models: use ClinicalComments

opencb · Aug 31, 2020 · eebbc63 · eebbc63
1 parent bbb9fca
commit eebbc63
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Showing 3 changed files with 11 additions and 111 deletions.
diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/Comment.java b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/Comment.java
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
@@ -19,7 +19,7 @@
 
 package org.opencb.biodata.models.clinical.interpretation;
 
-import org.opencb.biodata.models.clinical.Comment;
+import org.opencb.biodata.models.clinical.ClinicalComment;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.avro.VariantAvro;
 
@@ -32,7 +32,7 @@ public class ClinicalVariant extends Variant {
 
     private double deNovoQualityScore;
     private List<ClinicalVariantEvidence> evidences;
-    private List<Comment> comments;
+    private List<ClinicalComment> comments;
 
     private Status status;
 
@@ -55,8 +55,8 @@ public ClinicalVariant(VariantAvro avro) {
         this(avro, 0.0, new ArrayList<>(), new ArrayList<>(), Status.NOT_REVIEWED, new HashMap<>());
     }
 
-    public ClinicalVariant(VariantAvro avro, double deNovoQualityScore, List<ClinicalVariantEvidence> evidences, List<Comment> comments,
-                           Status status, Map<String, Object> attributes) {
+    public ClinicalVariant(VariantAvro avro, double deNovoQualityScore, List<ClinicalVariantEvidence> evidences,
+                           List<ClinicalComment> comments, Status status, Map<String, Object> attributes) {
         super(avro);
 
         this.deNovoQualityScore = deNovoQualityScore;
@@ -97,11 +97,11 @@ public ClinicalVariant setEvidences(List<ClinicalVariantEvidence> evidences) {
         return this;
     }
 
-    public List<Comment> getComments() {
+    public List<ClinicalComment> getComments() {
         return comments;
     }
 
-    public ClinicalVariant setComments(List<Comment> comments) {
+    public ClinicalVariant setComments(List<ClinicalComment> comments) {
         this.comments = comments;
         return this;
     }

diff --git a/...odels/src/main/java/org/opencb/biodata/models/clinical/interpretation/Interpretation.java b/...odels/src/main/java/org/opencb/biodata/models/clinical/interpretation/Interpretation.java
@@ -19,7 +19,7 @@
 
 package org.opencb.biodata.models.clinical.interpretation;
 
-import org.opencb.biodata.models.clinical.Comment;
+import org.opencb.biodata.models.clinical.ClinicalComment;
 
 import java.util.List;
 import java.util.Map;
@@ -40,7 +40,7 @@ public class Interpretation {
     private List<ClinicalVariant> primaryFindings;
     private List<ClinicalVariant> secondaryFindings;
 
-    private List<Comment> comments;
+    private List<ClinicalComment> comments;
 
     private String status;
     private String creationDate;
@@ -57,7 +57,7 @@ public Interpretation() {
 
     public Interpretation(String id, String uuid, String description, String clinicalAnalysisId, Analyst analyst,
                           List<InterpretationMethod> methods, List<ClinicalVariant> primaryFindings,
-                          List<ClinicalVariant> secondaryFindings, List<Comment> comments, String status, String creationDate,
+                          List<ClinicalVariant> secondaryFindings, List<ClinicalComment> comments, String status, String creationDate,
                           int version, Map<String, Object> attributes) {
         this.id = id;
         this.uuid = uuid;
@@ -166,11 +166,11 @@ public Interpretation setSecondaryFindings(List<ClinicalVariant> secondaryFindin
         return this;
     }
 
-    public List<Comment> getComments() {
+    public List<ClinicalComment> getComments() {
         return comments;
     }
 
-    public Interpretation setComments(List<Comment> comments) {
+    public Interpretation setComments(List<ClinicalComment> comments) {
         this.comments = comments;
         return this;
     }