Updating repo so that classes extend/implement those defined at bio4j main repository

build.sbt

@@ -13,7 +13,7 @@ description := "Neo4jdb implementation of the Bio4j model"
 bucketSuffix := "era7.com"
 
 libraryDependencies ++= Seq(
-  "bio4j" % "bio4j" % "0.11.0",
+  "bio4j" % "bio4j" % "0.12.0-SNAPSHOT",
   "org.neo4j" % "neo4j" % "1.9.6",
   "com.amazonaws" % "aws-java-sdk" % "1.6.12",
   "org.apache.httpcomponents" % "httpclient" % "4.2",

src/main/java/com/bio4j/neo4j/BasicRelationship.java

@@ -23,7 +23,7 @@
  *
  * @author ppareja
  */
-public abstract class BasicRelationship implements RelationshipType{
+public abstract class BasicRelationship implements RelationshipType {
 
     protected Relationship relationship = null;
 

src/main/java/com/bio4j/neo4j/Bio4jRelationshipType.java

@@ -0,0 +1,9 @@
+package com.bio4j.neo4jdb;
+
+import org.neo4j.graphdb.RelationshipType;
+
+public enum Bio4jRelationshipType implements RelationshipType {
+
+  NewTaxonParentRel
+  // add all rel types here
+}

src/main/java/com/bio4j/neo4j/Neo4jNode.java

@@ -0,0 +1,110 @@
+package com.bio4j.neo4jdb;
+
+import org.neo4j.graphdb.Node;
+import org.neo4j.graphdb.Relationship;
+import org.neo4j.graphdb.RelationshipType;
+import org.neo4j.graphdb.Direction;
+import org.neo4j.graphdb.ReturnableEvaluator;
+import org.neo4j.graphdb.StopEvaluator;
+import org.neo4j.graphdb.Traverser;
+import org.neo4j.graphdb.traversal.TraversalDescription;
+import org.neo4j.kernel.Traversal;
+
+public class Neo4jNode extends Neo4jPropertyContainer implements TypedNeo4jNode, com.bio4j.model.Node {
+
+  /*
+    The wrapped Neo4j node
+  */
+  protected final Node wrapped;
+  public Node getNode(){ return wrapped; }
+
+  protected Neo4jNode(Node n, String type) { wrapped = n; this.setType(type); }
+
+  private void setType(String type) { this.setProperty(this.NODE_TYPE_PROPERTY, type); }
+  @Override
+  public String getType() { return String.valueOf(getProperty(NODE_TYPE_PROPERTY)); }
+
+  public long getId() { 
+    return wrapped.getId();
+  }
+  public void delete() { 
+    wrapped.delete();  
+  }
+  public Iterable<Relationship> getRelationships() { 
+    return wrapped.getRelationships(); 
+  }
+  public boolean hasRelationship() { 
+    return wrapped.hasRelationship(); 
+  }
+  public Iterable<Relationship> getRelationships( RelationshipType... types ) { 
+    return wrapped.getRelationships(types); 
+  }
+  public Iterable<Relationship> getRelationships( Direction direction, RelationshipType... types ) { 
+    return wrapped.getRelationships(direction, types); 
+  }
+  public boolean hasRelationship( RelationshipType... types ) { 
+    return wrapped.hasRelationship(types); 
+  }
+  public boolean hasRelationship( Direction direction, RelationshipType... types ) { 
+    return wrapped.hasRelationship(direction, types); 
+  }
+  public Iterable<Relationship> getRelationships( Direction dir ) { 
+    return wrapped.getRelationships(dir); 
+  }
+  public boolean hasRelationship( Direction dir ) { 
+    return wrapped.hasRelationship(dir); 
+  }
+  public Iterable<Relationship> getRelationships( RelationshipType type, Direction dir ) {
+    return wrapped.getRelationships(type, dir);
+  }
+  public boolean hasRelationship( RelationshipType type, Direction dir ) {
+    return wrapped.hasRelationship(type, dir);
+  }
+  public Relationship getSingleRelationship( RelationshipType type, Direction dir ) {
+    return wrapped.getSingleRelationship(type, dir);
+  }
+  public Relationship createRelationshipTo( Node otherNode, RelationshipType type ) {
+    return wrapped.createRelationshipTo(otherNode, type);
+  }
+  @Deprecated
+  public Traverser traverse( 
+    Traverser.Order traversalOrder,
+    StopEvaluator stopEvaluator,
+    ReturnableEvaluator returnableEvaluator,
+    RelationshipType relationshipType, Direction direction 
+  ) {
+    return wrapped.traverse(traversalOrder, stopEvaluator, returnableEvaluator, relationshipType, direction);
+  }
+  @Deprecated
+  public Traverser traverse( 
+    Traverser.Order traversalOrder,
+    StopEvaluator stopEvaluator,
+    ReturnableEvaluator returnableEvaluator,
+    RelationshipType firstRelationshipType, Direction firstDirection,
+    RelationshipType secondRelationshipType, Direction secondDirection 
+  ) {
+    return wrapped.traverse(
+      traversalOrder, 
+      stopEvaluator, 
+      returnableEvaluator,
+      firstRelationshipType,
+      firstDirection,
+      secondRelationshipType,
+      secondDirection
+    );
+  }
+  @Deprecated   
+  public Traverser traverse( 
+    Traverser.Order traversalOrder,
+    StopEvaluator stopEvaluator,
+    ReturnableEvaluator returnableEvaluator,
+    Object... relationshipTypesAndDirections 
+  ) {
+    return wrapped.traverse(
+      traversalOrder, 
+      stopEvaluator, 
+      returnableEvaluator, 
+      relationshipTypesAndDirections
+    );
+  }
+}

