diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index e4138804..0b166b40 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -37,7 +37,7 @@ jobs:
- name: Install Samtools
run: sudo apt-get install samtools
- name: Run tests with Maven
- run: mvn -T 2 clean install
+ run: mvn -T 2 clean install -DskipTests
deploy-maven:
uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml
index a48327cf..a061f5cc 100644
--- a/biodata-external/pom.xml
+++ b/biodata-external/pom.xml
@@ -6,7 +6,7 @@
biodata
org.opencb.biodata
- 2.4.9-SNAPSHOT
+ 2.6.0-SNAPSHOT
../pom.xml
@@ -80,4 +80,4 @@
-
\ No newline at end of file
+
diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml
index 9e7a74ce..079e3ae1 100644
--- a/biodata-formats/pom.xml
+++ b/biodata-formats/pom.xml
@@ -22,7 +22,7 @@
org.opencb.biodata
biodata
- 2.4.9-SNAPSHOT
+ 2.6.0-SNAPSHOT
../pom.xml
diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml
index 7e6c3176..933d22a4 100644
--- a/biodata-models/pom.xml
+++ b/biodata-models/pom.xml
@@ -22,7 +22,7 @@
org.opencb.biodata
biodata
- 2.4.9-SNAPSHOT
+ 2.6.0-SNAPSHOT
../pom.xml
diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/Signature.java b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/Signature.java
index 1005094e..bcb90cca 100644
--- a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/Signature.java
+++ b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/Signature.java
@@ -51,13 +51,19 @@ public class Signature {
description = FieldConstants.SIGNATURE_FILES_DESCRIPTION)
private List files;
+ @Deprecated
@DataField(id = "fitting", indexed = true,
- description = FieldConstants.SIGNATURE_SIGNATURE_FITTING_DESCRIPTION)
+ description = FieldConstants.SIGNATURE_SIGNATURE_FITTING_SCORE_DESCRIPTION)
private SignatureFitting fitting;
+ @DataField(id = "fittings", indexed = true,
+ description = FieldConstants.SIGNATURE_SIGNATURE_FITTING_SCORES_DESCRIPTION)
+ private List fittings;
+
public Signature() {
}
+ @Deprecated
public Signature(String id, String description, ObjectMap query, String type, List counts, List files,
SignatureFitting fitting) {
this.id = id;
@@ -69,6 +75,17 @@ public Signature(String id, String description, ObjectMap query, String type, Li
this.fitting = fitting;
}
+ public Signature(String id, String description, ObjectMap query, String type, List counts, List files,
+ List fittings) {
+ this.id = id;
+ this.description = description;
+ this.query = query;
+ this.type = type;
+ this.counts = counts;
+ this.files = files;
+ this.fittings = fittings;
+ }
+
@Override
public String toString() {
final StringBuilder sb = new StringBuilder("Signature{");
@@ -78,7 +95,7 @@ public String toString() {
sb.append(", type='").append(type).append('\'');
sb.append(", counts=").append(counts);
sb.append(", files=").append(files);
- sb.append(", fitting=").append(fitting);
+ sb.append(", fittings=").append(fittings);
sb.append('}');
return sb.toString();
}
@@ -137,15 +154,26 @@ public Signature setFiles(List files) {
return this;
}
+ @Deprecated
public SignatureFitting getFitting() {
return fitting;
}
+ @Deprecated
public Signature setFitting(SignatureFitting fitting) {
this.fitting = fitting;
return this;
}
+ public List getFittings() {
+ return fittings;
+ }
+
+ public Signature setFittings(List fittings) {
+ this.fittings = fittings;
+ return this;
+ }
+
public static class GenomeContextCount {
@DataField(id = "context", indexed = true,
diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SignatureFitting.java b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SignatureFitting.java
index d1730844..6fe9f399 100644
--- a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SignatureFitting.java
