From db22e4cb9e9645c8a52906b423e0a90611642834 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Wed, 4 Oct 2023 09:40:51 +0200 Subject: [PATCH 01/29] models: update the function toString of ClinicalVariant according to Variant, #TASK-4158 --- .../clinical/interpretation/ClinicalVariant.java | 12 +----------- 1 file changed, 1 insertion(+), 11 deletions(-) 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 cfc93ab9..5e44e77d 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 @@ -94,17 +94,7 @@ 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(", 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() { From 16c42dd4ba549d66239936b2de5a5e9c9613f290 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 21 Dec 2023 18:54:22 +0100 Subject: [PATCH 02/29] Prepare portPatch --- 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 347042c9..f4125f70 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 2.12.1 + 2.13.0-SNAPSHOT ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index f0b0019e..8d0ec9b8 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.12.1 + 2.13.0-SNAPSHOT ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 81a8b17b..2c832ecf 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.12.1 + 2.13.0-SNAPSHOT ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index e2438f80..22732029 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.12.1 + 2.13.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 97688342..827c82dd 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.12.1 + 2.13.0-SNAPSHOT pom Biodata From df4bcbaef1c3bfe897a1d17319a1f6e5f86af849 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 3 Jan 2024 13:11:04 +0100 Subject: [PATCH 03/29] Updated dependencies --- biodata-formats/pom.xml | 4 ++-- biodata-models/pom.xml | 4 ++-- biodata-tools/pom.xml | 4 ++-- pom.xml | 24 +++++++++++++++--------- 4 files changed, 21 insertions(+), 15 deletions(-) diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index 8d0ec9b8..c838726d 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-models/pom.xml b/biodata-models/pom.xml index 2c832ecf..bd8d7d0e 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-tools/pom.xml b/biodata-tools/pom.xml index 22732029..1e5c2cc3 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -90,10 +90,10 @@ org.apache.commons commons-collections4 - + com.google.guava guava diff --git a/pom.xml b/pom.xml index 28eeb5bd..7bebf639 100644 --- a/pom.xml +++ b/pom.xml @@ -38,19 +38,19 @@ - 4.13.0-SNAPSHOT - 2.11.4 + 4.12.0-SNAPSHOT + 2.14.3 4.4 1.7.7 3.11.4 1.28.1 - 2.23.0 - 1.7.32 + 3.0.5 + 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 +229,11 @@ commons-lang3 ${commons-lang.version} - + org.apache.avro avro @@ -408,6 +408,12 @@ * + + * + + + org.codehaus.jackson:jackson-mapper-asl* + From f1bbf107d667a5169fdc8beab185db0d1c479b66 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 12 Jan 2024 09:42:03 +0100 Subject: [PATCH 04/29] Fix jcl dependency --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 827c82dd..28eeb5bd 100644 --- a/pom.xml +++ b/pom.xml @@ -38,7 +38,7 @@ - 4.12.0 + 4.13.0-SNAPSHOT 2.11.4 4.4 1.7.7 From 874a1386b47518f1636f06bf3e018fb202a3bc4d Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 15 Jan 2024 16:22:37 +0100 Subject: [PATCH 05/29] pom: Restore htsjdk version #TASK-4437 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index ce2980e0..72f8ecca 100644 --- a/pom.xml +++ b/pom.xml @@ -45,7 +45,7 @@ 1.7.7 3.11.4 1.28.1 - 3.0.5 + 2.23.0 1.7.36 3.0.2 3.14.0 From 6aea20b3d17628b7963e3a9e81d7913712921403 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 17 Jan 2024 10:24:31 +0100 Subject: [PATCH 06/29] pom: Delete codehaus imports #TASK-4437 --- .../formats/variant/annotation/io/VepFormatWriterTest.java | 2 +- .../org/opencb/biodata/models/alignment/RegionCoverage.java | 4 ++-- .../org/opencb/biodata/models/clinical/pedigree/Pedigree.java | 2 +- .../biodata/tools/alignment/stats/AlignmentGlobalStats.java | 4 ++-- .../opencb/biodata/tools/alignment/stats/SequenceKmers.java | 4 ++-- .../opencb/biodata/tools/alignment/stats/SequenceStats.java | 4 ++-- pom.xml | 3 --- 7 files changed, 10 insertions(+), 13 deletions(-) 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 7194668c..9092cbec 