Enable running integration test within VS (#239)

* Enable running integration test in VS
* Update docker compose template
* Remove nugetdefence scan
* Cleanup minio after scenario
* Update messaging lib to 0.1.11
* Use ubuntu-22.04 for integration test


Signed-off-by: Victor Chang <[email protected]>

Author: mocsharp

.github/workflows/ci.yml

@@ -149,13 +149,6 @@ jobs:
       run: dotnet build -c ${{ env.BUILD_CONFIG }} --nologo ${{ env.SOLUTION }}
       working-directory: ./src
 
-    - name: NuGetDefense Scanning
-      continue-on-error: true
-      run: |
-        sed -i "s/OSSINDEXAPI_TOKEN/$OSSINDEXAPI_TOKEN/g" NuGetDefense.json
-        sed -i "s/OSSINDEXAPI_USERNAME/$OSSINDEXAPI_USERNAME/g" NuGetDefense.json
-        nugetdefense -p src/${{ env.SOLUTION }} --settings-file NuGetDefense.json
-
     - name: Secret detection
       uses: gitleaks/[email protected]
 
@@ -237,9 +230,8 @@ jobs:
           verbose: true
 
   integration-test:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     timeout-minutes: 30
-    needs: [build]
     strategy:
       matrix:
         feature: [AcrApi, DicomDimseScp, DicomDimseScu, DicomWebExport, DicomWebStow, HealthLevel7, Fhir]
@@ -285,7 +277,6 @@ jobs:
           name: integration-${{ matrix.feature }}
           path: |
             ${{ github.workspace }}/LivingDoc.html
-            ${{ github.workspace }}/metrics.log
             ${{ github.workspace }}/services.log
             ${{ github.workspace }}/run.log
           retention-days: 30

doc/dependency_decisions.yml

@@ -791,14 +791,14 @@
   - :who: mocsharp
     :why: Apache-2.0 (https://github.com/Project-MONAI/monai-deploy-messaging/raw/main/LICENSE)
     :versions:
-    - 0.1.9
+    - 0.1.11
     :when: 2022-08-16 23:06:21.051573547 Z
 - - :approve
   - Monai.Deploy.Messaging.RabbitMQ
   - :who: mocsharp
     :why: Apache-2.0 (https://github.com/Project-MONAI/monai-deploy-messaging/raw/main/LICENSE)
     :versions:
-    - 0.1.9
+    - 0.1.11
     :when: 2022-08-16 23:06:21.511789690 Z
 - - :approve
   - Monai.Deploy.Storage

tests/Integration.Test/configs/orthanc.json renamed to docker-compose/configs/orthanc.json

@@ -15,7 +15,7 @@
 version: "3.9"
 services:
   rabbitmq:
-    image: rabbitmq:3-management
+    image: rabbitmq:3.10-management
     hostname: rabbitmq
     ports:
       - 5672:5672
@@ -27,9 +27,10 @@ services:
       RABBITMQ_ERLANG_COOKIE: "SWQOKODSQALRPCLNMEQG"
     healthcheck:
       test: rabbitmq-diagnostics -q ping
-      interval: 15s
+      start_period: 10s
+      interval: 5s
       timeout: 30s
-      retries: 3
+      retries: 5
     networks:
       - monaideploy
 
@@ -48,34 +49,53 @@ services:
       MINIO_ROOT_PASSWORD: minioadmin
     healthcheck:
       test: ["CMD", "curl", "-f", "http://localhost:9000/minio/health/live"]
-      interval: 15s
+      start_period: 10s
+      interval: 5s
       timeout: 30s
-      retries: 3
+      retries: 5
     networks:
       - monaideploy
 
-  createbuckets:
-    image: minio/mc
+  mongodb:
+    image: mongo:latest
     environment:
-      MINIO_ROOT_USER: minioadmin
-      MINIO_ROOT_PASSWORD: minioadmin
-      BUCKET_NAME: monaideploy
-      ENDPOINT: http://minio:9000
-    depends_on:
-      minio:
-        condition: service_healthy
+      MONGO_INITDB_ROOT_USERNAME: root
+      MONGO_INITDB_ROOT_PASSWORD: rootpassword
+    ports:
+      - 27017:27017
+    volumes:
+      - ./.run/mongodb/:/data/db
     networks:
       - monaideploy
-    entrypoint: >
-      /bin/sh -c "
-      until (/usr/bin/mc config host add myminio $$ENDPOINT $$MINIO_ROOT_USER $$MINIO_ROOT_PASSWORD) do echo '...waiting...' && sleep 1; done;
-      /usr/bin/mc mb myminio/$$BUCKET_NAME;
-      /usr/bin/mc policy set public myminio/$$BUCKET_NAME;
-      /usr/bin/mc ls myminio;
-      # exit 0
-      "
+    healthcheck:
+      test: echo 'db.runCommand("ping").ok' | mongo localhost:27017/productiondb --quiet
+      interval: 10s
+      timeout: 10s
+      retries: 5
+      start_period: 40s
+
+  orthanc:
+    image: osimis/orthanc:22.9.0
+    hostname: orthanc
+    volumes:
+      - ./configs/orthanc.json:/etc/orthanc/orthanc.json
+      - .run/orthanc:/var/lib/orthanc/db/
+    ports:
+      - "1114:1114"
+      - "8089:8089"
+    environment:
+      VERBOSE_ENABLED: "true"
+    networks:
+      - monaideploy
+    healthcheck:
+      test: ["CMD", "/probes/test-aliveness.py"]
+      start_period: 10s
+      retries: 3
+      interval: 15s
+      timeout: 30s
 
   elasticsearch:
+    profiles: [ 'elk' ]
     image: docker.elastic.co/elasticsearch/elasticsearch:${ELASTIC_VERSION}
     hostname: elasticsearch
     volumes:
@@ -98,6 +118,7 @@ services:
       retries: 50
 
   logstash:
+    profiles: [ 'elk' ]
     image: docker.elastic.co/logstash/logstash:${ELASTIC_VERSION}
     volumes:
       - ./configs/logstash.yml:/usr/share/logstash/config/logstash.yml:ro,Z
@@ -120,6 +141,7 @@ services:
       - monaideploy
 
   kibana:
+    profiles: [ 'elk' ]
     image: docker.elastic.co/kibana/kibana:${ELASTIC_VERSION}
     volumes:
       - ./configs/kibana.yml:/usr/share/kibana/config/kibana.yml:ro,Z
@@ -139,6 +161,7 @@ services:
       retries: 120
 
   kibana-setup:
+    profiles: [ 'elk' ]
     image: curlimages/curl:latest
     volumes:
       - ./configs/kibana.ndjson:/usr/share/kibana.ndjson