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 01/12] 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 f9db370edcef6e75785d3d8768ea8ffadc866b3a Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 20 Nov 2023 10:34:32 +0100 Subject: [PATCH 02/12] Prepare new development branch release-2.12.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 f4125f70..1a723eb5 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 2.13.0-SNAPSHOT + 2.12.1-SNAPSHOT ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index 8d0ec9b8..6643572a 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.13.0-SNAPSHOT + 2.12.1-SNAPSHOT ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 2c832ecf..bc4ab917 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.13.0-SNAPSHOT + 2.12.1-SNAPSHOT ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 22732029..b2675c3d 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.13.0-SNAPSHOT + 2.12.1-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 28eeb5bd..29f12bdd 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.13.0-SNAPSHOT + 2.12.1-SNAPSHOT pom Biodata @@ -38,7 +38,7 @@ - 4.13.0-SNAPSHOT + 4.12.1-SNAPSHOT 2.11.4 4.4 1.7.7 From f53640731990c72b93db2e549ae3ddac57f31579 Mon Sep 17 00:00:00 2001 From: pfurio Date: Wed, 29 Nov 2023 12:27:34 +0100 Subject: [PATCH 03/12] models: change ClinicalAnalyst models, #TASK-5198 --- .../models/clinical/ClinicalAnalyst.java | 40 +++++---- .../interpretation/ClinicalVariant.java | 41 +++++++++ .../clinical/interpretation/MiniPubmed.java | 90 +++++++++++++++++++ .../models/constants/FieldConstants.java | 4 +- 4 files changed, 154 insertions(+), 21 deletions(-) create mode 100644 biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/MiniPubmed.java diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAnalyst.java b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAnalyst.java index 2f2b5620..8048c118 100644 --- a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAnalyst.java +++ b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAnalyst.java @@ -3,6 +3,8 @@ import org.opencb.biodata.models.constants.FieldConstants; import org.opencb.commons.annotations.DataField; +import java.util.Map; + public class ClinicalAnalyst { @DataField(id = "id", indexed = true, @@ -17,23 +19,23 @@ public class ClinicalAnalyst { description = FieldConstants.CLINICAL_ANALYST_EMAIL_DESCRIPTION) private String email; - @DataField(id = "assignedBy", indexed = true, - description = FieldConstants.CLINICAL_ANALYST_ASSIGNED_BY_DESCRIPTION) - private String assignedBy; + @DataField(id = "role", indexed = true, + description = FieldConstants.CLINICAL_ANALYST_ROLE_DESCRIPTION) + private String role; - @DataField(id = "date", indexed = true, - description = FieldConstants.CLINICAL_ANALYST_DATE_DESCRIPTION) - private String date; + @DataField(id = "attributes", indexed = true, + description = FieldConstants.CLINICAL_ANALYST_ATTRIBUTES_DESCRIPTION) + private Map attributes; public ClinicalAnalyst() { } - public ClinicalAnalyst(String id, String name, String email, String assignedBy, String date) { + public ClinicalAnalyst(String id, String name, String email, String role, Map attributes) { this.id = id; this.name = name; this.email = email; - this.assignedBy = assignedBy; - this.date = date; + this.role = role; + this.attributes = attributes; } @Override @@ -42,8 +44,8 @@ public String toString() { sb.append("id='").append(id).append('\''); sb.append(", name='").append(name).append('\''); sb.append(", email='").append(email).append('\''); - sb.append(", assignedBy='").append(assignedBy).append('\''); - sb.append(", date='").append(date).append('\''); + sb.append(", role='").append(role).append('\''); + sb.append(", attributes=").append(attributes); sb.append('}'); return sb.toString(); } @@ -75,21 +77,21 @@ public ClinicalAnalyst setEmail(String email) { return this; } - public String getAssignedBy() { - return assignedBy; + public String getRole() { + return role; } - public ClinicalAnalyst setAssignedBy(String assignedBy) { - this.assignedBy = assignedBy; + public ClinicalAnalyst setRole(String role) { + this.role = role; return this; } - public String getDate() { - return date; + public Map