Merge branch 'develop' into TASK-6217

Author: j-coll

.github/workflows/compare-vulnerabilities.yml

@@ -0,0 +1,64 @@
+name: Compare vulnerabilities (Syft SBOM -> Grype) between two branches
+run-name: 'Compare vulnerabilities between ${{ inputs.branch_a }} (base) and ${{ inputs.branch_b }} (head) by @${{ github.actor }}'
+on:
+  workflow_call:
+    inputs:
+      branch_a:
+        type: string
+        description: 'Base branch (e.g. develop)'
+        required: true
+      branch_b:
+        type: string
+        description: 'Head branch (e.g. TASK-1234)'
+        required: true
+    secrets:
+      SLACK_SECURITY_WEBHOOK_URL:
+        required: false
+
+  workflow_dispatch:
+    inputs:
+      branch_a:
+        description: 'Base branch (e.g. develop)'
+        required: true
+        default: 'develop'
+      branch_b:
+        description: 'Head branch (e.g. TASK-1234)'
+        required: true
+
+jobs:
+  compare-branches:
+    runs-on: ${{ vars.UBUNTU_VERSION }}
+
+    steps:
+      # 1) Checkout head branch only
+      - name: Checkout head branch
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.inputs.branch_b }}
+          fetch-depth: 0
+          fetch-tags: true
+
+      - name: Set up JDK 8
+        uses: actions/setup-java@v4
+        with:
+          distribution: 'temurin'
+          java-version: '8'
+          cache: 'maven'
+      # 3) Run the action
+      - name: Vulnerability Diff (Syft+Grype)
+        uses: sec-open/vuln-diff-action@v2.0.0-alpha.1
+        with:
+          base_ref: ${{ github.event.inputs.branch_a }}   # pass 'develop'
+          head_ref: ${{ github.event.inputs.branch_b }}   # pass 'TASK-7908'
+          html_logo_url: "https://zettagenomics.com/wp-content/uploads/2022/10/Zetta-reversed-out-full-logo-dark-background.png"
+
+
+#          build_command: ""
+#          write_summary: "true"
+#          upload_artifact: "true"
+#          artifact_name: "vulnerability-diff-${{ github.event.inputs.branch_a }}-vs-${{ github.event.inputs.branch_b }}"
+#          report_html: "true"
+#          report_pdf: "true"
+#          min_severity: "LOW"
+#          title_logo_url: "https://zettagenomics.com/wp-content/uploads/2022/10/Zetta-reversed-out-full-logo-dark-background.png"
+

.github/workflows/deploy-maven-repository-workflow.yml

@@ -33,7 +33,7 @@ jobs:
           gpg-private-key: ${{ secrets.MAVEN_GPG_PRIVATE_KEY }}   # Value of the GPG private key to import
           gpg-passphrase: MAVEN_GPG_PASSPHRASE                    # env variable for GPG private key passphrase
       - name: Deploy to Maven Central repository
-        run: mvn clean deploy -DskipTests -P deploy-maven ${{ inputs.maven_opts }} --no-transfer-progress
+        run: mvn clean deploy -DskipTests -Pdeploy-maven ${{ inputs.maven_opts }} --no-transfer-progress
         env:
           MAVEN_NEXUS_USER: ${{ secrets.MAVEN_USER_TOKEN }}
           MAVEN_NEXUS_PASSWORD: ${{ secrets.MAVEN_PASSWORD_TOKEN }}
@@ -44,6 +44,6 @@ jobs:
           distribution: 'temurin'
           java-version: '8'
       - name: Deploy to GitHub Packages repository
-        run: mvn clean deploy -DskipTests -P deploy-github ${{ inputs.maven_opts }} --no-transfer-progress
+        run: mvn clean deploy -DskipTests -Pdeploy-github ${{ inputs.maven_opts }} --no-transfer-progress
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/deploy-zetta-docker-hub-workflow.yml

@@ -1,4 +1,4 @@
-name: Reusable workflow to push in DockerHub
+name: Reusable workflow to push in Zettagenomics DockerHub
 
 on:
   workflow_call:
@@ -46,4 +46,3 @@ jobs:
           logout: true
       - name: Deploy in Docker Hub
         run: ${{ inputs.cli }} --org zettagenomics
-

.github/workflows/pull-request-approved.yml

@@ -35,7 +35,7 @@ jobs:
   test:
     name: "Run all tests before merging"
     needs: calculate-xetabase-branch
-    uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@develop
+    uses: ./.github/workflows/test-xetabase-workflow.yml
     with:
       branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }}
       task: ${{ github.event.pull_request.head.ref }}

.github/workflows/test-analysis.yml

@@ -39,4 +39,4 @@ jobs:
           check_name: "Surefire tests report"
           report_paths: './**/surefire-reports/TEST-*.xml'
           commit: '${{ github.sha }}'
-          fail_on_test_failures: true
+          fail_on_test_failures: true

