Fixes

.gitattributes

@@ -0,0 +1 @@
+* text=auto

R/createDdl.R

@@ -71,7 +71,7 @@ createDdl <- function(cdmVersion){
     if ('person_id' %in% fieldNames){
       hintContent <- "--HINT DISTRIBUTE_ON_KEY(person_id)"
     } else {
-      hintContent <- "--HINT DISTRIBUTE_ON_KEY(RANDOM)"
+      hintContent <- "--HINT DISTRIBUTE_ON_RANDOM"
     }
 
     # Add SORT_ON_KEY if table is in sortKeyMap and has all the sort fields

R/writeDDL.R

@@ -44,18 +44,19 @@ writeDdl <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema
   sql <- createDdl(cdmVersion)
   sql <- SqlRender::render(sql = sql, cdmDatabaseSchema = cdmDatabaseSchema, targetDialect = targetDialect)
   sql <- SqlRender::translate(sql, targetDialect = targetDialect)
+  sql <- gsub("\r\n?", "\n", sql) ## force line endings to be LF
 
   # Post-processing: remove conditional markers and handle dialects
   lines <- strsplit(sql, "\n")[[1]]
-  
+
   if (tolower(targetDialect) == "redshift") {
     # For Redshift: remove conditional markers but keep the HINT lines
     lines <- lines[!grepl("\\{#?if|\\{/if\\}", lines)]
   } else {
     # For non-Redshift: remove HINT directives and conditional markers
     lines <- lines[!grepl("--HINT|\\{#?if|\\{/if\\}", lines)]
   }
-  
+
   sql <- paste(lines, collapse = "\n")
 
   filename <- paste("OMOPCDM", gsub(" ", "_", targetDialect), cdmVersion, "ddl.sql", sep = "_")
@@ -84,6 +85,7 @@ writePrimaryKeys <- function(targetDialect, cdmVersion, outputfolder, cdmDatabas
   sql <- createPrimaryKeys(cdmVersion)
   sql <- SqlRender::render(sql = sql, cdmDatabaseSchema = cdmDatabaseSchema, targetDialect = targetDialect)
   sql <- SqlRender::translate(sql, targetDialect = targetDialect)
+  sql <- gsub("\r\n?", "\n", sql) ## force line endings to be LF
 
   # Post-processing: remove any conditional markers that may have been added
   lines <- strsplit(sql, "\n")[[1]]
@@ -115,6 +117,7 @@ writeForeignKeys <- function(targetDialect, cdmVersion, outputfolder, cdmDatabas
   sql <- createForeignKeys(cdmVersion)
   sql <- SqlRender::render(sql = sql, cdmDatabaseSchema = cdmDatabaseSchema, targetDialect = targetDialect)
   sql <- SqlRender::translate(sql, targetDialect = targetDialect)
+  sql <- gsub("\r\n?", "\n", sql) ## force line endings to be LF
 
   # Post-processing: remove any conditional markers that may have been added
   lines <- strsplit(sql, "\n")[[1]]
@@ -147,6 +150,7 @@ writeIndex <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchem
   sql <- readr::read_file(system.file(file.path("sql", "sql_server", sqlFilename), package = "CommonDataModel"))
   sql <- SqlRender::render(sql, targetDialect = targetDialect, cdmDatabaseSchema = cdmDatabaseSchema)
   sql <- SqlRender::translate(sql, targetDialect = targetDialect)
+  sql <- gsub("\r\n?", "\n", sql) ## force line endings to be LF
 
   filename <- paste("OMOPCDM", gsub(" ", "_", targetDialect), cdmVersion, "indices.sql", sep = "_")
   # Use writeLines instead of SqlRender::writeSql to avoid line wrapping

