Merge branch 'develop' into TASK-7555

j-coll · j-coll · commit f225f5800a83 · 2025-11-11T10:31:05.000Z
diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml
@@ -7,17 +7,14 @@ on:
       - release-*
 
 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
 
   deploy-maven:
     uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
     needs: test
     with:
       maven_opts: -U -DskipTests
+      cache_key: ${{ needs.test.outputs.cache_key }}
     secrets: inherit
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -8,11 +8,19 @@ on:
 jobs:
   build:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
+    with:
+      maven_opts: --update-snapshots -DskipTests
+      upload_artifacts: false
+      needs_hadoop_preparation: false
+      dependency_repos: "java-common-libs"
+    secrets: inherit
 
   deploy-maven:
     uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
     needs: build
     secrets: inherit
+    with:
+      cache_key: ${{ needs.build.outputs.cache_key }}
 
   release:
     uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop
diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh
diff --git a/.github/workflows/task.yml b/.github/workflows/task.yml
@@ -6,10 +6,6 @@ on:
       - TASK-*
 
 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
diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml
@@ -1,13 +1,27 @@
 name: Build and test the project
 on:
   workflow_call:
+    outputs:
+      cache_key:
+        description: "Cache key used for Maven repository"
+        value: ${{ jobs.build.outputs.cache_key }}
     secrets:
       SONAR_TOKEN:
         required: true
 
 jobs:
+
+  build:
+    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
+    with:
+      needs_hadoop_preparation: false
+      upload_artifact: false
+      dependency_repos: "java-common-libs"
+    secrets: inherit
+
   test:
     name: Test and push Sonar analysis
+    needs: build
     runs-on: ${{ vars.UBUNTU_VERSION }}
     steps:
       - uses: actions/checkout@v4
@@ -19,16 +33,15 @@ jobs:
           distribution: 'temurin'
           java-version: '11'
           cache: 'maven'
+      - name: Cache local Maven repository
+        uses: actions/cache/restore@v4
+        with:
+          path: ~/.m2/repository
+          key: ${{ needs.build.outputs.cache_key }}
+          ## Force cache hit to avoid analyzing with incomplete dependencies
+          fail-on-cache-miss: true
       - 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
diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/stats/writer/VariantStatsPopulationFrequencyExporter.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/stats/writer/VariantStatsPopulationFrequencyExporter.java
@@ -96,7 +96,7 @@ public boolean write(Variant variant) {
                 PopulationFrequency populationFrequency = converter.convert(studyId,
                         variantStats, variant.getReference(), variant.getAlternate());
                 // Write only frequencies non zero
-                if (populationFrequency.getAltAlleleFreq() > 0 && !populationFrequency.getAltAlleleFreq().isNaN()) {
+                if (populationFrequency.getAltAlleleFreq() > 0 && !Float.isNaN(populationFrequency.getAltAlleleFreq())) {
                     frequencies.add(populationFrequency);
                 }
             }
diff --git a/biodata-tools/src/test/java/org/opencb/biodata/tools/variant/stats/SampleVariantStatsCalculatorTest.java b/biodata-tools/src/test/java/org/opencb/biodata/tools/variant/stats/SampleVariantStatsCalculatorTest.java
@@ -117,18 +117,18 @@ private void checkStats(List<SampleVariantStats> sampleStats) {
         for (SampleVariantStats sampleStat : sampleStats) {
             Assert.assertFalse(Float.isNaN(sampleStat.getQualityAvg()));
             Assert.assertFalse(Float.isInfinite(sampleStat.getQualityAvg()));
-            Assert.assertEquals(0, sampleStat.getDepthCount().getNa().intValue());
+            Assert.assertEquals(0, sampleStat.getDepthCount().getNa());
             int dp = Integer.parseInt(sampleStat.getId().substring(1)) * 10;
             if (dp < 5) {
-                Assert.assertNotEquals(0, sampleStat.getDepthCount().getLt5().intValue());
+                Assert.assertNotEquals(0, sampleStat.getDepthCount().getLt5());
             } else if (dp < 10) {
-                Assert.assertNotEquals(0, sampleStat.getDepthCount().getLt10().intValue());
+                Assert.assertNotEquals(0, sampleStat.getDepthCount().getLt10());
             } else if (dp < 15) {
-                Assert.assertNotEquals(0, sampleStat.getDepthCount().getLt15().intValue());
+                Assert.assertNotEquals(0, sampleStat.getDepthCount().getLt15());
             } else if (dp < 20) {
-                Assert.assertNotEquals(0, sampleStat.getDepthCount().getLt20().intValue());
+                Assert.assertNotEquals(0, sampleStat.getDepthCount().getLt20());
             } else {
-                Assert.assertNotEquals(0, sampleStat.getDepthCount().getGte20().intValue());
+                Assert.assertNotEquals(0, sampleStat.getDepthCount().getGte20());
             }
         }
     }
diff --git a/biodata-tools/src/test/java/org/opencb/biodata/tools/variant/stats/VariantSetStatsCalculatorTest.java b/biodata-tools/src/test/java/org/opencb/biodata/tools/variant/stats/VariantSetStatsCalculatorTest.java
@@ -132,10 +132,10 @@ public void testStudyStats() throws Exception {
 
