#255 keeping identifiers, machine tags and occurrence mappings in the…

… replaced entity

registry-integration-tests/src/test/java/org/gbif/registry/ws/it/collections/merge/BaseMergeServiceIT.java

@@ -161,18 +161,19 @@ public void mergeTest() {
     T replaced = crudService.get(toReplace.getKey());
     T replacementUpdated = crudService.get(replacement.getKey());
 
-    assertEquals(0, replaced.getIdentifiers().size());
+    assertEquals(1, replaced.getIdentifiers().size());
     assertNotEquals(toReplace.getModified(), replaced.getModified());
     assertEquals(user, replaced.getModifiedBy());
     assertEquals(user, replacementUpdated.getModifiedBy());
     assertEquals(2, replacementUpdated.getIdentifiers().size());
-    assertEquals(1, replaced.getMachineTags().size());
+    assertEquals(2, replaced.getMachineTags().size());
     assertEquals(1, replacementUpdated.getMachineTags().size());
     assertEquals(2, replacementUpdated.getContacts().size());
     assertEquals(a2, replacementUpdated.getAddress());
     assertEquals(ma1, replacementUpdated.getMailingAddress());
     assertEquals(replacement.getCreatedBy(), replacementUpdated.getCreatedBy());
     assertNull(replacementUpdated.getDeleted());
+    assertEquals(1, replaced.getOccurrenceMappings().size());
     assertEquals(1, replacementUpdated.getOccurrenceMappings().size());
 
     extraAsserts(replaced, replacement, replacementUpdated);

registry-persistence/src/main/java/org/gbif/registry/persistence/mapper/collections/MergeableMapper.java

@@ -23,19 +23,4 @@ public interface MergeableMapper {
 
   void replace(
       @Param("targetEntityKey") UUID targetEntityKey, @Param("replacementKey") UUID replacementKey);
-
-  void moveIdentifier(
-      @Param("sourceEntityKey") UUID sourceEntityKey,
-      @Param("targetEntityKey") UUID targetEntityKey,
-      @Param("identifierKey") int identifierKey);
-
-  void moveMachineTag(
-      @Param("sourceEntityKey") UUID sourceEntityKey,
-      @Param("targetEntityKey") UUID targetEntityKey,
-      @Param("machineTagKey") int machineTagKey);
-
-  void moveOccurrenceMapping(
-      @Param("sourceEntityKey") UUID sourceEntityKey,
-      @Param("targetEntityKey") UUID targetEntityKey,
-      @Param("occurrenceMappingKey") int occurrenceMappingKey);
 }

registry-persistence/src/main/resources/org/gbif/registry/persistence/mapper/collections/CollectionMapper.xml

@@ -572,26 +572,5 @@
     replaced_by = #{replacementKey,jdbcType=OTHER}
     WHERE key = #{targetEntityKey,jdbcType=OTHER} AND deleted IS NULL
   </update>
-
-  <update id="moveIdentifier">
-    UPDATE collection_identifier
-    SET collection_key = #{targetEntityKey,jdbcType=OTHER}
-    WHERE collection_key = #{sourceEntityKey,jdbcType=OTHER}
-    AND identifier_key = #{identifierKey,jdbcType=INTEGER}
-  </update>
-
-  <update id="moveMachineTag">
-    UPDATE collection_machine_tag
-    SET collection_key = #{targetEntityKey,jdbcType=OTHER}
-    WHERE collection_key = #{sourceEntityKey,jdbcType=OTHER}
-    AND machine_tag_key = #{machineTagKey,jdbcType=INTEGER}
-  </update>
-
-  <update id="moveOccurrenceMapping">
-    UPDATE collection_occurrence_mapping
-    SET collection_key = #{targetEntityKey,jdbcType=OTHER}
-    WHERE collection_key = #{sourceEntityKey,jdbcType=OTHER}
-    AND occurrence_mapping_key = #{occurrenceMappingKey,jdbcType=INTEGER}
-  </update>
   <!-- END MERGE -->
 </mapper>

registry-persistence/src/main/resources/org/gbif/registry/persistence/mapper/collections/InstitutionMapper.xml

