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 01/25] 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 02/25] 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 03/25] 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 04/25] 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 05/25] 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 06/25] 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 07/25] 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 08/25] 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 09/25] 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 10/25] 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 11/25] 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 12/25] 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 13/25] 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 14/25] 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 15/25] 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 16/25] 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 17/25] 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 18/25] 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 c83345c4a21c4bcaf6612a540ad5092a7dee1592 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 14 Jun 2024 09:30:28 +0200 Subject: [PATCH 19/25] 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 cf82c5ddca85df40d417bbb39fa817d7dc9a5f9f Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 8 Jul 2024 16:43:25 +0200 Subject: [PATCH 20/25] 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 21/25] 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 22/25] 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 23/25] 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 24/25] 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 25/25] 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