         System.out.println("stats = " + stats);
 
-        assertEquals(variants, stats.getVariantCount().intValue());
+        assertEquals(variants, stats.getVariantCount());
         assertEquals(((int) (files * variants * passVariants)), stats.getFilterCount().get("PASS").intValue());
-        assertEquals(files, stats.getFilesCount().intValue());
-        assertEquals(files * samplesPerFile, stats.getSampleCount().intValue());
+        assertEquals(files, stats.getFilesCount());
+        assertEquals(files * samplesPerFile, stats.getSampleCount());
         assertEquals(files * samplesPerFile * variants, stats.getGenotypeCount().values().stream().reduce(Long::sum).orElse(0L).intValue());
     }
 
@@ -154,10 +154,10 @@ public void testFileStats() throws Exception {
         }
         stDev = Math.sqrt(stDev / quals.length);
 
-        assertEquals(variants, stats.getVariantCount().intValue());
+        assertEquals(variants, stats.getVariantCount());
         assertEquals(((int) (variants * passVariants)), stats.getFilterCount().get("PASS").intValue());
-        assertEquals(1, stats.getFilesCount().intValue());
-        assertEquals(samplesPerFile, stats.getSampleCount().intValue());
+        assertEquals(1, stats.getFilesCount());
+        assertEquals(samplesPerFile, stats.getSampleCount());
         assertEquals(samplesPerFile * variants, stats.getGenotypeCount().values().stream().reduce(Long::sum).orElse(0L).intValue());
 
         assertEquals(mean, stats.getQualityAvg(), 0.000001);
diff --git a/pom.xml b/pom.xml
@@ -41,7 +41,7 @@
 
         <jackson.version>2.14.3</jackson.version>
         <collections.version>4.4</collections.version>
-        <avro.version>1.7.7</avro.version>
+        <avro.version>1.11.4</avro.version>
         <protobuf.version>3.11.4</protobuf.version>
         <grpc.version>1.28.1</grpc.version>
         <htsjdk.version>2.23.0</htsjdk.version>

Original file line number	Diff line number	Diff line change
`@@ -96,7 +96,7 @@ public boolean write(Variant variant) {`
`96`	`96`	`PopulationFrequency populationFrequency = converter.convert(studyId,`
`97`	`97`	`variantStats, variant.getReference(), variant.getAlternate());`
`98`	`98`	`// Write only frequencies non zero`
`99`		`- if (populationFrequency.getAltAlleleFreq() > 0 && !populationFrequency.getAltAlleleFreq().isNaN()) {`
	`99`	`+ if (populationFrequency.getAltAlleleFreq() > 0 && !Float.isNaN(populationFrequency.getAltAlleleFreq())) {`
`100`	`100`	`frequencies.add(populationFrequency);`
`101`	`101`	`}`
`102`	`102`	`}`