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/src/main/java/org/opencb/biodata/models/alignment/RegionCoverage.java b/biodata-models/src/main/java/org/opencb/biodata/models/alignment/RegionCoverage.java index e7f367e0..01b4b532 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/pedigree/Pedigree.java b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/pedigree/Pedigree.java index af190bd8..18fe4c71 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/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 a668fd29..128b5ed0 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 350f4304..b6eb0b19 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 b1129601..2cfae49b 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/pom.xml b/pom.xml index 72f8ecca..2d7c87ca 100644 --- a/pom.xml +++ b/pom.xml @@ -412,9 +412,6 @@ * - - org.codehaus.jackson:jackson-mapper-asl* - From 072f8765d83e60af0f1bbc68f7aeb6da30821ace Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 24 Jan 2024 12:42:07 +0100 Subject: [PATCH 07/29] Fix OpenCB repository versions to conform to XetaBase 2.0.0 version #TASK-5444 --- 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 f4125f70..ad285906 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index c838726d..5df2ddfe 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index bd8d7d0e..61629296 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 1e5c2cc3..83fddd53 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 2d7c87ca..c174e6ef 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT pom Biodata From 6ebf69d70b3d776beaa81b50961019169c568724 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 24 Jan 2024 13:08:32 +0100 Subject: [PATCH 08/29] Fix OpenCB repository versions to conform to XetaBase 2.0.0 version #TASK-5444 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index c174e6ef..cbe89ab1 100644 --- a/pom.xml +++ b/pom.xml @@ -38,7 +38,7 @@ - 4.13.0-SNAPSHOT + 5.0.0-SNAPSHOT 2.14.3 4.4 From 46ac2e9fe7ebce9480624c295cf50732c9096617 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 4 Mar 2024 12:06:12 +0100 Subject: [PATCH 09/29] Prepare release 3.0.0 --- 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 ad285906..bf843117 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 3.0.0-SNAPSHOT + 3.0.0 ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index 5df2ddfe..aaf09fd8 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.0.0-SNAPSHOT + 3.0.0 ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 61629296..aa53fa2c 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.0.0-SNAPSHOT + 3.0.0 ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 83fddd53..29615312 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.0.0-SNAPSHOT + 3.0.0 ../pom.xml diff --git a/pom.xml b/pom.xml index cbe89ab1..61383366 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.0.0-SNAPSHOT + 3.0.0 pom Biodata @@ -38,7 +38,7 @@ - 5.0.0-SNAPSHOT + 5.0.0 2.14.3 4.4 From 3dbb25f73a270738d71ac3c2acf93ee1d133bcfb Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 4 Mar 2024 12:06:48 +0100 Subject: [PATCH 10/29] Prepare new development branch release-3.0.x --- 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 bf843117..b4501e0a 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 3.0.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index aaf09fd8..f562bcdf 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.0.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index aa53fa2c..f5dbb058 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.0.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 29615312..2e7806d2 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.0.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 61383366..de858078 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.0.0 + 3.1.0-SNAPSHOT pom Biodata @@ -38,7 +38,7 @@ - 5.0.0 + 5.1.0-SNAPSHOT 2.14.3 4.4 From dcf13125dba0c6e6ead6a806a137ea7603218f5c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 5 Mar 2024 11:58:07 +0100 Subject: [PATCH 11/29] Merge pull request #255 from opencb/TASK-4158 --- 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 b4501e0a..ad285906 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 3.1.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index f562bcdf..5df2ddfe 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.1.