Update Docker Compose and Kubernetes configurations, fix Vocab_Uploader

IDEA4RC · Jan 31, 2024 · 792d004 · 792d004
1 parent e1ae8de
commit 792d004
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Showing 10 changed files with 648 additions and 39 deletions.
diff --git a/base_sql_scripts/001_OMOP-DDL.sql b/base_sql_scripts/001_OMOP-DDL.sql
@@ -1,4 +1,7 @@
 --postgresql CDM DDL Specification for OMOP Common Data Model 5.4
+
+CREATE SCHEMA IF NOT EXISTS omopSchema;
+
 --HINT DISTRIBUTE ON KEY (person_id)
 CREATE TABLE omopSchema.person (
 			person_id integer NOT NULL,
@@ -442,7 +445,6 @@ CREATE TABLE omopSchema.concept_class (
 			concept_class_id varchar(20) NOT NULL,
 			concept_class_name varchar(255) NOT NULL,
 			concept_class_concept_id integer NOT NULL );
-CREATE SCHEMA omopSchema;
 --HINT DISTRIBUTE ON RANDOM
 CREATE TABLE omopSchema.concept_relationship (
 			concept_id_1 integer NOT NULL,

diff --git a/docker-compose.yaml b/docker-compose.yaml
@@ -8,7 +8,7 @@ services:
     environment:
       - POSTGRES_USER=postgres
       - POSTGRES_PASSWORD=mysecretpassword
-      - POSTGRES_DB=test-omop
+      - POSTGRES_DB=omopdb
     volumes:
       - db-data:/var/lib/postgresql/data
     ports:

diff --git a/kubernetes/002_OMOP-CDM-Deployment.yaml b/kubernetes/002_OMOP-CDM-Deployment.yaml
@@ -13,20 +13,21 @@ spec:
         app: omop-postgres
     spec:
       containers:
-        - name: omop-postgres
-          image: ghcr.io/idea4rc/omop-deploy:latest
-          imagePullPolicy: IfNotPresent
-          env:
-            - name: POSTGRES_USER
-              secretKeyRef:
-                  name: omop-secrets
-                  key: POSTGRES_USER
-            - name: POSTGRES_PASSWORD
-              valueFrom:
-                secretKeyRef:
-                  name: omop-secrets
-                  key: POSTGRES_PASSWORD
-            - name: POSTGRES_DB
-              value: omopdb
-          ports:
-            - containerPort: 5432
+      - name: omop-postgres
+        image: ghcr.io/idea4rc/omop-deploy:latest
+        imagePullPolicy: IfNotPresent
+        env:
+        - name: POSTGRES_USER
+          valueFrom:
+            secretKeyRef:
+              name: omop-secrets
+              key: POSTGRES_USER
+        - name: POSTGRES_PASSWORD
+          valueFrom:
+            secretKeyRef:
+              name: omop-secrets
+              key: POSTGRES_PASSWORD
+        - name: POSTGRES_DB
+          value: omopdb
+        ports:
+        - containerPort: 5432
diff --git a/kubernetes/004_OMOP-Vocab-job.yaml b/kubernetes/004_OMOP-Vocab-job.yaml
@@ -7,24 +7,24 @@ spec:
   template:
     spec:
       containers:
-        - name: populate-db
-          image: ghcr.io/idea4rc/omop-vocab-uploader:latest
-          imagePullPolicy: IfNotPresent
-          env:
-            - name: VOCAB_PG_HOST
-              value: omop-postgres-service
-            - name: VOCAB_PG_DATABASE
-              value: omopdb
-            - name: VOCAB_PG_USER
-              valueFrom:
-                secretKeyRef:
-                  name: omop-secrets
-                  key: POSTGRES_USER
-            - name: VOCAB_PG_PASSWORD
-              valueFrom:
-                secretKeyRef:
-                  name: omop-secrets
-                  key: POSTGRES_PASSWORD
-            - name: VOCAB_PG_SCHEMA
-              value: omopcdm
+      - name: populate-db
+        image: ghcr.io/idea4rc/omop-vocab-uploader:latest
+        imagePullPolicy: IfNotPresent
+        env:
+        - name: VOCAB_PG_HOST
+          value: omop-postgres-service
+        - name: VOCAB_PG_DATABASE
+          value: omopdb
+        - name: VOCAB_PG_USER
+          valueFrom:
+            secretKeyRef:
+              name: omop-secrets
+              key: POSTGRES_USER
+        - name: VOCAB_PG_PASSWORD
+          valueFrom:
+            secretKeyRef:
+              name: omop-secrets
+              key: POSTGRES_PASSWORD
+        - name: VOCAB_PG_SCHEMA
+          value: omopschema
       restartPolicy: OnFailure
diff --git a/base_sql_scripts/002_OMOP-PrimaryKeys.sql → ...b_script/scripts/002_OMOP-PrimaryKeys.sql b/base_sql_scripts/002_OMOP-PrimaryKeys.sql → ...b_script/scripts/002_OMOP-PrimaryKeys.sql
diff --git a/base_sql_scripts/003_OMOP-Indices.sql → vocab_script/scripts/003_OMOP-Indices.sql b/base_sql_scripts/003_OMOP-Indices.sql → vocab_script/scripts/003_OMOP-Indices.sql
diff --git a/base_sql_scripts/004_OMOP-Constraints.sql → ...b_script/scripts/004_OMOP-Constraints.sql b/base_sql_scripts/004_OMOP-Constraints.sql → ...b_script/scripts/004_OMOP-Constraints.sql