TRM-27505: Add reason for entry deletion

ebi-uniprot · Apr 23, 2024 · c4e9010 · c4e9010
1 parent a8324b8
commit c4e9010
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Showing 8 changed files with 125 additions and 4 deletions.
diff --git a/core-domain/src/main/java/org/uniprot/core/uniprotkb/DeletedReason.java b/core-domain/src/main/java/org/uniprot/core/uniprotkb/DeletedReason.java
@@ -0,0 +1,48 @@
+package org.uniprot.core.uniprotkb;
+
+import org.uniprot.core.util.EnumDisplay;
+
+import javax.annotation.Nonnull;
+import java.util.Arrays;
+import java.util.List;
+
+public enum DeletedReason implements EnumDisplay {
+
+    UNKNOWN( "Unknown reason", 0, 4, 5, 7, 9, 12),
+    SOURCE_DELETION( "Sequence source deletion", 1, 6, 8, 11),
+    SWISSPROT_DELETION( "SwissProt deletion", 2),
+    REDUNDANCY( "Sequence redundancy", 3),
+    ENTRY_TYPE_CHANGE( "Entry type change", 10),
+    PROTEOME_REDUNDANCY( "Proteome Redundancy", 13),
+    PROTEOME_EXCLUSION( "Proteome Exclusion", 14),
+    OVERREPRESENTED( "Overrepresented sequence", 15);
+
+    private final List<Integer> ids;
+    private final String description;
+
+    DeletedReason(String description,Integer ... id) {
+        this.ids = Arrays.asList(id);
+        this.description = description;
+    }
+
+    @Nonnull
+    @Override
+    public String getName() {
+        return description;
+    }
+
+    public List<Integer> getIds() {
+        return ids;
+    }
+
+    public static DeletedReason fromId(String id) {
+        try {
+            return Arrays.stream(DeletedReason.values())
+                    .filter(reason -> reason.getIds().contains(Integer.parseInt(id)))
+                    .findFirst()
+                    .orElseThrow();
+        } catch (Exception e) {
+            throw new IllegalArgumentException("The DeletedReason id '" + id + "' doesn't exist.");
+        }
+    }
+}
diff --git a/core-domain/src/main/java/org/uniprot/core/uniprotkb/EntryInactiveReason.java b/core-domain/src/main/java/org/uniprot/core/uniprotkb/EntryInactiveReason.java
@@ -7,4 +7,6 @@ public interface EntryInactiveReason extends Serializable {
     InactiveReasonType getInactiveReasonType();
 
     List<String> getMergeDemergeTos();
+
+    DeletedReason getDeletedReason();
 }
diff --git a/core-domain/src/main/java/org/uniprot/core/uniprotkb/impl/EntryInactiveReasonBuilder.java b/core-domain/src/main/java/org/uniprot/core/uniprotkb/impl/EntryInactiveReasonBuilder.java
@@ -8,6 +8,7 @@
 import javax.annotation.Nonnull;
 
 import org.uniprot.core.Builder;
+import org.uniprot.core.uniprotkb.DeletedReason;
 import org.uniprot.core.uniprotkb.EntryInactiveReason;
 import org.uniprot.core.uniprotkb.InactiveReasonType;
 import org.uniprot.core.util.Utils;
@@ -17,11 +18,18 @@ public class EntryInactiveReasonBuilder implements Builder<EntryInactiveReason>
     private InactiveReasonType inactiveReasonType;
     private List<String> mergeDemergeTos = new ArrayList<>();
 
+    private DeletedReason deletedReason;
+
     public @Nonnull EntryInactiveReasonBuilder type(InactiveReasonType inactiveReasonType) {
         this.inactiveReasonType = inactiveReasonType;
         return this;
     }
 
+    public @Nonnull EntryInactiveReasonBuilder deletedReason(DeletedReason deletedReason) {
+        this.deletedReason = deletedReason;
+        return this;
+    }
+
     public @Nonnull EntryInactiveReasonBuilder mergeDemergeTosSet(List<String> mergeDemergeTo) {
         this.mergeDemergeTos = modifiableList(mergeDemergeTo);
         return this;
@@ -34,12 +42,13 @@ public class EntryInactiveReasonBuilder implements Builder<EntryInactiveReason>
 
