Merge pull request #71 from nitin-ebi/variant-history

EVA-2623: Variant history common changes
EBIvariation · Nov 23, 2021 · 907bf64 · 907bf64
2 parents 5aaa169 + 0d7dab6
commit 907bf64
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Showing 10 changed files with 96 additions and 15 deletions.
diff --git a/...mmons-core/src/main/java/uk/ac/ebi/ampt2d/commons/accession/core/models/HistoryEvent.java b/...mmons-core/src/main/java/uk/ac/ebi/ampt2d/commons/accession/core/models/HistoryEvent.java
@@ -17,7 +17,6 @@
  */
 package uk.ac.ebi.ampt2d.commons.accession.core.models;
 
-import sun.reflect.generics.reflectiveObjects.NotImplementedException;
 import uk.ac.ebi.ampt2d.commons.accession.persistence.models.IAccessionedObject;
 
 import java.time.LocalDateTime;
@@ -33,16 +32,22 @@ public class HistoryEvent<MODEL, ACCESSION> implements IEvent<MODEL, ACCESSION>
 
     private ACCESSION mergedInto;
 
+    private ACCESSION splitInto;
+
     private LocalDateTime localDateTime;
 
     private MODEL data;
 
-    public HistoryEvent(EventType eventType, ACCESSION accession, Integer version, ACCESSION mergedInto,
+    public HistoryEvent(EventType eventType, ACCESSION accession, Integer version, ACCESSION destinationAccession,
                         LocalDateTime localDateTime, MODEL data) {
         this.eventType = eventType;
         this.accession = accession;
         this.version = version;
-        this.mergedInto = mergedInto;
+        if(this.eventType == EventType.MERGED){
+            this.mergedInto = destinationAccession;
+        }else if(this.eventType == EventType.RS_SPLIT){
+            this.splitInto = destinationAccession;
+        }
         this.localDateTime = localDateTime;
         this.data = data;
     }
@@ -61,13 +66,14 @@ public Integer getVersion() {
         return version;
     }
 
+    @Override
     public ACCESSION getMergedInto() {
         return mergedInto;
     }
 
     @Override
     public ACCESSION getSplitInto() {
-        throw new NotImplementedException();
+        return splitInto;
     }
 
     @Override
@@ -113,6 +119,11 @@ public static <MODEL, ACCESSION> HistoryEvent<MODEL, ACCESSION> merged(ACCESSION
         return new HistoryEvent<>(EventType.MERGED, accession, null, mergedInto, localDateTime, null);
     }
 
+    public static <MODEL, ACCESSION> HistoryEvent<MODEL, ACCESSION> split(ACCESSION accession, ACCESSION splitInto,
+                                                                          LocalDateTime localDateTime) {
+        return new HistoryEvent<>(EventType.RS_SPLIT, accession, null, splitInto, localDateTime, null);
+    }
+
     public static <MODEL, ACCESSION> HistoryEvent<MODEL, ACCESSION> updated(ACCESSION accession, int version,
                                                                             MODEL data, LocalDateTime localDateTime) {
         return new HistoryEvent<>(EventType.UPDATED, accession, version, null, localDateTime, data);

diff --git a/...ion-commons-core/src/main/java/uk/ac/ebi/ampt2d/commons/accession/core/models/IEvent.java b/...ion-commons-core/src/main/java/uk/ac/ebi/ampt2d/commons/accession/core/models/IEvent.java
@@ -46,6 +46,13 @@ public interface IEvent<MODEL, ACCESSION> {
      */
     ACCESSION getSplitInto();
 
+    /**
+     * @return Accession of the target object resulted because of the event (merged, rs-split etc)
+     */
+    default ACCESSION getDestinationAccession() {
+        return getMergedInto() != null ? getMergedInto() : getSplitInto();
+    }
+
     /**
      * @return Type of the event like creation, update, etc, executed on the accessioned object
      */

diff --git a/.../java/uk/ac/ebi/ampt2d/commons/accession/persistence/repositories/IHistoryRepository.java b/.../java/uk/ac/ebi/ampt2d/commons/accession/persistence/repositories/IHistoryRepository.java
@@ -31,4 +31,9 @@ public interface IHistoryRepository<ACCESSION, OPERATION_ENTITY, ID extends Seri
 
     List<OPERATION_ENTITY> findAllByAccession(ACCESSION accession);
 