@@ -551,27 +551,6 @@
     WHERE key = #{targetEntityKey,jdbcType=OTHER} AND deleted IS NULL
   </update>
 
-  <update id="moveIdentifier">
-    UPDATE institution_identifier
-    SET institution_key = #{targetEntityKey,jdbcType=OTHER}
-    WHERE institution_key = #{sourceEntityKey,jdbcType=OTHER}
-    AND identifier_key = #{identifierKey,jdbcType=INTEGER}
-  </update>
-
-  <update id="moveMachineTag">
-    UPDATE institution_machine_tag
-    SET institution_key = #{targetEntityKey,jdbcType=OTHER}
-    WHERE institution_key = #{sourceEntityKey,jdbcType=OTHER}
-    AND machine_tag_key = #{machineTagKey,jdbcType=INTEGER}
-  </update>
-
-  <update id="moveOccurrenceMapping">
-    UPDATE institution_occurrence_mapping
-    SET institution_key = #{targetEntityKey,jdbcType=OTHER}
-    WHERE institution_key = #{sourceEntityKey,jdbcType=OTHER}
-    AND occurrence_mapping_key = #{occurrenceMappingKey,jdbcType=INTEGER}
-  </update>
-
   <update id="convertToCollection">
     UPDATE institution
     SET deleted = now(),

registry-service/src/main/java/org/gbif/registry/service/collections/merge/BaseMergeService.java

@@ -27,9 +27,11 @@
 import org.gbif.api.vocabulary.IdentifierType;
 import org.gbif.registry.persistence.ContactableMapper;
 import org.gbif.registry.persistence.mapper.IdentifierMapper;
+import org.gbif.registry.persistence.mapper.MachineTagMapper;
 import org.gbif.registry.persistence.mapper.collections.BaseMapper;
 import org.gbif.registry.persistence.mapper.collections.MergeableMapper;
 import org.gbif.registry.persistence.mapper.collections.OccurrenceMappeableMapper;
+import org.gbif.registry.persistence.mapper.collections.OccurrenceMappingMapper;
 import org.gbif.registry.persistence.mapper.collections.PersonMapper;
 
 import java.lang.reflect.InvocationTargetException;
@@ -58,20 +60,26 @@ public abstract class BaseMergeService<
   protected final IdentifierMapper identifierMapper;
   protected final OccurrenceMappeableMapper occurrenceMappeableMapper;
   protected final PersonMapper personMapper;
+  private final MachineTagMapper machineTagMapper;
+  private final OccurrenceMappingMapper occurrenceMappingMapper;
 
   protected BaseMergeService(
       BaseMapper<T> baseMapper,
       MergeableMapper mergeableMapper,
       ContactableMapper contactableMapper,
       IdentifierMapper identifierMapper,
       OccurrenceMappeableMapper occurrenceMappeableMapper,
-      PersonMapper personMapper) {
+      PersonMapper personMapper,
+      MachineTagMapper machineTagMapper,
+      OccurrenceMappingMapper occurrenceMappingMapper) {
     this.baseMapper = baseMapper;
     this.mergeableMapper = mergeableMapper;
     this.contactableMapper = contactableMapper;
     this.identifierMapper = identifierMapper;
     this.occurrenceMappeableMapper = occurrenceMappeableMapper;
     this.personMapper = personMapper;
+    this.machineTagMapper = machineTagMapper;
+    this.occurrenceMappingMapper = occurrenceMappingMapper;
   }
 
   @Override
@@ -118,13 +126,20 @@ public void merge(UUID entityToReplaceKey, UUID replacementKey, String user) {
     entityToReplace
         .getIdentifiers()
         .forEach(
-            i -> mergeableMapper.moveIdentifier(entityToReplaceKey, replacementKey, i.getKey()));
+            i -> {
+              identifierMapper.createIdentifier(i);
+              baseMapper.addIdentifier(replacementKey, i.getKey());
+            });
 
