Merge pull request #199 from ehrbase/develop

[pull] develop from ehrbase:develop
NUM-Forschungsdatenplattform · Jan 16, 2024 · e581a77 · e581a77
2 parents 0d079a0 + 77b0788
commit e581a77
Show file tree

Hide file tree

Showing 372 changed files with 19,820 additions and 2,475 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -207,6 +207,12 @@ workflows:
             - build-ehrbase
             - QUERYSERVICE-test-1
 
+      - STOREDQUERY-test:
+          context: org-global
+          requires:
+            - build-ehrbase
+            - QUERYSERVICE-test-1
+
       - QUERYSERVICE-test-1:
           context: org-global
           requires:
@@ -271,6 +277,7 @@ workflows:
             - EHRSERVICE-test
             - EHRSTATUS-test
             - KNOWLEDGE-test
+            - STOREDQUERY-test
             - QUERYSERVICE-test-1
             - QUERYSERVICE-test-2
             - NEWQUERY-test-set
@@ -467,6 +474,12 @@ workflows:
             - build-ehrbase
             - QUERYSERVICE-test-2
 
+      - STOREDQUERY-test:
+          context: org-global
+          requires:
+            - build-ehrbase
+            - QUERYSERVICE-test-2
+
       - QUERYSERVICE-test-1:
           context: org-global
           requires:
@@ -525,6 +538,7 @@ workflows:
             - EHRSERVICE-test
             - EHRSTATUS-test
             - KNOWLEDGE-test
+            - STOREDQUERY-test
             - QUERYSERVICE-test-1
             - QUERYSERVICE-test-2
             - NEWQUERY-test-set
@@ -745,6 +759,10 @@ workflows:
           context: org-global
           requires:
             - build package ehrbase with locally built sdk from sync-branch
+      - STOREDQUERY-test:
+          context: org-global
+          requires:
+            - build package ehrbase with locally built sdk from sync-branch
       - QUERYSERVICE-test-1:
           context: org-global
           requires:
@@ -797,6 +815,7 @@ workflows:
             - EHRSERVICE-test
             - EHRSTATUS-test
             - KNOWLEDGE-test
+            - STOREDQUERY-test
             - QUERYSERVICE-test-1
             - QUERYSERVICE-test-2
             - NEWQUERY-test-set
@@ -1227,6 +1246,19 @@ jobs:
           allow-template-overwrite: false
           cache-enabled: false
 
+  STOREDQUERY-test:
+    executor: docker-py3-postgres
+    steps:
+      - checkout
+      - restore-workspace
+      - git-clone-robot-integration-tests-repo
+      - move-integration-tests-content-to-local-tests-folder
+      - run-robot-tests:
+          include-tags: "stored_query"
+          test-suite-path: "STORED_QUERY_TESTS"
+          test-suite-name: "STORED_QUERY"
+          allow-template-overwrite: true
+
   QUERYSERVICE-test-1:
     executor: docker-py3-postgres
     steps:
@@ -1522,7 +1554,7 @@ commands:
                    --plugin-manager.plugin-dir='tests/test_plugin' \
                    --plugin-manager.plugin-config-dir='tests/test_plugin_config_dir' \
                    --cache.enabled=<< parameters.cache-enabled >> > log & app_pid=$!
-                timeout=60
+                timeout=360
                 while [ ! -f ./log ];
                     do
                         echo "Waiting for file ./log ..."
@@ -1536,6 +1568,7 @@ commands:
                 while ! (cat ./log | grep -m 1 "Started EhrBase in");
                     do
                         echo "waiting for EHRbase to be ready ...";
+                        tail -n 5 ./log
                         if [ "$timeout" == 0 ]; then
                             echo "WARNING: Did not see a startup message even after waiting 60s"
                             exit 1
@@ -1717,7 +1750,7 @@ commands:
           name: INSTALL SDK
           command: |
             cd ~/projects/openEHR_SDK
-              mvn install -Dmaven.javadoc.skip=true -Djacoco.skip=true -Dmaven.test.skip
+              mvn install -Dmaven.javadoc.skip=true -Djacoco.skip=true
   
 
   start-ehrbase-and-run-java-integration-sdk-tests:
@@ -1994,8 +2027,8 @@ commands:
           name: Save unit test results
           command: |
             mkdir -p ~/ehrbase-test-results/unit-tests/
-            find ~/projects -type f -regex ".*/target/surefire-reports/.*xml" -exec cp {} ~/ehrbase-test-results/unit-tests/ \;
-            find ~/projects -type f -regex ".*/target/surefire-reports/.*txt" -exec cp {} ~/ehrbase-test-results/unit-tests/ \;
+            find ~/projects -type f -regex ".*/target/surefire-reports/.*xml" -not -path "~/projects/openEHR_SDK/*" -exec cp {} ~/ehrbase-test-results/unit-tests/ \;
+            find ~/projects -type f -regex ".*/target/surefire-reports/.*txt" -not -path "~/projects/openEHR_SDK/*" -exec cp {} ~/ehrbase-test-results/unit-tests/ \;
           when: always
 