-}
+    List<OPERATION_ENTITY> findAllByAccessionOrMergeIntoOrSplitInto(ACCESSION accession, ACCESSION mergeInto, ACCESSION splitInto);
+
+    default List<OPERATION_ENTITY> findAllInvolvedIn(ACCESSION accession) {
+        return findAllByAccessionOrMergeIntoOrSplitInto(accession, accession, accession);
+    }
+}
diff --git a/...ain/java/uk/ac/ebi/ampt2d/commons/accession/persistence/services/BasicHistoryService.java b/...ain/java/uk/ac/ebi/ampt2d/commons/accession/persistence/services/BasicHistoryService.java
@@ -79,6 +79,11 @@ protected List<HistoryEvent<MODEL, ACCESSION>> generateHistory(
                     newEvent = HistoryEvent.merged(operation.getAccession(),
                             operation.getMergedInto(), operation.getCreatedDate());
                     break;
+                case RS_SPLIT:
+                    versionMap = mapVersions(operation.getInactiveObjects());
+                    newEvent = HistoryEvent.split(operation.getAccession(), operation.getSplitInto(),
+                            operation.getCreatedDate());
+                    break;
                 case UPDATED:
                     IAccessionedObject<MODEL, ?, ACCESSION> dataBeforeUpdate = operation.getInactiveObjects().get(0);
                     int version = dataBeforeUpdate.getVersion();

diff --git a/...ava/uk/ac/ebi/ampt2d/commons/accession/persistence/services/InactiveAccessionService.java b/...ava/uk/ac/ebi/ampt2d/commons/accession/persistence/services/InactiveAccessionService.java
@@ -50,4 +50,5 @@ public interface InactiveAccessionService<
 
     List<? extends IEvent<MODEL, ACCESSION>> getEvents(ACCESSION accession);
 
+    List<? extends IEvent<MODEL, ACCESSION>> getAllEventsInvolvedIn(ACCESSION accession);
 }
diff --git a/...mmons-core/src/main/java/uk/ac/ebi/ampt2d/commons/accession/rest/dto/HistoryEventDTO.java b/...mmons-core/src/main/java/uk/ac/ebi/ampt2d/commons/accession/rest/dto/HistoryEventDTO.java
@@ -31,15 +31,26 @@ public class HistoryEventDTO<ACCESSION, DTO> {
 
     private Integer version;
 
+    private ACCESSION splitInto;
+
     private ACCESSION mergedInto;
 
     private LocalDateTime localDateTime;
 
     private DTO data;
 
+    public HistoryEventDTO(){
+
+    }
+
     public <MODEL> HistoryEventDTO(HistoryEvent<MODEL, ACCESSION> event, Function<MODEL, DTO> modelToDTO) {
         this.type = event.getEventType();
         this.accession = event.getAccession();
+        if(event.getEventType() == EventType.MERGED){
+            this.mergedInto = event.getMergedInto();
+        }else if(event.getEventType() == EventType.RS_SPLIT){
+            this.splitInto = event.getSplitInto();
+        }
         this.mergedInto = event.getMergedInto();
         this.localDateTime = event.getLocalDateTime();
         this.data = modelToDTO.apply(event.getData());
@@ -61,6 +72,20 @@ public ACCESSION getMergedInto() {
         return mergedInto;
     }
 
+    public ACCESSION getSplitInto(){
+        return splitInto;
+    }
+
+    public ACCESSION getDestinationAccession(){
+        if(this.type == EventType.MERGED){
+            return mergedInto;
+        }else if(this.type == EventType.RS_SPLIT){
+            return splitInto;
+        }else{
+            return null;
+        }
+    }
+
     public LocalDateTime getLocalDateTime() {
         return localDateTime;
     }

diff --git a/...ain/java/uk/ac/ebi/ampt2d/commons/accession/persistence/jpa/entities/OperationEntity.java b/...ain/java/uk/ac/ebi/ampt2d/commons/accession/persistence/jpa/entities/OperationEntity.java
@@ -51,6 +51,9 @@ public abstract class OperationEntity<ACCESSION> {
     @Column
     private ACCESSION mergeInto;
 
+    @Column
+    private ACCESSION splitInto;
+
     @Enumerated(value = EnumType.STRING)
     @Column(nullable = false)
     private EventType eventType;
@@ -74,6 +77,10 @@ public ACCESSION getMergeInto() {
         return mergeInto;
     }
 
+    public ACCESSION getSplitInto() {
+        return splitInto;
+    }
+
     public EventType getEventType() {
         return eventType;
     }
@@ -89,7 +96,11 @@ public LocalDateTime getCreatedDate() {
     public void fill(EventType type, ACCESSION origin, ACCESSION destination, String reason) {
         this.eventType = type;
         this.accession = origin;
-        this.mergeInto = destination;
+        if (type == EventType.MERGED) {
+            this.mergeInto = destination;
+        } else if (type == EventType.RS_SPLIT) {
+            this.splitInto = destination;
+        }
         this.reason = reason;
     }
 }
diff --git a/...jpa/src/main/java/uk/ac/ebi/ampt2d/commons/accession/persistence/jpa/models/JpaEvent.java b/...jpa/src/main/java/uk/ac/ebi/ampt2d/commons/accession/persistence/jpa/models/JpaEvent.java
@@ -17,12 +17,11 @@
  */
 package uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.models;
 
