Merge branch 'release-3.2.x' into TASK-6647-rel

opencb · Aug 6, 2024 · ac9da0c · ac9da0c
2 parents da73175 + b4c2afb
commit ac9da0c
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Showing 14 changed files with 57 additions and 42 deletions.
diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
@@ -0,0 +1,15 @@
+name: Pull request approve workflow
+
+on:
+  pull_request_review:
+    types: [ submitted ]
+
+jobs:
+  build:
+    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
+
+  test:
+    name: "Test analysis"
+    uses: ./.github/workflows/test-analysis.yml
+    needs: build
+    secrets: inherit
diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml
@@ -10,11 +10,11 @@ jobs:
     name: Test and push Sonar analysis
     runs-on: ubuntu-22.04
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: '0'
       - name: Set up JDK 11
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
           java-version: '11'

diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml
@@ -88,11 +88,11 @@
             <groupId>org.apache.avro</groupId>
             <artifactId>avro</artifactId>
         </dependency>
-        <dependency>
+<!--        <dependency>
             <groupId>org.codehaus.jackson</groupId>
             <artifactId>jackson-mapper-asl</artifactId>
             <scope>test</scope>
-        </dependency>
+        </dependency>-->
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>

diff --git a/...s/src/test/java/org/opencb/biodata/formats/variant/annotation/io/VepFormatWriterTest.java b/...s/src/test/java/org/opencb/biodata/formats/variant/annotation/io/VepFormatWriterTest.java
@@ -19,7 +19,7 @@
 
 package org.opencb.biodata.formats.variant.annotation.io;
 
-import org.codehaus.jackson.map.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.junit.Test;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.avro.VariantAvro;

diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml
@@ -74,10 +74,10 @@
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
         </dependency>
-        <dependency>
+<!--        <dependency>
             <groupId>org.codehaus.jackson</groupId>
             <artifactId>jackson-mapper-asl</artifactId>
-        </dependency>
+        </dependency>-->
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>

diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/alignment/RegionCoverage.java b/biodata-models/src/main/java/org/opencb/biodata/models/alignment/RegionCoverage.java
@@ -1,7 +1,7 @@
 package org.opencb.biodata.models.alignment;
 
-import org.codehaus.jackson.map.ObjectMapper;
-import org.codehaus.jackson.map.ObjectWriter;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectWriter;
 import org.opencb.biodata.models.core.Region;
 
 import java.io.IOException;

diff --git a/...dels/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariant.java b/...dels/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariant.java
@@ -115,19 +115,7 @@ public ClinicalVariant(VariantAvro avro, List<ClinicalVariantEvidence> evidences
 
     @Override
     public String toString() {
-        final StringBuilder sb = new StringBuilder("ClinicalVariant{");
-        sb.append("evidences=").append(evidences);
-        sb.append(", comments=").append(comments);
-        sb.append(", filters=").append(filters);
-        sb.append(", recommendation='").append(recommendation).append('\'');
-        sb.append(", references=").append(references);
-        sb.append(", discussion=").append(discussion);
-        sb.append(", confidence=").append(confidence);
-        sb.append(", tags=").append(tags);
-        sb.append(", status=").append(status);
-        sb.append(", attributes=").append(attributes);
-        sb.append('}');
-        return sb.toString();
+        return super.toString();
     }
 
     public List<ClinicalVariantEvidence> getEvidences() {

diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/pedigree/Pedigree.java b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/pedigree/Pedigree.java
@@ -19,7 +19,7 @@
 
 package org.opencb.biodata.models.clinical.pedigree;
 
-import org.codehaus.jackson.map.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.opencb.biodata.models.clinical.Disorder;
 import org.opencb.biodata.models.clinical.Phenotype;
 

diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml
@@ -53,6 +53,12 @@
         <dependency>
             <groupId>com.databricks</groupId>
             <artifactId>SnpEff</artifactId>
+            <exclusions>
+                <exclusion>
+                    <groupId>distlib</groupId>
+                    <artifactId>distlib</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>org.rocksdb</groupId>
@@ -90,10 +96,10 @@
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-collections4</artifactId>
         </dependency>
-        <dependency>
+<!--        <dependency>
             <groupId>org.codehaus.jackson</groupId>
             <artifactId>jackson-mapper-asl</artifactId>
-        </dependency>
+        </dependency>-->
         <dependency>
             <groupId>com.google.guava</groupId>
             <artifactId>guava</artifactId>

diff --git a/...ta-tools/src/main/java/org/opencb/biodata/tools/alignment/stats/AlignmentGlobalStats.java b/...ta-tools/src/main/java/org/opencb/biodata/tools/alignment/stats/AlignmentGlobalStats.java
@@ -19,8 +19,8 @@
 
 package org.opencb.biodata.tools.alignment.stats;
 