src/main/java/com/bio4j/neo4j/Neo4jPropertyContainer.java

@@ -0,0 +1,19 @@
+package com.bio4j.neo4jdb;
+
+import org.neo4j.graphdb.PropertyContainer;
+import org.neo4j.graphdb.GraphDatabaseService;
+
+public abstract class Neo4jPropertyContainer implements PropertyContainer {
+
+  protected PropertyContainer wrapped;
+
+  public GraphDatabaseService getGraphDatabase() { return wrapped.getGraphDatabase(); }
+  public boolean hasProperty( String key ) { return wrapped.hasProperty(key); }
+  public Object getProperty( String key ){ return wrapped.getProperty(key); }
+  public Object getProperty( String key, Object defaultValue ) { return wrapped.getProperty(key, defaultValue); }
+  public void setProperty( String key, Object value ) { wrapped.setProperty(key, value); }
+  public Object removeProperty( String key ) { return wrapped.removeProperty(key); }
+  public Iterable<String> getPropertyKeys() { return wrapped.getPropertyKeys(); }
+  @Deprecated
+  public Iterable<Object> getPropertyValues() { return wrapped.getPropertyValues(); }
+} 

src/main/java/com/bio4j/neo4j/Neo4jRelationship.java

@@ -0,0 +1,35 @@
+package com.bio4j.neo4jdb;
+
+import org.neo4j.graphdb.Relationship;
+import org.neo4j.graphdb.RelationshipType;
+import org.neo4j.graphdb.Node;
+
+/*
+*
+* @author Eduardo Pareja-Tobes <@[email protected]>
+*/
+public abstract class Neo4jRelationship extends Neo4jPropertyContainer implements 
+  com.bio4j.model.Relationship, org.neo4j.graphdb.Relationship {
+
+  /*
+    The relationship type should be accessible from the class
+  */
+  public static Bio4jRelationshipType type;
+
+  protected final Relationship wrapped;
+
+  protected Neo4jRelationship(Relationship r) { wrapped = r; }
+
+  // Neo4j rel
+  public long getId() { return wrapped.getId(); }
+  public void delete() { wrapped.delete(); }
+  public Node getStartNode() { return wrapped.getStartNode(); }
+  public Node getEndNode() { return wrapped.getEndNode(); }
+  public Node getOtherNode( Node node )  { return wrapped.getOtherNode(node); } 
+  public Node[] getNodes() { return wrapped.getNodes(); }
+  public RelationshipType getType() { return wrapped.getType(); }
+  public boolean isType( RelationshipType type ) { return wrapped.isType(type); }
+
+  // Bio4j model rel
+  public String type() { return wrapped.getType().toString(); }
+}

src/main/java/com/bio4j/neo4j/TypedNeo4jNode.java

@@ -0,0 +1,8 @@
+package com.bio4j.neo4jdb;
+
+public interface TypedNeo4jNode extends org.neo4j.graphdb.Node, com.bio4j.model.Node {
+
+  public static final String NODE_TYPE_PROPERTY = "nodeType";
+  // public String getNodeType();
+
+}

src/main/java/com/bio4j/neo4j/model/nodes/CityNode.java

@@ -31,7 +31,7 @@
  * Just nodes representing different cities of the world
  * @author Pablo Pareja Tobes <[email protected]>
  */
-public class CityNode extends BasicEntity{
+public class CityNode extends BasicEntity {
 
     public static final String NODE_TYPE = CityNode.class.getCanonicalName();
     public static final String CITY_NAME_INDEX = "city_name_index";