inst/ddl/5.3/iris/OMOPCDM_iris_5.3_ddl.sql

@@ -209,7 +209,6 @@ CREATE TABLE @cdmDatabaseSchema.note (
 			visit_occurrence_id integer NULL,
 			visit_detail_id integer NULL,
 			note_source_value varchar(50) NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema.note_nlp (
 			note_nlp_id integer NOT NULL,
 			note_id integer NOT NULL,
@@ -242,14 +241,12 @@ CREATE TABLE @cdmDatabaseSchema.specimen (
 			unit_source_value varchar(50) NULL,
 			anatomic_site_source_value varchar(50) NULL,
 			disease_status_source_value varchar(50) NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema.fact_relationship (
 			domain_concept_id_1 integer NOT NULL,
 			fact_id_1 integer NOT NULL,
 			domain_concept_id_2 integer NOT NULL,
 			fact_id_2 integer NOT NULL,
 			relationship_concept_id integer NOT NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema.location (
 			location_id integer NOT NULL,
 			address_1 varchar(50) NULL,
@@ -259,15 +256,13 @@ CREATE TABLE @cdmDatabaseSchema.location (
 			zip varchar(9) NULL,
 			county varchar(20) NULL,
 			location_source_value varchar(50) NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema.care_site (
 			care_site_id integer NOT NULL,
 			care_site_name varchar(255) NULL,
 			place_of_service_concept_id integer NULL,
 			location_id integer NULL,
 			care_site_source_value varchar(50) NULL,
 			place_of_service_source_value varchar(50) NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema.provider (
 			provider_id integer NOT NULL,
 			provider_name varchar(255) NULL,
@@ -301,7 +296,6 @@ CREATE TABLE @cdmDatabaseSchema.payer_plan_period (
 			stop_reason_concept_id integer NULL,
 			stop_reason_source_value varchar(50) NULL,
 			stop_reason_source_concept_id integer NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema.cost (
 			cost_id integer NOT NULL,
 			cost_event_id integer NOT NULL,
@@ -351,7 +345,6 @@ CREATE TABLE @cdmDatabaseSchema.condition_era (
 			condition_era_start_date date NOT NULL,
 			condition_era_end_date date NOT NULL,
 			condition_occurrence_count integer NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema.metadata (
 			metadata_concept_id integer NOT NULL,
 			metadata_type_concept_id integer NOT NULL,
@@ -360,7 +353,6 @@ CREATE TABLE @cdmDatabaseSchema.metadata (
 			value_as_concept_id integer NULL,
 			metadata_date date NULL,
 			metadata_datetime datetime NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema.cdm_source (
 			cdm_source_name varchar(255) NOT NULL,
 			cdm_source_abbreviation varchar(25) NULL,
@@ -372,7 +364,6 @@ CREATE TABLE @cdmDatabaseSchema.cdm_source (
 			cdm_release_date date NULL,
 			cdm_version varchar(10) NULL,
 			vocabulary_version varchar(20) NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema.concept (
 			concept_id integer NOT NULL,
 			concept_name varchar(255) NOT NULL,
@@ -384,51 +375,43 @@ CREATE TABLE @cdmDatabaseSchema.concept (
 			valid_start_date date NOT NULL,
 			valid_end_date date NOT NULL,
 			invalid_reason varchar(1) NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema.vocabulary (
 			vocabulary_id varchar(20) NOT NULL,
 			vocabulary_name varchar(255) NOT NULL,
 			vocabulary_reference varchar(255) NOT NULL,
 			vocabulary_version varchar(255) NULL,
 			vocabulary_concept_id integer NOT NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema."DOMAIN"  (
 			domain_id varchar(20) NOT NULL,
 			domain_name varchar(255) NOT NULL,
 			domain_concept_id integer NOT NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema.concept_class (
 			concept_class_id varchar(20) NOT NULL,
 			concept_class_name varchar(255) NOT NULL,
 			concept_class_concept_id integer NOT NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema.concept_relationship (
 			concept_id_1 integer NOT NULL,
 			concept_id_2 integer NOT NULL,
 			relationship_id varchar(20) NOT NULL,
 			valid_start_date date NOT NULL,
 			valid_end_date date NOT NULL,
 			invalid_reason varchar(1) NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema.relationship (
 			relationship_id varchar(20) NOT NULL,
 			relationship_name varchar(255) NOT NULL,
 			is_hierarchical varchar(1) NOT NULL,
 			defines_ancestry varchar(1) NOT NULL,
 			reverse_relationship_id varchar(20) NOT NULL,
 			relationship_concept_id integer NOT NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema.concept_synonym (
 			concept_id integer NOT NULL,
 			concept_synonym_name varchar(1000) NOT NULL,
 			language_concept_id integer NOT NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema.concept_ancestor (
 			ancestor_concept_id integer NOT NULL,
 			descendant_concept_id integer NOT NULL,
 			min_levels_of_separation integer NOT NULL,
 			max_levels_of_separation integer NOT NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema.source_to_concept_map (
 			source_code varchar(50) NOT NULL,
 			source_concept_id integer NOT NULL,
@@ -439,7 +422,6 @@ CREATE TABLE @cdmDatabaseSchema.source_to_concept_map (
 			valid_start_date date NOT NULL,
 			valid_end_date date NOT NULL,
 			invalid_reason varchar(1) NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema.drug_strength (
 			drug_concept_id integer NOT NULL,
 			ingredient_concept_id integer NOT NULL,
@@ -453,7 +435,6 @@ CREATE TABLE @cdmDatabaseSchema.drug_strength (
 			valid_start_date date NOT NULL,
 			valid_end_date date NOT NULL,
 			invalid_reason varchar(1) NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema.cohort_definition (
 			cohort_definition_id integer NOT NULL,
 			cohort_definition_name varchar(255) NOT NULL,
@@ -462,7 +443,6 @@ CREATE TABLE @cdmDatabaseSchema.cohort_definition (
 			cohort_definition_syntax varchar(MAX) NULL,
 			subject_concept_id integer NOT NULL,
 			cohort_initiation_date date NULL );
- -- "haven't looked into this yet, skip it for now""
 CREATE TABLE @cdmDatabaseSchema.attribute_definition (
 			attribute_definition_id integer NOT NULL,
 			attribute_name varchar(255) NOT NULL,

