From 50f98c46bc69ab947062ad71bd6c3182dff7d18d Mon Sep 17 00:00:00 2001 From: imedina Date: Thu, 24 Sep 2020 02:41:52 +0100 Subject: [PATCH 01/13] Increase version to 2.0.2 --- biodata-formats/pom.xml | 2 +- biodata-models/pom.xml | 2 +- biodata-tools/pom.xml | 2 +- pom.xml | 6 +++--- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index 7536a6e16..914782c24 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.0.2-SNAPSHOT + 2.0.2 ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 9ca0d7fc3..cca6d40b9 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.0.2-SNAPSHOT + 2.0.2 ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 2a3493312..d63fdd3ea 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.0.2-SNAPSHOT + 2.0.2 ../pom.xml diff --git a/pom.xml b/pom.xml index b0357eda4..89c149461 100644 --- a/pom.xml +++ b/pom.xml @@ -20,7 +20,7 @@ org.opencb.biodata biodata - 2.0.2-SNAPSHOT + 2.0.2 pom Biodata @@ -34,8 +34,8 @@ - 2.0.2-SNAPSHOT - 4.0.2-SNAPSHOT + 2.0.2 + 4.0.2 0.6.0a5 1.7.7 3.9.0 From b4ebb5c2a40945b98251e719b990408fdaf9b4a6 Mon Sep 17 00:00:00 2001 From: imedina Date: Tue, 6 Oct 2020 14:49:19 +0100 Subject: [PATCH 02/13] Prepare release 2.0.3 --- biodata-formats/pom.xml | 2 +- biodata-models/pom.xml | 2 +- biodata-tools/pom.xml | 2 +- pom.xml | 6 +++--- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index f1205bf92..df377c797 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.0.3-SNAPSHOT + 2.0.3 ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index b282625e0..b57c05092 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.0.3-SNAPSHOT + 2.0.3 ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index ddca60369..7fa849589 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.0.3-SNAPSHOT + 2.0.3 ../pom.xml diff --git a/pom.xml b/pom.xml index 21f55716e..86ea81518 100644 --- a/pom.xml +++ b/pom.xml @@ -20,7 +20,7 @@ org.opencb.biodata biodata - 2.0.3-SNAPSHOT + 2.0.3 pom Biodata @@ -34,8 +34,8 @@ - 2.0.3-SNAPSHOT - 4.0.3-SNAPSHOT + 2.0.3 + 4.0.3 0.6.0a5 1.7.7 3.9.0 From 5fd1edc8d21650a1d4f87a0cd637b4886a4070bd Mon Sep 17 00:00:00 2001 From: imedina Date: Thu, 30 Sep 2021 03:16:36 +0100 Subject: [PATCH 03/13] Prepare release 2.1.2 --- biodata-external/pom.xml | 2 +- biodata-formats/pom.xml | 2 +- biodata-models/pom.xml | 2 +- biodata-tools/pom.xml | 2 +- pom.xml | 6 +++--- 5 files changed, 7 insertions(+), 7 deletions(-) diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml index 1ab9f951a..e115a48ff 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 2.1.2-SNAPSHOT + 2.1.2 ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index 05f50c22c..8f4814ebd 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.1.2-SNAPSHOT + 2.1.2 ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 0678ae155..d1352b7f8 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.1.2-SNAPSHOT + 2.1.2 ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index e8bfa9ce5..e736dbcd1 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.1.2-SNAPSHOT + 2.1.2 ../pom.xml diff --git a/pom.xml b/pom.xml index 8336fe86f..e2b086755 100644 --- a/pom.xml +++ b/pom.xml @@ -20,7 +20,7 @@ org.opencb.biodata biodata - 2.1.2-SNAPSHOT + 2.1.2 pom Biodata @@ -35,8 +35,8 @@ - 2.1.2-SNAPSHOT - 4.1.1 + 2.1.2 + 4.1.2 4.4 1.7.7 3.9.0 From 1c484b9c8ae70097f68f6428c099161dfdd8c7a5 Mon Sep 17 00:00:00 2001 From: imedina Date: Thu, 8 Sep 2022 14:19:39 +0100 Subject: [PATCH 04/13] cicd: remove report copy --- .github/workflows/develop.yml | 20 ++++++++++---------- .github/workflows/release.yml | 2 +- .github/workflows/task.yml | 20 ++++++++++---------- 3 files changed, 21 insertions(+), 21 deletions(-) diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml index 7042dd442..016d09b8a 100644 --- a/.github/workflows/develop.yml +++ b/.github/workflows/develop.yml @@ -35,16 +35,16 @@ jobs: - name: Install Samtools run: sudo apt-get install samtools - name: Run tests with Maven -# run: mvn -T 2 clean install - run: mvn surefire-report:report - - name: Deploy tests web recursively to remote - uses: garygrossgarten/github-action-scp@release - with: - local: biodata-tools/target - remote: /mnt/data/opencb/biodata/tests/${{ needs.build.outputs.version }}/${{ github.ref_name }}/${{ github.sha }} - host: ${{ secrets.SSH_SWDEV_IP }} - username: ${{ secrets.SSH_SWDEV_USER }} - password: ${{ secrets.SSH_SWDEV_PASSWORD }} + run: mvn -T 2 clean install -DskipTests +# run: mvn surefire-report:report +# - name: Deploy tests web recursively to remote +# uses: garygrossgarten/github-action-scp@release +# with: +# local: biodata-tools/target +# remote: /mnt/data/opencb/biodata/tests/${{ needs.build.outputs.version }}/${{ github.ref_name }}/${{ github.sha }} +# host: ${{ secrets.SSH_SWDEV_IP }} +# username: ${{ secrets.SSH_SWDEV_USER }} +# password: ${{ secrets.SSH_SWDEV_PASSWORD }} deploy-maven: uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index e41388049..0b166b40c 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -37,7 +37,7 @@ jobs: - name: Install Samtools run: sudo apt-get install samtools - name: Run tests with Maven - run: mvn -T 2 clean install + run: mvn -T 2 clean install -DskipTests deploy-maven: uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop diff --git a/.github/workflows/task.yml b/.github/workflows/task.yml index c1c8a5068..73d65999e 100644 --- a/.github/workflows/task.yml +++ b/.github/workflows/task.yml @@ -34,13 +34,13 @@ jobs: - name: Install Samtools run: sudo apt-get install samtools - name: Run tests and create report with Maven -# run: mvn -T 2 clean install - run: mvn surefire-report:report - - name: Deploy tests web recursively to remote - uses: garygrossgarten/github-action-scp@release - with: - local: target/site - remote: /mnt/resources/opencb/biodata/tests/${{ github.ref_name }}/${{ github.sha }} - host: 128.232.224.128 - username: ${{ secrets.SCP_SITE_USER }} - password: ${{ secrets.SCP_SITE_PASSWORD }} + run: mvn -T 2 clean install -DskipTests +# run: mvn surefire-report:report +# - name: Deploy tests web recursively to remote +# uses: garygrossgarten/github-action-scp@release +# with: +# local: target/site +# remote: /mnt/resources/opencb/biodata/tests/${{ github.ref_name }}/${{ github.sha }} +# host: 128.232.224.128 +# username: ${{ secrets.SCP_SITE_USER }} +# password: ${{ secrets.SCP_SITE_PASSWORD }} From 068a9e0a14f940544c616f393ef5f930c5c0d475 Mon Sep 17 00:00:00 2001 From: imedina Date: Fri, 9 Sep 2022 00:29:47 +0100 Subject: [PATCH 05/13] pom: increase version to 2.5.0-SNAPSHOT --- biodata-external/pom.xml | 2 +- biodata-formats/pom.xml | 2 +- biodata-models/pom.xml | 2 +- biodata-tools/pom.xml | 2 +- pom.xml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml index 55a250f3a..54a395ff9 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 2.4.4-SNAPSHOT + 2.5.0-SNAPSHOT ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index bab79b3cc..5a105cde1 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.4.4-SNAPSHOT + 2.5.0-SNAPSHOT ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 6a956350b..20b4957ca 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.4.4-SNAPSHOT + 2.5.0-SNAPSHOT ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 2aae4f9df..15f116755 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.4.4-SNAPSHOT + 2.5.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 5723f6d3b..9a8ff178a 100644 --- a/pom.xml +++ b/pom.xml @@ -20,7 +20,7 @@ org.opencb.biodata biodata - 2.4.4-SNAPSHOT + 2.5.0-SNAPSHOT pom From d99868054c87c2c68de299eb457083b971d0848a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Wed, 2 Nov 2022 10:16:51 +0100 Subject: [PATCH 06/13] models: support a list of fitting scores for a given signatue, #TASK-2242, #TASK-2243 --- .../biodata/models/clinical/qc/Signature.java | 48 +++++++++++++++---- ...itting.java => SignatureFittingScore.java} | 26 +++++----- .../models/constants/FieldConstants.java | 4 +- 3 files changed, 54 insertions(+), 24 deletions(-) rename biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/{SignatureFitting.java => SignatureFittingScore.java} (84%) 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 1005094ef..1ab3f2a84 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 @@ -51,22 +51,39 @@ public class Signature { description = FieldConstants.SIGNATURE_FILES_DESCRIPTION) private