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imedinaimedina
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Merge branch 'release-2.3.x'
2 parents 55773a3 + 5ca25ee commit 22aac92

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13 files changed

+289
-45
lines changed

13 files changed

+289
-45
lines changed

‎.github/workflows/develop.yml‎

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@@ -26,16 +26,12 @@ jobs:
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- uses: actions/checkout@v2
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with:
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fetch-depth: '10'
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- name: Set up JDK 1.8
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- name: Set up JDK 8
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uses: actions/setup-java@v2
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with:
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distribution: 'zulu'
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distribution: 'temurin'
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java-version: '8'
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- name: Setup Maven Action
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uses: s4u/[email protected]
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with:
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java-version: 8
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maven-version: 3.6.3
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cache: 'maven'
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- name: Cache Maven packages
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uses: actions/cache@v2
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with:

‎.github/workflows/release.yml‎

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@@ -28,16 +28,12 @@ jobs:
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- uses: actions/checkout@v2
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with:
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fetch-depth: '10'
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- name: Set up JDK 1.8
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- name: Set up JDK 8
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uses: actions/setup-java@v2
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with:
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distribution: 'zulu'
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distribution: 'temurin'
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java-version: '8'
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- name: Setup Maven Action
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uses: s4u/[email protected]
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with:
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java-version: 8
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maven-version: 3.6.3
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cache: 'maven'
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- name: Cache Maven packages
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uses: actions/cache@v2
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with:

‎.github/workflows/task.yml‎

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name: Push biodata develop
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on:
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push:
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branches:
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- TASK-*
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jobs:
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build:
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uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
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sonar:
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uses: opencb/java-common-libs/.github/workflows/sonar-analysis-workflow.yml@develop
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needs: build
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with:
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sonarProjectKey: opencb_biodata
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secrets:
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SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
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test:
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name: Test biodata
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runs-on: ubuntu-20.04
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needs: build
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: '10'
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- name: Set up JDK 8
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uses: actions/setup-java@v2
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with:
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distribution: 'temurin'
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java-version: '8'
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cache: 'maven'
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- name: Cache Maven packages
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uses: actions/cache@v2
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with:
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path: ~/.m2/repository
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key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
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restore-keys: ${{ runner.os }}-maven
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- name: Install Samtools
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run: sudo apt-get install samtools
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- name: Run tests with Maven
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run: mvn -T 2 clean install

‎biodata-external/pom.xml‎

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@@ -6,7 +6,7 @@
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<parent>
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<artifactId>biodata</artifactId>
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<groupId>org.opencb.biodata</groupId>
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<version>2.2.2</version>
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<version>2.3.0</version>
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<relativePath>../pom.xml</relativePath>
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</parent>
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‎biodata-formats/pom.xml‎

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@@ -22,7 +22,7 @@
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<parent>
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<groupId>org.opencb.biodata</groupId>
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<artifactId>biodata</artifactId>
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<version>2.2.2</version>
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<version>2.3.0</version>
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<relativePath>../pom.xml</relativePath>
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</parent>
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‎biodata-models/pom.xml‎

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@@ -22,7 +22,7 @@
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<parent>
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<groupId>org.opencb.biodata</groupId>
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<artifactId>biodata</artifactId>
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<version>2.2.2</version>
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<version>2.3.0</version>
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<relativePath>../pom.xml</relativePath>
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</parent>
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‎biodata-models/src/main/avro/variantAnnotation.avdl‎

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@@ -110,6 +110,10 @@ protocol VariantAnnotations {
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union { null, float } percentage;
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}
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record SpliceScores {
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string source;
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map<double> scores;
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}
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record ConsequenceType {
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union { null, string } geneId;
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union { null, string } geneName;
@@ -127,6 +131,8 @@ protocol VariantAnnotations {
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union { null, string } source;
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union { null, array<ExonOverlap> } exonOverlap;
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union { null, array<SpliceScores> } spliceScores;
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// DEPRECATED: replaced by transcriptFlags
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//@javaAnnotation("Deprecated")
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//union { null, array<string> } transcriptAnnotationFlags;

‎biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariant.java‎

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@@ -45,7 +45,8 @@ public enum Status {
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REVIEW_REQUESTED,
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REVIEWED,
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DISCARDED,
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REPORTED
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REPORTED,
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ARTIFACT
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}
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public ClinicalVariant() {

‎biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/Interpretation.java‎

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@@ -46,6 +46,7 @@ public class Interpretation {
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private InterpretationStats stats;
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private boolean locked;
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private Status status;
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private String creationDate;
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private String modificationDate;
@@ -63,7 +64,7 @@ public Interpretation() {
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public Interpretation(String id, String uuid, String description, String clinicalAnalysisId, ClinicalAnalyst analyst,
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InterpretationMethod method, List<ClinicalVariant> primaryFindings, List<ClinicalVariant> secondaryFindings,
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List<ClinicalComment> comments, InterpretationStats stats, Status status, String creationDate,
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String modificationDate, int version, Map<String, Object> attributes) {
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String modificationDate, boolean locked, int version, Map<String, Object> attributes) {
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this.id = id;
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this.uuid = uuid;
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this.description = description;
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this.status = status;
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this.creationDate = creationDate;
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this.modificationDate = modificationDate;
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this.locked = locked;
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this.version = version;
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this.attributes = attributes;
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}
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sb.append(", status=").append(status);
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sb.append(", creationDate='").append(creationDate).append('\'');
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sb.append(", modificationDate='").append(modificationDate).append('\'');
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sb.append(", locked='").append(locked).append('\'');
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sb.append(", version=").append(version);
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sb.append(", attributes=").append(attributes);
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sb.append('}');
@@ -220,6 +223,15 @@ public Interpretation setModificationDate(String modificationDate) {
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return this;
221224
}
222225