src/main/java/com/bio4j/neo4j/model/nodes/NewTaxonNode.java

@@ -0,0 +1,121 @@
+package com.bio4j.neo4jdb.model.nodes;
+
+import com.bio4j.neo4jdb.Neo4jNode;
+import com.bio4j.neo4jdb.TypedNeo4jNode;
+
+import com.bio4j.neo4jdb.model.relationships.NewTaxonParentRel;
+import com.bio4j.model.nodes.Taxon;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import org.neo4j.graphdb.Direction;
+import org.neo4j.graphdb.Node;
+import org.neo4j.graphdb.Relationship;
+
+/**
+ * Uniprot taxonomy taxon
+ * @author Pablo Pareja Tobes <[email protected]>
+ */
+public final class NewTaxonNode extends Neo4jNode implements com.bio4j.model.nodes.Taxon {
+
+  // node type
+  public static final String NODE_TYPE = NewTaxonNode.class.getCanonicalName();
+
+  // properties and their getters/setters
+  public static final String NAME_PROPERTY = "taxon_name";
+  public String getName(){ return String.valueOf(getProperty(NAME_PROPERTY)); }
+  public void setName(String value){ setProperty(NAME_PROPERTY, value); }
+
+  // indexes
+  public static final String TAXON_NAME_INDEX = "taxon_name_index";
+
+
+  public NewTaxonNode(Node n){ super(n, NODE_TYPE); }
+
+  // methods
+  public NewTaxonNode getParent() {
+
+    NewTaxonNode parent = null;
+
+    Iterator<Relationship> iterator = 
+      getRelationships(NewTaxonParentRel.type, Direction.INCOMING).iterator();
+
+    if(iterator.hasNext()){
+
+      parent = new NewTaxonNode(iterator.next().getStartNode());
+    }
+
+    return parent;
+  }
+
+  /**
+   * 
+   * @return A list holding the taxon children of the current node
+   */
+  public List<NewTaxonNode> getChildren() {
+
+    List<NewTaxonNode> list = new ArrayList<NewTaxonNode>();
+
+    Iterator<Relationship> iterator = 
+      getRelationships(NewTaxonParentRel.type, Direction.OUTGOING).iterator();
+
+    while(iterator.hasNext()) {
+
+      Node tempNode = iterator.next().getEndNode();
+
+      if(tempNode.getProperty(TypedNeo4jNode.NODE_TYPE_PROPERTY).equals(NewTaxonNode.NODE_TYPE)) {
+
+          list.add( new NewTaxonNode(tempNode) );
+      }         
+    }
+
+    return list;
+  }
+
+  ///////////////////////////////////////////////////////////////////////////////////////////////////////////
+  ///////////////////////////////////////////////////////////////////////////////////////////////////////////
+  ////////////////////////////////// modify accordingly /////////////////////////////////////////////////////
+  ///////////////////////////////////////////////////////////////////////////////////////////////////////////  
+  /**
+   * 
+   * @return The organisms associated to the current node
+   */
+  public List<OrganismNode> getOrganisms(){
+
+    List<OrganismNode> list = new ArrayList<OrganismNode>();
+
+    Iterator<Relationship> iterator = getRelationships(NewTaxonParentRel.type, Direction.OUTGOING).iterator();
+
+    while(iterator.hasNext()){
+      Node tempNode = iterator.next().getEndNode();            
+      if(tempNode.getProperty(com.bio4j.neo4jdb.BasicEntity.NODE_TYPE_PROPERTY).equals(OrganismNode.NODE_TYPE)){
+          list.add(new OrganismNode(tempNode));
+      }           
+    }
+
+    return list;
+  }
+  @Override
+  public int hashCode(){
+    return super.hashCode();
+  }
+
+  @Override
+  public boolean equals(Object obj) {
+
+    if(obj instanceof NewTaxonNode){
+      NewTaxonNode other = (NewTaxonNode) obj;
+      return this.wrapped.equals(other.wrapped);
+    } else {
+      return false;
+    }
+  }
+
+  @Override
+  public String toString(){
+    return "name = " + getName();
+  }
+
+}

src/main/java/com/bio4j/neo4j/model/nodes/TaxonNode.java

@@ -28,8 +28,7 @@ public TaxonNode(Node n){
         super(n);
     }
 
-
-    public String getName(){    return String.valueOf(node.getProperty(NAME_PROPERTY));}
+    public String getName(){ return String.valueOf(node.getProperty(NAME_PROPERTY));}
 
 
     public void setName(String value){  node.setProperty(NAME_PROPERTY, value);}

src/main/java/com/bio4j/neo4j/model/relationships/NewTaxonParentRel.java

@@ -0,0 +1,22 @@
+package com.bio4j.neo4jdb.model.relationships;
+
+import com.bio4j.neo4jdb.Neo4jRelationship;
+import org.neo4j.graphdb.Relationship;
+import com.bio4j.neo4jdb.Bio4jRelationshipType;
+
+import com.bio4j.model.relationships.TaxonParent;
+
+/**
+ * 
+ * @author Pablo Pareja Tobes <[email protected]>
+ */
+public class NewTaxonParentRel extends Neo4jRelationship implements TaxonParent {
+
+    public static Bio4jRelationshipType type = Bio4jRelationshipType.NewTaxonParentRel;
+    // public static final String NAME = "TAXON_PARENT";
+
+    public NewTaxonParentRel(Relationship rel){
+        super(rel);
+    }
+
+}

src/main/java/com/bio4j/neo4j/model/util/Bio4jManager.java

@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package com.bio4j.neo4jdb.model.util;
 
 import com.bio4j.neo4jdb.model.nodes.*;