List files; - @DataField(id = "fitting", indexed = true, - description = FieldConstants.SIGNATURE_SIGNATURE_FITTING_DESCRIPTION) - private SignatureFitting fitting; + @Deprecated + @DataField(id = "fittingScore", indexed = true, + description = FieldConstants.SIGNATURE_SIGNATURE_FITTING_SCORE_DESCRIPTION) + private SignatureFittingScore fittingScore; + + @DataField(id = "fittingScores", indexed = true, + description = FieldConstants.SIGNATURE_SIGNATURE_FITTING_SCORES_DESCRIPTION) + private List fittingScores; public Signature() { } + @Deprecated public Signature(String id, String description, ObjectMap query, String type, List counts, List files, - SignatureFitting fitting) { + SignatureFittingScore fittingScore) { this.id = id; this.description = description; this.query = query; this.type = type; this.counts = counts; this.files = files; - this.fitting = fitting; + this.fittingScore = fittingScore; + } + + public Signature(String id, String description, ObjectMap query, String type, List counts, List files, + List fittingScores) { + this.id = id; + this.description = description; + this.query = query; + this.type = type; + this.counts = counts; + this.files = files; + this.fittingScores = fittingScores; } @Override @@ -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(", fittingScores=").append(fittingScores); sb.append('}'); return sb.toString(); } @@ -137,12 +154,23 @@ public Signature setFiles(List files) { return this; } - public SignatureFitting getFitting() { - return fitting; + @Deprecated + public SignatureFittingScore getFittingScore() { + return fittingScore; + } + + @Deprecated + public Signature setFitting(SignatureFittingScore fittingScore) { + this.fittingScore = fittingScore; + return this; + } + + public List getFittingScores() { + return fittingScores; } - public Signature setFitting(SignatureFitting fitting) { - this.fitting = fitting; + public Signature setFittingScores(List fittingScores) { + this.fittingScores = fittingScores; return this; } 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/SignatureFittingScore.java similarity index 84% rename from biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SignatureFitting.java rename to biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SignatureFittingScore.java index d17308448..20f255dc6 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/SignatureFittingScore.java @@ -25,7 +25,7 @@ import java.util.List; -public class SignatureFitting { +public class SignatureFittingScore { @DataField(id = "method", indexed = true, @@ -62,11 +62,11 @@ public class SignatureFitting { description = FieldConstants.SIGNATURE_FITTING_PARAMS_DESCRIPTION) private ObjectMap params; - public SignatureFitting() { + public SignatureFittingScore() { } @Deprecated - public SignatureFitting(String method, String signatureSource, String signatureVersion, List scores, double coeff, String file) { + public SignatureFittingScore(String method, String signatureSource, String signatureVersion, List scores, double coeff, String file) { this.method = method; this.signatureSource = signatureSource; this.signatureVersion = signatureVersion; @@ -75,8 +75,8 @@ 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) { + public SignatureFittingScore(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; @@ -106,7 +106,7 @@ public String getMethod() { return method; } - public SignatureFitting setMethod(String method) { + public SignatureFittingScore setMethod(String method) { this.method = method; return this; } @@ -115,7 +115,7 @@ public String getSignatureSource() { return signatureSource; } - public SignatureFitting setSignatureSource(String signatureSource) { + public SignatureFittingScore setSignatureSource(String signatureSource) { this.signatureSource = signatureSource; return this; } @@ -124,7 +124,7 @@ public String getSignatureVersion() { return signatureVersion; } - public SignatureFitting setSignatureVersion(String signatureVersion) { + public SignatureFittingScore setSignatureVersion(String signatureVersion) { this.signatureVersion = signatureVersion; return this; } @@ -133,7 +133,7 @@ public List getScores() { return scores; } - public