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 @@ * + + * +