 
@@ -2515,7 +2548,7 @@ commands:
 orbs:
   maven: circleci/[email protected]
   openjdk-install: cloudesire/[email protected]
-  sonarcloud: sonarsource/sonarcloud@1.0.2
+  sonarcloud: sonarsource/sonarcloud@2.0.0
 
 executors:
   # https://hub.docker.com/u/cimg (circleci next-gen docker images)

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -12,3 +12,8 @@ updates:
     ignore:
        - dependency-name: "*"
          update-types: ["version-update:semver-major"]
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"
diff --git a/.github/workflows/build-multiarch-image-latest.yml b/.github/workflows/build-multiarch-image-latest.yml
@@ -15,27 +15,27 @@ jobs:
     steps:
       -
         name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
       -
         name: Build and push (AMD64)
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           context: .
           platforms: linux/amd64
           push: true
           tags: ehrbase/ehrbase:latest-amd64
       -
         name: Build and push (ARM64)
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           context: .
           platforms: linux/arm64

diff --git a/.github/workflows/build-multiarch-image-next.yml b/.github/workflows/build-multiarch-image-next.yml
@@ -31,27 +31,27 @@ jobs:
           # Set as Environment for all further steps 
           echo "TAG=${v}" >> $GITHUB_ENV
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
 
       - name: Login to DockerHub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
 
       - name: Build and push (AMD64)
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           context: .
           platforms: linux/amd64
           push: true
           tags: ehrbase/ehrbase:${{env.TAG}}-amd64
 
       - name: Build and push (ARM64)
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           context: .
           platforms: linux/arm64

diff --git a/.github/workflows/build-multiarch-image-tag.yml b/.github/workflows/build-multiarch-image-tag.yml
@@ -15,7 +15,7 @@ jobs:
     steps:
       -
         name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       -
         name: Create TAG ENV from version of release Branch
         run: |
@@ -27,24 +27,24 @@ jobs:
           echo "TAG=$TAG" >> $GITHUB_ENV
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
       -
         name: Build and push (AMD64)
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           context: .
           platforms: linux/amd64
           push: true
           tags: ehrbase/ehrbase:tag-amd64
       -
         name: Build and push (ARM64)
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           context: .
           platforms: linux/arm64

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -33,12 +33,12 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Setup Java
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
           java-version: '17'
@@ -48,7 +48,7 @@ jobs:
         run: mvn -B verify
 
       - name: Setup Maven Central
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
           java-version: '17'

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -53,18 +53,18 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Java
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
           java-version: '17'
           cache: 'maven'
 
       # Initializes the CodeQL tools for scanning.
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v2
+        uses: github/codeql-action/init@v3
         with:
           languages: ${{ matrix.language }}
           # If you wish to specify custom queries, you can do so here or in a config file.
@@ -78,7 +78,7 @@ jobs:
       # Autobuild attempts to build any compiled languages  (C/C++, C#, Go, or Java).
       # If this step fails, then you should remove it and run the build manually (see below)
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v2
+        uses: github/codeql-action/autobuild@v3
 
       # ℹ️ Command-line programs to run using the OS shell.
       # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
@@ -91,6 +91,6 @@ jobs:
       #     ./location_of_script_within_repo/buildscript.sh
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v2
+        uses: github/codeql-action/analyze@v3
         with:
           category: "/language:${{matrix.language}}"
diff --git a/.github/workflows/jdk-compat-robot.yml b/.github/workflows/jdk-compat-robot.yml
@@ -36,12 +36,12 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Setup Java
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
           java-version: ${{ matrix.java }}
@@ -69,14 +69,14 @@ jobs:
           cat /var/tmp/log.txt
           
       - name: Checkout robot
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
           repository: ehrbase/integration-tests
           ref: main
 
       - name: Install Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
 
@@ -103,14 +103,14 @@ jobs:
           
       - name: Archive code coverage results
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: robot-result
           path: /home/runner/work/ehrbase/ehrbase/tests/results/
 
       - name: Archive logs
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: log
           path: /var/tmp/log.txt
diff --git a/.github/workflows/jdk-compat.yml b/.github/workflows/jdk-compat.yml
@@ -28,12 +28,12 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Setup Java
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
           java-version: ${{ matrix.java }}