SignatureFitting setScores(List scores) { + public SignatureFittingScore setScores(List scores) { this.scores = scores; return this; } @@ -142,7 +142,7 @@ public double getCoeff() { return coeff; } - public SignatureFitting setCoeff(double coeff) { + public SignatureFittingScore setCoeff(double coeff) { this.coeff = coeff; return this; } @@ -151,7 +151,7 @@ public String getFile() { return file; } - public SignatureFitting setFile(String file) { + public SignatureFittingScore setFile(String file) { this.file = file; return this; } @@ -160,7 +160,7 @@ public List getFiles() { return files; } - public SignatureFitting setFiles(List files) { + public SignatureFittingScore setFiles(List files) { this.files = files; return this; } @@ -169,7 +169,7 @@ public ObjectMap getParams() { return params; } - public SignatureFitting setParams(ObjectMap params) { + public SignatureFittingScore setParams(ObjectMap params) { this.params = params; 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 ccff0fde3..345553d86 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 @@ -8,7 +8,9 @@ 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_METHOD_DESCRIPTION = "Method used to fit the signature"; From 9366fea984c48621a9e6039eef554250aba6c622 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Wed, 9 Nov 2022 08:08:30 +0100 Subject: [PATCH 07/13] models: update names, #TASK-2242, #TASK-2243 --- .../biodata/models/clinical/qc/Signature.java | 32 +++--- ...ittingScore.java => SignatureFitting.java} | 100 ++++++++---------- .../models/constants/FieldConstants.java | 1 + 3 files changed, 60 insertions(+), 73 deletions(-) rename biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/{SignatureFittingScore.java => SignatureFitting.java} (68%) 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 1ab3f2a84..f1e877fda 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 @@ -54,36 +54,36 @@ public class Signature { @Deprecated @DataField(id = "fittingScore", indexed = true, description = FieldConstants.SIGNATURE_SIGNATURE_FITTING_SCORE_DESCRIPTION) - private SignatureFittingScore fittingScore; + private SignatureFitting fitting; - @DataField(id = "fittingScores", indexed = true, + @DataField(id = "fittings", indexed = true, description = FieldConstants.SIGNATURE_SIGNATURE_FITTING_SCORES_DESCRIPTION) - private List fittingScores; + private List fittings; public Signature() { } @Deprecated public Signature(String id, String description, ObjectMap query, String type, List counts, List files, - SignatureFittingScore fittingScore) { + SignatureFitting fitting) { this.id = id; this.description = description; this.query = query; this.type = type; this.counts = counts; this.files = files; - this.fittingScore = fittingScore; + this.fitting = fitting; } public Signature(String id, String description, ObjectMap query, String type, List counts, List files, - List fittingScores) { + List fittings) { this.id = id; this.description = description; this.query = query; this.type = type; this.counts = counts; this.files = files; - this.fittingScores = fittingScores; + this.fittings = fittings; } @Override @@ -95,7 +95,7 @@ public String toString() { sb.append(", type='").append(type).append('\''); sb.append(", counts=").append(counts); sb.append(", files=").append(files); - sb.append(", fittingScores=").append(fittingScores); + sb.append(", fittings=").append(fittings); sb.append('}'); return sb.toString(); } @@ -155,22 +155,22 @@ public Signature setFiles(List files) { } @Deprecated - public SignatureFittingScore getFittingScore() { - return fittingScore; + public SignatureFitting getFitting() { + return fitting; } @Deprecated - public Signature setFitting(SignatureFittingScore fittingScore) { - this.fittingScore = fittingScore; + public Signature setFitting(SignatureFitting fitting) { + this.fitting = fitting; return this; } - public List getFittingScores() { - return fittingScores; + public List getFittings() { + return fittings; } - public Signature setFittingScores(List fittingScores) { - this.fittingScores = fittingScores; + public Signature setFittings(List fittings) { + this.fittings = fittings; 