3 +Not healed 4 \ No newline at end of file diff --git a/nbri_ehr/resources/data/wound_status_clinical.tsv b/nbri_ehr/resources/data/wound_status_clinical.tsv new file mode 100644 index 0000000..a2e6ce0 --- /dev/null +++ b/nbri_ehr/resources/data/wound_status_clinical.tsv @@ -0,0 +1,11 @@ +value sort_order +Healing well 1 +Mostly healed 2 +Completely healed 3 +Cannot visualize 4 +Dehiscence (wound opened) 5 +Necrotic tissue present 6 +Bone exposure on digit(s) 7 +Abscess 8 +Purulent exudate present 9 +Other 10 \ No newline at end of file diff --git a/nbri_ehr/resources/data/yes_no_only.tsv b/nbri_ehr/resources/data/yes_no_only.tsv new file mode 100644 index 0000000..9776fec --- /dev/null +++ b/nbri_ehr/resources/data/yes_no_only.tsv @@ -0,0 +1,3 @@ +value sort_order +Yes 1 +No 2 \ No newline at end of file diff --git a/nbri_ehr/resources/data/yes_no_order.tsv b/nbri_ehr/resources/data/yes_no_order.tsv new file mode 100644 index 0000000..90cd652 --- /dev/null +++ b/nbri_ehr/resources/data/yes_no_order.tsv @@ -0,0 +1,4 @@ +value sort_order +Yes 1 +No 2 +N/A 3 \ No newline at end of file diff --git a/nbri_ehr/resources/domain-templates/ehr.template.xml b/nbri_ehr/resources/domain-templates/ehr.template.xml new file mode 100644 index 0000000..281f4bd --- /dev/null +++ b/nbri_ehr/resources/domain-templates/ehr.template.xml @@ -0,0 +1,125 @@ + + + + + + + + diff --git a/nbri_ehr/resources/domain-templates/ehr_lookups.template.xml b/nbri_ehr/resources/domain-templates/ehr_lookups.template.xml new file mode 100644 index 0000000..36eb0f9 --- /dev/null +++ b/nbri_ehr/resources/domain-templates/ehr_lookups.template.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/ProjectAndAssignment.xml b/nbri_ehr/resources/etls/ProjectAndAssignment.xml new file mode 100644 index 0000000..ec6543c --- /dev/null +++ b/nbri_ehr/resources/etls/ProjectAndAssignment.xml @@ -0,0 +1,31 @@ + + + Project and Assignment + Project and assignment data + + + Copy to project target + + + + + + + + + Copy to assignment target + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/ProtocolAndAssignment.xml b/nbri_ehr/resources/etls/ProtocolAndAssignment.xml new file mode 100644 index 0000000..685afc3 --- /dev/null +++ b/nbri_ehr/resources/etls/ProtocolAndAssignment.xml @@ -0,0 +1,50 @@ + + + Protocol and Assignment + Protocol and assignment data + + + Copy to protocol target + + + + + + + + + + + + + + Copy to protocol amendments target + + + + + + + + + + + + + Copy to assignment target + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/account.xml b/nbri_ehr/resources/etls/account.xml new file mode 100644 index 0000000..41af548 --- /dev/null +++ b/nbri_ehr/resources/etls/account.xml @@ -0,0 +1,17 @@ + + + Account + Account data + + + Copy to account target + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/animalDelivery.xml b/nbri_ehr/resources/etls/animalDelivery.xml new file mode 100644 index 0000000..f1ef000 --- /dev/null +++ b/nbri_ehr/resources/etls/animalDelivery.xml @@ -0,0 +1,32 @@ + + + Animal Delivery + Animal delivery data + + + Copy to animal delivery target + + + + + + + + + + Copy to animal delivery esignature target + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/animalReqOrder.xml b/nbri_ehr/resources/etls/animalReqOrder.xml new file mode 100644 index 0000000..350dccf --- /dev/null +++ b/nbri_ehr/resources/etls/animalReqOrder.xml @@ -0,0 +1,36 @@ + + + Animal Req Order + Animal req order data + + + Copy to req order target + + + + + + + + + + + + + + Copy to req order esignature target + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/animalShipment.xml b/nbri_ehr/resources/etls/animalShipment.xml new file mode 100644 index 0000000..61e5798 --- /dev/null +++ b/nbri_ehr/resources/etls/animalShipment.xml @@ -0,0 +1,21 @@ + + + Animal Shipment + Animal shipment data + + + Copy to animal shipment target + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/animalVendor.xml b/nbri_ehr/resources/etls/animalVendor.xml new file mode 100644 index 0000000..bc7899e --- /dev/null +++ b/nbri_ehr/resources/etls/animalVendor.xml @@ -0,0 +1,17 @@ + + + Animal Vendor + Animal vendor data + + + Copy to animal vendor target + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/arrival.xml b/nbri_ehr/resources/etls/arrival.xml new file mode 100644 index 0000000..f77f752 --- /dev/null +++ b/nbri_ehr/resources/etls/arrival.xml @@ -0,0 +1,30 @@ + + + Arrival + Arrival data + + + Copy to arrival target + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/biopsy.xml b/nbri_ehr/resources/etls/biopsy.xml new file mode 100644 index 0000000..32ab5a3 --- /dev/null +++ b/nbri_ehr/resources/etls/biopsy.xml @@ -0,0 +1,30 @@ + + + Biopsies + Biopsies + + + Copy to biopsy target + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/birth.xml b/nbri_ehr/resources/etls/birth.xml new file mode 100644 index 0000000..9934ff7 --- /dev/null +++ b/nbri_ehr/resources/etls/birth.xml @@ -0,0 +1,29 @@ + + + Births + Births data + + + Copy to births target + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/blood.xml b/nbri_ehr/resources/etls/blood.xml new file mode 100644 index 0000000..dd086b1 --- /dev/null +++ b/nbri_ehr/resources/etls/blood.xml @@ -0,0 +1,30 @@ + + + Blood Draws + Blood Draw data + + + Copy to blood target + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/breeder.xml b/nbri_ehr/resources/etls/breeder.xml new file mode 100644 index 0000000..ef521b8 --- /dev/null +++ b/nbri_ehr/resources/etls/breeder.xml @@ -0,0 +1,30 @@ + + + Breeder + Breeder + + + Copy to breeder target + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/cageCard.xml b/nbri_ehr/resources/etls/cageCard.xml new file mode 100644 index 0000000..ff4257a --- /dev/null +++ b/nbri_ehr/resources/etls/cageCard.xml @@ -0,0 +1,33 @@ + + + Cage Card + Cage Card data + + + Copy to cage card target + + + + + + + + + + Copy to cage card history target + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/cases.xml b/nbri_ehr/resources/etls/cases.xml new file mode 100644 index 0000000..9b8bb41 --- /dev/null +++ b/nbri_ehr/resources/etls/cases.xml @@ -0,0 +1,28 @@ + + + Cases + Clinical Treatment Cases + + + Copy to cases temp table + + + + + + + + + + Copy from cases temp to cases + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/chemistryResults.xml b/nbri_ehr/resources/etls/chemistryResults.xml new file mode 100644 index 0000000..c20a59d --- /dev/null +++ b/nbri_ehr/resources/etls/chemistryResults.xml @@ -0,0 +1,30 @@ + + + Chemistry Results + Chemistry Results + + + Copy to chemistry results target + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/clinremarks.xml b/nbri_ehr/resources/etls/clinremarks.xml new file mode 100644 index 0000000..a692ff7 --- /dev/null +++ b/nbri_ehr/resources/etls/clinremarks.xml @@ -0,0 +1,30 @@ + + + Clinical Remarks + Comments/Clinical Remarks + + + Copy to clinremarks target + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/deaths.xml b/nbri_ehr/resources/etls/deaths.xml new file mode 100644 index 0000000..6dd2f6e --- /dev/null +++ b/nbri_ehr/resources/etls/deaths.xml @@ -0,0 +1,26 @@ + + + Deaths + Deaths data + + + Copy to deaths target + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/deletedRecord.xml b/nbri_ehr/resources/etls/deletedRecord.xml new file mode 100644 index 0000000..1ac7dae --- /dev/null +++ b/nbri_ehr/resources/etls/deletedRecord.xml @@ -0,0 +1,21 @@ + + + Deleted Records + Deleted Records data + + + Copy to account target + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/demographics.xml b/nbri_ehr/resources/etls/demographics.xml new file mode 100644 index 0000000..e2e7a22 --- /dev/null +++ b/nbri_ehr/resources/etls/demographics.xml @@ -0,0 +1,28 @@ + + + Demographics + Demographics data + + + Copy to Animal target + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/department.xml b/nbri_ehr/resources/etls/department.xml new file mode 100644 index 0000000..d94dce0 --- /dev/null +++ b/nbri_ehr/resources/etls/department.xml @@ -0,0 +1,21 @@ + + + Department + Department data + + + Copy to department target + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/departure.xml b/nbri_ehr/resources/etls/departure.xml new file mode 100644 index 0000000..eb01e0b --- /dev/null +++ b/nbri_ehr/resources/etls/departure.xml @@ -0,0 +1,26 @@ + + + Departure + Departure data + + + Copy to departure target + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/drug.xml b/nbri_ehr/resources/etls/drug.xml new file mode 100644 index 0000000..05c0232 --- /dev/null +++ b/nbri_ehr/resources/etls/drug.xml @@ -0,0 +1,30 @@ + + + Drug + Drug Administration + + + Copy to drug target + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/ehrRecords.xml b/nbri_ehr/resources/etls/ehrRecords.xml new file mode 100644 index 0000000..146b309 --- /dev/null +++ b/nbri_ehr/resources/etls/ehrRecords.xml @@ -0,0 +1,45 @@ + + + EHR Records + Housing, cases, notes, departures and deaths + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/ehr_lookups.xml b/nbri_ehr/resources/etls/ehr_lookups.xml new file mode 100644 index 0000000..c9bf07f --- /dev/null +++ b/nbri_ehr/resources/etls/ehr_lookups.xml @@ -0,0 +1,48 @@ + + + EHR Lookups + EHR Lookups data + + + Copy to lookups target + + + + + + + + + Copy to species code target + + + + + + + + + Copy to species target + + + + + + Copy to flag categories target + + + + + + Copy to flag values target + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/exemptions.xml b/nbri_ehr/resources/etls/exemptions.xml new file mode 100644 index 0000000..78c962f --- /dev/null +++ b/nbri_ehr/resources/etls/exemptions.xml @@ -0,0 +1,30 @@ + + + Exemptions + Exemptions data + + + Copy to exemption target + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/flags.xml b/nbri_ehr/resources/etls/flags.xml new file mode 100644 index 0000000..87c2979 --- /dev/null +++ b/nbri_ehr/resources/etls/flags.xml @@ -0,0 +1,30 @@ + + + Flags + Flag data + + + Copy to blood target + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/foster.xml b/nbri_ehr/resources/etls/foster.xml new file mode 100644 index 0000000..42c5a01 --- /dev/null +++ b/nbri_ehr/resources/etls/foster.xml @@ -0,0 +1,30 @@ + + + Fostering + Fostering + + + Copy to foster target + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/histopathology.xml b/nbri_ehr/resources/etls/histopathology.xml new file mode 100644 index 0000000..050c77e --- /dev/null +++ b/nbri_ehr/resources/etls/histopathology.xml @@ -0,0 +1,25 @@ + + + Histopathology + Histopathology data + + + Copy to histopathology target + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/historicalOther.xml b/nbri_ehr/resources/etls/historicalOther.xml new file mode 100644 index 0000000..7b62eff --- /dev/null +++ b/nbri_ehr/resources/etls/historicalOther.xml @@ -0,0 +1,25 @@ + + + HistoricalOther + Historical data + + + Copy to historicalOther target + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/housing.xml b/nbri_ehr/resources/etls/housing.xml new file mode 100644 index 0000000..cd92dc5 --- /dev/null +++ b/nbri_ehr/resources/etls/housing.xml @@ -0,0 +1,26 @@ + + + Housing + Housing data + + + Copy to arrival target + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/idHistory.xml b/nbri_ehr/resources/etls/idHistory.xml new file mode 100644 index 0000000..e85b3c8 --- /dev/null +++ b/nbri_ehr/resources/etls/idHistory.xml @@ -0,0 +1,17 @@ + + + ID History + Animal Id history data + + + Copy to study Id history target + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/locations.xml b/nbri_ehr/resources/etls/locations.xml new file mode 100644 index 0000000..849fd43 --- /dev/null +++ b/nbri_ehr/resources/etls/locations.xml @@ -0,0 +1,42 @@ + + + Locations + Locations data + + + Copy to areas target + + + + + + Copy to buildings target + + + + + + Copy to floors target + + + + + + Copy to rooms target + + + + + + Copy to cage target + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/lotNumber.xml b/nbri_ehr/resources/etls/lotNumber.xml new file mode 100644 index 0000000..efe1b04 --- /dev/null +++ b/nbri_ehr/resources/etls/lotNumber.xml @@ -0,0 +1,18 @@ + + + Animal Lot + Shipment lot data + + + Copy to lot number target + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/necropsy.xml b/nbri_ehr/resources/etls/necropsy.xml new file mode 100644 index 0000000..71b3897 --- /dev/null +++ b/nbri_ehr/resources/etls/necropsy.xml @@ -0,0 +1,30 @@ + + + Necropsy + Necropsy data + + + Copy to necropsy target + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/notes.xml b/nbri_ehr/resources/etls/notes.xml new file mode 100644 index 0000000..4e8430a --- /dev/null +++ b/nbri_ehr/resources/etls/notes.xml @@ -0,0 +1,26 @@ + + + Notes + Notes + + + Copy to notes target + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/obs.xml b/nbri_ehr/resources/etls/obs.xml new file mode 100644 index 0000000..dbec321 --- /dev/null +++ b/nbri_ehr/resources/etls/obs.xml @@ -0,0 +1,44 @@ + + + Observations + Observations data + + + Copy to observations target + + + + + + + + + + + + + Copy to alopecia target + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/pairings.xml b/nbri_ehr/resources/etls/pairings.xml new file mode 100644 index 0000000..d087c04 --- /dev/null +++ b/nbri_ehr/resources/etls/pairings.xml @@ -0,0 +1,30 @@ + + + Pairings + Pairings data + + + Copy to pairings target + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/physicalExam.xml b/nbri_ehr/resources/etls/physicalExam.xml new file mode 100644 index 0000000..b115465 --- /dev/null +++ b/nbri_ehr/resources/etls/physicalExam.xml @@ -0,0 +1,30 @@ + + + Physical Exam + Physical Exam data + + + Copy to physical exam target + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/prc.xml b/nbri_ehr/resources/etls/prc.xml new file mode 100644 index 0000000..bf0b199 --- /dev/null +++ b/nbri_ehr/resources/etls/prc.xml @@ -0,0 +1,30 @@ + + + Procedures + Procedures data + + + Copy to procedures target + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/pregnancy.xml b/nbri_ehr/resources/etls/pregnancy.xml new file mode 100644 index 0000000..0371f8d --- /dev/null +++ b/nbri_ehr/resources/etls/pregnancy.xml @@ -0,0 +1,30 @@ + + + Pregnancy Outcomes + Pregnancy Outcomes + + + Copy to pregnancy target + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/procedure.xml b/nbri_ehr/resources/etls/procedure.xml new file mode 100644 index 0000000..696ed36 --- /dev/null +++ b/nbri_ehr/resources/etls/procedure.xml @@ -0,0 +1,21 @@ + + + Reference Procedure List + Reference Procedure data + + + Copy to procedure target + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/protocolCounts.xml b/nbri_ehr/resources/etls/protocolCounts.xml new file mode 100644 index 0000000..061593e --- /dev/null +++ b/nbri_ehr/resources/etls/protocolCounts.xml @@ -0,0 +1,17 @@ + + + Protocol Counts + Protocol Counts data + + + Copy to protocol counts target + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/protocolSupplement.xml b/nbri_ehr/resources/etls/protocolSupplement.xml new file mode 100644 index 0000000..c7026bb --- /dev/null +++ b/nbri_ehr/resources/etls/protocolSupplement.xml @@ -0,0 +1,35 @@ + + + Protocol Supplement + Protocol Supplement data + + + Copy to protocol esig target + + + + + + + + + Copy to protocol stress target + + + + + + Copy to protocol procedures target + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/protocolUsage.xml b/nbri_ehr/resources/etls/protocolUsage.xml new file mode 100644 index 0000000..bcd448e --- /dev/null +++ b/nbri_ehr/resources/etls/protocolUsage.xml @@ -0,0 +1,17 @@ + + + Protocol Usage + Protocol Usage data + + + Copy to protocol usage target + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/questionResponse.xml b/nbri_ehr/resources/etls/questionResponse.xml new file mode 100644 index 0000000..d9b2952 --- /dev/null +++ b/nbri_ehr/resources/etls/questionResponse.xml @@ -0,0 +1,21 @@ + + + Question And Response + Question And Response data + + + Copy to Question target + + + + + + Copy to Question Response target + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/serology.xml b/nbri_ehr/resources/etls/serology.xml new file mode 100644 index 0000000..203ec45 --- /dev/null +++ b/nbri_ehr/resources/etls/serology.xml @@ -0,0 +1,30 @@ + + + Serology + Serology data + + + Copy to observations target + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/shipTo.xml b/nbri_ehr/resources/etls/shipTo.xml new file mode 100644 index 0000000..25e20c2 --- /dev/null +++ b/nbri_ehr/resources/etls/shipTo.xml @@ -0,0 +1,18 @@ + + + Ship To + Ship To data + + + Copy to ship to target + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/staff.xml b/nbri_ehr/resources/etls/staff.xml new file mode 100644 index 0000000..0f0e56e --- /dev/null +++ b/nbri_ehr/resources/etls/staff.xml @@ -0,0 +1,18 @@ + + + Staff + Staff data + + + Copy to user target + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/stress.xml b/nbri_ehr/resources/etls/stress.xml new file mode 100644 index 0000000..9ef78c9 --- /dev/null +++ b/nbri_ehr/resources/etls/stress.xml @@ -0,0 +1,18 @@ + + + Stress + Stress data + + + Copy to stress target + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/vitals.xml b/nbri_ehr/resources/etls/vitals.xml new file mode 100644 index 0000000..2d17dd3 --- /dev/null +++ b/nbri_ehr/resources/etls/vitals.xml @@ -0,0 +1,30 @@ + + + Vitals + Vital Signs data + + + Copy to observations target + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/etls/weight.xml b/nbri_ehr/resources/etls/weight.xml new file mode 100644 index 0000000..b3e0fa3 --- /dev/null +++ b/nbri_ehr/resources/etls/weight.xml @@ -0,0 +1,30 @@ + + + Weights + Weights data + + + Copy to weights target + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/folderTypes/NBRI_EHR.folderType.xml b/nbri_ehr/resources/folderTypes/NBRI_EHR.folderType.xml new file mode 100644 index 0000000..a65c1c0 --- /dev/null +++ b/nbri_ehr/resources/folderTypes/NBRI_EHR.folderType.xml @@ -0,0 +1,70 @@ + + NBRI EHR + Folder type used for New Iberia Research Center's EHR + + + + + + + Electronic Health Record + menu + + + Quick Search + menu + + + + + + overview + Overview + + + EHR Front Page + body + + + + + animalHistory + Animal History + + + animalHistory + + + + + NBRI Animal History + body + + + + + animalSearch + Animal Search + + + animalSearch + + + + + Animal Search + body + + + + + + Core + Study + DataIntegration + EHR + NBRI_EHR + + Core + false + diff --git a/nbri_ehr/resources/module.xml b/nbri_ehr/resources/module.xml new file mode 100644 index 0000000..62c8ba1 --- /dev/null +++ b/nbri_ehr/resources/module.xml @@ -0,0 +1,17 @@ + + + + false + This is the path to the orchard file location + + ADMIN + + + + + + + + + + diff --git a/nbri_ehr/resources/queries/dbo/auditDeleteEvent.sql b/nbri_ehr/resources/queries/dbo/auditDeleteEvent.sql new file mode 100644 index 0000000..2c58cdf --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/auditDeleteEvent.sql @@ -0,0 +1,23 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +-- subquery to extract an animal event from AUDIT_TRAIL.REFERENCE to identify delete event +SELECT + auditSubQuery.objectid, + auditSubQuery.modified, + auditSubQuery.REFERENCE, + trim(substring(auditSubQuery.event_partial, 1, (length(auditSubQuery.event_partial) - + (length('Event Datetime:') + length(event_datetime))))) as event_name --extract event name from REFERENCE +FROM ( + SELECT substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_EVENT_ID = ')) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE, + substring(adt.reference, + locate('Event:', adt.reference) + length('Event:')) AS event_partial, + substring(adt.reference, + locate('Event Datetime:', adt.reference) + length('Event Datetime:')) AS event_datetime + FROM AUDIT_TRAIL adt + WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' + AND adt.COLUMN_NAME = 'DELETE') auditSubQuery \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_account.sql b/nbri_ehr/resources/queries/dbo/q_account.sql new file mode 100644 index 0000000..c18eee7 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_account.sql @@ -0,0 +1,17 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + ac.ACCOUNT_ID as AccountId, + ac.ACCOUNT_NUMBER as AccountNumber, + ac.DEPARTMENT_ID as department, + ac.COST_TYPE_ID as costType, + ac.EXPENSE_CLASS_ID as expenseClass, + ac.PROJECT_CODE_ID as projectCode, + ac.ACCOUNT_DESC as description, + ac.ACTIVE_YN as active, + ar.area as area +FROM ACCOUNT ac + LEFT JOIN q_areas ar ON ar.area = ac.LOCATION_ID \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_alopecia.sql b/nbri_ehr/resources/queries/dbo/q_alopecia.sql new file mode 100644 index 0000000..322c104 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_alopecia.sql @@ -0,0 +1,25 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID AS objectid, + anmEvt.ANIMAL_ID.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS date, + (CASE + WHEN (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) IS NULL OR trim(anmEvt.STAFF_ID.STAFF_LAST_NAME) IS NULL) THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + anmEvt.RESULT || ev.NUMERIC_UNIT_ID.NAME AS observation, + anmEvt.RESULT AS resobservation, + ev.NUMERIC_UNIT_ID AS unitobservation, + anmEvt.DIAGNOSIS AS remark, + 'Alopecia Score' AS category, + CAST(COALESCE(adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id + LEFT JOIN EVENT ev on anmEvt.EVENT_ID = ev.EVENT_ID +WHERE anmEvt.EVENT_ID.EVENT_ID = 2293 + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates +-- 2293 Alopecia \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_alopecia_delete.sql b/nbri_ehr/resources/queries/dbo/q_alopecia_delete.sql new file mode 100644 index 0000000..cb1f016 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_alopecia_delete.sql @@ -0,0 +1,12 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_EVENT_ID = ')) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + (adt.REFERENCE LIKE '%Alopecia Event%') AND + adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_animal_delivery.sql b/nbri_ehr/resources/queries/dbo/q_animal_delivery.sql new file mode 100644 index 0000000..5cf3b54 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_animal_delivery.sql @@ -0,0 +1,31 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + ad.ANIMAL_DELIVERY_ID as AnimalDeliveryId, + ad.ANIMAL_SHIPMENT_ID as AnimalShipment, + ad.SHIPTO_ID as ShipTo, + cg.location as cage, + COALESCE(rm.room, cg.room) as room, + COALESCE(fl.floor, cg.floor, rm.floor) as floor, + COALESCE(bu.Name, cg.building, rm.building, fl.building) as building, + COALESCE(ar.area, cg.area, rm.area, fl.area, bu.area) as area, + ad.ANIMAL_REQ_ORDER_ID as AnimalReqOrder, + ad.DELIVERY_STATE_ID as DeliveryState, + ad.DELIVERY_NUMBER as DeliveryNumber, + ad.EXPECTED_DATE as ExpectedDate, + ad.PROJECT_CODE_ID as Project, + ad.BILL_TO_ACCOUNT_ID as BillToAccount, + ad.BILL_TO_STAFF_ID.STAFF_FIRST_NAME + || '|' || ad.BILL_TO_STAFF_ID.STAFF_LAST_NAME as BillToStaff, + ad.PER_DIEM_ACCOUNT_ID as PerDiemAccount, + ad.PER_DIEM_STAFF_ID.STAFF_FIRST_NAME + || '|' || ad.PER_DIEM_STAFF_ID.STAFF_LAST_NAME as PerDiemStaff, +FROM ANIMAL_DELIVERY ad + LEFT JOIN q_cages cg ON cg.location = ad.LOCATION_ID + LEFT JOIN q_rooms rm ON rm.room = ad.LOCATION_ID + LEFT JOIN q_floors fl ON fl.floor = ad.LOCATION_ID + LEFT JOIN q_buildings bu ON bu.name = ad.LOCATION_ID + LEFT JOIN q_areas ar ON ar.area = ad.LOCATION_ID \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_animal_delivery_esig.sql b/nbri_ehr/resources/queries/dbo/q_animal_delivery_esig.sql new file mode 100644 index 0000000..1210c26 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_animal_delivery_esig.sql @@ -0,0 +1,13 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + ID as EsigId, + ANIMAL_DELIVERY_ID as AnimalDelivery, + ESIGNATURE_EVENT_ID as EsigEvent, + USER_PROFILE_ID.STAFF_ID.STAFF_FIRST_NAME + || '|' || USER_PROFILE_ID.STAFF_ID.STAFF_LAST_NAME as UserProfile, + ESIG_DATETIME as EsigDateTime +FROM ANIMAL_DELIVERY_ESIG \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_animal_req_order.sql b/nbri_ehr/resources/queries/dbo/q_animal_req_order.sql new file mode 100644 index 0000000..f8222aa --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_animal_req_order.sql @@ -0,0 +1,46 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + ar.ANIMAL_REQ_ORDER_ID as AnimalReqOrderId, + ar.ANIMAL_VENDOR_ID as AnimalVendor, + ar.REQUISITIONER_STAFF_ID.STAFF_FIRST_NAME + || '|' || ar.REQUISITIONER_STAFF_ID.STAFF_LAST_NAME as RequisitionerStaff, + ar.REQUEST_NUMBER as RequestNumber, + ar.REQUISITION_NUMBER as RequisitionNumber, + ar.BILL_YN as Bill, + ar.SHIPPING_CONTACT as ShippingContact, + ar.CREATE_DATE as CreateDate, + ar.REQ_ORDER_TYPE_ID as ReqOrderType, + ar.REQ_ORDER_STATE_ID as ReqOrderState, + ar.BILL_TO_ACCOUNT_ID as BillToAccount, + ar.BILL_TO_STAFF_ID.STAFF_FIRST_NAME + || '|' || ar.BILL_TO_STAFF_ID.STAFF_LAST_NAME as BillToStaff, + ar.PER_DIEM_ACCOUNT_ID as PerDiemAccount, + ar.PER_DIEM_STAFF_ID.STAFF_FIRST_NAME + || '|' || ar.PER_DIEM_STAFF_ID.STAFF_LAST_NAME as PerDiemStaff, + ar.SUBMITTED_BY_STAFF_ID.STAFF_FIRST_NAME + || '|' || ar.SUBMITTED_BY_STAFF_ID.STAFF_LAST_NAME as SubmittedByStaff, + ar.APPROVED_BY_STAFF_ID.STAFF_FIRST_NAME + || '|' || ar.APPROVED_BY_STAFF_ID.STAFF_LAST_NAME as ApprovedByStaff, + ar.SUBMITTED_DATE as SubmittedDate, + ar.APPROVED_DATE as ApprovedDate, + s.SPECIES_ID as Species, + s.PROTOCOL_ID as Protocol, + ar.PROJECT_CODE_ID as Project, + cg.location as SiteCage, + COALESCE(rm.room, cg.room) as SiteRoom, + COALESCE(fl.floor, cg.floor, rm.floor) as SiteFloor, + COALESCE(bu.Name, cg.building, rm.building, fl.building) as SiteBuilding, + COALESCE(area.area, cg.area, rm.area, fl.area, bu.area) as SiteArea, + ar.CREATED_BY_STAFF_ID.STAFF_FIRST_NAME + || '|' || ar.CREATED_BY_STAFF_ID.STAFF_LAST_NAME as CreatedByStaff +FROM ANIMAL_REQ_ORDER ar + LEFT JOIN q_cages cg ON cg.location = ar.SITE_LOCATION_ID + LEFT JOIN q_rooms rm ON rm.room = ar.SITE_LOCATION_ID + LEFT JOIN q_floors fl ON fl.floor = ar.SITE_LOCATION_ID + LEFT JOIN q_areas area ON area.area = ar.SITE_LOCATION_ID + LEFT JOIN q_buildings bu ON bu.name = ar.SITE_LOCATION_ID + LEFT JOIN SEGMENT s ON ar.SEGMENT_ID = s.SEGMENT_ID diff --git a/nbri_ehr/resources/queries/dbo/q_animal_req_order_esig.sql b/nbri_ehr/resources/queries/dbo/q_animal_req_order_esig.sql new file mode 100644 index 0000000..bcce338 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_animal_req_order_esig.sql @@ -0,0 +1,13 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + ID as EsigId, + ANIMAL_REQ_ORDER_ID as AnimalReqOrder, + ESIGNATURE_EVENT_ID as EsigEvent, + USER_PROFILE_ID.STAFF_ID.STAFF_FIRST_NAME + || '|' || USER_PROFILE_ID.STAFF_ID.STAFF_LAST_NAME as UserProfile, + ESIG_DATETIME as EsigDateTime +FROM ANIMAL_REQ_ORDER_ESIG \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_animal_shipment.sql b/nbri_ehr/resources/queries/dbo/q_animal_shipment.sql new file mode 100644 index 0000000..decfb51 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_animal_shipment.sql @@ -0,0 +1,33 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + ans.ANIMAL_SHIPMENT_ID as AnimalShipmentId, + ans.RECEIVED_BY_STAFF_ID.STAFF_FIRST_NAME + || '|' || ans.RECEIVED_BY_STAFF_ID.STAFF_LAST_NAME as ReceivedByStaff, + cg.location as cage, + COALESCE(rm.room, cg.room) as room, + COALESCE(fl.floor, cg.floor, rm.floor) as floor, + COALESCE(bu.Name, cg.building, rm.building, fl.building) as building, + COALESCE(ar.area, cg.area, rm.area, fl.area, bu.area) as area, + ans.ANIMAL_DELIVERY_ID as AnimalDelivery, + ans.LOT_NUMBER_ID as LotNumber, + ans.RECEIVED_DATE as ReceivedDate, + ans.ANIMAL_BIRTH_DATE as BirthDate, + ans.NUMBER_MALES_RECEIVED as MalesReceived, + ans.NUMBER_FEMALES_RECEIVED as FemalesReceived, + ans.NUMBER_EITHER_RECEIVED as EitherReceived, + ans.CAN_UNRECEIVE_YN as CanUnreceive, + ans.COST_CENTER_ID as CostCenter, + ans.MATERNAL_ID as Dam, + ans.PATERNAL_ID as Sire, + ans.RECORDED_DATETIME as RecordedDate, + ans.RECORDED_BY_NAME as RecordedBy +FROM ANIMAL_SHIPMENT ans + LEFT JOIN q_cages cg ON cg.location = ans.LOCATION_ID + LEFT JOIN q_rooms rm ON rm.room = ans.LOCATION_ID + LEFT JOIN q_floors fl ON fl.floor = ans.LOCATION_ID + LEFT JOIN q_buildings bu ON bu.name = ans.LOCATION_ID + LEFT JOIN q_areas ar ON ar.area = ans.LOCATION_ID \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_animal_vendor.sql b/nbri_ehr/resources/queries/dbo/q_animal_vendor.sql new file mode 100644 index 0000000..34e9338 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_animal_vendor.sql @@ -0,0 +1,23 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + av.ANIMAL_VENDOR_ID as AnimalVendorId, + av.VENDOR_APPROVAL_CODE_ID as VendorApprovalCode, + av.VENDOR_Name as VendorName, + av.STREET_ADDRESS1 as StreetAddress1, + av.STREET_ADDRESS2 as StreetAddress2, + av.CITY as City, + av.STATE_PROV as StateProv, + av.COUNTRY as Country, + av.ZIP as Zip, + av.ZIP_EXT as ZipExt, + av.PHONE_NUMBER as PhoneNumber, + av.FAX_NUMBER as FaxNumber, + av.COMMENTS as Comments, + av.INTERNAL_VENDOR_YN as InternalVendor, + vpn.VENDOR_PRODUCTION_LOCATION_ID as VendorProductionLocation +FROM ANIMAL_VENDOR av +LEFT JOIN VENDOR_PRODUCTION_LOCATION vpn ON av.ANIMAL_VENDOR_ID = vpn.ANIMAL_VENDOR_ID diff --git a/nbri_ehr/resources/queries/dbo/q_areas.sql b/nbri_ehr/resources/queries/dbo/q_areas.sql new file mode 100644 index 0000000..9e896a7 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_areas.sql @@ -0,0 +1,9 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT LOCATION_ID AS area, + LOCATION_NAME AS description, +FROM LOCATION +WHERE LOCATION_TYPE_ID = 1 -- SITE \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_arrival.sql b/nbri_ehr/resources/queries/dbo/q_arrival.sql new file mode 100644 index 0000000..f4b836c --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_arrival.sql @@ -0,0 +1,25 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID AS objectid, + anm.ANIMAL_ID_NUMBER AS Id, + (CASE + WHEN (anmEvt.STAFF_ID.STAFF_FIRST_NAME IS NULL OR anmEvt.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + CAST(COALESCE(adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS eventDate, + NULL AS acqDateText, + 'Animal Event' AS source, + substring(Evt.NAME, length('Lab Transfer Fr ')) AS sourceFacility, + CASE WHEN anmEvt.ATTACHMENT_PATH IS NOT NULL THEN + ('C:\Program Files\Labkey\labkey\files\NBRI\EHR\@files\attachments' + || substring(anmEvt.ATTACHMENT_PATH, LENGTH('N:\'), LENGTH(anmEvt.ATTACHMENT_PATH))) + ELSE NULL END AS attachmentFile +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL anm ON anmEvt.ANIMAL_ID = anm.ANIMAL_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id + LEFT JOIN EVENT Evt ON anmEvt.EVENT_ID = Evt.EVENT_ID +WHERE anmEvt.EVENT_ID IN (SELECT EVENT_ID FROM EVENT WHERE NAME LIKE 'Lab Transfer Fr%') \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_arrival_delete.sql b/nbri_ehr/resources/queries/dbo/q_arrival_delete.sql new file mode 100644 index 0000000..e8f5bec --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_arrival_delete.sql @@ -0,0 +1,12 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_EVENT_ID = ')) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + (adt.REFERENCE LIKE '%Lab Transfer Fr%') AND + adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_assignment.sql b/nbri_ehr/resources/queries/dbo/q_assignment.sql new file mode 100644 index 0000000..8b6393f --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_assignment.sql @@ -0,0 +1,41 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT alt.ALTERNATE_ID AS "objectId", + anm.ANIMAL_ID, + anm.ANIMAL_ID_NUMBER AS "Id", + CASE WHEN (SUBSTRING(trim(alt.NAME),3,1) = '-' OR SUBSTRING(trim(alt.NAME),5,1) = '-') + THEN trim(SUBSTRING(trim(alt.NAME),0,11)) + ELSE trim(SUBSTRING(trim(alt.NAME), 0, 8)) + END as "projectName", + alt.NAME AS "description", + ae.EVENT_DATETIME AS assignmentDate, -- Set to arrival/birth then updated by trigger + CASE WHEN alt.DESCRIPTION IS NULL OR length(trim(alt.DESCRIPTION)) != 11 THEN NULL + ELSE COALESCE(TO_DATE(alt.DESCRIPTION, 'DD-Mon-RR'), COALESCE(dea.deathDate, dep.eventDate)) END as endDate, + (CASE + WHEN (ae.STAFF_ID.STAFF_FIRST_NAME IS NULL OR ae.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (trim(ae.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(ae.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + COALESCE(MAX(CAST(adt.CHANGE_DATETIME AS TIMESTAMP)), ae.CREATED_DATETIME) AS modified +FROM ALTERNATE alt +LEFT JOIN ANIMAL anm ON alt.ANIMAL_ID = anm.ANIMAL_ID +LEFT JOIN AUDIT_TRAIL adt ON alt.ALTERNATE_ID = substring(PRIMARY_KEY_VALUES, length('Alternate_ID = ')) + AND adt.TABLE_NAME = 'ALTERNATE' +LEFT JOIN ANIMAL_EVENT ae ON ae.ANIMAL_ID = anm.ANIMAL_ID AND EVENT_ID = 1 -- Received +LEFT JOIN q_deaths dea ON anm.ANIMAL_ID_NUMBER = dea.participantId +LEFT JOIN q_finalDeparture dep ON anm.ANIMAL_ID_NUMBER = dep.Id +WHERE alt.ALTERNATE_TYPE_ID = 6 -- Project Inventory Number for project transfers +GROUP BY alt.ALTERNATE_ID, + anm.ANIMAL_ID, + anm.ANIMAL_ID_NUMBER, + alt.NAME, + alt.DESCRIPTION, + ae.CREATED_DATETIME, + ae.EVENT_DATETIME, + ae.STAFF_ID.STAFF_FIRST_NAME, + ae.STAFF_ID.STAFF_LAST_NAME, + dea.deathDate, + dep.eventDate +ORDER BY anm.ANIMAL_ID,alt.ALTERNATE_ID ASC \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_assignment_delete.sql b/nbri_ehr/resources/queries/dbo/q_assignment_delete.sql new file mode 100644 index 0000000..41f7c47 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_assignment_delete.sql @@ -0,0 +1,11 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, length('Alternate_ID = ')) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +WHERE adt.TABLE_NAME = 'ALTERNATE' AND + adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_biopsy.sql b/nbri_ehr/resources/queries/dbo/q_biopsy.sql new file mode 100644 index 0000000..40e28a9 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_biopsy.sql @@ -0,0 +1,48 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID AS objectid, + anmEvt.ANIMAL_ID.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS biopsyDate, + (CASE + WHEN (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) IS NULL OR trim(anmEvt.STAFF_ID.STAFF_LAST_NAME) IS NULL) THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + anmEvt.EVENT_ID.NAME AS type, + CASE WHEN anmEvt.ATTACHMENT_PATH IS NOT NULL THEN + ('C:\Program Files\Labkey\labkey\files\NBRI\EHR\@files\attachments' + || substring(anmEvt.ATTACHMENT_PATH, LENGTH('N:\'), LENGTH(anmEvt.ATTACHMENT_PATH))) + ELSE NULL END AS attachmentFile, + anmEvt.DIAGNOSIS AS description, + anmCmt.TEXT AS remark, + CAST(COALESCE(adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id + +WHERE anmEvt.EVENT_ID.EVENT_ID IN ( + 1386, -- Hepatic Biopsy-Tru Cut + 1388, -- Liver precutaneous Biopsy + 1389, -- Skin Biopsy + 1390, -- Hepatic Biopsy-Menghini Technique + 1391, -- Lymph node Biopsy + 1392, -- Skeletal Muscle Biopsy + 1393, -- Lung Biopsy + 1394, -- White fat Biopsy + 1395, -- Renal Biopsy + 1396, -- Brown Fat Biopsy + 1397, -- Gastric Biopsy + 1398, -- Intestinal Biopsy + 1399, -- Cervical Biopsy + 1400, -- Rectal Biopsy + 1401, -- Uterine Biopsy + 1402, -- Vaginal Biopsy + 1403, -- Testicular Biopsy + 1404, -- Bone marrow Biopsy + 1603, -- Biopsy Collection + 1641, -- Biopsy Collection - Liver (punch) + 1642 -- Biopsy Collection - Lymph node + ) + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates diff --git a/nbri_ehr/resources/queries/dbo/q_biopsy_delete.sql b/nbri_ehr/resources/queries/dbo/q_biopsy_delete.sql new file mode 100644 index 0000000..4357b9c --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_biopsy_delete.sql @@ -0,0 +1,13 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +SELECT substring(adt.PRIMARY_KEY_VALUES, 18) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + adt.REFERENCE LIKE '%Biops%' AND + adt.COLUMN_NAME = 'DELETE' + diff --git a/nbri_ehr/resources/queries/dbo/q_births.sql b/nbri_ehr/resources/queries/dbo/q_births.sql new file mode 100644 index 0000000..3d6904c --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_births.sql @@ -0,0 +1,26 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anm.ANIMAL_ID_NUMBER AS participantId, + anm.BIRTH_DATE AS birthDate, + (CASE + WHEN (ae.STAFF_ID.STAFF_FIRST_NAME IS NULL OR ae.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (trim(ae.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(ae.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + -- audit timestamp for modifications or animal event received for created + COALESCE(MAX(CAST(adt.CHANGE_DATETIME AS TIMESTAMP)), ae.CREATED_DATETIME) AS modified +FROM Animal anm +LEFT JOIN ALTERNATE alt ON alt.ANIMAL_ID = anm.ANIMAL_ID +LEFT JOIN AUDIT_TRAIL adt ON anm.ANIMAL_ID = substring(PRIMARY_KEY_VALUES, length('ANIMAL_ID = ')) + AND adt.TABLE_NAME = 'ANIMAL' +LEFT JOIN ANIMAL_EVENT ae ON ae.ANIMAL_ID = anm.ANIMAL_ID AND EVENT_ID = 1 -- Received +WHERE alt.ALTERNATE_TYPE_ID = 7 -- 'Dam/Sire/Acq' +AND anm.ANIMAL_ID_NUMBER LIKE 'A%' -- Animal born in centers are pre-appended with A's (in animal Id) +AND alt.DESCRIPTION IS NOT NULL +GROUP BY anm.ANIMAL_ID_NUMBER, + anm.BIRTH_DATE, + ae.STAFF_ID.STAFF_FIRST_NAME, + ae.STAFF_ID.STAFF_LAST_NAME, + ae.CREATED_DATETIME \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_births_delete.sql b/nbri_ehr/resources/queries/dbo/q_births_delete.sql new file mode 100644 index 0000000..3101a85 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_births_delete.sql @@ -0,0 +1,11 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT an.ANIMAL_ID_NUMBER AS Id, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +LEFT JOIN ANIMAL an ON an.ANIMAL_ID = substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_ID = ')) +WHERE adt.TABLE_NAME = 'ANIMAL' AND adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_blood.sql b/nbri_ehr/resources/queries/dbo/q_blood.sql new file mode 100644 index 0000000..8a6f0b9 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_blood.sql @@ -0,0 +1,28 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID AS objectid, + anmEvt.ANIMAL_ID.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS bloodDate, + (CASE + WHEN (anmEvt.STAFF_ID.STAFF_FIRST_NAME IS NULL OR anmEvt.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + anmEvt.EVENT_ID.NAME AS type, + anmEvt.RESULT AS quantity, + ev.NUMERIC_UNIT_ID AS Units, + (CASE WHEN (anmEvt.DIAGNOSIS IS NOT NULL AND anmCmt.TEXT IS NOT NULL) THEN (anmEvt.DIAGNOSIS || ', ' || anmCmt.TEXT) WHEN (anmEvt.DIAGNOSIS IS NOT NULL AND anmCmt.TEXT IS NULL) THEN (anmEvt.DIAGNOSIS) ELSE (anmCmt.TEXT) END) AS remark, + CAST(COALESCE(adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id + LEFT JOIN EVENT ev ON anmEvt.EVENT_ID = ev.EVENT_ID + +WHERE anmEvt.EVENT_ID.EVENT_ID IN (1864, 1581, 2129, 219) + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates +-- 1864 Blood Sample Collection (with Volume) +-- 1581 Blood Sample Collection +-- 2129 Blood-Predose +-- 219 SRV Draw \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_blood_delete.sql b/nbri_ehr/resources/queries/dbo/q_blood_delete.sql new file mode 100644 index 0000000..c2171ba --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_blood_delete.sql @@ -0,0 +1,13 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +SELECT substring(adt.PRIMARY_KEY_VALUES, 18) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + adt.REFERENCE LIKE '%Blood Sample Collection%' AND + adt.COLUMN_NAME = 'DELETE' + diff --git a/nbri_ehr/resources/queries/dbo/q_breeder.sql b/nbri_ehr/resources/queries/dbo/q_breeder.sql new file mode 100644 index 0000000..fa4d1ac --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_breeder.sql @@ -0,0 +1,28 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID AS objectid, + anmEvt.ANIMAL_ID.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS administrationDate, + (CASE + WHEN (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) IS NULL OR trim(anmEvt.STAFF_ID.STAFF_LAST_NAME) IS NULL) THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + anmEvt.EVENT_ID.NAME AS type, + anmEvt.TEXT_RESULT AS result, + CASE WHEN anmEvt.ATTACHMENT_PATH IS NOT NULL THEN + ('C:\Program Files\Labkey\labkey\files\NBRI\EHR\@files\attachments' + || substring(anmEvt.ATTACHMENT_PATH, LENGTH('N:\'), LENGTH(anmEvt.ATTACHMENT_PATH))) + ELSE NULL END AS attachmentFile, + anmCmt.TEXT AS remark, + CAST(COALESCE(adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN EVENT_EVENT_GROUP evtEvtGrp ON evtEvtGrp.EVENT_ID = anmEvt.EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id + +WHERE evtEvtGrp.EVENT_GROUP_ID = 56 + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates +-- 56 Breeder \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_breeder_delete.sql b/nbri_ehr/resources/queries/dbo/q_breeder_delete.sql new file mode 100644 index 0000000..f756ce3 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_breeder_delete.sql @@ -0,0 +1,14 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_EVENT_ID = ')) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + (adt.REFERENCE LIKE '%Multiple Sires%' OR + adt.REFERENCE LIKE '%Multiple Dams%' OR + adt.REFERENCE LIKE '%Mating Event%') AND + adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_buildings.sql b/nbri_ehr/resources/queries/dbo/q_buildings.sql new file mode 100644 index 0000000..8dd5ddd --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_buildings.sql @@ -0,0 +1,12 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + building.LOCATION_ID AS name, + building.LOCATION_NAME AS description, + area.LOCATION_ID AS area +FROM LOCATION building +JOIN LOCATION area ON building.PARENT_LOCATION_ID = area.LOCATION_ID +WHERE building.LOCATION_TYPE_ID = 2 -- building \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_cage_card.sql b/nbri_ehr/resources/queries/dbo/q_cage_card.sql new file mode 100644 index 0000000..e9d6495 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_cage_card.sql @@ -0,0 +1,38 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + cc.CAGE_CARD_ID AS CageCardId, + s.PROTOCOL_ID AS Protocol, + s.SPECIES_ID AS Species, + cc.CARD_FORMAT_ID AS CardFormat, + cc.COST_CENTER_ID AS CostCenter, + cc.GENERATION_DATETIME AS GenerationDate, + cc.UPDATE_DATETIME AS UpdateDate, + cc.NUMBER_OF_ANIMALS AS NumberOfAnimals, + cg.location as cage, + COALESCE(rm.room, cg.room) as room, + COALESCE(fl.floor, cg.floor, rm.floor) as floor, + COALESCE(bu.Name, cg.building, rm.building, fl.building) as building, + COALESCE(ar.area, cg.area, rm.area, fl.area, bu.area) as area, + cc.STAFF_ACCOUNT_ACCOUNT_ID AS Account, + (CASE + WHEN (cc.STAFF_ACCOUNT_STAFF_ID.STAFF_FIRST_NAME IS NULL OR cc.STAFF_ACCOUNT_STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (trim(cc.STAFF_ACCOUNT_STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(cc.STAFF_ACCOUNT_STAFF_ID.STAFF_LAST_NAME)) END) AS AccountStaff, + cc.CENSUS_ACTIVITY_STATUS_ID AS CensusActivityStatus, + cc.CENSUS_ACTIVITY_DATE AS CensusActivityDate, + cc.ANIMAL_DELIVERY_ID AS AnimalDelivery, + (CASE + WHEN (cc.ANIMAL_REQUESTED_BY_STAFF_ID.STAFF_FIRST_NAME IS NULL OR cc.ANIMAL_REQUESTED_BY_STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (trim(cc.ANIMAL_REQUESTED_BY_STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(cc.ANIMAL_REQUESTED_BY_STAFF_ID.STAFF_LAST_NAME)) END) AS AnimalRequestedByStaff +FROM CAGE_CARD cc +LEFT JOIN SEGMENT s ON cc.SEGMENT_ID = s.SEGMENT_ID +LEFT JOIN q_cages cg ON cg.location = cc.LOCATION_ID +LEFT JOIN q_rooms rm ON rm.room = cc.LOCATION_ID +LEFT JOIN q_floors fl ON fl.floor = cc.LOCATION_ID +LEFT JOIN q_buildings bu ON bu.name = cc.LOCATION_ID +LEFT JOIN q_areas ar ON ar.area = cc.LOCATION_ID \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_cage_card_history.sql b/nbri_ehr/resources/queries/dbo/q_cage_card_history.sql new file mode 100644 index 0000000..0313509 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_cage_card_history.sql @@ -0,0 +1,47 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + cc.CAGE_CARD_ID AS CageCardId, + cc.ANIMAL_DELIVERY_ID AS AnimalDelivery, + s.PROTOCOL_ID AS Protocol, + s.SPECIES_ID AS Species, + cc.CARD_FORMAT_ID AS CardFormat, + cc.COST_CENTER_ID AS CostCenter, + cc.GENERATION_DATETIME AS GenerationDate, + cc.UPDATE_DATETIME AS UpdateDate, + cc.NUMBER_OF_ANIMALS AS NumberOfAnimals, + cg.location as cage, + COALESCE(rm.room, cg.room) as room, + COALESCE(fl.floor, cg.floor, rm.floor) as floor, + COALESCE(bu.Name, cg.building, rm.building, fl.building) as building, + COALESCE(ar.area, cg.area, rm.area, fl.area, bu.area) as area, + cc.STAFF_ACCOUNT_ACCOUNT_ID AS Account, + (CASE + WHEN (ast.STAFF_FIRST_NAME IS NULL OR ast.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (ast.STAFF_FIRST_NAME + || '|' || ast.STAFF_LAST_NAME) END) AS AccountStaff, + cc.CENSUS_ACTIVITY_STATUS_ID AS CensusActivityStatus, + cc.CENSUS_ACTIVITY_DATE AS CensusActivityDate, + cc.CENSUS_START_DATE AS CensusStartDate, + cc.CENSUS_STOP_DATE AS CensusStopDate, + cc.TRANSFER_DATE AS TransferDate, + cc.ACTION_DATE AS ActionDate, + cc.RETROSPECTIVE_STRESS_ID AS RetrospectiveStress, + (CASE + WHEN (rst.STAFF_FIRST_NAME IS NULL OR rst.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (rst.STAFF_FIRST_NAME + || '|' || rst.STAFF_LAST_NAME) END) AS AnimalRequestedByStaff + +FROM CAGE_CARD_HISTORY cc + LEFT JOIN SEGMENT s ON s.SEGMENT_ID = cc.SEGMENT_ID + LEFT JOIN STAFF ast ON ast.STAFF_ID = cc.STAFF_ACCOUNT_STAFF_ID + LEFT JOIN STAFF rst ON rst.STAFF_ID = cc.ANIMAL_REQUESTED_BY_STAFF_ID + LEFT JOIN q_cages cg ON cg.location = cc.LOCATION_ID + LEFT JOIN q_rooms rm ON rm.room = cc.LOCATION_ID + LEFT JOIN q_floors fl ON fl.floor = cc.LOCATION_ID + LEFT JOIN q_buildings bu ON bu.name = cc.LOCATION_ID + LEFT JOIN q_areas ar ON ar.area = cc.LOCATION_ID + diff --git a/nbri_ehr/resources/queries/dbo/q_cages.sql b/nbri_ehr/resources/queries/dbo/q_cages.sql new file mode 100644 index 0000000..f851e38 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_cages.sql @@ -0,0 +1,18 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + cage.LOCATION_ID AS location, + cage.LOCATION_NAME AS cage, + room.LOCATION_ID AS room, + floor.LOCATION_ID as floor, + building.LOCATION_ID as building, + area.LOCATION_ID as area +FROM LOCATION cage +JOIN LOCATION room ON cage.PARENT_LOCATION_ID = room.LOCATION_ID +JOIN LOCATION floor ON room.PARENT_LOCATION_ID = floor.LOCATION_ID +JOIN LOCATION building ON floor.PARENT_LOCATION_ID = building.LOCATION_ID +JOIN LOCATION area ON building.PARENT_LOCATION_ID = area.LOCATION_ID +WHERE cage.LOCATION_TYPE_ID = 5 -- Sub Room \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_cases.sql b/nbri_ehr/resources/queries/dbo/q_cases.sql new file mode 100644 index 0000000..9b8e4fb --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_cases.sql @@ -0,0 +1,36 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT * FROM ( + SELECT anmEvt.ANIMAL_EVENT_ID as objectid, + anm.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS caseDate, + CAST(COALESCE(adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified, + (CASE + WHEN (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) IS NULL OR trim(anmEvt.STAFF_ID.STAFF_LAST_NAME) IS NULL) + THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + (CASE WHEN anmEvt.EVENT_ID = 1580 THEN ('Open Remark: ' || COALESCE(anmCmt.TEXT, 'None') || '; Open Diagnosis: ' || COALESCE(anmEvt.DIAGNOSIS, 'None')) ELSE NULL END) AS openRemark, + (CASE WHEN anmEvt.EVENT_ID = 1677 THEN ('Close Remark: ' || COALESCE(anmCmt.TEXT, 'None') || '; Close Diagnosis: ' || COALESCE(anmEvt.DIAGNOSIS, 'None')) ELSE NULL END) AS closeRemark, + COALESCE(dea.deathDate, dep.eventDate) AS enddate, + anmEvt.EVENT_ID.NAME AS category, + CASE + WHEN anmEvt.ATTACHMENT_PATH IS NOT NULL THEN + ('C:\Program Files\Labkey\labkey\files\NBRI\EHR\@files\attachments' + || substring(anmEvt.ATTACHMENT_PATH, LENGTH('N:\'), LENGTH(anmEvt.ATTACHMENT_PATH))) + ELSE NULL END AS attachmentFile + FROM ANIMAL_EVENT anmEvt + LEFT JOIN staffInfo staff ON staff.staff_id = anmEvt.STAFF_ID + LEFT JOIN ANIMAL anm ON anmEvt.ANIMAL_ID = anm.ANIMAL_ID + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id + LEFT JOIN q_deaths dea ON anm.ANIMAL_ID_NUMBER = dea.participantId + LEFT JOIN q_finalDeparture dep ON anm.ANIMAL_ID_NUMBER = dep.Id + WHERE anmEvt.EVENT_ID = 1580 + OR anmEvt.EVENT_ID = 1677 -- 1580 Presenting Diagnosis, 1677 Clinical Resolution + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates + ) cas +ORDER BY cas.Id DESC, cas.caseDate DESC, cas.category ASC \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_cases_delete.sql b/nbri_ehr/resources/queries/dbo/q_cases_delete.sql new file mode 100644 index 0000000..b5e2104 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_cases_delete.sql @@ -0,0 +1,29 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT ade.objectid, + ade.modified, + ade.REFERENCE, + ct.event_id, + ade.event_name +FROM auditDeleteEvent ade + +LEFT JOIN -- on clinical treatments + +(SELECT e.name, e.event_id, eeg.event_group_id + FROM event_event_group eeg + LEFT JOIN event e ON eeg.event_id = e.event_id + WHERE (eeg.EVENT_GROUP_ID = 37) -- Clinical Treatments + GROUP BY eeg.event_group_id, e.event_id, e.name) ct + +ON ade.event_name = ct.name + +WHERE ct.name IS NOT NULL + +GROUP BY ade.objectid, + ade.modified, + ade.REFERENCE, + ct.event_id, + ade.event_name \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_chemistryResults.sql b/nbri_ehr/resources/queries/dbo/q_chemistryResults.sql new file mode 100644 index 0000000..a2983ff --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_chemistryResults.sql @@ -0,0 +1,23 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID AS objectid, + anmEvt.ANIMAL_ID.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS administrationDate, + (CASE + WHEN (anmEvt.STAFF_ID.STAFF_FIRST_NAME IS NULL OR anmEvt.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (anmEvt.STAFF_ID.STAFF_FIRST_NAME + || '|' || anmEvt.STAFF_ID.STAFF_LAST_NAME) END) AS performedby, + anmEvt.EVENT_ID.NAME AS type, + anmEvt.RESULT AS result, + anmCmt.TEXT AS remark, + CAST(COALESCE(adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN EVENT_EVENT_GROUP evtEvtGrp ON evtEvtGrp.EVENT_ID = anmEvt.EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id + +WHERE evtEvtGrp.EVENT_GROUP_ID = 64 -- 64 Hormones + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates diff --git a/nbri_ehr/resources/queries/dbo/q_chemistryResults_delete.sql b/nbri_ehr/resources/queries/dbo/q_chemistryResults_delete.sql new file mode 100644 index 0000000..9c51cfe --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_chemistryResults_delete.sql @@ -0,0 +1,11 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_EVENT_ID = ')) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_clinremarks.sql b/nbri_ehr/resources/queries/dbo/q_clinremarks.sql new file mode 100644 index 0000000..714998a --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_clinremarks.sql @@ -0,0 +1,27 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID AS objectid, + anmEvt.ANIMAL_ID.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS administrationDate, + (CASE + WHEN (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) IS NULL OR trim(anmEvt.STAFF_ID.STAFF_LAST_NAME) IS NULL) THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + ('Note: ' || COALESCE(anmCmt.TEXT, 'None') || '; Diagnosis: ' || COALESCE(anmEvt.DIAGNOSIS, 'None')) AS remark, + 'Clinical' AS category, + CASE WHEN anmEvt.ATTACHMENT_PATH IS NOT NULL THEN + ('C:\Program Files\Labkey\labkey\files\NBRI\EHR\@files\attachments' + || substring(anmEvt.ATTACHMENT_PATH, LENGTH('N:\'), LENGTH(anmEvt.ATTACHMENT_PATH))) + ELSE NULL END AS attachmentFile, + CAST(COALESCE(adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN EVENT_EVENT_GROUP evtEvtGrp ON evtEvtGrp.EVENT_ID = anmEvt.EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id + +WHERE evtEvtGrp.EVENT_GROUP_ID = 53 + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates +-- 53 Comments \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_clinremarks_delete.sql b/nbri_ehr/resources/queries/dbo/q_clinremarks_delete.sql new file mode 100644 index 0000000..d0395a2 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_clinremarks_delete.sql @@ -0,0 +1,31 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_EVENT_ID = ')) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + (adt.REFERENCE LIKE '%Gross Pathology%' OR + adt.REFERENCE LIKE '%Cardiopulmonary Disorder%' OR + adt.REFERENCE LIKE '%Dermatological Disorder%' OR + adt.REFERENCE LIKE '%Endocrine Disorder%' OR + adt.REFERENCE LIKE '%Environmental Exposure%' OR + adt.REFERENCE LIKE '%Gastrointestinal Disorder%' OR + adt.REFERENCE LIKE '%Hematological Disorder%' OR + adt.REFERENCE LIKE '%Iatrogenic%' OR + adt.REFERENCE LIKE '%Immune Disorder%' OR + adt.REFERENCE LIKE '%Infectious Disease%' OR + adt.REFERENCE LIKE '%Metabolic Disorder%' OR + adt.REFERENCE LIKE '%Musculoskeletal Disorder%' OR + adt.REFERENCE LIKE '%Neoplasia%' OR + adt.REFERENCE LIKE '%Neurological Disorder%' OR + adt.REFERENCE LIKE '%No Post Mortem exam%' OR + adt.REFERENCE LIKE '%Opthalmologic Disorder%' OR + adt.REFERENCE LIKE '%Reproductive Disorder%' OR + adt.REFERENCE LIKE '%Autolysis%' OR + adt.REFERENCE LIKE '%No gross abnormalities%' OR + adt.REFERENCE LIKE '%General Comment%') AND + adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_deaths.sql b/nbri_ehr/resources/queries/dbo/q_deaths.sql new file mode 100644 index 0000000..3a4c38a --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_deaths.sql @@ -0,0 +1,26 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +SELECT an.ANIMAL_ID_NUMBER AS participantId, + an.DEATH_DATE AS deathDate, + an.TERMINATION_REASON_ID as reason, + (CASE + WHEN (ae.STAFF_ID.STAFF_FIRST_NAME IS NULL OR ae.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (trim(ae.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(ae.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + COALESCE(MAX(CAST(adt.CHANGE_DATETIME AS TIMESTAMP)), ae.CREATED_DATETIME) AS modified +FROM Animal an +LEFT JOIN AUDIT_TRAIL adt ON an.ANIMAL_ID = substring(PRIMARY_KEY_VALUES, length('ANIMAL_ID = ')) + AND adt.TABLE_NAME = 'ANIMAL' AND adt.COLUMN_NAME = 'death_date' +LEFT JOIN ANIMAL_EVENT ae ON ae.ANIMAL_ID = an.ANIMAL_ID AND EVENT_ID = 1 -- Received +WHERE an.ANIMAL_DISPOSITION_ID = 4 -- died +AND an.TERMINATION_REASON_ID != 10 -- Invalid Id +GROUP BY an.ANIMAL_ID_NUMBER, + an.DEATH_DATE, + an.TERMINATION_REASON_ID, + ae.STAFF_ID.STAFF_FIRST_NAME, + ae.STAFF_ID.STAFF_LAST_NAME, + ae.CREATED_DATETIME \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_deaths_delete.sql b/nbri_ehr/resources/queries/dbo/q_deaths_delete.sql new file mode 100644 index 0000000..3101a85 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_deaths_delete.sql @@ -0,0 +1,11 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT an.ANIMAL_ID_NUMBER AS Id, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +LEFT JOIN ANIMAL an ON an.ANIMAL_ID = substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_ID = ')) +WHERE adt.TABLE_NAME = 'ANIMAL' AND adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_deleted_record.sql b/nbri_ehr/resources/queries/dbo/q_deleted_record.sql new file mode 100644 index 0000000..2a04497 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_deleted_record.sql @@ -0,0 +1,17 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + dr.ID AS Id, + dr.PROTOCOL_NUMBER AS Protocol, + dr.USER_REFERENCE_NUMBER AS UserReferenceNumber, + dr.PI_NAME AS Investigator, + dr.TITLE AS Title, + dre.ESIGNATURE_EVENT_ID AS EsigEvent, + dre.USER_PROFILE_ID.STAFF_ID.STAFF_FIRST_NAME + || '|' || dre.USER_PROFILE_ID.STAFF_ID.STAFF_LAST_NAME as EsigUser, + dre.ESIG_DATETIME AS EsigDate +FROM DELETED_RECORD dr +LEFT JOIN DELETED_RECORD_ESIG dre ON dr.ID = dre.DELETED_RECORD_ID \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_demographics.sql b/nbri_ehr/resources/queries/dbo/q_demographics.sql new file mode 100644 index 0000000..67bcb9f --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_demographics.sql @@ -0,0 +1,64 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +SELECT anm.ANIMAL_ID_NUMBER AS participantId, + anm.BIRTH_DATE, + anm.GENDER_ID AS gender, + anm.SSB_ID.SPECIES_ID AS species, + anm.BIRTH_DATE AS birth, + anm.DATE_WEANED AS weanedDate, + anm.DEATH_DATE AS death, + anm.ANIMAL_DISPOSITION_ID AS disposition, + anm.DESCRIPTION AS description, + anm.TERMINATION_REASON_ID AS termination, + anm.VENDOR_ANIMAL_NUMBER AS vendorNumber, + anm.ACTIVE_YN AS activeStatus, + anm.LOT_NUMBER_ID AS lotId, + st.status AS calculated_status, + alt.NAME AS damSire, + altImplant.Name AS implantNumber, + altOrigin.Name AS geographic_origin, + altSrc.Name AS source, + altCites.Name AS CITES, + (CASE + WHEN (ae.STAFF_ID.STAFF_FIRST_NAME IS NULL OR ae.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (trim(ae.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(ae.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + -- audit timestamp for modifications or animal event received for created + COALESCE(MAX(CAST(adt.CHANGE_DATETIME AS TIMESTAMP)), ae.CREATED_DATETIME) AS modified +FROM Animal anm +LEFT JOIN AUDIT_TRAIL adt ON anm.ANIMAL_ID = substring(PRIMARY_KEY_VALUES, length('ANIMAL_ID = ')) +AND adt.TABLE_NAME = 'ANIMAL' +LEFT JOIN q_status st ON st.Id = anm.ANIMAL_ID_NUMBER +LEFT JOIN ANIMAL_EVENT ae ON ae.ANIMAL_ID = anm.ANIMAL_ID AND EVENT_ID = 1 -- Received +LEFT JOIN ALTERNATE alt ON alt.ANIMAL_ID = anm.ANIMAL_ID AND alt.ALTERNATE_TYPE_ID = 7 -- Dam/sire +LEFT JOIN ALTERNATE altImplant ON altImplant.ANIMAL_ID = anm.ANIMAL_ID AND altImplant.ALTERNATE_TYPE_ID = 5 --Transponder number +LEFT JOIN ALTERNATE altOrigin ON altOrigin.ANIMAL_ID = anm.ANIMAL_ID AND altOrigin.ALTERNATE_TYPE_ID = 10 -- Country of origin +LEFT JOIN ALTERNATE altSrc ON altSrc.ANIMAL_ID = anm.ANIMAL_ID AND altSrc.ALTERNATE_TYPE_ID = 11 -- Source +LEFT JOIN ALTERNATE altCites ON altCites.ANIMAL_ID = anm.ANIMAL_ID AND altCites.ALTERNATE_TYPE_ID = 3 -- CITES number +WHERE anm.ANIMAL_DISPOSITION_ID IS NULL OR anm.ANIMAL_DISPOSITION_ID != 110 -- Invalid Id +GROUP BY anm.ANIMAL_ID_NUMBER, + anm.BIRTH_DATE, + anm.GENDER_ID, + anm.SSB_ID.SPECIES_ID, + anm.BIRTH_DATE, + anm.DATE_WEANED, + anm.DEATH_DATE, + anm.ANIMAL_DISPOSITION_ID, + anm.DESCRIPTION, + anm.TERMINATION_REASON_ID, + anm.VENDOR_ANIMAL_NUMBER, + anm.ACTIVE_YN, + anm.LOT_NUMBER_ID, + ae.STAFF_ID.STAFF_FIRST_NAME, + ae.STAFF_ID.STAFF_LAST_NAME, + st.status, + alt.NAME, + altImplant.Name, + altOrigin.Name, + altSrc.Name, + altCites.Name, + ae.CREATED_DATETIME diff --git a/nbri_ehr/resources/queries/dbo/q_demographics_delete.sql b/nbri_ehr/resources/queries/dbo/q_demographics_delete.sql new file mode 100644 index 0000000..cad208a --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_demographics_delete.sql @@ -0,0 +1,11 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT an.ANIMAL_ID_NUMBER AS Id, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +LEFT JOIN ANIMAL an ON an.ANIMAL_ID = substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_ID = ')) +WHERE adt.TABLE_NAME = 'ANIMAL' AND adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_department.sql b/nbri_ehr/resources/queries/dbo/q_department.sql new file mode 100644 index 0000000..8232785 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_department.sql @@ -0,0 +1,13 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + DEPARTMENT_ID as DepartmentId, + DEPARTMENT_NAME as Name, + DEPARTMENT_DESC as Description, + PARENT_DEPARTMENT_ID as ParentDepartment, + STAFF_ID.STAFF_FIRST_NAME + || '|' || STAFF_ID.STAFF_LAST_NAME as Staff +FROM DEPARTMENT \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_departure.sql b/nbri_ehr/resources/queries/dbo/q_departure.sql new file mode 100644 index 0000000..da11868 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_departure.sql @@ -0,0 +1,229 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +-- Used for departure ETL. There are some duplicate departures in ANIMAL_EVENTS thus the GROUP BY and MAX values +SELECT + i.*, + (CASE + WHEN (st.STAFF_FIRST_NAME IS NULL OR + st.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (st.STAFF_FIRST_NAME + || '|' || st.STAFF_LAST_NAME) END) AS performedby +FROM +( + SELECT MAX(anmEvt.ANIMAL_EVENT_ID) AS objectid, + anm.ANIMAL_ID_NUMBER AS Id, + src.NAME AS destination, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS eventDate, + evt.NAME AS description, + MAX(anmEvt.STAFF_ID) AS staff, + CAST(COALESCE(MAX(adt.modified), MAX(anmEvt.CREATED_DATETIME)) AS TIMESTAMP) AS modified + FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL anm ON anmEvt.ANIMAL_ID = anm.ANIMAL_ID + LEFT JOIN EVENT evt ON anmEvt.EVENT_ID = evt.EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id + LEFT JOIN ANIMAL_DISPOSITION src ON src.ID = anm.ANIMAL_DISPOSITION_ID + WHERE anmEvt.EVENT_ID IN (SELECT EVENT_ID FROM EVENT WHERE NAME LIKE 'Lab Transfer To%' OR NAME LIKE 'Lab Transfer to%') + GROUP BY anm.ANIMAL_ID_NUMBER, + anm.ANIMAL_DISPOSITION_ID, + anmEvt.EVENT_DATETIME, + evt.NAME, + src.NAME +) i +LEFT JOIN STAFF st ON i.staff = st.STAFF_ID +WHERE i.Id NOT IN + ( + '07-162', + '11C044', + '13A31451', + '16-4234', + '170239', + '18-4048', + '180176', + '20-4049', + '20-4069', + '20-4073', + '20-4079', + 'A10L018', + 'A10L131', + 'A10N037', + 'A10N096', + 'A10N127', + 'A10R025', + 'A11L055', + 'A11N119', + 'A11N123', + 'A11R024', + 'A12L162', + 'A13N113', + 'A13N130', + 'A13N159', + 'A14L023', + 'A14L078', + 'A14L114', + 'A15N026', + 'A15N090', + 'A15N118', + 'A15N137', + 'A15N152', + 'A16L053', + 'A16N009', + 'A16N057', + 'A16N106', + 'A16N154', + 'A17L125', + 'A17L145', + 'A18M014', + 'A18U011', + 'A19U013', + 'A1K036', + 'A20U002', + 'A20U003', + 'A20U006', + 'A20U008', + 'A21U004', + 'A21U005', + 'A21U006', + 'A21U007', + 'A25C058', + 'A25C059', + 'A25M103', + 'A25N094', + 'A25U031', + 'A2L070', + 'A2M062', + 'A3A005', + 'A3A021', + 'A3M058', + 'A4S005', + 'A5A006', + 'A5A008', + 'A5A010', + 'A5M022', + 'A5M044', + 'A6A003', + 'A6A004', + 'A6A012', + 'A6E081', + 'A6M005', + 'A6M037', + 'A6M052', + 'A7N086', + 'A7N137', + 'A7N156', + 'A8A007', + 'A8R029', + 'A8R032', + 'A9A002', + 'A9A011', + 'AK340I', + 'AM535I', + 'AM541J', + 'AR709D', + 'AT667F', + 'BF702G', + 'BF737H', + 'BY381J', + 'CKE036', + 'CKG004', + 'CKG005', + 'CKG016', + 'CKG026', + 'CKG041', + 'CKG047', + 'CKG080', + 'CKH026', + 'CKH051', + 'CKH078', + 'CKH084', + 'CKI003', + 'CKI038', + 'CKI080', + 'CR31', + 'CR45', + 'CT73', + 'CT74', + 'DCGM', + 'DE2E', + 'G97003', + 'GB75B', + 'JR29I', + 'N11801241', + 'N4544916', + 'N4591982', + 'N88411011', + 'N9961471', + 'N9961472', + 'O10831233', + 'O10831242', + 'O10831363', + 'O13131543', + 'O1344845', + 'O1344846', + 'O159341211', + 'O16253113', + 'O16253210', + 'O16451432', + 'O16651162', + 'O16651163', + 'O1669712', + 'O1669852', + 'O17202122', + 'O17202123', + 'O17312681', + 'O1842672', + 'O18732525', + 'O18732533', + 'O19612254', + 'O19612316', + 'O20121233', + 'O2071438', + 'O20813341', + 'O20813451', + 'O20813453', + 'O21162181', + 'O22082333', + 'O22517112', + 'O2301711', + 'O2301734', + 'O2307197', + 'O2418381', + 'O2659166', + 'O270573', + 'O2705731', + 'O2707213', + 'O2733136', + 'O2899141', + 'O3087125', + 'O311019', + 'O3345221', + 'O4001210', + 'O400129', + 'O5322112', + 'O644815', + 'O8253762', + 'O8284861', + 'O8456105', + 'O8711107', + 'O87117111', + 'O8711871', + 'O87641', + 'O88533', + 'O88803', + 'O89142', + 'O89152', + 'O915089', + 'O9184343', + 'O9184616', + 'O92861', + 'O94691', + 'RE3I', + 'S111221', + 'SZ218A', + 'U564', + 'U682', + 'VL111C', + 'YS94F' + ) diff --git a/nbri_ehr/resources/queries/dbo/q_departure_delete.sql b/nbri_ehr/resources/queries/dbo/q_departure_delete.sql new file mode 100644 index 0000000..81b1194 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_departure_delete.sql @@ -0,0 +1,12 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_EVENT_ID = ')) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + (adt.REFERENCE LIKE '%Lab Transfer To%') AND + adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_drug.sql b/nbri_ehr/resources/queries/dbo/q_drug.sql new file mode 100644 index 0000000..bdf7e1c --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_drug.sql @@ -0,0 +1,48 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID AS objectid, + anmEvt.ANIMAL_ID.