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index f5dbb058..61629296 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.1.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 2e7806d2..83fddd53 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.1.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index de858078..cbe89ab1 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.1.0-SNAPSHOT + 3.0.0-SNAPSHOT pom Biodata @@ -38,7 +38,7 @@ - 5.1.0-SNAPSHOT + 5.0.0-SNAPSHOT 2.14.3 4.4 From d25903c4e252eb0496a23a9388e1f045baa5c774 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 7 Mar 2024 16:46:51 +0100 Subject: [PATCH 12/29] Prepare release 3.0.0 --- 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 ad285906..bf843117 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 3.0.0-SNAPSHOT + 3.0.0 ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index 5df2ddfe..aaf09fd8 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.0.0-SNAPSHOT + 3.0.0 ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 61629296..aa53fa2c 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.0.0-SNAPSHOT + 3.0.0 ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 83fddd53..29615312 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.0.0-SNAPSHOT + 3.0.0 ../pom.xml diff --git a/pom.xml b/pom.xml index cbe89ab1..61383366 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.0.0-SNAPSHOT + 3.0.0 pom Biodata @@ -38,7 +38,7 @@ - 5.0.0-SNAPSHOT + 5.0.0 2.14.3 4.4 From 5e3010fc83f15a32bdac9704543544a529de0172 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 7 Mar 2024 16:47:28 +0100 Subject: [PATCH 13/29] Prepare new development branch release-3.0.x --- 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 bf843117..b4501e0a 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 3.0.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index aaf09fd8..f562bcdf 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.0.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index aa53fa2c..f5dbb058 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.0.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 29615312..2e7806d2 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.0.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 61383366..de858078 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.0.0 + 3.1.0-SNAPSHOT pom Biodata @@ -38,7 +38,7 @@ - 5.0.0 + 5.1.0-SNAPSHOT 2.14.3 4.4 From 96c9e00c9ddb646f647bd29dbd74d6f61edd79ee Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 26 Mar 2024 10:24:36 +0100 Subject: [PATCH 14/29] Create branch to test run.sh from opencga-enterprise #TASK-5605 --- pom.xml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/pom.xml b/pom.xml index de858078..c1ed8a30 100644 --- a/pom.xml +++ b/pom.xml @@ -230,11 +230,6 @@ commons-lang3 ${commons-lang.version} - org.apache.avro avro From 6c7db0aee16a577682f56d24cdcd707287a5c012 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 10 Apr 2024 18:15:07 +0200 Subject: [PATCH 15/29] Temporaly fix test --- .../org/opencb/biodata/tools/variant/VcfManagerTest.java | 7 +++++++ 1 file changed, 7 insertions(+) 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 1a4ac4c3..f75a2ae9 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(); } From 146f1b1afd30b8101f87c8183a84e94f4da2fbdb Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 20 May 2024 15:37:02 +0200 Subject: [PATCH 16/29] Prepare release 3.1.0 --- 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 b4501e0a..46b50c19 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index f562bcdf..167e16df 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index f5dbb058..fce0a389 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 2e7806d2..142deb3e 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/pom.xml b/pom.xml index c1ed8a30..8ae4a43a 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.1.0-SNAPSHOT + 3.1.0 pom Biodata @@ -38,7 +38,7 @@ - 5.1.0-SNAPSHOT + 5.1.0 2.14.3 4.4 From 1cfbcb2b5b52e79d5c1e36952c61900ac44cf45f Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 20 May 2024 15:37:35 +0200 Subject: [PATCH 17/29] Prepare new development branch release-3.1.x --- 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 46b50c19..c27bf0eb 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index 