Merge branch 'develop' into TASK-1111

.github/workflows/develop.yml

@@ -14,9 +14,6 @@ jobs:
     uses: ./.github/workflows/test-analysis.yml
     needs: build
     secrets: inherit
-    with:
-      report_context: development
-      report_dir: ${{ github.ref_name }}/biodata/${{ github.sha }}
 
   deploy-maven:
     uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop

.github/workflows/release.yml

@@ -9,14 +9,6 @@ jobs:
   build:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
 
-  test:
-    uses: ./.github/workflows/test-analysis.yml
-    needs: build
-    secrets: inherit
-    with:
-      report_context: xetabase
-      report_dir: biodata
-
   deploy-maven:
     uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
     needs: test

.github/workflows/scripts/get_same_branch.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+
+BRANCH_NAME=$1
+
+if [[ -z $BRANCH_NAME  ]]; then
+  echo "The first parameter is mandatory and must be a valid branch name."
+  exit 1
+fi
+
+if [[ $BRANCH_NAME != "TASK-"*   ]]; then
+  echo "No need to check dependencies."
+  exit 0
+fi
+
+function install(){
+  local REPO=$1
+  cd /home/runner/work/ || exit 2
+  git clone https://github.com/opencb/"$REPO".git -b "$BRANCH_NAME"
+  if [ -d "./$REPO" ]; then
+    cd "$REPO" || exit 2
+    echo "Branch name $BRANCH_NAME already exists."
+    mvn clean install -DskipTests
+  else
+    echo "$CURRENT Branch is NOT EQUALS $BRANCH_NAME "
+  fi
+}
+
+install "java-common-libs"

.github/workflows/task.yml

@@ -13,32 +13,3 @@ jobs:
     uses: ./.github/workflows/test-analysis.yml
     needs: build
     secrets: inherit
-    with:
-      report_context: development
-      report_dir: ${{ github.ref_name }}/biodata/${{ github.sha }}
-
-  deploy-maven:
-    name: Deploy in maven only for renamed versions
-    uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
-    needs: [ build, test ]
-    if: contains( needs.build.outputs.version ,'TASK')
-    secrets: inherit
-
-  #The following jobs are to see that the previous 'if' doesn't fail and that the maven deploy is executed because it is true
-  snapshot-version:
-    name: Check SNAPSHOT version
-    needs: [ build, test ]
-    if: contains(needs.build.outputs.version ,'SNAPSHOT')
-    runs-on: ubuntu-22.04
-    steps:
-      - name: test-version-from-check
-        run: echo "Project version is " ${{ needs.build.outputs.version }}
-
-  task-version:
-    name: Check TASK version
-    needs: [ build, test ]
-    if: contains(needs.build.outputs.version ,'TASK')
-    runs-on: ubuntu-22.04
-    steps:
-      - name: test-version-from-check
-        run: echo "Project version is " ${{ needs.build.outputs.version }}

