Curator tool

pom.xml

@@ -11,7 +11,7 @@
     <artifactId>graph-core</artifactId>
 
     <packaging>jar</packaging>
-    <version>2.0.9</version>
+    <version>2.0.12.CT</version>
     <name>Graph Core Next Generation</name>
 
     <description>

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

@@ -1,24 +1,29 @@
 package org.reactome.server.graph.domain.model;
 
-import com.fasterxml.jackson.annotation.JsonIdentityInfo;
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.ObjectIdGenerators;
+import java.io.Serializable;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.lang.reflect.ParameterizedType;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Objects;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
 import org.reactome.server.graph.domain.annotations.ReactomeProperty;
 import org.reactome.server.graph.domain.annotations.ReactomeSchemaIgnore;
 import org.reactome.server.graph.domain.annotations.ReactomeTransient;
+import org.reactome.server.graph.domain.relationship.ModifiedList;
 import org.reactome.server.graph.domain.result.DatabaseObjectLike;
 import org.springframework.data.neo4j.core.schema.Id;
 import org.springframework.data.neo4j.core.schema.Node;
 import org.springframework.data.neo4j.core.schema.Relationship;
 import org.springframework.lang.NonNull;
 
-import java.io.Serializable;
-import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Method;
-import java.lang.reflect.ParameterizedType;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Objects;
+import com.fasterxml.jackson.annotation.JsonIdentityInfo;
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.ObjectIdGenerators;
 
 /**
  * DatabaseObject contains the minimum fields used to define an instance of an Reactome entry
@@ -62,13 +67,21 @@ public abstract class DatabaseObject implements Serializable, Comparable<Databas
 
     @Relationship(type = "modified", direction = Relationship.Direction.INCOMING)
     private InstanceEdit modified;
+
+    // This is a list of InstanceEdits that have modified this DatabaseObject.
+    // So that we can track all modifications, not just the most recent one.
+    @Relationship(type = "modifiedList", direction = Relationship.Direction.INCOMING)
+    private SortedSet<ModifiedList> modifiedList;
+
+    @Relationship(type = "stableIdentifier")
+    private StableIdentifier stableIdentifier;
 
     public DatabaseObject() {
     }
 
     public DatabaseObject(Long dbId) {
         this.dbId = dbId;
-    }
+    } 
 
 //    @ReactomeSchemaIgnore
 //    public Long getId() {
@@ -79,6 +92,40 @@ public DatabaseObject(Long dbId) {
 //        this.id = id;
 //    }
 
+    public StableIdentifier getStableIdentifier() {
+        return stableIdentifier;
+    }
+
+    public void setStableIdentifier(StableIdentifier stableIdentifier) {
+        this.stableIdentifier = stableIdentifier;
+    }
+
+    public List<InstanceEdit> getModifiedList() {
+        if (this.modifiedList == null || this.modifiedList.isEmpty()) {
+            return null;
+        }
+
+        List<InstanceEdit> rtn = new ArrayList<>();
+        for (ModifiedList modified : this.modifiedList) {
+            rtn.add(modified.getInstanceEdit());
+        }
+        return rtn;
+    }
+
+    public void setModifiedList(List<InstanceEdit> modifiedList) {
+        if (modifiedList == null || modifiedList.isEmpty()) {
+            return;
+        }   
+        this.modifiedList = new TreeSet<>();
+        int order = 0;
+        for (InstanceEdit instanceEdit : modifiedList) {
+            ModifiedList aux = new ModifiedList();
+            aux.setInstanceEdit(instanceEdit);
+            aux.setOrder(order++);
+            this.modifiedList.add(aux);
+        }
+    }
+
     public Long getDbId() {
         return dbId;
     }

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

@@ -26,6 +26,9 @@ public class Deleted extends MetaDatabaseObject{
     @Deprecated
     @ReactomeProperty(originName = "deletedInstanceDB_ID")
     private List<Integer> deletedInstanceDbId;
+
+    @ReactomeProperty(originName = "replacementInstanceDB_IDs")
+    private List<Integer> replacementInstanceDbIds;
 
     public Deleted() {
     }
@@ -34,6 +37,14 @@ public String getCuratorComment() {
         return curatorComment;
     }
 