167e16df..e84416eb 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index fce0a389..c7d21a5f 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 142deb3e..826ca18f 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 8ae4a43a..e35210e0 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.1.0 + 3.2.0-SNAPSHOT pom Biodata @@ -38,7 +38,7 @@ - 5.1.0 + 5.2.0-SNAPSHOT 2.14.3 4.4 From 7ea67e48dd0d91782573e25b9a490529e431e03c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 30 May 2024 17:47:06 +0200 Subject: [PATCH 18/29] cicd: Update action version to test for compatibility with test and release process #TASK-6264 --- .github/workflows/test-analysis.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index d460871a..e9df51ec 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' From a4eb6dc3ee7760a3289e51dea0e25af96ade962f Mon Sep 17 00:00:00 2001 From: pfurio Date: Mon, 10 Jun 2024 12:26:59 +0200 Subject: [PATCH 19/29] models: deprecate status name, #TASK-5964 --- .../interpretation/Interpretation.java | 64 +++++++++++-------- .../opencb/biodata/models/common/Status.java | 19 +++--- 2 files changed, 48 insertions(+), 35 deletions(-) diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/Interpretation.java b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/Interpretation.java index 99fbff5d..36f9c7e0 100644 --- a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/Interpretation.java +++ b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/Interpretation.java @@ -28,29 +28,29 @@ public class Interpretation { - private String id; - private String uuid; - private String description; - private String clinicalAnalysisId; + protected String id; + protected String uuid; + protected String name; + protected String description; + protected String clinicalAnalysisId; /** * Interpretation algorithm tool used to generate this interpretation. */ - private ClinicalAnalyst analyst; - private InterpretationMethod method; + protected ClinicalAnalyst analyst; + protected InterpretationMethod method; - private List primaryFindings; - private List secondaryFindings; + protected List primaryFindings; + protected List secondaryFindings; - private List comments; + protected List comments; - private InterpretationStats stats; + protected InterpretationStats stats; - private boolean locked; - private Status status; - private String creationDate; - private String modificationDate; - private int version; + protected boolean locked; + protected String creationDate; + protected String modificationDate; + protected int version; /** * Users can add custom information in this field. @@ -61,12 +61,23 @@ public class Interpretation { public Interpretation() { } + @Deprecated public Interpretation(String id, String uuid, String description, String clinicalAnalysisId, ClinicalAnalyst analyst, InterpretationMethod method, List primaryFindings, List secondaryFindings, List comments, InterpretationStats stats, Status status, String creationDate, String modificationDate, boolean locked, int version, Map attributes) { + this(id, uuid, id, description, clinicalAnalysisId, analyst, method, primaryFindings, secondaryFindings, + comments, stats, locked, creationDate, modificationDate, version, attributes); + } + + public Interpretation(String id, String uuid, String name, String description, String clinicalAnalysisId, + ClinicalAnalyst analyst, InterpretationMethod method, List primaryFindings, + List secondaryFindings, List comments, + InterpretationStats stats, boolean locked, String creationDate, String modificationDate, + int version, Map attributes) { this.id = id; this.uuid = uuid; + this.name = name; this.description = description; this.clinicalAnalysisId = clinicalAnalysisId; this.analyst = analyst; @@ -75,10 +86,9 @@ public Interpretation(String id, String uuid, String description, String clinica this.secondaryFindings = secondaryFindings; this.comments = comments; this.stats = stats; - this.status = status; + this.locked = locked; this.creationDate = creationDate; this.modificationDate = modificationDate; - this.locked = locked; this.version = version; this.attributes = attributes; } @@ -88,6 +98,7 @@ public String toString() { final StringBuilder sb = new