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS administrationDate, + (CASE + WHEN (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) IS NULL OR trim(anmEvt.STAFF_ID.STAFF_LAST_NAME) IS NULL) THEN 'unknown' + WHEN (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) = ' ' OR trim(anmEvt.STAFF_ID.STAFF_LAST_NAME) = ' ') THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + anmEvt.EVENT_ID.NAME AS type, + anmEvt.RESULT AS amount, + CASE WHEN anmEvt.ATTACHMENT_PATH IS NOT NULL THEN + ('C:\Program Files\Labkey\labkey\files\NBRI\EHR\@files\attachments' + || substring(anmEvt.ATTACHMENT_PATH, LENGTH('N:\'), LENGTH(anmEvt.ATTACHMENT_PATH))) + ELSE NULL END AS attachmentFile, + (CASE WHEN (anmEvt.DIAGNOSIS IS NOT NULL AND anmCmt.TEXT IS NOT NULL) THEN (anmEvt.DIAGNOSIS || ', ' || anmCmt.TEXT) WHEN (anmEvt.DIAGNOSIS IS NOT NULL AND anmCmt.TEXT IS NULL) THEN (anmEvt.DIAGNOSIS) ELSE (anmCmt.TEXT) END) AS remark, + CAST(COALESCE(adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN EVENT_EVENT_GROUP evtEvtGrp ON evtEvtGrp.EVENT_ID = anmEvt.EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id + +WHERE (evtEvtGrp.EVENT_GROUP_ID = 31 AND evtEvtGrp.EVENT_ID = 2261) -- Sedation from Timed Procedures + OR evtEvtGrp.EVENT_GROUP_ID IN (3, 25, 34, 39, 51, 54, 65) + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates +-- 3 Vaccinations +-- 25 Dose Administration +-- 34 Medication Administration +-- 39 Behavioral Treatment +-- 51 Oral Dose Administration - Alert +-- 54 Fluid Administration +-- 65 Sedation +GROUP BY anmEvt.ANIMAL_EVENT_ID, + anmEvt.ANIMAL_ID.ANIMAL_ID_NUMBER, + anmEvt.EVENT_DATETIME, + anmEvt.STAFF_ID.STAFF_FIRST_NAME, + anmEvt.STAFF_ID.STAFF_LAST_NAME, + anmEvt.EVENT_ID.NAME, + anmEvt.RESULT, + anmEvt.ATTACHMENT_PATH, + anmEvt.DIAGNOSIS, + anmCmt.TEXT, + anmEvt.CREATED_DATETIME, + adt.modified \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_drug_delete.sql b/nbri_ehr/resources/queries/dbo/q_drug_delete.sql new file mode 100644 index 0000000..817ab35 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_drug_delete.sql @@ -0,0 +1,28 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT ade.objectid, + ade.modified, + ade.REFERENCE, + drugEvents.event_id, + ade.event_name +FROM auditDeleteEvent ade + +LEFT JOIN -- on drug events + + (SELECT e.name, e.event_id, eeg.event_group_id + FROM event_event_group eeg LEFT JOIN event e ON eeg.event_id = e.event_id + WHERE (eeg.EVENT_GROUP_ID = 31 AND eeg.EVENT_ID = 2261) -- Sedation from Timed Procedures + OR eeg.EVENT_GROUP_ID IN (3, 25, 34, 39, 51, 54, 65) + GROUP BY eeg.event_group_id, e.event_id, e.name) drugEvents + +ON ade.event_name = drugEvents.name WHERE drugEvents.name IS NOT NULL + +GROUP BY + ade.objectid, + ade.modified, + ade.REFERENCE, + drugEvents.event_id, + ade.event_name \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_exemptions.sql b/nbri_ehr/resources/queries/dbo/q_exemptions.sql new file mode 100644 index 0000000..3fdd35d --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_exemptions.sql @@ -0,0 +1,24 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID as objectid, + anm.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS exemptionDate, + CAST(COALESCE (adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified, + (CASE + WHEN (anmEvt.STAFF_ID.STAFF_FIRST_NAME IS NULL OR anmEvt.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + (CASE WHEN (anmEvt.DIAGNOSIS IS NOT NULL AND anmCmt.TEXT IS NOT NULL) THEN (anmEvt.DIAGNOSIS || ', ' || anmCmt.TEXT) WHEN (anmEvt.DIAGNOSIS IS NOT NULL AND anmCmt.TEXT IS NULL) THEN (anmEvt.DIAGNOSIS) ELSE (anmCmt.TEXT) END) AS remark, + anmEvt.EVENT_ID.NAME AS category +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL anm ON anmEvt.ANIMAL_ID = anm.ANIMAL_ID + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN EVENT_EVENT_GROUP evtEvtGrp ON evtEvtGrp.EVENT_ID = anmEvt.EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id +WHERE evtEvtGrp.EVENT_GROUP_ID IN (45,46) + -- 45 Food Enrichment Exemption + -- 46 Environmental Enrichment Exemption + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_exemptions_delete.sql b/nbri_ehr/resources/queries/dbo/q_exemptions_delete.sql new file mode 100644 index 0000000..4f8da71 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_exemptions_delete.sql @@ -0,0 +1,13 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_EVENT_ID = ')) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + (adt.REFERENCE LIKE '%Housing Exempt%' OR + adt.REFERENCE LIKE '%Food Exempt%' ) AND + adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_finalDeparture.sql b/nbri_ehr/resources/queries/dbo/q_finalDeparture.sql new file mode 100644 index 0000000..291c72f --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_finalDeparture.sql @@ -0,0 +1,15 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +-- Determines final departure dates including for animals that leave and return +SELECT dep.Id, + arr.latestArr, + dep.latestDep, + -- Animal can leave center and come back multiple times + CASE WHEN arr.latestArr IS NOT NULL AND dep.latestDep IS NOT NULL AND arr.latestArr > dep.latestDep THEN NULL + ELSE dep.latestDep END AS eventDate + FROM q_latestDeparture dep +LEFT JOIN q_latestArrival arr ON arr.Id = dep.Id \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_flag_categories.sql b/nbri_ehr/resources/queries/dbo/q_flag_categories.sql new file mode 100644 index 0000000..b2720cb --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_flag_categories.sql @@ -0,0 +1,15 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + NAME AS category, + 'FALSE' AS enforceUnique, + 'FALSE' AS omitFromOverview, + 'TRUE' AS doHighlight +FROM EVENT_GROUP +WHERE EVENT_GROUP_ID IN (26, 28, 67) +-- 26 Quarantine +-- 28 Surgical Procedures - Major +-- 67 Adverse Reaction to Medication diff --git a/nbri_ehr/resources/queries/dbo/q_flag_values.sql b/nbri_ehr/resources/queries/dbo/q_flag_values.sql new file mode 100644 index 0000000..20b38a8 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_flag_values.sql @@ -0,0 +1,18 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + CASE WHEN EVENT_ID = 1673 OR EVENT_ID = 1674 THEN 'Quarantine' + ELSE EVENT_ID.NAME + END AS value, + EVENT_ID AS code, + EVENT_ID AS objectid, + EVENT_ID.DESCRIPTION, + EVENT_GROUP_ID.NAME AS category +FROM EVENT_EVENT_GROUP +WHERE EVENT_GROUP_ID IN (26, 28, 67) +-- 26 Quarantine +-- 28 Surgical Procedures - Major +-- 67 Adverse Reaction to Medication diff --git a/nbri_ehr/resources/queries/dbo/q_flags.sql b/nbri_ehr/resources/queries/dbo/q_flags.sql new file mode 100644 index 0000000..b7fc253 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_flags.sql @@ -0,0 +1,51 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +-- Quarantine +SELECT anmEvt.ANIMAL_EVENT_ID AS objectid, + anmEvt.ANIMAL_ID.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS startdate, + CAST(ae.EVENT_DATETIME AS TIMESTAMP) AS enddate, + (CASE + WHEN (anmEvt.STAFF_ID.STAFF_FIRST_NAME IS NULL OR anmEvt.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + anmEvt.EVENT_ID AS flag, + CASE WHEN anmCmt.TEXT IS NOT NULL THEN (anmCmt.TEXT || '-' || ac.TEXT) + ELSE ac.TEXT END AS remark, + CAST(COALESCE(adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL_EVENT ae ON ae.ANIMAL_ID = anmEvt.ANIMAL_ID AND ae.EVENT_ID.EVENT_ID = 1674 + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN ANIMAL_EVENT_COMMENT ac ON ae.ANIMAL_EVENT_ID = ac.ANIMAL_EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id + +WHERE anmEvt.EVENT_ID.EVENT_ID = 1673 + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates +-- 1673 Quarantine - arrival +-- 1674 Quarantine - release +UNION + +-- Other flags +SELECT anmEvt.ANIMAL_EVENT_ID AS objectid, + anmEvt.ANIMAL_ID.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS startdate, + NULL AS enddate, + (CASE + WHEN (anmEvt.STAFF_ID.STAFF_FIRST_NAME IS NULL OR anmEvt.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + anmEvt.EVENT_ID AS flag, + anmCmt.TEXT AS remark, + CAST(COALESCE(adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id + LEFT JOIN EVENT_EVENT_GROUP evtEvtGrp ON evtEvtGrp.EVENT_ID = anmEvt.EVENT_ID + +WHERE evtEvtGrp.EVENT_GROUP_ID IN (28, 67) + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates +-- 28 Surgical Procedure - Major +-- 67 Medication Adverse Reaction diff --git a/nbri_ehr/resources/queries/dbo/q_flags_delete.sql b/nbri_ehr/resources/queries/dbo/q_flags_delete.sql new file mode 100644 index 0000000..b5f0cb9 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_flags_delete.sql @@ -0,0 +1,14 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, 18) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + (adt.REFERENCE LIKE '%Quarantine%' + OR adt.REFERENCE LIKE '%Adverse reaction%' + OR adt.REFERENCE LIKE '%Major Surgical%' + ) + AND adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_floors.sql b/nbri_ehr/resources/queries/dbo/q_floors.sql new file mode 100644 index 0000000..53d245f --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_floors.sql @@ -0,0 +1,14 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + floor.LOCATION_ID AS floor, + floor.LOCATION_NAME AS name, + building.LOCATION_ID AS building, + area.LOCATION_ID AS area +FROM LOCATION floor +JOIN LOCATION building ON floor.PARENT_LOCATION_ID = building.LOCATION_ID +JOIN LOCATION area ON building.PARENT_LOCATION_ID = area.LOCATION_ID +WHERE floor.LOCATION_TYPE_ID = 3 -- Floor \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_foster.sql b/nbri_ehr/resources/queries/dbo/q_foster.sql new file mode 100644 index 0000000..d88c76b --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_foster.sql @@ -0,0 +1,22 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID AS objectid, + anmEvt.ANIMAL_ID.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS fosterDate, + (CASE + WHEN (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) IS NULL OR trim(anmEvt.STAFF_ID.STAFF_LAST_NAME) IS NULL) THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + anmEvt.EVENT_ID.NAME AS type, + anmCmt.TEXT AS remark, + CAST(COALESCE(adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN EVENT_EVENT_GROUP evtEvtGrp ON evtEvtGrp.EVENT_ID = anmEvt.EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id + +WHERE evtEvtGrp.EVENT_GROUP_ID = 38 -- 38 Fostering + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates diff --git a/nbri_ehr/resources/queries/dbo/q_foster_delete.sql b/nbri_ehr/resources/queries/dbo/q_foster_delete.sql new file mode 100644 index 0000000..bf689e7 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_foster_delete.sql @@ -0,0 +1,12 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_EVENT_ID = ')) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + (adt.REFERENCE LIKE '%Foster%') AND + adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_histopathology.sql b/nbri_ehr/resources/queries/dbo/q_histopathology.sql new file mode 100644 index 0000000..3ebbb65 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_histopathology.sql @@ -0,0 +1,26 @@ +/* + * Copyright (c) 2023-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID as objectid, + anm.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS eventDate, + (CAST(COALESCE (adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP)) AS modified, + (CASE + WHEN (anmEvt.STAFF_ID.STAFF_FIRST_NAME IS NULL OR anmEvt.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (anmEvt.STAFF_ID.STAFF_FIRST_NAME + || '|' || anmEvt.STAFF_ID.STAFF_LAST_NAME) END) AS performedby, + anmCmt.TEXT AS remark, + anmEvt.DIAGNOSIS as diagnosis, + anmEvt.EVENT_ID.NAME AS category, + CASE WHEN anmEvt.ATTACHMENT_PATH IS NOT NULL THEN + ('C:\Program Files\Labkey\labkey\files\NBRI\EHR\@files\attachments' + || substring(anmEvt.ATTACHMENT_PATH, LENGTH('N:\'), LENGTH(anmEvt.ATTACHMENT_PATH))) + ELSE NULL END AS attachmentFile +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL anm ON anmEvt.ANIMAL_ID = anm.ANIMAL_ID + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id +WHERE anmEvt.EVENT_ID = 2236 -- 2236 Histopathology Report + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates diff --git a/nbri_ehr/resources/queries/dbo/q_historicalOther.sql b/nbri_ehr/resources/queries/dbo/q_historicalOther.sql new file mode 100644 index 0000000..950296c --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_historicalOther.sql @@ -0,0 +1,19 @@ +/* + * Copyright (c) 2023-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID AS objectId, +anm.ANIMAL_ID_NUMBER AS Id, +(CASE + WHEN (anmEvt.STAFF_ID.STAFF_FIRST_NAME IS NULL OR anmEvt.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (anmEvt.STAFF_ID.STAFF_FIRST_NAME + || '|' || anmEvt.STAFF_ID.STAFF_LAST_NAME) END) AS performedby, +CAST(anmEvt.CREATED_DATETIME AS TIMESTAMP) AS modified, +CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS eventDate, +aCom.TEXT AS remarks, +anmEvt.EVENT_ID.NAME AS type +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL_EVENT_COMMENT aCom ON aCom.ANIMAL_EVENT_ID = anmEvt.ANIMAL_EVENT_ID + LEFT JOIN ANIMAL anm ON anmEvt.ANIMAL_ID = anm.ANIMAL_ID +WHERE anmEvt.EVENT_ID IN (1, 3, 159, 160, 883, 1432, 1619, 1731, 1852, 2175, 2221, 2332, 2356) \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_housing.sql b/nbri_ehr/resources/queries/dbo/q_housing.sql new file mode 100644 index 0000000..64d830d --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_housing.sql @@ -0,0 +1,24 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +SELECT anmEvt.ANIMAL_EVENT_ID AS objectId, + anm.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS transferDate, + anmCmt.TEXT AS remark, + cg.location AS cage, + (CASE + WHEN (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) IS NULL OR trim(anmEvt.STAFF_ID.STAFF_LAST_NAME) IS NULL) THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + CAST(COALESCE(adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified +FROM ANIMAL_EVENT anmEvt +LEFT JOIN ANIMAL anm ON anmEvt.ANIMAL_ID = anm.ANIMAL_ID +LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID +LEFT JOIN q_cages cg ON cg.location = anmEvt.LOCATION_ID +LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id +WHERE anmEvt.EVENT_ID = 2 --Housing Transfer +AND anmCmt.TEXT LIKE '%Loc%' +ORDER BY anm.ANIMAL_ID_NUMBER,anmEvt.ANIMAL_EVENT_ID DESC \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_housing_delete.sql b/nbri_ehr/resources/queries/dbo/q_housing_delete.sql new file mode 100644 index 0000000..7b9b9c2 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_housing_delete.sql @@ -0,0 +1,12 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_EVENT_ID = ')) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + (adt.REFERENCE LIKE '%Location Transfer%') AND + adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_idHistory.sql b/nbri_ehr/resources/queries/dbo/q_idHistory.sql new file mode 100644 index 0000000..383fcb8 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_idHistory.sql @@ -0,0 +1,12 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + ANIMAL_ID.ANIMAL_ID_NUMBER AS Id, + ALTERNATE_TYPE_ID AS Type, + NAME +FROM ALTERNATE +WHERE ALTERNATE_TYPE_ID IN (1, 2, 4, 5) +GROUP BY ANIMAL_ID.ANIMAL_ID_NUMBER, NAME, ALTERNATE_TYPE_ID \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_latestArrival.sql b/nbri_ehr/resources/queries/dbo/q_latestArrival.sql new file mode 100644 index 0000000..2f74032 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_latestArrival.sql @@ -0,0 +1,11 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +-- Used in finalDeparture +SELECT Id, +MAX(eventDate) as latestArr, +FROM q_arrival +GROUP BY Id \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_latestDeparture.sql b/nbri_ehr/resources/queries/dbo/q_latestDeparture.sql new file mode 100644 index 0000000..b4bb160 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_latestDeparture.sql @@ -0,0 +1,11 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +-- Used in finalDeparture +SELECT Id, +MAX(eventDate) as latestDep, +FROM q_departure +GROUP BY Id \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_lookups.sql b/nbri_ehr/resources/queries/dbo/q_lookups.sql new file mode 100644 index 0000000..27753fe --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_lookups.sql @@ -0,0 +1,75 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT 'DISP_CD_' || ID AS objectid, +'disposition_codes' AS set_name, +ID AS "value", +DESCRIPTION AS description, +NAME AS title, +ID AS sort_order, +CASE ACTIVE_YN +WHEN 'Y' THEN NULL +WHEN 'N' THEN '1/1/1970' +END AS date_disabled, +NULL AS category +FROM ANIMAL_DISPOSITION + +UNION + +SELECT 'TERMINATION_RSN_CD_' || ID AS objectid, +'termination_reason_codes' AS set_name, +ID AS "value", +DESCRIPTION AS description, +NAME AS title, +ID AS sort_order, +CASE ACTIVE_YN +WHEN 'Y' THEN NULL +WHEN 'N' THEN '1/1/1970' +END AS date_disabled, +NULL AS category +FROM TERMINATION_REASON + +UNION + +SELECT 'KEYWORD_' || KEY_WORD_ID AS objectid, +'keyword' AS set_name, +KEY_WORD_ID AS "value", +NULL AS description, +KEY_WORD_NAME AS title, +KEY_WORD_ID AS sort_order, +NULL AS date_disabled, +NULL AS category +FROM KEY_WORD + +UNION + +SELECT +'CLINREMARKS_CATEGORY' || EVENT_ID.EVENT_ID as objectid, +'clinremarks_category' AS set_name, +EVENT_ID.EVENT_ID AS "value", +EVENT_ID.DESCRIPTION AS description, +EVENT_ID.NAME AS title, +EVENT_ID.EVENT_ID AS sort_order, +CASE + WHEN EVENT_ID.ACTIVE_YN = 'Y' AND EVENT_GROUP_ID.ACTIVE_YN = 'Y' THEN NULL + ELSE '1/1/1970' + END AS date_disabled, +NULL AS category, +FROM EVENT_EVENT_GROUP +WHERE EVENT_GROUP_ID.EVENT_GROUP_ID = 53 + +UNION + +SELECT + 'COST_CENTER' || COST_CENTER_ID as objectid, + 'cost_center' as set_name, + COST_CENTER_ID as "value", + COST_CENTER_DESC as description, + COST_CENTER_NAME as title, + COST_CENTER_ID as sort_order, + NULL AS date_disabled, + NULL AS category +FROM COST_CENTER + diff --git a/nbri_ehr/resources/queries/dbo/q_lot_number.sql b/nbri_ehr/resources/queries/dbo/q_lot_number.sql new file mode 100644 index 0000000..21595ac --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_lot_number.sql @@ -0,0 +1,11 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + LOT_NUMBER_ID as LotId, + ANIMAL_SHIPMENT_ID as AnimalShipment, + LOT_NUMBER_DATE as LotDate, + LOT_NUMBER_SEQUENCE as LotSequence +FROM LOT_NUMBER \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_modified_event.sql b/nbri_ehr/resources/queries/dbo/q_modified_event.sql new file mode 100644 index 0000000..d17f040 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_modified_event.sql @@ -0,0 +1,15 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + adt.modified, + substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_EVENT_ID = ')) as event_id FROM + (SELECT + MAX(AUDIT_TRAIL.CHANGE_DATETIME) as modified, + AUDIT_TRAIL.PRIMARY_KEY_VALUES + FROM AUDIT_TRAIL + WHERE AUDIT_TRAIL.PRIMARY_KEY_VALUES like '%ANIMAL_EVENT_ID =%' AND AUDIT_TRAIL.COLUMN_NAME != 'DELETE' + GROUP BY AUDIT_TRAIL.PRIMARY_KEY_VALUES + ) adt \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_necropsy.sql b/nbri_ehr/resources/queries/dbo/q_necropsy.sql new file mode 100644 index 0000000..6d855ba --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_necropsy.sql @@ -0,0 +1,26 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID as objectid, + anm.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS necropsyDate, + (CAST(COALESCE (adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP)) AS modified, + (CASE + WHEN (anmEvt.STAFF_ID.STAFF_FIRST_NAME IS NULL OR anmEvt.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + anmCmt.TEXT AS remark, + anmEvt.DIAGNOSIS as diagnosis, + anmEvt.EVENT_ID.NAME AS category, + CASE WHEN anmEvt.ATTACHMENT_PATH IS NOT NULL THEN + ('C:\Program Files\Labkey\labkey\files\NBRI\EHR\@files\attachments' + || substring(anmEvt.ATTACHMENT_PATH, LENGTH('N:\'), LENGTH(anmEvt.ATTACHMENT_PATH))) + ELSE NULL END AS attachmentFile +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL anm ON anmEvt.ANIMAL_ID = anm.ANIMAL_ID + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id +WHERE anmEvt.EVENT_ID = 1575 -- 1575 Necropsy + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates diff --git a/nbri_ehr/resources/queries/dbo/q_necropsy_delete.sql b/nbri_ehr/resources/queries/dbo/q_necropsy_delete.sql new file mode 100644 index 0000000..139e925 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_necropsy_delete.sql @@ -0,0 +1,15 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_EVENT_ID = ')) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + (adt.REFERENCE LIKE '%histopathology%' OR + adt.REFERENCE LIKE '%Animal Death/Necropsy%' OR + adt.REFERENCE LIKE '%Euthanized%' OR + adt.REFERENCE LIKE '%Toxological Cause of Death%' ) AND + adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_notes.sql b/nbri_ehr/resources/queries/dbo/q_notes.sql new file mode 100644 index 0000000..d2edc40 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_notes.sql @@ -0,0 +1,29 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID AS objectid, + anmEvt.ANIMAL_ID.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS noteDate, + (CASE + WHEN (anmEvt.STAFF_ID.STAFF_FIRST_NAME IS NULL OR anmEvt.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + anmEvt.EVENT_ID.NAME AS type, + CASE WHEN anmEvt.ATTACHMENT_PATH IS NOT NULL THEN + ('C:\Program Files\Labkey\labkey\files\NBRI\EHR\@files\attachments' + || substring(anmEvt.ATTACHMENT_PATH, LENGTH('N:\'), LENGTH(anmEvt.ATTACHMENT_PATH))) + ELSE NULL END AS attachmentFile, + anmCmt.TEXT AS remark, + CAST(COALESCE(adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN EVENT_EVENT_GROUP evtEvtGrp ON evtEvtGrp.EVENT_ID = anmEvt.EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id + +WHERE evtEvtGrp.EVENT_GROUP_ID = 19 + AND anmEvt.EVENT_ID.NAME NOT LIKE 'Lab Transfer Fr%' + AND anmEvt.EVENT_ID.NAME NOT LIKE 'Lab Transfer To%' + AND anmEvt.EVENT_ID NOT IN (SELECT EVENT_ID FROM EVENT_EVENT_GROUP WHERE EVENT_GROUP_ID = 14) -- Already in serology + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates diff --git a/nbri_ehr/resources/queries/dbo/q_notes_delete.sql b/nbri_ehr/resources/queries/dbo/q_notes_delete.sql new file mode 100644 index 0000000..ea2540c --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_notes_delete.sql @@ -0,0 +1,18 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, 18) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + adt.COLUMN_NAME = 'DELETE' AND + ( + adt.REFERENCE LIKE '%CRL Shipment%' OR + adt.REFERENCE LIKE '%Chimp Physical Exam%' OR + adt.REFERENCE LIKE '%Pregnancy Examination%' OR + adt.REFERENCE LIKE '%SALAR WP Shipment Staging%' OR + adt.REFERENCE LIKE '%Vendor Record Attached%' OR + adt.REFERENCE LIKE '%Medroxyprogesterone acetate tab%' + ) \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_observations.sql b/nbri_ehr/resources/queries/dbo/q_observations.sql new file mode 100644 index 0000000..3a4db23 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_observations.sql @@ -0,0 +1,30 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID AS objectid, + anmEvt.ANIMAL_ID.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS obsDate, + (CASE + WHEN (anmEvt.STAFF_ID.STAFF_FIRST_NAME IS NULL OR anmEvt.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + anmEvt.EVENT_ID.NAME AS category, + (CASE + WHEN evtEvtGrp.EVENT_GROUP_ID = 30 THEN 'Clinical' + WHEN evtEvtGrp.EVENT_GROUP_ID = 40 THEN 'Behavior' + ELSE 'Unknown' END) AS type, + (CASE + WHEN anmEvt.DIAGNOSIS IS NOT NULL THEN (anmCmt.TEXT || ';' || anmEvt.DIAGNOSIS) + ELSE anmCmt.TEXT END) AS remark, + CAST(COALESCE(adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN EVENT_EVENT_GROUP evtEvtGrp ON evtEvtGrp.EVENT_ID = anmEvt.EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id + +WHERE evtEvtGrp.EVENT_GROUP_ID IN (30, 40) + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates +-- 30 Observations +-- 40 Clinical Behavioral Assessment diff --git a/nbri_ehr/resources/queries/dbo/q_observations_delete.sql b/nbri_ehr/resources/queries/dbo/q_observations_delete.sql new file mode 100644 index 0000000..8821fe2 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_observations_delete.sql @@ -0,0 +1,24 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_EVENT_ID = ')) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + (adt.REFERENCE LIKE '%Normal observations%' OR + adt.REFERENCE LIKE '%Trauma%' OR + adt.REFERENCE LIKE '%Reduced appetite%' OR + adt.REFERENCE LIKE '%Abnormal stool consistency%' OR + adt.REFERENCE LIKE '%Dehydration%' OR + adt.REFERENCE LIKE '%Decreased activity%' OR + adt.REFERENCE LIKE '%Abnormal body condition%' OR + adt.REFERENCE LIKE '%Abnormal attitude%' OR + adt.REFERENCE LIKE '%No appetite%' OR + adt.REFERENCE LIKE '%No Stool%' OR + adt.REFERENCE LIKE '%Cage Appendage Entrapment%' OR + adt.REFERENCE LIKE '%Alopecia Event%' OR + adt.REFERENCE LIKE '%Behav Assess%') AND + adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_pairings.sql b/nbri_ehr/resources/queries/dbo/q_pairings.sql new file mode 100644 index 0000000..1f3c22d --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_pairings.sql @@ -0,0 +1,23 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +SELECT anmEvt.ANIMAL_EVENT_ID as objectid, + anm.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS pairingDate, + CAST(COALESCE (adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified, + (CASE + WHEN (anmEvt.STAFF_ID.STAFF_FIRST_NAME IS NULL OR anmEvt.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + anmCmt.TEXT AS remark, + anmEvt.EVENT_ID.NAME AS type +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL anm ON anmEvt.ANIMAL_ID = anm.ANIMAL_ID + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN EVENT_EVENT_GROUP evtEvtGrp ON evtEvtGrp.EVENT_ID = anmEvt.EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id +WHERE evtEvtGrp.EVENT_GROUP_ID IN (42, 43, 62) -- Behavioral Assessment, Group/Pair Formation, Pair Housing Type + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_pairings_delete.sql b/nbri_ehr/resources/queries/dbo/q_pairings_delete.sql new file mode 100644 index 0000000..2d2a969 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_pairings_delete.sql @@ -0,0 +1,29 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_EVENT_ID = ')) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + (adt.REFERENCE LIKE '%Pair Formation%' OR + adt.REFERENCE LIKE '%Group Formation%' OR + adt.REFERENCE LIKE '%Pair/Group-Compatible w/ Cagemates%' OR + adt.REFERENCE LIKE '%Pair/Group-Incompatible w/ Cagemates%' OR + adt.REFERENCE LIKE '%Pair/Group-Compatibility Undetermined%' OR + adt.REFERENCE LIKE '%Pair/Group-Dominant%' OR + adt.REFERENCE LIKE '%Pair/Group-Subordinate%' OR + adt.REFERENCE LIKE '%Pathological behavior%' OR + adt.REFERENCE LIKE '%intermittent pathological behavior%' OR + adt.REFERENCE LIKE '%Full Contact Pair%' OR + adt.REFERENCE LIKE '%Limited Contact Pair%' OR + adt.REFERENCE LIKE '%Pair Separation-Clinical%' OR + adt.REFERENCE LIKE '%Pair Separation-Behavioral%' OR + adt.REFERENCE LIKE '%Pair Separation-Other%' OR + adt.REFERENCE LIKE '%Compatible w/ adjacent groups%' OR + adt.REFERENCE LIKE '%Relocation only%' OR + adt.REFERENCE LIKE '%Reintroduction%' OR + adt.REFERENCE LIKE '%Introduction%' ) AND + adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_physicalExam.sql b/nbri_ehr/resources/queries/dbo/q_physicalExam.sql new file mode 100644 index 0000000..e89f139 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_physicalExam.sql @@ -0,0 +1,42 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID as objectid, + anm.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS physicalExamDate, + CAST(COALESCE (adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified, + (CASE + WHEN (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) IS NULL OR trim(anmEvt.STAFF_ID.STAFF_LAST_NAME) IS NULL) THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + (CASE WHEN (anmEvt.DIAGNOSIS IS NOT NULL AND anmCmt.TEXT IS NOT NULL) THEN (anmEvt.DIAGNOSIS || ', ' || anmCmt.TEXT) WHEN (anmEvt.DIAGNOSIS IS NOT NULL AND anmCmt.TEXT IS NULL) THEN (anmEvt.DIAGNOSIS) ELSE (anmCmt.TEXT) END) AS remark, + anmEvt.EVENT_ID.NAME AS exam, + anmEvt.RESULT, + ev.NUMERIC_UNIT_ID AS Units, + CASE WHEN anmEvt.ATTACHMENT_PATH IS NOT NULL THEN + ('C:\Program Files\Labkey\labkey\files\NBRI\EHR\@files\attachments' + || substring(anmEvt.ATTACHMENT_PATH, LENGTH('N:\'), LENGTH(anmEvt.ATTACHMENT_PATH))) + ELSE NULL END AS attachmentFile +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL anm ON anmEvt.ANIMAL_ID = anm.ANIMAL_ID + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN EVENT_EVENT_GROUP evtEvtGrp ON evtEvtGrp.EVENT_ID = anmEvt.EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id + LEFT JOIN EVENT ev on anmEvt.EVENT_ID = ev.EVENT_ID +WHERE evtEvtGrp.EVENT_GROUP_ID = 60 -- Physical Exam + -- filter out vital signs events + AND evtEvtGrp.EVENT_ID NOT IN (1349, 2165, 2166, 2167, 2168, 2169, 55, 56, 1643, 1647, 1652, 1653) + -- 1349 Body Weight + -- 2165 Blood Pressure-NHP + -- 2166 Heart Rate-NHP + -- 2167 Respiration Rate-NHP + -- 2168 Temperature-NHP + -- 2169 Pulse Rate-NHP + -- 55 Blood Pressure + -- 1652 Heart Rate + -- 56, 1647 Respiration Rate + -- 1643 Temperature + -- 1653 Pulse + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_physicalExam_delete.sql b/nbri_ehr/resources/queries/dbo/q_physicalExam_delete.sql new file mode 100644 index 0000000..c624ad1 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_physicalExam_delete.sql @@ -0,0 +1,33 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_EVENT_ID = ')) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + (adt.REFERENCE LIKE '%General Condition%' OR + adt.REFERENCE LIKE '%Assessment%' OR + adt.REFERENCE LIKE '%Specific System Exam%' OR + adt.REFERENCE LIKE '%EKG%' OR + adt.REFERENCE LIKE '%AGM Panel%' OR + adt.REFERENCE LIKE '%Macaque Panel%' OR + adt.REFERENCE LIKE '%General Health Panel%' OR + adt.REFERENCE LIKE '%TB Test Positive%' OR + adt.REFERENCE LIKE '%TB Test Negative%' OR + adt.REFERENCE LIKE '%TB Test Administered%' OR + adt.REFERENCE LIKE '%Ophthalmic Exam-Indirect%' OR + adt.REFERENCE LIKE '%Ophthalmic Exam-Direct%' OR + adt.REFERENCE LIKE '%Physical Exam%' OR + adt.REFERENCE LIKE '%Specific System Examination%' OR + adt.REFERENCE LIKE '%Pregnancy Examination by Ultrasound%' OR + adt.REFERENCE LIKE '%Deworm%' OR + adt.REFERENCE LIKE '%Max Planck Inst for Evol Anthroplogy%' OR + adt.REFERENCE LIKE '%Safety Assessment Staging%' OR + adt.REFERENCE LIKE '%Pre-shipment requirements%' OR + adt.REFERENCE LIKE '%Body Condition Score%' OR + adt.REFERENCE LIKE '%Pregnancy Examination%' OR + adt.REFERENCE LIKE '%Testicular Volume%' ) AND + adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_prc.sql b/nbri_ehr/resources/queries/dbo/q_prc.sql new file mode 100644 index 0000000..c4f0949 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_prc.sql @@ -0,0 +1,54 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID as objectid, + anm.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS prcDate, + CAST(COALESCE (adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified, + (CASE WHEN (anmEvt.DIAGNOSIS IS NOT NULL AND anmCmt.TEXT IS NOT NULL) THEN (anmEvt.DIAGNOSIS || ', ' || anmCmt.TEXT) WHEN (anmEvt.DIAGNOSIS IS NOT NULL AND anmCmt.TEXT IS NULL) THEN (anmEvt.DIAGNOSIS) ELSE (anmCmt.TEXT) END) AS remark, + (CASE + WHEN (anmEvt.STAFF_ID.STAFF_FIRST_NAME IS NULL OR anmEvt.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (anmEvt.STAFF_ID.STAFF_FIRST_NAME + || '|' || anmEvt.STAFF_ID.STAFF_LAST_NAME) END) AS performedby, + anmEvt.EVENT_ID.NAME AS type +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL anm ON anmEvt.ANIMAL_ID = anm.ANIMAL_ID + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN EVENT_EVENT_GROUP evtEvtGrp ON evtEvtGrp.EVENT_ID = anmEvt.EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id +WHERE evtEvtGrp.EVENT_GROUP_ID IN (6,10,27,50,52) + -- 6 Diagnostic Imaging + -- 10 Wound Care + -- 27 Dentistry Procedures + -- 28 Surgical Procedures Major + -- 29 Surgical Procedures Minor + -- 35 Diagnostic Tissue Collection + -- 50 Medical Treatment + -- 52 Protocol Associated Events + +OR -- Procedures from Diagnostic sample collection event group +(evtEvtGrp.EVENT_GROUP_ID = 36 AND (evtEvtGrp.EVENT_ID != 1581 AND evtEvtGrp.EVENT_ID != 1864)) + +OR -- Procedures from Timed sample collection event group minus blood draws and biopsies + (evtEvtGrp.EVENT_GROUP_ID = 32 AND (evtEvtGrp.EVENT_ID != 1581 AND evtEvtGrp.EVENT_ID != 1864 AND evtEvtGrp.EVENT_ID != 1641 AND evtEvtGrp.EVENT_ID != 1642)) + +OR -- Procedures from Diagnostic Procedures minus Biopsies + (evtEvtGrp.EVENT_GROUP_ID = 21 AND evtEvtGrp.EVENT_ID.Name NOT LIKE '%Biops%') + +OR -- Diagnostic Tissue Collection minus Biopsies + (evtEvtGrp.EVENT_GROUP_ID = 35 AND evtEvtGrp.EVENT_ID != 1603) + +OR -- Surgical Procedures minus Biopsies + (evtEvtGrp.EVENT_GROUP_ID = 29 AND (evtEvtGrp.EVENT_ID != 1641 AND evtEvtGrp.EVENT_ID != 1642)) + +OR -- Surgical Procedures minus Biopsies + (evtEvtGrp.EVENT_GROUP_ID = 28 AND evtEvtGrp.EVENT_ID != 1669) + +OR -- Procedures from Quarantine Period + (evtEvtGrp.EVENT_GROUP_ID = 26 AND evtEvtGrp.EVENT_ID = 1806) + +AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates +GROUP BY anmEvt.ANIMAL_EVENT_ID, anm.ANIMAL_ID_NUMBER, anmEvt.EVENT_DATETIME, adt.modified, anmEvt.CREATED_DATETIME, + anmEvt.DIAGNOSIS, anmCmt.TEXT, anmEvt.EVENT_ID.NAME, anmEvt.STAFF_ID.STAFF_FIRST_NAME, anmEvt.STAFF_ID.STAFF_LAST_NAME \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_prc_delete.sql b/nbri_ehr/resources/queries/dbo/q_prc_delete.sql new file mode 100644 index 0000000..3c7885a --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_prc_delete.sql @@ -0,0 +1,78 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_EVENT_ID = ')) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + adt.REFERENCE NOT LIKE '%Blood Sample Collection%' AND + ( + adt.REFERENCE LIKE '%Procedure%' OR + adt.REFERENCE LIKE '%Radiology%' OR + adt.REFERENCE LIKE '%Ultrasonography%' OR + adt.REFERENCE LIKE '%Endoscopy%' OR + adt.REFERENCE LIKE '%Laparoscopy%' OR + adt.REFERENCE LIKE '%Colonoscopy%' OR + adt.REFERENCE LIKE '%Cleaning%' OR + adt.REFERENCE LIKE '%Bandage%' OR + adt.REFERENCE LIKE '%bandage%' OR + adt.REFERENCE LIKE '%Debridement%' OR + adt.REFERENCE LIKE '%Cast%' OR + adt.REFERENCE LIKE '%Clip and clean%' OR + adt.REFERENCE LIKE '%Flush wound%' OR + adt.REFERENCE LIKE '%Furazolidone%' OR + adt.REFERENCE LIKE '%Hydrotherapy%' OR + adt.REFERENCE LIKE '%Preparation H application%' OR + adt.REFERENCE LIKE '%Purse string suture%' OR + adt.REFERENCE LIKE '%Rectal prolapse replacement%' OR + adt.REFERENCE LIKE '%Splint%' OR + adt.REFERENCE LIKE '%Suture%' OR + adt.REFERENCE LIKE '%TAO application%' OR + adt.REFERENCE LIKE '%Trypzyme application%' OR + adt.REFERENCE LIKE '%Hepatic Biopsy-Tru Cut%' OR + adt.REFERENCE LIKE '%Biopsy%' OR + adt.REFERENCE LIKE '%Bone Marrow Aspirates%' OR + adt.REFERENCE LIKE '%Splenectomy%' OR + adt.REFERENCE LIKE '%Thoracocentesis%' OR + adt.REFERENCE LIKE '%Abdominocentesis%' OR + adt.REFERENCE LIKE '%Catheter/Canula Placement%' OR + adt.REFERENCE LIKE '%Aspirate-Specify%' OR + adt.REFERENCE LIKE '%Ultrasound%' OR + adt.REFERENCE LIKE '%Embryo Transfer%' OR + adt.REFERENCE LIKE '%Oocyte Collection%' OR + adt.REFERENCE LIKE '%Electroejaculation%' OR + adt.REFERENCE LIKE '%Cesarian section%' OR + adt.REFERENCE LIKE '%Vasectomy%' OR + adt.REFERENCE LIKE '%Pulpectomy%' OR + adt.REFERENCE LIKE '%Pulpotomy%' OR + adt.REFERENCE LIKE '%Stool Analysis by Baermann Technique%' OR + adt.REFERENCE LIKE '%Pinworm test (Cellophane tape method)%' OR + adt.REFERENCE LIKE '%Root Canal%' OR + adt.REFERENCE LIKE '%Canine Blunting%' OR + adt.REFERENCE LIKE '%Prophylactic Cleaning%' OR + adt.REFERENCE LIKE '%Extraction%' OR + adt.REFERENCE LIKE '%Oophorectomy%' OR + adt.REFERENCE LIKE '%Transponder Implantation%' OR + adt.REFERENCE LIKE '%Tissue Culture%' OR + adt.REFERENCE LIKE '%Histopathology Tissue Collection%' OR + adt.REFERENCE LIKE '%IUD insertion%' OR + adt.REFERENCE LIKE '%Chair Training%' OR + adt.REFERENCE LIKE '%Vascular access port placement%' OR + adt.REFERENCE LIKE '%Vascular access port removal%' OR + adt.REFERENCE LIKE '%Disqualified from chair study%' OR + adt.REFERENCE LIKE '%Urine Collection (Cystocentesis)%' OR + adt.REFERENCE LIKE '%Sample Collection%' OR + adt.REFERENCE LIKE '%Specimen Collection%' OR + adt.REFERENCE LIKE '%Biopsy Collection%' OR + adt.REFERENCE LIKE '%Bronchial Lavage Sample Collection%' OR + adt.REFERENCE LIKE '%Stool (Pan) Collection%' OR + adt.REFERENCE LIKE '%Stool (Rectal Swab) Collection%' OR + adt.REFERENCE LIKE '%CSF tap%' OR + adt.REFERENCE LIKE '%Cervicovaginal Sample%' OR + adt.REFERENCE LIKE '%Nasal swab%' OR + adt.REFERENCE LIKE '%Quarantine - arrival%' OR + adt.REFERENCE LIKE '%Quarantine - release%' ) AND + adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_pregnancy.sql b/nbri_ehr/resources/queries/dbo/q_pregnancy.sql new file mode 100644 index 0000000..64b6791 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_pregnancy.sql @@ -0,0 +1,29 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID AS objectid, + anmEvt.ANIMAL_ID.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS administrationDate, + (CASE + WHEN (anmEvt.STAFF_ID.STAFF_FIRST_NAME IS NULL OR anmEvt.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (anmEvt.STAFF_ID.STAFF_FIRST_NAME + || '|' || anmEvt.STAFF_ID.STAFF_LAST_NAME) END) AS performedby, + anmEvt.EVENT_ID.NAME AS type, + anmEvt.TEXT_RESULT AS result, + anmEvt.DIAGNOSIS AS diagnosis, + CASE WHEN anmEvt.ATTACHMENT_PATH IS NOT NULL THEN + ('C:\Program Files\Labkey\labkey\files\NBRI\EHR\@files\attachments' + || substring(anmEvt.ATTACHMENT_PATH, LENGTH('N:\'), LENGTH(anmEvt.ATTACHMENT_PATH))) + ELSE NULL END AS attachmentFile, + anmCmt.TEXT AS remark, + CAST(COALESCE(adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id + +WHERE anmEvt.EVENT_ID.EVENT_ID IN (2170, 2171) + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates +-- 2170 Abort +-- 2171 Stillborn \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_pregnancy_delete.sql b/nbri_ehr/resources/queries/dbo/q_pregnancy_delete.sql new file mode 100644 index 0000000..7ed07e4 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_pregnancy_delete.sql @@ -0,0 +1,13 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_EVENT_ID = ')) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + (adt.REFERENCE LIKE '%Stillborn Event%' OR + adt.REFERENCE LIKE '%Abort Event%') AND + adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_procedures.sql b/nbri_ehr/resources/queries/dbo/q_procedures.sql new file mode 100644 index 0000000..b9473c1 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_procedures.sql @@ -0,0 +1,11 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + PROCEDURE_ID as procedureId, + ACTIVE_YN as active, + PROCEDURE_NAME as name, + PROCEDURE_DESC as description +FROM "PROCEDURE" \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_project.sql b/nbri_ehr/resources/queries/dbo/q_project.sql new file mode 100644 index 0000000..602ea73 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_project.sql @@ -0,0 +1,20 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +SELECT min(alt.ALTERNATE_ID) as project, + alt.project as name +FROM +( + SELECT + CASE WHEN (SUBSTRING(trim(NAME),3,1) = '-' OR SUBSTRING(trim(NAME),5,1) = '-') + THEN trim(SUBSTRING(trim(NAME),0,11)) + ELSE trim(SUBSTRING(trim(NAME), 0, 8)) + END as project, + ALTERNATE_ID + FROM ALTERNATE + WHERE ALTERNATE_TYPE_ID = 6 +) alt +GROUP BY alt.project \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_protocol.sql b/nbri_ehr/resources/queries/dbo/q_protocol.sql new file mode 100644 index 0000000..ed13fde --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_protocol.sql @@ -0,0 +1,61 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + p.PROTOCOL_ID AS objectid, + p.PROTOCOL_NUMBER AS title, + trim(p.PI_ID.STAFF_FIRST_NAME) + || '|' || trim(p.PI_ID.STAFF_LAST_NAME) as investigatorId, + trim(p.AUTHOR_ID.STAFF_FIRST_NAME) + || '|' || trim(p.AUTHOR_ID.STAFF_LAST_NAME) as authorId, + trim(p.OWNER_ID.STAFF_FIRST_NAME) + || '|' || trim(p.OWNER_ID.STAFF_LAST_NAME) as ownerId, + p.PROTOCOL_NUMBER AS external_id, + p.PROTOCOL_ID AS protocol, + p.DEPARTMENT_ID AS departmentId, + p.PROTOCOL_ID_PREFIX AS prefix, + p.PROTOCOL_ID_SUFFIX AS suffix, + p.PROTOCOL_SHORT_TITLE AS shortDescription, + p.APPROVAL_DATE AS approve, + p.EXPIRATION_DATE AS endDate, + p.RENEWAL_DATE AS renewalDate, + p.EMERGENCY_PHONE_NUM AS emergencyPhoneNumber, + p.INACTIVE_DATE AS inactiveDate, + p.NEXT_REVIEW_DATE AS nextReviewDate, + p.EFFECTIVE_DATE AS effectiveDate, + p.CURRENT_STATE AS currentState, + p.USER_REFERENCE_NUMBER AS userReferenceNumber, + p.UNRESTRICTED_VIEW_YN AS isUnrestrictedView, + p.AUDIT_YN AS isAudit, + p.AUDIT_YN_MODIFIED_YN AS isAuditModified, + p.PROTOCOL_TYPE_ID AS protocolTypeId, + p.PARENT_PROTOCOL_ID AS parentProtocolId, + p.QUESTIONNAIRE_ID AS questionnaireId, + p.AMENDMENT_REASON AS amendmentReason, + p.REQUESTED_EFFECTIVE_DATE AS requestedEffectiveDate, + p.PROTOCOL_CATEGORY_ID AS protocolCategoryId, + p.OBJECTIVE AS objective, + p.RATIONALE AS rationale, + p.TISSUE_HARVEST_YN AS isTissueHarvest, + p.ORDER_TRACKING_YN AS isOrderTracking, + p.LONG_TERM_YN AS isLongTerm, + p.IN_VIVO_YN AS isInVivo, + p.STOCK_YN AS isStock, + p.SUBMISSION_DATE AS submissionDate, + p.REVIEW_COMPLETION_DATE AS reviewCompletionDate, + p.HONOR_RESET_YN AS isHonorReset, + area.area AS area, + pd.text AS description, + COALESCE(X.modified, to_date('01/01/1970' ,'MM/DD/YYYY')) AS modified +FROM PROTOCOL p + LEFT JOIN ( + SELECT substring(PRIMARY_KEY_VALUES, length('PROTOCOL_ID = ')) AS protocolId, + MAX(CAST(CHANGE_DATETIME AS TIMESTAMP)) AS modified + FROM AUDIT_TRAIL + WHERE TABLE_NAME = 'PROTOCOL' + GROUP BY substring(PRIMARY_KEY_VALUES, length('PROTOCOL_ID = ')) + ) X ON X.protocolId = p.PROTOCOL_ID + LEFT JOIN q_areas area ON area.area = p.LOCATION_ID + LEFT JOIN PROTOCOL_DESCRIPTION pd ON pd.PROTOCOL_ID = p.PROTOCOL_ID diff --git a/nbri_ehr/resources/queries/dbo/q_protocolAssignment.sql b/nbri_ehr/resources/queries/dbo/q_protocolAssignment.sql new file mode 100644 index 0000000..478a61c --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_protocolAssignment.sql @@ -0,0 +1,52 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT * FROM +( + SELECT + anmEvt.ANIMAL_EVENT_ID AS "objectId", + anmEvt.ANIMAL_EVENT_ID AS "animalEventId", + anm.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS transferDate, + COALESCE(dea.deathDate, dep.eventDate) AS enddate, + (CASE + WHEN (anmEvt.STAFF_ID.STAFF_FIRST_NAME IS NULL OR anmEvt.STAFF_ID.STAFF_LAST_NAME IS NULL) + THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + REPLACE(anmCmt.TEXT, ';', ':') AS remark, + anmEvt.LOCATION_ID AS location + FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL anm ON anmEvt.ANIMAL_ID = anm.ANIMAL_ID + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN q_deaths dea ON anm.ANIMAL_ID_NUMBER = dea.participantId + LEFT JOIN q_finalDeparture dep ON anm.ANIMAL_ID_NUMBER = dep.Id + WHERE anmEvt.EVENT_ID = 2 --Animal Transfer + AND anmCmt.TEXT LIKE '%Pro%' + + UNION + + SELECT + ae.ANIMAL_EVENT_ID as objectId, + ae.ANIMAL_EVENT_ID as animalEventId, + an.ANIMAL_ID_NUMBER as Id, + CAST(ae.EVENT_DATETIME AS TIMESTAMP) as transferDate, + COALESCE(dea.deathDate, dep.eventDate) AS enddate, + (CASE + WHEN (ae.STAFF_ID.STAFF_FIRST_NAME IS NULL OR ae.STAFF_ID.STAFF_LAST_NAME IS NULL) + THEN 'unknown' + ELSE (ae.STAFF_ID.STAFF_FIRST_NAME + || '|' || ae.STAFF_ID.STAFF_LAST_NAME) END) AS performedby, + 'From Protocol: None: To Protocol: ' || pr.PROTOCOL_NUMBER as remark, + ae.LOCATION_ID as location + FROM ANIMAL an + JOIN CAGE_CARD cc ON an.CAGE_CARD_ID = cc.CAGE_CARD_ID + JOIN SEGMENT se ON cc.SEGMENT_ID = se.SEGMENT_ID + JOIN PROTOCOL pr ON se.PROTOCOL_ID = pr.PROTOCOL_ID + LEFT JOIN ANIMAL_EVENT ae ON ae.ANIMAL_ID = an.ANIMAL_ID AND EVENT_ID = 1 -- Received + LEFT JOIN q_deaths dea ON an.ANIMAL_ID_NUMBER = dea.participantId + LEFT JOIN q_finalDeparture dep ON an.ANIMAL_ID_NUMBER = dep.Id +) a +ORDER BY a.Id,a.transferDate DESC \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_protocol_amendments.sql b/nbri_ehr/resources/queries/dbo/q_protocol_amendments.sql new file mode 100644 index 0000000..c8dbaa9 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_protocol_amendments.sql @@ -0,0 +1,21 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT PROTOCOL_ID AS "protocolId", + CASE WHEN PROTOCOL_NUMBER IS NULL THEN 'missing' + ELSE PROTOCOL_NUMBER END AS "protocol", + RENEWAL_DATE AS "amendmentDate", + SUBMISSION_DATE AS "submitted", + APPROVAL_DATE AS "approved", + X.modified +FROM PROTOCOL p + LEFT JOIN ( + SELECT substring(PRIMARY_KEY_VALUES, length('PROTOCOL_ID = ')) AS protocolId, + COALESCE(MAX(CAST(CHANGE_DATETIME AS TIMESTAMP)), to_date('01/01/1970' ,'MM/DD/YYYY')) AS modified + FROM AUDIT_TRAIL + WHERE TABLE_NAME = 'PROTOCOL' + GROUP BY substring(PRIMARY_KEY_VALUES, length('PROTOCOL_ID = ')) +) X ON X.protocolId = p.PROTOCOL_ID +WHERE PROTOCOL_TYPE_ID IN (2,3,4) \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_protocol_counts.sql b/nbri_ehr/resources/queries/dbo/q_protocol_counts.sql new file mode 100644 index 0000000..9cb8726 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_protocol_counts.sql @@ -0,0 +1,33 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT pc.Protocol, pc.Species, COALESCE(pc.allowed, 0) as allowed, ssb.SSB_ID as ssb, eu.EUTHANASIA_TYPE_ID as Euthanasia FROM ( +SELECT + sub.Protocol, + sub.Species, + SUM(sub.Amt) as allowed, + --LISTAGG(sub.Stress, ', ') as StressLevels +FROM +( + SELECT sub1.Protocol, sub1.Species, sub2.STRESS_NAME AS Stress, sub2.AUTHORIZED_AMT AS Amt FROM + (SELECT + PROTOCOL_ID.PROTOCOL_ID AS Protocol, + SPECIES_ID.SPECIES_ID AS Species + FROM SEGMENT + GROUP BY + PROTOCOL_ID.PROTOCOL_ID, + SPECIES_ID.SPECIES_ID + ) sub1 + LEFT JOIN + (SELECT s.SEGMENT_ID, s.SPECIES_ID.SPECIES_ID, s.PROTOCOL_ID.PROTOCOL_ID, ss.STRESS_ID.STRESS_NAME, ss.AUTHORIZED_AMT FROM SEGMENT s + LEFT JOIN SEGMENT_STRESS ss ON ss.SEGMENT_ID = s.SEGMENT_ID) sub2 + ON sub2.PROTOCOL_ID = sub1.Protocol AND sub2.SPECIES_ID = sub1.Species AND sub2.AUTHORIZED_AMT > 0 +) sub +GROUP BY + sub.Protocol, sub.Species +) pc +LEFT JOIN SEGMENT_SSB ssb ON pc.Species = ssb.SEGMENT_ID.SPECIES_ID.SPECIES_ID AND pc.Protocol = ssb.SEGMENT_ID.PROTOCOL_ID.PROTOCOL_ID +LEFT JOIN SEGMENT_EUTHANASIA eu ON pc.Species = eu.SEGMENT_ID.SPECIES_ID.SPECIES_ID AND pc.Protocol = eu.SEGMENT_ID.PROTOCOL_ID.PROTOCOL_ID +WHERE Protocol IS NOT NULL AND Species IS NOT NULL \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_protocol_esig.sql b/nbri_ehr/resources/queries/dbo/q_protocol_esig.sql new file mode 100644 index 0000000..5766a60 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_protocol_esig.sql @@ -0,0 +1,13 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + ID as EsigId, + PROTOCOL_ID as Protocol, + ESIGNATURE_EVENT_ID as EsigEvent, + USER_PROFILE_ID.STAFF_ID.STAFF_FIRST_NAME + || '|' || USER_PROFILE_ID.STAFF_ID.STAFF_LAST_NAME as UserProfile, + ESIG_DATETIME as EsigDateTime, +FROM PROTOCOL_ESIG \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_protocol_procedures.sql b/nbri_ehr/resources/queries/dbo/q_protocol_procedures.sql new file mode 100644 index 0000000..ff350a7 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_protocol_procedures.sql @@ -0,0 +1,10 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + SEGMENT_ID.PROTOCOL_ID.PROTOCOL_ID AS Protocol, + SEGMENT_ID.SPECIES_ID AS Species, + PROCEDURE_ID.PROCEDURE_NAME AS Procedure +FROM SEGMENT_PROCEDURE \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_protocol_stress.sql b/nbri_ehr/resources/queries/dbo/q_protocol_stress.sql new file mode 100644 index 0000000..4619cd2 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_protocol_stress.sql @@ -0,0 +1,12 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + SEGMENT_ID.PROTOCOL_ID.PROTOCOL_ID AS Protocol, + SEGMENT_ID.SPECIES_ID AS Species, + STRESS_ID.STRESS_ID AS Stress, + AUTHORIZED_AMT AS Allowed +FROM SEGMENT_STRESS +WHERE AUTHORIZED_AMT > 0 AND SEGMENT_ID.SPECIES_ID IS NOT NULL \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_protocol_usage.sql b/nbri_ehr/resources/queries/dbo/q_protocol_usage.sql new file mode 100644 index 0000000..19c7865 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_protocol_usage.sql @@ -0,0 +1,25 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + put.PROTOCOL_NUMBER as Protocol, + put.USER_REFERENCE_NUMBER as UserReferenceNumber, + put.SHORT_TITLE as ShortTitle, + put.PI_NAME as Investigator, + put.PROTOCOL_TYPE as ProtocolType, + put.CURRENT_STATE as CurrentState, + put.SUBMIT_DATE as SubmitDate, + put.APPROVAL_DATE as ApprovalDate, + put.EXPIRATION_DATE as ExpirationDate, + put.EFFECTIVE_DATE as EffectiveDate, + put.RENEWAL_DATE as RenewalDate, + put.AUTHORIZED_AMT as AuthorizedAmt, + put.ON_ORDER_AMT as OnOrderAmt, + put.USED_AMT as UsedAmt, + put.AVAILABLE_AMT as AvailableAmt, + put.PERCENT_LEFT as PercentLeft, + s.SPECIES_ID as Species, +FROM PROTOCOL_USAGE_TEMP put +LEFT JOIN SEGMENT s ON put.SEGMENT_ID = s.SEGMENT_ID \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_question.sql b/nbri_ehr/resources/queries/dbo/q_question.sql new file mode 100644 index 0000000..81de8d2 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_question.sql @@ -0,0 +1,11 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + QUESTION_ID AS QuestionId, + QUESTION_TYPE_ID.QUESTION_TYPE_NAME AS Type, + QUESTION_TEXT AS Text, + QUESTION_CREATION_DATE as CreationDate +FROM QUESTION \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_question_response.sql b/nbri_ehr/resources/queries/dbo/q_question_response.sql new file mode 100644 index 0000000..6115895 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_question_response.sql @@ -0,0 +1,14 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + qr.QUESTION_RESPONSE_ID AS QuestionResponseId, + qr.PROTOCOL_ID AS Protocol, + rt.TEXT AS Response, + qq.QUESTION_ID AS Question, + qq.QUESTIONNAIRE_ID AS Questionnaire +FROM QUESTION_RESPONSE qr +LEFT JOIN RESPONSE_TEXT rt ON qr.QUESTION_RESPONSE_ID = rt.QUESTION_RESPONSE_ID +LEFT JOIN QUESTIONNAIRE_QUESTION qq ON qr.QUESTION_INSTANCE_ID = qq.QUESTION_INSTANCE_ID \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_rooms.sql b/nbri_ehr/resources/queries/dbo/q_rooms.sql new file mode 100644 index 0000000..c2148ee --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_rooms.sql @@ -0,0 +1,16 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + room.LOCATION_ID AS room, + room.LOCATION_NAME AS name, + floor.LOCATION_ID AS floor, + building.LOCATION_ID AS building, + area.LOCATION_ID AS area +FROM LOCATION room +JOIN LOCATION floor ON room.PARENT_LOCATION_ID = floor.LOCATION_ID +JOIN LOCATION building ON floor.PARENT_LOCATION_ID = building.LOCATION_ID +JOIN LOCATION area ON building.PARENT_LOCATION_ID = area.LOCATION_ID +WHERE room.LOCATION_TYPE_ID = 4 -- Room \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_serology.sql b/nbri_ehr/resources/queries/dbo/q_serology.sql new file mode 100644 index 0000000..13bf404 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_serology.sql @@ -0,0 +1,22 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID as objectid, + anm.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS serologyDate, + CAST(COALESCE (adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified, + (CASE + WHEN (anmEvt.STAFF_ID.STAFF_FIRST_NAME IS NULL OR anmEvt.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (anmEvt.STAFF_ID.STAFF_FIRST_NAME + || '|' || anmEvt.STAFF_ID.STAFF_LAST_NAME) END) AS performedby, + anmCmt.TEXT AS lab, + anmEvt.EVENT_ID.NAME AS type +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL anm ON anmEvt.ANIMAL_ID = anm.ANIMAL_ID + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN EVENT_EVENT_GROUP evtEvtGrp ON evtEvtGrp.EVENT_ID = anmEvt.EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id +WHERE evtEvtGrp.EVENT_GROUP_ID IN (14, 47, 49) -- Serology, CMV, Hepatitis B Events + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_serology_delete.sql b/nbri_ehr/resources/queries/dbo/q_serology_delete.sql new file mode 100644 index 0000000..4ccc49a --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_serology_delete.sql @@ -0,0 +1,83 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_EVENT_ID = ')) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + (adt.REFERENCE LIKE '%SRV -%' OR + adt.REFERENCE LIKE '%CMV Draw%' OR + adt.REFERENCE LIKE '%Hep B Draw%' OR + adt.REFERENCE LIKE '%B Virus%' OR + adt.REFERENCE LIKE '%Measles Positive%' OR + adt.REFERENCE LIKE '%Measles Negative%' OR + adt.REFERENCE LIKE '%Measles Equivocal%' OR + (adt.REFERENCE LIKE '%SIV%' AND adt.REFERENCE NOT LIKE '%SIV Draw%') OR + (adt.REFERENCE LIKE '%SRV%' AND adt.REFERENCE NOT LIKE '%SRV Draw%') OR + (adt.REFERENCE LIKE '%STLV-1%' AND adt.REFERENCE NOT LIKE '%STLV-1 Draw%') OR + adt.REFERENCE LIKE '%SA8%' OR + adt.REFERENCE LIKE '%SA11%' OR + (adt.REFERENCE LIKE '%Filovirus%' AND adt.REFERENCE NOT LIKE '%Filovirus Draw%') OR + (adt.REFERENCE LIKE '%CMV%' AND adt.REFERENCE NOT LIKE '%CMV Draw%') OR + adt.REFERENCE LIKE '%Foamy Virus%' OR + adt.REFERENCE LIKE '%Rabies Positive%' OR + adt.REFERENCE LIKE '%Rabies Negative%' OR + adt.REFERENCE LIKE '%Rabies Equivocal%' OR + adt.REFERENCE LIKE '%HIV AB Negative%' OR + adt.REFERENCE LIKE '%HEP A%' OR + adt.REFERENCE LIKE '%RSV AB%' OR + adt.REFERENCE LIKE '%SV40%' OR + adt.REFERENCE LIKE '%HIV PCR Qualitative%' OR + adt.REFERENCE LIKE '%Rheumatoid Arthritis%' OR + adt.REFERENCE LIKE '%HIV-1/HIV-2 AB%' OR + adt.REFERENCE LIKE '%Para Influenza Virus%' OR + adt.REFERENCE LIKE '%Ebola Virus%' OR + adt.REFERENCE LIKE '%Marburg Virus%' OR + adt.REFERENCE LIKE '%Polio Titer%' OR + adt.REFERENCE LIKE '%HEP B%' OR + adt.REFERENCE LIKE '%HEP C%' OR + adt.REFERENCE LIKE '%Herpes Simplex Virus%' OR + adt.REFERENCE LIKE '%HCV Genotyping%' OR + adt.REFERENCE LIKE '%HEP E%' OR + adt.REFERENCE LIKE '%NBRI Lab%' OR + adt.REFERENCE LIKE '%Enterovirus%' OR + adt.REFERENCE LIKE '%EBV%' OR + adt.REFERENCE LIKE '%WNV%' OR + adt.REFERENCE LIKE '%EMC AB%' OR + adt.REFERENCE LIKE '%LCM AB%' OR + adt.REFERENCE LIKE '%HCV Viral Load%' OR + adt.REFERENCE LIKE '%HBV Viral Load%' OR + adt.REFERENCE LIKE '%HIV 1/0/2 Abs-Reactive%' OR + adt.REFERENCE LIKE '%HIV 1/0/2 Abs-NonReactive%' OR + adt.REFERENCE LIKE '%HIV AB%' OR + adt.REFERENCE LIKE '%Plasmodium%' OR + adt.REFERENCE LIKE '%Anti-Noro Virus%' OR + adt.REFERENCE LIKE '%HBV Genotyping%' OR + adt.REFERENCE LIKE '%T. Cruzi%' OR + adt.REFERENCE LIKE '%SVV%' OR + adt.REFERENCE LIKE '%LCV%' OR + adt.REFERENCE LIKE '%MRV%' OR + adt.REFERENCE LIKE '%Introduction%' OR + adt.REFERENCE LIKE '%SIV Indeterminate%' OR + adt.REFERENCE LIKE '%Zika Virus%' OR + adt.REFERENCE LIKE '%Tuberculosis (TB) Multiplex Negative%' OR + adt.REFERENCE LIKE '%SHF Negative%' OR + adt.REFERENCE LIKE '%SA6%' OR + adt.REFERENCE LIKE '%K. PNEUMO Negative%' OR + adt.REFERENCE LIKE '%STLV-2 Negative%' OR + adt.REFERENCE LIKE '%MRSA Negative%' OR + adt.REFERENCE LIKE '%KLEBSIELLA CULTURE%' OR + adt.REFERENCE LIKE '%SRV-2%' OR + adt.REFERENCE LIKE '%Malaria%' OR + adt.REFERENCE LIKE '%SARS-CoV-2%' OR + adt.REFERENCE LIKE '%Spike-FL%' OR + adt.REFERENCE LIKE '%NP Equivocal%' OR + adt.REFERENCE LIKE '%NP Negative%' OR + adt.REFERENCE LIKE '%NP Positive%' OR + adt.REFERENCE LIKE '%SCMV Positive%' OR + adt.REFERENCE LIKE '%MTC Negative%' OR + adt.REFERENCE LIKE '%Y. pseudo tubercul Negative%' ) AND + adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_ship_to.sql b/nbri_ehr/resources/queries/dbo/q_ship_to.sql new file mode 100644 index 0000000..6ac7c2c --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_ship_to.sql @@ -0,0 +1,16 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + SHIPTO_ID as ShipToId, + SHIPTO_NICKNAME as Name, + COUNTRY as Country, + City as City, + STREET_ADDRESS1 as StreetAddress1, + STREET_ADDRESS2 as StreetAddress2, + STATE_PROV as StateProv, + ZIP as Zip, + ZIP_EXT as ZipExt +FROM SHIPTO \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_species.sql b/nbri_ehr/resources/queries/dbo/q_species.sql new file mode 100644 index 0000000..c57e9d2 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_species.sql @@ -0,0 +1,12 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + SPEC_NAME AS common, + SPEC_DESC AS scientific_name, + 3 AS blood_per_kg, + 1 AS max_draw_pct, + 7 blood_draw_interval +FROM SPECIES diff --git a/nbri_ehr/resources/queries/dbo/q_species_codes.sql b/nbri_ehr/resources/queries/dbo/q_species_codes.sql new file mode 100644 index 0000000..ace9b46 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_species_codes.sql @@ -0,0 +1,16 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +SELECT + SPECIES_ID AS code, + SPEC_NAME AS common_name, + replace(SPEC_DESC, CHR(13) || CHR(10), ' ') AS scientific_name, + SPECIES_GROUP_ID as species, + CASE ACTIVE_YN + WHEN 'Y' THEN NULL + WHEN 'N' THEN '1/1/1970' + END AS dateDisabled +FROM SPECIES \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_staff.sql b/nbri_ehr/resources/queries/dbo/q_staff.sql new file mode 100644 index 0000000..53d287b --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_staff.sql @@ -0,0 +1,50 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + STAFF_ID as staffId, + EMAIL_ADDRESS as email, + trim(STAFF_FIRST_NAME) as firstName, + trim(STAFF_LAST_NAME) as lastName, + STAFF_MIDDLE_NAME as middleName, + STAFF_NUMBER as displayName, + HIRE_DATE as hireDate, + LAST_EMPLOY_DATE as lastEmployDate, + OFFICE_TELEPHONE as officePhone, + OFFICE_PHONE_EXT as officePhoneExt, + OFFICE_FAX as officeFax, + HOME_TELEPHONE as homePhone, + BEEPER_TELEPHONE as beeperPhone, + CELLULAR_TELEPHONE as cellPhone, + EMERGENCY_CONTACT as emergencyContact, + EMERGENCY_TELEPHONE as emergencyPhone, + HOME_ADDRESS1 as homeAddress1, + HOME_ADDRESS2 as homeAddress2, + HOME_CITY as homeCity, + HOME_STATE_PROV as homeState, + HOME_ZIP as homeZip, + HOME_ZIP_EXT as homeZipExt, + HOME_COUNTRY as homeCountry, + OFFICE_ADDRESS1 as officeAddress1, + OFFICE_ADDRESS2 as officeAddress2, + OFFICE_CITY as officeCity, + OFFICE_STATE_PROV as officeState, + OFFICE_ZIP as officeZip, + OFFICE_ZIP_EXT as officeZipExt, + OFFICE_COUNTRY as officeCountry, + BIRTHDATE as birthDate, + HS_NAME_DESC as hsName, + COLLEGE_GRAD_DATE as collegeGradDate, + COLLEGE_DEGREE as collegeDegree, + COLLEGE_MAJOR as collegeMajor, + COLLEGE_NAME_DESC as collegeName, + SUPERVISOR_STAFF_ID as supervisor, + POSITION_NAME as positionName, + POSITION_DESCRIPTION as positionDesc, + ACTIVE_YN as active +FROM STAFF + + + diff --git a/nbri_ehr/resources/queries/dbo/q_status.sql b/nbri_ehr/resources/queries/dbo/q_status.sql new file mode 100644 index 0000000..8642f14 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_status.sql @@ -0,0 +1,14 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +-- Used in q_demographics +SELECT anm.ANIMAL_ID_NUMBER AS Id, + anm.ANIMAL_DISPOSITION_ID.NAME, + CASE WHEN anm.TERMINATION_REASON_ID.ID = 10 THEN 'Invalid' -- Invalid Id + WHEN anm.ANIMAL_DISPOSITION_ID IS NULL THEN 'Alive' + WHEN anm.ANIMAL_DISPOSITION_ID IN (2, 3, 4) THEN 'Dead' -- Died, Project Sacrifice, Moribund Sacrifice + WHEN anm.ANIMAL_DISPOSITION_ID IN (5, 6) THEN 'Other' -- Escaped, Misc + ELSE 'Shipped' END AS status +FROM Animal anm \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_stress.sql b/nbri_ehr/resources/queries/dbo/q_stress.sql new file mode 100644 index 0000000..0423d89 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_stress.sql @@ -0,0 +1,13 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + STRESS_ID AS StressId, + STRESS_NAME AS Name, + STRESS_DESCRIPTION AS Description, + STRESS_RANKING AS Ranking, + REGULATORY_STRESS_LEVEL_ID AS RegulatoryStressLevel, + ACTIVE_YN AS Active +FROM STRESS_NAME \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_vitals.sql b/nbri_ehr/resources/queries/dbo/q_vitals.sql new file mode 100644 index 0000000..822f26c --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_vitals.sql @@ -0,0 +1,42 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT anmEvt.ANIMAL_EVENT_ID as objectid, + anm.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS vitalDate, + (CASE + WHEN (anmEvt.STAFF_ID.STAFF_FIRST_NAME IS NULL OR anmEvt.STAFF_ID.STAFF_LAST_NAME IS NULL) THEN 'unknown' + ELSE (anmEvt.STAFF_ID.STAFF_FIRST_NAME + || '|' || anmEvt.STAFF_ID.STAFF_LAST_NAME) END) AS performedby, + CAST(COALESCE (adt.modified, anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified, + CASE WHEN anmEvt.EVENT_ID.NAME LIKE '%Blood Pressure%' THEN anmEvt.TEXT_RESULT END AS bloodPressure, + CASE WHEN anmEvt.EVENT_ID.NAME LIKE '%Heart Rate%' THEN anmEvt.RESULT END AS heartRate, + CASE WHEN anmEvt.EVENT_ID.NAME LIKE '%Respiration Rate%' THEN anmEvt.RESULT END AS respRate, + CASE WHEN anmEvt.EVENT_ID.NAME LIKE '%Temperature%' THEN anmEvt.RESULT END AS temp, + CASE WHEN anmEvt.EVENT_ID.NAME LIKE '%Pulse Rate%' THEN anmEvt.RESULT END AS pulseRate, + CASE WHEN anmEvt.EVENT_ID.NAME LIKE '%Pulse Oximetry%' THEN anmEvt.RESULT END AS pulseOximetry, + CASE WHEN anmEvt.EVENT_ID.NAME LIKE '%EKG%' THEN anmEvt.RESULT END AS ekg, + ev.NUMERIC_UNIT_ID AS Units, + anmEvt.EVENT_ID.NAME AS type +FROM ANIMAL_EVENT anmEvt + LEFT JOIN ANIMAL anm ON anmEvt.ANIMAL_ID = anm.ANIMAL_ID + LEFT JOIN ANIMAL_EVENT_COMMENT anmCmt ON anmEvt.ANIMAL_EVENT_ID = anmCmt.ANIMAL_EVENT_ID + LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id + LEFT JOIN EVENT ev on anmEvt.EVENT_ID = ev.EVENT_ID +WHERE anmEvt.EVENT_ID.EVENT_ID IN (55, 56, 57, 1643, 1647, 1652, 1653, 1654, 1655, 2165, 2166, 2167, 2168, 2169) + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates + -- 55 Blood Pressure + -- 57 EKG + -- 1643 Temperature + -- 56, 1647 Respiration Rate + -- 1652 Heart Rate + -- 1653 Pulse + -- 1654 Pulse Rate + -- 1655 Pulse Oximetry + -- 2165 Blood Pressure-NHP + -- 2166 Heart Rate-NHP + -- 2167 Respiration Rate-NHP + -- 2168 Temperature-NHP + -- 2169 Pulse Rate-NHP diff --git a/nbri_ehr/resources/queries/dbo/q_vitals_delete.sql b/nbri_ehr/resources/queries/dbo/q_vitals_delete.sql new file mode 100644 index 0000000..ee2658e --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_vitals_delete.sql @@ -0,0 +1,18 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, length('ANIMAL_EVENT_ID = ')) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified, + adt.REFERENCE +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + (adt.REFERENCE LIKE '%Blood Pressure%' OR + adt.REFERENCE LIKE '%Heart Rate%' OR + adt.REFERENCE LIKE '%Respiration Rate%' OR + adt.REFERENCE LIKE '%Temperature%' OR + adt.REFERENCE LIKE '%Pulse Oximetry%' OR + adt.REFERENCE LIKE '%EKG%' OR + adt.REFERENCE LIKE '%Pulse Rate%' ) AND + adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_weight.sql b/nbri_ehr/resources/queries/dbo/q_weight.sql new file mode 100644 index 0000000..d2f32b6 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_weight.sql @@ -0,0 +1,22 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +SELECT anmEvt.ANIMAL_EVENT_ID as objectid, + anm.ANIMAL_ID_NUMBER AS Id, + CAST(anmEvt.EVENT_DATETIME AS TIMESTAMP) AS weightDate, + CAST(COALESCE (adt.modified,anmEvt.CREATED_DATETIME) AS TIMESTAMP) AS modified, + (CASE + WHEN (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) IS NULL OR trim(anmEvt.STAFF_ID.STAFF_LAST_NAME) IS NULL) THEN 'unknown' + ELSE (trim(anmEvt.STAFF_ID.STAFF_FIRST_NAME) + || '|' || trim(anmEvt.STAFF_ID.STAFF_LAST_NAME)) END) AS performedby, + anmEvt.result AS weight, + ev.NUMERIC_UNIT_ID AS Units +FROM ANIMAL_EVENT anmEvt +LEFT JOIN ANIMAL anm ON anmEvt.ANIMAL_ID = anm.ANIMAL_ID +LEFT JOIN EVENT ev ON anmEvt.EVENT_ID = ev.EVENT_ID +LEFT JOIN q_modified_event adt ON anmEvt.ANIMAL_EVENT_ID = adt.event_id +WHERE anmEvt.EVENT_ID = 1349 -- Body weight + AND anmEvt.CREATED_DATETIME < now() -- there are rows in ANIMAL_EVENT table with future dates \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/q_weight_delete.sql b/nbri_ehr/resources/queries/dbo/q_weight_delete.sql new file mode 100644 index 0000000..e910243 --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/q_weight_delete.sql @@ -0,0 +1,11 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT substring(adt.PRIMARY_KEY_VALUES, 18) AS objectid, + CAST(adt.CHANGE_DATETIME AS TIMESTAMP) AS modified +FROM AUDIT_TRAIL adt +WHERE adt.PRIMARY_KEY_VALUES LIKE '%ANIMAL_EVENT_ID%' AND + adt.REFERENCE LIKE '%Event: Body Weight%' AND + adt.COLUMN_NAME = 'DELETE' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/dbo/staffInfo.sql b/nbri_ehr/resources/queries/dbo/staffInfo.sql new file mode 100644 index 0000000..6918dca --- /dev/null +++ b/nbri_ehr/resources/queries/dbo/staffInfo.sql @@ -0,0 +1,17 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +-- subquery to get staff info +-- email_prefix below (used for display name) and transformEmailDomain '@louisiana.edu' (defined in etl xml) +-- during user column transform creates a deactivated labkey user during an ETL run +SELECT +s.staff_id, +(s.staff_last_name ||', '|| s.staff_first_name) as staffName, +s.email_address, +(CASE + WHEN s.email_address IS NULL THEN 'unknown' + ELSE substring(s.email_address, 1, + locate('@', s.email_address) - 1) END) as email_prefix +FROM STAFF s \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr/activeProtocols.sql b/nbri_ehr/resources/queries/ehr/activeProtocols.sql new file mode 100644 index 0000000..6ee76fa --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/activeProtocols.sql @@ -0,0 +1,7 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT protocol, title FROM ehr.protocol pr +WHERE pr.inactiveDate IS NULL OR pr.inactiveDate > now() \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr/my_tasks.query.xml b/nbri_ehr/resources/queries/ehr/my_tasks.query.xml new file mode 100644 index 0000000..2a6ca88 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/my_tasks.query.xml @@ -0,0 +1,65 @@ + + + + + My Tasks + + + + RowId + + + Task Id + true + true + + + Task Type + + + Assigned To + true + + core + PrincipalsWithoutAdmin + userid + + + + Due Date + true + DateTime + + + Created By + + + Created + + + Modified By + + + Modified + + + + ehr.context + /ehr/studyButtons.js + + Grid Views + + + Charts + + + Export + + + Print + + +
