Merge branch 'release-2.4.x'

opencb · Aug 2, 2022 · 86856ba · 86856ba
2 parents 4f2a97e + df73148
commit 86856ba
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Showing 12 changed files with 80 additions and 18 deletions.
diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <artifactId>biodata</artifactId>
         <groupId>org.opencb.biodata</groupId>
-        <version>2.4.0</version>
+        <version>2.4.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>2.4.0</version>
+        <version>2.4.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>2.4.0</version>
+        <version>2.4.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalDiscussion.java b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/ClinicalDiscussion.java
@@ -0,0 +1,54 @@
+package org.opencb.biodata.models.clinical;
+
+public class ClinicalDiscussion {
+
+    private String author;
+    private String date;
+    private String text;
+
+    public ClinicalDiscussion() {
+    }
+
+    public ClinicalDiscussion(String author, String date, String text) {
+        this.author = author;
+        this.date = date;
+        this.text = text;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("ClinicalDiscussion{");
+        sb.append("author='").append(author).append('\'');
+        sb.append(", date='").append(date).append('\'');
+        sb.append(", text='").append(text).append('\'');
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public String getAuthor() {
+        return author;
+    }
+
+    public ClinicalDiscussion setAuthor(String author) {
+        this.author = author;
+        return this;
+    }
+
+    public String getDate() {
+        return date;
+    }
+
+    public ClinicalDiscussion setDate(String date) {
+        this.date = date;
+        return this;
+    }
+
+    public String getText() {
+        return text;
+    }
+
+    public ClinicalDiscussion setText(String text) {
+        this.text = text;
+        return this;
+    }
+}
diff --git a/...c/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalEvidenceReview.java b/...c/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalEvidenceReview.java
@@ -19,6 +19,7 @@
 
 package org.opencb.biodata.models.clinical.interpretation;
 
+import org.opencb.biodata.models.clinical.ClinicalDiscussion;
 import org.opencb.biodata.models.clinical.ClinicalProperty;
 
 import java.util.ArrayList;
@@ -32,15 +33,15 @@ public class ClinicalEvidenceReview {
     private String tier;
     private List<String> acmg;
     private ClinicalProperty.ClinicalSignificance clinicalSignificance;
-    private String discussion;
+    private ClinicalDiscussion discussion;
 
     public ClinicalEvidenceReview() {
         this.select = false;
         this.acmg = new ArrayList<>();
     }
 
     public ClinicalEvidenceReview(boolean select, String tier, List<String> acmg, ClinicalSignificance clinicalSignificance,
-                                  String discussion) {
+                                  ClinicalDiscussion discussion) {
         this.select = select;
         this.tier = tier;
         this.acmg = acmg;
@@ -96,11 +97,11 @@ public ClinicalEvidenceReview setClinicalSignificance(ClinicalSignificance clini
         return this;
     }
 
-    public String getDiscussion() {
+    public ClinicalDiscussion getDiscussion() {
         return discussion;
     }
 
-    public ClinicalEvidenceReview setDiscussion(String discussion) {
+    public ClinicalEvidenceReview setDiscussion(ClinicalDiscussion discussion) {
         this.discussion = discussion;
         return this;
     }

diff --git a/...dels/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariant.java b/...dels/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariant.java
@@ -20,6 +20,7 @@
 package org.opencb.biodata.models.clinical.interpretation;
 
 import org.opencb.biodata.models.clinical.ClinicalComment;
+import org.opencb.biodata.models.clinical.ClinicalDiscussion;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.avro.VariantAvro;
 
@@ -33,7 +34,7 @@ public class ClinicalVariant extends Variant {
     private List<ClinicalVariantEvidence> evidences;
     private List<ClinicalComment> comments;
     private Map<String, Object> filters;
-    private String discussion;
+    private ClinicalDiscussion discussion;
 
     private Status status;
 
@@ -54,11 +55,13 @@ public ClinicalVariant() {
     }
 
     public ClinicalVariant(VariantAvro avro) {
-        this(avro, new ArrayList<>(), new ArrayList<>(), new HashMap<>(), "", Status.NOT_REVIEWED, new HashMap<>());
+        this(avro, new ArrayList<>(), new ArrayList<>(), new HashMap<>(), new ClinicalDiscussion(), Status.NOT_REVIEWED,
+                new HashMap<>());
     }
 
     public ClinicalVariant(VariantAvro avro, List<ClinicalVariantEvidence> evidences, List<ClinicalComment> comments,
-                           Map<String, Object> filters, String discussion, Status status, Map<String, Object> attributes) {
+                           Map<String, Object> filters, ClinicalDiscussion discussion, Status status,
+                           Map<String, Object> attributes) {
         super(avro);
 
         this.evidences = evidences;
@@ -109,11 +112,11 @@ public ClinicalVariant setFilters(Map<String, Object> filters) {
         return this;
     }
 
-    public String getDiscussion() {
+    public ClinicalDiscussion getDiscussion() {
         return discussion;
     }
 
