Merge pull request #99 from OHDSI/CDM_5_2_bug_fixes

Bugfix issues #98, #97 and #96.

Author: clairblacketer

Impala/OMOP_CDM_ddl_Impala.sql

@@ -333,7 +333,7 @@ CREATE TABLE visit_occurrence (
  visit_source_concept_id INTEGER,
  admitting_source_concept_id	INTEGER,
  admitting_source_value			VARCHAR(50),
- discharge_to_concept_id		INTEGER(50),
+ discharge_to_concept_id		INTEGER,
  discharge_to_source_value		VARCHAR(50),
  preceding_visit_occurrence_id	INTEGER	
 )

Oracle/OMOP CDM constraints - Oracle.sql

@@ -353,8 +353,6 @@ ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_type_concept FOREIGN KEY (drug
 
 ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_route_concept FOREIGN KEY (route_concept_id)  REFERENCES concept (concept_id);
 
-ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_dose_unit_concept FOREIGN KEY (dose_unit_concept_id)  REFERENCES concept (concept_id);
-
 ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_provider FOREIGN KEY (provider_id)  REFERENCES provider (provider_id);
 
 ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_visit FOREIGN KEY (visit_occurrence_id)  REFERENCES visit_occurrence (visit_occurrence_id);

Oracle/OMOP CDM ddl - Oracle.sql

@@ -315,7 +315,7 @@ CREATE TABLE visit_occurrence
 	 visit_source_concept_id		INTEGER			NULL,
 	 admitting_source_concept_id	INTEGER			NULL ,
 	 admitting_source_value			VARCHAR(50)		NULL ,
-	 discharge_to_concept_id		INTEGER(50)		NULL ,
+	 discharge_to_concept_id		INTEGER		NULL ,
 	 discharge_to_source_value		VARCHAR(50)		NULL ,
 	 preceding_visit_occurrence_id	INTEGER			NULL
     ) 

Oracle/OMOP CDM indexes required - Oracle - With constraints.sql

@@ -113,7 +113,6 @@ CREATE INDEX idx_note_person_id ON note (person_id ASC);
 CREATE INDEX idx_note_concept_id ON note (note_type_concept_id ASC);
 CREATE INDEX idx_note_visit_id ON note (visit_occurrence_id ASC);
 
-CREATE INDEX idx_note_nlp_person_id ON note_nlp (person_id ASC);
 CREATE INDEX idx_note_nlp_note_id ON note_nlp (note_id ASC);
 CREATE INDEX idx_note_nlp_concept_id ON note_nlp (note_nlp_concept_id ASC);
 

Oracle/OMOP CDM indexes required - Oracle - Without constraints.sql

@@ -132,7 +132,6 @@ CREATE INDEX idx_note_person_id ON note (person_id ASC);
 CREATE INDEX idx_note_concept_id ON note (note_type_concept_id ASC);
 CREATE INDEX idx_note_visit_id ON note (visit_occurrence_id ASC);
 
-CREATE INDEX idx_note_nlp_person_id ON note_nlp (person_id ASC);
 CREATE INDEX idx_note_nlp_note_id ON note_nlp (note_id ASC);
 CREATE INDEX idx_note_nlp_concept_id ON note_nlp (note_nlp_concept_id ASC);
 

PostgreSQL/OMOP CDM constraints - PostgreSQL.sql

@@ -126,7 +126,7 @@ ALTER TABLE measurement ADD CONSTRAINT xpk_measurement PRIMARY KEY ( measurement
 
 ALTER TABLE note ADD CONSTRAINT xpk_note PRIMARY KEY ( note_id ) ;
 
-ALTER TABLE note_nlp ADD CONSTRAINT xpk_note_nlp PRIMARY KEY NONCLUSTERED ( note_nlp_id ) ;
+ALTER TABLE note_nlp ADD CONSTRAINT xpk_note_nlp PRIMARY KEY ( note_nlp_id ) ;
 
 ALTER TABLE observation  ADD CONSTRAINT xpk_observation PRIMARY KEY ( observation_id ) ;
 
@@ -352,8 +352,6 @@ ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_type_concept FOREIGN KEY (drug
 
 ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_route_concept FOREIGN KEY (route_concept_id)  REFERENCES concept (concept_id);
 
-ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_dose_unit_concept FOREIGN KEY (dose_unit_concept_id)  REFERENCES concept (concept_id);
-
 ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_provider FOREIGN KEY (provider_id)  REFERENCES provider (provider_id);
 
 ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_visit FOREIGN KEY (visit_occurrence_id)  REFERENCES visit_occurrence (visit_occurrence_id);

PostgreSQL/OMOP CDM ddl - PostgreSQL.sql

@@ -465,7 +465,7 @@ CREATE TABLE note_nlp
   note_id						INTEGER			NOT NULL ,
   section_concept_id			INTEGER			NULL ,
   snippet						VARCHAR(250)	NULL ,
-  offset						VARCHAR(250)	NULL ,
+  "offset"						VARCHAR(250)	NULL ,
   lexical_variant				VARCHAR(250)	NOT NULL ,
   note_nlp_concept_id			INTEGER			NULL ,
   note_nlp_source_concept_id	INTEGER			NULL ,

PostgreSQL/OMOP CDM indexes required - PostgreSQL.sql

@@ -153,9 +153,8 @@ CLUSTER  note  USING  idx_note_person_id ;
 CREATE INDEX idx_note_concept_id ON note (note_type_concept_id ASC);
 CREATE INDEX idx_note_visit_id ON note (visit_occurrence_id ASC);
 
-CREATE INDEX idx_note_nlp_person_id ON note_nlp (person_id ASC);
-CLUSTER note_nlp USING idx_note_nlp_person_id ;
 CREATE INDEX idx_note_nlp_note_id ON note_nlp (note_id ASC);
+CLUSTER note_nlp USING idx_note_nlp_note_id ;
 CREATE INDEX idx_note_nlp_concept_id ON note_nlp (note_nlp_concept_id ASC);
 
 CREATE INDEX  idx_observation_person_id  ON  observation  (person_id ASC);

Sql Server/OMOP CDM constraints - SQL Server.sql

@@ -352,8 +352,6 @@ ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_type_concept FOREIGN KEY (drug
 
 ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_route_concept FOREIGN KEY (route_concept_id)  REFERENCES concept (concept_id);
 
-ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_dose_unit_concept FOREIGN KEY (dose_unit_concept_id)  REFERENCES concept (concept_id);
-
 ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_provider FOREIGN KEY (provider_id)  REFERENCES provider (provider_id);
 
 ALTER TABLE drug_exposure ADD CONSTRAINT fpk_drug_visit FOREIGN KEY (visit_occurrence_id)  REFERENCES visit_occurrence (visit_occurrence_id);

Sql Server/OMOP CDM indexes required - SQL Server.sql

@@ -131,8 +131,7 @@ CREATE CLUSTERED INDEX idx_note_person_id ON note (person_id ASC);
 CREATE INDEX idx_note_concept_id ON note (note_type_concept_id ASC);
 CREATE INDEX idx_note_visit_id ON note (visit_occurrence_id ASC);
 
-CREATE CLUSTERED INDEX idx_note_nlp_person_id ON note_nlp (person_id ASC);
-CREATE INDEX idx_note_nlp_note_id ON note_nlp (note_id ASC);
+CREATE CLUSTERED INDEX idx_note_nlp_note_id ON note_nlp (note_id ASC);
 CREATE INDEX idx_note_nlp_concept_id ON note_nlp (note_nlp_concept_id ASC);
 
 CREATE CLUSTERED INDEX idx_observation_person_id ON observation (person_id ASC);