getAttributes() { + return attributes; } - public ClinicalAnalyst setDate(String date) { - this.date = date; + public ClinicalAnalyst setAttributes(Map attributes) { + this.attributes = attributes; return this; } } 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..67de7d60 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 @@ -34,6 +34,8 @@ public class ClinicalVariant extends Variant { private List evidences; private List comments; private Map filters; + private String recommendation; + private List references; private ClinicalDiscussion discussion; private ClinicalVariantConfidence confidence; private List tags; @@ -76,6 +78,7 @@ public ClinicalVariant(VariantAvro avro, List evidences this.attributes = attributes; } + @Deprecated public ClinicalVariant(VariantAvro avro, List evidences, List comments, Map filters, ClinicalDiscussion discussion, ClinicalVariantConfidence confidence, Status status, List tags, @@ -92,12 +95,32 @@ public ClinicalVariant(VariantAvro avro, List evidences this.attributes = attributes; } + public ClinicalVariant(VariantAvro avro, List evidences, List comments, + Map filters, String recommendation, List references, + ClinicalDiscussion discussion, ClinicalVariantConfidence confidence, Status status, + List tags, Map attributes) { + super(avro); + + this.evidences = evidences; + this.comments = comments; + this.filters = filters; + this.recommendation = recommendation; + this.references = references; + this.discussion = discussion; + this.status = status; + this.tags = tags; + this.confidence = confidence; + this.attributes = attributes; + } + @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(", recommendation='").append(recommendation).append('\''); + sb.append(", references=").append(references); sb.append(", discussion=").append(discussion); sb.append(", confidence=").append(confidence); sb.append(", tags=").append(tags); @@ -134,6 +157,24 @@ public ClinicalVariant setFilters(Map filters) { return this; } + public String getRecommendation() { + return recommendation; + } + + public ClinicalVariant setRecommendation(String recommendation) { + this.recommendation = recommendation; + return this; + } + + public List getReferences() { + return references; + } + + public ClinicalVariant setReferences(List references) { + this.references = references; + return this; + } + public ClinicalDiscussion getDiscussion() { return discussion; } diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/MiniPubmed.java b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/MiniPubmed.java new file mode 100644 index 00000000..c459e498 --- /dev/null +++ b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/interpretation/MiniPubmed.java @@ -0,0 +1,90 @@ +package org.opencb.biodata.models.clinical.interpretation; + +public class MiniPubmed { + + private String id; + private String name; + private String journal; + private String summary; + private String date; + private String url; + + public MiniPubmed() { + } + + public MiniPubmed(String id, String name, String summary, String date, String url, String journal) { + this.id = id; + this.name = name; + this.summary = summary; + this.date = date; + this.url = url; + this.journal = journal; + } + + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("MiniPubmed{"); + sb.append("id='").append(id).append('\''); + sb.append(", name='").append(name).append('\''); + sb.append(", summary='").append(summary).append('\''); + sb.append(", date=").append(date); + sb.append(", url='").append(url).append('\''); + sb.append(", journal='").append(journal).append('\''); + sb.append('}'); + return sb.toString(); + } + + public String getId() { + return id; + } + + public MiniPubmed setId(String id) { + this.id = id; + return this; + } + + public String getName() { + return name; + } + + public MiniPubmed setName(String name) { + this.name = name; + return this; + } + + public String getSummary() { + return summary; + } + + public MiniPubmed setSummary(String summary) { + this.summary = summary; + return this; + } + + public String getDate() { + return date; + } + + public MiniPubmed setDate(String date) { + this.date = date; + return this; + } + + public String getUrl() { + return url; + } + + public MiniPubmed