+ + + diff --git a/nbri_ehr/resources/queries/ehr/my_tasks.sql b/nbri_ehr/resources/queries/ehr/my_tasks.sql new file mode 100644 index 0000000..4105b20 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/my_tasks.sql @@ -0,0 +1,28 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + +taskid, +rowid, +updateTitle, +category, +title, +formtype, +qcstate, +assignedto, +duedate, +requestid, +datecompleted, +modifiedby, +modified, +createdby, +created, +description + + +FROM ehr.tasks t + +WHERE ISMEMBEROF(t.assignedto) \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr/my_tasks/.qview.xml b/nbri_ehr/resources/queries/ehr/my_tasks/.qview.xml new file mode 100644 index 0000000..8388595 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/my_tasks/.qview.xml @@ -0,0 +1,15 @@ + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr/my_tasks/Active Tasks.qview.xml b/nbri_ehr/resources/queries/ehr/my_tasks/Active Tasks.qview.xml new file mode 100644 index 0000000..069ab01 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/my_tasks/Active Tasks.qview.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr/my_tasks/Review Required.qview.xml b/nbri_ehr/resources/queries/ehr/my_tasks/Review Required.qview.xml new file mode 100644 index 0000000..d02c415 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/my_tasks/Review Required.qview.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr/observation_types.query.xml b/nbri_ehr/resources/queries/ehr/observation_types.query.xml new file mode 100644 index 0000000..16fbabe --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/observation_types.query.xml @@ -0,0 +1,17 @@ + + + + + Observation Types + + + false + + + true + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr/project.js b/nbri_ehr/resources/queries/ehr/project.js new file mode 100644 index 0000000..5f615b3 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/project.js @@ -0,0 +1,32 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +require("ehr/triggers").initScript(this); +var nextProjectNum = -1; + +function onInit(event, helper){ + + //ETL'd data has integer values in the 'project' column that is meaningless to the client, + //but since 'project' is a required field, find the highest num in the existing data and add 1 for inserting new Projects. + LABKEY.Query.executeSql({ + schemaName: 'ehr', + sql: 'SELECT MAX(project) AS latestProjectNum FROM ehr.project', + containerFilter: LABKEY.Query.containerFilter.allFolders, + success: function(data) { + nextProjectNum = data.rows[0].latestProjectNum + 1; + }, + failure: function (error) { + console.log("Error getting the latest 'Project Id' in project trigger onInit()\n" + error); + } + }); +} +function onUpsert(helper, scriptErrors, row, oldRow) { + if (!helper.isETL()) { + if (!row.project) { + row.project = nextProjectNum; + } + } +} \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr/project.query.xml b/nbri_ehr/resources/queries/ehr/project.query.xml new file mode 100644 index 0000000..d2db2ca --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/project.query.xml @@ -0,0 +1,75 @@ + + + + + + /EHR/projectDetails.view?project=${project} + + + + + + + Project + false + NBRI Project + + + Project Id + true + + + true + + + true + + + true + + + IACUC Protocol + true + + ehr + protocol + protocol + + + + true + + + true + + + true + + + true + + + true + + + true + + + Investigator + true + + + Requestor Name + true + + + true + + + true + + +
+ + + diff --git a/nbri_ehr/resources/queries/ehr/project/.qview.xml b/nbri_ehr/resources/queries/ehr/project/.qview.xml new file mode 100644 index 0000000..2022e60 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/project/.qview.xml @@ -0,0 +1,8 @@ + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr/protocol.js b/nbri_ehr/resources/queries/ehr/protocol.js new file mode 100644 index 0000000..3847f94 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/protocol.js @@ -0,0 +1,37 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +require("ehr/triggers").initScript(this); + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_INSERT, 'ehr', 'protocol', function (helper, scriptErrors, row, oldRow) { + + if (row.description) { + plainTextParts = row.description.split("\\loch\\af0") + let plainText = ""; + for(let i = 1; i < plainTextParts.length; i++) + { + let chunk = LABKEY.Utils.encodeHtml(plainTextParts[i].split("}")[0]); + chunk = chunk.replace("\\hich\\af0 \\'85", "…"); // ellipsis + chunk = chunk.replace("\\hich\\af0 \\'92", "'"); + chunk = chunk.replace("\\hich\\af0 \\'93", "\""); + chunk = chunk.replace("\\hich\\af0 \\'94", "\""); + chunk = chunk.replace("\\hich\\af0 \\'99", "™"); // trademark + chunk = chunk.replace("\\hich\\af0 \\'ae", "®"); // registered trademark + chunk = chunk.replace("\\hich\\af0 \\'b0", "°"); // Degree sign + chunk = chunk.replace("\\hich\\af0 \\'b5", "µ"); // Micro sign (Greek mu) + chunk = chunk.replace("\\hich\\af0 \\'b7", "·"); // Middle dot + chunk = chunk.replace("\\hich\\af0 \\'ef", "ï"); // i-diaeresis + // TODO: As a general catch all, could convert the hex value in the match to the HTML ascii entity + // Currently this covers all the cases though in the source data + + plainText += chunk.trim(); + plainText += " "; + + } + row.description = plainText.trim(); + } + +}); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr/protocol.query.xml b/nbri_ehr/resources/queries/ehr/protocol.query.xml new file mode 100644 index 0000000..82667e7 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/protocol.query.xml @@ -0,0 +1,91 @@ + + + + + + Protocol + + + PI + false + + core + Users + UserId + DisplayName + + + + true + + + Author + + core + Users + UserId + DisplayName + + + + Owner + + core + Users + UserId + DisplayName + + + + Protocol Type + + ehr_lookups + protocol_type + value + title + + + + Protocol Category + + ehr_lookups + protocol_category + value + title + + + + Current State + + ehr_lookups + protocol_state + value + title + + + + Parent Protocol + + ehr + protocol + protocol + displayName + + + + Questionnaire + + ehr_lookups + questionnaire + value + title + + + + Approval Date + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr/protocol/.qview.xml b/nbri_ehr/resources/queries/ehr/protocol/.qview.xml new file mode 100644 index 0000000..e2e125f --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/protocol/.qview.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr/protocolActiveAnimals.query.xml b/nbri_ehr/resources/queries/ehr/protocolActiveAnimals.query.xml new file mode 100644 index 0000000..623b9ea --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/protocolActiveAnimals.query.xml @@ -0,0 +1,29 @@ + + + + + Animals Actively Assigned to Each Protocol + + + true + + ehr + protocol + protocol + + + + /query/executeQuery.view?schemaName=study& + query.queryName=protocolAssignment& + query.viewName=Active Assignments& + query.protocol~eq=${protocol}& + + + + + + TotalActiveAnimals +
+ + + diff --git a/nbri_ehr/resources/queries/ehr/protocolActiveAnimals.sql b/nbri_ehr/resources/queries/ehr/protocolActiveAnimals.sql new file mode 100644 index 0000000..e30ff67 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/protocolActiveAnimals.sql @@ -0,0 +1,21 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + p.protocol, + p.title, + count(distinct a.Id) AS TotalActiveAnimals, + group_concat(distinct a.Id) AS ActiveAnimals + +FROM ehr.protocol p + +--we find total distinct animals ever assigned to this protocol +LEFT JOIN + (SELECT a.protocol, a.id, count(*) AS TotalAssignments, max(a.date) as LatestStart, + max(a.enddateCoalesced) as latestEnd + FROM study.protocolAssignment a + GROUP BY a.protocol, a.id) a ON (p.protocol = a.protocol.protocol) + +group by p.protocol, p.title \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr/protocolAnimals.query.xml b/nbri_ehr/resources/queries/ehr/protocolAnimals.query.xml new file mode 100644 index 0000000..f9500ac --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/protocolAnimals.query.xml @@ -0,0 +1,43 @@ + + + + + Distinct animals ever assigned to this protocol, over the full history + + + true + + ehr + protocol + protocol + + + + + study + animal + id + + + + + ehr_lookups + species + common + + + + + + /query/executeQuery.view?schemaName=study& + query.queryName=protocolAssignment& + query.protocol~eq=${protocol}& + query.id~eq=${id}& + query.sort=-Date& + + + +
+ + + diff --git a/nbri_ehr/resources/queries/ehr/protocolAnimals.sql b/nbri_ehr/resources/queries/ehr/protocolAnimals.sql new file mode 100644 index 0000000..193bc4c --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/protocolAnimals.sql @@ -0,0 +1,22 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + p.protocol, + p.approve, + a.id, + a.species, + + COALESCE(a.Total, 0) AS TotalAssignments + +FROM ehr.protocol p + +--we find total distinct animals ever assigned to this protocol, since the last approval date +LEFT JOIN + (SELECT a.protocol.displayName as protocol, a.id, a.id.dataset.demographics.Species AS Species, count(*) AS Total, max(a.date) as LatestStart, + max(a.enddateCoalesced) as latestEnd + FROM study.protocolAssignment a + GROUP BY a.protocol.displayName, a.id, a.id.dataset.demographics.species) a ON (p.displayName = a.protocol) + diff --git a/nbri_ehr/resources/queries/ehr/protocolHistoricAnimals.sql b/nbri_ehr/resources/queries/ehr/protocolHistoricAnimals.sql new file mode 100644 index 0000000..7ad4bd5 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/protocolHistoricAnimals.sql @@ -0,0 +1,26 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + p.protocol, + p.approve, + a.id, + a.species, + a.LatestStart, + a.LatestEnd, + + COALESCE(a.Total, 0) AS TotalAssignments + +FROM ehr.protocol p + +--we find total distinct animals ever assigned to this protocol +LEFT JOIN + (SELECT a.Project.protocol as protocol, a.id, a.id.dataset.demographics.Species AS Species, count(*) AS Total, max(a.date) as LatestStart, + max(a.enddateCoalesced) as latestEnd + FROM study.assignment a + GROUP BY a.project.protocol, a.id, a.id.dataset.demographics.species) a + ON (p.protocol = a.protocol) + +WHERE a.Total > 0 diff --git a/nbri_ehr/resources/queries/ehr/protocolTotalAnimalsBySpecies.query.xml b/nbri_ehr/resources/queries/ehr/protocolTotalAnimalsBySpecies.query.xml new file mode 100644 index 0000000..302482d --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/protocolTotalAnimalsBySpecies.query.xml @@ -0,0 +1,36 @@ + + + + + Total Animals Assigned To Each Protocol, By Species + + + true + + ehr + protocol + protocol + + + + Species + + ehr_lookups + species + common + + + + + /query/executeQuery.view?schemaName=ehr& + query.queryName=protocolAnimals& + query.protocol~eq=${protocol}& + query.species~eq=${species}& + + + + TotalAnimals +
+ + + diff --git a/nbri_ehr/resources/queries/ehr/protocolTotalAnimalsBySpecies.sql b/nbri_ehr/resources/queries/ehr/protocolTotalAnimalsBySpecies.sql new file mode 100644 index 0000000..3521c6a --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/protocolTotalAnimalsBySpecies.sql @@ -0,0 +1,18 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT i.* FROM ( + SELECT + p.protocol as protocol, + pa.species, + group_concat(DISTINCT pa.id) as Animals, + CONVERT(Count(pa.id), INTEGER) AS TotalAnimals + FROM ehr.protocol p + LEFT JOIN ehr.protocolAnimals pa ON (p.protocol = pa.protocol) + GROUP BY p.protocol, pa.species +) i +WHERE i.species IS NOT NULL + + diff --git a/nbri_ehr/resources/queries/ehr/protocol_counts.query.xml b/nbri_ehr/resources/queries/ehr/protocol_counts.query.xml new file mode 100644 index 0000000..6586f91 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/protocol_counts.query.xml @@ -0,0 +1,30 @@ + + + + + NHPs Allowed Per Protocol + + + + Species + + ehr_lookups + species_codes + code + scientific_name + + + + Euthanasia + + ehr_lookups + euthanasia_type + value + title + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr/protocol_counts/.qview.xml b/nbri_ehr/resources/queries/ehr/protocol_counts/.qview.xml new file mode 100644 index 0000000..c932369 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/protocol_counts/.qview.xml @@ -0,0 +1,9 @@ + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr/tasks/.qview.xml b/nbri_ehr/resources/queries/ehr/tasks/.qview.xml new file mode 100644 index 0000000..b60dc1d --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/tasks/.qview.xml @@ -0,0 +1,19 @@ + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr/tasks/Active Tasks.qview.xml b/nbri_ehr/resources/queries/ehr/tasks/Active Tasks.qview.xml new file mode 100644 index 0000000..33364dc --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/tasks/Active Tasks.qview.xml @@ -0,0 +1,8 @@ + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr/tasks/Review Required.qview.xml b/nbri_ehr/resources/queries/ehr/tasks/Review Required.qview.xml new file mode 100644 index 0000000..ac3cbd6 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/tasks/Review Required.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/ageclass.query.xml b/nbri_ehr/resources/queries/ehr_lookups/ageclass.query.xml new file mode 100644 index 0000000..7aa4864 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/ageclass.query.xml @@ -0,0 +1,45 @@ + + + + + Age Class + + + Key + false + true + true + + + Species + + ehr_lookups + species_codes + code + common_name + + + + Gender + + ehr_lookups + gender_codes + code + meaning + + + + Age Class + + + Min + + + Max + + + key +
+ + + diff --git a/nbri_ehr/resources/queries/ehr_lookups/areas/.qview.xml b/nbri_ehr/resources/queries/ehr_lookups/areas/.qview.xml new file mode 100644 index 0000000..bac04f3 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/areas/.qview.xml @@ -0,0 +1,7 @@ + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/buildings.js b/nbri_ehr/resources/queries/ehr_lookups/buildings.js new file mode 100644 index 0000000..14ca220 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/buildings.js @@ -0,0 +1,53 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +var LABKEY = require("labkey"); + +var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); + +function onUpsert(row, oldRow, errors){ + if (extraContext.dataSource != "etl") { + if (!row.description) { + errors['description'] = 'Building description is required.'; + return; + } + + if (!row.area) { + errors['area'] = 'Area is required.'; + return; + } + + if (!row.name) { + if (oldRow && oldRow.name && oldRow.name[0]) { + row.name = oldRow.name[0]; + return; + } + + row.name = row.description + '-' + row.area; + } + } +} + +function beforeInsert(row, errors){ + onUpsert(row, undefined, errors); +} + +function beforeUpdate(row, oldRow, errors){ + onUpsert(row, oldRow, errors); +} + +function beforeDelete(row, errors) { + if (extraContext.dataSource != "etl") { + if (!row.name) { + errors[null] = 'Building name is required.'; + } + else { + let totalRecords = triggerHelper.totalRecords("ehr_lookups", "floors", "building", row.name); + if (totalRecords > 0) { + errors[null] = 'Cannot delete. There are ' + totalRecords + ' floors currently registered in this building. Delete floors before deleting this building.'; + } + } + } +} \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/buildings.query.xml b/nbri_ehr/resources/queries/ehr_lookups/buildings.query.xml new file mode 100644 index 0000000..90dd3ea --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/buildings.query.xml @@ -0,0 +1,31 @@ + + + + + Buildings + + + + + Area + + ehr_lookups + areas + area + description + + + + true + false + false + false + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/buildings/.qview.xml b/nbri_ehr/resources/queries/ehr_lookups/buildings/.qview.xml new file mode 100644 index 0000000..6dab0af --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/buildings/.qview.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/cage.js b/nbri_ehr/resources/queries/ehr_lookups/cage.js new file mode 100644 index 0000000..0d5c704 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/cage.js @@ -0,0 +1,50 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +var LABKEY = require("labkey"); + +var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); + +function onUpsert(row, oldRow, errors){ + if (extraContext.dataSource != "etl") { + if (!row.location) { + if (oldRow && oldRow.location && oldRow.location[0]) { + row.location = oldRow.location[0]; + return; + } + + if (!row.room) { + errors['room'] = 'Room is required.'; + return; + } + + row.location = row.room; + if (row.cage) + row.location += '-' + row.cage; + } + } +} + +function beforeInsert(row, errors){ + onUpsert(row, undefined, errors); +} + +function beforeUpdate(row, oldRow, errors){ + onUpsert(row, oldRow, errors); +} + +function beforeDelete(row, errors) { + if (extraContext.dataSource != "etl") { + if (!row.location) { + errors[null] = 'Location is required.'; + } + else { + let currentlyHoused = triggerHelper.totalHousingRecords(row.location); + if (currentlyHoused > 0) { + errors[null] = 'Cannot delete. There are ' + currentlyHoused + ' animals currently housed in this cage.'; + } + } + } +} \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/cage.query.xml b/nbri_ehr/resources/queries/ehr_lookups/cage.query.xml new file mode 100644 index 0000000..97b1549 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/cage.query.xml @@ -0,0 +1,29 @@ + + + + + Cages + + + /nbri_ehr/cageDetails.view?room=${room}&cage=${location}& + + + Room + + + true + false + + + Indoor/Outdoor + + ehr_lookups + indoor_outdoor + value + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/cage/.qview.xml b/nbri_ehr/resources/queries/ehr_lookups/cage/.qview.xml new file mode 100644 index 0000000..5f0ff5c --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/cage/.qview.xml @@ -0,0 +1,12 @@ + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/country.query.xml b/nbri_ehr/resources/queries/ehr_lookups/country.query.xml new file mode 100644 index 0000000..0cfb2c9 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/country.query.xml @@ -0,0 +1,20 @@ + + + + + Country + + + Category + + ehr_lookups + country_category + value + title + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/floors.js b/nbri_ehr/resources/queries/ehr_lookups/floors.js new file mode 100644 index 0000000..4577e1a --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/floors.js @@ -0,0 +1,53 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +var LABKEY = require("labkey"); + +var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); + +function onUpsert(row, oldRow, errors){ + if (extraContext.dataSource != "etl") { + if (!row.name) { + errors['name'] = 'Floor name is required.'; + return; + } + + if (!row.building) { + errors['building'] = 'Building is required.'; + return; + } + + if (!row.floor) { + if (oldRow && oldRow.floor && oldRow.floor[0]) { + row.floor = oldRow.floor[0]; + return; + } + + row.floor = row.name + '-' + row.building; + } + } +} + +function beforeInsert(row, errors){ + onUpsert(row, undefined, errors); +} + +function beforeUpdate(row, oldRow, errors){ + onUpsert(row, oldRow, errors); +} + +function beforeDelete(row, errors) { + if (extraContext.dataSource != "etl") { + if (!row.floor) { + errors[null] = 'Floor is required.'; + } + else { + let totalRecords = triggerHelper.totalRecords("ehr_lookups", "rooms", "floor", row.floor); + if (totalRecords > 0) { + errors[null] = 'Cannot delete. There are ' + totalRecords + ' rooms currently registered on this floor. Delete rooms before deleting this floor.'; + } + } + } +} \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/floors.query.xml b/nbri_ehr/resources/queries/ehr_lookups/floors.query.xml new file mode 100644 index 0000000..ba3ff03 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/floors.query.xml @@ -0,0 +1,28 @@ + + + + + Floors + + + + + Building + + ehr_lookups + buildings + name + description + + + + true + false + false + false + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/floors/.qview.xml b/nbri_ehr/resources/queries/ehr_lookups/floors/.qview.xml new file mode 100644 index 0000000..f8c6e5e --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/floors/.qview.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/procedures/.qview.xml b/nbri_ehr/resources/queries/ehr_lookups/procedures/.qview.xml new file mode 100644 index 0000000..a2af545 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/procedures/.qview.xml @@ -0,0 +1,7 @@ + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/roomUtilization.query.xml b/nbri_ehr/resources/queries/ehr_lookups/roomUtilization.query.xml new file mode 100644 index 0000000..dacb1a3 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/roomUtilization.query.xml @@ -0,0 +1,22 @@ + + + + + Room Utilization + + + + Total Animals + /query/executeQuery.view? + schemaName=study& + query.queryName=Housing& + query.room~eq=${room}& + query.sort=Id& + query.enddate~isblank + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/roomUtilization.sql b/nbri_ehr/resources/queries/ehr_lookups/roomUtilization.sql new file mode 100644 index 0000000..8abd391 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/roomUtilization.sql @@ -0,0 +1,16 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +SELECT + r.room, + count(DISTINCT h.id) as TotalAnimals, + r.building, + r.area, +FROM ehr_lookups.rooms r +LEFT JOIN study.housing h +ON r.room = h.room + +GROUP BY r.room, r.building, r.area \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/roomUtilizationByBuilding.query.xml b/nbri_ehr/resources/queries/ehr_lookups/roomUtilizationByBuilding.query.xml new file mode 100644 index 0000000..8177e14 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/roomUtilizationByBuilding.query.xml @@ -0,0 +1,81 @@ + + + + + Room Utilization By Building + + + + true + + + Total Cage Spaces + 40 + /query/executeQuery.view? + schemaName=ehr_lookups& + query.queryName=cage& + query.room/building~eq=${building}& + query.sort=cage& + + + + Total Cages Present + 40 + /query/executeQuery.view? + schemaName=ehr_lookups& + query.queryName=availableCages& + query.room/building~eq=${building}& + query.isAvailable~eq=true& + query.sort=cage& + + + + Cages Used + 40 + /query/executeQuery.view? + schemaName=ehr_lookups& + query.queryName=cage& + query.room/building~eq=${building}& + query.availability/isAvailable~eq=true& + query.totalAnimals/totalAnimals~gt=0& + query.sort=cage& + + + + Cages Empty + 40 + /query/executeQuery.view? + schemaName=ehr_lookups& + query.queryName=cage& + query.room/building~eq=${building}& + query.availability/isAvailable~eq=true& + query.totalAnimals/totalAnimals~isblank& + query.sort=cage& + + + + 40 + % Used + 0.## + + + 40 + % Empty + 0.## + + + Total Animals + 40 + /query/executeQuery.view? + schemaName=study& + query.queryName=Demographics& + query.viewName=By Location& + query.Id/curLocation/room/building~eq=${building}& + query.sort=Id& + + + +
+ + + diff --git a/nbri_ehr/resources/queries/ehr_lookups/roomUtilizationByBuilding.sql b/nbri_ehr/resources/queries/ehr_lookups/roomUtilizationByBuilding.sql new file mode 100644 index 0000000..17c695b --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/roomUtilizationByBuilding.sql @@ -0,0 +1,30 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + t1.building, + t1.totalRooms, +-- t1.totalCages, +-- t1.availableCages, +-- t1.cagesUsed, +-- t1.cagesEmpty, +-- cast(((CAST(t1.cagesUsed as double) / t1.availableCages) * 100) as double) as pctUsed, +-- cast((100.0 - ((CAST(t1.cagesUsed as double) / t1.availableCages) * 100)) as double) as pctEmpty, + t1.totalAnimals + +FROM ( +SELECT + r.room.building as building, + count(DISTINCT r.room) as totalRooms, +-- sum(r.totalCages) as totalCages, +-- sum(r.availableCages) as availableCages, +-- sum(r.cagesUsed) as cagesUsed, +-- sum(r.cagesEmpty) as cagesEmpty, + sum(r.totalAnimals) as totalAnimals + +FROM ehr_lookups.roomUtilization r +GROUP BY r.room.building + +) t1 \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/rooms.js b/nbri_ehr/resources/queries/ehr_lookups/rooms.js new file mode 100644 index 0000000..63e936b --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/rooms.js @@ -0,0 +1,54 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +var LABKEY = require("labkey"); +var console = require("console"); + +var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); + +function onUpsert(row, oldRow, errors){ + if (extraContext.dataSource != "etl") { + if (!row.name) { + errors['name'] = 'Room name is required.'; + return; + } + + if (!row.floor) { + errors['floor'] = 'Floor is required.'; + return; + } + + if (!row.room) { + if (oldRow && oldRow.room && oldRow.room[0]) { + row.room = oldRow.room[0]; + return; + } + + row.room = row.name + '-' + row.floor; + } + } +} + +function beforeInsert(row, errors){ + onUpsert(row, undefined, errors); +} + +function beforeUpdate(row, oldRow, errors){ + onUpsert(row, oldRow, errors); +} + +function beforeDelete(row, errors) { + if (extraContext.dataSource != "etl") { + if (!row.room) { + errors[null] = 'Room is required.'; + } + else { + let totalRecords = triggerHelper.totalRecords("ehr_lookups", "cage", "room", row.room); + if (totalRecords > 0) { + errors[null] = 'Cannot delete. There are ' + totalRecords + ' cages currently registered in this room. Delete cages before deleting this room.'; + } + } + } +} \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/rooms.query.xml b/nbri_ehr/resources/queries/ehr_lookups/rooms.query.xml new file mode 100644 index 0000000..dd7b89f --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/rooms.query.xml @@ -0,0 +1,24 @@ + + + + + + Rooms + + + + + true + false + false + + + true + false + false + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/rooms/.qview.xml b/nbri_ehr/resources/queries/ehr_lookups/rooms/.qview.xml new file mode 100644 index 0000000..0bfbf5b --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/rooms/.qview.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/snomed.query.xml b/nbri_ehr/resources/queries/ehr_lookups/snomed.query.xml new file mode 100644 index 0000000..4613f3e --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/snomed.query.xml @@ -0,0 +1,9 @@ + + + + + Treatments +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/species_codes.query.xml b/nbri_ehr/resources/queries/ehr_lookups/species_codes.query.xml new file mode 100644 index 0000000..fab66c2 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/species_codes.query.xml @@ -0,0 +1,19 @@ + + + + + + + Scientific Name + + ehr_lookups + species + scientific_name + scientific_name + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/ehr_lookups/vendor_production_location.query.xml b/nbri_ehr/resources/queries/ehr_lookups/vendor_production_location.query.xml new file mode 100644 index 0000000..058877b --- /dev/null +++ b/nbri_ehr/resources/queries/ehr_lookups/vendor_production_location.query.xml @@ -0,0 +1,19 @@ + + + + + + + Country + + ehr_lookups + country + value + title + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/Account.query.xml b/nbri_ehr/resources/queries/nbri_ehr/Account.query.xml new file mode 100644 index 0000000..7f498db --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/Account.query.xml @@ -0,0 +1,48 @@ + + + + + Account + + + + Department + + nbri_ehr + Department + DepartmentId + Name + + + + Cost Type + + ehr_lookups + cost_type + value + title + + + + Expense Class + + ehr_lookups + expense_class + value + description + + + + Project + + ehr + project + project + displayName + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/AnimalDelivery.query.xml b/nbri_ehr/resources/queries/nbri_ehr/AnimalDelivery.query.xml new file mode 100644 index 0000000..e19c0a8 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/AnimalDelivery.query.xml @@ -0,0 +1,86 @@ + + + + + Animal Delivery + + + + Animal Delivery Id + + + Animal Shipment + + nbri_ehr + AnimalShipment + AnimalShipmentId + AnimalShipmentId + + + + Ship To + + nbri_ehr + ShipTo + ShipToId + Name + + + + Animal Req Order + + nbri_ehr + AnimalReqOrder + AnimalReqOrderId + AnimalReqOrder + + + + Delivery State + + ehr_lookups + delivery_state + value + title + + + + Project + + ehr + project + project + displayName + + + + Bill To Account + + nbri_ehr + Account + AccountId + AccountNumber + + + + Bill To Staff + http://www.labkey.org/types#userId + + + Per Diem Account + + nbri_ehr + Account + AccountId + AccountNumber + + + + Per Diem Staff + http://www.labkey.org/types#userId + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/AnimalDeliveryEsig.query.xml b/nbri_ehr/resources/queries/nbri_ehr/AnimalDeliveryEsig.query.xml new file mode 100644 index 0000000..0c74ac4 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/AnimalDeliveryEsig.query.xml @@ -0,0 +1,36 @@ + + + + + Animal Delivery ESignature + + + Animal Delivery + + nbri_ehr + AnimalDelivery + AnimalDeliveryId + AnimalDeliveryId + + + + Esig Event + + ehr_lookups + esig_events + value + title + + + + User Profile + http://www.labkey.org/types#userId + + + Esig Date + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/AnimalReqOrder.query.xml b/nbri_ehr/resources/queries/nbri_ehr/AnimalReqOrder.query.xml new file mode 100644 index 0000000..5c829e1 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/AnimalReqOrder.query.xml @@ -0,0 +1,135 @@ + + + + + Animal Req Order + + + + Animal Vendor + + nbri_ehr + AnimalVendor + AnimalVendorId + VendorName + + + + Requisitioner Staff + http://www.labkey.org/types#userId + + + Req Order Type + + ehr_lookups + req_order_type + value + title + + + + Req Order State + + ehr_lookups + req_order_state + value + title + + + + Bill To Account + + nbri_ehr + Account + AccountId + AccountNumber + + + + Bill To Staff + http://www.labkey.org/types#userId + + + Per Diem Account + + nbri_ehr + Account + AccountId + AccountNumber + + + + Per Diem Staff + http://www.labkey.org/types#userId + + + Submitted By Staff + http://www.labkey.org/types#userId + + + Approved By Staff + http://www.labkey.org/types#userId + + + Project + + ehr + project + project + displayName + + + + Site Cage + /nbri_ehr/cageDetails.view?room=${SiteCage/room}&cage=${SiteCage}& + + ehr_lookups + cage + location + cage + + + + Site Room + /nbri_ehr/cageDetails.view?room=${SiteRoom}& + + ehr_lookups + rooms + room + name + + + + Site Floor + + ehr_lookups + floors + floor + name + + + + Site Building + + ehr_lookups + buildings + name + + + + Site Area + + ehr_lookups + areas + area + + + + Created By Staff + http://www.labkey.org/types#userId + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/AnimalReqOrderEsig.query.xml b/nbri_ehr/resources/queries/nbri_ehr/AnimalReqOrderEsig.query.xml new file mode 100644 index 0000000..2d8bfb2 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/AnimalReqOrderEsig.query.xml @@ -0,0 +1,36 @@ + + + + + Animal Req Order ESignature + + + Animal Req Order + + nbri_ehr + AnimalReqOrder + AnimalReqOrderId + AnimalReqOrderId + + + + Esig Event + + ehr_lookups + esig_events + value + title + + + + User Profile + http://www.labkey.org/types#userId + + + Esig Date + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/AnimalShipment.query.xml b/nbri_ehr/resources/queries/nbri_ehr/AnimalShipment.query.xml new file mode 100644 index 0000000..60aa8de --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/AnimalShipment.query.xml @@ -0,0 +1,42 @@ + + + + + Animal Shipment + + + + Received By Staff + http://www.labkey.org/types#userId + + + Animal Delivery + + nbri_ehr + AnimalDelivery + AnimalDeliveryId + AnimalDeliveryId + + + + Lot Id + + nbri_ehr + lot + lotId + + + + Cost Center + + ehr_lookups + cost_center + value + title + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/AnimalVendor.query.xml b/nbri_ehr/resources/queries/nbri_ehr/AnimalVendor.query.xml new file mode 100644 index 0000000..426952f --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/AnimalVendor.query.xml @@ -0,0 +1,29 @@ + + + + + Animal Vendor + + + Vendor Approval Code + + ehr_lookups + vendor_approval_code + value + title + + + + Vendor Production Location + + ehr_lookups + vendor_production_location + value + title + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/AnimalVendor/.qview.xml b/nbri_ehr/resources/queries/nbri_ehr/AnimalVendor/.qview.xml new file mode 100644 index 0000000..9691552 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/AnimalVendor/.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/CageCard.query.xml b/nbri_ehr/resources/queries/nbri_ehr/CageCard.query.xml new file mode 100644 index 0000000..e70dfc5 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/CageCard.query.xml @@ -0,0 +1,56 @@ + + + + + Cage Card + + + + Account Staff + http://www.labkey.org/types#userId + + + Account Staff + http://www.labkey.org/types#userId + + + Animal Delivery + + nbri_ehr + AnimalDelivery + AnimalDeliveryId + AnimalDeliveryId + + + + Cost Center + + ehr_lookups + cost_center + value + title + + + + Card Format + + ehr_lookups + card_format + value + title + + + + Census Activity Status + + ehr_lookups + census_activity_status + value + title + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/CageCardHistory.query.xml b/nbri_ehr/resources/queries/nbri_ehr/CageCardHistory.query.xml new file mode 100644 index 0000000..088f8b4 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/CageCardHistory.query.xml @@ -0,0 +1,65 @@ + + + + + Cage Card History + + + + Account Staff + http://www.labkey.org/types#userId + + + Account Staff + http://www.labkey.org/types#userId + + + Animal Delivery + + nbri_ehr + AnimalDelivery + AnimalDeliveryId + AnimalDeliveryId + + + + Cost Center + + ehr_lookups + cost_center + value + title + + + + Card Format + + ehr_lookups + card_format + value + title + + + + Census Activity Status + + ehr_lookups + census_activity_status + value + title + + + + Account + + nbri_ehr + Account + AccountId + AccountNumber + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/DeletedRecord.query.xml b/nbri_ehr/resources/queries/nbri_ehr/DeletedRecord.query.xml new file mode 100644 index 0000000..6b894a7 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/DeletedRecord.query.xml @@ -0,0 +1,24 @@ + + + + + Deleted Record + + + Esig Event + + ehr_lookups + esig_events + value + title + + + + ESignature User + http://www.labkey.org/types#userId + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/Department.query.xml b/nbri_ehr/resources/queries/nbri_ehr/Department.query.xml new file mode 100644 index 0000000..91062cf --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/Department.query.xml @@ -0,0 +1,25 @@ + + + + + Department + + + + Parent Department + + nbri_ehr + Department + DepartmentId + Name + + + + Staff + http://www.labkey.org/types#userId + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/IdHistory.query.xml b/nbri_ehr/resources/queries/nbri_ehr/IdHistory.query.xml new file mode 100644 index 0000000..686bf4c --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/IdHistory.query.xml @@ -0,0 +1,29 @@ + + + + + Id History + + + Id + + study + Animal + Id + Id + + + + Type + + ehr_lookups + id_history_type + Value + Title + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/Lot.query.xml b/nbri_ehr/resources/queries/nbri_ehr/Lot.query.xml new file mode 100644 index 0000000..a5de660 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/Lot.query.xml @@ -0,0 +1,20 @@ + + + + + Animal Lot + + + Animal Shipment + + nbri_ehr + AnimalShipment + AnimalShipmentId + AnimalShipmentId + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/ProtocolEsig.query.xml b/nbri_ehr/resources/queries/nbri_ehr/ProtocolEsig.query.xml new file mode 100644 index 0000000..366d740 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/ProtocolEsig.query.xml @@ -0,0 +1,31 @@ + + + + + Protocol ESignature + + + + Esig Id + + + Esig Event + + ehr_lookups + esig_events + value + title + + + + User Profile + http://www.labkey.org/types#userId + + + Esig Date + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/ProtocolProcedures.query.xml b/nbri_ehr/resources/queries/nbri_ehr/ProtocolProcedures.query.xml new file mode 100644 index 0000000..27ee2e0 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/ProtocolProcedures.query.xml @@ -0,0 +1,21 @@ + + + + + Protocol Procedures + + + + Procedures + + ehr_lookups + procedures + name + name + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/ProtocolStress.query.xml b/nbri_ehr/resources/queries/nbri_ehr/ProtocolStress.query.xml new file mode 100644 index 0000000..2b1ca94 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/ProtocolStress.query.xml @@ -0,0 +1,21 @@ + + + + + Protocol Stress + + + + Stress + + nbri_ehr + Stress + StressId + Name + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/QuestionResponse.js b/nbri_ehr/resources/queries/nbri_ehr/QuestionResponse.js new file mode 100644 index 0000000..aa03638 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/QuestionResponse.js @@ -0,0 +1,35 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_INSERT, 'nbri_ehr', 'QuestionResponse', function (helper, scriptErrors, row, oldRow) { + + if (row.Response) { + plainTextParts = row.Response.split("\\loch\\af0") + let plainText = ""; + for(let i = 1; i < plainTextParts.length; i++) + { + let chunk = LABKEY.Utils.encodeHtml(plainTextParts[i].split("}")[0]); + chunk = chunk.replace("\\hich\\af0 \\'85", "…"); // ellipsis + chunk = chunk.replace("\\hich\\af0 \\'92", "'"); + chunk = chunk.replace("\\hich\\af0 \\'93", "\""); + chunk = chunk.replace("\\hich\\af0 \\'94", "\""); + chunk = chunk.replace("\\hich\\af0 \\'99", "™"); // trademark + chunk = chunk.replace("\\hich\\af0 \\'ae", "®"); // registered trademark + chunk = chunk.replace("\\hich\\af0 \\'b0", "°"); // Degree sign + chunk = chunk.replace("\\hich\\af0 \\'b5", "µ"); // Micro sign (Greek mu) + chunk = chunk.replace("\\hich\\af0 \\'b7", "·"); // Middle dot + chunk = chunk.replace("\\hich\\af0 \\'ef", "ï"); // i-diaeresis + // TODO: As a general catch all, could convert the hex value in the match to the HTML ascii entity + // Currently this covers all the cases though in the source data + + plainText += chunk.trim(); + plainText += " "; + } + row.Response = plainText.trim(); + } + +}); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/QuestionResponse.query.xml b/nbri_ehr/resources/queries/nbri_ehr/QuestionResponse.query.xml new file mode 100644 index 0000000..218470d --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/QuestionResponse.query.xml @@ -0,0 +1,38 @@ + + + + + Question Response + + + Protocol + + ehr + protocol + objectid + protocol + + + + Question + + nbri_ehr + Question + QuestionId + Text + + + + Questionnaire + + ehr_lookups + questionnaire + value + title + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/casesSource.sql b/nbri_ehr/resources/queries/nbri_ehr/casesSource.sql new file mode 100644 index 0000000..7055821 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/casesSource.sql @@ -0,0 +1,19 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +-- Only used for ETL from staging table to cases table +SELECT objectid, + Id, + date, + performedby, + openRemark, + closeRemark, + openDiagnosis, + closeDiagnosis, + enddate, + 'Clinical' as category, + attachmentFile +FROM CasesTemp +WHERE category = 'Presenting Diagnosis' AND (openRemark IS NULL OR openRemark NOT LIKE 'Error:%') \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/casesTemp.js b/nbri_ehr/resources/queries/nbri_ehr/casesTemp.js new file mode 100644 index 0000000..58e77be --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/casesTemp.js @@ -0,0 +1,42 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); + +var prevRow; + +function getEnddate(row, enddate){ + var closeDate = new Date(enddate); + + if (row.enddate) { + var deathOrDep = new Date(row.enddate); + + if (deathOrDep < closeDate) + return deathOrDep; + } + return EHR.Server.Utils.datetimeToString(closeDate); +} + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_INSERT, 'nbri_ehr', 'casesTemp', function (helper, scriptErrors, row, oldRow) { + + // Align resolved cases with case openings + if (helper.isETL()) { + if (prevRow && prevRow.Id == row.Id) { + if (row.category == "Presenting Diagnosis" && prevRow.category == "Presenting Diagnosis") { + row.openRemark = "Error: Consecutive Presenting Diagnosis" + } + else if (row.category == "Clinical Resolution" && prevRow.category == "Clinical Resolution") { + row.openRemark = "Error: Consecutive Clinical Resolution" + } + else if (row.category == "Presenting Diagnosis") { + row.closeRemark = prevRow.closeRemark || null; + row.closeDiagnosis = prevRow.closeDiagnosis || null; + row.enddate = getEnddate(row, prevRow.date); + } + } + + prevRow = row; + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/dateRange.sql b/nbri_ehr/resources/queries/nbri_ehr/dateRange.sql new file mode 100644 index 0000000..a9aa810 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/dateRange.sql @@ -0,0 +1,25 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +PARAMETERS(StartDate TIMESTAMP, NumDays INTEGER DEFAULT 1) + +SELECT +i.date, +CAST(i.date as date) as dateOnly, +cast(dayofyear(i.date) as integer) as DayOfYear, +cast(dayofmonth(i.date) as integer) as DayOfMonth, +cast(dayofweek(i.date) as integer) as DayOfWeek, +ceiling(cast(dayofmonth(i.date) as float) / 7.0) as WeekOfMonth, +cast(week(i.date) as integer) as WeekOfYear, +CAST(StartDate AS TIMESTAMP) as startDate @hidden, +cast(NumDays as integer) as numDays @hidden + +FROM (SELECT + +timestampadd('SQL_TSI_DAY', i.value, CAST(COALESCE(CAST(StartDate as date), curdate()) AS TIMESTAMP)) as date + +FROM ldk.integers i + +WHERE i.value < NumDays) i diff --git a/nbri_ehr/resources/queries/nbri_ehr/locationTypes/.qview.xml b/nbri_ehr/resources/queries/nbri_ehr/locationTypes/.qview.xml new file mode 100644 index 0000000..b1d4016 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/locationTypes/.qview.xml @@ -0,0 +1,5 @@ + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/locations.query.xml b/nbri_ehr/resources/queries/nbri_ehr/locations.query.xml new file mode 100644 index 0000000..3f4fe51 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/locations.query.xml @@ -0,0 +1,19 @@ + + + + + + + Location Type + + nbri_ehr + locationTypes + locationTypeId + name + + + +
+ + + diff --git a/nbri_ehr/resources/queries/nbri_ehr/locations/.qview.xml b/nbri_ehr/resources/queries/nbri_ehr/locations/.qview.xml new file mode 100644 index 0000000..08af13d --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/locations/.qview.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/locationsMapping.query.xml b/nbri_ehr/resources/queries/nbri_ehr/locationsMapping.query.xml new file mode 100644 index 0000000..d2357c7 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/locationsMapping.query.xml @@ -0,0 +1,28 @@ + + + + + + + Location + + nbri_ehr + locations + locationId + name + + + + Parent Location + + nbri_ehr + locations + locationId + name + + + +
+ + + diff --git a/nbri_ehr/resources/queries/nbri_ehr/locationsMapping/.qview.xml b/nbri_ehr/resources/queries/nbri_ehr/locationsMapping/.qview.xml new file mode 100644 index 0000000..6496f3b --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/locationsMapping/.qview.xml @@ -0,0 +1,7 @@ + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/necropsyTasks.query.xml b/nbri_ehr/resources/queries/nbri_ehr/necropsyTasks.query.xml new file mode 100644 index 0000000..578d354 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/necropsyTasks.query.xml @@ -0,0 +1,28 @@ + + + + + + Necropsies + + + + + + + + FBEC5D + + + + + + FBEC5D + + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/necropsyTasks.sql b/nbri_ehr/resources/queries/nbri_ehr/necropsyTasks.sql new file mode 100644 index 0000000..b428c81 --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/necropsyTasks.sql @@ -0,0 +1,26 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + t.taskid, + d.Id AS animalId, + t.updateTitle AS form, + t.assignedTo, + t.created, + t.createdBy, + t.modified, + t.modifiedBy, + CASE WHEN t.qcstate.Label = 'Request: Pending' THEN 'Death Entered: Necropsy Pending' + WHEN t.qcstate.Label = 'Review Required' THEN 'Necropsy Entered: Review Required' + ELSE t.qcstate.Label + END AS status, + CASE WHEN t.qcstate.Label = 'Request: Pending' THEN 1 + WHEN t.qcstate.Label = 'Review Required' THEN 2 + WHEN t.qcstate.Label = 'Completed' THEN 3 + ELSE 4 + END AS statusOrder +FROM ehr.tasks t +LEFT JOIN study.deaths d ON d.taskid = t.taskid +WHERE formType = 'Necropsy' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/necropsyTasks/.qview.xml b/nbri_ehr/resources/queries/nbri_ehr/necropsyTasks/.qview.xml new file mode 100644 index 0000000..908527e --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/necropsyTasks/.qview.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/staff.query.xml b/nbri_ehr/resources/queries/nbri_ehr/staff.query.xml new file mode 100644 index 0000000..c39c37c --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/staff.query.xml @@ -0,0 +1,128 @@ + + + + + Staff + + + First Name + + + Last Name + + + Middle Name + + + Display Name + + + Hire Date + + + Last Employ Date + + + Office Phone + + + Office Phone Ext + + + Office Fax + + + Home Phone + + + Beeper Phone + + + Cell Phone + + + Emergency Contact + + + Emergency Phone + + + Home Address 1 + + + Home Address2 + + + Home City + + + Home State + + + Home Zip + + + Home Zip Ext + + + Home Country + + + Office Address 1 + + + Office Address 2 + + + Office City + + + Office State + + + Office Zip + + + Office Zip Ext + + + Office Country + + + Birth Date + + + High School Name + + + College Grad Date + + + College Degree + + + College Major + + + College Name + + + Supervisor + + nbri_ehr + staff + staffId + displayName + + + + Position Name + + + Position Description + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/nbri_ehr/stress.query.xml b/nbri_ehr/resources/queries/nbri_ehr/stress.query.xml new file mode 100644 index 0000000..590673d --- /dev/null +++ b/nbri_ehr/resources/queries/nbri_ehr/stress.query.xml @@ -0,0 +1,20 @@ + + + + + Stress Levels + + + Regulatory Stress Level + + ehr_lookups + regulatory_stress_levels + value + title + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/AcquisitionReport.sql b/nbri_ehr/resources/queries/study/AcquisitionReport.sql new file mode 100644 index 0000000..0f86bec --- /dev/null +++ b/nbri_ehr/resources/queries/study/AcquisitionReport.sql @@ -0,0 +1,14 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT d.Id, + d.gender, + d.species, + d.Birth, + d.Id.MostRecentArrival.Center_Arrival, + cpp.project +FROM study.demographics d + LEFT JOIN CurrentProtocolProjectReport cpp ON cpp.Id = d.Id +ORDER BY d.Id ASC \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/AcquisitionReportBySpecies.sql b/nbri_ehr/resources/queries/study/AcquisitionReportBySpecies.sql new file mode 100644 index 0000000..03dbac6 --- /dev/null +++ b/nbri_ehr/resources/queries/study/AcquisitionReportBySpecies.sql @@ -0,0 +1,18 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +PARAMETERS(StartDate TIMESTAMP, EndDate TIMESTAMP, Project VARCHAR) + +SELECT s.species, s.project, s.speciesName, COUNT(*) as Total FROM + ( + SELECT + species, + species.scientific_name AS speciesName, + Center_Arrival, + project + FROM study.AcquisitionReport ar + WHERE CAST(COALESCE(StartDate, '1900-01-01') as date) <= ar.Center_Arrival AND CAST(COALESCE(EndDate, curdate()) as date) >= CAST(ar.Center_Arrival as date) AND Project = ar.project + ) s +GROUP BY s.species, s.project, s.speciesName \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/BehaviorClinRemarks.sql b/nbri_ehr/resources/queries/study/BehaviorClinRemarks.sql new file mode 100644 index 0000000..fbd179d --- /dev/null +++ b/nbri_ehr/resources/queries/study/BehaviorClinRemarks.sql @@ -0,0 +1,7 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT * FROM study.clinremarks +WHERE category = 'Behavior' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/BehaviorClinRemarks/.qview.xml b/nbri_ehr/resources/queries/study/BehaviorClinRemarks/.qview.xml new file mode 100644 index 0000000..4e381e4 --- /dev/null +++ b/nbri_ehr/resources/queries/study/BehaviorClinRemarks/.qview.xml @@ -0,0 +1,16 @@ + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/ClinicalClinRemarks.sql b/nbri_ehr/resources/queries/study/ClinicalClinRemarks.sql new file mode 100644 index 0000000..9584233 --- /dev/null +++ b/nbri_ehr/resources/queries/study/ClinicalClinRemarks.sql @@ -0,0 +1,7 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT * FROM study.clinremarks +WHERE category = 'Clinical' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/ClinicalClinRemarks/.qview.xml b/nbri_ehr/resources/queries/study/ClinicalClinRemarks/.qview.xml new file mode 100644 index 0000000..c3ca1ea --- /dev/null +++ b/nbri_ehr/resources/queries/study/ClinicalClinRemarks/.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/CurrentProtocolProjectReport.sql b/nbri_ehr/resources/queries/study/CurrentProtocolProjectReport.sql new file mode 100644 index 0000000..c8478fb --- /dev/null +++ b/nbri_ehr/resources/queries/study/CurrentProtocolProjectReport.sql @@ -0,0 +1,17 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +SELECT DISTINCT Id, protocol.title as protocol, project FROM + ( + SELECT DISTINCT d.Id, + a.project.name as project, a.enddate AS projectenddate, + pa.protocol, pa.enddate AS protocolenddate + FROM study.demographics d + JOIN study.assignment a ON a.Id = d.Id + JOIN study.protocolAssignment pa ON pa.Id = d.Id + WHERE a.enddate IS NULL + ) sub +WHERE sub.protocolenddate IS NULL \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/MHC.js b/nbri_ehr/resources/queries/study/MHC.js new file mode 100644 index 0000000..1c4b50a --- /dev/null +++ b/nbri_ehr/resources/queries/study/MHC.js @@ -0,0 +1,7 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +require("ehr/triggers").initScript(this); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/MHC.query.xml b/nbri_ehr/resources/queries/study/MHC.query.xml new file mode 100644 index 0000000..c513a9e --- /dev/null +++ b/nbri_ehr/resources/queries/study/MHC.query.xml @@ -0,0 +1,14 @@ + + + + + + + false + false + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/Pedigree.sql b/nbri_ehr/resources/queries/study/Pedigree.sql new file mode 100644 index 0000000..fa450ba --- /dev/null +++ b/nbri_ehr/resources/queries/study/Pedigree.sql @@ -0,0 +1,31 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + + d.id as Id, + d.dam as Dam, + d.sire as Sire, + d.modified, + + CASE (d.id.demographics.gender.meaning) + WHEN 'male' THEN 1 + WHEN 'female' THEN 2 + ELSE 3 + END AS gender, + d.id.demographics.gender.meaning as gender_code, + CASE (d.id.demographics.calculated_status) + WHEN 'Alive' THEN 0 + ELSE 1 + END + AS status, + d.id.demographics.calculated_status as status_code, + d.id.demographics.species.common_name as species, + '' as Display, + 'Demographics' as source, + d.modified + +FROM study.demographics d +WHERE d.Dam IS NOT NULL OR d.Sire IS NOT NULL diff --git a/nbri_ehr/resources/queries/study/Weight.js b/nbri_ehr/resources/queries/study/Weight.js new file mode 100644 index 0000000..2694fe9 --- /dev/null +++ b/nbri_ehr/resources/queries/study/Weight.js @@ -0,0 +1,91 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); + +function onInit(event, helper){ + helper.decodeExtraContextProperty('skipIdNotFoundError'); + + if (helper.getProperty('skipIdNotFoundError')['form'] === 'arrival'|| + helper.getProperty('skipIdNotFoundError')['form'] === 'birth') { + helper.setScriptOptions({ + allowAnyId: true + }); + } + + helper.registerRowProcessor(function(helper, row){ + if (!row) + return; + + if (!row.Id || !row.weight){ + return; + } + + var weightInTransaction = helper.getProperty('weightInTransaction'); + weightInTransaction = weightInTransaction || {}; + weightInTransaction[row.Id] = weightInTransaction[row.Id] || []; + + var shouldAdd = true; + if (row.objectid){ + LABKEY.ExtAdapter.each(weightInTransaction[row.Id], function(r){ + if (r.objectid == row.objectid){ + if (r.weight != row.weight){ + r.weight = row.weight; + } + else { + shouldAdd = false; + return false; + } + } + }, this); + } + + if (shouldAdd){ + weightInTransaction[row.Id].push({ + objectid: row.objectid, + date: row.date, + qcstate: row.QCState, + weight: row.weight + }); + } + + helper.setProperty('weightInTransaction', weightInTransaction); + }); +} + +function onUpsert(helper, scriptErrors, row, oldRow){ + if (!row.weight){ + EHR.Server.Utils.addError(scriptErrors, 'weight', 'This field is required', 'WARN'); + } + + // warn if more than 10% different from last weight + // the highest error this can produce is WARN. therefore skip this check if we would ignore it anyway in order to save the overhead. + // this would normally occur when finalizing a form + if (!helper.isETL() && row.Id && row.weight && EHR.Server.Utils.shouldIncludeError('WARN', helper.getErrorThreshold(), helper)){ + EHR.Server.Utils.findDemographics({ + participant: row.Id, + helper: helper, + scope: this, + callback: function(data){ + if (!data) + return; + + if (data.mostRecentWeight && (row.weight <= data.mostRecentWeight * 0.9)){ + EHR.Server.Utils.addError(scriptErrors, 'weight', 'Weight drop of >10%. Last weight ' + data.mostRecentWeight + ' kg', 'INFO'); + } + else if (data.mostRecentWeight && (row.weight >= data.mostRecentWeight / 0.9)){ + EHR.Server.Utils.addError(scriptErrors, 'weight', 'Weight gain of >10%. Last weight ' + data.mostRecentWeight + ' kg', 'INFO'); + } + + if (data && data.species){ + var msg = helper.getJavaHelper().verifyWeightRange(row.id, row.weight, data.species); + if (msg != null){ + EHR.Server.Utils.addError(scriptErrors, 'weight', msg, 'WARN'); + } + } + } + }); + } +} \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeAssignments.sql b/nbri_ehr/resources/queries/study/activeAssignments.sql new file mode 100644 index 0000000..6361e73 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeAssignments.sql @@ -0,0 +1,22 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT pa.Id, + pa.protocol.title AS protocolTitle, + pa.protocol.InvestigatorId AS investigatorId, + pa.protocol.InvestigatorId.DisplayName AS investigatorName, + pa.protocol.InvestigatorId.LastName AS investigatorLastName, + a.project.name AS project, + a.isActive AS isActiveAssignment, + pa.isActive AS isActiveProtocolAssignment, + a.qcstate.publicData AS isPublicAssignment, + pa.qcstate.publicData AS isPublicProtocolAssignment + + FROM protocolAssignment pa +FULL OUTER JOIN assignment a ON pa.Id = a.Id +WHERE pa.isActive = true AND + a.isActive = true AND + a.qcstate.publicData = true AND + pa.qcstate.publicData = true diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases.sql b/nbri_ehr/resources/queries/study/activeBehaviorCases.sql new file mode 100644 index 0000000..fab5ea2 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases.sql @@ -0,0 +1,7 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT * FROM study.cases +WHERE category = 'Behavior' AND isOpen = TRUE \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/.qview.xml new file mode 100644 index 0000000..b08797c --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/.qview.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Area 11.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Area 11.qview.xml new file mode 100644 index 0000000..edcb23f --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Area 11.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Area 51.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Area 51.qview.xml new file mode 100644 index 0000000..d1274dc --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Area 51.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 10.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 10.qview.xml new file mode 100644 index 0000000..2aa8535 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 10.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 10C.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 10C.qview.xml new file mode 100644 index 0000000..8136896 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 10C.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 27.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 27.qview.xml new file mode 100644 index 0000000..b369423 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 27.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 28.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 28.qview.xml new file mode 100644 index 0000000..7cd8a6d --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 28.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 29.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 29.qview.xml new file mode 100644 index 0000000..6798f6c --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 29.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 30.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 30.qview.xml new file mode 100644 index 0000000..8225a43 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 30.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 31.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 31.qview.xml new file mode 100644 index 0000000..2bdc6ca --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 31.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 31C.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 31C.qview.xml new file mode 100644 index 0000000..e86d068 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 31C.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 31D.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 31D.qview.xml new file mode 100644 index 0000000..c75ade9 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 31D.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 32.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 32.qview.xml new file mode 100644 index 0000000..4fafe49 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 32.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 34.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 34.qview.xml new file mode 100644 index 0000000..19c1701 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 34.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 37.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 37.qview.xml new file mode 100644 index 0000000..d22bd89 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 37.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 41.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 41.qview.xml new file mode 100644 index 0000000..5eaf22e --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 41.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 42.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 42.qview.xml new file mode 100644 index 0000000..5598b7c --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 42.