     @Override
     public @Nonnull EntryInactiveReason build() {
-        return new EntryInactiveReasonImpl(inactiveReasonType, mergeDemergeTos);
+        return new EntryInactiveReasonImpl(inactiveReasonType, mergeDemergeTos, deletedReason);
     }
 
     public static @Nonnull EntryInactiveReasonBuilder from(@Nonnull EntryInactiveReason instance) {
         return new EntryInactiveReasonBuilder()
                 .type(instance.getInactiveReasonType())
-                .mergeDemergeTosSet(instance.getMergeDemergeTos());
+                .mergeDemergeTosSet(instance.getMergeDemergeTos())
+                .deletedReason(instance.getDeletedReason());
     }
 }
diff --git a/core-domain/src/main/java/org/uniprot/core/uniprotkb/impl/EntryInactiveReasonImpl.java b/core-domain/src/main/java/org/uniprot/core/uniprotkb/impl/EntryInactiveReasonImpl.java
@@ -3,6 +3,7 @@
 import java.util.Collections;
 import java.util.List;
 
+import org.uniprot.core.uniprotkb.DeletedReason;
 import org.uniprot.core.uniprotkb.EntryInactiveReason;
 import org.uniprot.core.uniprotkb.InactiveReasonType;
 import org.uniprot.core.util.Utils;
@@ -11,14 +12,16 @@ public class EntryInactiveReasonImpl implements EntryInactiveReason {
     private static final long serialVersionUID = 1358481260367130982L;
     private InactiveReasonType inactiveReasonType;
     private List<String> mergeDemergeTo;
+    private DeletedReason deletedReason;
 
     EntryInactiveReasonImpl() {
         this.mergeDemergeTo = Collections.emptyList();
     }
 
-    EntryInactiveReasonImpl(InactiveReasonType inactiveReasonType, List<String> mergeDemergeTo) {
+    EntryInactiveReasonImpl(InactiveReasonType inactiveReasonType, List<String> mergeDemergeTo, DeletedReason deletedReason) {
         this.inactiveReasonType = inactiveReasonType;
         this.mergeDemergeTo = Utils.unmodifiableList(mergeDemergeTo);
+        this.deletedReason = deletedReason;
     }
 
     @Override
@@ -31,13 +34,19 @@ public List<String> getMergeDemergeTos() {
         return mergeDemergeTo;
     }
 
+    @Override
+    public DeletedReason getDeletedReason() {
+        return deletedReason;
+    }
+
     @Override
     public int hashCode() {
         final int prime = 31;
         int result = 1;
         result =
                 prime * result + ((inactiveReasonType == null) ? 0 : inactiveReasonType.hashCode());
         result = prime * result + ((mergeDemergeTo == null) ? 0 : mergeDemergeTo.hashCode());
+        result = prime * result + ((deletedReason == null) ? 0 : deletedReason.hashCode());
         return result;
     }
 
@@ -48,6 +57,7 @@ public boolean equals(Object obj) {
         if (getClass() != obj.getClass()) return false;
         EntryInactiveReasonImpl other = (EntryInactiveReasonImpl) obj;
         if (inactiveReasonType != other.inactiveReasonType) return false;
+        if (deletedReason != other.deletedReason) return false;
         return mergeDemergeTo.equals(other.mergeDemergeTo);
     }
 }
diff --git a/core-domain/src/test/java/org/uniprot/core/uniprotkb/DeletedReasonTest.java b/core-domain/src/test/java/org/uniprot/core/uniprotkb/DeletedReasonTest.java
@@ -0,0 +1,36 @@
+package org.uniprot.core.uniprotkb;
+
+import org.junit.jupiter.api.Test;
+
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+class DeletedReasonTest {
+
+    @Test
+    void canGetIds() {
+        assertEquals(List.of(2), DeletedReason.SWISSPROT_DELETION.getIds());
+    }
+
+    @Test
+    void canGetName() {
+        assertEquals("Overrepresented sequence", DeletedReason.OVERREPRESENTED.getName());
+    }
+
+    @Test
+    void canGetFromIdWithValidSingleId() {
+        assertEquals(DeletedReason.PROTEOME_REDUNDANCY, DeletedReason.fromId("13"));
+    }
+
+    @Test
+    void canGetFromIdWithValidMultipleId() {
+        assertEquals(DeletedReason.SOURCE_DELETION, DeletedReason.fromId("8"));
+    }
+
+    @Test
+    void canGetFromIdWithInValidIdThrowsException() {
+        IllegalArgumentException exception = assertThrows(IllegalArgumentException.class, () -> DeletedReason.fromId("99"));
+        assertEquals("The DeletedReason id '99' doesn't exist.", exception.getMessage());
+    }
+}
diff --git a/...-domain/src/test/java/org/uniprot/core/uniprotkb/impl/EntryInactiveReasonBuilderTest.java b/...-domain/src/test/java/org/uniprot/core/uniprotkb/impl/EntryInactiveReasonBuilderTest.java
@@ -3,6 +3,7 @@
 import static org.junit.jupiter.api.Assertions.*;
 