inst/ddl/5.3/netezza/OMOPCDM_netezza_5.3_ddl.sql

@@ -230,7 +230,7 @@ CREATE TABLE @cdmDatabaseSchema.note_nlp (
 			term_exists varchar(1) NULL,
 			term_temporal varchar(50) NULL,
 			term_modifiers varchar(2000) NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;
 CREATE TABLE @cdmDatabaseSchema.specimen (
 			specimen_id integer NOT NULL,
 			person_id integer NOT NULL,
@@ -254,7 +254,7 @@ CREATE TABLE @cdmDatabaseSchema.fact_relationship (
 			domain_concept_id_2 integer NOT NULL,
 			fact_id_2 integer NOT NULL,
 			relationship_concept_id integer NOT NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;
 CREATE TABLE @cdmDatabaseSchema.location (
 			location_id integer NOT NULL,
 			address_1 varchar(50) NULL,
@@ -264,15 +264,15 @@ CREATE TABLE @cdmDatabaseSchema.location (
 			zip varchar(9) NULL,
 			county varchar(20) NULL,
 			location_source_value varchar(50) NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;
 CREATE TABLE @cdmDatabaseSchema.care_site (
 			care_site_id integer NOT NULL,
 			care_site_name varchar(255) NULL,
 			place_of_service_concept_id integer NULL,
 			location_id integer NULL,
 			care_site_source_value varchar(50) NULL,
 			place_of_service_source_value varchar(50) NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;
 CREATE TABLE @cdmDatabaseSchema.provider (
 			provider_id integer NOT NULL,
 			provider_name varchar(255) NULL,
@@ -287,7 +287,7 @@ CREATE TABLE @cdmDatabaseSchema.provider (
 			specialty_source_concept_id integer NULL,
 			gender_source_value varchar(50) NULL,
 			gender_source_concept_id integer NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;
 CREATE TABLE @cdmDatabaseSchema.payer_plan_period (
 			payer_plan_period_id integer NOT NULL,
 			person_id integer NOT NULL,
@@ -330,7 +330,7 @@ CREATE TABLE @cdmDatabaseSchema.cost (
 			revenue_code_source_value varchar(50) NULL,
 			drg_concept_id integer NULL,
 			drg_source_value varchar(3) NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;
 SORT_ON_KEY(INTERLEAVED:drug_concept_id,person_id)
 CREATE TABLE @cdmDatabaseSchema.drug_era (
 			drug_era_id integer NOT NULL,
@@ -366,7 +366,7 @@ CREATE TABLE @cdmDatabaseSchema.metadata (
 			value_as_concept_id integer NULL,
 			metadata_date date NULL,
 			metadata_datetime TIMESTAMP NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;
 CREATE TABLE @cdmDatabaseSchema.cdm_source (
 			cdm_source_name varchar(255) NOT NULL,
 			cdm_source_abbreviation varchar(25) NULL,
@@ -378,7 +378,7 @@ CREATE TABLE @cdmDatabaseSchema.cdm_source (
 			cdm_release_date date NULL,
 			cdm_version varchar(10) NULL,
 			vocabulary_version varchar(20) NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;
 CREATE TABLE @cdmDatabaseSchema.concept (
 			concept_id integer NOT NULL,
 			concept_name varchar(255) NOT NULL,
@@ -390,51 +390,51 @@ CREATE TABLE @cdmDatabaseSchema.concept (
 			valid_start_date date NOT NULL,
 			valid_end_date date NOT NULL,
 			invalid_reason varchar(1) NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;
 CREATE TABLE @cdmDatabaseSchema.vocabulary (
 			vocabulary_id varchar(20) NOT NULL,
 			vocabulary_name varchar(255) NOT NULL,
 			vocabulary_reference varchar(255) NOT NULL,