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 43.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 43.qview.xml new file mode 100644 index 0000000..d864dbe --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 43.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 44.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 44.qview.xml new file mode 100644 index 0000000..3c0e4c6 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 44.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 45.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 45.qview.xml new file mode 100644 index 0000000..49d52f6 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 45.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 46.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 46.qview.xml new file mode 100644 index 0000000..9944c43 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 46.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 50.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 50.qview.xml new file mode 100644 index 0000000..7e86728 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 50.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 52.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 52.qview.xml new file mode 100644 index 0000000..7860808 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 52.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 53.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 53.qview.xml new file mode 100644 index 0000000..7c63231 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 53.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 54A.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 54A.qview.xml new file mode 100644 index 0000000..b2f3a2b --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 54A.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 54B.qview.xml b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 54B.qview.xml new file mode 100644 index 0000000..449c6ac --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeBehaviorCases/Building 54B.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases.sql b/nbri_ehr/resources/queries/study/activeClinicalCases.sql new file mode 100644 index 0000000..63be8fa --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases.sql @@ -0,0 +1,7 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT * FROM study.cases +WHERE category = 'Clinical' AND isOpen = TRUE \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/.qview.xml new file mode 100644 index 0000000..b08797c --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/.qview.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Area 11.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Area 11.qview.xml new file mode 100644 index 0000000..edcb23f --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Area 11.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Area 51.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Area 51.qview.xml new file mode 100644 index 0000000..d1274dc --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Area 51.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 10.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 10.qview.xml new file mode 100644 index 0000000..1bf0575 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 10.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 10C.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 10C.qview.xml new file mode 100644 index 0000000..8136896 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 10C.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 27.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 27.qview.xml new file mode 100644 index 0000000..b369423 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 27.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 28.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 28.qview.xml new file mode 100644 index 0000000..7cd8a6d --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 28.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 29.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 29.qview.xml new file mode 100644 index 0000000..6798f6c --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 29.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 30.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 30.qview.xml new file mode 100644 index 0000000..8225a43 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 30.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 31.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 31.qview.xml new file mode 100644 index 0000000..2bdc6ca --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 31.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 31C.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 31C.qview.xml new file mode 100644 index 0000000..e86d068 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 31C.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 31D.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 31D.qview.xml new file mode 100644 index 0000000..c75ade9 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 31D.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 32.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 32.qview.xml new file mode 100644 index 0000000..4fafe49 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 32.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 34.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 34.qview.xml new file mode 100644 index 0000000..19c1701 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 34.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 37.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 37.qview.xml new file mode 100644 index 0000000..d22bd89 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 37.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 41.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 41.qview.xml new file mode 100644 index 0000000..5eaf22e --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 41.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 42.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 42.qview.xml new file mode 100644 index 0000000..5598b7c --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 42.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 43.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 43.qview.xml new file mode 100644 index 0000000..d864dbe --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 43.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 44.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 44.qview.xml new file mode 100644 index 0000000..3c0e4c6 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 44.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 45.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 45.qview.xml new file mode 100644 index 0000000..49d52f6 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 45.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 46.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 46.qview.xml new file mode 100644 index 0000000..9944c43 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 46.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 50.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 50.qview.xml new file mode 100644 index 0000000..7e86728 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 50.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 52.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 52.qview.xml new file mode 100644 index 0000000..7860808 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 52.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 53.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 53.qview.xml new file mode 100644 index 0000000..7c63231 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 53.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 54A.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 54A.qview.xml new file mode 100644 index 0000000..b2f3a2b --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 54A.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeClinicalCases/Building 54B.qview.xml b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 54B.qview.xml new file mode 100644 index 0000000..449c6ac --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeClinicalCases/Building 54B.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeProjectsFromHousing.sql b/nbri_ehr/resources/queries/study/activeProjectsFromHousing.sql new file mode 100644 index 0000000..e3af892 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeProjectsFromHousing.sql @@ -0,0 +1,10 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + Id.activeProjectAssignments.project, + COUNT(*) as Total +FROM housing +GROUP BY Id.activeProjectAssignments.project \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/activeTreatmentOrders.sql b/nbri_ehr/resources/queries/study/activeTreatmentOrders.sql new file mode 100644 index 0000000..bd47d25 --- /dev/null +++ b/nbri_ehr/resources/queries/study/activeTreatmentOrders.sql @@ -0,0 +1,25 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + Id, + date, + enddate, + code, + frequency, + route, + volume, + vol_units, + amount, + amount_units, + concentration, + conc_units, + dosage, + dosage_units, + performedBy, + description, + remark +FROM treatment_order +WHERE enddate IS NULL OR enddate >= NOW() -- calculated col. isActive is false when the enddate is in the future, so using this condition instead \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/alias.js b/nbri_ehr/resources/queries/study/alias.js new file mode 100644 index 0000000..f4d5931 --- /dev/null +++ b/nbri_ehr/resources/queries/study/alias.js @@ -0,0 +1,6 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/alias.query.xml b/nbri_ehr/resources/queries/study/alias.query.xml new file mode 100644 index 0000000..c67c110 --- /dev/null +++ b/nbri_ehr/resources/queries/study/alias.query.xml @@ -0,0 +1,29 @@ + + + + + + + + + + + + + + Type + + ehr_lookups + alias_category + value + title + + + + Alias + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/aliases.sql b/nbri_ehr/resources/queries/study/aliases.sql new file mode 100644 index 0000000..98a5e77 --- /dev/null +++ b/nbri_ehr/resources/queries/study/aliases.sql @@ -0,0 +1,19 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +-- This query is used to match upper and lowercase names in animal history + +SELECT Id, + Id as alias +FROM study.Animal where Dataset.Demographics.calculated_status != 'Alive - In Progress' +UNION +SELECT Id, + Name as alias +FROM nbri_ehr.IdHistory +UNION +SELECT Id, + Alias as alias +FROM study.alias where Id.demographics.calculated_status != 'Alive - In Progress' +' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/alopecia/.qview.xml b/nbri_ehr/resources/queries/study/alopecia/.qview.xml new file mode 100644 index 0000000..f889f92 --- /dev/null +++ b/nbri_ehr/resources/queries/study/alopecia/.qview.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/arrival.js b/nbri_ehr/resources/queries/study/arrival.js new file mode 100644 index 0000000..6f1757c --- /dev/null +++ b/nbri_ehr/resources/queries/study/arrival.js @@ -0,0 +1,176 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); + +var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_UPSERT, 'study', 'Arrival', function(helper, scriptErrors, row, oldRow) { + + if(!row.rearrival){ + helper.setScriptOptions({requiresStatusRecalc: true}); + } + + // Due to order of operation, this needs to be done in upsert instead of insert + if (!row.rearrival && helper.getEvent() == 'insert' && row.Id && triggerHelper.animalIdExists(row.Id)) { + EHR.Server.Utils.addError(scriptErrors, 'Id', 'Animal Id ' + row.Id + ' is already in use. Please use a different Id.', 'ERROR'); + } + + if (row.eventDate) { + row.date = row.eventDate; + } + + helper.registerArrival(row.Id, row.date); + + //Insert or update demographic and birth records + if (!row.rearrival && !helper.isETL() && !helper.isGeneratedByServer() && !helper.isValidateOnly()) { + + // this allows demographic records in qcstates other than completed + var extraDemographicsFieldMappings = { + 'taskid': row.taskid, + 'qcstate': helper.getJavaHelper().getQCStateForLabel(row.QCStateLabel).getRowId() + } + + // null (not undefined) required for call to java trigger helper + row.dam = row['Id/demographics/dam'] || null; + row.sire = row['Id/demographics/sire'] || null; + row.species = row['Id/demographics/species'] || null; + row.birth = row['Id/demographics/birth'] || null; + row.gender = row['Id/demographics/gender'] || null; + row.geographic_origin = row['Id/demographics/geographic_origin'] || null; + row.source = row.sourceFacility || null; + + if (row.QCStateLabel) { + row.qcstate = helper.getJavaHelper().getQCStateForLabel(row.QCStateLabel).getRowId(); + } + + if (row.birth) { + var birthInfo = { + Id: row.Id, + date: row.birth, + qcstate: row.qcstate, + taskid: row.taskid, + performedby: row.performedby + } + + var birthErrors = triggerHelper.saveBirthRecord(row.Id, birthInfo); + if (birthErrors){ + EHR.Server.Utils.addError(scriptErrors, 'birth', birthErrors, 'ERROR'); + } + } + + if (row.Id && row.date) { + + let assignmentRec = { + Id: row.Id, + date: row.date, + taskid: row.taskid, + remark: row.remark, + qcstate: row.qcstate, + performedby: row.performedby + } + + if (row.project) { + assignmentRec['project'] = row.project; + triggerHelper.createAssignmentRecord("assignment", row.Id, assignmentRec); + } + + if (row.arrivalProtocol) { + assignmentRec['protocol'] = row.arrivalProtocol; + triggerHelper.createAssignmentRecord("protocolAssignment", row.Id, assignmentRec); + } + } + + // if 'cage', labeled as "Initial Location" is provided, then insert into housing. + if (row.cage && row.Id && row.date) { + var housingRec = { + Id: row.Id, + date: row.date, + cage: row.cage, + taskid: row.taskid, + qcstate: row.qcstate, + reason: row.arrivalType, + performedby: row.performedby + } + + var housingErrors = triggerHelper.createHousingRecord(row.Id, housingRec, "arrival"); + if (housingErrors) { + EHR.Server.Utils.addError(scriptErrors, 'Id', housingErrors, 'ERROR'); + } + } + + row.calculated_status = (row.QCStateLabel.toUpperCase() === 'IN PROGRESS' || row.QCStateLabel.toUpperCase() === 'REVIEW REQUIRED') ? 'Alive - In Progress' : 'Alive'; + + if(!oldRow) { + //if not already present, insert into demographics + helper.getJavaHelper().createDemographicsRecord(row.Id, row, extraDemographicsFieldMappings); + } + else { + //Update demographics records + var ar = helper.getJavaHelper().getDemographicRecord(row.id); + var data = ar || {}; + + var obj = {}; + var hasUpdates = false; + + if (row.gender && row.gender !== data.gender ) + { + obj.gender = row.gender; + hasUpdates = true; + } + + if (row.species && row.species !== data.species ) + { + obj.species = row.species; + hasUpdates = true; + } + + if (row.geographic_origin && row.geographic_origin !== data.geographic_origin ) + { + obj.geographic_origin = row.geographic_origin; + hasUpdates = true; + } + + if (row.birth && row.birth !== data.birth) + { + obj.birth = row.birth; + hasUpdates = true; + } + + if (row.sire && row.sire !== data.sire) + { + obj.sire = row.sire; + hasUpdates = true; + } + + if (row.dam && row.dam !== data.dam) + { + obj.dam = row.dam; + hasUpdates = true; + } + + if (row.QCStateLabel && row.QCStateLabel !== data.QCStateLabel) + { + obj.QCStateLabel = row.QCStateLabel; + hasUpdates = true; + } + + if (row.performedby && row.performedby !== data.performedby) + { + obj.performedby = row.performedby; + hasUpdates = true; + } + + if (hasUpdates) + { + console.info("Arrival update for animal Id " + row.Id + " included demographic changes Demographic record updated."); + obj.Id = row.Id; + var demographicsUpdates = [obj]; + helper.getJavaHelper().updateDemographicsRecord(demographicsUpdates); + helper.cacheDemographics(row.Id, row); + } + } + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/arrival.query.xml b/nbri_ehr/resources/queries/study/arrival.query.xml new file mode 100644 index 0000000..ffe2108 --- /dev/null +++ b/nbri_ehr/resources/queries/study/arrival.query.xml @@ -0,0 +1,79 @@ + + + + + + + + + + + + + Arrival Date + + + Arrival Type + + ehr_lookups + arrival_type + value + + + + Acquisition Type + + ehr_lookups + acquisition_type + value + + + + true + + + 80 + Initial Location + true + true + + ehr_lookups + cage + location + cage + + + + Project + + ehr + project + project + name + + + + Protocol + + ehr + protocol + protocol + title + + + + Source Facility + + ehr_lookups + source + meaning + + + + Rearrival + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/arrival/.qview.xml b/nbri_ehr/resources/queries/study/arrival/.qview.xml new file mode 100644 index 0000000..9aa2dd4 --- /dev/null +++ b/nbri_ehr/resources/queries/study/arrival/.qview.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/assignment.js b/nbri_ehr/resources/queries/study/assignment.js new file mode 100644 index 0000000..512b732 --- /dev/null +++ b/nbri_ehr/resources/queries/study/assignment.js @@ -0,0 +1,91 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); +var projectData = {}; +var prevAnimalId; +var prevDate; +var count = 0; + +function getLastAssignment(id){ + var batchLatestEnddate; + + LABKEY.Query.selectRows({ + schemaName: 'study', + queryName: 'assignment', + columns: 'Id,enddate', + filterArray: [LABKEY.Filter.create('Id', id)], + sort: '-enddate', + success: function (results) { + if (results.rows.length) { + batchLatestEnddate = results.rows[0].enddate; + } + }, + scope: this + }); + + return batchLatestEnddate; +} + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'assignment', function(event, helper){ + + if (helper.isETL()) { + LABKEY.Query.selectRows({ + schemaName: 'ehr', + queryName: 'project', + columns: 'project,name', + success: function (results) { + if (results.rows.length) { + for (var i = 0; i < results.rows.length; i++) { + let rec = results.rows[i]; + projectData[rec.name] = rec.project; + } + } + }, + scope: this + }); + } +}); + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_INSERT, 'study', 'assignment', function (helper, scriptErrors, row, oldRow) { + + if (helper.isETL()) { + if (prevAnimalId === row.Id) { + row.date = prevDate; + } + else if (count === 0) { + // This handles batch boundary row for full truncate ETL, which is the only ETL setup for this currently. + // Gets previous enddate from db for first row + var batchLatestEnddate = getLastAssignment(row.Id); + if (batchLatestEnddate) { + row.date = batchLatestEnddate; + } + } + + if (!row.projectName) { + console.log("project name is missing for Id: " + row.Id); + } + else { + var projectName = row.projectName.split(' ' + row.Id)[0]; + var projectId = projectData[projectName]; + + if (projectId) { + row.project = projectId; + } + else { + row.description = projectName; + console.log("project cannot be found: " + projectName + " for Id: " + row.Id); + } + } + prevAnimalId = row.Id; + if (!(!row.endDate || row.endDate === 'undefined')) { + prevDate = row.endDate; + } + + count++; + } + +}); + diff --git a/nbri_ehr/resources/queries/study/assignment.query.xml b/nbri_ehr/resources/queries/study/assignment.query.xml new file mode 100644 index 0000000..1cf7a36 --- /dev/null +++ b/nbri_ehr/resources/queries/study/assignment.query.xml @@ -0,0 +1,28 @@ + + + + + + + + DateTime + + + + + ehr + project + project + name + + + + + + true + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/behaviorCases.sql b/nbri_ehr/resources/queries/study/behaviorCases.sql new file mode 100644 index 0000000..635574c --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases.sql @@ -0,0 +1,7 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT * FROM study.cases +WHERE category = 'Behavior' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/.qview.xml new file mode 100644 index 0000000..b08797c --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/.qview.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Area 11.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Area 11.qview.xml new file mode 100644 index 0000000..edcb23f --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Area 11.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Area 51.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Area 51.qview.xml new file mode 100644 index 0000000..d1274dc --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Area 51.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 10.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 10.qview.xml new file mode 100644 index 0000000..1bf0575 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 10.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 10C.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 10C.qview.xml new file mode 100644 index 0000000..8136896 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 10C.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 27.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 27.qview.xml new file mode 100644 index 0000000..b369423 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 27.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 28.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 28.qview.xml new file mode 100644 index 0000000..7cd8a6d --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 28.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 29.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 29.qview.xml new file mode 100644 index 0000000..6798f6c --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 29.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 30.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 30.qview.xml new file mode 100644 index 0000000..8225a43 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 30.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 31.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 31.qview.xml new file mode 100644 index 0000000..2bdc6ca --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 31.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 31C.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 31C.qview.xml new file mode 100644 index 0000000..e86d068 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 31C.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 31D.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 31D.qview.xml new file mode 100644 index 0000000..c75ade9 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 31D.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 32.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 32.qview.xml new file mode 100644 index 0000000..4fafe49 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 32.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 34.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 34.qview.xml new file mode 100644 index 0000000..19c1701 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 34.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 37.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 37.qview.xml new file mode 100644 index 0000000..d22bd89 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 37.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 41.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 41.qview.xml new file mode 100644 index 0000000..5eaf22e --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 41.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 42.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 42.qview.xml new file mode 100644 index 0000000..5598b7c --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 42.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 43.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 43.qview.xml new file mode 100644 index 0000000..d864dbe --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 43.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 44.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 44.qview.xml new file mode 100644 index 0000000..3c0e4c6 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 44.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 45.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 45.qview.xml new file mode 100644 index 0000000..49d52f6 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 45.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 46.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 46.qview.xml new file mode 100644 index 0000000..9944c43 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 46.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 50.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 50.qview.xml new file mode 100644 index 0000000..7e86728 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 50.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 52.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 52.qview.xml new file mode 100644 index 0000000..7860808 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 52.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 53.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 53.qview.xml new file mode 100644 index 0000000..7c63231 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 53.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 54A.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 54A.qview.xml new file mode 100644 index 0000000..b2f3a2b --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 54A.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorCases/Building 54B.qview.xml b/nbri_ehr/resources/queries/study/behaviorCases/Building 54B.qview.xml new file mode 100644 index 0000000..449c6ac --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorCases/Building 54B.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations.sql b/nbri_ehr/resources/queries/study/behaviorObservations.sql new file mode 100644 index 0000000..38bac33 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations.sql @@ -0,0 +1,7 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT * FROM study.clinical_observations +WHERE type = 'Behavior' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/.qview.xml new file mode 100644 index 0000000..a48d5a5 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/.qview.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Area 11.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Area 11.qview.xml new file mode 100644 index 0000000..02bbb1c --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Area 11.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Area 51.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Area 51.qview.xml new file mode 100644 index 0000000..f1e9bde --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Area 51.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 10.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 10.qview.xml new file mode 100644 index 0000000..6c5a2df --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 10.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 10C.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 10C.qview.xml new file mode 100644 index 0000000..0ebcf0a --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 10C.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 27.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 27.qview.xml new file mode 100644 index 0000000..2760754 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 27.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 28.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 28.qview.xml new file mode 100644 index 0000000..2ed3cc1 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 28.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 29.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 29.qview.xml new file mode 100644 index 0000000..e40c6bf --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 29.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 30.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 30.qview.xml new file mode 100644 index 0000000..8220278 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 30.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 31.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 31.qview.xml new file mode 100644 index 0000000..96f771c --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 31.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 31C.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 31C.qview.xml new file mode 100644 index 0000000..17a41c2 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 31C.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 31D.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 31D.qview.xml new file mode 100644 index 0000000..5d65614 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 31D.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 32.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 32.qview.xml new file mode 100644 index 0000000..284f684 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 32.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 34.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 34.qview.xml new file mode 100644 index 0000000..2ec2783 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 34.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 37.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 37.qview.xml new file mode 100644 index 0000000..4880b02 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 37.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 41.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 41.qview.xml new file mode 100644 index 0000000..fca1205 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 41.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 42.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 42.qview.xml new file mode 100644 index 0000000..2b2ed75 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 42.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 43.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 43.qview.xml new file mode 100644 index 0000000..065334b --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 43.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 44.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 44.qview.xml new file mode 100644 index 0000000..db70e10 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 44.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 45.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 45.qview.xml new file mode 100644 index 0000000..36036ee --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 45.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 46.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 46.qview.xml new file mode 100644 index 0000000..d13731e --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 46.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 50.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 50.qview.xml new file mode 100644 index 0000000..d9d616f --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 50.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 52.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 52.qview.xml new file mode 100644 index 0000000..49b3e35 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 52.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 53.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 53.qview.xml new file mode 100644 index 0000000..4bdb49b --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 53.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 54A.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 54A.qview.xml new file mode 100644 index 0000000..ce9d4e1 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 54A.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/behaviorObservations/Building 54B.qview.xml b/nbri_ehr/resources/queries/study/behaviorObservations/Building 54B.qview.xml new file mode 100644 index 0000000..d0c9046 --- /dev/null +++ b/nbri_ehr/resources/queries/study/behaviorObservations/Building 54B.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/birth.js b/nbri_ehr/resources/queries/study/birth.js new file mode 100644 index 0000000..3801823 --- /dev/null +++ b/nbri_ehr/resources/queries/study/birth.js @@ -0,0 +1,169 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); +EHR.Server.Utils = require("ehr/utils").EHR.Server.Utils; + +var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); + +function onInit(event, helper){ + helper.setScriptOptions({ + allowAnyId: true, + requiresStatusRecalc: true, + allowDeadIds: true, + skipIdFormatCheck: true, + skipHousingCheck: true, + announceAllModifiedParticipants: true, + allowDatesInDistantPast: true, + removeTimeFromDate: true, + skipAssignmentCheck: true, + }); + + helper.decodeExtraContextProperty('birthsInTransaction'); +} + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_UPSERT, 'study', 'birth', function(helper, scriptErrors, row, oldRow) { + + if (!oldRow && row.Id && triggerHelper.birthExists(row.Id)) { + EHR.Server.Utils.addError(scriptErrors, 'Id', 'Birth record already exists for this Id, update existing record to change birth information', 'ERROR'); + } + + if (!helper.isETL()) { + + if (row.QCStateLabel) { + row.qcstate = helper.getJavaHelper().getQCStateForLabel(row.QCStateLabel).getRowId(); + } + + if (row.Id && row.date) { + + let assignmentRec = { + Id: row.Id, + date: row.date, + taskid: row.taskid, + remark: row.remark, + qcstate: row.qcstate, + performedby: row.performedby + } + + if (row.project) { + assignmentRec['project'] = row.project; + triggerHelper.createAssignmentRecord("assignment", row.Id, assignmentRec); + } + + if (row.birthProtocol) { + assignmentRec['protocol'] = row.birthProtocol; + triggerHelper.createAssignmentRecord("protocolAssignment", row.Id, assignmentRec); + } + } + + if (!helper.isGeneratedByServer() && !helper.isValidateOnly()) { + + // if 'cage', labeled as "Birth Location" is provided, then insert into housing. + if (row.cage && row.Id && row.date) { + var housingRec = { + Id: row.Id, + date: row.date, + cage: row.cage, + taskid: row.taskid, + qcstate: row.qcstate, + reason: 'Husbandry', + performedby: row.performedby + } + + var housingErrors = triggerHelper.createHousingRecord(row.Id, housingRec, "birth"); + if (housingErrors) { + EHR.Server.Utils.addError(scriptErrors, 'Id', housingErrors, 'ERROR'); + } + } + + // this allows demographic records in qcstates other than completed + var extraDemographicsFieldMappings = { + 'qcstate': helper.getJavaHelper().getQCStateForLabel(row.QCStateLabel).getRowId() + } + + var calc_status = (row.QCStateLabel.toUpperCase() === 'IN PROGRESS' || row.QCStateLabel.toUpperCase() === 'REVIEW REQUIRED') ? 'Alive - In Progress' : 'Alive'; + + var obj = { + Id: row.Id, + date: row.date, + calculated_status: calc_status, + dam: row['Id/demographics/dam'] || null, + sire: row['Id/demographics/sire'] || null, + species: row['Id/demographics/species'] || null, + birth: row.date || null, + gender: row['Id/demographics/gender'] || null, + taskid: row.taskid, + remark: row.remark, + QCStateLabel: row.QCStateLabel, + performedby: row.performedby + }; + + //find dam, if provided + if (obj.dam && !obj.origin) { + obj.origin = helper.getJavaHelper().getGeographicOrigin(obj.dam); + } + + if (obj.dam && !obj.species) { + obj.species = helper.getJavaHelper().getSpecies(obj.dam); + } + + if (!oldRow) { + //if not already present, we insert into demographics + helper.getJavaHelper().createDemographicsRecord(row.Id, obj, extraDemographicsFieldMappings); + } + else { + //Update demographics records + var ar = helper.getJavaHelper().getDemographicRecord(obj.Id); + var data = ar || {}; + + var record = {}; + var hasUpdates = false; + + if (obj.gender && obj.gender !== data.gender) { + record.gender = obj.gender; + hasUpdates = true; + } + + if (obj.species && obj.species !== data.species) { + record.species = obj.species; + hasUpdates = true; + } + + if (obj.birth && obj.birth !== data.birth) { + record.birth = obj.birth; + hasUpdates = true; + } + + if (obj.sire && obj.sire !== data.sire) { + record.sire = obj.sire; + hasUpdates = true; + } + + if (obj.dam && obj.dam !== data.dam) { + record.dam = obj.dam; + hasUpdates = true; + } + + if (obj.performedby && obj.performedby !== data.performedby) { + record.performedby = obj.performedby; + hasUpdates = true; + } + + if (obj.QCStateLabel && obj.QCStateLabel !== data.QCStateLabel) { + record.QCStateLabel = obj.QCStateLabel; + hasUpdates = true; + } + + if (hasUpdates) { + console.info("Birth update for animal Id " + row.Id + " included demographic changes. Demographic record updated."); + record.Id = obj.Id; + var demographicsUpdates = [record]; + helper.getJavaHelper().updateDemographicsRecord(demographicsUpdates); + helper.cacheDemographics(row.Id, row); + } + } + } + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/birth.query.xml b/nbri_ehr/resources/queries/study/birth.query.xml new file mode 100644 index 0000000..4084988 --- /dev/null +++ b/nbri_ehr/resources/queries/study/birth.query.xml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + Birth Date + + + Birth Location + 80 + true + true + + ehr_lookups + cage + location + cage + + + + Project + + ehr + project + project + name + + + + Protocol + + ehr + protocol + protocol + title + + + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/blood/.qview.xml b/nbri_ehr/resources/queries/study/blood/.qview.xml new file mode 100644 index 0000000..831d6b5 --- /dev/null +++ b/nbri_ehr/resources/queries/study/blood/.qview.xml @@ -0,0 +1,19 @@ + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/bloodDrawChanges.sql b/nbri_ehr/resources/queries/study/bloodDrawChanges.sql new file mode 100644 index 0000000..b550417 --- /dev/null +++ b/nbri_ehr/resources/queries/study/bloodDrawChanges.sql @@ -0,0 +1,66 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +--this query is designed to return any dates when allowable blood draw volume changes +--this includes dates of blood draws, plus the date those draws drop off +PARAMETERS(DATE_INTERVAL INTEGER) + +SELECT + b2.id, + b2.dateOnly, + b2.quantity, + DATE_INTERVAL as blood_draw_interval, + TIMESTAMPADD('SQL_TSI_DAY', (-1 * DATE_INTERVAL), b2.dateOnly) as minDate, + TIMESTAMPADD('SQL_TSI_DAY', DATE_INTERVAL, b2.dateOnly) as maxDate, + +FROM ( + SELECT + b.id, + b.dateOnly, + sum(b.quantity) as quantity + + FROM ( + --find all blood draws within the interval, looking backwards + SELECT + b.id, + b.dateOnly, + b.quantity, + FROM study.blood b + WHERE b.dateOnly > timestampadd('SQL_TSI_DAY', -1 * DATE_INTERVAL, curdate()) + + UNION ALL + + --join 1 row for the current date + SELECT + d1.id, + curdate() as dateOnly, + 0 as quantity, + FROM study.demographics d1 + WHERE d1.calculated_status = 'Alive' + + UNION ALL + + --add one row for each date when the draw drops off the record + SELECT + b.id, + timestampadd('SQL_TSI_DAY', DATE_INTERVAL, b.dateOnly), + 0 as quantity, + FROM study.blood b + WHERE timestampadd('SQL_TSI_DAY', DATE_INTERVAL, b.dateOnly) >= timestampadd('SQL_TSI_DAY', -1 * DATE_INTERVAL, curdate()) + + ) b + + GROUP BY b.id, b.dateOnly + ) b2 \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/breeder/.qview.xml b/nbri_ehr/resources/queries/study/breeder/.qview.xml new file mode 100644 index 0000000..448bd0f --- /dev/null +++ b/nbri_ehr/resources/queries/study/breeder/.qview.xml @@ -0,0 +1,15 @@ + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/cases.js b/nbri_ehr/resources/queries/study/cases.js new file mode 100644 index 0000000..0a14bc7 --- /dev/null +++ b/nbri_ehr/resources/queries/study/cases.js @@ -0,0 +1,71 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +const console = require("console"); +require("ehr/triggers").initScript(this); + +var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); + +function onInit(event, helper) { + helper.decodeExtraContextProperty('ordersInTransaction'); +} + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_UPSERT, 'study', 'cases', function(helper, errors, row, oldRow){ + if (!helper.isETL()) { + var error = false; + if (row.enddate) { + if (!row.closeRemark) { + EHR.Server.Utils.addError(errors, 'closeRemark', 'Close remark required when closing a case.', 'ERROR'); + error = true; + } + + if(!triggerHelper.canCloseCase(row.category)) { + EHR.Server.Utils.addError(errors, 'enddate', 'Veterinarian permission required to close a case.', 'ERROR'); + error = true; + } + } + + if (!row.performedby) { + EHR.Server.Utils.addError(errors, 'performedby', 'Opened By is a required field.', 'ERROR'); + error = true; + } + + if (!helper.isValidateOnly() && row.caseid && row.enddate && oldRow && (row.enddate != oldRow.enddate)) { + triggerHelper.closeDailyClinicalObs(row.caseid, row.enddate); + } + + if (!helper.isValidateOnly() && !error) { + var qc; + if (row.QCStateLabel) { + qc = EHR.Server.Security.getQCStateByLabel(row.QCStateLabel); + } + else if (row.QCState) { + qc = EHR.Server.Security.getQCStateByRowId(row.QCState); + } + + if (!qc) { + console.error('Unable to find QCState: ' + row.QCState + '/' + row.QCStateLabel); + } + else { + + // Don't allow taking an existing non-draft case back to draft + if (oldRow && qc.Label == 'In Progress') { + var oldQc = EHR.Server.Security.getQCStateByLabel(oldRow.QCStateLabel); + if (oldQc.Label != 'In Progress') { + EHR.Server.Utils.addError(errors, null, 'Cannot save a draft copy of a case already opened or in review.', 'ERROR'); + } + } else if (row.category == 'Clinical' && (qc.Label == 'Completed' || qc.Label == 'Review Required') && row.caseid && row.Id && row.performedby && row.taskid && !row.enddate) { + var ordersInTransaction = helper.getProperty('ordersInTransaction'); + var oit = []; + if (ordersInTransaction && ordersInTransaction.length) { + oit = ordersInTransaction; + } + triggerHelper.ensureDailyClinicalObservationOrders(row.Id, row.caseid, row.date, row.performedby, qc.RowId, row.taskid, oit); + } + } + } + } +}); diff --git a/nbri_ehr/resources/queries/study/cases.query.xml b/nbri_ehr/resources/queries/study/cases.query.xml new file mode 100644 index 0000000..b2b7762 --- /dev/null +++ b/nbri_ehr/resources/queries/study/cases.query.xml @@ -0,0 +1,71 @@ + + + + + + + + + + + + + Open Date + + + Close Date + false + + + Problem Area + + ehr_lookups + problem_list_category + value + + + + Problem Subcategory + + ehr_lookups + problem_list_subcategory + value + + + + textarea + 5 + + + Case Plan + textarea + 5 + + + textarea + 5 + + + Opened By + + + Category + true + false + + ehr_lookups + data_category + value + + + + true + + + false + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/cases/.qview.xml b/nbri_ehr/resources/queries/study/cases/.qview.xml new file mode 100644 index 0000000..340d770 --- /dev/null +++ b/nbri_ehr/resources/queries/study/cases/.qview.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/cases/Active Behavior Cases.qview.xml b/nbri_ehr/resources/queries/study/cases/Active Behavior Cases.qview.xml new file mode 100644 index 0000000..8333562 --- /dev/null +++ b/nbri_ehr/resources/queries/study/cases/Active Behavior Cases.qview.xml @@ -0,0 +1,29 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/cases/Active Clinical Cases.qview.xml b/nbri_ehr/resources/queries/study/cases/Active Clinical Cases.qview.xml new file mode 100644 index 0000000..6081418 --- /dev/null +++ b/nbri_ehr/resources/queries/study/cases/Active Clinical Cases.qview.xml @@ -0,0 +1,32 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/cases/All Behavior Cases.qview.xml b/nbri_ehr/resources/queries/study/cases/All Behavior Cases.qview.xml new file mode 100644 index 0000000..261b1bb --- /dev/null +++ b/nbri_ehr/resources/queries/study/cases/All Behavior Cases.qview.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/cases/All Clinical Cases.qview.xml b/nbri_ehr/resources/queries/study/cases/All Clinical Cases.qview.xml new file mode 100644 index 0000000..73fb0b2 --- /dev/null +++ b/nbri_ehr/resources/queries/study/cases/All Clinical Cases.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/chemistryResults.query.xml b/nbri_ehr/resources/queries/study/chemistryResults.query.xml new file mode 100644 index 0000000..caa0e9e --- /dev/null +++ b/nbri_ehr/resources/queries/study/chemistryResults.query.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + Date + + + Type + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/chemistryResults/.qview.xml b/nbri_ehr/resources/queries/study/chemistryResults/.qview.xml new file mode 100644 index 0000000..02467cb --- /dev/null +++ b/nbri_ehr/resources/queries/study/chemistryResults/.qview.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases.sql b/nbri_ehr/resources/queries/study/clinicalCases.sql new file mode 100644 index 0000000..fa3b774 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases.sql @@ -0,0 +1,7 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT * FROM study.cases +WHERE category = 'Clinical' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/.qview.xml new file mode 100644 index 0000000..b08797c --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/.qview.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Area 11.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Area 11.qview.xml new file mode 100644 index 0000000..edcb23f --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Area 11.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Area 51.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Area 51.qview.xml new file mode 100644 index 0000000..d1274dc --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Area 51.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 10.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 10.qview.xml new file mode 100644 index 0000000..1bf0575 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 10.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 10C.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 10C.qview.xml new file mode 100644 index 0000000..8136896 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 10C.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 27.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 27.qview.xml new file mode 100644 index 0000000..b369423 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 27.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 28.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 28.qview.xml new file mode 100644 index 0000000..7cd8a6d --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 28.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 29.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 29.qview.xml new file mode 100644 index 0000000..6798f6c --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 29.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 30.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 30.qview.xml new file mode 100644 index 0000000..8225a43 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 30.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 31.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 31.qview.xml new file mode 100644 index 0000000..2bdc6ca --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 31.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 31C.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 31C.qview.xml new file mode 100644 index 0000000..e86d068 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 31C.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 31D.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 31D.qview.xml new file mode 100644 index 0000000..c75ade9 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 31D.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 32.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 32.qview.xml new file mode 100644 index 0000000..4fafe49 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 32.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 34.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 34.qview.xml new file mode 100644 index 0000000..19c1701 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 34.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 37.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 37.qview.xml new file mode 100644 index 0000000..d22bd89 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 37.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 41.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 41.qview.xml new file mode 100644 index 0000000..5eaf22e --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 41.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 42.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 42.qview.xml new file mode 100644 index 0000000..5598b7c --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 42.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 43.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 43.qview.xml new file mode 100644 index 0000000..d864dbe --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 43.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 44.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 44.qview.xml new file mode 100644 index 0000000..3c0e4c6 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 44.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 45.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 45.qview.xml new file mode 100644 index 0000000..49d52f6 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 45.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 46.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 46.qview.xml new file mode 100644 index 0000000..9944c43 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 46.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 50.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 50.qview.xml new file mode 100644 index 0000000..7e86728 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 50.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 52.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 52.qview.xml new file mode 100644 index 0000000..7860808 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 52.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 53.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 53.qview.xml new file mode 100644 index 0000000..7c63231 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 53.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 54A.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 54A.qview.xml new file mode 100644 index 0000000..b2f3a2b --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 54A.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalCases/Building 54B.qview.xml b/nbri_ehr/resources/queries/study/clinicalCases/Building 54B.qview.xml new file mode 100644 index 0000000..449c6ac --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalCases/Building 54B.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations.sql b/nbri_ehr/resources/queries/study/clinicalObservations.sql new file mode 100644 index 0000000..0f97920 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations.sql @@ -0,0 +1,7 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT * FROM study.clinical_observations +WHERE type = 'Clinical' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/.qview.xml new file mode 100644 index 0000000..7b1fc1a --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/.qview.xml @@ -0,0 +1,17 @@ + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Area 11.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Area 11.qview.xml new file mode 100644 index 0000000..d6bc389 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Area 11.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Area 51.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Area 51.qview.xml new file mode 100644 index 0000000..afba1b7 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Area 51.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 10.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 10.qview.xml new file mode 100644 index 0000000..81afb77 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 10.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 10C.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 10C.qview.xml new file mode 100644 index 0000000..cd80d91 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 10C.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 27.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 27.qview.xml new file mode 100644 index 0000000..40176ca --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 27.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 28.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 28.qview.xml new file mode 100644 index 0000000..081bda6 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 28.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 29.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 29.qview.xml new file mode 100644 index 0000000..e1a5e46 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 29.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 30.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 30.qview.xml new file mode 100644 index 0000000..2a1d832 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 30.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 31.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 31.qview.xml new file mode 100644 index 0000000..3a35f29 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 31.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 31C.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 31C.qview.xml new file mode 100644 index 0000000..ee6575a --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 31C.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 31D.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 31D.qview.xml new file mode 100644 index 0000000..8189627 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 31D.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 32.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 32.qview.xml new file mode 100644 index 0000000..c6c4d4e --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 32.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 34.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 34.qview.xml new file mode 100644 index 0000000..159b5cd --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 34.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 37.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 37.qview.xml new file mode 100644 index 0000000..0cb4ba2 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 37.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 41.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 41.qview.xml new file mode 100644 index 0000000..ecf5453 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 41.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 42.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 42.qview.xml new file mode 100644 index 0000000..9ce6c0a --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 42.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 43.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 43.qview.xml new file mode 100644 index 0000000..c7cb4d6 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 43.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 44.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 44.qview.xml new file mode 100644 index 0000000..71daaac --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 44.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 45.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 45.qview.xml new file mode 100644 index 0000000..6f5e934 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 45.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 46.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 46.qview.xml new file mode 100644 index 0000000..536923d --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 46.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 50.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 50.qview.xml new file mode 100644 index 0000000..8a45fab --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 50.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 52.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 52.qview.xml new file mode 100644 index 0000000..a87ccca --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 52.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 53.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 53.qview.xml new file mode 100644 index 0000000..d443280 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 53.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 54A.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 54A.qview.xml new file mode 100644 index 0000000..2dbdacf --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 54A.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinicalObservations/Building 54B.qview.xml b/nbri_ehr/resources/queries/study/clinicalObservations/Building 54B.qview.xml new file mode 100644 index 0000000..ed14674 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinicalObservations/Building 54B.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observations.js b/nbri_ehr/resources/queries/study/clinical_observations.js new file mode 100644 index 0000000..cbad6bf --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observations.js @@ -0,0 +1,77 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +const console = require("console"); +require("ehr/triggers").initScript(this); + +var animalIdCasesMap = {}; +var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); + +function onInit(event, helper) { + helper.decodeExtraContextProperty('orderTasksInTransaction'); + triggerHelper.clearScheduledObsTaskMap(); +} + +function onUpsert(helper, scriptErrors, row, oldRow) { + + if (!helper.isETL() && !helper.isGeneratedByServer()) { + + if (!row.observation && !row.remark) { + EHR.Server.Utils.addError(scriptErrors, 'observation', 'Must enter an observation or remark', 'WARN'); + EHR.Server.Utils.addError(scriptErrors, 'remark', 'Must enter an observation or remark', 'WARN'); + } + + if (row.category === "Verified Id?" && row.observation === "No" && !row.remark) { + EHR.Server.Utils.addError(scriptErrors, 'remark', "You selected 'No' for 'Verified Id?', please enter Remark", "WARN"); + } + + if (row.category === "Daily Enrichment" && row.observation === "Other" && !row.remark) { + EHR.Server.Utils.addError(scriptErrors, 'remark', "You selected 'Other' for 'Daily Enrichment', please enter Remark", "WARN"); + } + + if (row.category === "Alopecia Score" && !row.observation) { + EHR.Server.Utils.addError(scriptErrors, 'observation', "Score required for 'Alopecia Score'.", "WARN"); + } + + if (row.category === "Alopecia Score" && !row.remark) { + EHR.Server.Utils.addError(scriptErrors, 'remark', "Remark required for 'Alopecia Score'.", "WARN"); + } + + var yesRemarkRequired = (row.category === "Self Biting Observed" || row.category === "New Injury Observed" || row.category === "Other Stereotopy" || row.category === "Environmental Change" || row.category === "Special Enrichment"); + if (yesRemarkRequired && row.observation === "Yes" && !row.remark) { + EHR.Server.Utils.addError(scriptErrors, 'remark', "You selected 'Yes' for " + row.category + ", please explain in the Remark", "WARN"); + } + + // Handle scheduled observations + if (!helper.isValidateOnly() && row.scheduledDate) { + var qc; + if (row.QCStateLabel) { + qc = EHR.Server.Security.getQCStateByLabel(row.QCStateLabel); + } + else if (row.QCState) { + qc = EHR.Server.Security.getQCStateByRowId(row.QCState); + } + + if (!qc) { + console.error('Unable to find QCState: ' + row.QCState + '/' + row.QCStateLabel); + } + else { + var orderTasks = helper.getProperty('orderTasksInTransaction'); + if (orderTasks && orderTasks.length > 0) { + var orderData = triggerHelper.handleScheduledObservations(row, qc.RowId, orderTasks[0]); + + if (orderData) { + row.caseId = orderData.caseId; + row.orderid = orderData.orderId; + row.area = orderData.area; + row.type = orderData.type; + row.taskid = orderData.taskId; + } + } + } + } + } +} \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observations.query.xml b/nbri_ehr/resources/queries/study/clinical_observations.query.xml new file mode 100644 index 0000000..7b058cf --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observations.query.xml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + Category + + + Area + + ehr_lookups + observation_areas + value + + + + Observation/Score + + + Remark + + + Case + + + Performed By + + + Scheduled Date + + + Type + true + + + Order Id + true + + study + observation_order + objectid + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observations/.qview.xml b/nbri_ehr/resources/queries/study/clinical_observations/.qview.xml new file mode 100644 index 0000000..daaa82d --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observations/.qview.xml @@ -0,0 +1,19 @@ + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observations/Alopecia Scores.qview.xml b/nbri_ehr/resources/queries/study/clinical_observations/Alopecia Scores.qview.xml new file mode 100644 index 0000000..0a05b82 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observations/Alopecia Scores.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observations/Behavior.qview.xml b/nbri_ehr/resources/queries/study/clinical_observations/Behavior.qview.xml new file mode 100644 index 0000000..f7566f3 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observations/Behavior.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observations/Clinical.qview.xml b/nbri_ehr/resources/queries/study/clinical_observations/Clinical.qview.xml new file mode 100644 index 0000000..adf8cf8 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observations/Clinical.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary.sql b/nbri_ehr/resources/queries/study/clinical_observationsSummary.sql new file mode 100644 index 0000000..58afbb2 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary.sql @@ -0,0 +1,29 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + Id, + date, + category, + area, + observation, + remark, + performedBy, + scheduledDate, + QCState, + type +FROM clinical_observations +WHERE type = 'Clinical' +GROUP BY + Id, + date, + category, + area, + observation, + remark, + performedBy, + scheduledDate, + QCState, + type \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/.qview.xml new file mode 100644 index 0000000..a48d5a5 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/.qview.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Area 11.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Area 11.qview.xml new file mode 100644 index 0000000..02bbb1c --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Area 11.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Area 51.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Area 51.qview.xml new file mode 100644 index 0000000..f1e9bde --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Area 51.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 10.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 10.qview.xml new file mode 100644 index 0000000..6c5a2df --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 10.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 10C.