     // copy iDigBio machine tags
+    // TODO: what if the replacement has idigbio machine tags already?
     entityToReplace.getMachineTags().stream()
         .filter(mt -> mt.getNamespace().equals("iDigBio.org"))
         .forEach(
-            mt -> mergeableMapper.moveMachineTag(entityToReplaceKey, replacementKey, mt.getKey()));
+            mt -> {
+              machineTagMapper.createMachineTag(mt);
+              baseMapper.addMachineTag(replacementKey, mt.getKey());
+            });
 
     // merge contacts
     Objects.requireNonNull(entityToReplace.getContacts()).stream()
@@ -141,9 +156,10 @@ public void merge(UUID entityToReplaceKey, UUID replacementKey, String user) {
     // update occurrence mappings
     List<OccurrenceMapping> occMappings =
         occurrenceMappeableMapper.listOccurrenceMappings(entityToReplaceKey);
-    occMappings.forEach(
-        om ->
-            mergeableMapper.moveOccurrenceMapping(entityToReplaceKey, replacementKey, om.getKey()));
+    occMappings.forEach(om -> {
+      occurrenceMappingMapper.createOccurrenceMapping(om);
+      occurrenceMappeableMapper.addOccurrenceMapping(replacementKey, om.getKey());
+    });
 
     additionalOperations(entityToReplace, replacement);
   }

registry-service/src/main/java/org/gbif/registry/service/collections/merge/CollectionMergeService.java

@@ -19,7 +19,9 @@
 import org.gbif.api.model.collections.Collection;
 import org.gbif.api.model.collections.Person;
 import org.gbif.registry.persistence.mapper.IdentifierMapper;
+import org.gbif.registry.persistence.mapper.MachineTagMapper;
 import org.gbif.registry.persistence.mapper.collections.CollectionMapper;
+import org.gbif.registry.persistence.mapper.collections.OccurrenceMappingMapper;
 import org.gbif.registry.persistence.mapper.collections.PersonMapper;
 
 import java.util.List;
@@ -35,14 +37,18 @@ public class CollectionMergeService extends BaseMergeService<Collection> {
   protected CollectionMergeService(
       CollectionMapper collectionMapper,
       IdentifierMapper identifierMapper,
-      PersonMapper personMapper) {
+      PersonMapper personMapper,
+      MachineTagMapper machineTagMapper,
+      OccurrenceMappingMapper occurrenceMappingMapper) {
     super(
         collectionMapper,
         collectionMapper,
         collectionMapper,
         identifierMapper,
         collectionMapper,
-        personMapper);
+        personMapper,
+        machineTagMapper,
+        occurrenceMappingMapper);
   }
 
   @Override

registry-service/src/main/java/org/gbif/registry/service/collections/merge/InstitutionMergeService.java

@@ -63,7 +63,9 @@ public InstitutionMergeService(
         institutionMapper,
         identifierMapper,
         institutionMapper,
-        personMapper);
+        personMapper,
+        machineTagMapper,
+        occurrenceMappingMapper);
     this.institutionMapper = institutionMapper;
     this.collectionMapper = collectionMapper;
     this.machineTagMapper = machineTagMapper;
@@ -136,7 +138,6 @@ public UUID convertToCollection(
         .getIdentifiers()
         .forEach(
             i -> {
-              institutionMapper.deleteIdentifier(institutionKey, i.getKey());
               identifierMapper.createIdentifier(i);
               collectionMapper.addIdentifier(newCollection.getKey(), i.getKey());
             });
@@ -146,7 +147,6 @@ public UUID convertToCollection(
         .getMachineTags()
         .forEach(
             mt -> {
-              institutionMapper.deleteMachineTag(institutionKey, mt.getKey());
               machineTagMapper.createMachineTag(mt);
               collectionMapper.addMachineTag(newCollection.getKey(), mt.getKey());
             });
@@ -156,7 +156,6 @@ public UUID convertToCollection(
         .getOccurrenceMappings()
         .forEach(
             om -> {
-              institutionMapper.deleteOccurrenceMapping(institutionKey, om.getKey());
               occurrenceMappingMapper.createOccurrenceMapping(om);
               collectionMapper.addOccurrenceMapping(newCollection.getKey(), om.getKey());
             });