Merge pull request #2293 from opencb/TASK-4445

TASK-4445 - Opencga long test fails
opencb · Jul 26, 2023 · 476848b · 476848b
2 parents 18d2cd4 + c7b53d1
commit 476848b
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Showing 6 changed files with 93 additions and 21 deletions.
diff --git a/.github/workflows/check-junit-test.yml b/.github/workflows/check-junit-test.yml
@@ -0,0 +1,56 @@
+name: Check junits
+
+on:
+  workflow_dispatch:
+    inputs:
+      short_tests:
+        type: boolean
+        required: false
+        default: true
+      medium_tests:
+        type: boolean
+        required: false
+        default: false
+      long_tests:
+        type: boolean
+        required: false
+        default: false
+      mvn_opts:
+        type: string
+        required: false
+        default: ""
+
+jobs:
+  get_profiles:
+    name: Test JUnit
+    runs-on: ubuntu-22.04
+    outputs:
+      profiles: ${{ steps.getter.outputs.profiles }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: '10'
+      - name: Building string profiles to run
+        id: getter
+        run: |
+          if [ -f "./.github/workflows/scripts/get_profiles.sh" ]; then
+            chmod +x ./.github/workflows/scripts/get_profiles.sh
+            echo "profiles=$(./.github/workflows/scripts/get_profiles.sh ${{ inputs.short_tests }} ${{ inputs.medium_tests }} ${{ inputs.long_tests }})" >> $GITHUB_OUTPUT
+          fi
+
+  echo_log:
+    needs: get_profiles
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Echo profiles
+        id: log
+        run: echo "Executing testing profiles -> ${{ needs.get_profiles.outputs.profiles }}"
+
+  test:
+    needs: [ get_profiles, echo_log ]
+    uses: ./.github/workflows/test-analysis.yml
+    with:
+      test_profile: ${{ needs.get_profiles.outputs.profiles }}
+      report_context: development
+      mvn_opts: ${{ inputs.mvn_opts }}
+    secrets: inherit
diff --git a/.github/workflows/scripts/get_profiles.sh b/.github/workflows/scripts/get_profiles.sh
@@ -0,0 +1,30 @@
+#!/bin/bash
+
+if [ $# -eq 0 ];  then
+    echo "The arguments must be 3"
+    exit 1
+fi
+PROFILE=""
+
+if [ $1 == "true" ]; then
+  PROFILE="${PROFILE}runShortTests,"
+fi
+if [ $2 == "true" ]; then
+  PROFILE="${PROFILE}runMediumTests,"
+fi
+if [ $3 == "true" ]; then
+  PROFILE="${PROFILE}runLongTests"
+fi
+
+if [[ "${PROFILE}" == *"," ]]; then
+  PROFILE="${PROFILE%?}"
+fi
+
+if [ -z "${PROFILE}" ]; then
+  echo "There must be at least one active profile"
+  exit 1
+fi
+
+echo "${PROFILE}"
+exit 0
+
diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml
@@ -8,6 +8,10 @@ on:
       report_context:
         type: string
         required: true
+      mvn_opts:
+        type: string
+        required: false
+        default: ""
     secrets:
       SONAR_TOKEN:
         required: true
@@ -61,7 +65,7 @@ jobs:
           mongodb-version: 6.0
           mongodb-replica-set: rs-test
       - name: Run Junit tests
-        run: mvn -B verify surefire-report:report -P storage-hadoop,hdp3.1,${{ inputs.test_profile }} -Dcheckstyle.skip -Popencga-storage-hadoop-deps -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6'
+        run: mvn -B verify surefire-report:report -P storage-hadoop,hdp3.1,${{ inputs.test_profile }} -Dcheckstyle.skip -Popencga-storage-hadoop-deps -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' ${{ inputs.mvn_opts }}
       - name: Upload result dir
         uses: actions/upload-artifact@v3
         with:
@@ -73,7 +77,7 @@ jobs:
     needs: test
     strategy:
       matrix:
-        module: ["opencga-app", "opencga-catalog", "opencga-client", "opencga-clinical", "opencga-core", "opencga-master", "opencga-server", "opencga-storage", "opencga-storage/opencga-storage-app", "opencga-storage/opencga-storage-benchmark", "opencga-storage/opencga-storage-core", "opencga-storage/opencga-storage-hadoop", "opencga-storage/opencga-storage-server", "opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core", "opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps"]
+        module: [ "opencga-app", "opencga-catalog", "opencga-client", "opencga-clinical", "opencga-core", "opencga-master", "opencga-server", "opencga-storage", "opencga-storage/opencga-storage-app", "opencga-storage/opencga-storage-benchmark", "opencga-storage/opencga-storage-core", "opencga-storage/opencga-storage-hadoop", "opencga-storage/opencga-storage-server", "opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core", "opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps" ]
     steps:
       - name: Download result dir
         uses: actions/download-artifact@v3

diff --git a/.github/workflows/test-long-test-analysis.yml b/.github/workflows/test-long-test-analysis.yml
diff --git a/...e-core/src/main/java/org/opencb/opencga/storage/core/metadata/models/ProjectMetadata.java b/...e-core/src/main/java/org/opencb/opencga/storage/core/metadata/models/ProjectMetadata.java
@@ -85,10 +85,6 @@ public VariantAnnotationMetadata() {
             sourceVersion = new ArrayList<>();
         }
 
-        public VariantAnnotationMetadata(int id, String name, Date creationDate, VariantAnnotatorProgram annotator,
-                                         List<ObjectMap> sourceVersion, DataRelease dataRelease) {
-
-        }
         public VariantAnnotationMetadata(int id, String name, Date creationDate, VariantAnnotatorProgram annotator,
                                          List<ObjectMap> sourceVersion, DataRelease dataRelease, List<String> privateSources) {
             this.id = id;

diff --git a/.../src/test/java/org/opencb/opencga/storage/core/variant/annotation/DummyTestAnnotator.java b/.../src/test/java/org/opencb/opencga/storage/core/variant/annotation/DummyTestAnnotator.java
@@ -59,7 +59,7 @@ public List<VariantAnnotation> annotate(List<Variant> variants) throws VariantAn
     public ProjectMetadata.VariantAnnotationMetadata getVariantAnnotationMetadata() throws VariantAnnotatorException {
         return new ProjectMetadata.VariantAnnotationMetadata(-1, null, null,
                 new ProjectMetadata.VariantAnnotatorProgram("MyAnnotator", key, null),
-                Collections.singletonList(new ObjectMap("data", "genes")), null);
+                Collections.singletonList(new ObjectMap("data", "genes")), null, null);
     }
 
 }