Added container run smoke tests and test.compose.yml to the analytics-dev container

Author: bp1183

.github/workflows/check.container-run.yml

@@ -0,0 +1,49 @@
+name: Check Container Entrypoints
+
+on:
+  push:
+    branches: [main, deliverable/add-ci-and-refine-tests]
+
+jobs:
+  bunny-run:
+    name: Run bunny integration test
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v4
+
+      - name: Run bunny integration test
+        working-directory: docker/bunny-wrapper
+        run: docker compose -f test.compose.yml up --build --abort-on-container-exit --exit-code-from bunny 
+    
+      - name: Verify bunny output
+        working-directory: docker/bunny-wrapper
+        run: | 
+          OUTPUT=$(cat test-output/output.json)
+          COUNT=$(echo "$OUTPUT" | jq '.queryResult' | jq '.count')
+          STATUS=$(echo "$OUTPUT" | jq '.status')
+
+          [ "$COUNT" = "40" ] || (echo "Expected count=40, got "$COUNT" && exit 1)
+          [ "$STATUS" = "ok" ] || (echo "Expected status=ok, got "$STATUS" && exit 1)
+
+  analytics-dev-run:
+    name: Run analytics dev integration tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v4
+
+      - name: Run analytics dev integration test
+        working-directory: docker/analytics-dev
+        run: docker compose -f test.compose.yml up --build --abort-on-container-exit --exit-code-from analytics-dev
+
+      - name: Verify analytics dev output 
+        working-directory: docker/analytics-dev
+        run: |
+          OUTPUT=$(cat test-output/output.json)
+          N=$(echo "$OUTPUT" | jq '.n')
+          TOTAL=$(echo "$OUTPUT" | jq '.total')
+
+          [ "$N" = "10836" ] || (echo "Expected n=10836, got "$N" && exit 1)
+          [ "$TOTAL" = "54109.0" ] || (echo "Expected total=54109.0, got "$TOTAL" && exit 1)
+            

.gitignore

@@ -73,6 +73,7 @@ logs/
 *.temp
 temp/
 tmp/
+test-output/
 
 # Jupyter Notebook
 .ipynb_checkpoints

docker/analytics-dev/test.compose.yml

@@ -0,0 +1,51 @@
+services:
+  db:
+    image: postgres:18
+    ports:
+      - "5432:5432"
+    environment:
+      POSTGRES_PASSWORD: postgres
+      POSTGRES_DB: omop
+    healthcheck:
+      test: ["CMD", "pg_isready", "-U", "postgres", "-d", "omop"]
+      interval: 5s
+      timeout: 5s
+      retries: 5
+
+  omop-lite:
+    image: ghcr.io/health-informatics-uon/omop-lite:sha-c6054ef
+    depends_on:
+      db:
+        condition: service_healthy
+    environment:
+      DB_HOST: db
+      DB_PASSWORD: postgres
+      DB_NAME: omop
+      SYNTHETIC: true
+      SYNTHETIC_NUMBER: 1000
+
+  analytics-dev: 
+    build:
+      context: ../../
+      dockerfile: docker/analytics-dev/Dockerfile
+    command:
+      - "--user-query"
+      - "SELECT value_as_number FROM measurement WHERE measurement_concept_id = 43055141 AND value_as_number IS NOT NULL"
+      - "--analysis"
+      - "mean"
+      - "--output-filename"
+      - "/tmp/output/output"
+      - "--output-format"
+      - "json"
+    volumes:
+      - ./test-output:/tmp/output
+    depends_on:
+      omop-lite:
+        condition: service_completed_successfully
+    environment:
+      postgresServer: db
+      postgresPort: 5432
+      postgresSchema: public
+      postgresDatabase: omop
+      postgresUsername: postgres
+      postgresPassword: postgres

docker/bunny-wrapper/test.compose.yml

@@ -14,13 +14,15 @@ services:
       DB_PASSWORD: postgres
       DB_NAME: omop
       SYNTHETIC: true
+  
   bunny:
     build: .
     command:
       - "--body /var/queries/availability.json"
-      - "--output /tmp/output.json"
+      - "--output /tmp/output/output.json"
     volumes:
       - ./availability.json:/var/queries/availability.json
+      - ./test-output:/tmp/output
     environment:
       postgresServer: db
       postgresPort: 5432

examples/analysis_examples.py

@@ -5,7 +5,7 @@
 from string import Template 
 from typing import List, Dict, Any 
 
-from five_safes_tes_analytics.clients.analytics_tes import AnalyticsTES
+from five_safes_tes_analytics.clients.analytics_tes_client import AnalyticsTES
 from five_safes_tes_analytics.runners.analysis_runner import AnalysisRunner