StringBuilder("Interpretation{"); sb.append("id='").append(id).append('\''); sb.append(", uuid='").append(uuid).append('\''); + sb.append(", name='").append(name).append('\''); sb.append(", description='").append(description).append('\''); sb.append(", clinicalAnalysisId='").append(clinicalAnalysisId).append('\''); sb.append(", analyst=").append(analyst); @@ -96,7 +107,6 @@ public String toString() { sb.append(", secondaryFindings=").append(secondaryFindings); sb.append(", comments=").append(comments); sb.append(", stats=").append(stats); - sb.append(", status=").append(status); sb.append(", creationDate='").append(creationDate).append('\''); sb.append(", modificationDate='").append(modificationDate).append('\''); sb.append(", locked='").append(locked).append('\''); @@ -124,6 +134,15 @@ public Interpretation setUuid(String uuid) { return this; } + public String getName() { + return name; + } + + public Interpretation setName(String name) { + this.name = name; + return this; + } + public String getDescription() { return description; } @@ -196,15 +215,6 @@ public Interpretation setStats(InterpretationStats stats) { return this; } - public Status getStatus() { - return status; - } - - public Interpretation setStatus(Status status) { - this.status = status; - return this; - } - public String getCreationDate() { return creationDate; } diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/common/Status.java b/biodata-models/src/main/java/org/opencb/biodata/models/common/Status.java index 7563ce9e..65ffd889 100644 --- a/biodata-models/src/main/java/org/opencb/biodata/models/common/Status.java +++ b/biodata-models/src/main/java/org/opencb/biodata/models/common/Status.java @@ -19,17 +19,22 @@ public class Status { protected String id; - protected String name; protected String description; protected String date; public Status() { - this("", "", "", ""); + this("", "", ""); } + public Status(String id, String description, String date) { + this.id = id; + this.description = description; + this.date = date; + } + + @Deprecated public Status(String id, String name, String description, String date) { this.id = id; - this.name = name; this.description = description; this.date = date; } @@ -38,7 +43,6 @@ public Status(String id, String name, String description, String date) { public String toString() { final StringBuilder sb = new StringBuilder("Status{"); sb.append("id='").append(id).append('\''); - sb.append(", name='").append(name).append('\''); sb.append(", description='").append(description).append('\''); sb.append(", date='").append(date).append('\''); sb.append('}'); @@ -53,7 +57,6 @@ public boolean equals(Object o) { Status status = (Status) o; if (!id.equals(status.id)) return false; - if (name != null ? !name.equals(status.name) : status.name != null) return false; if (description != null ? !description.equals(status.description) : status.description != null) return false; return date != null ? date.equals(status.date) : status.date == null; } @@ -61,7 +64,6 @@ public boolean equals(Object o) { @Override public int hashCode() { int result = id.hashCode(); - result = 31 * result + (name != null ? name.hashCode() : 0); result = 31 * result + (description != null ? description.hashCode() : 0); result = 31 * result + (date != null ? date.hashCode() : 0); return result; @@ -76,12 +78,13 @@ public Status setId(String id) { return this; } + @Deprecated public String getName() { - return name; + return id; } + @Deprecated public Status setName(String name) { - this.name = name; return this; } From c83345c4a21c4bcaf6612a540ad5092a7dee1592 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 14 Jun 2024 09:30:28 +0200 Subject: [PATCH 20/29] cicd: Pull request approve workflow #TASK-4970 --- .github/workflows/pull-request-approved.yml | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 .github/workflows/pull-request-approved.yml diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml new file mode 100644 index 00000000..eb410c9c --- /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 From 50a2be94aed6556d7cb83eee48f3a4170fd4d20f Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 26 Jun 2024 20:07:24 +0200 Subject: [PATCH 21/29] cicd: Modify pull request approve #TASK-6399 --- .github/workflows/pull-request-approved.yml | 34 +++++++++++++--- .github/workflows/scripts/xetabase-branch.sh | 42 ++++++++++++++++++++ 2 files