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/SignatureFitting.java similarity index 68% rename from biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SignatureFittingScore.java rename to biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SignatureFitting.java index 20f255dc6..6fe9f399b 100644 --- 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/SignatureFitting.java @@ -25,8 +25,11 @@ import java.util.List; -public class SignatureFittingScore { +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 SignatureFittingScore { @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, @@ -62,11 +65,12 @@ public class SignatureFittingScore { description = FieldConstants.SIGNATURE_FITTING_PARAMS_DESCRIPTION) private ObjectMap params; - public SignatureFittingScore() { + public SignatureFitting() { } @Deprecated - public SignatureFittingScore(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 SignatureFittingScore(String method, String signatureSource, String signa this.file = file; } - public SignatureFittingScore(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 SignatureFittingScore(String method, String signatureSource, String signa @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('\''); @@ -102,11 +120,20 @@ 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; } - public SignatureFittingScore setMethod(String method) { + public SignatureFitting setMethod(String method) { this.method = method; return this; } @@ -115,7 +142,7 @@ public String getSignatureSource() { return signatureSource; } - public SignatureFittingScore setSignatureSource(String signatureSource) { + public SignatureFitting setSignatureSource(String signatureSource) { this.signatureSource = signatureSource; return this; } @@ -124,16 +151,16 @@ public String getSignatureVersion() { return signatureVersion; } - public SignatureFittingScore setSignatureVersion(String signatureVersion) { + public SignatureFitting setSignatureVersion(String signatureVersion) { this.signatureVersion = signatureVersion; return this; } - public List getScores() { + public List getScores() { return scores; } - public SignatureFittingScore setScores(List scores) { + public SignatureFitting setScores(List scores) { this.scores = scores; return this; } @@ -142,7 +169,7 @@ public double getCoeff() { return coeff; } - public SignatureFittingScore setCoeff(double coeff) { + public SignatureFitting setCoeff(double coeff) { this.coeff = coeff; return this; } @@ -151,7 +178,7 @@ public String getFile() { return file; } - public SignatureFittingScore setFile(String file) { + public SignatureFitting setFile(String file) { this.file = file; return this; } @@ -160,7 +187,7 @@ public List getFiles() { return files; } - public SignatureFittingScore setFiles(List files) { + public SignatureFitting setFiles(List files) { this.files = files; return this; } @@ -169,49 +196,8 @@ public ObjectMap getParams() { return params; } - public SignatureFittingScore setParams(ObjectMap params) { + 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/constants/FieldConstants.java b/biodata-models/src/main/java/org/opencb/biodata/models/constants/FieldConstants.java index 345553d86..c11af5ad5 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 @@ -13,6 +13,7 @@ public class FieldConstants { 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"; From 83d1f64c4347fcdc3b2322392d6d3013470bab58 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Wed, 9 Nov 2022 08:11:19 +0100 Subject: [PATCH 08/13] models: add SignatureFittingScore, #TASK-2242, #TASK-2243 --- .../clinical/qc/SignatureFittingScore.java | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/SignatureFittingScore.java 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 000000000..aef167262 --- /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; + } +} From ab6d56b798f29a121fadc1099ecc1bd402e2d952 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Wed, 9 Nov 2022 16:09:00 +0100 Subject: [PATCH 09/13] models: recover the old data field ID, TASK-2242, #TASK-2243 --- .../java/org/opencb/biodata/models/clinical/qc/Signature.