-import sun.reflect.generics.reflectiveObjects.NotImplementedException;
 import uk.ac.ebi.ampt2d.commons.accession.core.models.EventType;
-import uk.ac.ebi.ampt2d.commons.accession.persistence.models.IAccessionedObject;
 import uk.ac.ebi.ampt2d.commons.accession.core.models.IEvent;
 import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.entities.InactiveAccessionEntity;
 import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.entities.OperationEntity;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.models.IAccessionedObject;
 
 import java.io.Serializable;
 import java.time.LocalDateTime;
@@ -34,6 +33,8 @@ public class JpaEvent<MODEL, ACCESSION extends Serializable> implements IEvent<M
 
     private ACCESSION mergeInto;
 
+    private ACCESSION splitInto;
+
     private EventType eventType;
 
     private String reason;
@@ -45,8 +46,12 @@ public class JpaEvent<MODEL, ACCESSION extends Serializable> implements IEvent<M
     public JpaEvent(OperationEntity<ACCESSION> lastOperation,
                     List<? extends InactiveAccessionEntity<MODEL, ACCESSION>> inactiveEntities) {
         this.accession = lastOperation.getAccession();
-        this.mergeInto = lastOperation.getMergeInto();
         this.eventType = lastOperation.getEventType();
+        if(this.eventType == EventType.MERGED){
+            this.mergeInto = lastOperation.getMergeInto();
+        }else if(this.eventType == EventType.RS_SPLIT){
+            this.splitInto = lastOperation.getSplitInto();
+        }
         this.reason = lastOperation.getReason();
         this.createdDate = lastOperation.getCreatedDate();
         this.inactiveEntities = inactiveEntities;
@@ -64,7 +69,7 @@ public ACCESSION getMergedInto() {
 
     @Override
     public ACCESSION getSplitInto() {
-        throw new NotImplementedException();
+        return splitInto;
     }
 
     @Override

diff --git a/...bi/ampt2d/commons/accession/persistence/jpa/service/BasicJpaInactiveAccessionService.java b/...bi/ampt2d/commons/accession/persistence/jpa/service/BasicJpaInactiveAccessionService.java
@@ -17,15 +17,16 @@
  */
 package uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.service;
 
+import sun.reflect.generics.reflectiveObjects.NotImplementedException;
 import uk.ac.ebi.ampt2d.commons.accession.core.models.EventType;
-import uk.ac.ebi.ampt2d.commons.accession.persistence.services.BasicInactiveAccessionService;
-import uk.ac.ebi.ampt2d.commons.accession.persistence.models.IAccessionedObject;
-import uk.ac.ebi.ampt2d.commons.accession.persistence.repositories.IHistoryRepository;
 import uk.ac.ebi.ampt2d.commons.accession.core.models.IEvent;
-import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.repositories.InactiveAccessionRepository;
 import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.entities.InactiveAccessionEntity;
 import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.entities.OperationEntity;
 import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.models.JpaEvent;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.repositories.InactiveAccessionRepository;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.models.IAccessionedObject;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.repositories.IHistoryRepository;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.services.BasicInactiveAccessionService;
 
 import java.io.Serializable;
 import java.util.List;
@@ -67,7 +68,7 @@ protected void saveHistory(EventType type, ACCESSION accession, ACCESSION mergeI
         OPERATION_ENTITY operation = historyEntitySupplier.get();
         operation.fill(type, accession, mergeInto, reason);
         final OPERATION_ENTITY savedOperation = historyRepository.save(operation);
-        if(accessionInactiveEntities!=null) {
+        if (accessionInactiveEntities != null) {
             accessionInactiveEntities.forEach(entity -> entity.setHistoryId(savedOperation.getId()));
             inactiveAccessionRepository.saveAll(accessionInactiveEntities);
         }
@@ -99,4 +100,9 @@ public List<IEvent<MODEL, ACCESSION>> getEvents(ACCESSION accession) {
         return operations.stream().map(this::toJpaOperation).collect(Collectors.toList());
     }
 
+    @Override
+    public List<? extends IEvent<MODEL, ACCESSION>> getAllEventsInvolvedIn(ACCESSION accession) {
+        throw new NotImplementedException();
+    }
+
 }
diff --git a/...d/commons/accession/persistence/mongodb/service/BasicMongoDbInactiveAccessionService.java b/...d/commons/accession/persistence/mongodb/service/BasicMongoDbInactiveAccessionService.java
@@ -78,4 +78,9 @@ public IEvent<MODEL, ACCESSION> getLastEvent(ACCESSION accession) {
     public List<? extends IEvent<MODEL, ACCESSION>> getEvents(ACCESSION accession) {
         return historyRepository.findAllByAccession(accession);
     }
+
+    @Override
+    public List<? extends IEvent<MODEL, ACCESSION>> getAllEventsInvolvedIn(ACCESSION accession) {
+        return historyRepository.findAllInvolvedIn(accession);
+    }
 }
Original file line number	Diff line number	Diff line change
Expand Up		@@ -50,4 +50,5 @@ public interface InactiveAccessionService<

		List<? extends IEvent<MODEL, ACCESSION>> getEvents(ACCESSION accession);

		List<? extends IEvent<MODEL, ACCESSION>> getAllEventsInvolvedIn(ACCESSION accession);
		}