+    public List<Integer> getReplacementInstanceDbIds() {
+        return replacementInstanceDbIds;
+    }
+
+    public void setReplacementInstanceDbIds(List<Integer> replacementInstanceDbIds) {
+        this.replacementInstanceDbIds = replacementInstanceDbIds;
+    }
+
     public void setCuratorComment(String curatorComment) {
         this.curatorComment = curatorComment;
     }

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

@@ -1,14 +1,21 @@
 package org.reactome.server.graph.domain.model;
 
-import com.fasterxml.jackson.annotation.JsonIgnore;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+import java.util.SortedSet;
+import java.util.TreeSet;
+import java.util.stream.Collectors;
+
 import org.reactome.server.graph.domain.annotations.ReactomeProperty;
 import org.reactome.server.graph.domain.annotations.ReactomeSchemaIgnore;
 import org.reactome.server.graph.domain.annotations.ReactomeTransient;
 import org.reactome.server.graph.domain.relationship.HasCompartment;
+import org.reactome.server.graph.domain.relationship.StructureModified;
 import org.springframework.data.neo4j.core.schema.Node;
 import org.springframework.data.neo4j.core.schema.Relationship;
 
-import java.util.*;
+import com.fasterxml.jackson.annotation.JsonIgnore;
 
 @SuppressWarnings({"unused"})
 
@@ -31,6 +38,8 @@ public abstract class Event extends DatabaseObject implements Trackable, Deletab
     private String releaseStatus;
     @ReactomeProperty(addedField = true)
     private String speciesName;
+    @ReactomeProperty(originName = "_doRelease")
+    private Boolean doRelease;
 
     @Relationship(type = "authored", direction = Relationship.Direction.INCOMING)
     private List<InstanceEdit> authored;
@@ -114,8 +123,13 @@ public abstract class Event extends DatabaseObject implements Trackable, Deletab
     @Relationship(type = "internalReviewed", direction = Relationship.Direction.INCOMING)
     private List<InstanceEdit> internalReviewed;
 
+    // For some reason, we have to define a relationship to keep the order
+    // for newly added InstanceEdit in this attribute. Not sure why.
+    // Use SortedSet to make sure the order is correct. Most likely
+    // the sorting is conducted when the list, which is generated by the framework(?), is
+    // converted into a SortedSet. 
     @Relationship(type = "structureModified", direction = Relationship.Direction.INCOMING)
-    private List<InstanceEdit> structureModified;
+    private SortedSet<StructureModified> structureModified;
 
     @ReactomeTransient
     @Relationship(type = "replacementInstances", direction = Relationship.Direction.INCOMING)
@@ -392,11 +406,26 @@ public void setInternalReviewed(List<InstanceEdit> internalReviewed) {
     }
 
     public List<InstanceEdit> getStructureModified() {
-        return structureModified;
+        if (structureModified == null || structureModified.isEmpty())
+            return null;
+        return this.structureModified.stream().map(s -> s.getInstanceEdit()).collect(Collectors.toList());
     }
 
     public void setStructureModified(List<InstanceEdit> structureModified) {
-        this.structureModified = structureModified;
+        if (structureModified != null && structureModified.size() > 0) {
+            int order = 0;
+            this.structureModified = new TreeSet<>();
+            for (InstanceEdit ie : structureModified) {
+                StructureModified sm = new StructureModified();
+                sm.setId(ie.getDbId());
+                sm.setInstanceEdit(ie);
+                sm.setOrder(order);
+                order ++;
+                this.structureModified.add(sm);
+            }
+        }
+        else
+            this.structureModified = null;
     }
 
     @Override
@@ -416,4 +445,13 @@ public List<UpdateTracker> getUpdateTrackers() {
     public void setUpdateTrackers(List<UpdateTracker> updateTrackers) {
         this.updateTrackers = updateTrackers;
     }
+
+
+    public Boolean getDoRelease() {
+        return doRelease;
+    }
+
+    public void setDoRelease(Boolean doRelease) {
+        this.doRelease = doRelease;
+    }
 }