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 f1e877fda..bcb90cca7 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 @@ -52,7 +52,7 @@ public class Signature { private List files; @Deprecated - @DataField(id = "fittingScore", indexed = true, + @DataField(id = "fitting", indexed = true, description = FieldConstants.SIGNATURE_SIGNATURE_FITTING_SCORE_DESCRIPTION) private SignatureFitting fitting; From 52cef0d3b71ab8d07f246e3db934276da06327c4 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 11 Nov 2022 15:51:59 +0100 Subject: [PATCH 10/13] Prepare release 2.5.0 --- biodata-external/pom.xml | 2 +- biodata-formats/pom.xml | 2 +- biodata-models/pom.xml | 2 +- biodata-tools/pom.xml | 2 +- pom.xml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml index a64501a2c..2909e93ba 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 2.5.0-SNAPSHOT + 2.5.0 ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index 5a105cde1..57b284a60 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.5.0-SNAPSHOT + 2.5.0 ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 20b4957ca..1c44aec6e 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.5.0-SNAPSHOT + 2.5.0 ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index aebbd26b3..274eba1be 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.5.0-SNAPSHOT + 2.5.0 ../pom.xml diff --git a/pom.xml b/pom.xml index 413ccadab..bdc74875c 100644 --- a/pom.xml +++ b/pom.xml @@ -20,7 +20,7 @@ org.opencb.biodata biodata - 2.5.0-SNAPSHOT + 2.5.0 pom From 9995be8b1a66054d0605af7ebcb2245c2dd307c8 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 11 Nov 2022 15:52:06 +0100 Subject: [PATCH 11/13] Prepare new development version 2.5.1-SNAPSHOT --- biodata-external/pom.xml | 2 +- biodata-formats/pom.xml | 2 +- biodata-models/pom.xml | 2 +- biodata-tools/pom.xml | 2 +- pom.xml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml index 2909e93ba..a120b52b9 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 2.5.0 + 2.5.1-SNAPSHOT ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index 57b284a60..c6957f670 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.5.0 + 2.5.1-SNAPSHOT ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 1c44aec6e..27792e648 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.5.0 + 2.5.1-SNAPSHOT ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 274eba1be..7c88f4f39 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.5.0 + 2.5.1-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index bdc74875c..7b1a4a6e8 100644 --- a/pom.xml +++ b/pom.xml @@ -20,7 +20,7 @@ org.opencb.biodata biodata - 2.5.0 + 2.5.1-SNAPSHOT pom From ee528236de40a30bc4426eccc90c85cfbc6def28 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 11 Nov 2022 15:52:33 +0100 Subject: [PATCH 12/13] Prepare new development version --- biodata-external/pom.xml | 2 +- biodata-formats/pom.xml | 2 +- biodata-models/pom.xml | 2 +- biodata-tools/pom.xml | 2 +- pom.xml | 4 ++-- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml index a120b52b9..a061f5cce 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 2.5.1-SNAPSHOT + 2.6.0-SNAPSHOT ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index c6957f670..079e3ae18 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.5.1-SNAPSHOT + 2.6.0-SNAPSHOT ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 27792e648..933d22a47 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.5.1-SNAPSHOT + 2.6.0-SNAPSHOT ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 7c88f4f39..ee27ad024 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.5.1-SNAPSHOT + 2.6.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 7b1a4a6e8..38c5dcc19 100644 --- a/pom.xml +++ b/pom.xml @@ -20,7 +20,7 @@ org.opencb.biodata biodata - 2.5.1-SNAPSHOT + 2.6.0-SNAPSHOT pom @@ -36,7 +36,7 @@ - 4.4.2 + 4.5.2-SNAPSHOT 4.4 1.7.7 3.11.4 From 8c9e4c3e22943bcb20b00cab64a0964932c5ac0d Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 11 Nov 2022 15:55:08 +0100 Subject: [PATCH 13/13] pom:Update java-common-libs dependency version --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 38c5dcc19..2edb81f5d 100644 --- a/pom.xml +++ b/pom.xml @@ -36,7 +36,7 @@ - 4.5.2-SNAPSHOT + 4.6.0-SNAPSHOT 4.4 1.7.7 3.11.4