changed, 70 insertions(+), 6 deletions(-) create mode 100644 .github/workflows/scripts/xetabase-branch.sh diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index eb410c9c..8a60928f 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -1,15 +1,37 @@ name: Pull request approve workflow +run-name: 'Pull request approve workflow ${{ github.event.pull_request.head.ref }} -> ${{ github.event.pull_request.base.ref }} by @${{ github.actor }}' on: pull_request_review: types: [ submitted ] jobs: - build: - uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop + calculate-xetabase-branch: + name: Calculate Xetabase branch + runs-on: ubuntu-22.04 + outputs: + xetabase_branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }} + steps: + - name: Clone java-common-libs + uses: actions/checkout@v4 + with: + fetch-depth: '10' + - id: get_xetabase_branch + name: "Get current branch for Xetabase from target branch" + run: | + chmod +x ./.github/workflows/scripts/xetabase-branch.sh + ls ./.github/workflows/scripts/ + ls ./.github/workflows/ + bash --version + xetabase_branch=$(./.github/workflows/scripts/xetabase-branch.sh ${{ github.event.pull_request.base.ref }}) + echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} + echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT test: - name: "Test analysis" - uses: ./.github/workflows/test-analysis.yml - needs: build - secrets: inherit + name: "Run all tests before merging" + needs: calculate-xetabase-branch + uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@TASK-6399 + with: + branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }} + task: ${{ github.event.pull_request.head.ref }} + secrets: inherit \ No newline at end of file diff --git a/.github/workflows/scripts/xetabase-branch.sh b/.github/workflows/scripts/xetabase-branch.sh new file mode 100644 index 00000000..af17f7f1 --- /dev/null +++ b/.github/workflows/scripts/xetabase-branch.sh @@ -0,0 +1,42 @@ +#!/bin/bash + +# Function to calculate the corresponding branch of Xetabase project +get_xetabase_branch() { + # Input parameter (branch name) + input_branch="$1" + + # Check if the branch name is "develop" in that case return the same branch name + if [[ "$input_branch" == "develop" ]]; then + echo "develop" + return 0 + fi + + # Check if the branch name starts with "release-" and follows the patterns "release-a.b.x" or "release-a.b.c.x" + if [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.x$ ]] || [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.([0-9]+)\.x$ ]]; then + # Extract the MAJOR part of the branch name + MAJOR=${BASH_REMATCH[1]} + # Calculate the XETABASE_MAJOR by subtracting 3 from MAJOR + XETABASE_MAJOR=$((MAJOR - 3)) + # Check if the XETABASE_MAJOR is negative + if (( XETABASE_MAJOR < 0 )); then + echo "Error: 'MAJOR' digit after subtraction results in a negative number." + return 1 + fi + # Construct and echo the new branch name + echo "release-$XETABASE_MAJOR.${input_branch#release-$MAJOR.}" + return 0 + fi + + # If the branch name does not match any of the expected patterns + echo "Error: The branch name is not correct." + return 1 +} + +# Check if the script receives exactly one argument +if [ "$#" -ne 1 ]; then + echo "Usage: $0 " + exit 1 +fi + +# Call the function with the input branch name +get_xetabase_branch "$1" From 10aa6c8019c3a4e876d2477f1c1e67c493c5b2b7 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 1 Jul 2024 17:36:40 +0200 Subject: [PATCH 22/29] cicd: Modify pull request approve #TASK-6399 --- .github/workflows/pull-request-approved.yml | 7 ++----- .../{xetabase-branch.sh => get-xetabase-branch.sh} | 10 +++++++++- 2 files changed, 11 insertions(+), 6 deletions(-) rename .github/workflows/scripts/{xetabase-branch.sh => get-xetabase-branch.sh} (80%) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index 8a60928f..a0d481fa 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -19,11 +19,8 @@ jobs: - id: get_xetabase_branch name: "Get current branch for Xetabase from target branch" run: | - chmod +x ./.github/workflows/scripts/xetabase-branch.sh - ls ./.github/workflows/scripts/ - ls ./.github/workflows/ - bash --version - xetabase_branch=$(./.github/workflows/scripts/xetabase-branch.sh ${{ github.event.pull_request.base.ref }}) + chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh + xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.base.ref }}) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT diff --git a/.github/workflows/scripts/xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh similarity index 80% rename from .github/workflows/scripts/xetabase-branch.sh rename to .github/workflows/scripts/get-xetabase-branch.sh index af17f7f1..e971f990 100644 --- a/.github/workflows/scripts/xetabase-branch.sh +++ b/.github/workflows/scripts/get-xetabase-branch.sh @@ -5,6 +5,14 @@ get_xetabase_branch() { # Input parameter (branch name) input_branch="$1" + # If the branch begins with 'TASK' and exists in the opencga-enterprise repository, I return it + if [[ $input_branch == TASK* ]]; then + if [ "$(git ls-remote https://github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then + echo "$GIT_BRANCH"; + exit 0; + fi + fi + # Check if the branch name is "develop" in that case return the same branch name if [[ "$input_branch" == "develop" ]]; then echo "develop" @@ -16,7 +24,7 @@ get_xetabase_branch() { # Extract the MAJOR part of the branch name MAJOR=${BASH_REMATCH[1]} # Calculate the XETABASE_MAJOR by subtracting 3 from MAJOR - XETABASE_MAJOR=$((MAJOR - 3)) + XETABASE_MAJOR=$((MAJOR - 1)) # Check if the XETABASE_MAJOR is negative if (( XETABASE_MAJOR < 0 )); then echo "Error: 'MAJOR' digit after subtraction results in a negative number." From cf82c5ddca85df40d417bbb39fa817d7dc9a5f9f Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 8 Jul 2024 16:43:25 +0200 Subject: [PATCH 23/29] exclude distlib dependency --- biodata-tools/pom.xml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 826ca18f..d63983d3 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -53,6 +53,12 @@ com.databricks SnpEff + + + distlib + distlib + + org.rocksdb From b3d21ca549639a2c8c5398fbac33d9b637a6e87a Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 8 Jul 2024 16:43:25 +0200 Subject: [PATCH 24/29] pom: exclude distlib dependency #TASK-6481 --- biodata-tools/pom.xml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 826ca18f..d63983d3 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -53,6 +53,12 @@ com.databricks SnpEff + + + distlib + distlib + + org.rocksdb From 6d83ad3706c1d9c62cbd18fa933d77da368161da Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Thu, 25 Apr 2024 15:53:04 +0100 Subject: [PATCH 25/29] tools: Fix normalization of variants wiht ins seq. (cherry-pick from 941cb51e) #TASK-6266 --- .../opencb/biodata/tools/variant/VariantNormalizer.java | 2 ++ .../biodata/tools/variant/VariantNormalizerTest.java | 8 ++++++++ 2 files changed, 10 insertions(+) diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/VariantNormalizer.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/VariantNormalizer.java index 990d61e8..e3bb3d6e 100644 --- a/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/VariantNormalizer.java +++ b/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/VariantNormalizer.java @@ -1394,6 +1394,8 @@ private Variant newVariant(Variant variant, VariantKeyFields keyFields, Structur normalizedVariant.getSv().setCiStartRight(sv.getCiStartRight()); normalizedVariant.getSv().setCiEndLeft(sv.getCiEndLeft()); normalizedVariant.getSv().setCiEndRight(sv.getCiEndRight()); + normalizedVariant.getSv().setLeftSvInsSeq(sv.getLeftSvInsSeq()); + normalizedVariant.getSv().setRightSvInsSeq(sv.getRightSvInsSeq()); // Variant will never have CopyNumber, because the Alternate is normalized from to normalizedVariant.getSv().setCopyNumber(keyFields.getCopyNumber()); diff --git a/biodata-tools/src/test/java/org/opencb/biodata/tools/variant/VariantNormalizerTest.java b/biodata-tools/src/test/java/org/opencb/biodata/tools/variant/VariantNormalizerTest.java index 95265190..a4a62f06 100644 --- a/biodata-tools/src/test/java/org/opencb/biodata/tools/variant/VariantNormalizerTest.java +++ b/biodata-tools/src/test/java/org/opencb/biodata/tools/variant/VariantNormalizerTest.java @@ -784,6 +784,14 @@ public void testNormalizeSvToIndel() throws NonStandardCompliantSampleField { } + @Test + public void testNormalizeWithInsSeq() throws NonStandardCompliantSampleField { + Variant variant = new Variant("1:799984<800001<800022:-:ACCACACCCACACAACACACA...TGTGGTGTGTGTGGTGTG"); + Variant normVar = new VariantNormalizer().normalize(Collections.singletonList(variant), false).get(0); + assertEquals(variant, normVar); + assertEquals(variant.toString(), normVar.toString()); + } + @Test public void testNormalizeBND() throws NonStandardCompliantSampleField { normalizeBnd(newVariant(101, 100, "", ".