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

@@ -4,7 +4,7 @@
 
 @SuppressWarnings("unused")
 @Node
-public class GO_BiologicalProcess extends GO_Term{
+public class GO_BiologicalProcess extends GO_Term {
 
     public GO_BiologicalProcess() {}
 

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

@@ -43,13 +43,6 @@ public void setHasPart(List<GO_CellularComponent> hasPart) {
         this.hasPart = hasPart;
     }
 
-    public List<GO_CellularComponent> getInstanceOf() {
-        return instanceOf;
-    }
-
-    public void setInstanceOf(List<GO_CellularComponent> instanceOf) {
-        this.instanceOf = instanceOf;
-    }
 
     public List<GO_CellularComponent> getSurroundedBy() {
         return surroundedBy;

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

@@ -12,73 +12,14 @@
  */
 @SuppressWarnings("unused")
 @Node
-public abstract class GO_Term extends DatabaseObject{
-
-    @ReactomeProperty
-    private String accession;
-    // will be filled together with url
-    private String databaseName;
-    @ReactomeProperty
-    private String definition;
-    @ReactomeProperty
-    private String name;
-    @ReactomeProperty(addedField = true)
-    private String url;
-    @Relationship(type = "referenceDatabase")
-    private ReferenceDatabase referenceDatabase;
+public abstract class GO_Term extends ExternalOntology {
 
     public GO_Term() {}
-
+    
     public GO_Term(Long dbId) {
-        super(dbId);
-    }
-
-    public String getAccession() {
-        return accession;
+        super();
+        setDbId(dbId);
     }
 
-    public void setAccession(String accession) {
-        this.accession = accession;
-    }
-
-    public String getDatabaseName() {
-        return databaseName;
-    }
-
-    public void setDatabaseName(String databaseName) {
-        this.databaseName = databaseName;
-    }
-
-    public String getDefinition() {
-        return definition;
-    }
-
-    public void setDefinition(String definition) {
-        this.definition = definition;
-    }
-
-    public String getName() {
-        return name;
-    }
-
-    public void setName(String name) {
-        this.name = name;
-    }
-
-    public String getUrl() {
-        return url;
-    }
-
-    public void setUrl(String url) {
-        this.url = url;
-    }
-
-    public ReferenceDatabase getReferenceDatabase() {
-        return referenceDatabase;
-    }
-
-    public void setReferenceDatabase(ReferenceDatabase referenceDatabase) {
-        this.referenceDatabase = referenceDatabase;
-    }
 }
 

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

@@ -2,6 +2,7 @@
 
 import org.reactome.server.graph.domain.annotations.ReactomeProperty;
 import org.springframework.data.neo4j.core.schema.Node;
+import org.springframework.data.neo4j.core.schema.Relationship;
 
 @SuppressWarnings("unused")
 @Node
@@ -19,9 +20,20 @@ public class LiteratureReference extends Publication {
     private Integer volume;
     @ReactomeProperty
     private Integer year;
+
+    @Relationship(type = "retractionStatus")
+    private RetractionStatus retractionStatus;
 
     public LiteratureReference() {}
 
+    public RetractionStatus getRetractionStatus() {
+        return retractionStatus;
+    }
+
+    public void setRetractionStatus(RetractionStatus retractionStatus) {
+        this.retractionStatus = retractionStatus;
+    }
+
     public LiteratureReference(Long dbId) {
         super(dbId);
     }

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

@@ -37,7 +37,7 @@ public class Pathway extends Event {
     private Integer diagramHeight;
 
     @ReactomeProperty
-    private String isCanonical;
+    private Boolean isCanonical;
 
     @ReactomeProperty
     private String lastUpdatedDate;
@@ -102,11 +102,11 @@ public void setDiagramHeight(Integer diagramHeight) {
         this.diagramHeight = diagramHeight;
     }
 
-    public String getIsCanonical() {
+    public Boolean getIsCanonical() {
         return isCanonical;
     }
 
-    public void setIsCanonical(String isCanonical) {
+    public void setIsCanonical(Boolean isCanonical) {
         this.isCanonical = isCanonical;
     }