Merge branch 'main' into uniparc_light_vd_v2

ebi-uniprot · Oct 4, 2024 · e21338c · e21338c
2 parents da162c6 + 244c338
commit e21338c
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Showing 5 changed files with 44 additions and 8 deletions.
diff --git a/core-domain/src/main/java/org/uniprot/core/publication/CommunityAnnotation.java b/core-domain/src/main/java/org/uniprot/core/publication/CommunityAnnotation.java
@@ -1,6 +1,9 @@
 package org.uniprot.core.publication;
 
+import org.uniprot.core.util.Utils;
+
 import java.io.Serializable;
+import java.time.LocalDate;
 
 /**
  * Created 02/12/2020
@@ -15,4 +18,6 @@ public interface CommunityAnnotation extends Serializable {
     String getDisease();
 
     String getComment();
+
+    LocalDate getSubmissionDate();
 }
diff --git a/core-domain/src/main/java/org/uniprot/core/publication/impl/CommunityAnnotationBuilder.java b/core-domain/src/main/java/org/uniprot/core/publication/impl/CommunityAnnotationBuilder.java
@@ -5,6 +5,8 @@
 import org.uniprot.core.Builder;
 import org.uniprot.core.publication.CommunityAnnotation;
 
+import java.time.LocalDate;
+
 /**
  * Created 02/12/2020
  *
@@ -15,6 +17,7 @@ public class CommunityAnnotationBuilder implements Builder<CommunityAnnotation>
     private String function;
     private String disease;
     private String comment;
+    private LocalDate submissionDate;
 
     public CommunityAnnotationBuilder proteinOrGene(String proteinOrGene) {
         this.proteinOrGene = proteinOrGene;
@@ -36,17 +39,28 @@ public CommunityAnnotationBuilder comment(String comment) {
         return this;
     }
 
+    public CommunityAnnotationBuilder submissionDate(String submissionDate) {
+        this.submissionDate = LocalDate.parse(submissionDate);
+        return this;
+    }
+
+    public CommunityAnnotationBuilder submissionDate(LocalDate submissionDate) {
+        this.submissionDate = submissionDate;
+        return this;
+    }
+
     @Nonnull
     @Override
     public CommunityAnnotation build() {
-        return new CommunityAnnotationImpl(proteinOrGene, function, disease, comment);
+        return new CommunityAnnotationImpl(proteinOrGene, function, disease, comment, submissionDate);
     }
 
     public static CommunityAnnotationBuilder from(@Nonnull CommunityAnnotation instance) {
         return new CommunityAnnotationBuilder()
                 .function(instance.getFunction())
                 .disease(instance.getDisease())
                 .comment(instance.getComment())
-                .proteinOrGene(instance.getProteinOrGene());
+                .proteinOrGene(instance.getProteinOrGene())
+                .submissionDate(instance.getSubmissionDate());
     }
 }
diff --git a/core-domain/src/main/java/org/uniprot/core/publication/impl/CommunityAnnotationImpl.java b/core-domain/src/main/java/org/uniprot/core/publication/impl/CommunityAnnotationImpl.java
@@ -1,5 +1,6 @@
 package org.uniprot.core.publication.impl;
 
+import java.time.LocalDate;
 import java.util.Objects;
 
 import org.uniprot.core.publication.CommunityAnnotation;
@@ -10,23 +11,25 @@
  * @author Edd
  */
 public class CommunityAnnotationImpl implements CommunityAnnotation {
-    private static final long serialVersionUID = 6579256221026737892L;
+    private static final long serialVersionUID = 8368111594497409648L;
 
     private final String proteinOrGene;
     private final String function;
     private final String disease;
     private final String comment;
+    private final LocalDate submissionDate;
 
     public CommunityAnnotationImpl() {
-        this(null, null, null, null);
+        this(null, null, null, null, null);
     }
 
     public CommunityAnnotationImpl(
-            String proteinOrGene, String function, String disease, String comment) {
+            String proteinOrGene, String function, String disease, String comment, LocalDate submissionDate) {
         this.proteinOrGene = proteinOrGene;
         this.function = function;
         this.disease = disease;
         this.comment = comment;
+        this.submissionDate = submissionDate;
     }
 
     @Override
@@ -49,6 +52,11 @@ public String getComment() {
         return comment;
     }
 
+    @Override
+    public LocalDate getSubmissionDate() {
+        return submissionDate;
+    }
+
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;
@@ -57,12 +65,13 @@ public boolean equals(Object o) {
         return Objects.equals(proteinOrGene, that.proteinOrGene)
                 && Objects.equals(function, that.function)
                 && Objects.equals(disease, that.disease)
-                && Objects.equals(comment, that.comment);
+                && Objects.equals(comment, that.comment)
+                && Objects.equals(submissionDate, that.submissionDate);
     }
 
     @Override
     public int hashCode() {
-        return Objects.hash(proteinOrGene, function, disease, comment);
+        return Objects.hash(proteinOrGene, function, disease, comment, submissionDate);
     }
 
     @Override
@@ -80,6 +89,9 @@ public String toString() {
                 + ", comment='"
                 + comment
                 + '\''
+                + ", submissionDate='"
+                + submissionDate
+                + '\''
                 + '}';
     }
 }
diff --git a/.../src/main/java/org/uniprot/core/json/parser/publication/MappedPublicationsJsonConfig.java b/.../src/main/java/org/uniprot/core/json/parser/publication/MappedPublicationsJsonConfig.java
@@ -9,6 +9,7 @@
 import org.uniprot.core.citation.impl.*;
 import org.uniprot.core.impl.CrossReferenceImpl;
 import org.uniprot.core.json.parser.JsonConfig;
+import org.uniprot.core.json.parser.deserializer.LocalDateDeserializer;
 import org.uniprot.core.json.parser.serializer.*;
 import org.uniprot.core.json.parser.uniprot.serializer.*;
 import org.uniprot.core.publication.*;
@@ -64,6 +65,8 @@ private ObjectMapper initFullObjectMapper() {
 
         // customise the default mapper
         SimpleModule mod = new SimpleModule();
+        mod.addSerializer(LocalDate.class, new LocalDateSerializer());
+        mod.addDeserializer(LocalDate.class, new LocalDateDeserializer());
         mod.addAbstractTypeMapping(MappedPublications.class, MappedPublicationsImpl.class);
         mod.addAbstractTypeMapping(
                 CommunityMappedReference.class, CommunityMappedReferenceImpl.class);

diff --git a/.../test/java/org/uniprot/core/json/parser/publication/MappedPublicationsJsonConfigTest.java b/.../test/java/org/uniprot/core/json/parser/publication/MappedPublicationsJsonConfigTest.java
@@ -4,6 +4,7 @@
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.not;
 
+import java.time.LocalDate;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
@@ -109,7 +110,8 @@ static CommunityMappedReference getCompleteCommunityMappedReference() {
                 .comment(comment)
                 .proteinOrGene(protOrGene)
                 .function(function)
-                .disease(disease);
+                .disease(disease)
+                .submissionDate(LocalDate.of(2024,9,16));
         CommunityMappedReferenceBuilder builder = new CommunityMappedReferenceBuilder();
         builder.communityAnnotation(communityAnnotationBuilder.build());
         builder.uniProtKBAccession(accession).source(mappedSource);