.github/workflows/test-analysis.yml

@@ -1,26 +1,10 @@
 name: Build and test the project
 on:
   workflow_call:
-    inputs:
-      report_dir:
-        type: string
-        required: true
-      report_context:
-        type: string
-        required: true
     secrets:
       SONAR_TOKEN:
         required: true
-      SSH_TESTING_SERVER_HOST:
-        required: true
-      SSH_TESTING_SERVER_PORT:
-        required: true
-      SSH_TESTING_SERVER_USER:
-        required: true
-      SSH_TESTING_SERVER_PASSWORD:
-        required: true
-env:
-  xb_version: "1.7.0"
+
 jobs:
   test:
     name: Test and push Sonar analysis
@@ -37,35 +21,26 @@ jobs:
           cache: 'maven'
       - name: Install Samtools
         run: sudo apt-get install samtools
+      - name: Install dependencies branches
+        run: |
+          if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then
+            chmod +x ./.github/workflows/scripts/get_same_branch.sh
+            ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }}
+          else
+             echo "./.github/workflows/scripts/get_same_branch.sh does not exist."
+          fi
       - name: Test and Analyze
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-        run: mvn -B verify surefire-report:report  org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=opencb_biodata
-      - name: Upload result dir
-        uses: actions/upload-artifact@v3
-        with:
-          name: workdir
-          path: "**/target/site"
-  publish-test:
-    name: Publish test results
-    runs-on: ubuntu-22.04
-    needs: test
-    strategy:
-      matrix:
-        module: ["biodata-tools", "biodata-models"]
-    steps:
-      - name: Download result dir
-        uses: actions/download-artifact@v3
-        with:
-          name: workdir
-      - name: Deploy unit tests web recursively to remote
-        uses: garygrossgarten/github-action-scp@release
+        run: mvn -B verify surefire-report:report --fail-never org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=opencb_biodata
+      - name: Publish Test Report
+        uses: scacap/action-surefire-report@v1
+        ## Skip cancelled()
+        ## https://docs.github.com/en/actions/learn-github-actions/expressions#cancelled
+        if: success() || failure()
         with:
-          local: ${{ matrix.module }}/target/site
-          remote: /var/www/html/reports/${{ inputs.report_context }}/${{ env.xb_version }}/${{ inputs.report_dir }}/unit/${{ matrix.module }}
-          host: ${{ secrets.SSH_TESTING_SERVER_HOST}}
-          port: ${{ secrets.SSH_TESTING_SERVER_PORT}}
-          username: ${{ secrets.SSH_TESTING_SERVER_USER }}
-          password: ${{ secrets.SSH_TESTING_SERVER_PASSWORD }}
-          concurrency: 2
+          check_name: "Surefire tests report"
+          report_paths: './**/surefire-reports/TEST-*.xml'
+          commit: '${{ github.sha }}'
+          fail_on_test_failures: true

biodata-external/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <artifactId>biodata</artifactId>
         <groupId>org.opencb.biodata</groupId>
-        <version>2.9.0-SNAPSHOT</version>
+        <version>2.10.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

biodata-formats/pom.xml

@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>2.9.0-SNAPSHOT</version>
+        <version>2.10.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

biodata-models/pom.xml

@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>2.9.0-SNAPSHOT</version>
+        <version>2.10.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

biodata-models/src/main/java/org/opencb/biodata/models/core/AnnotationEvidence.java

@@ -16,6 +16,8 @@
 
 package org.opencb.biodata.models.core;
 
+import org.opencb.commons.utils.PrintUtils;
+
 import java.util.Set;
 
 public class AnnotationEvidence {

biodata-tools/pom.xml

@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>2.9.0-SNAPSHOT</version>
+        <version>2.10.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/ClinicalVariantCreator.java

@@ -33,6 +33,7 @@
 import org.opencb.biodata.models.variant.avro.ConsequenceType;
 import org.opencb.biodata.models.variant.avro.GeneCancerAssociation;
 import org.opencb.biodata.models.variant.avro.SequenceOntologyTerm;
+import org.opencb.commons.utils.PrintUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -94,6 +95,7 @@ public ClinicalVariantCreator(List<DiseasePanel> diseasePanels, Disorder disorde
         this.modeOfInheritances = modeOfInheritances;
         this.penetrance = penetrance;
         this.assembly = assembly;
+        PrintUtils.printSpace();
 
         this.biotypeSet = new HashSet<>();
         if (CollectionUtils.isNotEmpty(biotypes)) {

pom.xml

@@ -20,7 +20,7 @@
 
     <groupId>org.opencb.biodata</groupId>
     <artifactId>biodata</artifactId>
-    <version>2.9.0-SNAPSHOT</version>
+    <version>2.10.0-SNAPSHOT</version>
     <packaging>pom</packaging>
     <name>Biodata</name>
     <description>Biological entities and their equivalents in different file formats typically used in bioinformatics</description>
@@ -34,7 +34,7 @@
     </modules>
 
     <properties>
-        <java-common-libs.version>4.9.0-SNAPSHOT</java-common-libs.version>
+        <java-common-libs.version>4.10.0-SNAPSHOT</java-common-libs.version>
         <collections.version>4.4</collections.version>
         <avro.version>1.7.7</avro.version>
         <protobuf.version>3.11.4</protobuf.version>