🚧 update data model to have updateTracker

Author: cqgong

pom.xml

@@ -11,7 +11,7 @@
     <artifactId>graph-core</artifactId>
 
     <packaging>jar</packaging>
-    <version>2.0.8</version>
+    <version>2.0.9-SNAPSHOT</version>
     <name>Graph Core Next Generation</name>
 
     <description>

src/main/java/org/reactome/server/graph/domain/annotations/ReactomeProperty.java

@@ -16,4 +16,5 @@
 
     boolean addedField() default false;
 
+    String originName() default "";
 }

src/main/java/org/reactome/server/graph/domain/model/DBInfo.java

@@ -1,28 +1,14 @@
 package org.reactome.server.graph.domain.model;
 
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import org.springframework.data.neo4j.core.schema.Id;
 import org.springframework.data.neo4j.core.schema.Node;
 
 @Node
-public class DBInfo {
-
-    @JsonIgnore
-    @Id
-    private Long id;
+public class DBInfo extends Release {
 
     private String name;
-    private Integer version;
     private Long checksum;
 
-    public DBInfo() { }
-
-    public Long getId() {
-        return id;
-    }
-
-    public void setId(Long id) {
-        this.id = id;
+    public DBInfo() {
     }
 
     public String getName() {
@@ -33,13 +19,6 @@ public void setName(String name) {
         this.name = name;
     }
 
-    public Integer getVersion() {
-        return version;
-    }
-
-    public void setVersion(Integer version) {
-        this.version = version;
-    }
 
     public Long getChecksum() {
         return checksum;

src/main/java/org/reactome/server/graph/domain/model/Deletable.java

@@ -0,0 +1,11 @@
+package org.reactome.server.graph.domain.model;
+
+
+import org.reactome.server.graph.domain.result.DatabaseObjectLike;
+
+import java.util.List;
+
+public interface Deletable extends DatabaseObjectLike {
+
+    List<Deleted> getDeleted();
+}

src/main/java/org/reactome/server/graph/domain/model/Deleted.java

@@ -0,0 +1,82 @@
+package org.reactome.server.graph.domain.model;
+
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import org.reactome.server.graph.domain.annotations.ReactomeProperty;
+import org.reactome.server.graph.domain.annotations.ReactomeSchemaIgnore;
+import org.springframework.data.neo4j.core.schema.Node;
+import org.springframework.data.neo4j.core.schema.Relationship;
+
+import java.util.List;
+
+@Node
+public class Deleted extends MetaDatabaseObject{
+
+    @ReactomeProperty
+    private String curatorComment;
+
+    @Relationship(type = "deletedInstance")
+    private List<DeletedInstance> deletedInstance;
+
+    @Relationship(type="reason")
+    private DeletedControlledVocabulary reason;
+
+    @Relationship(type="replacementInstances")
+    private List<Deletable> replacementInstances;
+
+    @Deprecated
+    @ReactomeProperty(originName = "deletedInstanceDB_ID")
+    private List<Integer> deletedInstanceDbId;
+
+    public Deleted() {
+    }
+
+    public String getCuratorComment() {
+        return curatorComment;
+    }
+
+    public void setCuratorComment(String curatorComment) {
+        this.curatorComment = curatorComment;
+    }
+
+    public List<DeletedInstance> getDeletedInstance() {
+        return deletedInstance;
+    }
+
+    public void setDeletedInstance(List<DeletedInstance> deletedInstance) {
+        this.deletedInstance = deletedInstance;
+    }
+
+    public DeletedControlledVocabulary getReason() {
+        return reason;
+    }
+
+    public void setReason(DeletedControlledVocabulary reason) {
+        this.reason = reason;
+    }
+
+    public List<Deletable> getReplacementInstances() {
+        return replacementInstances;
+    }
+
+    public void setReplacementInstances(List<Deletable> replacementInstances) {
+        this.replacementInstances = replacementInstances;
+    }
+
+    @Deprecated
+    public List<Integer> getDeletedInstanceDbId() {
+        return deletedInstanceDbId;
+    }
+
+    @Deprecated
+    public void setDeletedInstanceDbId(List<Integer> deletedInstanceDbId) {
+        this.deletedInstanceDbId = deletedInstanceDbId;
+    }
+
+    @ReactomeSchemaIgnore
+    @Override
+    @JsonIgnore
+    public String getExplanation() {
+        //todo
+        return "Deleted";
+    }
+}

src/main/java/org/reactome/server/graph/domain/model/DeletedControlledVocabulary.java

@@ -0,0 +1,8 @@
+package org.reactome.server.graph.domain.model;
+
+import org.springframework.data.neo4j.core.schema.Node;
+
+@Node
+public class DeletedControlledVocabulary extends ControlledVocabulary{
+
+}