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 10C.qview.xml new file mode 100644 index 0000000..0ebcf0a --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 10C.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 27.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 27.qview.xml new file mode 100644 index 0000000..2760754 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 27.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 28.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 28.qview.xml new file mode 100644 index 0000000..2ed3cc1 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 28.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 29.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 29.qview.xml new file mode 100644 index 0000000..e40c6bf --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 29.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 30.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 30.qview.xml new file mode 100644 index 0000000..8220278 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 30.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 31.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 31.qview.xml new file mode 100644 index 0000000..96f771c --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 31.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 31C.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 31C.qview.xml new file mode 100644 index 0000000..17a41c2 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 31C.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 31D.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 31D.qview.xml new file mode 100644 index 0000000..5d65614 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 31D.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 32.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 32.qview.xml new file mode 100644 index 0000000..284f684 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 32.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 34.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 34.qview.xml new file mode 100644 index 0000000..2ec2783 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 34.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 37.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 37.qview.xml new file mode 100644 index 0000000..4880b02 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 37.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 41.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 41.qview.xml new file mode 100644 index 0000000..fca1205 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 41.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 42.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 42.qview.xml new file mode 100644 index 0000000..2b2ed75 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 42.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 43.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 43.qview.xml new file mode 100644 index 0000000..065334b --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 43.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 44.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 44.qview.xml new file mode 100644 index 0000000..db70e10 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 44.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 45.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 45.qview.xml new file mode 100644 index 0000000..36036ee --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 45.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 46.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 46.qview.xml new file mode 100644 index 0000000..d13731e --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 46.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 50.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 50.qview.xml new file mode 100644 index 0000000..d9d616f --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 50.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 52.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 52.qview.xml new file mode 100644 index 0000000..49b3e35 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 52.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 53.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 53.qview.xml new file mode 100644 index 0000000..4bdb49b --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 53.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 54A.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 54A.qview.xml new file mode 100644 index 0000000..ce9d4e1 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 54A.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 54B.qview.xml b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 54B.qview.xml new file mode 100644 index 0000000..d0c9046 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinical_observationsSummary/Building 54B.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinremarks.js b/nbri_ehr/resources/queries/study/clinremarks.js new file mode 100644 index 0000000..0dc73f6 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinremarks.js @@ -0,0 +1,31 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + + +const console = require("console"); +require("ehr/triggers").initScript(this); + +function onInit(event, helper) { + helper.decodeExtraContextProperty('casesInTransaction'); +} + +function onUpsert(helper, scriptErrors, row, oldRow) { + if (!helper.isETL()) { + + var caseMap = helper.getProperty('casesInTransaction'); + var remarkCase = []; + if (caseMap && caseMap[row.Id]){ + remarkCase = caseMap[row.Id]; + } + + var hasCaseEnddate = remarkCase.length > 0 && remarkCase[0].enddate + + if (!row.s && !row.o && !row.a && !row.p && !row.remark && !hasCaseEnddate) { + EHR.Server.Utils.addError(scriptErrors, 'remark', 'Must enter at least one comment', 'WARN'); + EHR.Server.Utils.addError(scriptErrors, 's', 'Must enter at least one comment', 'WARN'); + } + } +} \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinremarks.query.xml b/nbri_ehr/resources/queries/study/clinremarks.query.xml new file mode 100644 index 0000000..a221d11 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinremarks.query.xml @@ -0,0 +1,63 @@ + + + + + + + + + History + + + Subjective + textarea + ALWAYS_OFF + + + Objective + textarea + ALWAYS_OFF + + + Assessment + textarea + ALWAYS_OFF + + + Plan + textarea + ALWAYS_OFF + + + Category + + ehr_lookups + data_category + value + + + + + textarea + 5 + + + Vet Review + textarea + 5 + true + + + Vet Review Date + Date + true + + + Date + true + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinremarks/.qview.xml b/nbri_ehr/resources/queries/study/clinremarks/.qview.xml new file mode 100644 index 0000000..903f88d --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinremarks/.qview.xml @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinremarks/Behavior.qview.xml b/nbri_ehr/resources/queries/study/clinremarks/Behavior.qview.xml new file mode 100644 index 0000000..24f5a40 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinremarks/Behavior.qview.xml @@ -0,0 +1,19 @@ + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/clinremarks/Clinical.qview.xml b/nbri_ehr/resources/queries/study/clinremarks/Clinical.qview.xml new file mode 100644 index 0000000..6cb3771 --- /dev/null +++ b/nbri_ehr/resources/queries/study/clinremarks/Clinical.qview.xml @@ -0,0 +1,24 @@ + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/colonyPopulationByAgeClass.query.xml b/nbri_ehr/resources/queries/study/colonyPopulationByAgeClass.query.xml new file mode 100644 index 0000000..27edcf5 --- /dev/null +++ b/nbri_ehr/resources/queries/study/colonyPopulationByAgeClass.query.xml @@ -0,0 +1,30 @@ + + + + + Population Summary, By Age and Species + + + Species + + ehr_lookups + species_codes + code + common_name + + + + Animal Count + /query/executeQuery.view?schemaName=study& + query.queryName=demographics& + query.species~eq=${species}& + query.gender~eq=${gender}& + query.Id/ageClass/label~eq=${ageclass}& + query.viewName=Alive%2C at Center& + + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/colonyPopulationChange.sql b/nbri_ehr/resources/queries/study/colonyPopulationChange.sql new file mode 100644 index 0000000..cac3cf8 --- /dev/null +++ b/nbri_ehr/resources/queries/study/colonyPopulationChange.sql @@ -0,0 +1,59 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +PARAMETERS(StartDate TIMESTAMP, EndDate TIMESTAMP) + +SELECT + T1.id, +-- T1.id.dataset.demographics.species as species, + 'Births' AS Category, + T1.date, + convert(year(T1.date), integer) AS Year + +FROM study.Birth T1 +WHERE T1.date IS NOT NULL +and cast(COALESCE(STARTDATE, '1900-01-01') as date) <= T1.date and cast(COALESCE(ENDDATE, curdate()) as date) >= cast(T1.date as date) + +UNION ALL + +SELECT + T2.id, +-- T2.id.dataset.demographics.species, + 'Arrivals' AS Category, + T2.date, + convert(year(T2.date), INTEGER) AS Year + +FROM study.Arrival T2 +WHERE T2.date IS NOT NULL +AND T2.qcstate.publicdata = true +and cast(COALESCE(STARTDATE, '1900-01-01') as date) <= T2.date and cast(COALESCE(ENDDATE, curdate()) as date) >= cast(T2.date as date) + +UNION ALL + +SELECT + T3.id, +-- T3.id.dataset.demographics.species, + 'Departures' AS Category, + T3.date, + convert(year(T3.date), INTEGER) AS Year + +FROM study.Departure T3 +WHERE T3.date IS NOT NULL +AND T3.qcstate.publicdata = true +and cast(COALESCE(STARTDATE, '1900-01-01') as date) <= T3.date and cast(COALESCE(ENDDATE, curdate()) as date) >= cast(T3.date as date) + +UNION ALL + +SELECT + T4.id, +-- T4.id.dataset.demographics.species, + 'Deaths' AS Category, + T4.date, + convert(year(T4.date), INTEGER) AS Year + +FROM study.Deaths T4 +WHERE T4.date IS NOT NULL +-- and (t4.notAtCenter is null or t4.notAtCenter = false) +and cast(COALESCE(STARTDATE, '1900-01-01') as date) <= T4.date and cast(COALESCE(ENDDATE, curdate()) as date) >= cast(T4.date as date) diff --git a/nbri_ehr/resources/queries/study/colonyPopulationSummary.query.xml b/nbri_ehr/resources/queries/study/colonyPopulationSummary.query.xml new file mode 100644 index 0000000..1005e5d --- /dev/null +++ b/nbri_ehr/resources/queries/study/colonyPopulationSummary.query.xml @@ -0,0 +1,28 @@ + + + + + Population Summary, By Species + + + Species + + ehr_lookups + species_codes + code + common_name + + + + Animal Count + /query/executeQuery.view?schemaName=study& + query.queryName=demographics& + query.species~eq=${species}& + query.viewName=Alive%2C at Center + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/currentBloodDraws.sql b/nbri_ehr/resources/queries/study/currentBloodDraws.sql new file mode 100644 index 0000000..557648f --- /dev/null +++ b/nbri_ehr/resources/queries/study/currentBloodDraws.sql @@ -0,0 +1,84 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +SELECT + t.id, + t.date, + cast(t.quantity as double) as quantity, + t.species, + t.max_draw_pct, + t.blood_draw_interval, + t.blood_per_kg, + t.mostRecentWeight, + t.mostRecentWeightDate, + t.death, + cast(t.allowableBlood as double) as maxAllowableBlood, + cast(t.bloodPrevious as double) as bloodPrevious, + cast((t.allowableBlood - t.bloodPrevious) as double) as allowablePrevious, + + cast(t.bloodFuture as double) as bloodFuture, + cast((t.allowableBlood - t.bloodFuture) as double) as allowableFuture, + + --if the draw is historic, always consider previous draws only. + --otherwise, look both forward and backwards, then take the interval with the highest volume + cast(case + WHEN t.date < curdate() THEN (t.allowableBlood - t.bloodPrevious) + WHEN t.bloodPrevious < t.bloodFuture THEN (t.allowableBlood - t.bloodFuture) + ELSE (t.allowableBlood - t.bloodPrevious) + end as double) as allowableBlood, + t.minDate, + t.maxDate + +FROM ( + + SELECT + bd.id, + bd.dateOnly as date, + bd.quantity, + d.species, + d.death, + d.id.mostRecentWeight.MostRecentWeight, + d.id.mostRecentWeight.MostRecentWeightDate, + d.species.scientific_name.blood_per_kg, + d.species.scientific_name.max_draw_pct, + bd.blood_draw_interval, + (d.id.mostRecentWeight.MostRecentWeight * d.species.scientific_name.blood_per_kg * d.species.scientific_name.max_draw_pct) AS allowableBlood, + bd.minDate, + bd.maxDate, + COALESCE( + (SELECT SUM(coalesce(draws.quantity, 0)) AS _expr + FROM study.blood draws + WHERE draws.id = bd.id + AND draws.dateOnly > bd.minDate + AND draws.dateOnly <= bd.dateOnly + --NOTE: this has been changed to include pending/non-approved draws + AND draws.countsAgainstVolume = true + ), 0) AS BloodPrevious, + + COALESCE( + (SELECT SUM(coalesce(draws.quantity, 0)) AS _expr + FROM study.blood draws + WHERE draws.id = bd.id + AND draws.dateOnly < bd.maxDate + AND draws.dateOnly >= bd.dateOnly + --NOTE: this has been changed to include pending/non-approved draws + AND draws.countsAgainstVolume = true + ), 0) AS BloodFuture + + FROM study.bloodDrawChanges bd + JOIN study.demographics d ON (d.id = bd.id) + + ) t \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/currentproject.sql b/nbri_ehr/resources/queries/study/currentproject.sql new file mode 100644 index 0000000..e69c367 --- /dev/null +++ b/nbri_ehr/resources/queries/study/currentproject.sql @@ -0,0 +1,11 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +-- This query is used to find the current project + +SELECT DISTINCT assignment.Id, +assignment.project +FROM assignment +WHERE assignment.enddate is null \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/deathNotification.sql b/nbri_ehr/resources/queries/study/deathNotification.sql new file mode 100644 index 0000000..3516c49 --- /dev/null +++ b/nbri_ehr/resources/queries/study/deathNotification.sql @@ -0,0 +1,13 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +SELECT + Id, + date, + taskid, + performedBy.DisplayName AS performedBy, + reason.title AS reason +FROM study.deaths \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/deaths.js b/nbri_ehr/resources/queries/study/deaths.js new file mode 100644 index 0000000..d319fb5 --- /dev/null +++ b/nbri_ehr/resources/queries/study/deaths.js @@ -0,0 +1,180 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); + +var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); +var validIds = []; +var idMap = {}; +var deathIdMap = {}; + +function onInit(event, helper){ + + helper.decodeExtraContextProperty('deathsInTransaction'); + + // Cache valid Ids for check on each row + LABKEY.Query.selectRows({ + requiredVersion: 9.1, + schemaName: 'study', + queryName: 'demographics', + columns: ['Id', 'calculated_status', 'QCState/Label'], + scope: this, + success: function (results) { + if (!results || !results.rows || results.rows.length < 1) + return; + + for(var i=0; i < results.rows.length; i++) { + validIds.push(results.rows[i]["Id"]["value"]) + idMap[results.rows[i]["Id"]["value"]] = {calculated_status: results.rows[i]["calculated_status"]["value"], QCStateLabel: results.rows[i]["QCState/Label"]["value"]}; + // console.log(idMap[results.rows[i]["Id"]["value"]]); + } + }, + failure: function (error) { + console.log("error getting demographics data in death trigger onInit()\n" + error); + } + }); + + LABKEY.Query.selectRows({ + requiredVersion: 9.1, + schemaName: 'study', + queryName: 'deaths', + columns: ['Id', 'QCState/Label'], + scope: this, + success: function (results) { + if (!results || !results.rows || results.rows.length < 1) + return; + + for(var i=0; i < results.rows.length; i++) { + deathIdMap[results.rows[i]["Id"]["value"]] = {QCStateLabel: results.rows[i]["QCState/Label"]["value"]}; + } + }, + failure: function (error) { + console.log("error getting death data in death trigger onInit()\n" + error); + } + }); +} + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.AFTER_DELETE, 'study', 'Deaths', function(helper, errors, row, oldRow) { + + var demographicsUpdates = []; + demographicsUpdates.push({ + Id: row.Id, + death: null, + calculated_status: 'Alive', + QCState: helper.getJavaHelper().getQCStateForLabel('Completed').getRowId(), + }); + + console.log('removing demographics death date for animal:' + row.Id); + helper.getJavaHelper().updateDemographicsRecord(demographicsUpdates); +}); + +function onUpsert(helper, scriptErrors, row, oldRow) { + + var demographicsUpdates = []; + + if (!helper.isETL()) { + + //skip other checks so that the admins can update a death record + if (helper.getEvent() === 'update' && LABKEY.Security.currentUser.isAdmin) { + return; + } + + //only allow death record to be created if the animal is in the demographics table + if (idMap[row.Id]) { + + // check if a death record already exists for this animal + if (idMap[row.Id].calculated_status.toUpperCase() === 'DEAD' && deathIdMap[row.Id].QCStateLabel.toUpperCase() === 'COMPLETED') { + EHR.Server.Utils.addError(scriptErrors, 'Id', 'Death record already exists for this animal.', 'ERROR'); + } + // check if the animal is at the center + else if (idMap[row.Id].calculated_status.toUpperCase() === 'SHIPPED') { + EHR.Server.Utils.addError(scriptErrors, 'Id', 'Animal is not at the center.', 'ERROR'); + } + // Check if an animal that's being entered is pending any request/review. + // Note 1: When trying to enter a new record for an animal, the QCState = 'IN PROGRESS'. + // Note 2: Upon 'Submit Death', the QCState will get set to 'REQUEST: PENDING', and upon 'Submit Necropsy for Review', + // the QCState will get set to 'Review Required' - this way we can distinguish between the two states in the Death/Necropsy workflow. + // If a user tries to submit a new Death record (identified by QCState = 'IN PROGRESS') for an animal that + // already has a pending request/review status in study.deaths, then below error message will be displayed. + else if (row.QCStateLabel.toUpperCase() === 'IN PROGRESS' && + deathIdMap[row.Id] && deathIdMap[row.Id].QCStateLabel && + (deathIdMap[row.Id].QCStateLabel.toUpperCase() === 'REQUEST: PENDING' || + deathIdMap[row.Id].QCStateLabel.toUpperCase() === 'REVIEW REQUIRED')) { + EHR.Server.Utils.addError(scriptErrors, 'Id', 'Death record is pending review for this animal', 'ERROR'); + } + // if 'Save Draft' record already exists, it doesn't allow to 'Save Draft' or 'Submit Death' + // on the same animal again - throws an error "duplicate key value violates unique constraint" + // So, added this check to allow 'Save Draft' record to be saved only once. + else if (oldRow === undefined && row.QCStateLabel.toUpperCase() === 'IN PROGRESS' && + deathIdMap[row.Id] && deathIdMap[row.Id].QCStateLabel && + deathIdMap[row.Id].QCStateLabel.toUpperCase() === 'IN PROGRESS') { + EHR.Server.Utils.addError(scriptErrors, 'Id', 'Death/Necropsy data entry is in progress for this animal', 'ERROR'); + } + else if (!helper.isValidateOnly() && row.Id && row.date && row.QCStateLabel.toUpperCase() === 'COMPLETED') { + + if (validIds.indexOf(row.id) !== -1) { + + // update demographics + demographicsUpdates.push({ + Id: row.Id, + death: row.date, + calculated_status: 'Dead', + QCState: helper.getJavaHelper().getQCStateForLabel(row.QCStateLabel).getRowId() + }); + + console.log('updating demographics death date for animal: ' + row.Id); + helper.getJavaHelper().updateDemographicsRecord(demographicsUpdates); + console.log('updated demographics death date for animal: ' + row.Id); + } + else { + console.log(row.id + " is not a valid animal id"); + } + } + + if(row.QCStateLabel && EHR.Server.Security.getQCStateByLabel(row.QCStateLabel).PublicData) { + var qcstate = helper.getJavaHelper().getQCStateForLabel(row.QCStateLabel).getRowId(); + + //add/update weight record + var weightRecord = { + Id: row.Id, + date: row.date, + weight: row.deathWeight, + taskid: row.taskid, + qcstate: qcstate, + performedby: row.performedby + }; + triggerHelper.upsertWeightRecord(weightRecord); + } + } + } +} + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.AFTER_INSERT, 'study', 'deaths', function(helper, scriptErrors, row, oldRow) { + helper.registerDeath(row.Id, row.date); + triggerHelper.reportDataChange("study", "deaths", [row.Id]); +}); + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.COMPLETE, 'study', 'Deaths', function(event, errors, helper){ + var rows = helper.getRows() || []; + for (var i = 0; i < rows.length; i++) { + var row = rows[i].row; + var oldRow = rows[i].oldRow; + + // Notification will get sent when: + // 1) a brand-new row saved directly as 'Request: Pending' (i.e., when a user clicks 'Submit Death'), or + // 2) a draft death record moving from 'In Progress' to 'Request: Pending'. + if (!helper.isETL() && + row && row.Id && + row.QCStateLabel && + row.QCStateLabel.toUpperCase() === 'REQUEST: PENDING' && + (!oldRow || !oldRow.QCStateLabel || oldRow.QCStateLabel.toUpperCase() === 'IN PROGRESS')) { + console.log("Sending NBRI Death Notification") + triggerHelper.sendDeathNotification(row.Id); + + console.log("Updating Procedure Orders to Completed for Animal: " + row.Id + "") + triggerHelper.updateProcedureOrdersToCompleted([row.Id]); + } + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/deaths.query.xml b/nbri_ehr/resources/queries/study/deaths.query.xml new file mode 100644 index 0000000..35c2e6a --- /dev/null +++ b/nbri_ehr/resources/queries/study/deaths.query.xml @@ -0,0 +1,34 @@ + + + + + + + + Death Date + + + Disposition + + ehr_lookups + death_reason + value + title + + + + Death Weight (kg) + + + + + true + + + true + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/deaths/.qview.xml b/nbri_ehr/resources/queries/study/deaths/.qview.xml new file mode 100644 index 0000000..fdc063c --- /dev/null +++ b/nbri_ehr/resources/queries/study/deaths/.qview.xml @@ -0,0 +1,14 @@ + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/demographics.js b/nbri_ehr/resources/queries/study/demographics.js new file mode 100644 index 0000000..068afbb --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographics.js @@ -0,0 +1,80 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +require("ehr/triggers").initScript(this); + +let triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); +let animalIds = []; + +function onInit(event, helper){ + helper.setScriptOptions({ + allowAnyId: true, + requiresStatusRecalc: false, + allowDatesInDistantPast: true + }); +} + +function onUpsert(helper, scriptErrors, row, oldRow){ + //NOTE: this should be getting set by the birth, death, arrival & departure tables + //ALSO: it should be rare to insert directly into this table. usually this record will be created by inserting into either birth or arrival + if (!row.calculated_status && !helper.isETL()){ + row.calculated_status = helper.getJavaHelper().getCalculatedStatusValue(row.Id); + } + + if (helper.isETL() && row.damSire) { + let damSire = row.damSire.split('DAM:'); + if (damSire.length === 1) { + row.damSire.split('DAM'); + } + + if (damSire.length > 1) { + let damAndSire = damSire[1].split("SIRE:") + if (damAndSire.length === 1) { + row.damSire.split('SIRE'); + } + if (damAndSire[0].trim() === row.Id) + { + console.log(row.Id + " listed as it's own dam") + } + if (damAndSire[0].trim() !== 'UNK' && damAndSire[0].trim() !== row.Id) + row.dam = damAndSire[0].trim(); + + if (damAndSire.length > 1 && damAndSire[1].trim() === row.Id) + { + console.log(row.Id + " listed as it's own sire") + } + if (damAndSire.length > 1 && damAndSire[1].trim() !== 'UNK' && damAndSire[1].trim() !== row.Id) + row.sire = damAndSire[1].trim(); + + if (row.sire === row.dam) { + row.sire = ''; + row.dam = ''; + } + } + } +} + +function onComplete(event, errors, helper){ + if (!helper.isValidateOnly() && !helper.isETL()) { + var updateRows = helper.getRows(); + + // When closing previous records, we don't need to update the orchard file. Use the same flag as demographics providers. + var skipAnnounceChangedParticipants = false; + var extraContext = helper.getProperty('extraContext'); + if (extraContext) { + skipAnnounceChangedParticipants = extraContext.skipAnnounceChangedParticipants; + } + + if (updateRows && updateRows.length > 0 && + updateRows[0].row.taskid && + updateRows[0].row.QCStateLabel && + EHR.Server.Security.getQCStateByLabel(updateRows[0].row.QCStateLabel).PublicData && + !skipAnnounceChangedParticipants + ) { + triggerHelper.generateOrchardFile(updateRows[0].row.taskid); + } + } +} \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/demographics.query.xml b/nbri_ehr/resources/queries/study/demographics.query.xml new file mode 100644 index 0000000..bff3d17 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographics.query.xml @@ -0,0 +1,112 @@ + + + + + + + true + + + Sex + + + Species + + + Date + Birth + /query/executeQuery.view? + schemaName=study& + query.queryName=Birth& + query.Id~eq=${Id} + + + + Date + Death + /query/executeQuery.view? + schemaName=study& + query.queryName=Deaths& + query.Id~eq=${Id} + + + + Dam + + study + animal + id + + /ehr/participantView.view?participantId=${dam} + + + Sire + + study + animal + id + + /ehr/participantView.view?participantId=${sire} + + + Disposition + + ehr_lookups + disposition_codes + value + title + + + + Termination + + ehr_lookups + termination_reason_codes + value + title + + + + Date Weaned + Date + + + Implant Number + + + Vendor Number + + + Active Status + + + Animal Status + + + Lot + + nbri_ehr + Lot + LotId + + + + Origin + + ehr_lookups + geographic_origins + meaning + meaning + + + + Source + + + CITES + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/demographics/.qview.xml b/nbri_ehr/resources/queries/study/demographics/.qview.xml new file mode 100644 index 0000000..56f1f23 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographics/.qview.xml @@ -0,0 +1,23 @@ + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/demographicsActiveFlags.sql b/nbri_ehr/resources/queries/study/demographicsActiveFlags.sql new file mode 100644 index 0000000..b3c176e --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsActiveFlags.sql @@ -0,0 +1,24 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + f1.Id, + group_concat(DISTINCT f1.flag, chr(10)) as flags + +FROM ( + SELECT + f.Id, + CASE + WHEN f.flag is null THEN null + WHEN f.flag.category IS NULL THEN f.flag.value + ELSE cast((CAST(f.flag.category as varchar(100)) || CAST(': ' as varchar(2)) || CAST(f.flag.value as varchar(100))) as varchar(202)) + END as flag + + FROM study.flags f + WHERE f.isActive = true + + ) f1 + +GROUP BY f1.Id \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/demographicsActiveProjectAssignment.sql b/nbri_ehr/resources/queries/study/demographicsActiveProjectAssignment.sql new file mode 100644 index 0000000..8789900 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsActiveProjectAssignment.sql @@ -0,0 +1,10 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + d.id, + a.project.name as project +FROM study.demographics d +LEFT JOIN study.assignment a ON (a.id = d.id AND a.enddate IS NULL) \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/demographicsActiveProtocolAssignment.query.xml b/nbri_ehr/resources/queries/study/demographicsActiveProtocolAssignment.query.xml new file mode 100644 index 0000000..e7d003f --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsActiveProtocolAssignment.query.xml @@ -0,0 +1,29 @@ + + + + + Active Protocol Assignments + + + + Protocol + 100 + + + 180 + + + ALWAYS_OFF + Total Protocols + /query/executeQuery.view?schemaName=study&query.queryName=Assignment&query.id~eq=${id}&query.isActive~eq=true + + + ALWAYS_OFF + # Active Assignments + /query/executeQuery.view?schemaName=study&query.queryName=Assignment&query.id~eq=${id}&query.isActive~eq=true + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/demographicsActiveProtocolAssignment.sql b/nbri_ehr/resources/queries/study/demographicsActiveProtocolAssignment.sql new file mode 100644 index 0000000..817a7f0 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsActiveProtocolAssignment.sql @@ -0,0 +1,18 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + d.id, + a.protocol.displayName as protocolDisplayName, + initcap(a.protocol.investigatorId.firstName) ||' '|| initcap(a.protocol.investigatorId.lastName) as investigator, + a.protocol.title as protocolTitle, + a.lsid, + cast(CASE + WHEN a.protocol.investigatorId.lastName IS NOT NULL THEN (a.protocol.investigatorId.lastName || ' - ' || a.protocol.displayName) + ELSE a.protocol.displayName + END as varchar(500)) as protocolString + +FROM study.demographics d +LEFT JOIN study.protocolAssignment a ON (a.id = d.id AND a.enddate IS NULL) \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/demographicsAliases.query.xml b/nbri_ehr/resources/queries/study/demographicsAliases.query.xml new file mode 100644 index 0000000..09b31f9 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsAliases.query.xml @@ -0,0 +1,9 @@ + + + + + Animal Aliases +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/demographicsAliases.sql b/nbri_ehr/resources/queries/study/demographicsAliases.sql new file mode 100644 index 0000000..cb979e8 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsAliases.sql @@ -0,0 +1,11 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT Id, + GROUP_CONCAT(alias, ', ') alias, + category.title as aliasType +FROM alias +GROUP BY Id, category.title + PIVOT alias BY aliasType IN (SELECT title FROM ehr_lookups.alias_category) \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/demographicsCagemates.query.xml b/nbri_ehr/resources/queries/study/demographicsCagemates.query.xml new file mode 100644 index 0000000..c4877dd --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsCagemates.query.xml @@ -0,0 +1,24 @@ + + + + + Animals Per Pairing + + + true + + + false + + + Total Animals In Pairing + /query/executeQuery.view?schemaName=study&query.queryName=Demographics&query.id/numPaired/room~eq=${room}&query.id/numPaired/effectiveCage~eq=${effectiveCage} + + + Category + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/demographicsCagemates.sql b/nbri_ehr/resources/queries/study/demographicsCagemates.sql new file mode 100644 index 0000000..a309200 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsCagemates.sql @@ -0,0 +1,33 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + d.id, +-- t.room, + t.cage, + t.total, + cast(t.animals as varchar(4000)) as animals + +FROM study.demographics d +LEFT JOIN ( +SELECT + h.id, +-- h.room, + h.cage, + count(distinct h2.id) as total, + group_concat(distinct h2.id, ', ') as animals + +FROM study.housing h + +JOIN study.housing h2 +ON (h2.Id.demographics.calculated_status = 'Alive' + AND (h.cage = h2.cage)) + +WHERE h.enddateTimeCoalesced >= now() +GROUP BY h.id, h.room, h.cage + +) t ON (t.id = d.id) + +WHERE d.calculated_status = 'Alive' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/demographicsCurLocation.query.xml b/nbri_ehr/resources/queries/study/demographicsCurLocation.query.xml new file mode 100644 index 0000000..de68430 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsCurLocation.query.xml @@ -0,0 +1,35 @@ + + + + + + + true + true + + + + ehr_lookups + cage + location + + + + + 100 + + + /query/executeQuery.view?schemaName=study& + query.queryName=housing& + query.room~eq=${room}& + query.cage~eq=${cage}& + query.enddate~isblank& + query.sort=Id& + + + + Location +
+ + + diff --git a/nbri_ehr/resources/queries/study/demographicsCurLocation.sql b/nbri_ehr/resources/queries/study/demographicsCurLocation.sql new file mode 100644 index 0000000..e50160a --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsCurLocation.sql @@ -0,0 +1,37 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + +d2.id, + +d2.cage AS Location, + +d2.room.area, + +d2.room, + +d2.cage AS cage, + +ifdefined(d2.cond) as cond, + +d2.date, + +d2.reason, + +d2.remark, + +coalesce(d2.room, '') as room_order, +d2.room_sortValue @hidden, + +coalesce(d2.cage, '') as cage_order, +d2.cage_sortValue @hidden, + +d2.performedBy.displayName AS performedBy + +FROM study.housing d2 + +WHERE d2.enddate IS NULL +AND d2.qcstate.publicdata = true \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/demographicsLastProject.query.xml b/nbri_ehr/resources/queries/study/demographicsLastProject.query.xml new file mode 100644 index 0000000..d01971e --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsLastProject.query.xml @@ -0,0 +1,13 @@ + + + + + + + Last Project + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/demographicsLastProject.sql b/nbri_ehr/resources/queries/study/demographicsLastProject.sql new file mode 100644 index 0000000..b4f45e9 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsLastProject.sql @@ -0,0 +1,15 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +SELECT + d2.id, + d2.project, + h.enddate as enddate + +FROM study.assignment d2 + JOIN (SELECT id, max(date) as maxDate, max(enddate) as enddate FROM study.assignment h GROUP BY id) h + ON (h.id = d2.id and d2.date = h.maxdate) +WHERE d2.qcstate.publicdata = true \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/demographicsLastProtocol.query.xml b/nbri_ehr/resources/queries/study/demographicsLastProtocol.query.xml new file mode 100644 index 0000000..94265b7 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsLastProtocol.query.xml @@ -0,0 +1,13 @@ + + + + + + + Last Protocol + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/demographicsLastProtocol.sql b/nbri_ehr/resources/queries/study/demographicsLastProtocol.sql new file mode 100644 index 0000000..d4ec209 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsLastProtocol.sql @@ -0,0 +1,15 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +SELECT + d2.id, + d2.protocol, + h.enddate as enddate + +FROM study.protocolAssignment d2 + JOIN (SELECT id, max(date) as maxDate, max(enddate) as enddate FROM study.protocolAssignment h GROUP BY id) h + ON (h.id = d2.id and d2.date = h.maxdate) +WHERE d2.qcstate.publicdata = true \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/demographicsOffspring.query.xml b/nbri_ehr/resources/queries/study/demographicsOffspring.query.xml new file mode 100644 index 0000000..877be40 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsOffspring.query.xml @@ -0,0 +1,20 @@ + + + + + + + true + + + + study + animal + Id + + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/demographicsOffspring.sql b/nbri_ehr/resources/queries/study/demographicsOffspring.sql new file mode 100644 index 0000000..e40fbc8 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsOffspring.sql @@ -0,0 +1,21 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + + d.id as Id, + d2.id AS Offspring, + d2.birth AS date, +d2.sire, +d2.dam, +d2.gender AS sex, +d.qcstate + +FROM study.Demographics d + + INNER JOIN study.Demographics d2 +ON ((d2.sire = d.id OR d2.dam = d.id) AND d.id != d2.id) + +group by d.id, d2.id, d2.birth, d2.sire, d2.dam, d2.gender, d.qcstate diff --git a/nbri_ehr/resources/queries/study/demographicsParents.query.xml b/nbri_ehr/resources/queries/study/demographicsParents.query.xml new file mode 100644 index 0000000..a151cf1 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsParents.query.xml @@ -0,0 +1,31 @@ + + + + + Parents + + + true + + + + study + animal + id + + + + + study + animal + id + + + + Number of Parents Known + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/demographicsParents.sql b/nbri_ehr/resources/queries/study/demographicsParents.sql new file mode 100644 index 0000000..b36eb8e --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsParents.sql @@ -0,0 +1,30 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +SELECT + d.id, + d.dam as dam, + 'Observed' as damType, + d.sire as sire, + 'Observed' as sireType, + CASE + WHEN d.dam IS NOT NULL AND d.sire IS NOT NULL THEN 2 + WHEN d.dam IS NOT NULL OR d.sire IS NOT NULL THEN 1 + ELSE 0 + END as numParents +FROM study.demographics d + +-- TODO: Incorporate fostering? Genetic testing? + diff --git a/nbri_ehr/resources/queries/study/demographicsSiblings.query.xml b/nbri_ehr/resources/queries/study/demographicsSiblings.query.xml new file mode 100644 index 0000000..a97b1d1 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsSiblings.query.xml @@ -0,0 +1,44 @@ + + Siblings of Any Animal + + + + Siblings of Any Animal + + + true + + + + /query/executeQuery.view?schemaName=study& + query.queryName=demographicsSiblings& + query.Id~eq=${Id} + + + + + study + animal + Id + + + + + study + animal + Id + + + + + study + animal + Id + + + + Relationship +
+ + + diff --git a/nbri_ehr/resources/queries/study/demographicsSiblings.sql b/nbri_ehr/resources/queries/study/demographicsSiblings.sql new file mode 100644 index 0000000..0990440 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsSiblings.sql @@ -0,0 +1,36 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + + d1.id, + + CASE + WHEN (COALESCE(d1.id.parents.sire, '') = COALESCE(d2.id.parents.sire, '') and COALESCE(d1.id.parents.dam, '') = COALESCE(d2.id.parents.dam, '') AND COALESCE(d1.id.parents.sire, '')!='' AND COALESCE(d1.id.parents.dam, '')!='') + THEN 'Full Sib' + WHEN (COALESCE(d1.id.parents.sire, '') = COALESCE(d2.id.parents.sire, '') AND COALESCE(d1.id.parents.sire, '') != '' AND (COALESCE(d1.id.parents.dam, '') != COALESCE(d2.id.parents.dam, '') OR COALESCE(d1.id.parents.dam, '') = '')) + THEN 'Half-Sib Paternal' + WHEN (COALESCE(d1.id.parents.dam, '') = COALESCE(d2.id.parents.dam, '') AND COALESCE(d1.id.parents.dam, '') != '' AND (COALESCE(d1.id.parents.sire, '') != COALESCE(d2.id.parents.sire, '') OR COALESCE(d1.id.parents.sire, '') = '')) + THEN 'Half-Sib Maternal' + WHEN (COALESCE(d1.id.parents.sire, '') != COALESCE(d2.id.parents.sire, '') and COALESCE(d1.id.parents.dam, '') != COALESCE(d2.id.parents.dam, '')) + THEN 'ERROR' + END AS Relationship, + + d2.id AS Sibling, + + d2.id.parents.dam AS SiblingDam, + d2.id.parents.sire AS SiblingSire, + d1.qcstate + +FROM study.Demographics d1 + +--removed left join + JOIN study.Demographics d2 + ON ((d2.id.parents.sire = d1.id.parents.sire OR d2.id.parents.dam = d1.id.parents.dam) AND d1.id != d2.id) + +WHERE d2.id is not null + +-- ) t + diff --git a/nbri_ehr/resources/queries/study/demographicsSource.query.xml b/nbri_ehr/resources/queries/study/demographicsSource.query.xml new file mode 100644 index 0000000..98ae435 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsSource.query.xml @@ -0,0 +1,17 @@ + + + + + Source + + + Days Since Center Arrival + + + From Center? + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/demographicsSource.sql b/nbri_ehr/resources/queries/study/demographicsSource.sql new file mode 100644 index 0000000..27c7810 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsSource.sql @@ -0,0 +1,35 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +SELECT + d.Id AS Id, + + T1.mostRecentArrival, + T1.earliestArrival, + d.birth, + coalesce(T1.EarliestArrival, d.birth) as center_Arrival, + timestampdiff('SQL_TSI_DAY', coalesce(T1.EarliestArrival, d.birth), now()) as daysSinceCenterArrival, + + CASE + WHEN T1.EarliestArrival IS NULL AND d.birth IS NOT NULL THEN true + ELSE false + END as fromCenter, + d.source as source, + + CASE + WHEN T1.EarliestArrival IS NULL AND d.birth IS NOT NULL THEN 'Born at NBRI' + WHEN T1.EarliestArrival IS NOT NULL AND T2.sourceFacility IS NOT NULL THEN T2.sourceFacility.meaning + ELSE 'Unknown' + END as type + +FROM study.demographics d + +LEFT JOIN + (select T1.Id, max(T1.date) as MostRecentArrival, min(T1.date) as EarliestArrival FROM study.arrival T1 WHERE T1.qcstate.publicdata = true GROUP BY T1.Id) T1 + ON (T1.Id = d.Id) + +LEFT JOIN study.arrival T2 ON (t2.id = d.id AND t2.date = t1.earliestArrival) + diff --git a/nbri_ehr/resources/queries/study/demographicsTotalOffspring.query.xml b/nbri_ehr/resources/queries/study/demographicsTotalOffspring.query.xml new file mode 100644 index 0000000..d42f72b --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsTotalOffspring.query.xml @@ -0,0 +1,34 @@ + + + + + + + true + true + + + /query/executeQuery.view?schemaName=study& + query.queryName=demographicsOffspring& + query.Id~eq=${Id} + + + + /query/executeQuery.view?schemaName=study& + query.queryName=demographicsOffspring& + query.Offspring/demographics/calculated_status~eq=Alive& + query.Id~eq=${Id} + + + + Earliest Birth + + + Latest Birth + + + TotalOffspring +
+ + + diff --git a/nbri_ehr/resources/queries/study/demographicsTotalOffspring.sql b/nbri_ehr/resources/queries/study/demographicsTotalOffspring.sql new file mode 100644 index 0000000..e8fe9ef --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsTotalOffspring.sql @@ -0,0 +1,42 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + + d.id, + group_concat(DISTINCT d2.id) as Offspring, + count(DISTINCT d2.id) as TotalOffspring, + SUM(CASE WHEN d2.calculated_status = 'Alive' THEN 1 ELSE 0 END) as TotalLivingOffspring, + + min(d2.birth) as earliestBirth, + max(d2.birth) as latestBirth + +FROM study.Demographics d + + JOIN study.Demographics d2 + ON (d.id = d2.id.parents.sire OR d.id = d2.id.parents.dam) + +GROUP BY d.id + +UNION + +SELECT + + d3.id, + NULL as Offspring, + 0 as TotalOffspring, + 0 as TotalLivingOffspring, + + NULL as earliestBirth, + NULL as latestBirth + +FROM study.Demographics d3 + +WHERE (d3.id NOT IN ( + SELECT d4.id.parents.sire FROM study.demographics d4 WHERE (d4.id.parents.sire IS NOT NULL) + UNION + SELECT d4.id.parents.dam FROM study.demographics d4 WHERE (d4.id.parents.dam IS NOT NULL))) + +GROUP BY d3.id diff --git a/nbri_ehr/resources/queries/study/departure.js b/nbri_ehr/resources/queries/study/departure.js new file mode 100644 index 0000000..b0f8b0b --- /dev/null +++ b/nbri_ehr/resources/queries/study/departure.js @@ -0,0 +1,31 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); + +var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); +var departures = []; + +function onInit(event, helper){ + helper.setScriptOptions({ + requiresStatusRecalc: false + }); + +} + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.AFTER_INSERT, 'study', 'departure', function(helper, scriptErrors, row, oldRow) { + + if (row.id) { + departures.push(row.id); + } +}); + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.COMPLETE, 'study', 'departure', function(event, errors, helper){ + + if (!helper.isETL() && helper.isEHRDataEntry()) { + triggerHelper.updateProcedureOrdersToCompleted(departures); + } +}); + diff --git a/nbri_ehr/resources/queries/study/departure.query.xml b/nbri_ehr/resources/queries/study/departure.query.xml new file mode 100644 index 0000000..19845d1 --- /dev/null +++ b/nbri_ehr/resources/queries/study/departure.query.xml @@ -0,0 +1,23 @@ + + + + + + + + + + + + Destination + + ehr_lookups + source + meaning + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/departure/.qview.xml b/nbri_ehr/resources/queries/study/departure/.qview.xml new file mode 100644 index 0000000..31e17cb --- /dev/null +++ b/nbri_ehr/resources/queries/study/departure/.qview.xml @@ -0,0 +1,14 @@ + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/drug.js b/nbri_ehr/resources/queries/study/drug.js new file mode 100644 index 0000000..fbbc9f8 --- /dev/null +++ b/nbri_ehr/resources/queries/study/drug.js @@ -0,0 +1,28 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +require("ehr/triggers").initScript(this); + +let triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_INSERT, 'study', 'drug', function(helper, scriptErrors, row, oldRow) { + if(row.treatmentid && row.scheduledDate && triggerHelper.isTreatmentOrderEntered(row.treatmentid, row.scheduledDate)) { + EHR.Server.Utils.addError(scriptErrors, 'scheduledDate', 'A treatment has already been entered for this order for this date and time.', 'ERROR'); + } +}); + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_UPSERT, 'study', 'drug', function(helper, scriptErrors, row, oldRow) { + // Max reasonable amount warning. Error when the amount is greater than the max reasonable amount + if (row.code) { + let drugFormulary = triggerHelper.getFormularyForDrug(row.code); + if (drugFormulary && drugFormulary.maxAmount && row.amount > drugFormulary.maxAmount) { + EHR.Server.Utils.addError(scriptErrors, 'amount', 'Amount is greater than the maximum reasonable amount: ' + drugFormulary.maxAmount, 'ERROR'); + } + } + if (row.volume && !row.vol_units) { + EHR.Server.Utils.addError(scriptErrors, 'volume', 'Units required for volume.', 'ERROR'); + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/drug.query.xml b/nbri_ehr/resources/queries/study/drug.query.xml new file mode 100644 index 0000000..95051db --- /dev/null +++ b/nbri_ehr/resources/queries/study/drug.query.xml @@ -0,0 +1,111 @@ + + + + + /ehr/drugDetails.view?lsid=${lsid} + + + + + + + + Date + + + Treatment + + ehr_lookups + snomed + code + meaning + + + + Route + + ehr_lookups + routes + route + + + + + Volume + + + Vol Units + + ehr_lookups + volume_units + unit + + + + + Amount + + + Amount Units + + ehr_lookups + amount_units + unit + + + + + Drug Conc + + + Conc Units + + ehr_lookups + conc_units + unit + + + + + Dosage + + + Dosage Units + + ehr_lookups + dosage_units + unit + + + + + Remark + + + Category + + ehr_lookups + data_category + value + + + + + Treatment Id + true + + study + treatment_order + objectid + + + + + + Scheduled Date + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/drug/.qview.xml b/nbri_ehr/resources/queries/study/drug/.qview.xml new file mode 100644 index 0000000..3b72268 --- /dev/null +++ b/nbri_ehr/resources/queries/study/drug/.qview.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/drug/Behavior.qview.xml b/nbri_ehr/resources/queries/study/drug/Behavior.qview.xml new file mode 100644 index 0000000..a9769cb --- /dev/null +++ b/nbri_ehr/resources/queries/study/drug/Behavior.qview.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/exemptions.js b/nbri_ehr/resources/queries/study/exemptions.js new file mode 100644 index 0000000..f4d5931 --- /dev/null +++ b/nbri_ehr/resources/queries/study/exemptions.js @@ -0,0 +1,6 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/exemptions.query.xml b/nbri_ehr/resources/queries/study/exemptions.query.xml new file mode 100644 index 0000000..db997ae --- /dev/null +++ b/nbri_ehr/resources/queries/study/exemptions.query.xml @@ -0,0 +1,29 @@ + + + + + + + + + + + + + + true + + + Category + false + + ehr_lookups + exemption_category + value + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/exemptions/.qview.xml b/nbri_ehr/resources/queries/study/exemptions/.qview.xml new file mode 100644 index 0000000..7e4278b --- /dev/null +++ b/nbri_ehr/resources/queries/study/exemptions/.qview.xml @@ -0,0 +1,14 @@ + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/flags.js b/nbri_ehr/resources/queries/study/flags.js new file mode 100644 index 0000000..f4d5931 --- /dev/null +++ b/nbri_ehr/resources/queries/study/flags.js @@ -0,0 +1,6 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/flags.query.xml b/nbri_ehr/resources/queries/study/flags.query.xml new file mode 100644 index 0000000..570a645 --- /dev/null +++ b/nbri_ehr/resources/queries/study/flags.query.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + Animal Id + + + Date Added + + + Date Removed + false + + + Flag + + ehr_lookups + flag_values + objectid + value + + + + Value + true + + + + + true + + + true + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/flags/.qview.xml b/nbri_ehr/resources/queries/study/flags/.qview.xml new file mode 100644 index 0000000..bf12e57 --- /dev/null +++ b/nbri_ehr/resources/queries/study/flags/.qview.xml @@ -0,0 +1,19 @@ + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/grossPathology.js b/nbri_ehr/resources/queries/study/grossPathology.js new file mode 100644 index 0000000..f4d5931 --- /dev/null +++ b/nbri_ehr/resources/queries/study/grossPathology.js @@ -0,0 +1,6 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/grossPathology.query.xml b/nbri_ehr/resources/queries/study/grossPathology.query.xml new file mode 100644 index 0000000..a7fce7d --- /dev/null +++ b/nbri_ehr/resources/queries/study/grossPathology.query.xml @@ -0,0 +1,41 @@ + + + + + + + Organ Systems Examined + + ehr_lookups + organ_systems + value + + + + Appearance + + ehr_lookups + organ_appearance + value + + + + true + + + true + + + true + + + true + + + true + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/grossPathology/.qview.xml b/nbri_ehr/resources/queries/study/grossPathology/.qview.xml new file mode 100644 index 0000000..798d1da --- /dev/null +++ b/nbri_ehr/resources/queries/study/grossPathology/.qview.xml @@ -0,0 +1,12 @@ + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/histopathology.query.xml b/nbri_ehr/resources/queries/study/histopathology.query.xml new file mode 100644 index 0000000..e35e753 --- /dev/null +++ b/nbri_ehr/resources/queries/study/histopathology.query.xml @@ -0,0 +1,16 @@ + + + + + + + Diagnosis + + + Category + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/historicalOther.query.xml b/nbri_ehr/resources/queries/study/historicalOther.query.xml new file mode 100644 index 0000000..37e2754 --- /dev/null +++ b/nbri_ehr/resources/queries/study/historicalOther.query.xml @@ -0,0 +1,13 @@ + + + + + + + Type + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/housing.js b/nbri_ehr/resources/queries/study/housing.js new file mode 100644 index 0000000..e80bd1e --- /dev/null +++ b/nbri_ehr/resources/queries/study/housing.js @@ -0,0 +1,166 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); +var prevAnimalId; +var prevDate; + +let triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); +let animalIds = []; + +function onInit(event, helper){ + helper.setScriptOptions({ + skipHousingCheck: true + }); + + helper.decodeExtraContextProperty('housingInTransaction'); + + helper.registerRowProcessor(function(helper, row){ + if (!row) + return; + + if (!row.Id || !row.room){ + return; + } + + var housingInTransaction = helper.getProperty('housingInTransaction'); + housingInTransaction = housingInTransaction || {}; + housingInTransaction[row.Id] = housingInTransaction[row.Id] || []; + + // this is a failsafe in case the client did not provide housing JSON. it ensures + // the current row is part of housingInTransaction + var shouldAdd = true; + if (row.objectid){ + LABKEY.ExtAdapter.each(housingInTransaction[row.Id], function(r){ + if (r.objectid == row.objectid){ + shouldAdd = false; + return false; + } + }, this); + } + + if (shouldAdd){ + housingInTransaction[row.Id].push({ + objectid: row.objectid, + date: row.date, + enddate: row.enddate, + qcstate: row.QCState, + room: row.room, + cage: row.cage, + divider: row.divider + }); + } + + helper.setProperty('housingInTransaction', housingInTransaction); + }); +} + +function onUpsert(helper, scriptErrors, row, oldRow){ + //verify we dont have 2 opened records for the same ID + if (!helper.isETL() && !row.enddate && row.Id){ + var map = helper.getProperty('housingInTransaction'); + if (map && map[row.Id]){ + var housingRecords = map[row.Id]; + for (var i=0;i 0) { + // Only need boundary rows for batch. Changing batch size on ETL may require change here. Incremental updates + // should update all incoming rows so don't do this. + if (helper.isETL() && updateRows.length > 4000) { + console.log("Batch import: only closing boundary housing record") + updateRows = [updateRows[0]]; + } + var idsToClose = []; + for (var i = 0; i < updateRows.length; i++) { + if (EHR.Server.Security.getQCStateByLabel(updateRows[i].row.QCStateLabel).PublicData && updateRows[i].row.date) { + idsToClose.push({ + Id: updateRows[i].row.Id, + date: EHR.Server.Utils.datetimeToString(updateRows[i].row.date), //stringify to serialize properly + objectid: updateRows[i].row.objectid + }); + if (animalIds.indexOf(updateRows[i].row.Id) === -1) { + animalIds.push(updateRows[i].row.Id); + } + } + } + if (idsToClose.length){ + helper.getJavaHelper().closeHousingRecords(idsToClose); + } + + // When closing previous records, we don't need to update the orchard file. Use the same flag as demographics providers. + var skipAnnounceChangedParticipants = false; + var extraContext = helper.getProperty('extraContext'); + if (extraContext) { + skipAnnounceChangedParticipants = extraContext.skipAnnounceChangedParticipants; + } + + if (updateRows && updateRows.length > 0 && + updateRows[0].row.taskid && + updateRows[0].row.QCStateLabel && + EHR.Server.Security.getQCStateByLabel(updateRows[0].row.QCStateLabel).PublicData && + !skipAnnounceChangedParticipants + ) { + triggerHelper.generateOrchardFile(updateRows[0].row.taskid); + } + } + } +} + diff --git a/nbri_ehr/resources/queries/study/housing.query.xml b/nbri_ehr/resources/queries/study/housing.query.xml new file mode 100644 index 0000000..eeb5e0d --- /dev/null +++ b/nbri_ehr/resources/queries/study/housing.query.xml @@ -0,0 +1,52 @@ + + + + + + + + In Date + + + true + false + true + true + Out Date + + + Location + /nbri_ehr/cageDetails.view?room=${room}&cage=${cage}& + + ehr_lookups + cage + location + cage + + + + Room + /nbri_ehr/cageDetails.view?room=${room}& + + ehr_lookups + rooms + room + name + + + + Reason For Move + + ehr_lookups + housing_reason + value + + + + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/housing/.qview.xml b/nbri_ehr/resources/queries/study/housing/.qview.xml new file mode 100644 index 0000000..bc780a5 --- /dev/null +++ b/nbri_ehr/resources/queries/study/housing/.qview.xml @@ -0,0 +1,15 @@ + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/housing/Active Housing.qview.xml b/nbri_ehr/resources/queries/study/housing/Active Housing.qview.xml new file mode 100644 index 0000000..4fc3eeb --- /dev/null +++ b/nbri_ehr/resources/queries/study/housing/Active Housing.qview.xml @@ -0,0 +1,24 @@ + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/necropsy.js b/nbri_ehr/resources/queries/study/necropsy.js new file mode 100644 index 0000000..65a914d --- /dev/null +++ b/nbri_ehr/resources/queries/study/necropsy.js @@ -0,0 +1,59 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); +var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); + +var deathIdMap = {}; + +function onInit(event, helper){ + + if (!helper.isETL() && event != 'truncate') { + LABKEY.Query.selectRows({ + requiredVersion: 9.1, + schemaName: 'study', + queryName: 'deaths', + columns: ['Id', 'QCState/Label'], + scope: this, + success: function (results) { + if (!results || !results.rows || results.rows.length < 1) + return; + + for (var i = 0; i < results.rows.length; i++) { + deathIdMap[results.rows[i]["Id"]["value"]] = {QCStateLabel: results.rows[i]["QCState/Label"]["value"]}; + } + }, + failure: function (error) { + console.log("error getting death data in death trigger onInit()\n" + error); + } + }); + } +} + +function onUpsert(helper, scriptErrors, row, oldRow) { + + if (!helper.isETL()) { + + if (deathIdMap[row.Id] && deathIdMap[row.Id].QCStateLabel && + (deathIdMap[row.Id].QCStateLabel.toUpperCase() === 'REQUEST: PENDING' || + deathIdMap[row.Id].QCStateLabel.toUpperCase() === 'REVIEW REQUIRED')) { + + if (!row.specimenCondition) + EHR.Server.Utils.addError(scriptErrors, 'specimenCondition', "'Condition of Specimen' is required", 'ERROR'); + if (!row.physicalCondition) + EHR.Server.Utils.addError(scriptErrors, 'physicalCondition', "'Physical Condition' is required", 'ERROR'); + if (!row.diagnosis) + EHR.Server.Utils.addError(scriptErrors, 'diagnosis', "'Diagnosis' is required", 'ERROR'); + if (!row.grossAbnormalities) + EHR.Server.Utils.addError(scriptErrors, 'grossAbnormalities', "'Gross Abnormalities' is required", 'ERROR'); + if (!row.accessionNumber) + EHR.Server.Utils.addError(scriptErrors, 'accessionNumber', "'Accession Number' is required", 'ERROR'); + } + } +} + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.AFTER_INSERT, 'study', 'necropsy', function(helper, scriptErrors, row, oldRow) { + triggerHelper.reportDataChange("study", "necropsy", [row.Id]); +}); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/necropsy.query.xml b/nbri_ehr/resources/queries/study/necropsy.query.xml new file mode 100644 index 0000000..35290a8 --- /dev/null +++ b/nbri_ehr/resources/queries/study/necropsy.query.xml @@ -0,0 +1,43 @@ + + + + + + + Exam Date + + + Category + + + Diagnosis + + + + ehr_lookups + necropsy_specimen_condition + value + + + + + ehr_lookups + necropsy_physical_condition + value + + + + true + + + true + + + + true + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/necropsy/.qview.xml b/nbri_ehr/resources/queries/study/necropsy/.qview.xml new file mode 100644 index 0000000..2a4be61 --- /dev/null +++ b/nbri_ehr/resources/queries/study/necropsy/.qview.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/necropsyStatus.sql b/nbri_ehr/resources/queries/study/necropsyStatus.sql new file mode 100644 index 0000000..622185d --- /dev/null +++ b/nbri_ehr/resources/queries/study/necropsyStatus.sql @@ -0,0 +1,10 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + demo.Id, + CASE WHEN d.QCState.Label = 'Request: Pending' OR d.QCState.Label = 'Review Required' THEN 'Necropsy Pending' ELSE demo.calculated_status END AS necropsy_status + FROM study.demographics demo +LEFT JOIN study.deaths d ON d.Id = demo.Id \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/nhpTraining.js b/nbri_ehr/resources/queries/study/nhpTraining.js new file mode 100644 index 0000000..f4d5931 --- /dev/null +++ b/nbri_ehr/resources/queries/study/nhpTraining.js @@ -0,0 +1,6 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/nhpTraining.query.xml b/nbri_ehr/resources/queries/study/nhpTraining.query.xml new file mode 100644 index 0000000..ecf5a11 --- /dev/null +++ b/nbri_ehr/resources/queries/study/nhpTraining.query.xml @@ -0,0 +1,46 @@ + + + + + Animal Training + + + + + Training Type + + ehr_lookups + nhp_training_type + value + + + + Reason + + ehr_lookups + nhp_training_reason + value + + + + Result + + ehr_lookups + nhp_training_result + value + + + + Training Staff + + + true + + + true + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/notes.js b/nbri_ehr/resources/queries/study/notes.js new file mode 100644 index 0000000..f4d5931 --- /dev/null +++ b/nbri_ehr/resources/queries/study/notes.js @@ -0,0 +1,6 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/notes.query.xml b/nbri_ehr/resources/queries/study/notes.query.xml new file mode 100644 index 0000000..e45f321 --- /dev/null +++ b/nbri_ehr/resources/queries/study/notes.query.xml @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + true + + + true + + + Type + true + + + Note + false + + + true + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/notes/.qview.xml b/nbri_ehr/resources/queries/study/notes/.qview.xml new file mode 100644 index 0000000..6cd9bab --- /dev/null +++ b/nbri_ehr/resources/queries/study/notes/.qview.xml @@ -0,0 +1,16 @@ + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/notificationAnimalProject.sql b/nbri_ehr/resources/queries/study/notificationAnimalProject.sql new file mode 100644 index 0000000..7437677 --- /dev/null +++ b/nbri_ehr/resources/queries/study/notificationAnimalProject.sql @@ -0,0 +1,13 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +-- Add more here to make a single query for animal details in notifications +SELECT + Id, + date, + project.name AS project, + enddate +FROM study.assignment +WHERE enddate IS NULL \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationOrdersByDate.sql b/nbri_ehr/resources/queries/study/observationOrdersByDate.sql new file mode 100644 index 0000000..6153c06 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationOrdersByDate.sql @@ -0,0 +1,59 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT +s.*, +co.qcstate.label AS obsStatus +FROM + (SELECT + s1.*, + timestampadd('SQL_TSI_MINUTE', ((s1.hours * 60) + s1.minutes), s1.origDate) AS date, + ((s1.hours * 60) + s1.minutes) AS timeOffset + + FROM ( + SELECT + t1.lsid, + t1.dataset, + t1.id AS animalid, + coalesce(ft.hourofday, ((hour(t1.date) * 100) + minute(t1.date))) AS time, + (coalesce(ft.hourofday, (hour(t1.date) * 100)) / 100) AS hours, + + CASE WHEN ft.hourofday IS NOT NULL + THEN (((ft.hourofday / 100.0) - floor(ft.hourofday / 100)) * 100) + ELSE minute(t1.date) + END AS minutes, + + dr.date AS origDate, + + t1.frequency.meaning AS frequency, + t1.date AS startDate, + timestampdiff('SQL_TSI_DAY', cast(t1.dateOnly AS timestamp), dr.dateOnly) + 1 AS daysElapsed, + t1.enddate, + t1.category, + t1.area, + t1.performedby, + t1.remark, + t1.caseid.objectid AS caseid, + t1.taskid, + t1.type, + t1.objectid, + + t1.qcstate + FROM nbri_ehr.dateRange dr + JOIN + + -- order by category to replace string with Daily Obs + (SELECT * FROM study.observation_order ORDER BY category) t1 + ON (dr.dateOnly >= t1.dateOnly AND (dr.dateOnly <= t1.enddate OR t1.enddate IS NULL) AND + --technically the first day of the treatment is day 1, not day 0 + ((mod(CAST(timestampdiff('SQL_TSI_DAY', CAST(t1.dateOnly AS timestamp), dr.dateOnly) AS integer), t1.frequency.intervalindays) = 0 AND t1.frequency.intervalindays IS NOT NULL AND t1.frequency.dayofweek IS NULL)) + AND (t1.frequency.weekDays IS NULL OR LOCATE(CAST(dr.DayOfWeek AS VARCHAR), t1.frequency.weekDays) > 0) + ) + LEFT JOIN ehr_lookups.treatment_frequency_times ft ON ft.frequency = t1.frequency.meaning + WHERE t1.date IS NOT NULL + + ) s1 +) s +LEFT JOIN study.clinical_observations co ON co.scheduledDate IS NOT NULL AND s.date = co.scheduledDate AND co.orderId = s.objectid \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule.query.xml b/nbri_ehr/resources/queries/study/observationSchedule.query.xml new file mode 100644 index 0000000..4d03aac --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule.query.xml @@ -0,0 +1,20 @@ + + + + + + Observation Schedule + + + + Scheduled Date/Time + + + Observations + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule.sql b/nbri_ehr/resources/queries/study/observationSchedule.sql new file mode 100644 index 0000000..7862407 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule.sql @@ -0,0 +1,49 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + g.id, + g.scheduledDate, + COUNT(g.caseid) cases, + o.observations, + SUM(g.obsCount) AS obsCount, + o.orderIds, + o.status, + o.taskids, + MAX(g.type) AS type, + MAX(g.caseid) AS caseid +FROM +( + SELECT + sch.animalId as id, + sch.date AS scheduledDate, + sch.caseid, + sch.type, + COUNT(sch.category) AS obsCount + FROM observationOrdersByDate sch + GROUP BY + sch.animalId, + sch.date, + sch.caseid, + sch.type +) g +LEFT JOIN ( + SELECT + obs.animalId AS id, + obs.date AS scheduledDate, + GROUP_CONCAT(DISTINCT obs.category, ';') AS observations, + GROUP_CONCAT(obs.objectid, ';') AS orderIds, + GROUP_CONCAT(obs.obsStatus, ';') AS status, + GROUP_CONCAT(DISTINCT(obs.taskid), ';') AS taskids + FROM observationOrdersByDate obs + GROUP BY obs.animalId, obs.date +) o ON g.id = o.id AND g.scheduledDate = o.scheduledDate +GROUP BY + g.id, + g.scheduledDate, + o.observations, + o.orderIds, + o.status, + o.taskids diff --git a/nbri_ehr/resources/queries/study/observationSchedule/.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/.qview.xml new file mode 100644 index 0000000..b91d5d4 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/.qview.xml @@ -0,0 +1,17 @@ + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Area 11.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Area 11.qview.xml new file mode 100644 index 0000000..0049449 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Area 11.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Area 51.