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Merge branch 'develop' into TASK-6647-dev
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juanfeSanahuja committed Aug 6, 2024
2 parents 71d7e85 + b66f3ea commit ddc1135
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Showing 14 changed files with 57 additions and 42 deletions.
15 changes: 15 additions & 0 deletions .github/workflows/pull-request-approved.yml
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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
4 changes: 2 additions & 2 deletions .github/workflows/test-analysis.yml
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Expand Up @@ -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'
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4 changes: 2 additions & 2 deletions biodata-formats/pom.xml
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Expand Up @@ -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>
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Expand Up @@ -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;
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4 changes: 2 additions & 2 deletions biodata-models/pom.xml
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Expand Up @@ -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>
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@@ -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;
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Expand Up @@ -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() {
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Expand Up @@ -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;

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10 changes: 8 additions & 2 deletions biodata-tools/pom.xml
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Expand Up @@ -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>
Expand Down Expand Up @@ -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>
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Expand Up @@ -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;
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Expand Up @@ -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;
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Expand Up @@ -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;
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@@ -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;
Expand All @@ -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;

Expand All @@ -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();
}
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21 changes: 10 additions & 11 deletions pom.xml
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Expand Up @@ -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>5.3.0-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>
Expand Down Expand Up @@ -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>
Expand Down Expand Up @@ -408,6 +404,9 @@
<ignoredUnusedDeclaredDependencies>
<ignoredUnusedDeclaredDependency>*</ignoredUnusedDeclaredDependency>
</ignoredUnusedDeclaredDependencies>
<ignoredNonTestScopedDependencies>
<ignoredNonTestScopedDependency>*</ignoredNonTestScopedDependency>
</ignoredNonTestScopedDependencies>
</configuration>
</execution>
</executions>
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