 			vocabulary_version varchar(255) NULL,
 			vocabulary_concept_id integer NOT NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;
 CREATE TABLE @cdmDatabaseSchema.domain (
 			domain_id varchar(20) NOT NULL,
 			domain_name varchar(255) NOT NULL,
 			domain_concept_id integer NOT NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;
 CREATE TABLE @cdmDatabaseSchema.concept_class (
 			concept_class_id varchar(20) NOT NULL,
 			concept_class_name varchar(255) NOT NULL,
 			concept_class_concept_id integer NOT NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;
 CREATE TABLE @cdmDatabaseSchema.concept_relationship (
 			concept_id_1 integer NOT NULL,
 			concept_id_2 integer NOT NULL,
 			relationship_id varchar(20) NOT NULL,
 			valid_start_date date NOT NULL,
 			valid_end_date date NOT NULL,
 			invalid_reason varchar(1) NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;
 CREATE TABLE @cdmDatabaseSchema.relationship (
 			relationship_id varchar(20) NOT NULL,
 			relationship_name varchar(255) NOT NULL,
 			is_hierarchical varchar(1) NOT NULL,
 			defines_ancestry varchar(1) NOT NULL,
 			reverse_relationship_id varchar(20) NOT NULL,
 			relationship_concept_id integer NOT NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;
 CREATE TABLE @cdmDatabaseSchema.concept_synonym (
 			concept_id integer NOT NULL,
 			concept_synonym_name varchar(1000) NOT NULL,
 			language_concept_id integer NOT NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;
 CREATE TABLE @cdmDatabaseSchema.concept_ancestor (
 			ancestor_concept_id integer NOT NULL,
 			descendant_concept_id integer NOT NULL,
 			min_levels_of_separation integer NOT NULL,
 			max_levels_of_separation integer NOT NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;
 CREATE TABLE @cdmDatabaseSchema.source_to_concept_map (
 			source_code varchar(50) NOT NULL,
 			source_concept_id integer NOT NULL,
@@ -445,7 +445,7 @@ CREATE TABLE @cdmDatabaseSchema.source_to_concept_map (
 			valid_start_date date NOT NULL,
 			valid_end_date date NOT NULL,
 			invalid_reason varchar(1) NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;
 CREATE TABLE @cdmDatabaseSchema.drug_strength (
 			drug_concept_id integer NOT NULL,
 			ingredient_concept_id integer NOT NULL,
@@ -459,7 +459,7 @@ CREATE TABLE @cdmDatabaseSchema.drug_strength (
 			valid_start_date date NOT NULL,
 			valid_end_date date NOT NULL,
 			invalid_reason varchar(1) NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;
 CREATE TABLE @cdmDatabaseSchema.cohort_definition (
 			cohort_definition_id integer NOT NULL,
 			cohort_definition_name varchar(255) NOT NULL,
@@ -468,11 +468,11 @@ CREATE TABLE @cdmDatabaseSchema.cohort_definition (
 			cohort_definition_syntax VARCHAR(1000) NULL,
 			subject_concept_id integer NOT NULL,
 			cohort_initiation_date date NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;
 CREATE TABLE @cdmDatabaseSchema.attribute_definition (
 			attribute_definition_id integer NOT NULL,
 			attribute_name varchar(255) NOT NULL,
 			attribute_description VARCHAR(1000) NULL,
 			attribute_type_concept_id integer NOT NULL,
 			attribute_syntax VARCHAR(1000) NULL )
-DISTRIBUTE ON (RANDOM);
+DISTRIBUTE ON RANDOM;