src/main/java/org/reactome/server/graph/domain/model/DeletedInstance.java

@@ -0,0 +1,79 @@
+package org.reactome.server.graph.domain.model;
+
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import org.reactome.server.graph.domain.annotations.ReactomeProperty;
+import org.reactome.server.graph.domain.annotations.ReactomeSchemaIgnore;
+import org.springframework.data.neo4j.core.schema.Node;
+import org.springframework.data.neo4j.core.schema.Relationship;
+
+import java.util.List;
+
+@Node
+public class DeletedInstance extends MetaDatabaseObject {
+
+    @ReactomeProperty(originName = "class")
+    private String clazz;
+
+    @ReactomeProperty(originName = "deletedInstanceDB_ID")
+    private Integer deletedInstanceDbId;
+
+    @ReactomeProperty
+    private String name;
+
+    @ReactomeProperty(addedField = true)
+    private String deletedStId;
+
+    @Relationship(type = "species")
+    private List<Taxon> species;
+
+    public DeletedInstance() {
+    }
+
+    public String getClazz() {
+        return clazz;
+    }
+
+    public void setClazz(String clazz) {
+        this.clazz = clazz;
+    }
+
+    public Integer getDeletedInstanceDbId() {
+        return deletedInstanceDbId;
+    }
+
+    public void setDeletedInstanceDbId(Integer deletedInstanceDbId) {
+        this.deletedInstanceDbId = deletedInstanceDbId;
+    }
+
+    public String getDeletedStId() {
+        return deletedStId;
+    }
+
+    public void setDeletedStId(String deletedStId) {
+        this.deletedStId = deletedStId;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public List<Taxon> getSpecies() {
+        return species;
+    }
+
+    public void setSpecies(List<Taxon> species) {
+        this.species = species;
+    }
+
+    @ReactomeSchemaIgnore
+    @Override
+    @JsonIgnore
+    public String getExplanation() {
+        //todo
+        return "DeletedInstance";
+    }
+}

src/main/java/org/reactome/server/graph/domain/model/Event.java

@@ -13,7 +13,7 @@
 @SuppressWarnings({"unused"})
 
 @Node
-public abstract class Event extends DatabaseObject {
+public abstract class Event extends DatabaseObject implements Trackable, Deletable {
 
     @ReactomeProperty
     private String definition;
@@ -117,6 +117,14 @@ public abstract class Event extends DatabaseObject {
     @Relationship(type = "structureModified", direction = Relationship.Direction.INCOMING)
     private List<InstanceEdit> structureModified;
 
+    @ReactomeTransient
+    @Relationship(type = "replacementInstances", direction = Relationship.Direction.INCOMING)
+    private List<Deleted> deleted;
+
+    @ReactomeTransient
+    @Relationship(type = "updatedInstance", direction = Relationship.Direction.INCOMING)
+    private List<UpdateTracker> updateTrackers;
+
 
     public Event() {}
 
@@ -390,4 +398,22 @@ public List<InstanceEdit> getStructureModified() {
     public void setStructureModified(List<InstanceEdit> structureModified) {
         this.structureModified = structureModified;
     }
+
+    @Override
+    public List<Deleted> getDeleted() {
+        return deleted;
+    }
+
+    public void setDeletedList(List<Deleted> deleted) {
+        this.deleted = deleted;
+    }
+
+    @Override
+    public List<UpdateTracker> getUpdateTrackers() {
+        return updateTrackers;
+    }
+
+    public void setUpdateTrackers(List<UpdateTracker> updateTrackers) {
+        this.updateTrackers = updateTrackers;
+    }
 }

src/main/java/org/reactome/server/graph/domain/model/MetaDatabaseObject.java

@@ -0,0 +1,8 @@
+package org.reactome.server.graph.domain.model;
+
+import org.springframework.data.neo4j.core.schema.Node;
+
+@Node
+public abstract class MetaDatabaseObject extends DatabaseObject{
+
+}

src/main/java/org/reactome/server/graph/domain/model/Pathway.java

@@ -39,6 +39,9 @@ public class Pathway extends Event {
     @ReactomeProperty
     private String isCanonical;
 
+    @ReactomeProperty
+    private String lastUpdatedDate;
+
     @Relationship(type = "hasEvent")
     private SortedSet<HasEvent> hasEvent;
 
@@ -159,6 +162,14 @@ public void setNormalPathway(Pathway normalPathway) {
         this.normalPathway = normalPathway;
     }
 
+    public String getLastUpdatedDate() {
+        return lastUpdatedDate;
+    }
+
+    public void setLastUpdatedDate(String lastUpdatedDate) {
+        this.lastUpdatedDate = lastUpdatedDate;
+    }
+
     @ReactomeSchemaIgnore
     @Override
     @JsonIgnore

src/main/java/org/reactome/server/graph/domain/model/PhysicalEntity.java

@@ -12,7 +12,7 @@
 
 @SuppressWarnings("unused")
 @Node
-public abstract class PhysicalEntity extends DatabaseObject {
+public abstract class PhysicalEntity extends DatabaseObject implements Trackable, Deletable {
 
     @ReactomeProperty
     private String definition;
@@ -134,6 +134,14 @@ public abstract class PhysicalEntity extends DatabaseObject {
     @Relationship(type = "marker", direction = Relationship.Direction.INCOMING)
     private List<MarkerReference> markingReferences;
 
+    @ReactomeTransient
+    @Relationship(type = "replacementInstances", direction = Relationship.Direction.INCOMING)
+    private List<Deleted> deleted;
+
+    @ReactomeTransient
+    @Relationship(type = "updatedInstance", direction = Relationship.Direction.INCOMING)
+    private List<UpdateTracker> updateTrackers;
+
     public PhysicalEntity() {}
 
     public PhysicalEntity(Long dbId) {
@@ -477,4 +485,22 @@ public List<CellType> getCellType() {
     public void setCellType(List<CellType> cellType) {
         this.cellType = cellType;
     }
+
+    @Override
+    public List<Deleted> getDeleted() {
+        return deleted;
+    }
+
+    public void setDeleted(List<Deleted> deleted) {
+        this.deleted = deleted;
+    }
+
+    @Override
+    public List<UpdateTracker> getUpdateTrackers() {
+        return updateTrackers;
+    }
+
+    public void setUpdateTrackers(List<UpdateTracker> updateTrackers) {
+        this.updateTrackers = updateTrackers;
+    }
 }