226+
public boolean isLocked() {
227+
return locked;
228+
}
229+
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public Interpretation setLocked(boolean locked) {
231+
this.locked = locked;
232+
return this;
233+
}
234+
223235
public int getVersion() {
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return version;
225237
}

‎biodata-models/src/main/java/org/opencb/biodata/models/core/SpliceScore.java‎

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package org.opencb.biodata.models.core;
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import java.util.ArrayList;
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import java.util.List;
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public class SpliceScore {
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private String chromosome;
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private int position;
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private String refAllele;
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private String geneId;
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private String geneName;
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private String transcriptId;
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private String exonId;
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private int exonNumber;
15+
private String source;
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private List<SpliceScoreAlternate> alternates;
17+
18+
public SpliceScore() {
19+
this.alternates = new ArrayList<>();
20+
}
21+
22+
public SpliceScore(String chromosome, int position, String refAllele, String geneId, String geneName, String transcriptId,
23+
String exonId, int exonNumber, String source, List<SpliceScoreAlternate> alternates) {
24+
this.chromosome = chromosome;
25+
this.position = position;
26+
this.refAllele = refAllele;
27+
this.geneId = geneId;
28+
this.geneName = geneName;
29+
this.transcriptId = transcriptId;
30+
this.exonId = exonId;
31+
this.exonNumber = exonNumber;
32+
this.source = source;
33+
this.alternates = alternates;
34+
}
35+
36+
@Override
37+
public String toString() {
38+
final StringBuilder sb = new StringBuilder("SpliceScore{");
39+
sb.append("chromosome='").append(chromosome).append('\'');
40+
sb.append(", position=").append(position);
41+
sb.append(", refAllele='").append(refAllele).append('\'');
42+
sb.append(", geneId='").append(geneId).append('\'');
43+
sb.append(", geneName='").append(geneName).append('\'');
44+
sb.append(", transcriptId='").append(transcriptId).append('\'');
45+
sb.append(", exonId='").append(exonId).append('\'');
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sb.append(", exonNumber=").append(exonNumber);
47+
sb.append(", source='").append(source).append('\'');
48+
sb.append(", alternates=").append(alternates);
49+
sb.append('}');
50+
return sb.toString();
51+
}
52+
53+
public String getChromosome() {
54+
return chromosome;
55+
}
56+
57+
public SpliceScore setChromosome(String chromosome) {
58+
this.chromosome = chromosome;
59+
return this;
60+
}
61+
62+
public int getPosition() {
63+
return position;
64+
}
65+
66+
public SpliceScore setPosition(int position) {
67+
this.position = position;
68+
return this;
69+
}
70+
71+
public String getRefAllele() {
72+
return refAllele;
73+
}
74+
75+
public SpliceScore setRefAllele(String refAllele) {
76+
this.refAllele = refAllele;
77+
return this;
78+
}
79+
80+
public String getGeneId() {
81+
return geneId;
82+
}
83+
84+
public SpliceScore setGeneId(String geneId) {
85+
this.geneId = geneId;
86+
return this;
87+
}
88+
89+
public String getGeneName() {
90+
return geneName;
91+
}
92+
93+
public SpliceScore setGeneName(String geneName) {
94+
this.geneName = geneName;
95+
return this;
96+
}
97+
98+
public String getTranscriptId() {
99+
return transcriptId;
100+
}
101+
102+
public SpliceScore setTranscriptId(String transcriptId) {
103+
this.transcriptId = transcriptId;
104+
return this;
105+
}
106+
107+
public String getExonId() {
108+
return exonId;
109+
}
110+
111+
public SpliceScore setExonId(String exonId) {
112+
this.exonId = exonId;
113+
return this;
114+
}
115+
116+
public int getExonNumber() {
117+
return exonNumber;
118+
}
119+
120+
public SpliceScore setExonNumber(int exonNumber) {
121+
this.exonNumber = exonNumber;
122+
return this;
123+
}
124+
125+
public String getSource() {
126+
return source;
127+
}
128+
129+
public SpliceScore setSource(String source) {
130+
this.source = source;
131+
return this;
132+
}
133+
134+
public List<SpliceScoreAlternate> getAlternates() {
135+
return alternates;
136+
}
137+
138+
public SpliceScore setAlternates(List<SpliceScoreAlternate> alternates) {
139+
this.alternates = alternates;
140+
return this;
141+
}
142+
}

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