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Area 51.qview.xml new file mode 100644 index 0000000..2a79261 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Area 51.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 10.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 10.qview.xml new file mode 100644 index 0000000..0730ade --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 10.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 10C.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 10C.qview.xml new file mode 100644 index 0000000..921c9a0 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 10C.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 27.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 27.qview.xml new file mode 100644 index 0000000..01bb682 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 27.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 28.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 28.qview.xml new file mode 100644 index 0000000..ebeef38 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 28.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 29.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 29.qview.xml new file mode 100644 index 0000000..ffbf857 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 29.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 30.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 30.qview.xml new file mode 100644 index 0000000..b0c0052 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 30.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 31.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 31.qview.xml new file mode 100644 index 0000000..28e5f72 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 31.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 31C.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 31C.qview.xml new file mode 100644 index 0000000..f9d36e5 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 31C.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 31D.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 31D.qview.xml new file mode 100644 index 0000000..f4724dd --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 31D.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 32.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 32.qview.xml new file mode 100644 index 0000000..3c7b8bc --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 32.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 34.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 34.qview.xml new file mode 100644 index 0000000..9258df6 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 34.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 37.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 37.qview.xml new file mode 100644 index 0000000..80b0bc5 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 37.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 41.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 41.qview.xml new file mode 100644 index 0000000..3858990 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 41.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 42.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 42.qview.xml new file mode 100644 index 0000000..2d323bc --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 42.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 43.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 43.qview.xml new file mode 100644 index 0000000..6cd00cd --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 43.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 44.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 44.qview.xml new file mode 100644 index 0000000..cf80abb --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 44.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 45.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 45.qview.xml new file mode 100644 index 0000000..f76ad48 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 45.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 46.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 46.qview.xml new file mode 100644 index 0000000..4772424 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 46.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 50.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 50.qview.xml new file mode 100644 index 0000000..2d1b266 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 50.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 52.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 52.qview.xml new file mode 100644 index 0000000..8082c4c --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 52.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 53.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 53.qview.xml new file mode 100644 index 0000000..8a02077 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 53.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 54A.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 54A.qview.xml new file mode 100644 index 0000000..1a245ff --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 54A.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observationSchedule/Building 54B.qview.xml b/nbri_ehr/resources/queries/study/observationSchedule/Building 54B.qview.xml new file mode 100644 index 0000000..3ab71fc --- /dev/null +++ b/nbri_ehr/resources/queries/study/observationSchedule/Building 54B.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observation_order.js b/nbri_ehr/resources/queries/study/observation_order.js new file mode 100644 index 0000000..f4d5931 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observation_order.js @@ -0,0 +1,6 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observation_order.query.xml b/nbri_ehr/resources/queries/study/observation_order.query.xml new file mode 100644 index 0000000..ec28463 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observation_order.query.xml @@ -0,0 +1,45 @@ + + + + + Observation Orders + + + + DateTime + + + false + DateTime + + + Category + + + Area + + ehr_lookups + observation_areas + value + + + + + Frequency + + ehr_lookups + treatment_frequency + meaning + + + + Ordered By + + + Type + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observation_order/.qview.xml b/nbri_ehr/resources/queries/study/observation_order/.qview.xml new file mode 100644 index 0000000..c02d2fb --- /dev/null +++ b/nbri_ehr/resources/queries/study/observation_order/.qview.xml @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observation_order/Active Behavior Orders.qview.xml b/nbri_ehr/resources/queries/study/observation_order/Active Behavior Orders.qview.xml new file mode 100644 index 0000000..d4c5c11 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observation_order/Active Behavior Orders.qview.xml @@ -0,0 +1,24 @@ + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observation_order/Active Clinical Orders.qview.xml b/nbri_ehr/resources/queries/study/observation_order/Active Clinical Orders.qview.xml new file mode 100644 index 0000000..1638c87 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observation_order/Active Clinical Orders.qview.xml @@ -0,0 +1,24 @@ + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observation_order/Behavior Orders.qview.xml b/nbri_ehr/resources/queries/study/observation_order/Behavior Orders.qview.xml new file mode 100644 index 0000000..343d9b8 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observation_order/Behavior Orders.qview.xml @@ -0,0 +1,23 @@ + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/observation_order/Clinical Orders.qview.xml b/nbri_ehr/resources/queries/study/observation_order/Clinical Orders.qview.xml new file mode 100644 index 0000000..5e1e749 --- /dev/null +++ b/nbri_ehr/resources/queries/study/observation_order/Clinical Orders.qview.xml @@ -0,0 +1,23 @@ + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/orchardData.sql b/nbri_ehr/resources/queries/study/orchardData.sql new file mode 100644 index 0000000..7597aa1 --- /dev/null +++ b/nbri_ehr/resources/queries/study/orchardData.sql @@ -0,0 +1,18 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + d.Id, + d.gender, + d.birth, + d.species.scientific_name as species, + pa.protocol.title as protocol, + InitCap(pa.protocol.InvestigatorId.LastName) || ', ' || InitCap(pa.protocol.InvestigatorId.FirstName) as PI, + InitCap(pa.protocol.AuthorId.LastName) || ', ' || InitCap(pa.protocol.AuthorId.FirstName) as Vet, + h.cage.cage as cage, + d.calculated_status as alive +FROM demographics d +LEFT JOIN housing h ON d.Id = h.Id +LEFT JOIN protocolAssignment pa ON d.Id = pa.Id AND pa.endDate is null \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/orchardIdsForTaskid.sql b/nbri_ehr/resources/queries/study/orchardIdsForTaskid.sql new file mode 100644 index 0000000..261c592 --- /dev/null +++ b/nbri_ehr/resources/queries/study/orchardIdsForTaskid.sql @@ -0,0 +1,17 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +PARAMETERS (MYTASKID VARCHAR) + +SELECT Id FROM (SELECT Id, taskid + FROM study.demographics + UNION + SELECT Id, taskid + FROM study.housing + UNION + SELECT Id, taskid + FROM study.protocolAssignment + ) u +WHERE u.taskid IS NOT NULL AND u.taskid = MYTASKID; \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/pairingSummary.query.xml b/nbri_ehr/resources/queries/study/pairingSummary.query.xml new file mode 100644 index 0000000..0d3b843 --- /dev/null +++ b/nbri_ehr/resources/queries/study/pairingSummary.query.xml @@ -0,0 +1,24 @@ + + + + + Pairing Summary + + + + 80 + + + Remark on Formation + + + Remark on Separation + + + Formation/Separation Type + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/pairingSummary.sql b/nbri_ehr/resources/queries/study/pairingSummary.sql new file mode 100644 index 0000000..3192d31 --- /dev/null +++ b/nbri_ehr/resources/queries/study/pairingSummary.sql @@ -0,0 +1,25 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + p.updatePairing, + p.Id, + (SELECT group_concat(distinct p2.Id, chr(10)) AS Ids FROM study.pairings p2 WHERE p.Id != p2.id AND p.pairId = p2.pairId) as otherIds, + p.pairid, + p.date, + p.enddate, + TIMESTAMPDIFF('SQL_TSI_DAY', p.date, coalesce(p.enddate,curdate())) as duration, + p.reason, + p.goal, + p.endState, + p.observation, + p.separationreason, + p.remark as formationRemark, + p.separationRemark, + p.performedby, + p.taskid, + p.type + +FROM study.pairings p \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/pairingSummary/.qview.xml b/nbri_ehr/resources/queries/study/pairingSummary/.qview.xml new file mode 100644 index 0000000..f0fdcf4 --- /dev/null +++ b/nbri_ehr/resources/queries/study/pairingSummary/.qview.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/nbri_ehr/resources/queries/study/pairingSummary/Active Pairing.qview.xml b/nbri_ehr/resources/queries/study/pairingSummary/Active Pairing.qview.xml new file mode 100644 index 0000000..14e0dfe --- /dev/null +++ b/nbri_ehr/resources/queries/study/pairingSummary/Active Pairing.qview.xml @@ -0,0 +1,29 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/nbri_ehr/resources/queries/study/pairingSummary/Pairing History.qview.xml b/nbri_ehr/resources/queries/study/pairingSummary/Pairing History.qview.xml new file mode 100644 index 0000000..1a11617 --- /dev/null +++ b/nbri_ehr/resources/queries/study/pairingSummary/Pairing History.qview.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/nbri_ehr/resources/queries/study/pairings.js b/nbri_ehr/resources/queries/study/pairings.js new file mode 100644 index 0000000..62c522d --- /dev/null +++ b/nbri_ehr/resources/queries/study/pairings.js @@ -0,0 +1,15 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); + +var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_UPSERT, 'study', 'pairings', function(helper, scriptErrors, row, oldRow) { + + if (row.cage && row.Id && row.date && !triggerHelper.validateHousing(row.Id, row.cage, row.date)){ + EHR.Server.Utils.addError(scriptErrors, 'cage', 'Not housed in this location on this date', 'INFO'); + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/pairings.query.xml b/nbri_ehr/resources/queries/study/pairings.query.xml new file mode 100644 index 0000000..727a724 --- /dev/null +++ b/nbri_ehr/resources/queries/study/pairings.query.xml @@ -0,0 +1,90 @@ + + + + + + + + + + false + + + Pair Id + + + Location + + ehr_lookups + cage + location + cage + + + + Introduction Reason + 150 + + ehr_lookups + pairing_reason + value + + + + Goal + 100 + + ehr_lookups + pairing_goal + value + + + + Formation Type + + ehr_lookups + pairing_formation_types + value + + + + Remark on Formation + 200 + + + Interaction Summary + + ehr_lookups + pairing_observation + value + + + + End State + 100 + + ehr_lookups + pairing_goal + value + + + + Separation Reason + 100 + + ehr_lookups + pairing_separation_reason + value + + + + + Remark on Separation + 200 + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/pairings/.qview.xml b/nbri_ehr/resources/queries/study/pairings/.qview.xml new file mode 100644 index 0000000..26a8731 --- /dev/null +++ b/nbri_ehr/resources/queries/study/pairings/.qview.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/nbri_ehr/resources/queries/study/parentageSummary.query.xml b/nbri_ehr/resources/queries/study/parentageSummary.query.xml new file mode 100644 index 0000000..1efefbc --- /dev/null +++ b/nbri_ehr/resources/queries/study/parentageSummary.query.xml @@ -0,0 +1,25 @@ + + + + + Parentage Summary + + + Parent + + study + animal + id + + + + Relationship + + + Method + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/parentageSummary.sql b/nbri_ehr/resources/queries/study/parentageSummary.sql new file mode 100644 index 0000000..e9299ee --- /dev/null +++ b/nbri_ehr/resources/queries/study/parentageSummary.sql @@ -0,0 +1,36 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +SELECT + d.Id, + d.date, + d.dam as parent, + 'Dam' as relationship, + 'Observed' as method + +FROM study.demographics d +WHERE d.qcstate.publicdata = true + +UNION ALL + +SELECT + d.Id, + d.date, + d.sire as parent, + 'Sire' as relationship, + 'Observed' as method + +FROM study.demographics d +WHERE d.qcstate.publicdata = true diff --git a/nbri_ehr/resources/queries/study/physicalExam/.qview.xml b/nbri_ehr/resources/queries/study/physicalExam/.qview.xml new file mode 100644 index 0000000..caf3fb0 --- /dev/null +++ b/nbri_ehr/resources/queries/study/physicalExam/.qview.xml @@ -0,0 +1,16 @@ + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prc.js b/nbri_ehr/resources/queries/study/prc.js new file mode 100644 index 0000000..b3123b8 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prc.js @@ -0,0 +1,32 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +require("ehr/triggers").initScript(this); + +var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_INSERT, 'study', 'prc', function(helper, scriptErrors, row, oldRow) { + if(row.orderid && triggerHelper.isProcedureOrderEntered(row.orderid)) { + EHR.Server.Utils.addError(scriptErrors, 'orderid', 'Procedure order has already been closed.', 'ERROR'); + } +}); + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.COMPLETE, 'study', 'prc', function (event, errors, helper) { + + if (!helper.isValidateOnly()){ + var rows = helper.getRows(); + var orderIds = []; + for (var i=0;i + + + + + + + + Category + + ehr_lookups + data_category + value + + + + + Procedure + false + + ehr_lookups + procedures + rowid + name + + + + Order Id + + study + prc_order + objectid + + + + + ehr.context + /ehr/studyButtons.js + EHR.DatasetButtons.moreActionsHandler + + Grid Views + + + Charts + + + Export + + + Print + + + + + EHR.DatasetButtons.historyHandler(dataRegion, dataRegionName); + + + + + EHR.window.GetDistinctWindow.getDistinctHandler(dataRegionName); + + + + + EHR.DatasetButtons.showAuditHistoryHandler(dataRegionName); + + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prc/.qview.xml b/nbri_ehr/resources/queries/study/prc/.qview.xml new file mode 100644 index 0000000..f5ed643 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prc/.qview.xml @@ -0,0 +1,14 @@ + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcOverdue.query.xml b/nbri_ehr/resources/queries/study/prcOverdue.query.xml new file mode 100644 index 0000000..2cf3260 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcOverdue.query.xml @@ -0,0 +1,154 @@ + + + + + Overdue Procedures + objectid + + + true + + + true + + + + study + animal + Id + + + + 250 + + + 40 + + ehr_lookups + rooms + Room + + + + 40 + + + true + + core + qcstate + rowid + + + + false + true + Procedure Status + 150 + + + + + + FBEC5D + + + + + + FBEC5D + + + + + + FBEC5D + + + + + + FF0000 + + + + + + FBEC5D + + + + + + FBEC5D + + + + + + FF0000 + + + + + + FBEC5D + + + + + true + Task Id + + ehr + tasks + taskid + + /ehr/taskDetails.view?formtype=${taskid/formtype}&taskid=${taskid} + + + + ehr.context + /ehr/studyButtons.js + nbri_ehr/buttons/RecordProcedureButton.js + nbri_ehr/buttons/ProcedureOrderCompleteButton.js + EHR.DatasetButtons.moreActionsHandler + + Grid Views + + + Charts + + + Export + + + Print + + + + + NBRI_EHR.RecordProcedureButton.recordProceduresHandler(dataRegion); + + + + + NBRI_EHR.ProcedureOrderCompleteButton.procedureOrderCompleteHandler(dataRegion); + + + + + EHR.DatasetButtons.historyHandler(dataRegion, dataRegionName); + + + + + EHR.window.GetDistinctWindow.getDistinctHandler(dataRegionName); + + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcOverdue.sql b/nbri_ehr/resources/queries/study/prcOverdue.sql new file mode 100644 index 0000000..8bf6ff8 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcOverdue.sql @@ -0,0 +1,20 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + po.procedureRecord, + po.Id, + po.procedure, + po.windowStart, + po.windowEnd, + timestampdiff('SQL_TSI_DAY', po.windowEnd, now()) as daysOverdue, + po.orderedby, + po.remark, + po.caseid, + po.objectid, + po.lsid, + CASE WHEN po.qcstate.label = 'Completed' THEN 'Completed' ELSE '' END as status +FROM prc_order po +WHERE now() > windowEnd AND po.qcstate.label != 'Completed' \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcOverdue/.qview.xml b/nbri_ehr/resources/queries/study/prcOverdue/.qview.xml new file mode 100644 index 0000000..b8bf120 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcOverdue/.qview.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcOverdueNotification.sql b/nbri_ehr/resources/queries/study/prcOverdueNotification.sql new file mode 100644 index 0000000..f9b41fc --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcOverdueNotification.sql @@ -0,0 +1,18 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + pod.Id, + pod.Id.demographics.species.common_name AS species, + pod.Id.curLocation.room.name AS room, + pod.Id.curLocation.cage.cage AS cage, + pod.procedure.name AS procedure, + pod.orderedby.displayName AS orderedBy, + pod.windowStart, + pod.windowEnd, + pod.daysOverdue, + pod.remark, +FROM prcOverdue pod +ORDER BY pod.daysOverdue DESC \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcOverdueNotification/.qview.xml b/nbri_ehr/resources/queries/study/prcOverdueNotification/.qview.xml new file mode 100644 index 0000000..c647e7b --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcOverdueNotification/.qview.xml @@ -0,0 +1,5 @@ + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule.query.xml b/nbri_ehr/resources/queries/study/prcSchedule.query.xml new file mode 100644 index 0000000..05c09db --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule.query.xml @@ -0,0 +1,154 @@ + + + + + Procedure Schedule + objectid + + + true + + + true + + + + study + animal + Id + + + + 250 + + + 40 + + ehr_lookups + rooms + Room + + + + 40 + + + true + + core + qcstate + rowid + + + + false + true + Procedure Status + 150 + + + + + + FBEC5D + + + + + + FBEC5D + + + + + + FBEC5D + + + + + + FF0000 + + + + + + FBEC5D + + + + + + FBEC5D + + + + + + FF0000 + + + + + + FBEC5D + + + + + true + Task Id + + ehr + tasks + taskid + + /ehr/taskDetails.view?formtype=${taskid/formtype}&taskid=${taskid} + + + + ehr.context + /ehr/studyButtons.js + nbri_ehr/buttons/RecordProcedureButton.js + nbri_ehr/buttons/ProcedureOrderCompleteButton.js + EHR.DatasetButtons.moreActionsHandler + + Grid Views + + + Charts + + + Export + + + Print + + + + + NBRI_EHR.RecordProcedureButton.recordProceduresHandler(dataRegion); + + + + + NBRI_EHR.ProcedureOrderCompleteButton.procedureOrderCompleteHandler(dataRegion); + + + + + EHR.DatasetButtons.historyHandler(dataRegion, dataRegionName); + + + + + EHR.window.GetDistinctWindow.getDistinctHandler(dataRegionName); + + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule.sql b/nbri_ehr/resources/queries/study/prcSchedule.sql new file mode 100644 index 0000000..c4dbce3 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule.sql @@ -0,0 +1,20 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +SELECT + po.procedureRecord, + po.Id, + po.procedure, + po.windowStart, + po.windowEnd, + po.orderedby, + po.remark, + po.caseid, + po.objectid, + po.lsid, + CASE WHEN po.qcstate.label = 'Completed' THEN 'Completed' ELSE '' END as status +FROM prc_order po +WHERE now() >= windowStart AND now() <= windowEnd \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/.qview.xml new file mode 100644 index 0000000..4604b77 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/.qview.xml @@ -0,0 +1,23 @@ + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Area 11.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Area 11.qview.xml new file mode 100644 index 0000000..2aef3b2 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Area 11.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Area 51.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Area 51.qview.xml new file mode 100644 index 0000000..f97a204 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Area 51.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 10.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 10.qview.xml new file mode 100644 index 0000000..6c5eaa2 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 10.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 10C.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 10C.qview.xml new file mode 100644 index 0000000..614726e --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 10C.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 27.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 27.qview.xml new file mode 100644 index 0000000..8bdd55c --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 27.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 28.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 28.qview.xml new file mode 100644 index 0000000..e42b1c0 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 28.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 29.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 29.qview.xml new file mode 100644 index 0000000..6d5dc4e --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 29.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 30.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 30.qview.xml new file mode 100644 index 0000000..e1bc3c7 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 30.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 31.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 31.qview.xml new file mode 100644 index 0000000..e44e698 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 31.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 31C.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 31C.qview.xml new file mode 100644 index 0000000..0a00bd5 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 31C.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 31D.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 31D.qview.xml new file mode 100644 index 0000000..98001ff --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 31D.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 32.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 32.qview.xml new file mode 100644 index 0000000..9dba6f2 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 32.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 34.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 34.qview.xml new file mode 100644 index 0000000..cd9c218 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 34.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 37.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 37.qview.xml new file mode 100644 index 0000000..4690ac7 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 37.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 41.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 41.qview.xml new file mode 100644 index 0000000..c7de509 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 41.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 42.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 42.qview.xml new file mode 100644 index 0000000..132d694 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 42.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 43.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 43.qview.xml new file mode 100644 index 0000000..c75574b --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 43.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 44.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 44.qview.xml new file mode 100644 index 0000000..e14ac0c --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 44.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 45.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 45.qview.xml new file mode 100644 index 0000000..7715928 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 45.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 46.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 46.qview.xml new file mode 100644 index 0000000..37d8849 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 46.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 50.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 50.qview.xml new file mode 100644 index 0000000..c454e30 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 50.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 52.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 52.qview.xml new file mode 100644 index 0000000..f65d618 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 52.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 53.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 53.qview.xml new file mode 100644 index 0000000..7b1c4a0 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 53.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 54A.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 54A.qview.xml new file mode 100644 index 0000000..671bbcc --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 54A.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prcSchedule/Building 54B.qview.xml b/nbri_ehr/resources/queries/study/prcSchedule/Building 54B.qview.xml new file mode 100644 index 0000000..2d51bae --- /dev/null +++ b/nbri_ehr/resources/queries/study/prcSchedule/Building 54B.qview.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prc_order.js b/nbri_ehr/resources/queries/study/prc_order.js new file mode 100644 index 0000000..d206b3e --- /dev/null +++ b/nbri_ehr/resources/queries/study/prc_order.js @@ -0,0 +1,14 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +require("ehr/triggers").initScript(this); + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_INSERT, 'study', 'prc_order', function (helper, scriptErrors, row, oldRow) { + if (!helper.isValidateOnly()) { + row.qcstate = helper.getJavaHelper().getQCStateForLabel('Request: Approved').getRowId(); + row.qcstateLabel = 'Request: Approved'; + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prc_order.query.xml b/nbri_ehr/resources/queries/study/prc_order.query.xml new file mode 100644 index 0000000..ef4dba7 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prc_order.query.xml @@ -0,0 +1,84 @@ + + + + + Procedure Orders + + + + + + + + + Window Start + false + + + Window End + false + + + Category + + ehr_lookups + data_category + value + + + + + Procedure + false + + ehr_lookups + procedures + rowid + name + + + + + ehr.context + /ehr/studyButtons.js + nbri_ehr/buttons/ProcedureOrderCompleteButton.js + EHR.DatasetButtons.moreActionsHandler + + Grid Views + + + Charts + + + Export + + + Print + + + + + NBRI_EHR.ProcedureOrderCompleteButton.procedureOrderCompleteHandler(dataRegion); + + + + + EHR.DatasetButtons.historyHandler(dataRegion, dataRegionName); + + + + + EHR.window.GetDistinctWindow.getDistinctHandler(dataRegionName); + + + + + EHR.DatasetButtons.showAuditHistoryHandler(dataRegionName); + + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prc_order/.qview.xml b/nbri_ehr/resources/queries/study/prc_order/.qview.xml new file mode 100644 index 0000000..b9de6c1 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prc_order/.qview.xml @@ -0,0 +1,17 @@ + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prc_order_report.query.xml b/nbri_ehr/resources/queries/study/prc_order_report.query.xml new file mode 100644 index 0000000..ad316a0 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prc_order_report.query.xml @@ -0,0 +1,84 @@ + + + + + Procedure Order Report + + + + + + + + + Window Start + false + + + Window End + false + + + Category + + ehr_lookups + data_category + value + + + + + Procedure + false + + ehr_lookups + procedures + rowid + name + + + + + ehr.context + /ehr/studyButtons.js + nbri_ehr/buttons/ProcedureOrderCompleteButton.js + EHR.DatasetButtons.moreActionsHandler + + Grid Views + + + Charts + + + Export + + + Print + + + + + NBRI_EHR.ProcedureOrderCompleteButton.procedureOrderCompleteHandler(dataRegion); + + + + + EHR.DatasetButtons.historyHandler(dataRegion, dataRegionName); + + + + + EHR.window.GetDistinctWindow.getDistinctHandler(dataRegionName); + + + + + EHR.DatasetButtons.showAuditHistoryHandler(dataRegionName); + + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prc_order_report.sql b/nbri_ehr/resources/queries/study/prc_order_report.sql new file mode 100644 index 0000000..0488ae9 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prc_order_report.sql @@ -0,0 +1,6 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT *, CASE WHEN qcstate.label = 'Completed' THEN 'Completed' ELSE '' END as status FROM study.prc_order \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/prc_order_report/.qview.xml b/nbri_ehr/resources/queries/study/prc_order_report/.qview.xml new file mode 100644 index 0000000..62d20f0 --- /dev/null +++ b/nbri_ehr/resources/queries/study/prc_order_report/.qview.xml @@ -0,0 +1,17 @@ + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/pregnancy.js b/nbri_ehr/resources/queries/study/pregnancy.js new file mode 100644 index 0000000..7717a71 --- /dev/null +++ b/nbri_ehr/resources/queries/study/pregnancy.js @@ -0,0 +1,20 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); + +var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.ON_BECOME_PUBLIC, 'study', 'pregnancy', function(scriptErrors, helper, row, oldRow) { + if (!helper.isETL()) { + + var outcomeRec = { + Id: row.Id, + date: row.date, + result: row.result + } + triggerHelper.sendPregnancyOutcomeNotification(row.Id, outcomeRec); + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/pregnancy.query.xml b/nbri_ehr/resources/queries/study/pregnancy.query.xml new file mode 100644 index 0000000..35663f8 --- /dev/null +++ b/nbri_ehr/resources/queries/study/pregnancy.query.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + + Delivery Date + + + Outcome + + ehr_lookups + pregnancy_result + value + title + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/protocolAssignment.js b/nbri_ehr/resources/queries/study/protocolAssignment.js new file mode 100644 index 0000000..32c56ce --- /dev/null +++ b/nbri_ehr/resources/queries/study/protocolAssignment.js @@ -0,0 +1,153 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); +var protocolData = {}; +var prevAnimalId; +var prevDate; + +var missing = []; + +var count = 0; + +var triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); + +function getLastAssignment(id){ + var batchLastDate; + + LABKEY.Query.selectRows({ + schemaName: 'study', + queryName: 'protocolAssignment', + columns: 'Id,date', + filterArray: [LABKEY.Filter.create('Id', id)], + sort: '-date', + success: function (results) { + if (results.rows.length) { + batchLastDate = results.rows[0].date; + } + }, + scope: this + }); + + return batchLastDate; +} + +function onInit(event, helper){ + + if (helper.isETL()) { + LABKEY.Query.selectRows({ + schemaName: 'ehr', + queryName: 'protocol', + columns: 'title,objectid', + success: function (results) { + if (results.rows.length) { + for (var i = 0; i < results.rows.length; i++) { + let rec = results.rows[i]; + protocolData[rec.objectid] = rec.title; + } + } + }, + scope: this + }); + } +} + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_INSERT, 'study', 'protocolAssignment', function (helper, scriptErrors, row, oldRow) { + + if (helper.isETL()) { + var isTransfer = prevAnimalId === row.Id; + + if (row.remark) { + var remarkTextArr = row.remark.split(':'); + var toProtocol = remarkTextArr[3].split(' (')[0]; // Get "To Protocol:" value without segment + var protocolId; + + protocolId = getProtocolIdByName(toProtocol); + if (!protocolId || protocolId === 'undefined') { + if (missing.indexOf(toProtocol) === -1) + missing.push(toProtocol) + } + else { + row.protocol = protocolId; + } + if (isTransfer) { + if (row.enddate) { + // End date will initially have animal death/departure. Override if the transfer is older. + var death = new Date(row.enddate); + var prev = new Date(prevDate); + + // Sanity check + if (prev < death) { + row.enddate = prevDate; + } + } + else { + row.enddate = prevDate; + } + } + else if (count === 0) { + // This handles batch boundary row for full truncate ETL, which is the only ETL setup for this currently. + // Gets previous date from db for first row in batch + var batchLastDate = getLastAssignment(row.Id); + if (batchLastDate) { + row.enddate = batchLastDate; + } + } + + if (row.enddate === 'undefined') { + console.log("end date not found for animal event - " + row.animalEventId); + } + } + + prevAnimalId = row.Id; + prevDate = row.date; + count++; + } + +}); + + +function getProtocolIdByName(protocolName) { + var protocols = Object.keys(protocolData); + + // Search protocols for exact case-insensitive match + for (var i = 0; i< protocols.length; i++) { + var pName = protocolData[protocols[i]] ; + if (pName && protocolName.trim().toLowerCase() === pName.toString().toLowerCase()) { + return protocols[i]; + } + } + + // If exact match not found, search for partial match at beginning of protocol + for (i = 0; i< protocols.length; i++) { + pName = protocolData[protocols[i]] ; + if (pName && protocolName.trim().toLowerCase().indexOf(pName.toString().toLowerCase()) === 0) { + return protocols[i]; + } + } +} + +function onComplete(event, errors, helper){ + + if (!helper.isValidateOnly() && !helper.isETL()) { + var updateRows = helper.getRows(); + + // When closing previous records, we don't need to update the orchard file. Use the same flag as demographics providers. + var skipAnnounceChangedParticipants = false; + var extraContext = helper.getProperty('extraContext'); + if (extraContext) { + skipAnnounceChangedParticipants = extraContext.skipAnnounceChangedParticipants; + } + + if (updateRows && updateRows.length > 0 && + updateRows[0].row.taskid && + updateRows[0].row.QCStateLabel && + EHR.Server.Security.getQCStateByLabel(updateRows[0].row.QCStateLabel).PublicData && + !skipAnnounceChangedParticipants + ) { + triggerHelper.generateOrchardFile(updateRows[0].row.taskid); + } + } +} diff --git a/nbri_ehr/resources/queries/study/protocolAssignment.query.xml b/nbri_ehr/resources/queries/study/protocolAssignment.query.xml new file mode 100644 index 0000000..ac61d1c --- /dev/null +++ b/nbri_ehr/resources/queries/study/protocolAssignment.query.xml @@ -0,0 +1,30 @@ + + + + + + + + + + true + + + Protocol + + ehr + protocol + protocol + title + + + + + + true + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/protocolAssignment/Active Assignments.qview.xml b/nbri_ehr/resources/queries/study/protocolAssignment/Active Assignments.qview.xml new file mode 100644 index 0000000..1f07c5a --- /dev/null +++ b/nbri_ehr/resources/queries/study/protocolAssignment/Active Assignments.qview.xml @@ -0,0 +1,8 @@ + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/recentCases.sql b/nbri_ehr/resources/queries/study/recentCases.sql new file mode 100644 index 0000000..7e65271 --- /dev/null +++ b/nbri_ehr/resources/queries/study/recentCases.sql @@ -0,0 +1,11 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +PARAMETERS(SubjectId VARCHAR, CaseCategory VARCHAR) + +SELECT * FROM study.cases +WHERE Id = SubjectId AND category = CaseCategory +ORDER BY date DESC LIMIT 20 \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/serology.query.xml b/nbri_ehr/resources/queries/study/serology.query.xml new file mode 100644 index 0000000..99f97bd --- /dev/null +++ b/nbri_ehr/resources/queries/study/serology.query.xml @@ -0,0 +1,25 @@ + + + + + + + + + + + + + Date + + + Lab + + + Type + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/serology/.qview.xml b/nbri_ehr/resources/queries/study/serology/.qview.xml new file mode 100644 index 0000000..2effb18 --- /dev/null +++ b/nbri_ehr/resources/queries/study/serology/.qview.xml @@ -0,0 +1,11 @@ + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/tissueDisposition.js b/nbri_ehr/resources/queries/study/tissueDisposition.js new file mode 100644 index 0000000..f4d5931 --- /dev/null +++ b/nbri_ehr/resources/queries/study/tissueDisposition.js @@ -0,0 +1,6 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +require("ehr/triggers").initScript(this); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/tissueDisposition.query.xml b/nbri_ehr/resources/queries/study/tissueDisposition.query.xml new file mode 100644 index 0000000..494a4ab --- /dev/null +++ b/nbri_ehr/resources/queries/study/tissueDisposition.query.xml @@ -0,0 +1,40 @@ + + + + + + + Tissue + 80 + + ehr_lookups + necropsy_tissue + value + + + + Tissue Disposition Code + 180 + + ehr_lookups + necropsy_disposition_codes + value + + + + true + + + true + + + true + + + true + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/tissueDisposition/.qview.xml b/nbri_ehr/resources/queries/study/tissueDisposition/.qview.xml new file mode 100644 index 0000000..428b937 --- /dev/null +++ b/nbri_ehr/resources/queries/study/tissueDisposition/.qview.xml @@ -0,0 +1,12 @@ + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule.query.xml b/nbri_ehr/resources/queries/study/treatmentSchedule.query.xml new file mode 100644 index 0000000..59d1f2e --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule.query.xml @@ -0,0 +1,187 @@ + + + + + Treatment Schedule + /EHR/treatmentDetails.view?key=${lsid} + primaryKey + + + true + + + true + true + + + true + + + + study + animal + Id + + + + Treatment Start Date + DateTime + + + false + Treatment + + ehr_lookups + snomed + code + + + + + true + + ehr_lookups + treatment_frequency + meaning + + + + 250 + + + 40 + + ehr_lookups + rooms + Room + + + + 40 + + + true + + + true + + core + qcstate + rowid + + + + Concentration + + + Amount + + + Volume + + + false + true + Treatment Status + 150 + + + + + + FBEC5D + + + + + + FBEC5D + + + + + + FBEC5D + + + + + + FF0000 + + + + + + FBEC5D + + + + + + FBEC5D + + + + + + FF0000 + + + + + + FBEC5D + + + + + false + Task Id + + ehr + tasks + taskid + + /ehr/taskDetails.view?formtype=${taskid/formtype}&taskid=${taskid} + + + + ehr.context + /ehr/studyButtons.js + nbri_ehr/buttons/RecordTreatmentButton.js + EHR.DatasetButtons.moreActionsHandler + + Grid Views + + + Charts + + + Export + + + Print + + + + + NBRI_EHR.RecordTreatmentButton.recordTreatmentsHandler(dataRegion); + + + + + EHR.DatasetButtons.historyHandler(dataRegion, dataRegionName); + + + + + EHR.window.GetDistinctWindow.getDistinctHandler(dataRegionName); + + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule.sql b/nbri_ehr/resources/queries/study/treatmentSchedule.sql new file mode 100644 index 0000000..2cfd6a1 --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule.sql @@ -0,0 +1,79 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +SELECT +d.id, +d_alias.alias AS Name, +d.calculated_status, +s.*, +s.objectid AS treatmentid, +drug.treatmentStatus, +s.objectid || '-pkSeparator-' || s.date AS primaryKey -- -pkSeparator- is used to separate the two parts of the primary key in RecordTreatmentButton.js +FROM study.demographics d +JOIN( + SELECT + s1.*, + timestampadd('SQL_TSI_MINUTE', ((s1.hours * 60) + s1.minutes), s1.origDate) AS date, + ((s1.hours * 60) + s1.minutes) AS timeOffset + FROM ( + SELECT + t1.lsid, + t1.objectid, + t1.dataset, + t1.id AS animalid, + + COALESCE(ft.hourofday, ((hour(t1.date) * 100) + minute(t1.date))) AS time, + (COALESCE(ft.hourofday, (hour(t1.date) * 100)) / 100) AS hours, + CASE + WHEN (ft.hourofday IS NOT NULL) THEN (((ft.hourofday / 100.0) - floor(ft.hourofday / 100)) * 100) + ELSE minute(t1.date) + END AS minutes, + dr.date AS origDate, + t1.category, + t1.frequency.meaning AS frequency, + t1.date AS startDate, + timestampdiff('SQL_TSI_DAY', cast(t1.dateOnly AS timestamp), dr.dateOnly) + 1 AS daysElapsed, + t1.enddate, + t1.code, + t1.treatmentRecord, + t1.volume, + t1.vol_units, + t1.concentration, + t1.conc_units, + t1.amount, + t1.amount_units, + t1.amountWithUnits, + t1.amountAndVolume, + t1.dosage, + t1.dosage_units, + t1.route, + IFDEFINED(t1.reason) AS reason, + t1.performedby, + t1.remark, + t1.caseid, + t1.orderedby, + t1.qcstate + FROM nbri_ehr.dateRange dr + JOIN study."Treatment Orders" t1 ON (dr.dateOnly >= t1.dateOnly AND + --technically the first day of the treatment is day 1, not day 0 + ((mod(CAST(timestampdiff('SQL_TSI_DAY', CAST(t1.dateOnly AS timestamp), dr.dateOnly) AS integer), t1.frequency.intervalindays) = 0 AND t1.frequency.intervalindays IS NOT NULL AND t1.frequency.dayofweek IS NULL )) + AND (t1.frequency.weekDays IS NULL OR LOCATE(CAST(dr.DayOfWeek AS VARCHAR), t1.frequency.weekDays) > 0) + ) + LEFT JOIN ehr_lookups.treatment_frequency_times ft ON ft.frequency = t1.frequency.meaning + --NOTE: if we run this report on a future interval, we want to include those treatments + WHERE t1.date IS NOT NULL + + ) s1 + +) s ON (s.animalid = d.id) +LEFT JOIN ( + SELECT treatmentid, IFDEFINED(scheduledDate) AS scheduledDate, MAX(qcstate.label) AS treatmentStatus + FROM study.drug + GROUP BY treatmentid, IFDEFINED(scheduledDate) +) drug ON s.objectid = drug.treatmentid AND s.date = drug.scheduledDate +LEFT JOIN (SELECT Id, GROUP_CONCAT(alias, ', ') alias FROM alias WHERE category.title = 'Name' GROUP BY Id) d_alias ON d.id = d_alias.id +WHERE (d.lastDayatCenter IS NULL OR d.lastDayAtCenter > s.enddate OR s.enddate IS NULL) + AND s.date >= s.startDate AND (s.enddate IS NULL OR s.date <= s.enddate) \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/.qview.xml new file mode 100644 index 0000000..4c57f0b --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/.qview.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Area 11.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Area 11.qview.xml new file mode 100644 index 0000000..ffd2a51 --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Area 11.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Area 51.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Area 51.qview.xml new file mode 100644 index 0000000..af198fa --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Area 51.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 10.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 10.qview.xml new file mode 100644 index 0000000..6ad2225 --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 10.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 10C.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 10C.qview.xml new file mode 100644 index 0000000..3c284c8 --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 10C.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 27.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 27.qview.xml new file mode 100644 index 0000000..1c63b9e --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 27.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 28.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 28.qview.xml new file mode 100644 index 0000000..71626c2 --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 28.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 29.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 29.qview.xml new file mode 100644 index 0000000..51b805f --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 29.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 30.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 30.qview.xml new file mode 100644 index 0000000..b60a8d8 --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 30.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 31.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 31.qview.xml new file mode 100644 index 0000000..5600c8c --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 31.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 31C.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 31C.qview.xml new file mode 100644 index 0000000..d8a6f0e --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 31C.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 31D.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 31D.qview.xml new file mode 100644 index 0000000..b323a42 --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 31D.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 32.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 32.qview.xml new file mode 100644 index 0000000..45336bf --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 32.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 34.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 34.qview.xml new file mode 100644 index 0000000..0a36b29 --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 34.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 37.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 37.qview.xml new file mode 100644 index 0000000..3598574 --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 37.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 41.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 41.qview.xml new file mode 100644 index 0000000..88a2791 --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 41.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 42.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 42.qview.xml new file mode 100644 index 0000000..53c001b --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 42.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 43.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 43.qview.xml new file mode 100644 index 0000000..159dcd3 --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 43.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 44.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 44.qview.xml new file mode 100644 index 0000000..92044fa --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 44.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 45.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 45.qview.xml new file mode 100644 index 0000000..3b4bdf4 --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 45.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 46.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 46.qview.xml new file mode 100644 index 0000000..ab88e99 --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 46.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 50.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 50.qview.xml new file mode 100644 index 0000000..696895c --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 50.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 52.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 52.qview.xml new file mode 100644 index 0000000..dc6ad0a --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 52.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 53.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 53.qview.xml new file mode 100644 index 0000000..73ca7b1 --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 53.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 54A.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 54A.qview.xml new file mode 100644 index 0000000..4943b37 --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 54A.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Building 54B.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 54B.qview.xml new file mode 100644 index 0000000..58ae6bd --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Building 54B.qview.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatmentSchedule/Clinical Medications.qview.xml b/nbri_ehr/resources/queries/study/treatmentSchedule/Clinical Medications.qview.xml new file mode 100644 index 0000000..5698039 --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatmentSchedule/Clinical Medications.qview.xml @@ -0,0 +1,8 @@ + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatment_order.js b/nbri_ehr/resources/queries/study/treatment_order.js new file mode 100644 index 0000000..0b04f2c --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatment_order.js @@ -0,0 +1,23 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +require("ehr/triggers").initScript(this); + +let triggerHelper = new org.labkey.nbri_ehr.query.NBRI_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id); + +EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_UPSERT, 'study', 'treatment_order', function(helper, scriptErrors, row, oldRow) { + // Max reasonable amount warning. Error when the amount is greater than the max reasonable amount + if (row.code) { + let drugFormulary = triggerHelper.getFormularyForDrug(row.code); + if (drugFormulary && drugFormulary.maxAmount && row.amount > drugFormulary.maxAmount) { + EHR.Server.Utils.addError(scriptErrors, 'amount', 'Amount is greater than the maximum reasonable amount: ' + drugFormulary.maxAmount, 'ERROR'); + } + } + + if (row.volume && !row.vol_units) { + EHR.Server.Utils.addError(scriptErrors, 'volume', 'Units required for volume.', 'ERROR'); + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatment_order.query.xml b/nbri_ehr/resources/queries/study/treatment_order.query.xml new file mode 100644 index 0000000..c2849aa --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatment_order.query.xml @@ -0,0 +1,170 @@ + + + + + /EHR/treatmentDetails.view?key=${lsid} + + + + + + + + + Begin Date + + + End Date + false + + + + ehr + project + project + + + + Category + + ehr_lookups + data_category + value + + + Depending on what is selected, the treatment will appear on a different schedule (ie. Clinical, Surgical, etc) + + + false + Treatment + + ehr_lookups + snomed + code + + + + Frequency + + ehr_lookups + treatment_frequency + meaning + + + + + + + + + Route + + ehr_lookups + routes + route + + + 40 + + + Volume + + + Volume Units + + ehr_lookups + volume_units + unit + + + + + Amount + + + Amount Units + + ehr_lookups + amount_units + unit + + + + + Drug Conc + + + Conc Units + + ehr_lookups + conc_units + unit + + + + + Dosage + + + Dosage Units + + ehr_lookups + dosage_units + unit + + + + + true + + + false + + + Parent ID + + + + ehr.context + /ehr/studyButtons.js + /nbri_ehr/window/MarkTreatmentCompletedWindow.js + EHR.DatasetButtons.moreActionsHandler + + Grid Views + + + Charts + + + Export + + + Print + + + + + EHR.DatasetButtons.historyHandler(dataRegion, dataRegionName); + + + + + EHR.window.GetDistinctWindow.getDistinctHandler(dataRegionName); + + + + + EHR.DatasetButtons.showAuditHistoryHandler(dataRegionName); + + + + + NBRI_EHR.window.MarkTreatmentCompletedWindow.buttonHandler(dataRegionName, 'study', 'treatment_order', 'datefield', 'lsid'); + + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatment_order/.qview.xml b/nbri_ehr/resources/queries/study/treatment_order/.qview.xml new file mode 100644 index 0000000..27608af --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatment_order/.qview.xml @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatment_order/Behavior Active Treatment Orders.qview.xml b/nbri_ehr/resources/queries/study/treatment_order/Behavior Active Treatment Orders.qview.xml new file mode 100644 index 0000000..a495f9e --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatment_order/Behavior Active Treatment Orders.qview.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/treatment_order/Clinical Active Treatment Orders.qview.xml b/nbri_ehr/resources/queries/study/treatment_order/Clinical Active Treatment Orders.qview.xml new file mode 100644 index 0000000..6fc59ae --- /dev/null +++ b/nbri_ehr/resources/queries/study/treatment_order/Clinical Active Treatment Orders.qview.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/vitals.js b/nbri_ehr/resources/queries/study/vitals.js new file mode 100644 index 0000000..1cb1b32 --- /dev/null +++ b/nbri_ehr/resources/queries/study/vitals.js @@ -0,0 +1,7 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +require("ehr/triggers").initScript(this); \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/vitals.query.xml b/nbri_ehr/resources/queries/study/vitals.query.xml new file mode 100644 index 0000000..29e22d9 --- /dev/null +++ b/nbri_ehr/resources/queries/study/vitals.query.xml @@ -0,0 +1,33 @@ + + + + + + + + + Category + + ehr_lookups + data_category + value + + + + + + + + + + EKG + + + Pulse Oximetry + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/vitals/.qview.xml b/nbri_ehr/resources/queries/study/vitals/.qview.xml new file mode 100644 index 0000000..f3b831c --- /dev/null +++ b/nbri_ehr/resources/queries/study/vitals/.qview.xml @@ -0,0 +1,19 @@ + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/weight.query.xml b/nbri_ehr/resources/queries/study/weight.query.xml new file mode 100644 index 0000000..d9ee743 --- /dev/null +++ b/nbri_ehr/resources/queries/study/weight.query.xml @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + Weight (kg) + 0.### + true + + + true + + + Category + true + + ehr_lookups + data_category + value + + + + + +
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/queries/study/weight/.qview.xml b/nbri_ehr/resources/queries/study/weight/.qview.xml new file mode 100644 index 0000000..b27ffe4 --- /dev/null +++ b/nbri_ehr/resources/queries/study/weight/.qview.xml @@ -0,0 +1,14 @@ + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/referenceStudy/.labkey/protocols/kinship/default.xml b/nbri_ehr/resources/referenceStudy/.labkey/protocols/kinship/default.xml new file mode 100644 index 0000000..b1fede0 --- /dev/null +++ b/nbri_ehr/resources/referenceStudy/.labkey/protocols/kinship/default.xml @@ -0,0 +1,3 @@ + + + true \ No newline at end of file diff --git a/nbri_ehr/resources/referenceStudy/folder.xml b/nbri_ehr/resources/referenceStudy/folder.xml new file mode 100644 index 0000000..0abf4b0 --- /dev/null +++ b/nbri_ehr/resources/referenceStudy/folder.xml @@ -0,0 +1,4 @@ + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/referenceStudy/study/datasets/PrimateElectronicHealthRecord.dataset b/nbri_ehr/resources/referenceStudy/study/datasets/PrimateElectronicHealthRecord.dataset new file mode 100644 index 0000000..9a762dd --- /dev/null +++ b/nbri_ehr/resources/referenceStudy/study/datasets/PrimateElectronicHealthRecord.dataset @@ -0,0 +1,19 @@ +# default group can be used to avoid repeating definitions for each dataset +# +# action=[REPLACE,APPEND,DELETE] (default:REPLACE) +# deleteAfterImport=[TRUE|FALSE] (default:FALSE) + +default.action=REPLACE +default.deleteAfterImport=FALSE + +# map a source tsv column (right side) to a property name or full propertyURI (left) +# predefined properties: ParticipantId, SiteId, VisitId, Created +default.property.ParticipantId=ptid +default.property.Created=dfcreate + +# use to map from filename->datasetid +# NOTE: if there are NO explicit import definitions, we will try to import all files matching pattern +# NOTE: if there are ANY explicit mapping, we will only import listed datasets + +default.filePattern=dataset(\\d*).tsv +default.importAllMatches=FALSE \ No newline at end of file diff --git a/nbri_ehr/resources/referenceStudy/study/datasets/datasets_manifest.xml b/nbri_ehr/resources/referenceStudy/study/datasets/datasets_manifest.xml new file mode 100644 index 0000000..1d03f01 --- /dev/null +++ b/nbri_ehr/resources/referenceStudy/study/datasets/datasets_manifest.xml @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml b/nbri_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml new file mode 100644 index 0000000..f8d49b0 --- /dev/null +++ b/nbri_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml @@ -0,0 +1,1514 @@ + + + + + + varchar + urn:ehr.labkey.org/#TaskId + + + varchar + urn:ehr.labkey.org/#ParentId + + + Performed By + varchar + urn:ehr.labkey.org/#PerformedBy + + + varchar + urn:ehr.labkey.org/#Description + + + varchar + urn:ehr.labkey.org/#Remark + + + entityid + urn:ehr.labkey.org/#ObjectId + true + + + + + Alias + Records alternative identifiers and aliases assigned to individual primates within the facility. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + varchar + + + varchar + + + varchar + + +
+ + Arrival + Tracks the arrival of primates into the research facility, including source, acquisition type, and associated documentation. + + + entityid + urn:ehr.labkey.org/#ObjectId + false + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + Location + varchar + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + Source Facility + varchar + + + Attachment File + varchar + http://cpas.fhcrc.org/exp/xml#fileLink + + + varchar + + + integer + urn:ehr.labkey.org/#Project + + + varchar + + + varchar + + + varchar + + + boolean + + +
+ + Project Assignments + Records project assignments for individual primates, linking animals to specific research projects with start and end dates. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + timestamp + + + integer + urn:ehr.labkey.org/#Project + + +
+ + Biopsy + Documents biopsy procedures performed on primates, including tissue type and associated pathology reports. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + Type + varchar + + + Attachment File + varchar + http://cpas.fhcrc.org/exp/xml#fileLink + + +
+ + Protocol Assignments + Tracks the assignment of primates to IACUC-approved research protocols with effective date ranges. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + timestamp + + + varchar + + +
+ + Birth + Records birth events for primates born within the facility, including location and associated protocols. + + + entityid + urn:ehr.labkey.org/#ObjectId + false + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + varchar + Location + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + integer + urn:ehr.labkey.org/#Project + + + varchar + + +
+ + Blood Draws + Tracks blood draw procedures performed on primates, including volume, sample type, tube type, and purpose. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + Type + varchar + + + double + + + varchar + urn:ehr.labkey.org/#CaseId + + + varchar + + + varchar + + + double + + + varchar + + + integer + + + varchar + + +
+ + Breeder + Records breeding evaluations and reproductive assessments for primates in the colony breeding program. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + Type + varchar + + + Result + varchar + + + Attachment File + varchar + http://cpas.fhcrc.org/exp/xml#fileLink + + +
+ + Clinical/Behavior Observations + Documents clinical and behavioral observations recorded during routine monitoring and veterinary assessments of primates. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + timestamp + + + Type + varchar + + + varchar + + + varchar + + + varchar + urn:ehr.labkey.org/#CaseId + + + varchar + + + varchar + + +
+ + Clinical Remarks + Stores veterinary clinical remarks and SOAP notes associated with primate health assessments and case management. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + varchar + + + varchar + + + varchar + + + varchar + + + varchar + + + varchar + + + varchar + + + timestamp + + + timestamp + + + timestamp + + + varchar + urn:ehr.labkey.org/#CaseId + + + Attachment File + varchar + http://cpas.fhcrc.org/exp/xml#fileLink + + +
+ + Demographics + Contains core demographic information for each primate, including species, sex, parentage, birth and death dates, and colony status. + + + entityid + urn:ehr.labkey.org/#ObjectId + false + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + varchar + sex + + + varchar + + + varchar + + + timestamp + + + timestamp + + + varchar + + + timestamp + + + varchar + + + varchar + + + varchar + + + varchar + + + varchar + + + varchar + + + integer + + + varchar + + + varchar + + + varchar + + +
+ + Departure + Records the departure of primates from the research facility, including destination information. + + + entityid + urn:ehr.labkey.org/#ObjectId + false + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + varchar + + +
+ + Deaths + Documents primate deaths, including date, cause of death, and terminal body weight. + + + entityid + urn:ehr.labkey.org/#ObjectId + false + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + varchar + + + double + + +
+ + Exemptions + Tracks approved exemptions from standard care or procedural requirements for individual primates. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + timestamp + urn:ehr.labkey.org/#EndDate + + + varchar + + + varchar + + +
+ + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + varchar + + + timestamp + urn:ehr.labkey.org/#EndDate + + + Animal Record Flags + Stores active record flags and status indicators applied to individual primates for colony management purposes. +
+ + Histopathology + Records histopathology findings from tissue examinations performed on primates, including diagnoses and associated reports. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + varchar + + + varchar + + + varchar + + + Attachment File + varchar + http://cpas.fhcrc.org/exp/xml#fileLink + + +
+ + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + varchar + + + varchar + + + Historical Other + Captures miscellaneous historical health and research records for primates that do not fit other specific categories. +
+ + Housing + Tracks housing assignments and location transfers for primates within the research facility. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + Location + varchar + + + varchar + + + varchar + + + timestamp + + + varchar + urn:ehr.labkey.org/#CaseId + + + + + cage + + +
+ + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + double + + + timestamp + urn:ehr.labkey.org/#EndDate + + + Inbreeding Coefficients + Records calculated inbreeding coefficients for primates to support genetic management of the colony. +