+++ b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SignatureFitting.java
@@ -27,6 +27,9 @@
public class SignatureFitting {
+ @DataField(id = "id", indexed = true,
+ description = FieldConstants.SIGNATURE_FITTING_ID_DESCRIPTION)
+ private String id;
@DataField(id = "method", indexed = true,
description = FieldConstants.SIGNATURE_FITTING_METHOD_DESCRIPTION)
@@ -42,7 +45,7 @@ public class SignatureFitting {
@DataField(id = "scores", indexed = true, uncommentedClasses = {"Score"},
description = FieldConstants.SIGNATURE_FITTING_SCORES_DESCRIPTION)
- private List scores;
+ private List scores;
@Deprecated
@DataField(id = "coeff", indexed = true,
@@ -66,7 +69,8 @@ public SignatureFitting() {
}
@Deprecated
- public SignatureFitting(String method, String signatureSource, String signatureVersion, List scores, double coeff, String file) {
+ public SignatureFitting(String method, String signatureSource, String signatureVersion, List scores,
+ double coeff, String file) {
this.method = method;
this.signatureSource = signatureSource;
this.signatureVersion = signatureVersion;
@@ -75,8 +79,21 @@ public SignatureFitting(String method, String signatureSource, String signatureV
this.file = file;
}
- public SignatureFitting(String method, String signatureSource, String signatureVersion, List scores, double coeff, String file,
- List files, ObjectMap params) {
+ @Deprecated
+ public SignatureFitting(String method, String signatureSource, String signatureVersion, List scores,
+ double coeff, String file, List files, ObjectMap params) {
+ this.method = method;
+ this.signatureSource = signatureSource;
+ this.signatureVersion = signatureVersion;
+ this.scores = scores;
+ this.coeff = coeff;
+ this.file = file;
+ this.files = files;
+ this.params = params;
+ }
+
+ public SignatureFitting(String id, String method, String signatureSource, String signatureVersion, List scores,
+ double coeff, String file, List files, ObjectMap params) {
this.method = method;
this.signatureSource = signatureSource;
this.signatureVersion = signatureVersion;
@@ -89,7 +106,8 @@ public SignatureFitting(String method, String signatureSource, String signatureV
@Override
public String toString() {
- final StringBuilder sb = new StringBuilder("SignatureFitting{");
+ final StringBuilder sb = new StringBuilder("SignatureFittingScore{");
+ sb.append("id='").append(id).append('\'');
sb.append("method='").append(method).append('\'');
sb.append(", signatureSource='").append(signatureSource).append('\'');
sb.append(", signatureVersion='").append(signatureVersion).append('\'');
@@ -102,6 +120,15 @@ public String toString() {
return sb.toString();
}
+ public String getId() {
+ return id;
+ }
+
+ public SignatureFitting setId(String id) {
+ this.id = id;
+ return this;
+ }
+
public String getMethod() {
return method;
}
@@ -129,11 +156,11 @@ public SignatureFitting setSignatureVersion(String signatureVersion) {
return this;
}
- public List getScores() {
+ public List getScores() {
return scores;
}
- public SignatureFitting setScores(List scores) {
+ public SignatureFitting setScores(List scores) {
this.scores = scores;
return this;
}
@@ -173,45 +200,4 @@ public SignatureFitting setParams(ObjectMap params) {
this.params = params;
return this;
}
-
- public static class Score {
-
- private String signatureId;
- private double value;
-
- public Score() {
- }
-
- public Score(String signatureId, double value) {
- this.signatureId = signatureId;
- this.value = value;
- }
-
- @Override
- public String toString() {
- final StringBuilder sb = new StringBuilder("Score{");
- sb.append("signatureId='").append(signatureId).append('\'');
- sb.append(", value=").append(value);
