diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
new file mode 100644
index 000000000..eb410c9cb
--- /dev/null
+++ 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
index d460871a6..e9df51ecd 100644
--- 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
index 3fdf0a651..c3332c2e4 100644
--- a/biodata-formats/pom.xml
+++ b/biodata-formats/pom.xml
@@ -88,11 +88,11 @@
org.apache.avro
avro
-
+
junit
junit
diff --git a/biodata-formats/src/test/java/org/opencb/biodata/formats/variant/annotation/io/VepFormatWriterTest.java b/biodata-formats/src/test/java/org/opencb/biodata/formats/variant/annotation/io/VepFormatWriterTest.java
index 7194668c9..9092cbec4 100644
--- a/biodata-formats/src/test/java/org/opencb/biodata/formats/variant/annotation/io/VepFormatWriterTest.java
+++ b/biodata-formats/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
index b95a085ee..7325a3831 100644
--- a/biodata-models/pom.xml
+++ b/biodata-models/pom.xml
@@ -74,10 +74,10 @@
com.fasterxml.jackson.core
jackson-databind
-
+
junit
junit
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
index e7f367e0e..01b4b532a 100644
--- 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/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariant.java b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariant.java
index 67de7d60b..50f4e2d6a 100644
--- a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariant.java
+++ b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariant.java
@@ -115,19 +115,7 @@ public ClinicalVariant(VariantAvro avro, List 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 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
index af190bd80..18fe4c71b 100644
--- 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
index 3edebe40d..e8d90adad 100644
--- a/biodata-tools/pom.xml
+++ b/biodata-tools/pom.xml
@@ -53,6 +53,12 @@
com.databricks
SnpEff
+
+
+ distlib
+ distlib
+
+
org.rocksdb
@@ -90,10 +96,10 @@
org.apache.commons
commons-collections4
-
+
com.google.guava
guava
diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/alignment/stats/AlignmentGlobalStats.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/alignment/stats/AlignmentGlobalStats.java
index a668fd296..128b5ed00 100644
--- a/biodata-tools/src/main/java/org/opencb/biodata/tools/alignment/stats/AlignmentGlobalStats.java
+++ b/biodata-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
index 350f43043..b6eb0b190 100644
--- 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
index b11296015..2cfae49b7 100644
--- 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
index 1a4ac4c3f..f75a2ae9b 100644
--- 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
index 1770c6822..faf0f65b2 100644
--- a/pom.xml
+++ b/pom.xml
@@ -38,19 +38,20 @@
- 4.12.0
- 2.11.4
+ 5.3.0-SNAPSHOT
+
+ 2.14.3
4.4
1.7.7
3.11.4
1.28.1
2.23.0
- 1.7.32
+ 1.7.36
3.0.2
- 3.12.0
- 1.9.13
+ 3.14.0
+
19.0
- 2.4
+ 2.12.0
5.0.0
0.6.0a5
4.3.1
@@ -229,11 +230,6 @@
commons-lang3
${commons-lang.version}
-
- org.codehaus.jackson
- jackson-mapper-asl
- ${jackson-mapper.version}
-
org.apache.avro
avro
@@ -408,6 +404,9 @@
*
+
+ *
+