+ + Necropsy + Documents necropsy (postmortem) examination findings for primates, including gross and histological observations, diagnoses, and reports. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + Category + varchar + + + Accession Number + varchar + + + Condition of Specimen + varchar + + + Physical Condition + varchar + + + Relevant History + varchar + + + Gross Abnormalities + varchar + + + Diagnosis + varchar + + + Name/State/License no. (quarantine only) + varchar + + + varchar + + + Attachment File + varchar + http://cpas.fhcrc.org/exp/xml#fileLink + + +
+ + Gross Pathology + Records gross pathology findings observed during necropsy examinations of primates. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + Date of Exam + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + varchar + + + varchar + + +
+ + Tissue Disposition + Tracks the disposition of tissue samples collected during necropsy of primates. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + varchar + + + varchar + + +
+ + Pairings + Records social pairing and group housing arrangements for primates, including formation type, compatibility observations, and separation details. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + timestamp + urn:ehr.labkey.org/#EndDate + + + varchar + + + varchar + + + Location + varchar + + + varchar + + + varchar + + + varchar + + + varchar + + + varchar + + + varchar + + + varchar + + +
+ + Physical Exam + Documents physical examination findings and measurements recorded during veterinary assessments of primates. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + varchar + + + double + + + Units + integer + + + varchar + + + Attachment File + varchar + http://cpas.fhcrc.org/exp/xml#fileLink + + +
+ + Procedures + Records research and veterinary procedures performed on primates, including procedure type, category, and associated case information. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + varchar + + + varchar + + + varchar + urn:ehr.labkey.org/#CaseId + + + varchar + + + integer + + + Ordered By + varchar + + + varchar + + +
+ + Procedure Orders + Tracks scheduled procedure orders for primates, including ordering veterinarian and scheduling windows. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + integer + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + Window Start + timestamp + + + Window End + timestamp + + + varchar + urn:ehr.labkey.org/#CaseId + + + varchar + + + Ordered By + varchar + + +
+ + Serology + Records serological test results for primates, used for infectious disease screening and colony health monitoring. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + varchar + + + varchar + + +
+ + Problem List + Maintains the active and historical problem list for individual primates, supporting ongoing veterinary case management. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + varchar + + + varchar + + + timestamp + + +
+ + Drug Administration + Records drug and medication administrations for primates, including dosage, route, concentration, and ordering clinician. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + Type + varchar + + + Amount + double + + + Attachment File + varchar + http://cpas.fhcrc.org/exp/xml#fileLink + + + varchar + + + varchar + + + double + + + varchar + + + varchar + + + double + + + varchar + + + double + + + varchar + + + varchar + + + varchar + urn:ehr.labkey.org/#CaseId + + + timestamp + + + varchar + + + Ordered By + varchar + + +
+ + Treatment Cases + Tracks veterinary treatment cases for primates, supporting clinical case management from opening through resolution. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + timestamp + urn:ehr.labkey.org/#EndDate + + + varchar + + + Case category + varchar + + + Open Remark + varchar + + + Close Remark + varchar + + + Attachment File + varchar + http://cpas.fhcrc.org/exp/xml#fileLink + + + varchar + + + varchar + + + varchar + + + varchar + urn:ehr.labkey.org/#VetReview + + + timestamp + urn:ehr.labkey.org/#VetReviewDate + + + varchar + urn:ehr.labkey.org/#CaseId + + + varchar + + +
+ + Treatment Orders + Stores standing treatment orders for primates, including medication details, dosing frequency, and prescribing veterinarian. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + varchar + + + timestamp + + + varchar + + + varchar + + + double + + + varchar + + + varchar + + + double + + + varchar + + + double + + + varchar + + + varchar + + + varchar + + + varchar + urn:ehr.labkey.org/#CaseId + + + Ordered By + varchar + + + End Treatment Ordered By + varchar + + +
+ + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + Blood Pressure + varchar + + + Temperature + double + + + Heart Rate + double + + + Respiration Rate + double + + + Pulse Rate + double + + + double + + + double + + + Type + varchar + + + Units + integer + + + varchar + urn:ehr.labkey.org/#CaseId + + + varchar + + + Vital Signs + Records vital sign measurements for primates, including temperature, heart rate, respiration rate, blood pressure, and pulse oximetry. +
+ + Weight + Tracks body weight measurements for primates, used for health monitoring and drug dosage calculations. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + double + + + Units + integer + + + varchar + urn:ehr.labkey.org/#CaseId + + + varchar + + +
+ + Pregnancy Outcomes + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + Type + varchar + + + Result + varchar + + + Diagnosis + varchar + + + Attachment File + varchar + http://cpas.fhcrc.org/exp/xml#fileLink + + +
+ + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + timestamp + + + varchar + + + Attachment File + varchar + http://cpas.fhcrc.org/exp/xml#fileLink + + + Notes +
+ + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + varchar + + + Result + double + + + Chemistry Results +
+ + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + varchar + + + Fostering +
+ + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + varchar + + + varchar + + + varchar + urn:ehr.labkey.org/#CaseId + + + timestamp + urn:ehr.labkey.org/#EndDate + + + integer + + + varchar + + + varchar + + + Observation Orders +
+ + Animal Training + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + timestamp + urn:ehr.labkey.org/#EndDate + + + varchar + + + varchar + + + varchar + + + varchar + + +
+ \ No newline at end of file diff --git a/nbri_ehr/resources/referenceStudy/study/study.xml b/nbri_ehr/resources/referenceStudy/study/study.xml new file mode 100644 index 0000000..7f13240 --- /dev/null +++ b/nbri_ehr/resources/referenceStudy/study/study.xml @@ -0,0 +1,7 @@ + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/reports/additionalReports.tsv b/nbri_ehr/resources/reports/additionalReports.tsv new file mode 100644 index 0000000..98acfbe --- /dev/null +++ b/nbri_ehr/resources/reports/additionalReports.tsv @@ -0,0 +1,52 @@ +reportname category reporttype reporttitle visible containerpath schemaname queryname viewname report datefieldname todayonly queryhaslocation sort_order QCStateLabelFieldName description +MHC Genetics query MHC TRUE study MHC FALSE FALSE qcstate/publicdata This report shows MHC type +assignment Colony Management query Protocol Assignment TRUE study protocolAssignment FALSE FALSE qcstate/publicdata This report shows protocol assignments +grossPathology Pathology query Gross Pathology TRUE study grossPathology FALSE FALSE qcstate/publicdata This is for histopathology reports +tissueDisposition Pathology query Tissue Disposition TRUE study tissueDisposition FALSE FALSE qcstate/publicdata This is for histopathology reports +histopathology Pathology query Histopathology TRUE study histopathology FALSE FALSE qcstate/publicdata This is for histopathology reports +clinical_observations Clinical query Clinical Observations TRUE study clinical_observationsSummary Clinical date FALSE FALSE qcstate/publicdata This report displays clinical observations for the selected animal +foster Reproductive Management query Fostering TRUE study foster FALSE FALSE qcstate/publicdata This is for animal fostering data +projects Colony Management query Project Assignment TRUE study assignment FALSE FALSE qcstate/publicdata This is for project assignments +chemistry Clinical query Chemistry TRUE study chemistryResults FALSE FALSE qcstate/publicdata This is for chemistry results +alias Colony Management query Aliases true study demographicsAliases false false qcstate/publicdata This report shows the animal aliases +notes Colony Management query Notes true study notes false false qcstate/publicdata This report shows the animal notes +activeClinTreatmentOrders Clinical query Active Clinical Medication Orders true study treatment_order Clinical Active Treatment Orders date false false qcstate/publicdata This report contains the treatment orders entered for each animal +activeBehaviorTreatmentOrders Behavior query Active Behavior Medication Orders true study treatment_order Behavior Active Treatment Orders date false false qcstate/publicdata This report contains the treatment orders entered for each animal +allTreatments Clinical query All Treatment Orders true study treatment_order false false qcstate/publicdata This report shows all treatment orders +behTreatments Behavior query All Behavior Medication Orders true study treatment_order behavior false false qcstate/publicdata This report shows all behavior treatment orders +behDrug Behavior query Behavior Drug Administration true study drug Behavior false false qcstate/publicdata This report shows all behavior drug administrations +FileRepository General js File Repository true study FileRepository false false qcstate/publicdata File Repository for uploading and viewing animal related files +observationSchedule Daily Reports js Today's Observation Schedule true study observationSchedule date false false qcstate/publicdata This report contains a list of today's treatments to be administered +activeClinicalObservationOrders Clinical query Active Clinical Observation Orders true study observation_order Active Clinical Orders date false false qcstate/publicdata This report contains a list of today's treatments to be administered +activeBehaviorObservationOrders Behavior query Active Behavior Observation Orders true study observation_order Active Behavior Orders date false false qcstate/publicdata This report contains a list of today's treatments to be administered +observationOrders Clinical query Observation Orders true study observation_order date false false qcstate/publicdata This report contains a list of today's treatments to be administered +alopecia Behavior query Alopecia Scores TRUE study clinical_observations Alopecia Scores date FALSE FALSE qcstate/publicdata This report contains the alopecia scores for the animal +behaviorCases Behavior query Active Behavior Cases true study activeBehaviorCases date false false qcstate/publicdata This displays active behavioral cases +allBehaviorCases Behavior query Behavior Cases true study behaviorCases date false false qcstate/publicdata This displays all behavioral cases +bloodSchedule +cases Clinical query Active Clinical Cases true study activeClinicalCases date false false qcstate/publicdata This displays active clinical cases +clinCases Clinical query All Clinical Cases true study clinicalCases date false false qcstate/publicdata This report contains one record for each clinical case +prcOrders Clinical query Procedure Orders true study prc_order_report date false false qcstate/publicdata This report contains one record for each procedure order +prcOverdue Daily Reports query Overdue Procedures true study prcOverdue date false false qcstate/publicdata This report contains one record for each overdue procedure +clinMedicationSchedule Daily Reports js Today's Medication Schedule true study clinMedicationSchedule date false false qcstate/publicdata This report contains a list of today's treatments to be administered +prcSchedule Daily Reports query Today's Procedure Schedule true study prcSchedule date false false qcstate/publicdata This report contains a list of today's procedures to be administered +dietSchedule +drug +incompleteTreatments Daily Reports js Incomplete Treatments true study incompleteTreatments date false false qcstate/publicdata This report contains a list of incomplete treatments for the previous 30 days +incompleteObservations Daily Reports js Incomplete Observations true study incompleteObservations date false false qcstate/publicdata This report contains a list of incomplete observations for the previous 30 days +pairingsBehavior +pairingHousingSummary +pairingSummary Behavior query Pairing Summary TRUE study pairingSummary date FALSE FALSE qcstate/publicdata This report displays animal pairings +activePairing Behavior query Active Pairing TRUE study pairingSummary Active Pairing date FALSE FALSE qcstate/publicdata This report displays animal pairings +pairingHistory +nhpTraining Behavior query Animal Training TRUE study nhpTraining date FALSE FALSE qcstate/publicdata This report displays animal training data +roommateHistoryBehavior +surgicalCases +surgMedicationSchedule +surgMedicationScheduleDaily +pairings +behaviorRemarks Behavior query Behavior Remarks true study BehaviorClinRemarks date false false qcstate/publicdata This report contains the behavior remarks entered about each animal +clinObsBehavior Behavior query Observations true study behaviorObservations date false false qcstate/publicdata This report contains one record for each encounter with each animal, including surergies, exams, procedures, etc. +clinremarks Clinical query Clinical Remarks true study ClinicalClinRemarks date false false qcstate/publicdata This report contains the clinical remarks entered about each animal +physicalExam Clinical query Exam History True study physicalExam date false false qcstate/publicdata This report displays physical exam data for the selected animal +historicalOther General query Historical True study historicalOther date false false qcstate/publicdata This report displays historical events from legacy systems \ No newline at end of file diff --git a/nbri_ehr/resources/schemas/dbscripts/postgresql/nbri_ehr-0.000-25.000.sql b/nbri_ehr/resources/schemas/dbscripts/postgresql/nbri_ehr-0.000-25.000.sql new file mode 100644 index 0000000..86962df --- /dev/null +++ b/nbri_ehr/resources/schemas/dbscripts/postgresql/nbri_ehr-0.000-25.000.sql @@ -0,0 +1,611 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +CREATE SCHEMA nbri_ehr; + +CREATE TABLE nbri_ehr.LocationTypes +( + RowId SERIAL NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + Container entityId NOT NULL, + + NAME TEXT, + LocationTypeId INTEGER, + + CONSTRAINT PK_LocationTypes PRIMARY KEY (RowId), + CONSTRAINT FK_LocationTypes_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_nbri_ehr_LocationTypes_Container ON nbri_ehr.LocationTypes (Container); + +CREATE TABLE nbri_ehr.Locations +( + RowId SERIAL NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + Container entityId NOT NULL, + + NAME TEXT, + LocationId INTEGER, + LocationType INTEGER, + + CONSTRAINT PK_Locations PRIMARY KEY (RowId), + CONSTRAINT FK_Locations_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_nbri_ehr_Locations_Container ON nbri_ehr.Locations (Container); + +CREATE TABLE nbri_ehr.LocationsMapping +( + RowId SERIAL NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + Container entityId NOT NULL, + + ParentLocation INTEGER, + ChildLocation INTEGER, + NAME TEXT, + + CONSTRAINT PK_LocationsMapping PRIMARY KEY (RowId), + CONSTRAINT FK_LocationsMapping_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_nbri_ehr_LocationsMapping_Container ON nbri_ehr.LocationsMapping (Container); + +CREATE TABLE nbri_ehr.Staff +( + staffId INTEGER NOT NULL, + email TEXT, + firstName TEXT, + lastName TEXT, + middleName TEXT, + displayName TEXT, + hireDate TIMESTAMP, + lastEmployDate TIMESTAMP, + officePhone TEXT, + officePhoneExt TEXT, + officeFax TEXT, + homePhone TEXT, + beeperPhone TEXT, + cellPhone TEXT, + emergencyContact TEXT, + emergencyPhone TEXT, + homeAddress1 TEXT, + homeAddress2 TEXT, + homeCity TEXT, + homeState TEXT, + homeZip TEXT, + homeZipExt TEXT, + homeCountry TEXT, + officeAddress1 TEXT, + officeAddress2 TEXT, + officeCity TEXT, + officeState TEXT, + officeZip TEXT, + officeZipExt TEXT, + officeCountry TEXT, + birthDate TIMESTAMP, + hsName TEXT, + collegeGradDate TEXT, + collegeDegree TEXT, + collegeMajor TEXT, + collegeName TEXT, + supervisor INTEGER, + positionName TEXT, + positionDesc TEXT, + active BOOLEAN, + Container entityId NOT NULL, + CONSTRAINT PK_STAFF PRIMARY KEY (staffId), + CONSTRAINT FK_STAFF_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_nbri_ehr_Staff_Container ON nbri_ehr.Staff (Container); + +CREATE TABLE nbri_ehr.Lot +( + LotId INTEGER, + AnimalShipment INTEGER, + Date TIMESTAMP, + LotSequence INTEGER, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_LOT PRIMARY KEY (LotId), + CONSTRAINT FK_LOT_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_Lot_Container ON nbri_ehr.Lot (Container); + +CREATE TABLE nbri_ehr.AnimalShipment +( + AnimalShipmentId INTEGER, + ReceivedByStaff USERID, + Cage TEXT, + Room TEXT, + Building TEXT, + Area TEXT, + AnimalDelivery INTEGER, + LotNumber INTEGER, + ReceivedDate TIMESTAMP, + BirthDate TIMESTAMP, + MalesReceived INTEGER, + FemalesReceived INTEGER, + EitherReceived INTEGER, + CanUnreceive BOOLEAN, + CostCenter INTEGER, + Dam TEXT, + Sire TEXT, + RecordedDate TIMESTAMP, + RecordedBy TEXT, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_ANIMALSHIPMENT PRIMARY KEY (AnimalShipmentId), + CONSTRAINT FK_ANIMALSHIPMENT_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_Animal_Shipment_Container ON nbri_ehr.AnimalShipment (Container); + +CREATE TABLE nbri_ehr.AnimalDelivery +( + AnimalDeliveryId INTEGER, + AnimalShipment INTEGER, + ShipTo INTEGER, + cage TEXT, + room TEXT, + building TEXT, + area TEXT, + AnimalReqOrder INTEGER, + DeliveryState INTEGER, + DeliveryNumber INTEGER, + ExpectedDate TIMESTAMP, + Project INTEGER, + BillToAccount INTEGER, + BillToStaff USERID, + PerDiemAccount INTEGER, + PerDiemStaff USERID, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_ANIMALDELIVERY PRIMARY KEY (AnimalDeliveryId), + CONSTRAINT FK_ANIMALDELIVER_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_Animal_Delivery_Container ON nbri_ehr.AnimalDelivery (Container); + +CREATE TABLE nbri_ehr.AnimalDeliveryEsig +( + EsigId INTEGER, + AnimalDelivery INTEGER, + EsigEvent INTEGER, + UserProfile USERID, + EsigDateTime TIMESTAMP, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_ANIMALDELIVERYESIG PRIMARY KEY (EsigId), + CONSTRAINT FK_ANIMALDELIVERESIG_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_Animal_Delivery_Esig_Container ON nbri_ehr.AnimalDeliveryEsig (Container); + +CREATE TABLE nbri_ehr.AnimalReqOrder +( + AnimalReqOrderId INTEGER, + AnimalVendor INTEGER, + RequisitionerStaff USERID, + RequestNumber TEXT, + RequisitionNumber TEXT, + Bill BOOLEAN, + ShippingContact TEXT, + CreateDate TIMESTAMP, + ReqOrderType INTEGER, + ReqOrderState INTEGER, + BillToAccount INTEGER, + BillToStaff USERID, + PerDiemAccount INTEGER, + PerDiemStaff USERID, + SubmittedByStaff USERID, + ApprovedByStaff USERID, + SubmittedDate TIMESTAMP, + ApprovedDate TIMESTAMP, + Segment INTEGER, + Project INTEGER, + SiteCage TEXT, + SiteRoom TEXT, + SiteBuilding TEXT, + SiteArea TEXT, + CreatedByStaff USERID, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_ANIMALREQORDER PRIMARY KEY (AnimalReqOrderId), + CONSTRAINT FK_ANIMALREQORDER_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_Animal_Req_Order_Container ON nbri_ehr.AnimalReqOrder (Container); + +CREATE TABLE nbri_ehr.AnimalReqOrderEsig +( + EsigId INTEGER, + AnimalReqOrder INTEGER, + EsigEvent INTEGER, + UserProfile USERID, + EsigDateTime TIMESTAMP, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_ANIMALREQORDERESIG PRIMARY KEY (EsigId), + CONSTRAINT FK_ANIMALREQORDERESIG_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_Animal_Req_Order_Esig_Container ON nbri_ehr.AnimalReqOrderEsig (Container); + +CREATE TABLE nbri_ehr.AnimalVendor +( + AnimalVendorId INTEGER, + VendorApprovalCode INTEGER, + VendorName TEXT, + StreetAddress1 TEXT, + StreetAddress2 TEXT, + City TEXT, + StateProv TEXT, + Country TEXT, + Zip TEXT, + ZipExt TEXT, + PhoneNumber TEXT, + FaxNumber TEXT, + Comments TEXT, + InternalVendor TEXT, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_ANIMALVENDOR PRIMARY KEY (AnimalVendorId), + CONSTRAINT FK_ANIMALVENDOR_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_Animal_Vendor_Container ON nbri_ehr.AnimalVendor (Container); + +CREATE TABLE nbri_ehr.ShipTo +( + ShipToId INTEGER, + Name TEXT, + Country TEXT, + City TEXT, + StreetAddress1 TEXT, + StreetAddress2 TEXT, + StateProv TEXT, + Zip TEXT, + ZipExt TEXT, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_SHIPTO PRIMARY KEY (ShipToId), + CONSTRAINT FK_SHIPTO_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_Ship_To_Container ON nbri_ehr.ShipTo (Container); + +ALTER TABLE nbri_ehr.Staff + ADD COLUMN Created TIMESTAMP, + ADD COLUMN CreatedBy USERID, + ADD COLUMN Modified TIMESTAMP, + ADD COLUMN ModifiedBy USERID; + +CREATE TABLE nbri_ehr.ProtocolEsig +( + EsigId INTEGER, + Protocol INTEGER, + EsigEvent INTEGER, + UserProfile USERID, + EsigDateTime TIMESTAMP, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_PROTOCOLESIG PRIMARY KEY (EsigId), + CONSTRAINT FK_PROTOCOLESIG_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_Protocol_Esig_Container ON nbri_ehr.ProtocolEsig (Container); + +CREATE TABLE nbri_ehr.ProtocolUsage +( + Protocol TEXT, + UserReferenceNumber TEXT, + ShortTitle TEXT, + Investigator TEXT, + ProtocolType TEXT, + CurrentState TEXT, + SubmitDate TIMESTAMP, + ApprovalDate TIMESTAMP, + ExpirationDate TIMESTAMP, + EffectiveDate TIMESTAMP, + RenewalDate TIMESTAMP, + AuthorizedAmt FLOAT, + OnOrderAmt FLOAT, + UsedAmt FLOAT, + AvailableAmt FLOAT, + PercentLeft FLOAT, + SegmentId INTEGER, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT FK_PROTOCOLUSAGE_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_Protocol_Usage_Container ON nbri_ehr.ProtocolUsage (Container); + +CREATE TABLE nbri_ehr.Account +( + AccountId INTEGER, + AccountNumber TEXT, + Department INTEGER, + CostType INTEGER, + ExpenseClass INTEGER, + ProjectCode INTEGER, + Description TEXT, + Active BOOLEAN, + Cage TEXT, + Room TEXT, + Building TEXT, + Area TEXT, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_ACCOUNT PRIMARY KEY (AccountId), + CONSTRAINT FK_ACCOUNT_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_Account_Container ON nbri_ehr.Account (Container); + + +CREATE TABLE nbri_ehr.Department +( + DepartmentId INTEGER, + Name TEXT, + Description TEXT, + ParentDepartment INTEGER, + Staff USERID, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_DEPARTMENT PRIMARY KEY (DepartmentId), + CONSTRAINT FK_DEPARTMENT_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_Department_Container ON nbri_ehr.Department (Container); + +ALTER TABLE nbri_ehr.AnimalShipment ADD COLUMN Floor VARCHAR; +ALTER TABLE nbri_ehr.AnimalDelivery ADD COLUMN Floor VARCHAR; + +CREATE TABLE nbri_ehr.IdHistory +( + Id VARCHAR, + Name VARCHAR, + Type INTEGER, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_IDHISTORY PRIMARY KEY (Id, Name), + CONSTRAINT FK_IDHISTORY_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_ID_History_Container ON nbri_ehr.IdHistory (Container); + +CREATE TABLE nbri_ehr.DeletedRecord +( + Id INTEGER, + Protocol VARCHAR, + UserReferenceNumber VARCHAR, + Investigator VARCHAR, + Title VARCHAR, + EsigEvent INTEGER, + EsigUser USERID, + EsigDate TIMESTAMP, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_DELETEDRECORD PRIMARY KEY (Id), + CONSTRAINT FK_DELETEDRECORD_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_Deleted_Record_Container ON nbri_ehr.DeletedRecord (Container); + +CREATE TABLE nbri_ehr.Question +( + QuestionId INTEGER, + Type VARCHAR, + Text VARCHAR, + CreationDate TIMESTAMP, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_QUESTION PRIMARY KEY (QuestionId), + CONSTRAINT FK_QUESTION_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_Question_Container ON nbri_ehr.Question (Container); + +CREATE TABLE nbri_ehr.QuestionResponse +( + QuestionResponseId INTEGER, + Protocol INTEGER, + Response VARCHAR, + Question INTEGER, + Questionnaire INTEGER, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_QUESTIONRESPONSE PRIMARY KEY (QuestionResponseId), + CONSTRAINT FK_QUESTIONRESPONSE_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_Question_Response_Container ON nbri_ehr.QuestionResponse (Container); + +ALTER TABLE nbri_ehr.AnimalVendor ADD COLUMN VendorProductionLocation INTEGER; + +ALTER TABLE nbri_ehr.ProtocolUsage DROP COLUMN SegmentId; +ALTER TABLE nbri_ehr.ProtocolUsage ADD COLUMN Species integer; + +ALTER TABLE nbri_ehr.AnimalReqOrder DROP COLUMN Segment; +ALTER TABLE nbri_ehr.AnimalReqOrder ADD COLUMN Protocol integer; +ALTER TABLE nbri_ehr.AnimalReqOrder ADD COLUMN Species integer; + +ALTER TABLE nbri_ehr.Account DROP COLUMN cage; +ALTER TABLE nbri_ehr.Account DROP COLUMN room; +ALTER TABLE nbri_ehr.Account DROP COLUMN building; + +CREATE TABLE nbri_ehr.ProtocolStress +( + RowId SERIAL NOT NULL, + Protocol INTEGER, + Species VARCHAR, + Stress INTEGER, + Allowed INTEGER, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_PROTOCOLSTRESS PRIMARY KEY (RowId), + CONSTRAINT FK_PROTOCOLSTRESS_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_ProtocolStress_Container ON nbri_ehr.ProtocolStress (Container); + +CREATE TABLE nbri_ehr.Stress +( + StressId INTEGER, + Name VARCHAR, + Description VARCHAR, + Ranking INTEGER, + RegulatoryStressLevel INTEGER, + Active BOOLEAN, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_STRESS PRIMARY KEY (StressId), + CONSTRAINT FK_STRESS_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_Stress_Container ON nbri_ehr.Stress (Container); + +CREATE TABLE nbri_ehr.ProtocolProcedures +( + RowId SERIAL NOT NULL, + Protocol INTEGER, + Species VARCHAR, + Procedure VARCHAR, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_PROTOCOLPROCEDURES PRIMARY KEY (RowId), + CONSTRAINT FK_PROTOCOLPROCEDURES_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_ProtocolProcedures_Container ON nbri_ehr.ProtocolProcedures (Container); + +CREATE TABLE nbri_ehr.CageCard +( + CageCardId INTEGER, + Protocol INTEGER, + Species INTEGER, + CardFormat INTEGER, + CostCenter INTEGER, + GenerationDate TIMESTAMP, + UpdateDate TIMESTAMP, + NumberOfAnimals INTEGER, + Cage INTEGER, + Room INTEGER, + Floor INTEGER, + Building INTEGER, + Area INTEGER, + Account INTEGER, + AccountStaff USERID, + CensusActivityStatus VARCHAR, + CensusActivityDate TIMESTAMP, + AnimalDelivery INTEGER, + AnimalRequestedByStaff USERID, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_CAGECARD PRIMARY KEY (CageCardId), + CONSTRAINT FK_CAGECARD_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_Cage_Card_Container ON nbri_ehr.CageCard (Container); + +CREATE TABLE nbri_ehr.CageCardHistory +( + RowId SERIAL NOT NULL, + CageCardId INTEGER, + AnimalDelivery INTEGER, + Protocol INTEGER, + Species INTEGER, + CardFormat INTEGER, + CostCenter INTEGER, + GenerationDate TIMESTAMP, + UpdateDate TIMESTAMP, + NumberOfAnimals INTEGER, + Cage INTEGER, + Room INTEGER, + Floor INTEGER, + Building INTEGER, + Area INTEGER, + Account INTEGER, + AccountStaff USERID, + CensusActivityStatus VARCHAR, + CensusActivityDate TIMESTAMP, + CensusStartDate TIMESTAMP, + CensusStopDate TIMESTAMP, + TransferDate TIMESTAMP, + ActionDate TIMESTAMP, + RetrospectiveStress INTEGER, + AnimalRequestedByStaff USERID, + Container entityId NOT NULL, + Created TIMESTAMP, + CreatedBy USERID, + Modified TIMESTAMP, + ModifiedBy USERID, + CONSTRAINT PK_CAGECARDHISTORY PRIMARY KEY (RowId), + CONSTRAINT FK_CAGECARDHISTORY_Container FOREIGN KEY (Container) REFERENCES core.Containers (EntityId) +); +CREATE INDEX IX_Nbri_Ehr_Cage_Card_History_Container ON nbri_ehr.CageCardHistory (Container); + +CREATE TABLE nbri_ehr.CasesTemp +( + Id TEXT, + date TIMESTAMP, + enddate TIMESTAMP, + objectid TEXT, + category TEXT, + openDiagnosis TEXT, + closeDiagnosis TEXT, + openRemark TEXT, + closeRemark TEXT, + attachmentFile TEXT, + performedby USERID +); diff --git a/nbri_ehr/resources/schemas/dbscripts/postgresql/nbri_ehr-25.000-25.001.sql b/nbri_ehr/resources/schemas/dbscripts/postgresql/nbri_ehr-25.000-25.001.sql new file mode 100644 index 0000000..3c2b808 --- /dev/null +++ b/nbri_ehr/resources/schemas/dbscripts/postgresql/nbri_ehr-25.000-25.001.sql @@ -0,0 +1,6 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT core.executeJavaUpgradeCode('reloadFolder'); \ No newline at end of file diff --git a/nbri_ehr/resources/schemas/nbri_ehr.xml b/nbri_ehr/resources/schemas/nbri_ehr.xml new file mode 100644 index 0000000..ab2223f --- /dev/null +++ b/nbri_ehr/resources/schemas/nbri_ehr.xml @@ -0,0 +1,588 @@ + + + + + Location Types + DETAILED + + + + + + + + + + +
+ + + Locations + DETAILED + + + + + + + + + + + +
+ + + Locations Mapping + DETAILED + + + + + + + + + + + +
+ + + Staff + DETAILED + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + Lot + DETAILED + + + + + + + + + + + +
+ + + Animal Shipment + DETAILED + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + Animal Delivery + DETAILED + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + Animal Delivery ESignature + DETAILED + + + + + + + + + + + + +
+ + + Animal Req Order + DETAILED + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + Animal Req Order ESignature + DETAILED + + + + + + + + + + + + +
+ + + Animal Vendor + DETAILED + + + + + + + + + + + + + + + + + + + + + + +
+ + + Ship To + DETAILED + + + + + + + + + + + + + + + + +
+ + + Protocol ESignature + DETAILED + + + + + + + + + + + + +
+ + + Protocol Usage + DETAILED + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + Account + DETAILED + + + + + + + + + + + + + + + + +
+ + + Department + DETAILED + + + + + + + + + + + + +
+ + + Id History + DETAILED + + + + + + + + + + +
+ + + Deleted Record + DETAILED + + + + + + + + + + + + + + + +
+ + + Question + DETAILED + + + + + + + + + + + +
+ + + Question Response + DETAILED + + + + + + + + + + + + +
+ + + Protocol Stress + DETAILED + + + + + + + + + + + + +
+ + + Stress + DETAILED + + + + + + + + + + + + + +
+ + + Protocol Procedures + DETAILED + + + + + + + + + + + +
+ + + Cage Card + DETAILED + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + Cage Card History + DETAILED + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + Cases Staging For ETL + + + + + + + + + + + + + +
+ + \ No newline at end of file diff --git a/nbri_ehr/resources/scripts/nbri_triggers.js b/nbri_ehr/resources/scripts/nbri_triggers.js new file mode 100644 index 0000000..5b2ef5d --- /dev/null +++ b/nbri_ehr/resources/scripts/nbri_triggers.js @@ -0,0 +1,150 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +var console = require("console"); +var LABKEY = require("labkey"); + +// For more complicated logic, I highly recommend implementing this in java. This provides much better debugging, and the full use of the server-side java APIs +// Methods on this TriggerHelper can be called from JS, and can return values to the JS code. In general, I try to only pass primitives; however, that may not always be required + +// NOTE: NBRI specific script options should be set here in INIT triggers + +exports.init = function (EHR) { + + + EHR.Server.TriggerManager.registerHandler(EHR.Server.TriggerManager.Events.INIT, function (event, helper, EHR) { + + EHR.Server.TriggerManager.unregisterAllHandlersForQueryNameAndEvent('ehr_lookups', 'cage', EHR.Server.TriggerManager.Events.BEFORE_UPSERT); + EHR.Server.TriggerManager.unregisterAllHandlersForQueryNameAndEvent('ehr_lookups', 'procedures', EHR.Server.TriggerManager.Events.BEFORE_DELETE); + EHR.Server.TriggerManager.unregisterAllHandlersForQueryNameAndEvent('study', 'assignment', EHR.Server.TriggerManager.Events.BEFORE_UPSERT); + EHR.Server.TriggerManager.unregisterAllHandlersForQueryNameAndEvent('study', 'clinremarks', EHR.Server.TriggerManager.Events.BEFORE_UPSERT); + EHR.Server.TriggerManager.unregisterAllHandlersForQueryNameAndEvent('study', 'clinremarks', EHR.Server.TriggerManager.Events.AFTER_UPSERT); + EHR.Server.TriggerManager.unregisterAllHandlersForQueryNameAndEvent('study', 'blood', EHR.Server.TriggerManager.Events.BEFORE_UPSERT); + EHR.Server.TriggerManager.unregisterAllHandlersForQueryNameAndEvent('study', 'cases', EHR.Server.TriggerManager.Events.AFTER_UPSERT); + EHR.Server.TriggerManager.unregisterAllHandlersForQueryNameAndEvent('study', 'cases', EHR.Server.TriggerManager.Events.AFTER_DELETE); + + helper.setScriptOptions({ + datasetsToClose: ['assignment', 'protocolAssignment' , 'housing', 'treatment_order', 'observation_order', 'cases', 'pairings', 'exemptions', 'flags'] + }); + }); + + EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'arrival', function(event, helper) { + helper.setScriptOptions({ + allowAnyId: true, + requiresStatusRecalc: false, // set in upsert to handle rearrival + allowDatesInDistantPast: true, + skipAssignmentCheck: true, + }); + }); + + EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'protocolAssignment', function(event, helper) { + helper.setScriptOptions({ + allowAnyId: false, + requiresStatusRecalc: false, + allowDatesInDistantPast: true + }); + }); + + EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'assignment', function(event, helper) { + helper.setScriptOptions({ + allowAnyId: false, + requiresStatusRecalc: false, + allowDatesInDistantPast: true, + skipAssignmentCheck: true, + removeTimeFromDate: false, + doStandardProtocolCountValidation: false + }); + + helper.decodeExtraContextProperty('assignmentsInTransaction', []); + + helper.registerRowProcessor(function(helper, row){ + if (!row) + return; + + if (!row.Id || !row.project){ + return; + } + + var assignmentsInTransaction = helper.getProperty('assignmentsInTransaction'); + assignmentsInTransaction = assignmentsInTransaction || []; + + var shouldAdd = true; + if (row.objectid){ + LABKEY.ExtAdapter.each(assignmentsInTransaction, function(r){ + if (r.objectid === row.objectid){ + shouldAdd = false; + return false; + } + }, this); + } + + if (shouldAdd){ + assignmentsInTransaction.push({ + Id: row.Id, + objectid: row.objectid, + date: row.date, + enddate: row.enddate, + qcstate: row.QCState, + project: row.project + }); + } + + helper.setProperty('assignmentsInTransaction', assignmentsInTransaction); + }); + }); + + EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'alias', function(event, helper) { + helper.setScriptOptions({ + allowDatesInDistantPast: true, + removeTimeFromDate: false, + }); + }); + + EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'drug', function(event, helper) { + helper.setScriptOptions({ + allowDeadIds: true, + }); + }); + + EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'treatment_order', function(event, helper) { + helper.setScriptOptions({ + allowFutureDates: true, + }); + }); + + EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'observation_order', function(event, helper, EHR) { + helper.setScriptOptions({ + allowFutureDates: true, + }); + }); + + EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'deaths', function(event, helper) { + + helper.setScriptOptions({ + datasetsToClose: ['assignment', 'protocolAssignment' , 'housing', 'treatment_order', 'observation_order', 'cases', 'pairings', 'exemptions', 'flags'], + allowShippedIds: false, + allowDeadIds: false, + requiresStatusRecalc: true, + allowRequestsInPast: true, + removeTimeFromDate: false, + allowDatesInDistantPast: true, + allowAnyId: true + }); + }); + + EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'necropsy', function(event, helper) { + + helper.setScriptOptions({ + removeTimeFromDate: false + }); + }); + + EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'cases', function(event, helper) { + helper.setScriptOptions({ + allowDatesInDistantPast: true + }); + }); +} diff --git a/nbri_ehr/resources/views/NBRI_amimalHistory.webpart.xml b/nbri_ehr/resources/views/NBRI_amimalHistory.webpart.xml new file mode 100644 index 0000000..ad91414 --- /dev/null +++ b/nbri_ehr/resources/views/NBRI_amimalHistory.webpart.xml @@ -0,0 +1,3 @@ + + + \ No newline at end of file diff --git a/nbri_ehr/resources/views/acquisitionReport.html b/nbri_ehr/resources/views/acquisitionReport.html new file mode 100644 index 0000000..f1ecf91 --- /dev/null +++ b/nbri_ehr/resources/views/acquisitionReport.html @@ -0,0 +1,217 @@ + + +
+
+ + +
+ +
+ + +
+ +
+ + +
+ + +
+ +
+
+
+ + diff --git a/nbri_ehr/resources/views/acquisitionReport.view.xml b/nbri_ehr/resources/views/acquisitionReport.view.xml new file mode 100644 index 0000000..bbbab5f --- /dev/null +++ b/nbri_ehr/resources/views/acquisitionReport.view.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/views/animalHistory.html b/nbri_ehr/resources/views/animalHistory.html new file mode 100644 index 0000000..5c2c43a --- /dev/null +++ b/nbri_ehr/resources/views/animalHistory.html @@ -0,0 +1,107 @@ + diff --git a/nbri_ehr/resources/views/animalHistory.view.xml b/nbri_ehr/resources/views/animalHistory.view.xml new file mode 100644 index 0000000..885cf5f --- /dev/null +++ b/nbri_ehr/resources/views/animalHistory.view.xml @@ -0,0 +1,13 @@ + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/views/begin.html b/nbri_ehr/resources/views/begin.html new file mode 100644 index 0000000..0987b92 --- /dev/null +++ b/nbri_ehr/resources/views/begin.html @@ -0,0 +1,251 @@ + \ No newline at end of file diff --git a/nbri_ehr/resources/views/begin.view.xml b/nbri_ehr/resources/views/begin.view.xml new file mode 100644 index 0000000..2132d52 --- /dev/null +++ b/nbri_ehr/resources/views/begin.view.xml @@ -0,0 +1,5 @@ + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/views/begin.webpart.xml b/nbri_ehr/resources/views/begin.webpart.xml new file mode 100644 index 0000000..6082de1 --- /dev/null +++ b/nbri_ehr/resources/views/begin.webpart.xml @@ -0,0 +1,7 @@ + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/views/cageDetails.html b/nbri_ehr/resources/views/cageDetails.html new file mode 100644 index 0000000..a0c5da2 --- /dev/null +++ b/nbri_ehr/resources/views/cageDetails.html @@ -0,0 +1,83 @@ + \ No newline at end of file diff --git a/nbri_ehr/resources/views/cageDetails.view.xml b/nbri_ehr/resources/views/cageDetails.view.xml new file mode 100644 index 0000000..68b5372 --- /dev/null +++ b/nbri_ehr/resources/views/cageDetails.view.xml @@ -0,0 +1,5 @@ + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/views/clinicalHistoryExport.html b/nbri_ehr/resources/views/clinicalHistoryExport.html new file mode 100644 index 0000000..e96bab9 --- /dev/null +++ b/nbri_ehr/resources/views/clinicalHistoryExport.html @@ -0,0 +1,87 @@ +
+ ULL Logo + The University of Louisiana at Lafayette New Iberia Research Center
Animal Record +
+ + \ No newline at end of file diff --git a/nbri_ehr/resources/views/clinicalHistoryExport.view.xml b/nbri_ehr/resources/views/clinicalHistoryExport.view.xml new file mode 100644 index 0000000..35f09e3 --- /dev/null +++ b/nbri_ehr/resources/views/clinicalHistoryExport.view.xml @@ -0,0 +1,5 @@ + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/views/datasets.html b/nbri_ehr/resources/views/datasets.html new file mode 100644 index 0000000..f6a4150 --- /dev/null +++ b/nbri_ehr/resources/views/datasets.html @@ -0,0 +1,130 @@ + diff --git a/nbri_ehr/resources/views/datasets.view.xml b/nbri_ehr/resources/views/datasets.view.xml new file mode 100644 index 0000000..895d3d0 --- /dev/null +++ b/nbri_ehr/resources/views/datasets.view.xml @@ -0,0 +1,5 @@ + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/views/enterData.html b/nbri_ehr/resources/views/enterData.html new file mode 100644 index 0000000..2d9c84f --- /dev/null +++ b/nbri_ehr/resources/views/enterData.html @@ -0,0 +1,43 @@ +
+ + diff --git a/nbri_ehr/resources/views/enterData.view.xml b/nbri_ehr/resources/views/enterData.view.xml new file mode 100644 index 0000000..a2ae43f --- /dev/null +++ b/nbri_ehr/resources/views/enterData.view.xml @@ -0,0 +1,9 @@ + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/views/nbri_login.html b/nbri_ehr/resources/views/nbri_login.html new file mode 100644 index 0000000..30a475a --- /dev/null +++ b/nbri_ehr/resources/views/nbri_login.html @@ -0,0 +1,48 @@ +
+
Sign In
+
+
+ + + +
+ Forgot password +
+ + Remember my email address + + +
+ + + + +
+ + + + + +
+
+ + + \ No newline at end of file diff --git a/nbri_ehr/resources/views/nbri_login.view.xml b/nbri_ehr/resources/views/nbri_login.view.xml new file mode 100644 index 0000000..ec29417 --- /dev/null +++ b/nbri_ehr/resources/views/nbri_login.view.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/views/necropsy.html b/nbri_ehr/resources/views/necropsy.html new file mode 100644 index 0000000..f1c3d1a --- /dev/null +++ b/nbri_ehr/resources/views/necropsy.html @@ -0,0 +1,99 @@ + + +
+ ULL Logo + The University of Louisiana at Lafayette New Iberia Research Center
Necropsy +
+
+ + +
+
+
+
+ +
+
+
+
+
+ + diff --git a/nbri_ehr/resources/views/necropsy.view.xml b/nbri_ehr/resources/views/necropsy.view.xml new file mode 100644 index 0000000..e10c578 --- /dev/null +++ b/nbri_ehr/resources/views/necropsy.view.xml @@ -0,0 +1,3 @@ + + + \ No newline at end of file diff --git a/nbri_ehr/resources/views/participantView.html b/nbri_ehr/resources/views/participantView.html new file mode 100644 index 0000000..89f88bf --- /dev/null +++ b/nbri_ehr/resources/views/participantView.html @@ -0,0 +1,31 @@ + \ No newline at end of file diff --git a/nbri_ehr/resources/views/participantView.view.xml b/nbri_ehr/resources/views/participantView.view.xml new file mode 100644 index 0000000..c41ebae --- /dev/null +++ b/nbri_ehr/resources/views/participantView.view.xml @@ -0,0 +1,15 @@ + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/nbri_ehr/resources/web/ehr/metadata/Default.js b/nbri_ehr/resources/web/ehr/metadata/Default.js new file mode 100644 index 0000000..ff00e03 --- /dev/null +++ b/nbri_ehr/resources/web/ehr/metadata/Default.js @@ -0,0 +1,21 @@ +/* + * Copyright (c) 2022-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + + +EHR.model.DataModelManager.registerMetadata('Default', { + byQuery: { + 'study.MHC': { + QCState: { + getInitialValue: function(v){ + var qc; + if (!v && EHR.Security.getQCStateByLabel('Completed')) + qc = EHR.Security.getQCStateByLabel('Completed').RowId; + return v || qc; + }, + } + } + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/buttons/ProcedureOrderCompleteButton.js b/nbri_ehr/resources/web/nbri_ehr/buttons/ProcedureOrderCompleteButton.js new file mode 100644 index 0000000..4e226a1 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/buttons/ProcedureOrderCompleteButton.js @@ -0,0 +1,112 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +Ext4.namespace('NBRI_EHR.ProcedureOrderCompleteButton'); + +Ext4.define('NBRI_EHR.window.ProcedureOrderCompleteWindow', { + extend: 'Ext.window.Window', + returnLocation: null, + + initComponent: function() { + Ext4.apply(this, { + title: 'Mark Procedure Order Completed', + modal: true, + width: 450, + bodyStyle: 'padding: 5px;', + closeAction: 'destroy', + items: [{ + xtype: 'panel', + border: false, + html: '

This will mark the procedure order(s) completed without entering a procedure. Ensure the procedure has been entered separately if it should be recorded.

', + }], + buttons: [{ + text:'Submit', + scope: this, + handler: function (btn) { + this.recordProcedure(btn, this.dataRegion); + } + },{ + text: 'Cancel', + scope: this, + handler: function(btn){ + btn.up('window').close(); + } + }] + }); + + this.callParent(arguments); + }, + + recordProcedure: function(btn, dataRegion) { + let win = btn.up('window'); + const selectedRows = [...new Set(dataRegion.getChecked())]; + var me = this; + btn.setDisabled(true); + Ext4.Msg.wait('Completing procedure orders...'); + + LABKEY.Query.selectRows({ + schemaName: 'core', + queryName: 'QCState', + filterArray: [LABKEY.Filter.create('label', 'Completed', LABKEY.Filter.Types.EQUALS)], + scope: this, + ignoreFilter: true, + columns: 'RowId', + success: function (data) { + const rowsToInsert = []; + const completedRowId = data?.rows?.[0]?.RowId; + if (completedRowId) { + for (const row of selectedRows) { + rowsToInsert.push({ + lsid: row, + qcstate: completedRowId + }); + } + } + + LABKEY.Query.updateRows({ + schemaName: 'study', + queryName: 'prc_order', + rows: rowsToInsert, + scope: this, + success: function() { + Ext4.Msg.alert('Success', 'Procedure order(s) marked completed.', function(){ + dataRegion.clearSelected(); + window.location = me.returnLocation; + window.location.reload(); + }); + win.close(); + }, + failure: function(error) { + btn.setDisabled(false); + Ext4.Msg.alert('Error', error?.exception ?? 'An error occurred while recording procedure orders.'); + console.error(error); + } + }); + }, + failure: function(error) { + btn.setDisabled(false); + Ext4.Msg.alert('Error', error?.exception ?? 'An error occurred querying qcstates.'); + console.error(error); + } + }); + } + +}); + +NBRI_EHR.ProcedureOrderCompleteButton = new function () { + return { + procedureOrderCompleteHandler: function(dataRegion) { + if (dataRegion && dataRegion.getChecked().length > 0) { + Ext4.create('NBRI_EHR.window.ProcedureOrderCompleteWindow', { + dataRegion: dataRegion, + returnLocation: window.location.href + }).show(); + } + else { + Ext4.Msg.alert('Error', 'Please select at least one procedure order.'); + } + }, + } +} diff --git a/nbri_ehr/resources/web/nbri_ehr/buttons/RecordProcedureButton.js b/nbri_ehr/resources/web/nbri_ehr/buttons/RecordProcedureButton.js new file mode 100644 index 0000000..9286775 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/buttons/RecordProcedureButton.js @@ -0,0 +1,149 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +Ext4.namespace('NBRI_EHR.RecordProcedureButton'); + +Ext4.define('NBRI_EHR.window.RecordProcedureWindow', { + extend: 'Ext.window.Window', + returnLocation: null, + + initComponent: function() { + Ext4.apply(this, { + title: 'Record Procedures', + modal: true, + width: 450, + bodyStyle: 'padding: 5px;', + closeAction: 'destroy', + items: [{ + xtype: 'labkey-combo', + fieldLabel: 'Performed By', + width: 350, + labelWidth: 100, + value: LABKEY.Security.currentUser.id, + itemId: 'performedBy', + displayField: 'DisplayName', + valueField: 'UserId', + queryMode: 'local', + forceSelection: true, + matchFieldWidth: false, + store: { + type: 'labkey-store', + schemaName: 'core', + queryName: 'PrincipalsWithoutAdmin', + columns: 'UserId,DisplayName,FirstName,LastName', + sort: 'Type,DisplayName', + autoLoad: true + }, + anyMatch: true, + caseSensitive: false, + }, { + xtype: 'xdatetime', + itemId: 'dateField', + width: 350, + labelWidth: 100, + fieldLabel: 'Date', + allowBlank: false, + name: 'date', + value: new Date() + },], + buttons: [{ + text:'Submit', + scope: this, + handler: function (btn) { + this.recordProcedure(btn, this.dataRegion); + } + },{ + text: 'Cancel', + scope: this, + handler: function(btn){ + btn.up('window').close(); + } + }] + }); + + this.callParent(arguments); + }, + + recordProcedure: function(btn, dataRegion) { + let win = btn.up('window'); + let windDate = win.down('#dateField').getValue(); + let performedBy = win.down('#performedBy').getValue(); + const selectedRows = [...new Set(dataRegion.getChecked())]; + var me = this; + btn.setDisabled(true); + Ext4.Msg.wait('Recording procedures...'); + + LABKEY.Query.selectRows({ + schemaName: 'study', + queryName: 'prc_order', + filterArray: [LABKEY.Filter.create('lsid', selectedRows.join(';'), LABKEY.Filter.Types.EQUALS_ONE_OF)], + scope: this, + ignoreFilter: true, + columns: 'Id,objectid,procedure,category,caseid,orderedby,lsid', + success: function (data) { + const rowsToInsert = []; + Ext4.each(data.rows, function(row) { + Ext4.each(selectedRows, function(selectedRow) { + if (row.lsid === selectedRow) { + rowsToInsert.push({ + Id: row.Id, + procedure: row.procedure, + orderid: row.objectid, + date: windDate, + performedby: performedBy, + objectid: LABKEY.Utils.generateUUID(), + orderedby: row.orderedby, + category: row.category, + caseid: row.caseid + }); + } + }); + }); + + LABKEY.Query.insertRows({ + schemaName: 'study', + queryName: 'prc', + rows: rowsToInsert, + scope: this, + success: function() { + Ext4.Msg.alert('Success', 'Procedures recorded successfully.', function(){ + dataRegion.clearSelected(); + window.location = me.returnLocation; + window.location.reload(); + }); + win.close(); + }, + failure: function(error) { + btn.setDisabled(false); + Ext4.Msg.alert('Error', error?.exception ?? 'An error occurred while recording procedures.'); + console.error(error); + } + }); + }, + failure: function(error) { + btn.setDisabled(false); + Ext4.Msg.alert('Error', error?.exception ?? 'An error occurred querying procedures.'); + console.error(error); + } + }); + } + +}); + +NBRI_EHR.RecordProcedureButton = new function () { + return { + recordProceduresHandler: function(dataRegion) { + if (dataRegion && dataRegion.getChecked().length > 0) { + Ext4.create('NBRI_EHR.window.RecordProcedureWindow', { + dataRegion: dataRegion, + returnLocation: window.location.href + }).show(); + } + else { + Ext4.Msg.alert('Error', 'Please select at least one procedure.'); + } + }, + } +} diff --git a/nbri_ehr/resources/web/nbri_ehr/buttons/RecordTreatmentButton.js b/nbri_ehr/resources/web/nbri_ehr/buttons/RecordTreatmentButton.js new file mode 100644 index 0000000..7432d47 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/buttons/RecordTreatmentButton.js @@ -0,0 +1,165 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +Ext4.namespace('NBRI_EHR.RecordTreatmentButton'); + +Ext4.define('NBRI_EHR.window.RecordTreatmentWindow', { + extend: 'Ext.window.Window', + returnLocation: null, + + initComponent: function() { + Ext4.apply(this, { + title: 'Bulk Record Treatments', + modal: true, + width: 450, + bodyStyle: 'padding: 5px;', + closeAction: 'destroy', + items: [{ + xtype: 'labkey-combo', + fieldLabel: 'Performed By', + width: 350, + labelWidth: 100, + value: LABKEY.Security.currentUser.id, + itemId: 'performedBy', + displayField: 'DisplayName', + valueField: 'UserId', + queryMode: 'local', + forceSelection: true, + matchFieldWidth: false, + store: { + type: 'labkey-store', + schemaName: 'core', + queryName: 'PrincipalsWithoutAdmin', + columns: 'UserId,DisplayName,FirstName,LastName', + sort: 'Type,DisplayName', + autoLoad: true + }, + anyMatch: true, + caseSensitive: false, + }, { + xtype: 'xdatetime', + itemId: 'dateField', + width: 350, + labelWidth: 100, + fieldLabel: 'Date', + allowBlank: false, + name: 'date', + value: new Date() + },], + buttons: [{ + text:'Submit', + scope: this, + handler: function (btn) { + this.recordTreatment(btn, this.dataRegion); + } + },{ + text: 'Cancel', + scope: this, + handler: function(btn){ + btn.up('window').close(); + } + }] + }); + + this.callParent(arguments); + }, + + recordTreatment: function(btn, dataRegion) { + let win = btn.up('window'); + let windDate = win.down('#dateField').getValue(); + let performedBy = win.down('#performedBy').getValue(); + const selectedRows = [...new Set(dataRegion.getChecked())]; + const objectIds = selectedRows.map(row => row.split('-pkSeparator-')[0]); + var me = this; + btn.setDisabled(true); + Ext4.Msg.wait('Recording treatments...'); + + LABKEY.Query.selectRows({ + schemaName: 'study', + queryName: 'treatment_order', + filterArray: [LABKEY.Filter.create('objectid', objectIds.join(';'), LABKEY.Filter.Types.EQUALS_ONE_OF)], + scope: this, + ignoreFilter: true, + columns: 'Id,objectid,code,route,amount,amount_units,concentration,volume,vol_units,conc_units,dosage,dosage_units,orderedby,category,caseid', + success: function (data) { + const rowsToInsert = []; + Ext4.each(data.rows, function(row) { + let scheduledDate; + Ext4.each(selectedRows, function(selectedRow) { + const parts = selectedRow.split('-pkSeparator-'); + const objectId = parts[0]; + const date = parts[1]; + if (row.objectid === objectId) { + scheduledDate = date; + rowsToInsert.push({ + Id: row.Id, + treatmentid: row.objectid, + date: windDate, + performedby: performedBy, + objectid: LABKEY.Utils.generateUUID(), + scheduledDate: scheduledDate, + code: row.code, + route: row.route, + amount: row.amount, + amount_units: row.amount_units, + concentration: row.concentration, + conc_units: row.conc_units, + dosage: row.dosage, + dosage_units: row.dosage_units, + volume: row.volume, + vol_units: row.vol_units, + orderedby: row.orderedby, + category: row.category, + caseid: row.caseid + }); + } + }); + }); + + LABKEY.Query.insertRows({ + schemaName: 'study', + queryName: 'drug', + rows: rowsToInsert, + scope: this, + success: function() { + Ext4.Msg.alert('Success', 'Treatments recorded successfully.', function(){ + dataRegion.clearSelected(); + window.location = me.returnLocation; + window.location.reload(); + }); + win.close(); + }, + failure: function(error) { + btn.setDisabled(false); + Ext4.Msg.alert('Error', error?.exception ?? 'An error occurred while recording treatments.'); + console.error(error); + } + }); + }, + failure: function(error) { + btn.setDisabled(false); + Ext4.Msg.alert('Error', error?.exception ?? 'An error occurred querying treatments.'); + console.error(error); + } + }); + } + +}); + +NBRI_EHR.RecordTreatmentButton = new function () { + return { + recordTreatmentsHandler: function(dataRegion) { + if (dataRegion && dataRegion.getChecked().length > 0) { + Ext4.create('NBRI_EHR.window.RecordTreatmentWindow', { + dataRegion: dataRegion, + returnLocation: window.location.href + }).show(); + } + else { + Ext4.Msg.alert('Error', 'Please select at least one treatment.'); + } + }, + } +} diff --git a/nbri_ehr/resources/web/nbri_ehr/buttons/SelectCaseButton.js b/nbri_ehr/resources/web/nbri_ehr/buttons/SelectCaseButton.js new file mode 100644 index 0000000..6411c0d --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/buttons/SelectCaseButton.js @@ -0,0 +1,95 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +Ext4.define('NBRI_EHR.form.field.SelectCaseButton', { + extend: 'Ext.button.Button', + alias: 'widget.nbri_ehr-selectcasebutton', + + text: 'Use Existing Case', + margin: '0 0 0 20', + animalId: null, + + handleCaseSelect: function(caseid, hideEdit){ + this.enableBubble('animalchange'); + + const store = this.getStore(caseid); + this.on('storeloaded', function(panel){ + + const rec = store.getAt(0); + EHR.DemographicsCache.reportCaseSelected(rec); + panel.fireEvent('animalchange', rec.data.Id); + + let editCases = this.up('#upperPanel')?.query('nbri_ehr-editCases')?.[0]; + editCases.fieldEnableChange(true); + if (hideEdit) + editCases.editBtn.hide(); + }); + }, + + onRender: function(){ + this.callParent(arguments); + + const caseid = LABKEY.ActionURL.getParameter('caseid'); + const edit = LABKEY.ActionURL.getParameter('edit'); + if (caseid){ + this.handleCaseSelect(caseid, !edit); + } + else { + const taskid = LABKEY.ActionURL.getParameter('taskId') || LABKEY.ActionURL.getParameter('taskid'); + if (taskid) { + let record = EHR.DataEntryUtils.getBoundRecord(this.up('panel')); + if (!record || !record.get('Id')) { + let tasksPanel = this.up('#upperPanel')?.query('ehr-formpanel')?.find(panel => panel.formConfig.name === 'tasks'); + let caseid = tasksPanel?.store?.data?.get(0)?.get('caseid'); + if (caseid) { + this.handleCaseSelect(caseid, false); + } + } + } + } + }, + + onAnimalChange: function(id){ + this.animalId = id; + }, + + handler: function(btn){ + if (this.animalId){ + var casepanel = this.up('panel').up('panel'); + Ext4.create('NBRI_EHR.window.SelectCaseWindow', {animalId: this.animalId, casepanel: casepanel}).show(); + } + else { + console.log('no id'); + } + }, + + getStore: function(caseid){ + if (this.store) + return this.store; + + this.store = Ext4.create('LABKEY.ext4.data.Store', { + schemaName: 'study', + queryName: 'Cases', + columns: 'lsid,objectid,caseid,taskid,Id,date,enddate,reviewdate,category,openRemark,closeRemark,performedby,plan,problemCategory,problemSubcategory', + filterArray: [ + LABKEY.Filter.create('objectid', caseid, LABKEY.Filter.Types.EQUAL), + ], + autoLoad: true, + listeners: { + scope: this, + load: function(store){ + //NOTE: consumed by SnapshotPanel + this.fireEvent('storeloaded', this); + }, + exception: function(store){ + //NOTE: refresh the store in order to avoid invalid data on the client + store.load(); + } + } + }); + + return this.store; + }, +}); diff --git a/nbri_ehr/resources/web/nbri_ehr/buttons/addClinicalObsButton.js b/nbri_ehr/resources/web/nbri_ehr/buttons/addClinicalObsButton.js new file mode 100644 index 0000000..34f9411 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/buttons/addClinicalObsButton.js @@ -0,0 +1,85 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +EHR.DataEntryUtils.registerGridButton('NBRI_DAILY_CLINICAL_OBS', function(config){ + return Ext4.Object.merge({ + text: 'Daily Observations', + tooltip: 'Click to add daily observations', + handler: function(btn) { + LABKEY.Query.selectRows({ + schemaName: 'ehr', + queryName: 'observation_types', + ignoreFilter: true, + success: function (results) { + var grid = btn.up('gridpanel'); + if (results?.rows?.length > 0) { + for (var i = 0; i < results.rows.length; i++) { + var row = results.rows[i]; + if (row.value === 'Verified Id?' || row.value === 'Stool' || row.value === 'Activity' || + row.value === 'Appetite' || row.value === 'Hydration' || row.value === 'BCS') { + + var newRecord = grid.store.createModel({}); + newRecord.set({ + category: row.value, + }); + grid.store.add(newRecord); + } + } + } + else { + Ext4.Msg.alert('Unable to load observation types. Please contact the system administrator.'); + } + }, + failure: function (error) { + Ext4.Msg.alert('Unable to load observation types. Please contact the system administrator.'); + console.log('Error loading observation types: ' + error); + }, + scope: this + }); + } + }, config); +}); + +EHR.DataEntryUtils.registerGridButton('NBRI_DAILY_CLINICAL_OBS_ORDERS', function(config){ + return Ext4.Object.merge({ + text: 'Daily Observations', + tooltip: 'Click to add daily observation orders', + handler: function(btn) { + + LABKEY.Query.selectRows({ + schemaName: 'ehr', + queryName: 'observation_types', + ignoreFilter: true, + success: function (results) { + var grid = btn.up('gridpanel'); + if (results?.rows?.length > 0) { + for (var i = 0; i < results.rows.length; i++) { + var row = results.rows[i]; + if (row.value === 'Verified Id?' || row.value === 'Stool' || row.value === 'Activity' || + row.value === 'Appetite' || row.value === 'Hydration' || row.value === 'BCS') { + + var newRecord = grid.store.createModel({}); + newRecord.set({ + category: row.value, + frequency: 'SID' + }); + grid.store.add(newRecord); + } + } + } + else { + Ext4.Msg.alert('Unable to load observation types. Please contact the system administrator.'); + } + }, + failure: function (error) { + Ext4.Msg.alert('Unable to load observation types. Please contact the system administrator.'); + console.log('Error loading observation types: ' + error); + }, + scope: this + }); + } + }, config); +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/buttons/clinicalObsGridButton.js b/nbri_ehr/resources/web/nbri_ehr/buttons/clinicalObsGridButton.js new file mode 100644 index 0000000..b017e0a --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/buttons/clinicalObsGridButton.js @@ -0,0 +1,59 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +EHR.DataEntryUtils.registerGridButton('NBRI_AUTO_POPULATE_DAILY_OBS', function(config){ + return Ext4.Object.merge({ + text: 'Auto Populate Clinical Obs', + xtype: 'button', + hidden: true, + listeners: { + render: function(btn){ + const id = LABKEY.ActionURL.getParameter('id'); + const caseid = LABKEY.ActionURL.getParameter('caseid'); + const scheduledDate = LABKEY.ActionURL.getParameter('scheduledDate'); + const scheduled = id && caseid && scheduledDate; + + LABKEY.Query.selectRows({ + schemaName: 'ehr', + queryName: 'observation_types', + ignoreFilter: true, + success: function (results) { + var grid = btn.up('gridpanel'); + if (grid?.store?.data?.getCount() === 0) { + if (results?.rows?.length > 0) { + for (var i = 0; i < results.rows.length; i++) { + var row = results.rows[i]; + if (row.value === 'Verified Id?' || row.value === 'Stool' || row.value === 'Activity' || + row.value === 'Appetite' || row.value === 'Hydration' || row.value === 'BCS') { + + var newRecord = grid.store.createModel({}); + newRecord.set({ + category: row.value, + }); + + if (scheduled) { + newRecord.set('Id', id); + newRecord.set('caseid', caseid); + newRecord.set('scheduledDate', scheduledDate); + } + grid.store.add(newRecord); + } + } + + if (scheduled) { + this.addEvents('animalchange'); + this.enableBubble('animalchange'); + this.fireEvent('animalchange', id); + grid.fireEvent('panelDataChange'); + } + } + } + }, + scope: this + }); + } + } + }, config); +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/buttons/deathNecropsyButtons.js b/nbri_ehr/resources/web/nbri_ehr/buttons/deathNecropsyButtons.js new file mode 100644 index 0000000..084923b --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/buttons/deathNecropsyButtons.js @@ -0,0 +1,144 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +/** + * Buttons specific to the Death-Necropsy form + */ + +EHR.DataEntryUtils.registerDataEntryFormButton('DEATHSUBMIT', { + text: 'Submit Death', + name: 'submitDeath', + errorThreshold: 'ERROR', + successURL: LABKEY.ActionURL.buildURL('ehr', 'enterData.view'), + itemId: 'submitDeathBtn', + disabled: true, + requiredQC: 'Request: Pending', + targetQC: 'Request: Pending', + handler: function(submitDeathBtn){ + Ext4.Msg.confirm('Confirm', 'You are about to submit a death record (any necropsy info entered will be discarded during this step). This will send an email notification to the appropriate parties to enter Necropsy. Submit death?', function(val){ + if (val == 'yes') { + var panel = submitDeathBtn.up('ehr-dataentrypanel'); + panel.storeCollection.clientStores.each((store) => { + if (store.storeId && (store.storeId.indexOf('necropsy') > -1) || store.storeId.indexOf('grossPathology') > -1 || store.storeId.indexOf('tissueDisposition') > -1) { + store.removeAll(); + } + }); + + // get and set 'Veterinarians' as the assignedTo value + var assignedToCombo = panel.down('ehr-usersandgroupscombo'); + if (assignedToCombo) { + var assignedToStore = assignedToCombo.getStore(); + if (assignedToStore.count() > 0) { + var assignedToRec = assignedToStore.findRecord('DisplayName', 'Veterinarians'); + if (assignedToRec) { + var taskStore = panel.storeCollection.getServerStoreForQuery('ehr', 'tasks'); + taskStore.getAt(0).set('assignedto', assignedToRec.get('UserId')); + panel.storeCollection.transformServerToClient(); + } + } + } + + panel.onSubmit(submitDeathBtn); + } + }, this); + }, + disableOn: 'ERROR' +}); + +EHR.DataEntryUtils.registerDataEntryFormButton('DEATH_NECROPSY_VET_REVIEW', { + text: 'Submit Necropsy for Review', + name: 'review', + requiredQC: 'Review Required', + targetQC: 'Review Required', + errorThreshold: 'WARN', + successURL: LABKEY.ActionURL.getParameter('returnUrl') || LABKEY.ActionURL.buildURL('ehr', 'enterData.view'), + disabled: true, + itemId: 'reviewBtn', + disableOn: 'ERROR', + handler: function(btn){ + var panel = btn.up('ehr-dataentrypanel'); + + Ext4.create('NBRI_EHR.window.DeathNecropsySubmitForReviewWindow', { + dataEntryPanel: panel, + dataEntryBtn: btn, + reviewRequiredRecipient: panel.formConfig.defaultReviewRequiredPrincipal + }).show(); + + } +}); + +Ext4.define('NBRI_EHR.window.DeathNecropsySubmitForReviewWindow', { + extend: 'Ext.window.Window', + + initComponent: function(){ + Ext4.apply(this, { + closeAction: 'destroy', + modal: true, + title: 'Submit For Review', + width: 430, + buttons: [{ + text:'Submit', + disabled:false, + itemId: 'submit', + scope: this, + handler: function(btn){ + var win = btn.up('window'); + var assignedTo = win.down('#assignedTo').getValue(); + if(!assignedTo){ + alert('Must assign this task to someone'); + return; + } + + var taskStore = this.dataEntryPanel.storeCollection.getServerStoreForQuery('ehr', 'tasks'); + taskStore.getAt(0).set('assignedto', assignedTo); + this.dataEntryPanel.storeCollection.transformServerToClient(); + this.dataEntryPanel.onSubmit(this.dataEntryBtn); + win.close(); + } + },{ + text: 'Cancel', + scope: this, + handler: function(btn){ + btn.up('window').hide(); + } + }], + items: [{ + bodyStyle: 'padding:5px;', + items: [{ + html: this.reviewRecipientMsg || '', + border: false, + style: 'padding-bottom: 10px;', + hidden: !this.reviewRecipientMsg + },{ + xtype: 'labkey-combo', + forceSelection: true, + fieldLabel: 'Assign To', + width: 400, + queryMode: 'local', + store: { + type: 'labkey-store', + schemaName: 'ehr_lookups', + queryName: 'veterinarians', + columns: 'UserId, DisplayName', + autoLoad: true + }, + value: this.getDefaultRecipient(), + displayField: 'DisplayName', + valueField: 'UserId', + itemId: 'assignedTo', + id: 'assignedTo', + anyMatch: true, + caseSensitive: false, + }] + }] + }); + + this.callParent(arguments); + }, + + getDefaultRecipient: function(){ + return this.reviewRequiredRecipient; + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/buttons/necropsyGridButtons.js b/nbri_ehr/resources/web/nbri_ehr/buttons/necropsyGridButtons.js new file mode 100644 index 0000000..352587c --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/buttons/necropsyGridButtons.js @@ -0,0 +1,37 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +EHR.DataEntryUtils.registerGridButton('ADDGROSSPATHOLOGY', function(config){ + return Ext4.Object.merge({ + text: 'Add', + xtype: 'button', + hidden: true, + listeners: { + render: function(btn){ + LABKEY.Query.selectRows({ + schemaName: 'ehr_lookups', + queryName: 'necropsy_organ_systems', + ignoreFilter: true, + success: function (results) { + var grid = btn.up('gridpanel'); + if (grid && grid.store && grid.store.data && grid.store.data.getCount() === 0) { + if (results && results.rows && results.rows.length > 0) { + for (var i = 0; i < results.rows.length; i++) { + var row = results.rows[i]; + var newRecord = grid.store.createModel({}); + newRecord.set({ + systemExamined: row.title, + }); + grid.store.add(newRecord); + } + } + } + }, + scope: this + }); + } + } + }, config); +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/buttons/saveDraftButton.js b/nbri_ehr/resources/web/nbri_ehr/buttons/saveDraftButton.js new file mode 100644 index 0000000..44c4f59 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/buttons/saveDraftButton.js @@ -0,0 +1,20 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +EHR.DataEntryUtils.registerDataEntryFormButton('NBRISAVEDRAFTBUTTON', { + text: 'Save Draft', + name: 'nbriSaveDraft', + errorThreshold: 'ERROR', + successURL: LABKEY.ActionURL.buildURL('ehr', 'enterData.view'), + itemId: 'nbriSaveDraftBtn', + disabled: false, + requiredQC: 'In Progress', + targetQC: 'In Progress', + handler: function(btn){ + var panel = btn.up('ehr-dataentrypanel'); + panel.onSubmit(btn, false, true); + }, + disableOn: 'ERROR' +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/buttons/treatmentSubmit.js b/nbri_ehr/resources/web/nbri_ehr/buttons/treatmentSubmit.js new file mode 100644 index 0000000..4d4a342 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/buttons/treatmentSubmit.js @@ -0,0 +1,273 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +EHR.DataEntryUtils.registerDataEntryFormButton('NBRI_TREATMENT_SUBMIT', { + text: 'Submit Final', + name: 'submit', + requiredQC: 'Completed', + targetQC: 'Completed', + errorThreshold: 'INFO', + successURL: LABKEY.ActionURL.getParameter('returnUrl') || LABKEY.ActionURL.buildURL('ehr', 'enterData.view'), + disabled: true, + itemId: 'submitBtn', + handler: function(btn){ + + const panel = btn.up('ehr-dataentrypanel'); + const casesStore = panel?.storeCollection?.getClientStoreByName('cases'); + if (casesStore) { + const rec = casesStore.getAt(0); + const caseid = casesStore.getAt(0).get('caseid'); + const qcstate = casesStore.getAt(0).get('qcstate/label'); + if (!caseid || (qcstate && qcstate !