.github/workflows/test-xetabase-workflow.yml

@@ -77,17 +77,6 @@ jobs:
         with:
           mongodb-version: 6.0
           mongodb-replica-set: rs-test
-      - name: K8s Tunnel MongoDB
-        run: |
-          wget https://dl.k8s.io/release/v1.28.2/bin/linux/amd64/kubectl
-          chmod +x ./kubectl
-          echo "${{ secrets.AZURE_KUBE_CONFIG }}" > admin.conf
-          ./kubectl -n cellbase-db port-forward services/cellbase-rs0-svc 27018:27017 --kubeconfig ./admin.conf &
-      - name: DockerHub login
-        uses: docker/login-action@v3
-        with:
-          username: ${{ env.DOCKER_HUB_USER }}
-          password: ${{ env.DOCKER_HUB_PASSWORD }}
       - name: Install sshpass
         run: sudo apt-get install sshpass
       - name: Add SSH Host to known_hosts
@@ -97,11 +86,11 @@ jobs:
         env:
           SSH_HOST: ${{ env.SSH_HOST }}
           SSH_PORT: ${{ env.SSH_PORT }}
-      - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, cellbase, opencga and opencga-enterprise
+      - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, opencga and opencga-enterprise
         run: |
           cd opencga-enterprise
           ln -s ../opencga opencga-home
-          ./build.sh -t -l runShortTests -b -s -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1
+          ./build.sh -t -l runShortTests -b -s -T ${{ inputs.task }}
       - name: Upload reports results to Github
         uses: actions/upload-artifact@v4
         with:

commons-datastore/commons-datastore-core/pom.xml

@@ -13,6 +13,10 @@
     <artifactId>commons-datastore-core</artifactId>
     <packaging>jar</packaging>
 
+    <name>OpenCB commons-datastore-core project</name>
+    <description>OpenCB commons project contains several Java libs for Bioinformatics</description>
+    <url>http://www.opencb.org</url>
+
     <dependencies>
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>

commons-datastore/commons-datastore-core/src/main/java/org/opencb/commons/datastore/core/ObjectMap.java

@@ -38,7 +38,6 @@ public class ObjectMap implements Map<String, Object>, Serializable {
 
     private static final Pattern KEY_SPLIT_PATTERN = Pattern.compile("(^[^\\[\\].]+(?:\\[[^\\]]+\\])?)(?:\\.(.*))*");
     private static final Pattern LIST_FILTER_PATTERN = Pattern.compile("([^\\[\\]]+)\\[([^=]*?)(?:[=]?)([^=]+)\\]$");
-    public static final Pattern COMMA_SEPARATED_LIST_SPLIT_PATTERN = Pattern.compile("((?:(?!,\\S).)+)+");
 
     public ObjectMap() {
         objectMap = new LinkedHashMap<>();

commons-datastore/commons-datastore-core/src/test/java/org/opencb/commons/datastore/core/ObjectMapTest.java

@@ -263,35 +263,4 @@ public void testGetWithFilterFromList() {
         assertEquals("CGHI", objectMap.get("nestedList[nested.value=G].nested.list[id=Cghi].name"));
     }
 
-    @Test
-    public void testPatternListSplit() {
-        List<String> originalValues = Arrays.asList("disorder1", "disorder2, blabla", "disorder3");
-        objectMap.put("key", StringUtils.join(originalValues, ","));
-        objectMap.put("key1", "");
-        objectMap.put("key2", "my value");
-        objectMap.put("key3", Arrays.asList("1", "2"));
-        objectMap.put("key4", Arrays.asList(1, 2));
-
-        List<String> values = objectMap.getAsStringList("key", ObjectMap.COMMA_SEPARATED_LIST_SPLIT_PATTERN);
-        assertEquals(originalValues.size(), values.size());
-        assertTrue(originalValues.containsAll(values));
-
-        values = objectMap.getAsStringList("key1", ObjectMap.COMMA_SEPARATED_LIST_SPLIT_PATTERN);
-        assertEquals(1, values.size());
-        assertEquals("", values.get(0));
-
-        values = objectMap.getAsStringList("key2", ObjectMap.COMMA_SEPARATED_LIST_SPLIT_PATTERN);
-        assertEquals(1, values.size());
-        assertEquals("my value", values.get(0));
-
-        values = objectMap.getAsStringList("key3", ObjectMap.COMMA_SEPARATED_LIST_SPLIT_PATTERN);
-        assertEquals(2, values.size());
-        assertEquals("1", values.get(0));
-        assertEquals("2", values.get(1));
-
-        values = objectMap.getAsStringList("key4", ObjectMap.COMMA_SEPARATED_LIST_SPLIT_PATTERN);
-        assertEquals(2, values.size());
-        assertEquals("1", values.get(0));
-        assertEquals("2", values.get(1));
-    }
 }

commons-datastore/commons-datastore-mongodb/pom.xml

@@ -13,6 +13,10 @@
     <artifactId>commons-datastore-mongodb</artifactId>
     <packaging>jar</packaging>
 
+    <name>OpenCB commons-datastore-mongodb project</name>
+    <description>OpenCB commons project contains several Java libs for Bioinformatics</description>
+    <url>http://www.opencb.org</url>
+
     <dependencies>
         <dependency>
             <groupId>org.opencb.commons</groupId>