-    public ClinicalVariant setDiscussion(String discussion) {
+    public ClinicalVariant setDiscussion(ClinicalDiscussion discussion) {
         this.discussion = discussion;
         return this;
     }

diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>2.4.0</version>
+        <version>2.4.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/ClinicalVariantCreator.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/ClinicalVariantCreator.java
@@ -22,6 +22,7 @@
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.collections4.MapUtils;
 import org.apache.commons.lang3.StringUtils;
+import org.opencb.biodata.models.clinical.ClinicalDiscussion;
 import org.opencb.biodata.models.clinical.ClinicalProperty;
 import org.opencb.biodata.models.clinical.ClinicalProperty.ModeOfInheritance;
 import org.opencb.biodata.models.clinical.Disorder;
@@ -132,7 +133,7 @@ public List<ClinicalVariant> createSecondaryFindings(List<Variant> variants) {
             // If we have clinical variant evidences, then we have to create the clinical variant
             if (CollectionUtils.isNotEmpty(clinicalVariantEvidences)) {
                 ClinicalVariant clinicalVariant = new ClinicalVariant(variant.getImpl(), Collections.emptyList(), Collections.emptyList(),
-                        Collections.emptyMap(), "", ClinicalVariant.Status.NOT_REVIEWED, Collections.emptyMap());
+                        Collections.emptyMap(), new ClinicalDiscussion(), ClinicalVariant.Status.NOT_REVIEWED, Collections.emptyMap());
                 clinicalVariant.setEvidences(clinicalVariantEvidences);
 
                 // Add variant to the list

diff --git a/...-tools/src/main/java/org/opencb/biodata/tools/clinical/DefaultClinicalVariantCreator.java b/...-tools/src/main/java/org/opencb/biodata/tools/clinical/DefaultClinicalVariantCreator.java
@@ -21,6 +21,7 @@
 
 import org.apache.commons.collections.CollectionUtils;
 import org.apache.commons.collections.MapUtils;
+import org.opencb.biodata.models.clinical.ClinicalDiscussion;
 import org.opencb.biodata.models.clinical.ClinicalProperty;
 import org.opencb.biodata.models.clinical.ClinicalProperty.ModeOfInheritance;
 import org.opencb.biodata.models.clinical.ClinicalProperty.Penetrance;
@@ -126,7 +127,7 @@ public List<ClinicalVariant> create(List<Variant> variants) {
             // Create a clinical variant only if we have evidences
             if (CollectionUtils.isNotEmpty(clinicalVariantEvidences)) {
                 ClinicalVariant clinicalVariant = new ClinicalVariant(variant.getImpl(), Collections.emptyList(), Collections.emptyList(),
-                        Collections.emptyMap(), "", ClinicalVariant.Status.NOT_REVIEWED, Collections.emptyMap());
+                        Collections.emptyMap(), new ClinicalDiscussion(), ClinicalVariant.Status.NOT_REVIEWED, Collections.emptyMap());
                 clinicalVariant.setEvidences(clinicalVariantEvidences);
 
                 // Add variant to the list

diff --git a/...ata-tools/src/main/java/org/opencb/biodata/tools/clinical/TeamClinicalVariantCreator.java b/...ata-tools/src/main/java/org/opencb/biodata/tools/clinical/TeamClinicalVariantCreator.java
@@ -21,6 +21,7 @@
 
 import org.apache.commons.collections.CollectionUtils;
 import org.apache.commons.collections.MapUtils;
+import org.opencb.biodata.models.clinical.ClinicalDiscussion;
 import org.opencb.biodata.models.clinical.ClinicalProperty.ModeOfInheritance;
 import org.opencb.biodata.models.clinical.ClinicalProperty.Penetrance;
 import org.opencb.biodata.models.clinical.ClinicalProperty.RoleInCancer;
@@ -124,7 +125,7 @@ public List<ClinicalVariant> create(List<Variant> variants) throws Interpretatio
             // If we have clinical variant evidences, then we have to create the clinical variant
             if (CollectionUtils.isNotEmpty(clinicalVariantEvidences)) {
                 ClinicalVariant clinicalVariant = new ClinicalVariant(variant.getImpl(), Collections.emptyList(), Collections.emptyList(),
-                        Collections.emptyMap(), "", ClinicalVariant.Status.NOT_REVIEWED, Collections.emptyMap());
+                        Collections.emptyMap(), new ClinicalDiscussion(), ClinicalVariant.Status.NOT_REVIEWED, Collections.emptyMap());
                 clinicalVariant.setEvidences(clinicalVariantEvidences);
 
                 // Add variant to the list

diff --git a/...-tools/src/main/java/org/opencb/biodata/tools/clinical/TieringClinicalVariantCreator.java b/...-tools/src/main/java/org/opencb/biodata/tools/clinical/TieringClinicalVariantCreator.java
@@ -22,6 +22,7 @@
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.collections4.MapUtils;
 import org.apache.commons.lang3.StringUtils;
+import org.opencb.biodata.models.clinical.ClinicalDiscussion;
 import org.opencb.biodata.models.clinical.ClinicalProperty.ModeOfInheritance;
 import org.opencb.biodata.models.clinical.ClinicalProperty.Penetrance;
 import org.opencb.biodata.models.clinical.interpretation.ClinicalVariant;
@@ -270,7 +271,7 @@ public List<ClinicalVariant> create(List<Variant> variants, Map<String, List<Mod
             if (CollectionUtils.isNotEmpty(clinicalVariantEvidences)) {
                 logger.debug(variant.toStringSimple() + ": reported, num. evidences: " + clinicalVariantEvidences.size());
                 ClinicalVariant clinicalVariant = new ClinicalVariant(variant.getImpl(), Collections.emptyList(), Collections.emptyList(),
-                        Collections.emptyMap(), "", ClinicalVariant.Status.NOT_REVIEWED, Collections.emptyMap());
+                        Collections.emptyMap(), new ClinicalDiscussion(), ClinicalVariant.Status.NOT_REVIEWED, Collections.emptyMap());
                 clinicalVariant.setEvidences(clinicalVariantEvidences);
 
                 // Add variant to the list

diff --git a/pom.xml b/pom.xml
@@ -20,7 +20,7 @@
 
     <groupId>org.opencb.biodata</groupId>
     <artifactId>biodata</artifactId>
-    <version>2.4.0</version>
+    <version>2.4.1</version>
     <packaging>pom</packaging>
 
     <name>Biodata</name>