== 'Completed')) { // only check for new cases or cases going from some other state to Completed + const id = rec.get('Id'); + const problemCategory = rec.get('problemCategory'); + const category = rec.get('category'); + if (id && problemCategory && category) { + const filters = [ + LABKEY.Filter.create('Id', id), + LABKEY.Filter.create('category', category), + LABKEY.Filter.create('problemCategory', problemCategory), + LABKEY.Filter.create('isActive', true), + LABKEY.Filter.create('QCState/Label', "Completed", LABKEY.Filter.Types.EQUAL) + ] + const caseid = rec.get('caseid'); + if (caseid) { + filters.push(LABKEY.Filter.create('caseid', caseid, LABKEY.Filter.Types.NEQ)) + } + LABKEY.Query.selectRows({ + schemaName: 'study', + queryName: 'cases', + filterArray: filters, + columns: 'problemSubcategory', + scope: this, + ignoreFilter: true, + failure: LDK.Utils.getErrorCallback(), + success: function (results) { + if (results.rows.length > 0) { + const subcategories = []; + for (let i = 0; i < results.rows.length; i++) { + subcategories.push(results.rows[i].problemSubcategory); + } + let msg; + if (subcategories.length === 1) { + msg = 'This animal already has a case with the problem ' + problemCategory + '. The subcategory is ' + results.rows[0].problemSubcategory + '. Do you still want to submit this case?'; + } + else { + msg = 'This animal already has ' + subcategories.length + ' cases with the problem ' + problemCategory + '. The subcategories are ' + subcategories.join(', ') + '. Do you still want to submit this case?'; + } + + Ext4.Msg.confirm('Similar Case Exists', msg, function (v) { + if (v == 'yes') + this.onSubmit(btn); + }, this); + } + else { + Ext4.Msg.confirm('Finalize Form', 'You are about to finalize this form. Do you want to do this?', function (v) { + if (v == 'yes') + this.onSubmit(btn); + }, this); + } + } + }); + } + else { + Ext4.Msg.confirm('Finalize Form', 'You are about to finalize this form. Do you want to do this?', function (v) { + if (v == 'yes') + this.onSubmit(btn); + }, this); + } + } + else { + Ext4.Msg.confirm('Finalize Form', 'You are about to finalize this form. Do you want to do this?', function (v) { + if (v == 'yes') + this.onSubmit(btn); + }, this); + } + } + else { + Ext4.Msg.confirm('Finalize Form', 'You are about to finalize this form. Do you want to do this?', function (v) { + if (v == 'yes') + this.onSubmit(btn); + }, this); + } + }, + listeners: { + afterRender: function(btn){ + const treatmentid = LABKEY.ActionURL.getParameter('treatmentid'); + const scheduledDate = LABKEY.ActionURL.getParameter('scheduledDate'); + const obsTask = LABKEY.ActionURL.getParameter('obsTask'); + const id = LABKEY.ActionURL.getParameter('id'); + const observations = LABKEY.ActionURL.getParameter('observations'); + const prcOrderId = LABKEY.ActionURL.getParameter('prcOrderId'); + + if (treatmentid) { + + this.addEvents('animalchange'); + this.enableBubble('animalchange'); + + function onSuccess(results) { + if (results.rows.length === 0) { + console.error('No treatment order found for treatmentid ' + treatmentid); + return; + } + + const drugGrid = this.up('ehr-dataentrypanel').query('grid').find(e => e.title === "Medications/Treatments Given"); + if (!drugGrid) { + console.error('Medication/Treatments grid not found'); + return; + } + + const row = results.rows[0]; + const record = { + Id: row.Id?.value, + category: row.category?.value, + code: row.code?.value, + route: row.route?.value, + concentration: row.concentration?.value, + conc_units: row.conc_units?.value, + amount: row.amount?.value, + amount_units: row.amount_units?.value, + dosage: row.dosage?.value, + dosage_units: row.dosage_units?.value, + volume: row.volume?.value, + vol_units: row.vol_units?.value, + orderedby: row.orderedby?.value, + treatmentid: row.objectid?.value, + caseid: row.caseid?.value + }; + + if (scheduledDate) { + record.scheduledDate = scheduledDate; + } + + drugGrid.store.add(record); + + this.fireEvent('animalchange', row.Id?.value); + drugGrid.fireEvent('panelDataChange'); + } + + LABKEY.Query.selectRows({ + requiredVersion: 9.1, + schemaName: 'study', + queryName: 'treatment_order', + columns: 'Id,meaning,code,qualifier,route,concentration,conc_units,amount,amount_units,dosage,dosage_units,volume,vol_units,remark,category,objectid,orderedby', + filterArray: [LABKEY.Filter.create('objectid', treatmentid, LABKEY.Filter.Types.EQUAL)], + scope: this, + ignoreFilter: true, + success: onSuccess, + failure: LDK.Utils.getErrorCallback() + }); + + } + + if (id && observations) { + this.addEvents('animalchange'); + this.enableBubble('animalchange'); + + function onObsSuccess(results) { + if (results.rows.length === 0) { + console.error('No observations found for taskid ' + obsTask + ' and id ' + id); + return; + } + + const obsGrid = this.up('ehr-dataentrypanel').query('grid').find(e => e.title === "Observations"); + if (!obsGrid) { + console.error('Observations grid not found'); + return; + } + + const categories = []; + for (let i = 0; i < results.rows.length; i++) { + let row = results.rows[i]; + + if (!categories.includes(row.category.value)) { + let record = { + Id: row.Id?.value, + category: row.category?.value, + area: row.area?.value, + orderId: row.objectid?.value, + caseid: row.caseid?.value + }; + + if (scheduledDate) { + record.scheduledDate = scheduledDate; + } + + obsGrid.store.add(record); + categories.push(row.category?.value); + } + } + + this.fireEvent('animalchange', results.rows[0].Id.value); + obsGrid.fireEvent('panelDataChange'); + } + + LABKEY.Query.selectRows({ + requiredVersion: 9.1, + schemaName: 'study', + queryName: 'observation_order', + columns: 'Id,category,area,objectid,caseid', + filterArray: [LABKEY.Filter.create('taskid', obsTask, LABKEY.Filter.Types.EQUALS_ONE_OF), + LABKEY.Filter.create('id', id, LABKEY.Filter.Types.EQUAL), + LABKEY.Filter.create('category', observations, LABKEY.Filter.Types.EQUALS_ONE_OF)], + scope: this, + ignoreFilter: true, + success: onObsSuccess, + failure: LDK.Utils.getErrorCallback() + }); + } + + if (prcOrderId) { + + this.addEvents('animalchange'); + this.enableBubble('animalchange'); + + function onSuccess(results) { + if (results.rows.length === 0) { + console.error('No procedure order found for procedure id ' + prcOrderId); + return; + } + + const prcGrid = this.up('ehr-dataentrypanel').query('grid').find(e => e.title === "Procedures"); + if (!prcGrid) { + console.error('Procedures grid not found'); + return; + } + + const row = results.rows[0]; + const record = { + Id: row.Id?.value, + category: row.category?.value, + procedure: row.procedure?.value, + caseid: row.caseid?.value, + orderedby: row.orderedby?.value, + orderid: row.objectid?.value + }; + + prcGrid.store.add(record); + + this.fireEvent('animalchange', row.Id.value); + prcGrid.fireEvent('panelDataChange'); + } + + LABKEY.Query.selectRows({ + requiredVersion: 9.1, + schemaName: 'study', + queryName: 'prc_order', + columns: 'Id,procedure,remark,category,objectid,orderedby,caseid', + filterArray: [LABKEY.Filter.create('objectid', prcOrderId, LABKEY.Filter.Types.EQUAL)], + ignoreFilter: true, + scope: this, + success: onSuccess, + failure: LDK.Utils.getErrorCallback() + }); + + } + + } + }, + disableOn: 'WARN' +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/data/AssignmentsAnyIdClientStore.js b/nbri_ehr/resources/web/nbri_ehr/data/AssignmentsAnyIdClientStore.js new file mode 100644 index 0000000..e61c52f --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/data/AssignmentsAnyIdClientStore.js @@ -0,0 +1,16 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +Ext4.define('NBRI_EHR.data.AssignmentsAnyIdClientStore', { + extend: 'NBRI_EHR.data.AssignmentsClientStore', + + getExtraContext: function () { + var ret = this.callParent(arguments) || {}; + + // Tell the trigger scripts to allow any Id. Requires handling in trigger script to fully enable. + ret['allowAnyId'] = true; + return ret; + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/data/AssignmentsClientStore.js b/nbri_ehr/resources/web/nbri_ehr/data/AssignmentsClientStore.js new file mode 100644 index 0000000..d12fde9 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/data/AssignmentsClientStore.js @@ -0,0 +1,60 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +/** + * @param fieldConfigs + */ +Ext4.define('NBRI_EHR.data.AssignmentsClientStore', { + extend: 'EHR.data.DataEntryClientStore', + + getExtraContext: function(){ + var rows = []; + var allRecords = this.getRange(); + for (var idx = 0; idx < allRecords.length; ++idx){ + var record = allRecords[idx]; + + var date = record.get('date'); + var id = record.get('Id'); + var protocol = record.get('protocol'); + var project = record.get('project'); + if (!id || !date || !protocol || !project) + continue; + + date = Ext4.Date.format(date, LABKEY.extDefaultDateFormat); + + if (protocol) { + rows.push({ + Id: id, + objectid: record.get('objectid'), + date: date, + enddate: record.get('enddate'), + qcstate: record.get('QCState'), + protocol: record.get('protocol') + }); + } + else if (project) { + rows.push({ + Id: id, + objectid: record.get('objectid'), + date: date, + enddate: record.get('enddate'), + qcstate: record.get('QCState'), + project: record.get('project') + }); + } + + } + + if (!Ext4.isEmpty(rows)){ + rows = Ext4.encode(rows); + + return { + assignmentsInTransaction: rows + } + } + + return null; + } +}); diff --git a/nbri_ehr/resources/web/nbri_ehr/data/CaseClientStore.js b/nbri_ehr/resources/web/nbri_ehr/data/CaseClientStore.js new file mode 100644 index 0000000..35d41e5 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/data/CaseClientStore.js @@ -0,0 +1,47 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +Ext4.define('NBRI_EHR.data.CaseClientStore', { + extend: 'EHR.data.ParentClientStore', + + getExtraContext: function(){ + // Pass through cases for validation in clinremarks + var caseMap = {}; + var allRecords = this.getRange(); + for (var idx = 0; idx < allRecords.length; ++idx){ + var record = allRecords[idx]; + if (record.get('objectid')){ + var id = record.get('Id'); + var date = record.get('date'); + if (!id || !date) + continue; + + date = Ext4.Date.format(date, LABKEY.extDefaultDateFormat); + + if (!caseMap[id]) + caseMap[id] = []; + + caseMap[id].push({ + objectid: record.get('objectid'), + date: date, + qcstate: record.get('QCState'), + caseid: record.get('caseid'), + enddate: record.get('enddate') + }); + } + } + + if (!LABKEY.Utils.isEmptyObj(caseMap)){ + caseMap = Ext4.encode(caseMap); + + return { + casesInTransaction: caseMap + } + } + + return null; + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/data/CaseStoreCollection.js b/nbri_ehr/resources/web/nbri_ehr/data/CaseStoreCollection.js new file mode 100644 index 0000000..5c70473 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/data/CaseStoreCollection.js @@ -0,0 +1,240 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +Ext4.define('NBRI_EHR.data.CaseStoreCollection', { + extend: 'EHR.data.StoreCollection', + + constructor: function(){ + this.callParent(arguments); + + this.mon(EHR.DemographicsCache, 'caseselected', this.onCaseSelected, this); + this.mon(EHR.DemographicsCache, 'casecreated', this.onCaseCreated, this); + }, + + onCaseCreated: function(){ + var record = this.getClientCaseRec(); + if (record){ + // iterate through record properties and set them to null + Ext4.Object.each(record.data, function(key, value){ + if(key !== 'Id' && key !== 'category') + record.set(key, null); + }); + + } + + record = this.getServerCaseRec(); + if (record){ + // iterate through record properties and set them on the case record + Ext4.Object.each(record.data, function(key, value){ + if(key !== 'Id' && key !== 'category') + record.set(key, null); + }); + + } + }, + + onCaseSelected: function(record){ + var rec = this.getClientCaseRec(); + if (rec && record){ + // iterate through record properties and set them on the case record + Ext4.Object.each(record.data, function(key, value){ + if (rec.fields.keys.indexOf(key) !== -1) + rec.set(key, value); + }); + + // Required to not try to insert a new case. Indicates if a record is not saved in the db. This one is already saved. + rec.phantom = false; + } + + rec = this.getServerCaseRec(); + if (rec && record){ + // iterate through record properties and set them on the case record + Ext4.Object.each(record.data, function(key, value){ + if (rec.fields.keys.indexOf(key) !== -1) + rec.set(key, value); + }); + + // Required to not try to insert a new case. Indicates if a record is not saved in the db. This one is already saved. + rec.phantom = false; + } + + this.validateAll(); + }, + + getClientCaseStore: function(){ + if (this.clientCaseStore){ + return this.clientCaseStore; + } + + this.clientCaseStore = this.getClientStoreByName('cases'); + LDK.Assert.assertNotEmpty('Unable to find cases store in CaseStoreCollection', this.clientCaseStore); + + return this.clientCaseStore; + }, + + getClientCaseRec: function(){ + var caseStore = this.getClientCaseStore(); + if (caseStore){ + LDK.Assert.assertTrue('More than 1 record found in Cases store, actual: ' + caseStore.getCount(), caseStore.getCount() <= 1); + if (caseStore.getCount() == 1){ + return caseStore.getAt(0); + } + } + }, + + getServerCaseStore: function(){ + if (this.serverCaseStore){ + return this.serverCaseStore; + } + + this.serverCaseStore = this.getServerStoreByName('study.cases'); + LDK.Assert.assertNotEmpty('Unable to find cases store in CaseStoreCollection', this.serverCaseStore); + + return this.serverCaseStore; + }, + + getServerCaseRec: function(){ + var caseStore = this.getServerCaseStore(); + if (caseStore){ + LDK.Assert.assertTrue('More than 1 record found in Cases store, actual: ' + caseStore.getCount(), caseStore.getCount() <= 1); + if (caseStore.getCount() == 1){ + return caseStore.getAt(0); + } + } + }, + + getDefaultValues: function(){ + var rec = this.getClientCaseRec(); + if (rec){ + return { + Id: rec.get('Id'), + caseid: rec.get('objectid') + } + } + + return null; + }, + + onClientStoreUpdate: function(){ + this.doUpdateRecords(); + this.callParent(arguments); + }, + + doUpdateRecords: function(){ + var newValues = this.getDefaultValues() || {}; + var cacheKey = newValues ? (newValues.Id + '||' + newValues.caseid) : null; + + if (cacheKey !== this._cachedKey){ + var caseStore = this.getClientCaseStore(); + this.clientStores.each(function(cs){ + if (cs.storeId == caseStore.storeId){ + return; + } + + var toSet = {}; + + if (cs.getFields().get('Id') != null){ + toSet.Id = newValues.Id; + } + if (cs.getFields().get('caseid') != null){ + toSet.caseid = newValues.caseid; + } + + if (Ext4.Object.isEmpty(toSet)){ + return; + } + + var storeChanged = false; + cs.suspendEvents(); + cs.each(function(rec){ + var needsUpdate = false; + for (var field in toSet){ + if (toSet[field] !== rec.get(field)){ + needsUpdate = true; + } + } + + if (needsUpdate){ + storeChanged = true; + rec.set(toSet); + } + }, this); + cs.resumeEvents(); + + if (storeChanged) + cs.fireEvent('datachanged', cs); + }, this); + } + // Only validate once stores have loaded, otherwise can have perf issues when loading existing cases + else if( this.haveStoresLoaded ) { + // Validate across the sections, such as clin_remark not required if case close date entered + this.validateAll(); + } + + this._cachedKey = cacheKey; + }, + + getTaskId: function(){ + if (this.taskId) { + return this.taskId; + } + + var model = this.getServerStoreForQuery('ehr', 'tasks').getAt(0); + if (model){ + return model.get('taskid'); + } + + console.error('Unable to find taskid'); + return null + }, + + setClientModelDefaults: function(model){ + if (!model.get('taskid')){ + model.suspendEvents(); + model.set('taskid', this.getTaskId()); + model.resumeEvents(); + } + + return this.callParent([model]); + }, + + commitChanges: function(){ + // ensure all records are using this taskId and alert if not + var taskid = this.getTaskId(); + if (taskid){ + this.clientStores.each(function(cs){ + if (cs.getFields().get('taskid') != null && cs.storeId !== this.collectionId + '-cases'){ + cs.each(function(r){ + if (taskid != r.get('taskid')){ + LDK.Assert.assertEquality('Incorrect taskid for client store:' + cs.storeId, taskid, r.get('taskid')); + r.beginEdit(); + r.set('taskid', this.getTaskId()); + r.endEdit(true); + } + }, this); + } + }, this); + + this.serverStores.each(function(cs){ + if (cs.getFields().get('taskid') != null && cs.storeId.indexOf('|cases|') === -1){ + cs.each(function(r){ + if (r.isRemovedRequest){ + return; //do not check these records. they have deliberately been separated. + } + + if (taskid != r.get('taskid')){ + LDK.Assert.assertEquality('Incorrect taskid for server store:' + cs.storeId, taskid, r.get('taskid')); + r.beginEdit(); + r.set('taskid', this.getTaskId()); + r.endEdit(true); + } + }, this); + } + }, this); + } + + return this.callParent(arguments); + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/data/ClinicalObservationClientStore.js b/nbri_ehr/resources/web/nbri_ehr/data/ClinicalObservationClientStore.js new file mode 100644 index 0000000..bb7b9b3 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/data/ClinicalObservationClientStore.js @@ -0,0 +1,24 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +Ext4.define('NBRI_EHR.data.ClinicalObservationsClientStore', { + extend: 'EHR.data.DataEntryClientStore', + + constructor: function(){ + this.callParent(arguments); + + this.observationTypesStore = EHR.DataEntryUtils.getObservationTypesStore(); + }, + + getExtraContext: function(){ + // Pass through tasks for entering observations from schedule + const obsTask = LABKEY.ActionURL.getParameter('obsTask'); + + return { + orderTasksInTransaction: [obsTask] + + } + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/data/DrugAdministrationRunsChildClientStore.js b/nbri_ehr/resources/web/nbri_ehr/data/DrugAdministrationRunsChildClientStore.js new file mode 100644 index 0000000..df4a978 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/data/DrugAdministrationRunsChildClientStore.js @@ -0,0 +1,33 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +Ext4.define('NBRI_EHR.data.DrugAdministrationRunsChildClientStore', { + extend: 'NBRI_EHR.data.DrugAdministrationRunsClientStore', + + insert: function(index, records) { + var ret = this.callParent(arguments); + + // after insert of a new, track down the parent record to get the fields to inherit + if (this.sectionCfg && this.sectionCfg.extraProperties && this.sectionCfg.extraProperties.parentQueryName) { + var parentQuery = this.sectionCfg.extraProperties.parentQueryName; + var parentStore = this.storeCollection.getClientStoreByName(parentQuery); + var parentRecord = parentStore ? parentStore.getAt(0) : null; + if (parentRecord && Ext4.isFunction(parentStore.onRecordUpdate)) { + // get the set of inherited field names + var inheritFieldNames = []; + Ext4.each(this.getFields().items, function(field) { + if (field.inheritFromParent) { + inheritFieldNames.push(field.name); + } + }); + + parentStore.onRecordUpdate(parentRecord, inheritFieldNames); + } + } + + return ret; + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/data/DrugAdministrationRunsClientStore.js b/nbri_ehr/resources/web/nbri_ehr/data/DrugAdministrationRunsClientStore.js new file mode 100644 index 0000000..a4b53c5 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/data/DrugAdministrationRunsClientStore.js @@ -0,0 +1,59 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +Ext4.define('NBRI_EHR.data.DrugAdministrationRunsClientStore', { + extend: 'EHR.data.DrugAdministrationRunsClientStore', + + // This override adds a special case for frequency to align formulary frequency.rowid with data frequency.meaning + onRecordUpdate: function (record, modifiedFieldNames) { + if (record.get('code')) { + modifiedFieldNames = modifiedFieldNames || []; + + if (modifiedFieldNames.indexOf('code') == -1) { + return; + } + + if (!this.formularyStore) { + LDK.Utils.logToServer({ + message: 'Unable to find formulary store in DrugAdministrationRunsClientStore' + }); + console.error('Unable to find formulary store in DrugAdministrationRunsClientStore'); + + return; + } + + var values = this.formularyStore.getFormularyValues(record.get('code')); + if (!Ext4.Object.isEmpty(values)) { + var params = {}; + + for (var fieldName in this.fieldMap) { + if (!this.getFields().get(fieldName)) { + continue; + } + + if (modifiedFieldNames.indexOf(this.fieldMap[fieldName]) != -1) { + continue; + } + + let def = values[fieldName]; + + // Special case for frequency to align the formulary frequency rowid with data stored as the meaning + if (fieldName.toLowerCase() === 'frequency') + def = values['frequency/meaning'] + + if (Ext4.isDefined(def)) { + params[this.fieldMap[fieldName]] = def; + } + } + + if (!LABKEY.Utils.isEmptyObj(params)) { + record.beginEdit(); + record.set(params); + record.endEdit(true); + } + } + } + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/data/ObsOrderChildClientStore.js b/nbri_ehr/resources/web/nbri_ehr/data/ObsOrderChildClientStore.js new file mode 100644 index 0000000..efa14af --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/data/ObsOrderChildClientStore.js @@ -0,0 +1,33 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +Ext4.define('NBRI_EHR.data.ObsOrderChildClientStore', { + extend: 'NBRI_EHR.data.ObsOrdersClientStore', + + insert: function(index, records) { + var ret = this.callParent(arguments); + + // after insert of a new, track down the parent record to get the fields to inherit + if (this.sectionCfg && this.sectionCfg.extraProperties && this.sectionCfg.extraProperties.parentQueryName) { + var parentQuery = this.sectionCfg.extraProperties.parentQueryName; + var parentStore = this.storeCollection.getClientStoreByName(parentQuery); + var parentRecord = parentStore ? parentStore.getAt(0) : null; + if (parentRecord && Ext4.isFunction(parentStore.onRecordUpdate)) { + // get the set of inherited field names + var inheritFieldNames = []; + Ext4.each(this.getFields().items, function(field) { + if (field.inheritFromParent) { + inheritFieldNames.push(field.name); + } + }); + + parentStore.onRecordUpdate(parentRecord, inheritFieldNames); + } + } + + return ret; + } + +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/data/ObsOrdersClientStore.js b/nbri_ehr/resources/web/nbri_ehr/data/ObsOrdersClientStore.js new file mode 100644 index 0000000..5700e0e --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/data/ObsOrdersClientStore.js @@ -0,0 +1,45 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +Ext4.define('NBRI_EHR.data.ObsOrdersClientStore', { + extend: 'EHR.data.DataEntryClientStore', + + constructor: function(){ + this.callParent(arguments); + + this.observationTypesStore = EHR.DataEntryUtils.getObservationTypesStore(); + }, + + getExtraContext: function(){ + // Pass through cases for validation in clinremarks + var orders = []; + var allRecords = this.getRange(); + for (var idx = 0; idx < allRecords.length; ++idx){ + var record = allRecords[idx]; + if (record.get('category')){ + var id = record.get('Id'); + var date = record.get('date'); + if (!id || !date) + continue; + + date = Ext4.Date.format(date, LABKEY.extDefaultDateFormat); + + orders.push({ + id: id, + objectid: record.get('objectid'), + date: date, + qcstate: record.get('QCState'), + taskid: record.get('taskid'), + category: record.get('category'), + frequency: record.get('frequency') + }); + } + } + + return { + ordersInTransaction: orders + } + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/field/AnimalIdCases.js b/nbri_ehr/resources/web/nbri_ehr/field/AnimalIdCases.js new file mode 100644 index 0000000..23813fd --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/field/AnimalIdCases.js @@ -0,0 +1,71 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +Ext4.define('NBRI_EHR.form.AnimalIdCases', { + extend: 'Ext.panel.Panel', + alias: 'widget.nbri_ehr-animalIdCases', + layout: { + type: 'hbox', + }, + + initComponent: function(){ + this.on('resize', function(){ + this.setWidth(700); + }); + + this.idField = Ext4.create('EHR.form.AnimalIdUpperField', { + id: 'animal_id', + name: 'Id', + width: 245 + }); + + this.existingCasesBtn = Ext4.create('NBRI_EHR.form.field.SelectCaseButton', { + id: 'existing_cases', + }); + + this.label = Ext4.create('Ext.form.Label', { + text: 'Id:', + forId: 'animal_id', + margin: '0 138 0 0', + cls: 'black-text-color' + }); + + this.items = [ + this.label, + this.idField, + this.existingCasesBtn + ] + + this.existingCasesBtn.disable(); + + if (this.idField){ + this.mon(this.idField, 'animalchange', this.onAnimalChange, this, {buffer: 1000}); + } + + this.callParent(); + }, + + onAnimalChange: function(){ + this.existingCasesBtn.onAnimalChange(this.idField.getValue()); + this.existingCasesBtn.enable(); + }, + + setValue: function(value){ + this.idField.setValue(value); + }, + + disable: function(){ + this.idField.disable(); + this.label.addCls('form-panel-input-disabled'); + this.idField.inputEl.addCls('form-panel-input-disabled'); + + }, + + enable: function(){ + this.idField.enable(); + this.label.removeCls('form-panel-input-disabled'); + this.idField.inputEl.removeCls('form-panel-input-disabled'); + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/field/DrugVolumeField.js b/nbri_ehr/resources/web/nbri_ehr/field/DrugVolumeField.js new file mode 100644 index 0000000..fb4a405 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/field/DrugVolumeField.js @@ -0,0 +1,61 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +Ext4.define('NBRI_EHR.field.DrugVolumeField', { + extend: 'EHR.form.field.DrugVolumeField', + alias: 'widget.nbri_ehr-drugvolumefield', + + triggerCls: 'x4-form-search-trigger', + triggerToolTip: 'Click to calculate amount based on concentration and volume', + + initComponent: function(){ + this.callParent(arguments); + this.getSnomedStore(); + }, + + getSnomedStore: function(){ + if (NBRI_EHR._snomedStore) + return NBRI_EHR._snomedStore; + + var storeId = ['ehr_lookups', 'snomed', 'code', 'meaning'].join('||'); + + NBRI_EHR._snomedStore = Ext4.create('LABKEY.ext4.data.Store', { + type: 'labkey-store', + schemaName: 'ehr_lookups', + queryName: 'snomed', + columns: 'code,meaning', + sort: 'meaning', + storeId: storeId, + autoLoad: true, + getRecordForCode: function(code){ + var recIdx = this.findExact('code', code); + if (recIdx != -1){ + return this.getAt(recIdx); + } + } + }); + + return NBRI_EHR._snomedStore; + }, + + onTriggerClick: function(){ + var record = EHR.DataEntryUtils.getBoundRecord(this); + if (!record){ + return; + } + + if (!record.get('code') || !record.get('Id')){ + Ext4.Msg.alert('Error', 'Must enter the Animal Id and treatment'); + return; + } + + Ext4.create('NBRI_EHR.window.DrugAmountWindow', { + targetStore: record.store, + formConfig: record.sectionCfg, + boundRecord: record + }).show(); + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/field/EditCase.js b/nbri_ehr/resources/web/nbri_ehr/field/EditCase.js new file mode 100644 index 0000000..3e50113 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/field/EditCase.js @@ -0,0 +1,115 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +Ext4.define('NBRI_EHR.form.EditCases', { + extend: 'Ext.panel.Panel', + alias: 'widget.nbri_ehr-editCases', + layout: { + type: 'hbox', + }, + editing: false, + disabled: false, + readonly: false, + + initComponent: function(){ + this.on('resize', function () { + this.setWidth(700); + }); + + let caseid = LABKEY.ActionURL.getParameter('caseid'); + let taskid = LABKEY.ActionURL.getParameter('taskId'); + + this.editBtn = Ext4.create('Ext.button.Button', { + text: 'Edit', + margin: '20 10 0 0', + hidden: !caseid && !taskid, + scope: this, + handler: this.onEditButtonClick + }); + + this.items = [ + this.editBtn, + ] + + this.mon(EHR.DemographicsCache, 'caseselected', this.onCaseSelect, this); + + this.callParent(); + }, + + disableItem(item, disable) { + if (disable) { + item.disable(); + } + else { + item.enable(); + } + }, + + disabledDisplay: function(item, disable){ + if (item.labelEl && item.inputEl) { + if (disable) { + item.labelEl.addCls('form-panel-input-disabled'); + item.inputEl.addCls('form-panel-input-disabled'); + } + else { + item.labelEl.removeCls('form-panel-input-disabled'); + item.inputEl.removeCls('form-panel-input-disabled'); + } + } + + if (item.labelEl && item.containerEl) { + if (disable) { + item.labelEl.addCls('form-panel-input-disabled'); + item.containerEl.addCls('form-panel-input-disabled'); + } + else { + item.labelEl.removeCls('form-panel-input-disabled'); + item.containerEl.removeCls('form-panel-input-disabled'); + } + } + }, + + fieldEnableChange: function(disable){ + var panel = this.up('panel'); + panel.items.each(function(item){ + if (item.name != 'objectid'){ + this.disableItem(item, disable); + this.disabledDisplay(item, disable); + } + }, this); + }, + + onEditButtonClick: function(){ + if (this.disabled) { + this.disabled = false; + this.fieldEnableChange(false); + } + else { + this.disabled = true; + this.fieldEnableChange(true); + } + }, + + onCaseSelect: function(){ + this.fieldEnableChange(true); + if (this.readonly) { + return; + } + this.editing = true; + this.disabled = true; + this.editBtn.show(); + }, + + onNewCase: function(){ + EHR.DemographicsCache.reportCaseCreated(); + this.editing = false; + this.editBtn.hide(); + this.fieldEnableChange(false); + }, + + disable: function(){}, + + enable: function(){} +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/field/LocationField.js b/nbri_ehr/resources/web/nbri_ehr/field/LocationField.js new file mode 100644 index 0000000..b42ceac --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/field/LocationField.js @@ -0,0 +1,42 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + * + * @cfg pairedWithRoomField. Note: if true, you must implement getRoomField(), which returns the cognate ehr-roomfield + */ +Ext4.define('NBRI_EHR.field.LocationField', { + extend: 'Ext.ux.CheckCombo', + alias: 'widget.nbri_ehr-locationField', + + fieldLabel: 'Location', + nullCaption: '[Blank]', + editable: true, + expandToFitContent: true, + addAllSelector: true, + typeAhead: true, + + initComponent: function(){ + Ext4.apply(this, { + displayField:'cage', + valueField: 'rowid', + queryMode: 'local', + anyMatch: true, + store: Ext4.create('LABKEY.ext4.data.Store', { + type: 'labkey-store', + schemaName: 'ehr_lookups', + queryName: 'cage', + sort: 'cage', + autoLoad: true, + columns: 'rowid,cage', + }) + }); + + if (!Ext4.isDefined(this.initialConfig.multiSelect)){ + this.multiSelect = true; + } + + this.callParent(arguments); + }, + +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/images/ull-logo-main-subsite.png b/nbri_ehr/resources/web/nbri_ehr/images/ull-logo-main-subsite.png new file mode 100644 index 0000000000000000000000000000000000000000..24c9f7cb9b9990671cb667debcaa564573767f4b GIT binary patch literal 7359 zcmaKRcQjmI_qUQDdX4BkdT-GqdYKUnMmHFpVGKqWC3+VvdW~oiz4sP91Ve~2Nkk{2 zmsg(O^L>8rAMf+tb?-gr?6p6i{W*K@yVhOnM85>85#iI~V_;wqX{amf-H(9#M-dO_ z{+%|)J$66PAXLBzeV84>2Lgv;DB8lTq0Abt5PPT|6k_Y^F$$H%z`$mA1c4D?fVQ*^ z%vAvL*GB;9>VA*Lz>rlyx(RQH2J z_5FY#8$V|oDO*+rd1hIp^gV$q6aisIy1KY|N+ac1|HUhPKmThMWM%%B3&L5B^?yWx z0WX=AU~nk2xPU0XjgYV~vxJ0zu$Z`ngfJhoh>);|pwRs-!7nT(EiNG~BFX&ki}gMl z+}2K7Pg(WfvF=xLtPTi-yR@L7kB^UlkEj3)ZZ9Y-B_;KjLqvrC-him}D=n!crKl<* zp&}xwa-VkBwOu(tn;RsFBnzs=z4ejiyG z3U~B|+N#1~uFU`1w6x=Y*P`@a`TmWy{qI_o|0`DTUX0-1(*9qi{>OCRKYyqHY25q8 ze_9{vcHi&t`^Hv$Jh6QLO$lo#D}sx9Ali~4C>s!}|x%7TJ-1(nR2YA+$b%hOFMwl}^(3a6xk=yl$`^7in-j(Yj%qiJF4*x|>S@L5isjZ_`^^;zWCTw>aVkGd4) zfXxQd;N#-_VLxn?@gcgJLdQ%`?{xu#mws8toU&3Cii7$ zP_aXHuh&iQ#doOsv=f=ul4f6n+seDN5=f%5e0fZr3EXY}GDqy?HGqTIv=bP`J3 zzcD?fN-Rd|Ce5%p9oGm}-Ikl+gA3R8i@7+owe4r0h;{}?J8?e0?~+@W_IxD%MNAxO z@lIc?)a;dYIfG24^I>>mGo9F(e`3weYa zY>}2PRTjSydupcQ_8eQThvXpJ-|0-}x&HT&_KjP&P0wDf5(6|jN7!h41D>UpmDQd^ zna;LA^=ByMOr6ydN^v?nWC#DixX?xLZ@F06t9JE`t6i}CsLz`XgiWW_R%4%3`Nty7 zhV<=$dIA@JfDQw~{XPcb>POShmF#6m_9Ia)KWHqvUq8q`?nb8Do9dTXCPZYRc}B@n zHuB}(`u#w2-^GMtHRz8_tCxoFzH)oF;*TM4oaC1IWa9aP&gGEkh?saY%H;{*%#;GP zVhoB)<%Gvo@EGJPBlR}vDn6nCmbGt9}^3yUs}`9 z=VE8Z(9qCO5y^7Fm8*{l{~d0Ug5Dg~iOQg>L?0UByvR+$*x8uEqc+YZyHfM|Szh9L z#qby_xv+YbK!#V#eRolp)PbAa;kqJ7Z?$?hI)?(&2*0MV=siAdBduakP=^B4uk%)| z?d}&*NZ0p*qwBSl*>at;TnT$(Lzl03W2IW%$Pvo?wQu$MCix0-H;8=0Y7;=2R`3te z$M#cxF&^bTnPbND;cMXo%X-jah@8^T%XR zM(?|yv5%@AlATj`2B0|2+v;KdXHcyrgzc1{12~0nLq4M`@T!gtg*xF8J=^_eX?C^5 zG%n?as`+uAHIByQL!za2gg~80v(gtK+L*A17rp2*AtqU6OGxQ28m?rM3$FuXSWrxGy;C)U zT`f~Hei!>n*x}60BarbS!Bn$99{2;PH=HYivdCb{pQI5A4X{(%{7zu*q+e3PZZq+N zKhrCKb4bwSL29$l+E*G;r0l{EL+z=Po2%1kGFr{|Q@6+IFKa}nx}Vds*<300PO4>t z6+xu!%um=Le6ZGZ7MG!zOQ1o&BK-pX2_aL!Bg@ z2}*vmk=-E(8YAX>TJI^xXjA2(by@^u+g@z+ChXC%s}HAGu! zMh`g2=3RRU0ax*_tS1T4O>T+Xl{C|z*hUmbgj(Mb)_;n99-=W9hL~CJF}h_zW_Ea@ zBkDg$?Vbxf*gEW$2Df?lW}Pyu>1QjFsfyJs8F0ZDqmEjw^thsy-W5FElXv82x$Rvm zKUQHkUzYWF88S0y7izpT|-vGxdLXOhp%;#P&$Nah-vqM#o+B57wl0&JQD zxI*QML`70xjHZc5&5nHMOKPwQnM`%XC#IOnNf7!dR|j~a<7+T}6{*trsWlIE;)!@q~%P2D713H#`=A} zx~mFy;nQha%ltfgvFZm)kKp7A57eSIHB`6fMT70cPgWa;0LB_(i}iZB3s*(gP|K%& zmm+k&KQ}=Ots`J>9@gySQ5&6jzXYH4;-*?v3}u1&PL0|W>&7Wp_~<|3^k^AqU~lH!tx|6D0qfCLhrcecAO?(Jx?s< z&Co!d?R!C4jyGZ6hs~khD}iL2iPC{TC^sm-f-ib)_UzDLXeQW#D<$0I7*TWC`sjVh zzL8QFQ0vszviczj`lq7Wls`9`i~Z_E@j0mrCHVwzk>t-V-2P&@!t|?`&kTH5{7p*b zwGU4Rk3YgcW)brdKE=PDaBAsV4$r>HFaBo0;5`Ql$-zM>`&gnyvbMsmIcrsK*mGG; zr5lT$MDj~Oex@O~)4O&)e~*3l{yl!HBc{KX!5ivvL&u1bM=Ooie0)#CqYHONTH3Zd ztynf)%1A29zDd7Y!K8JhXK52U+%{0w2YW`;a5#QJPOe4xIED0ijcpY_IT<}8gEFVo zxa$+*exXt#E^Up(eVsuS3+W;&0UwqBT-x)B4L;hK;zga&r8VL}Ix>pQqAKiGAslLtjw()9Utp zRTRUW(4@7u7dY9P!ETRsv15?3UTzN#4zg3V^Kf$`e#~zXm(FjBAJa32{$ySBfLK_( zPh$t?NyiaXJaDo%?9gpC{XK}({d9-nSHY}JRx8d*lpCiP!z1LDhsPjahp`6L%UlU8 zc5!hkrl507IQNh7k#R1R&)V}KZ|^4P!D{E$a&v6~O-DY~vm)m2Vk2hD7r17H`Ks&j zRwpOp?OEtkK?*w{wQ8E&71o$PgijKQ&IM_+=|}CrIypw%$VP=yz~mGfq#C>_(Xy&J z&pbA~1SQ6|`gd*PYE_2olpw;PCwZ=@^w0)bI5_}?5X?miC|26|qMut=@GDv;(nELO zjJia<-cD}q+~BS4=v)2~1mV%3OR=iBd6L4Zacn=8xA$}m-mGSjqBemaTO`jeEDurZ zzLl=EIh{Dk1K?|EsqD72NDXG!0wL0v*~@fZnp&Ggk2QO*yYWvFiGuy!A=QAnlkrh3 zf|<&Ue97W$Cc+?RTi(Zf)}pEUD08@E%S4nV;E>2Ve$+F=%QvZRQ)*yTdqYX(`k6x# zp0;|*oyxKAsoZx`YFEiG|NG!0V1RBDFgvNuO7G)xGBqC2SA<$(moQQ*4uYV zoMAXn{GIt^D^R<@5j!F~CnT4UYX%EsRFwTr6&fU;!1$@>lFk1^(hf~)PEQENF-zZx z1jlG{(dEw)zT+1uahJ(J`0pRul?$UT;&$4{r^-{m%cpl=?Pp4On>}1%@)h0qL+1+G zx2maL@$fmTIi5CO_K5D<33y35$s{)!5DiTwow{ZQh8r;WqiRhbdLP2QXj2PS4otu z33s!jTNP{z*DZ}GQsN)QbU`&uXyzqyvJt2=^6>JS9u)XoV`HU%z7WlM8 zQ3GvVm&W%%oH!Ra<9L5a<}{_-nke&o_~Aigx?_pDqE13lNlA&J$YoLD_tMgz2d!ro z5`mNL9hO%bvg&=mq>RkNj}JF*vQX;)E~_uw9&Z# z+lrhK-@_DSpNeFzVYbQh*dm45Lpmj})HT^|R_b=DA_&fJO4-kC;?dKX(Y{>Az!132eR zLfF5}e~cEc1lv_Oq3BJ#oa5+PPRU70u&?(*Bf z#nnp?=t3P7vuxPad3zw~PqqCG)j$`$zZ*dyP6@2Li4Op4H70P(Al}-G)PagfCe)X{ zR8vfgs%o^iq*IZ#LXRd;^!gaiz@`|E2CEyd)hd!1B5&D@y4r541D!LrF4}K#?8$&X z-sK^Le;OL%=ZL4k9a?)5u>Co5V- zx91dOD4%no+B$!wrSvspV{3%t1U=8PtvYU+W13Ix+jLO~~#%)?nYoi*CzIi1y2oX-9L? zayyDAe32F#dwlhvjUviT;!xi3&H+IQ`r%vhx#)N)nhIRE4GHtX(PhOZjh?MEK zW4;>v?eL|<+~CyY3HP)m)e}NC4-VeIlYtm(?UQ3F$MWuMUXJuFOwU`zwjZHW1)Rd; z7}^!^+8w>5=tOL6mHqA|N9sS@4njy7R_1a{T8G0Sr92!o%5@C{K47`DcT+FO)do1l z@jmDgc9wGT?c!NvDvp!KirVqzzs#JpJ@FBbc^+=^NT-#2Hdgbw=4;&`%uIOox!D+$qXAc(2hZwKxWU~ofIEV)W@5*d%7 z;8ZaLecuh$BdMtPfUiQV1KV5-HJ;j&i1@E!nycEoLqh zUyjG$%RseGbrQ4XXf_0oYf4w*oBRk?*<+5k8UyIX7Fff#J(35V)DqUk-v_63YY=M6 zJF>%qy;NAz7xdO-97Xb*#&)1nbmO-TD4ml%PmaL3{F(f?i`~9hTTk?1VFf#D?Jd_SvZ>*32q&JSzHEUvOeu#odDX8kxdbii zZbyywW96@-JW>Yt_s1>7TZ+RJ*7d*^_(jnsXTt6N?!UqQ)WzNe19 zmFKA1c)TDBYxPz6;Prs+M8lx46`IJG6KDEKIN>TP8_E8&NvpM%Ql3(T@M<89&g(5( zGuAe5IAQD(jlrdI<==_u-73)*_T^{=F=5@0>A4(^})?U;DHOBCJR zK$rY;tvSi%sc~@d**>?a1Z*f`aM*sQha zJ&xjfkU_cjeztS5_mP0*9cWAzf-I0(JU6O)z7!-0KeVdTvRJ~uj9|Yz@bUS5?2(u! zSNVdKt*+0I?Q!DWHpSMe<(Lxa4Xwli71Em#Bk@?1{(N7*ip`vekU%AW_|mj=+$D^+ znYIBxUbWtKC~aYIbkj(%II)>T+PCFy!^FT;i%&6Z?MN^LkQHM@@YMxEJ3~v7J8bk> zb?dc}TjMa9maBjfpsHc|qcB%oUAP^q=TXxA4+LkV$mxDS)A&>_%cI0NTVQ0ru7cL` zOZ0-RRFG?{CI-OlqeJquUzVAI5^M+f(a$rNFnkrsCMR=WWt0H^Fa@{Z!6P<^7&nRv z)4zF?hz!Ls@;7iB{#yMta#m;_OKb-yan+l;{e^1d6QV7;Hq1M9)|4HMCf-}-J>6Z2 z9iqgVU@1Q|aU>IQwQF!fk>e6GqPbItK6?lB6QvWvoLd?0Tqn6xFe{B}6|JpVfs0jJ z7Vf$jkEy9+8=VKgDgH@M-#E`_E#D-*VMFC-yt&1^6@;xe(CF&whL%S}M%v8!yd|Zi zziv}DWD37haF*6cImdO_7ZH_Z4Y=MnZx=fGRbJ;g?5#X}f53pKxYE%^K10OWx0Q|* z^-`f+ukU6VIceCc>G^L_a@7qv_RdiSH~ARY7~Ic{=P!0?(0`8 0) { + return necropsyStore.data.items[0].data.date; + } + } + }, + remark: { + hidden: true, + showInGrid: false + }, + project: { + hidden: true, + showInGrid: false + }, + systemExamined: { + columnConfig: { + width: 200 + } + }, + performedby: { + hidden: true, + showInGrid: false + }, + appearance: { + defaultValue: 'Normal', + lookup: { + schemaName: 'ehr_lookups', + queryName: 'necropsy_organ_appearance', + keyColumn: 'title', + displayColumn: 'title', + defaultValue: 'Normal' + } + } + }, + 'study.tissueDisposition': { + date: { + hidden: true, + getInitialValue: function(v, rec){ + const necropsyStore = rec.storeCollection.getClientStoreByName('necropsy'); + if (necropsyStore) { + return necropsyStore.data.items[0].data.date; + } + } + }, + project: { + hidden: true, + showInGrid: false + }, + performedby: { + hidden: true, + showInGrid: false + }, + necropsyDispositionCode: { + columnConfig: { + fixed: true, + width: 200 + }, + } + } + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/model/sources/MedicationEndDate.js b/nbri_ehr/resources/web/nbri_ehr/model/sources/MedicationEndDate.js new file mode 100644 index 0000000..86b0334 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/model/sources/MedicationEndDate.js @@ -0,0 +1,53 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +EHR.model.DataModelManager.registerMetadata('MedicationEndDate', { + allQueries: { + 'code': { + editorConfig: { + listeners: { + // End date calculated from Default Duration in the formulary and the date field of data entry grid. + // Only calculate end date when treatment is selected and there is a date in the field. + // Don’t recalculate if changing drug multiple times. + change: function (field, newVal, oldVal) { + if (newVal && !oldVal) { + let record = EHR.DataEntryUtils.getBoundRecord(field); + if (record) { + LABKEY.Query.selectRows({ + schemaName: 'ehr_lookups', + queryName: 'drug_defaults', + columns: ['duration','offset'], + scope: this, + ignoreFilter: true, + filterArray: [LABKEY.Filter.create('code', newVal)], + success: function (data) { + if (data.rows && data.rows.length > 0) { + let defaultDuration = data.rows[0].duration; + let offset = data.rows[0].offset; + let date = record.get('date'); + if (defaultDuration && date) { + let endDate = new Date(date); + endDate.setDate(endDate.getDate() + defaultDuration); + if (offset) { + endDate.setHours(endDate.getHours() + offset); + } + EHR.DataEntryUtils.setSiblingFields(field, { + enddate: endDate + }); + } + } + }, + failure: function(error) { + console.error(error); + } + }); + } + } + } + } + } + } + }, +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/model/sources/NBRIDefault.js b/nbri_ehr/resources/web/nbri_ehr/model/sources/NBRIDefault.js new file mode 100644 index 0000000..00e9da7 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/model/sources/NBRIDefault.js @@ -0,0 +1,353 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +EHR.model.DataModelManager.registerMetadata('Default', { + allQueries: { + Id: { + xtype: 'ehr-animalIdUpperField', + }, + 'Id/demographics/dam': { + xtype: 'ehr-animalIdUpperField', + }, + 'Id/demographics/sire': { + xtype: 'ehr-animalIdUpperField', + }, + performedby: { + hidden: false, + allowBlank: true, + defaultValue: LABKEY.Security.currentUser.id, + getInitialValue: function (v, rec) { + if (Number.isInteger(Number(v))){ + return v; + } + + return LABKEY.Security.currentUser.id; + }, + editorConfig: { + store: { + type: 'labkey-store', + schemaName: 'core', + + // 'performedby' is a text field in the dataset and its lookup to the userid is an int field - this mismatch causes it to disappear + // from the display when a value is selected from the dropdown even though the 'userid' value gets saved as a text (this behavior was only seen + // in the form panel but not in the grid panel). + // casting it as a varchar when loading the store fixes this issue. + sql: "SELECT CAST (UserId AS VARCHAR) AS UserId,DisplayName,FirstName,LastName FROM core.PrincipalsWithoutAdmin WHERE active = TRUE AND Type = 'u'", + autoLoad: true + } + } + }, + orderedby: { + hidden: false, + allowBlank: false, + defaultValue: null, + columnConfig: { + width: 160 + }, + editorConfig: { + store: { + type: 'labkey-store', + schemaName: 'ehr_lookups', + + // 'orderedby' is a text field in the dataset and its lookup to the userid is an int field - this mismatch causes it to disappear + // from the display when a value is selected from the dropdown even though the 'userid' value gets saved as a text. + // Casting it as a varchar when loading the store fixes this issue. + sql: 'SELECT CAST (UserId AS VARCHAR) AS UserId,DisplayName FROM ehr_lookups.veterinarians', + autoLoad: true + } + } + }, + scheduleddate: { + header: 'Scheduled Date/Time', + label: 'Scheduled Date/Time', + hidden: false, + userEditable: false, + nullable: true, + columnConfig: { + width: 180 + } + }, + date: { + columnConfig: { + fixed: true, + width: 150 + } + }, + enddate: { + columnConfig: { + fixed: true, + width: 150 + } + }, + 'cage': { + columnConfig: { + fixed: true, + width: 150 + }, + }, + QCState: { + hidden: true, + editable: false, + editorConfig: { + hidden: true, + editable: false + }, + getInitialValue: function (v) { + var qc; + if (!v && EHR.Security.getQCStateByLabel('In Progress')) + qc = EHR.Security.getQCStateByLabel('In Progress').RowId; + return v || qc || 'In Progress'; + } + }, + 'qcstate/label': { + hidden: true, + editable: false, + editorConfig: { + hidden: true, + editable: false + } + } + }, + byQuery: { + 'study.housing': { + room: { + allowBlank: true, + hidden: true + }, + 'cage': { + allowBlank: false + }, + 'enddate': { + hidden: true + }, + reason: { + defaultValue: null, + allowBlank: false, + columnConfig: { + width: 180 + }, + lookup: { + filterArray: [LABKEY.Filter.create('date_disabled', null, LABKEY.Filter.Types.ISBLANK)] + } + }, + performedby: { + hidden: false, + allowBlank: true, + defaultValue: LABKEY.Security.currentUser.id, + lookup: { + schemaName: 'core', + queryName: 'users', + keyColumn: 'UserId', + displayColumn: 'DisplayName', + columns: 'UserId,DisplayName,FirstName,LastName', + sort: 'Type,DisplayName' + }, + getInitialValue: function (v, rec) { + if (Number.isInteger(Number(v))){ + return v; + } + + return LABKEY.Security.currentUser.id; + }, + editorConfig: { + store: { + type: 'labkey-store', + schemaName: 'core', + + // 'performedby' is a text field in the dataset and its lookup to the userid is an int field - this mismatch causes it to disappear + // from the display when a value is selected from the dropdown even though the 'userid' value gets saved as a text (this behavior was only seen + // in the form panel but not in the grid panel). + // casting it as a varchar when loading the store fixes this issue. + sql: "SELECT CAST (UserId AS VARCHAR) AS UserId,DisplayName,FirstName,LastName FROM core.PrincipalsWithoutAdmin WHERE active = TRUE AND Type = 'u'", + autoLoad: true + } + } + }, + }, + 'study.arrival': { + initialRoom: { + allowBlank: true, + hidden: true + } + }, + 'study.birth': { + room: { + allowBlank: true, + hidden: true + } + }, + 'study.exemptions': { + category: { + columnConfig: { + width: 300 + } + } + }, + 'study.notes': { + remark: { + hidden: false, + columnConfig: { + width: 400 + } + } + }, + 'study.treatment_order': { + endTreatmentOrderedBy: { + columnConfig: { + width: 200 + }, + editorConfig: { + store: { + type: 'labkey-store', + schemaName: 'ehr_lookups', + + // see 'orderedby' comment above. + sql: 'SELECT CAST (UserId AS VARCHAR) AS UserId,DisplayName FROM ehr_lookups.veterinarians', + autoLoad: true + } + } + }, + frequency: { + columnConfig: { + width: 180 + }, + nullable: false, + allowBlank: true, + lookup: { + filterArray: [LABKEY.Filter.create('active', true, LABKEY.Filter.Types.EQUAL)] + }, + } + }, + 'study.drug': { + treatmentid: { + hidden: true, + nullable: true + }, + performedby: { + allowBlank: true, + } + }, + 'study.observation_order': { + category: { + allowBlank: false, + editorConfig: { + plugins: [Ext4.create('LDK.plugin.UserEditableCombo', { + allowChooseOther: false + })] + }, + lookup: { + columns: 'value,description' + }, + columnConfig: { + width: 200 + } + }, + area: { + defaultValue: 'N/A', + columnConfig: { + width: 200 + } + }, + observation: { + columnConfig: { + width: 200 + } + }, + remark: { + columnConfig: { + width: 300 + } + }, + frequency: { + columnConfig: { + width: 180 + }, + nullable: false, + allowBlank: true, + lookup: { + filterArray: [LABKEY.Filter.create('active', true, LABKEY.Filter.Types.EQUAL)] + }, + } + }, + 'study.pairings': { + date: { + header: 'Start Date', + getInitialValue: function(v, rec){ + if (v) + return v; + + return new Date(); + } + }, + type: { + hidden: true + }, + pairid: { + hidden: false, + nullable: false, + columnConfig: { + width: 150 + }, + }, + formationType: { + columnConfig: { + width: 150 + } + }, + reason: { + columnConfig: { + width: 150 + }, + }, + goal: { + columnConfig: { + width: 150 + }, + }, + endState: { + columnConfig: { + width: 150 + }, + }, + remark: { + title: 'Remark on Formation', + columnConfig: { + width: 200 + } + }, + separationRemark: { + columnConfig: { + width: 200 + } + } + }, + 'study.flags': { + flag: { + allowBlank: false, + lookup: { + columns: 'objectid,value,category,code', + sort: 'category,code,value', + filterArray: [LABKEY.Filter.create('datedisabled', null, LABKEY.Filter.Types.ISBLANK)] + }, + columnConfig: { + width: 300 + }, + editorConfig: { + caseSensitive: false, + anyMatch: true, + plugins: [Ext4.create('LDK.plugin.UserEditableCombo', { + allowChooseOther: false + })], + listConfig: { + innerTpl: '{[(values.category ? ("" + LABKEY.Utils.encodeHtml(values.category) + ": ") : "") + LABKEY.Utils.encodeHtml(values.value)]}', + getInnerTpl: function () { + return this.innerTpl; + } + } + } + } + } + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/model/sources/ObsDefaults.js b/nbri_ehr/resources/web/nbri_ehr/model/sources/ObsDefaults.js new file mode 100644 index 0000000..73b8950 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/model/sources/ObsDefaults.js @@ -0,0 +1,25 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +EHR.model.DataModelManager.registerMetadata('ObsDefaults', { + byQuery: { + 'study.clinical_observations': { + category: { + lookup: { + columns: 'value,description', + filterArray: [] + } + }, + }, + 'study.observation_order': { + category: { + lookup: { + columns: 'value,description', + filterArray: [] + } + } + } + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/model/sources/ParentChild.js b/nbri_ehr/resources/web/nbri_ehr/model/sources/ParentChild.js new file mode 100644 index 0000000..b548795 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/model/sources/ParentChild.js @@ -0,0 +1,25 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +EHR.model.DataModelManager.registerMetadata('ParentChild', { + allQueries: { + Id: { + inheritFromParent: true, + editable: false, + hidden: true, + columnConfig: { + editable: false + } + }, + caseid: { + inheritFromParent: true, + editable: false, + hidden: true, + columnConfig: { + editable: false + } + } + } +}); diff --git a/nbri_ehr/resources/web/nbri_ehr/model/sources/Pregnancy.js b/nbri_ehr/resources/web/nbri_ehr/model/sources/Pregnancy.js new file mode 100644 index 0000000..a6961bf --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/model/sources/Pregnancy.js @@ -0,0 +1,31 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +EHR.model.DataModelManager.registerMetadata('Pregnancy', { + allQueries: { + + }, + byQuery: { + 'study.pregnancy': { + project: { + hidden: true, + }, + type: { + hidden: true, + }, + diagnosis: { + hidden: true, + }, + attachmentFile: { + hidden: true, + }, + result: { + allowBlank: false, + nullable: false, + } + }, + + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/model/sources/Rearrival.js b/nbri_ehr/resources/web/nbri_ehr/model/sources/Rearrival.js new file mode 100644 index 0000000..059847e --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/model/sources/Rearrival.js @@ -0,0 +1,62 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +EHR.model.DataModelManager.registerMetadata('Rearrival', { + + byQuery: { + 'study.arrival': { + rearrival: { + getInitialValue: function (v, rec) { + return true + }, + editable: false, + hidden: true, + columnConfig: { + editable: false + } + }, + performedby: { + hidden: true, + showInGrid: false + }, + sourceFacility: { + allowBlank: false, + columnConfig: { + fixed: true, + width: 150 + }, + }, + acquisitionType: { + allowBlank: false, + columnConfig: { + fixed: true, + width: 150 + }, + }, + arrivalType: { + allowBlank: false, + columnConfig: { + width: 200 + } + }, + 'cage': { + allowBlank: true, + hidden: true, + showInGrid: false + }, + project: { + allowBlank: true, + hidden: true, + showInGrid: false + }, + arrivalProtocol: { + allowBlank: true, + hidden: true, + showInGrid: false + }, + } + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/model/sources/TreatmentSchedule.js b/nbri_ehr/resources/web/nbri_ehr/model/sources/TreatmentSchedule.js new file mode 100644 index 0000000..0759c99 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/model/sources/TreatmentSchedule.js @@ -0,0 +1,72 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +EHR.model.DataModelManager.registerMetadata('TreatmentSchedule', { + allQueries: { + project: { + hidden: true, + allowBlank: true + }, + code: { + allowBlank: false, + inheritFromParent: false, + editorConfig: { + xtype: 'labkey-combo', + displayField: 'meaning', + valueField: 'code', + anyMatch: true, + queryMode: 'local', + store: { + type: 'labkey-store', + schemaName: 'ehr_lookups', + queryName: 'snomed', + columns: 'code,meaning', + sort: 'meaning,code', + filterArray: [LABKEY.Filter.create('dateDisabled', null, LABKEY.Filter.Types.ISBLANK)], + autoLoad: true, + getRecordForCode: function(code){ + debugger + var recIdx = this.findExact('code', code); + if (recIdx !== -1){ + return this.getAt(recIdx); + } + } + } + } + }, + volume: { + inheritFromParent: false, + shownInGrid: true, + compositeField: 'Volume', + xtype: 'nbri_ehr-drugvolumefield', + noSaveInTemplateByDefault: true, + editorConfig: { + decimalPrecision: 3 + }, + header: 'Vol', + columnConfig: { + width: 90 + } + }, + type: { + hidden: true + }, + attachmentFile: { + hidden: true + } + }, + byQuery: { + 'study.drug': { + date: { + header: 'Date/Time', + } + }, + 'study.treatment_order': { + enddate: { + allowBlank: true, + } + } + } +}); \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/nbri.css b/nbri_ehr/resources/web/nbri_ehr/nbri.css new file mode 100644 index 0000000..fe5808a --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/nbri.css @@ -0,0 +1,7 @@ + +input.form-panel-input-disabled, +textarea.form-panel-input-disabled, +label.form-panel-input-disabled { + color: gray; + opacity: 1 !important; +} \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/nbriOverrides.js b/nbri_ehr/resources/web/nbri_ehr/nbriOverrides.js new file mode 100644 index 0000000..3c74896 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/nbriOverrides.js @@ -0,0 +1,16 @@ +/* + * Copyright (c) 2024-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +EHR.Utils.rowEditorPlugin = 'NBRI_EHR.plugin.RowEditor'; + +EHR.Utils.editUIButtonHandler = function(schemaName, queryName, dataRegionName, paramMap, copyFilters){ + var params = { + schemaName: schemaName, + 'query.queryName': queryName, + showImport: false + }; + + this.editUIButtonCore(schemaName, queryName, dataRegionName, paramMap, undefined, params); +}; \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/nbriReports.js b/nbri_ehr/resources/web/nbri_ehr/nbriReports.js new file mode 100644 index 0000000..0c1905e --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/nbriReports.js @@ -0,0 +1,287 @@ +/* + * Copyright (c) 2021-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +Ext4.namespace('EHR.reports'); + +EHR.reports.clinicalHistoryPanelXtype = 'nbri_ehr-snapshotpanel'; + + +EHR.reports.snapshot = function(panel, tab, showActionsBtn){ + if (tab.filters.subjects){ + renderSubjects(tab.filters.subjects, tab); + } + else + { + panel.resolveSubjectsFromHousing(tab, renderSubjects, this); + } + + function renderSubjects(subjects, tab){ + var toAdd = []; + if (!subjects.length){ + toAdd.push({ + html: 'No animals were found.', + border: false + }); + } + else if (subjects.length < 10) { + for (var i=0;i
If there have been recent blood draws for the animal, a graph will show the available blood over time. On the graph, dots indicate dates when either blood was drawn or a previous blood draw fell off. The horizontal lines indicate the maximum allowable blood that can be drawn on that date.', + border: false, + style: 'padding-bottom: 20px;' + }); + + tab.add({ + xtype: 'ldk-querycmp', + style: 'margin-bottom: 10px;', + queryConfig: panel.getQWPConfig({ + title: 'Summary', + schemaName: 'study', + queryName: 'Demographics', + viewName: 'Blood Draws', + filterArray: filterArray.removable.concat(filterArray.nonRemovable) + }) + }); + + var subjects = tab.filters.subjects || []; + + if (subjects.length){ + tab.add({ + xtype: 'nbri-bloodsummarypanel', + subjects: subjects + }); + } + else + { + panel.resolveSubjectsFromHousing(tab, function(subjects, tab){ + tab.add({ + xtype: 'nbri-bloodsummarypanel', + subjects: subjects + }); + }, this); + } +}; + +EHR.reports.clinicalHistory = function(panel, tab, showActionsBtn, includeAll){ + if (tab.filters.subjects){ + renderSubjects(tab.filters.subjects, tab); + } + else + { + panel.resolveSubjectsFromHousing(tab, renderSubjects, this); + } + + function renderSubjects(subjects, tab){ + if (subjects.length > 10){ + tab.add({ + html: 'Because more than 10 subjects were selected, the condensed report is being shown. Note that you can click the animal ID to open this same report in a different tab, showing that animal in more detail or click the link labeled \'Show Hx\'.', + style: 'padding-bottom: 20px;', + border: false + }); + + var filterArray = panel.getFilterArray(tab); + var title = panel.getTitleSuffix(); + tab.add({ + xtype: 'ldk-querycmp', + style: 'margin-bottom:20px;', + queryConfig: { + title: 'Overview' + title, + schemaName: 'study', + queryName: 'demographics', + viewName: 'Snapshot', + filterArray: filterArray.removable.concat(filterArray.nonRemovable) + } + }); + + return; + } + + if (!subjects.length){ + tab.add({ + html: 'No animals were found.', + border: false + }); + + return; + } + + tab.addCls('ehr-snapshotsubpanel'); + + var minDate = includeAll ? null : Ext4.Date.add(new Date(), Ext4.Date.YEAR, -30); + var toAdd = []; + Ext4.each(subjects, function(s){ + toAdd.push({ + html: 'Animal: ' + Ext4.htmlEncode(s) + '', + style: 'padding-bottom: 20px;', + border: false + }); + + toAdd.push({ + xtype: EHR.reports.clinicalHistoryPanelXtype, + showActionsButton: !!showActionsBtn, + hrefTarget: '_blank', + border: false, + subjectId: s + }); + + toAdd.push({ + html: 'Chronological History:
', + style: 'padding-top: 5px;', + border: false + }); + + toAdd.push({ + xtype: 'nbri_ehr-clinicalhistorypanel', + border: true, + subjectId: s, + autoLoadRecords: true, + minDate: minDate, + //maxGridHeight: 1000, + hrefTarget: '_blank', + style: 'margin-bottom: 20px;' + }); + }, this); + + if (toAdd.length){ + tab.add(toAdd); + } + } +}; + +EHR.reports.observationSchedule = function(panel, tab, viewName){ + var filterArray = panel.getFilterArray(tab); + var title = panel.getTitleSuffix(); + + var date = Ext4.Date.format(new Date(), LABKEY.extDefaultDateFormat); + tab.add({ + xtype: 'ldk-querypanel', + style: 'margin-bottom:20px;', + queryConfig: panel.getQWPConfig({ + schemaName: 'study', + queryName: 'observationSchedule', + title: 'Observation Schedule ' + title, + filters: filterArray.nonRemovable, + removeableFilters: filterArray.removable, + parameters: { + StartDate: date, + NumDays: 1 + } + }) + }); +} + +EHR.reports.incompleteTreatments = function(panel, tab, viewName){ + const currentDate = new Date(); + const previousDate = new Date(); + previousDate.setDate(currentDate.getDate() - 30); + + const gridFilterArray = panel.getFilterArray(tab); + const filterArray = gridFilterArray.nonRemovable.concat(LABKEY.Filter.create('treatmentStatus', "Completed", LABKEY.Filter.Types.NEQ_OR_NULL)); + + const config = panel.getQWPConfig({ + title: 'Incomplete Treatments For Past 30 Days', + schemaName: 'study', + queryName: 'treatmentSchedule', + dataRegionName: 'incomplete_treatments', + parameters: { + StartDate: `${String(previousDate.getMonth() + 1).padStart(2, '0')}/${String(previousDate.getDate()).padStart(2, '0')}/${previousDate.getFullYear()}`, + NumDays: 30 + }, + filters: filterArray, + removeableFilters: gridFilterArray.removable, + frame: true + }); + + tab.add({ + xtype: 'ldk-querycmp', + style: 'margin-bottom:20px;', + queryConfig: config + }); +} + +EHR.reports.incompleteObservations = function(panel, tab, viewName){ + const currentDate = new Date(); + const previousDate = new Date(); + previousDate.setDate(currentDate.getDate() - 30); + + const gridFilterArray = panel.getFilterArray(tab); + const filterArray = gridFilterArray.nonRemovable.concat( + [LABKEY.Filter.create('status', "Completed", LABKEY.Filter.Types.DOES_NOT_CONTAIN), + ] + ); + + const config = panel.getQWPConfig({ + title: 'Incomplete Observations For Past 30 Days', + schemaName: 'study', + queryName: 'observationSchedule', + dataRegionName: 'incomplete_observations', + parameters: { + StartDate: `${String(previousDate.getMonth() + 1).padStart(2, '0')}/${String(previousDate.getDate()).padStart(2, '0')}/${previousDate.getFullYear()}`, + NumDays: 30 + }, + filters: filterArray, + removeableFilters: gridFilterArray.removable, + frame: true + }); + + tab.add({ + xtype: 'ldk-querycmp', + style: 'margin-bottom:20px;', + queryConfig: config + }); +} \ No newline at end of file diff --git a/nbri_ehr/resources/web/nbri_ehr/nbri_ehr_api.lib.xml b/nbri_ehr/resources/web/nbri_ehr/nbri_ehr_api.lib.xml new file mode 100644 index 0000000..b75e07e --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/nbri_ehr_api.lib.xml @@ -0,0 +1,9 @@ + + +