-import org.codehaus.jackson.map.ObjectMapper;
-import org.codehaus.jackson.map.ObjectWriter;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectWriter;
 
 import java.io.IOException;
 import java.util.HashMap;

diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/alignment/stats/SequenceKmers.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/alignment/stats/SequenceKmers.java
@@ -19,8 +19,8 @@
 
 package org.opencb.biodata.tools.alignment.stats;
 
-import org.codehaus.jackson.map.ObjectMapper;
-import org.codehaus.jackson.map.ObjectWriter;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectWriter;
 
 import java.io.IOException;
 import java.util.HashMap;

diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/alignment/stats/SequenceStats.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/alignment/stats/SequenceStats.java
@@ -19,8 +19,8 @@
 
 package org.opencb.biodata.tools.alignment.stats;
 
-import org.codehaus.jackson.map.ObjectMapper;
-import org.codehaus.jackson.map.ObjectWriter;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectWriter;
 
 import java.io.IOException;
 import java.util.HashMap;

diff --git a/biodata-tools/src/test/java/org/opencb/biodata/tools/variant/VcfManagerTest.java b/biodata-tools/src/test/java/org/opencb/biodata/tools/variant/VcfManagerTest.java
@@ -1,6 +1,7 @@
 package org.opencb.biodata.tools.variant;
 
 import htsjdk.variant.variantcontext.VariantContext;
+import org.junit.BeforeClass;
 import org.junit.Test;
 import org.opencb.biodata.models.core.Region;
 import org.opencb.biodata.models.variant.Variant;
@@ -13,6 +14,7 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.List;
+import java.util.Locale;
 
 import static org.junit.Assert.assertEquals;
 
@@ -22,6 +24,11 @@
 public class VcfManagerTest {
     String filename = "/ibs.vcf";
 
+    @BeforeClass
+    public static void setUp(){
+        Locale.setDefault(new Locale("en", "EN"));
+    }
+
     private Path index(VcfManager vcfManager) throws IOException {
         return vcfManager.createIndex();
     }

diff --git a/pom.xml b/pom.xml
@@ -38,19 +38,20 @@
 
     <properties>
         <!-- All dependency versions must be defined here -->
-        <java-common-libs.version>4.12.0</java-common-libs.version>
-        <jackson.version>2.11.4</jackson.version>
+        <java-common-libs.version>5.2.1-SNAPSHOT</java-common-libs.version>
+
+        <jackson.version>2.14.3</jackson.version>
         <collections.version>4.4</collections.version>
         <avro.version>1.7.7</avro.version>
         <protobuf.version>3.11.4</protobuf.version>
         <grpc.version>1.28.1</grpc.version>
         <htsjdk.version>2.23.0</htsjdk.version>
-        <slf4j.version>1.7.32</slf4j.version>
+        <slf4j.version>1.7.36</slf4j.version>
         <jsr.version>3.0.2</jsr.version>
-        <commons-lang.version>3.12.0</commons-lang.version>
-        <jackson-mapper.version>1.9.13</jackson-mapper.version>
+        <commons-lang.version>3.14.0</commons-lang.version>
+       <!-- <jackson-mapper.version>2.9.9</jackson-mapper.version>-->
         <guava.version>19.0</guava.version>
-        <commons-io.version>2.4</commons-io.version>
+        <commons-io.version>2.12.0</commons-io.version>
         <biojava-core.version>5.0.0</biojava-core.version>
         <ga4gh.version>0.6.0a5</ga4gh.version>
         <SnpEff.version>4.3.1</SnpEff.version>
@@ -229,11 +230,6 @@
                 <artifactId>commons-lang3</artifactId>
                 <version>${commons-lang.version}</version>
             </dependency>
-            <dependency>
-                <groupId>org.codehaus.jackson</groupId>
-                <artifactId>jackson-mapper-asl</artifactId>
-                <version>${jackson-mapper.version}</version>
-            </dependency>
             <dependency>
                 <groupId>org.apache.avro</groupId>
                 <artifactId>avro</artifactId>
@@ -408,6 +404,9 @@
                             <ignoredUnusedDeclaredDependencies>
                                 <ignoredUnusedDeclaredDependency>*</ignoredUnusedDeclaredDependency>
                             </ignoredUnusedDeclaredDependencies>
+                            <ignoredNonTestScopedDependencies>
+                                <ignoredNonTestScopedDependency>*</ignoredNonTestScopedDependency>
+                            </ignoredNonTestScopedDependencies>
                         </configuration>
                     </execution>
                 </executions>