[9:10["), newVariant(100, 99, "A", "A[chr9:10[")); From 2b43895bc954d33afa2bf48348c08696a10a5cf7 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 17 Jul 2024 10:41:39 +0200 Subject: [PATCH 26/29] Prepare release 3.2.0 --- 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 c27bf0eb..12a6b4f5 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 3.2.0-SNAPSHOT + 3.2.0 ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index e84416eb..bfef3117 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.2.0-SNAPSHOT + 3.2.0 ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index c7d21a5f..887ce92d 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.2.0-SNAPSHOT + 3.2.0 ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index d63983d3..03bfa0e2 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.2.0-SNAPSHOT + 3.2.0 ../pom.xml diff --git a/pom.xml b/pom.xml index e35210e0..c1c07dc3 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.2.0-SNAPSHOT + 3.2.0 pom Biodata @@ -38,7 +38,7 @@ - 5.2.0-SNAPSHOT + 5.2.0 2.14.3 4.4 From 234ebdb3cb48496360151d0ef1995c369176ce58 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 17 Jul 2024 10:42:13 +0200 Subject: [PATCH 27/29] Prepare new development branch release-3.2.x --- 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 12a6b4f5..d6d1acdd 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 3.2.0 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index bfef3117..c3332c2e 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.2.0 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 887ce92d..7325a383 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.2.0 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 03bfa0e2..e8d90ada 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.2.0 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index c1c07dc3..faf0f65b 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.2.0 + 3.3.0-SNAPSHOT pom Biodata @@ -38,7 +38,7 @@ - 5.2.0 + 5.3.0-SNAPSHOT 2.14.3 4.4 From b4c2afb5bd4659e3d90a11446935797d595685bb Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 17 Jul 2024 10:42:33 +0200 Subject: [PATCH 28/29] Prepare new development branch release-3.2.x --- 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 d6d1acdd..bb85a556 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 3.3.0-SNAPSHOT + 3.2.1-SNAPSHOT ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index c3332c2e..238588ca 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.3.0-SNAPSHOT + 3.2.1-SNAPSHOT ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 7325a383..f9cf2628 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.3.0-SNAPSHOT + 3.2.1-SNAPSHOT ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index e8d90ada..c7c32361 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.3.0-SNAPSHOT + 3.2.1-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index faf0f65b..cee50cbd 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 3.3.0-SNAPSHOT + 3.2.1-SNAPSHOT pom Biodata @@ -38,7 +38,7 @@ - 5.3.0-SNAPSHOT + 5.2.1-SNAPSHOT 2.14.3 4.4 From da73175ec437c88a62a572c4960c572272acf306 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 6 Aug 2024 17:35:52 +0200 Subject: [PATCH 29/29] Prepare Port Patch Cellbase 2.12.2 -> 3.2.1 #TASK-6647 --- 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 3a98861e..bb85a556 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 2.12.2 + 3.2.1-SNAPSHOT ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index fe80d521..ce1f093f 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.12.2 + 3.2.1-SNAPSHOT ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 79a1954e..b10170a1 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.12.2 + 3.2.1-SNAPSHOT ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 45d41e63..9ccec982 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.12.2 + 3.2.1-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index a051029f..bc1643f8 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.12.2 + 3.2.1-SNAPSHOT pom Biodata