setUrl(String url) { + this.url = url; + return this; + } + + public String getJournal() { + return journal; + } + + public MiniPubmed setJournal(String journal) { + this.journal = journal; + 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 64febe28..4171448f 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 @@ -59,8 +59,8 @@ public class FieldConstants { public static final String RELATEDNESS_REPORT_SCORES_DESCRIPTION = "Relatedness scores for pair of samples"; public static final String RELATEDNESS_REPORT_FILES_DESCRIPTION = "List of files of Relatedness Report"; - public static final String CLINICAL_ANALYST_DATE_DESCRIPTION = "Date of the clinical analyst"; - public static final String CLINICAL_ANALYST_ASSIGNED_BY_DESCRIPTION = "Assigned by field"; + public static final String CLINICAL_ANALYST_ROLE_DESCRIPTION = "Analyst role"; + public static final String CLINICAL_ANALYST_ATTRIBUTES_DESCRIPTION = "Analyst attributes"; public static final String CLINICAL_ANALYST_EMAIL_DESCRIPTION = "Email of the analyst"; public static final String AUDIT_AUTHOR_DESCRIPTION = "Audit author"; From 681f1da6a2c46ab229b65f1d2c78331f3281c1bd Mon Sep 17 00:00:00 2001 From: pfurio Date: Tue, 5 Dec 2023 13:51:46 +0100 Subject: [PATCH 04/12] models: add deprecated fields, #TASK-5373 --- .../models/clinical/ClinicalAnalyst.java | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAnalyst.java b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAnalyst.java index 8048c118..260e901e 100644 --- a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAnalyst.java +++ b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalAnalyst.java @@ -1,5 +1,6 @@ package org.opencb.biodata.models.clinical; +import com.fasterxml.jackson.annotation.JsonIgnore; import org.opencb.biodata.models.constants.FieldConstants; import org.opencb.commons.annotations.DataField; @@ -27,6 +28,14 @@ public class ClinicalAnalyst { description = FieldConstants.CLINICAL_ANALYST_ATTRIBUTES_DESCRIPTION) private Map attributes; + @Deprecated + @DataField(id = "assignedBy") + private String assignedBy; + + @Deprecated + @DataField(id = "date") + private String date; + public ClinicalAnalyst() { } @@ -94,4 +103,26 @@ public ClinicalAnalyst setAttributes(Map attributes) { this.attributes = attributes; return this; } + + @JsonIgnore + @Deprecated + public String getAssignedBy() { + return assignedBy; + } + + @Deprecated + public ClinicalAnalyst setAssignedBy(String assignedBy) { + return this; + } + + @JsonIgnore + @Deprecated + public String getDate() { + return date; + } + + @Deprecated + public ClinicalAnalyst setDate(String date) { + return this; + } } From aaa326005c0a60944955c9ce70bad2ebbac9314b Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 20 Dec 2023 10:50:06 +0100 Subject: [PATCH 05/12] Prepare release 2.12.1 --- 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 1a723eb5..347042c9 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 2.12.1-SNAPSHOT + 2.12.1 ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index 6643572a..f0b0019e 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.12.1-SNAPSHOT + 2.12.1 ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index bc4ab917..81a8b17b 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.12.1-SNAPSHOT + 2.12.1 ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index b2675c3d..e2438f80 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.12.1-SNAPSHOT + 2.12.1 ../pom.xml diff --git a/pom.xml b/pom.xml index 29f12bdd..97688342 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.12.1-SNAPSHOT + 2.12.1 pom Biodata @@ -38,7 +38,7 @@ - 4.12.1-SNAPSHOT + 4.12.0 2.11.4 4.4 1.7.7 From 16c42dd4ba549d66239936b2de5a5e9c9613f290 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 21 Dec 2023 18:54:22 +0100 Subject: [PATCH 06/12] 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 07/12] 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 08/12] 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 09/12] 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 10/12] 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 11/12] 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 12/12] 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