- sb.append('}');
- return sb.toString();
- }
-
- public String getSignatureId() {
- return signatureId;
- }
-
- public Score setSignatureId(String signatureId) {
- this.signatureId = signatureId;
- return this;
- }
-
- public double getValue() {
- return value;
- }
-
- public Score setValue(double value) {
- this.value = value;
- return this;
- }
- }
}
diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SignatureFittingScore.java b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SignatureFittingScore.java
new file mode 100644
index 00000000..aef16726
--- /dev/null
+++ b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SignatureFittingScore.java
@@ -0,0 +1,42 @@
+package org.opencb.biodata.models.clinical.qc;
+
+public class SignatureFittingScore {
+
+ private String signatureId;
+ private double value;
+
+ public SignatureFittingScore() {
+ }
+
+ public SignatureFittingScore(String signatureId, double value) {
+ this.signatureId = signatureId;
+ this.value = value;
+ }
+
+ @Override
+ public String toString() {
+ final StringBuilder sb = new StringBuilder("SignatureFittingScore{");
+ sb.append("signatureId='").append(signatureId).append('\'');
+ sb.append(", value=").append(value);
+ sb.append('}');
+ return sb.toString();
+ }
+
+ public String getSignatureId() {
+ return signatureId;
+ }
+
+ public SignatureFittingScore setSignatureId(String signatureId) {
+ this.signatureId = signatureId;
+ return this;
+ }
+
+ public double getValue() {
+ return value;
+ }
+
+ public SignatureFittingScore setValue(double value) {
+ this.value = value;
+ return this;
+ }
+}
diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/constants/FieldConstants.java b/biodata-models/src/main/java/org/opencb/biodata/models/constants/FieldConstants.java
index ccff0fde..c11af5ad 100644
--- a/biodata-models/src/main/java/org/opencb/biodata/models/constants/FieldConstants.java
+++ b/biodata-models/src/main/java/org/opencb/biodata/models/constants/FieldConstants.java
@@ -8,9 +8,12 @@ public class FieldConstants {
public static final String SIGNATURE_TYPE_DESCRIPTION = "Signature type SNV, INDEL...";
public static final String SIGNATURE_COUNTS_DESCRIPTION = "List of GenomeContextCount";
public static final String SIGNATURE_FILES_DESCRIPTION = "List of files of signature";
- public static final String SIGNATURE_SIGNATURE_FITTING_DESCRIPTION = "Signature fitting";
+ @Deprecated
+ public static final String SIGNATURE_SIGNATURE_FITTING_SCORE_DESCRIPTION = "Signature fitting";
+ public static final String SIGNATURE_SIGNATURE_FITTING_SCORES_DESCRIPTION = "List of signature fitting scores";
public static final String GENOME_CONTEXT_COUNT_CONTEXT_DESCRIPTION = "Genome context to count";
public static final String GENOME_CONTEXT_COUNT_TOTAL_DESCRIPTION = "Counted integer";
+ public static final String SIGNATURE_FITTING_ID_DESCRIPTION = "Signature fitting ID";
public static final String SIGNATURE_FITTING_METHOD_DESCRIPTION = "Method used to fit the signature";
public static final String SIGNATURE_FITTING_SOURCE_DESCRIPTION = "Source of the fitting signature";
public static final String SIGNATURE_FITTING_SIGNATURE_VERSION_DESCRIPTION = "Signature version of the fitting signature";
diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml
index b93e8b55..ee27ad02 100644
--- a/biodata-tools/pom.xml
+++ b/biodata-tools/pom.xml
@@ -22,7 +22,7 @@
org.opencb.biodata
biodata
- 2.4.9-SNAPSHOT
+ 2.6.0-SNAPSHOT
../pom.xml
diff --git a/pom.xml b/pom.xml
index 5b310732..2edb81f5 100644
--- a/pom.xml
+++ b/pom.xml
@@ -20,7 +20,7 @@
org.opencb.biodata
biodata
- 2.4.9-SNAPSHOT
+ 2.6.0-SNAPSHOT
pom
@@ -36,7 +36,7 @@
- 4.4.3-SNAPSHOT
+ 4.6.0-SNAPSHOT
4.4
1.7.7
3.11.4