 import org.junit.jupiter.api.Test;
+import org.uniprot.core.uniprotkb.DeletedReason;
 import org.uniprot.core.uniprotkb.EntryInactiveReason;
 
 class EntryInactiveReasonBuilderTest {
@@ -16,6 +17,16 @@ void canBuildWithMergeDemergeTo() {
         assertEquals("merge", reason.getMergeDemergeTos().get(0));
     }
 
+    @Test
+    void canBuildWithDeletedReason() {
+        DeletedReason deletedReason = DeletedReason.SWISSPROT_DELETION;
+        EntryInactiveReason reason = new EntryInactiveReasonBuilder()
+                .deletedReason(deletedReason)
+                .build();
+        assertNotNull(reason.getDeletedReason());
+        assertEquals(deletedReason, reason.getDeletedReason());
+    }
+
     @Test
     void canCreateBuilderFromInstance() {
         EntryInactiveReason reason = new EntryInactiveReasonBuilder().build();

diff --git a/core-domain/src/test/java/org/uniprot/core/uniprotkb/impl/EntryInactiveReasonImplTest.java b/core-domain/src/test/java/org/uniprot/core/uniprotkb/impl/EntryInactiveReasonImplTest.java
@@ -6,6 +6,7 @@
 import java.util.Collections;
 
 import org.junit.jupiter.api.Test;
+import org.uniprot.core.uniprotkb.DeletedReason;
 import org.uniprot.core.uniprotkb.EntryInactiveReason;
 import org.uniprot.core.uniprotkb.InactiveReasonType;
 
@@ -35,12 +36,15 @@ void testEntryInactiveReasonImplMerge() {
 
     @Test
     void testEntryInactiveReasonImplDelete() {
+        DeletedReason deletedReason = DeletedReason.PROTEOME_REDUNDANCY;
         EntryInactiveReason reason =
                 new EntryInactiveReasonBuilder()
                         .type(InactiveReasonType.DELETED)
+                        .deletedReason(deletedReason)
                         .mergeDemergeTosSet(null)
                         .build();
         assertEquals(InactiveReasonType.DELETED, reason.getInactiveReasonType());
+        assertEquals(deletedReason, reason.getDeletedReason());
         assertTrue(reason.getMergeDemergeTos().isEmpty());
     }
 

diff --git a/json-parser/src/test/java/org/uniprot/core/json/parser/uniprot/UniProtKBEntryIT.java b/json-parser/src/test/java/org/uniprot/core/json/parser/uniprot/UniProtKBEntryIT.java
@@ -34,13 +34,14 @@
 /** @author lgonzales */
 public class UniProtKBEntryIT {
 
-    private static Logger logger = LoggerFactory.getLogger(UniProtKBEntryIT.class);
+    private static final Logger logger = LoggerFactory.getLogger(UniProtKBEntryIT.class);
 
     @Test
     void testInactiveUniProtEntryComplete() {
         EntryInactiveReason inactiveReason =
                 new EntryInactiveReasonBuilder()
                         .type(InactiveReasonType.MERGED)
+                        .deletedReason(DeletedReason.SWISSPROT_DELETION)
                         .mergeDemergeTosAdd("merge id")
                         .build();