Create nbri_ehr module

.github/workflows/branch_release.yml

@@ -8,16 +8,20 @@ on:
     tags:
       - '*'
 
+permissions:
+  pull-requests: write
+  contents: write
+
 jobs:
   branch_release:
     if: github.event.created && github.event.sender.login == 'labkey-teamcity'
     runs-on: ubuntu-latest
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Create branches and PRs
         uses: LabKey/gitHubActions/branch-release@develop
         with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
+          github_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/merge_release.yml

@@ -8,6 +8,10 @@ on:
     types:
       - submitted
 
+permissions:
+  pull-requests: write
+  contents: write
+
 jobs:
   merge_release:
     if: >
@@ -17,12 +21,12 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Merge PR
         uses: LabKey/gitHubActions/merge-release@develop
         with:
           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 }}
+          github_token: ${{ secrets.GITHUB_TOKEN }}

.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 }}
+          github_token: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -1,6 +1,11 @@
 .gradle
 build/
 
+# Log Files
+nbri_ehr/resources/referenceStudy/etlLogs/
+nbri_ehr/resources/referenceStudy/*.log
+nbri_ehr/test/sampledata/nbri_ehr/study/*.log
+
 # Ignore Gradle GUI config
 gradle-app.setting
 
@@ -21,4 +26,4 @@ gradle-app.setting
 *.ear
 
 # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
-hs_err_pid*
+hs_err_pid*

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'
+        }
+}

gradle.properties

@@ -0,0 +1 @@
+moduleContainer=:server:modules:nbriEHRModules

nbri_ehr/build.gradle

@@ -0,0 +1,32 @@
+/*
+ * Copyright (c) 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) }

nbri_ehr/module.properties

@@ -0,0 +1,2 @@
+ModuleClass: org.labkey.nbri_ehr.NBRI_EHRModule
+ManageVersion: true

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

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

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)

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

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

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

nbri_ehr/resources/data/alopecia_regrowth.tsv

@@ -0,0 +1,4 @@
+value	sort_order
+Yes	1
+No	2
+Not Evaluated	3

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

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

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

nbri_ehr/resources/data/app_score.tsv

@@ -0,0 +1,6 @@
+value
+NPO
+Normal
+Normal to low
+Low
+Unknown

nbri_ehr/resources/data/arrival_type.tsv

@@ -0,0 +1,3 @@
+value
+Non-quarantine Arrival
+Quarantine Arrival

nbri_ehr/resources/data/att_score.tsv

@@ -0,0 +1,6 @@
+value
+BAR
+QAR
+Lethargic
+Sedated
+Unknown

nbri_ehr/resources/data/bandage_observations.tsv

@@ -0,0 +1,4 @@
+value	sort_order
+Intact	1
+Removed or partially removed	2
+Other	3

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

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

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

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

nbri_ehr/resources/data/blood_draw_reason.tsv

@@ -0,0 +1,3 @@
+value	title
+Clinical	Clinical
+Research	Research

nbri_ehr/resources/data/blood_draw_tube_type.tsv

@@ -0,0 +1,5 @@
+type	color
+EDTA	Purple
+Heparin	Green
+No Additive	Red
+SST	Striped

nbri_ehr/resources/data/blood_sample_type.tsv

@@ -0,0 +1,3 @@
+value
+Whole Blood
+Bone Marrow