Open Biomedical Ontologies

Revision: 1299
          http://obo.svn.sourceforge.net/obo/?rev=1299&view=rev
Author:   cmungall
Date:     2007-12-09 16:56:49 -0800 (Sun, 09 Dec 2007)

Log Message:
-----------


Modified Paths:
--------------
    obdapi/trunk/OBDAPI/src/org/obd/model/Node.java
    obdapi/trunk/OBDAPI/src/org/obd/model/Shard.java
    obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBOBridge.java
    obdapi/trunk/OBDAPI/src/org/obd/model/impl/MultiShard.java
    obdapi/trunk/OBDAPI/src/org/obd/model/impl/OBDSQLShard.java
    obdapi/trunk/OBDAPI/src/org/obd/model/impl/OBOSessionShard.java
    obdapi/trunk/OBDAPI/src/org/obd/ws/OBDQueryService.java

Added Paths:
-----------
    obdapi/trunk/OBDAPI/src/org/obd/model/AnnotationNode.java
    obdapi/trunk/OBDAPI/src/org/obd/model/EquivalenceStatement.java
    obdapi/trunk/OBDAPI/src/org/obd/model/Graph.java
    obdapi/trunk/OBDAPI/src/org/obd/model/LinkStatement.java
    obdapi/trunk/OBDAPI/src/org/obd/model/LiteralStatement.java
    obdapi/trunk/OBDAPI/src/org/obd/model/NodeAlias.java
    obdapi/trunk/OBDAPI/src/org/obd/model/Statement.java
    obdapi/trunk/OBDAPI/src/org/obd/model/stats/
    obdapi/trunk/OBDAPI/src/org/obd/model/stats/AggregateStatistic.java
    obdapi/trunk/OBDAPI/src/org/obd/model/stats/AggregateStatisticCollection.java
    obdapi/trunk/OBDAPI/src/org/obd/model/stats/CountStatistic.java
    obdapi/trunk/OBDAPI/src/org/obd/model/stats/MeasuredEntity.java
    obdapi/trunk/OBDAPI/src/org/obd/model/stats/SummaryStatistics.java
    obdapi/trunk/OBDAPI/src/org/obd/query/
    obdapi/trunk/OBDAPI/src/org/obd/query/GraphQuery.java
    obdapi/trunk/OBDAPI/src/org/obd/test/
    obdapi/trunk/OBDAPI/src/org/obd/test/OBDQueryServiceTest.java

Removed Paths:
-------------
    obdapi/trunk/OBDAPI/src/org/obd/model/Statement.java

Added: obdapi/trunk/OBDAPI/src/org/obd/model/AnnotationNode.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/AnnotationNode.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/AnnotationNode.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -0,0 +1,17 @@
+package org.obd.model;
+
+import java.util.Collection;
+
+public class AnnotationNode extends Node {
+	Collection<Statement> posits;
+
+	public Collection<Statement> getPosits() {
+		return posits;
+	}
+
+	public void setPosits(Collection<Statement> posits) {
+		this.posits = posits;
+	}
+	
+	
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/model/EquivalenceStatement.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/EquivalenceStatement.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/EquivalenceStatement.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -0,0 +1,11 @@
+package org.obd.model;
+
+public class EquivalenceStatement extends LinkStatement {
+
+	/**
+	 * true  if is owl:equivalentClass semantics
+	 */ 
+	public boolean isEquivalentClass() {
+		return this.isAppliesToAllInstancesOf();
+	}
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/model/Graph.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/Graph.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/Graph.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -0,0 +1,153 @@
+package org.obd.model;
+
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.Map;
+
+/**
+ * @author cjm
+ *
+ */
+/**
+ * @author cjm
+ *
+ */
+public class Graph {
+	
+	protected Map<String,Node> nodeMap = new HashMap<String,Node> ();
+	protected Collection<Statement> statements;
+	
+	public Graph() {
+		super();
+		clearNodes();
+		clearStatements();
+	}
+
+	public Graph(Collection<Statement> statements) {
+		super();
+		setStatements(statements);
+	}
+
+	public Graph(Collection<Node> nodes, Collection<Statement> statements) {
+		super();
+		setNodes(nodes);
+		setStatements(statements);
+	}
+
+	public Node[] getNodes() {
+		System.out.println("nm="+nodeMap);
+		return  (Node[]) nodeMap.values().toArray(new Node[0]);
+	}
+	
+	public String[] getReferencedNodeIds() {
+		HashSet<String> nids = new HashSet<String>();
+		for (Statement s : getAllStatements()) {
+			nids.add(s.getNodeId());
+			nids.add(s.getTargetId());
+			nids.add(s.getRelationId());
+		}
+		return (String[]) nids.toArray(new String[0]);
+	}
+
+
+	public void addNode(Node n) {
+		if (n != null)
+			nodeMap.put(n.getId(), n);
+	}
+	public void addNodes(Collection<Node> nodes) {
+		for (Node n : nodes)
+			nodeMap.put(n.getId(), n);
+	}
+	public void addNodes(Node[] nodeArr) {
+		LinkedList<Node> nodes = new LinkedList<Node>();
+		nodes.addAll(Arrays.asList(nodeArr));
+		addNodes(nodes);
+	}
+	public void setNodes(Collection<Node> nodes) {
+		clearNodes();
+		for (Node n : nodes)
+			nodeMap.put(n.getId(), n);
+	}
+	
+	public void clearNodes() {
+		nodeMap = new HashMap<String,Node> ();
+	}
+	/**
+	 * all statements not nested under nodes
+	 */
+	public Statement[] getStatements() {
+		return (Statement[])statements.toArray(new Statement[0]);
+	}
+	
+	/**
+	 * all statements in the graph, whether or not they are nested under nodes
+	 * or not
+	 */
+	private Statement[] getAllStatements() {
+		LinkedList<Statement> statements = new LinkedList<Statement>();
+		statements.addAll(Arrays.asList(getStatements()));
+		for (Node n : getNodes()) {
+			statements.addAll(Arrays.asList(n.getStatements()));
+		}
+		return (Statement[])statements.toArray(new Statement[0]);
+	}
+	public void setStatements(Collection<Statement> statements) {
+		this.statements = statements;
+	}
+	
+
+	
+	public void addStatement(Statement statement) {
+		if (statements == null)
+			statements = new HashSet<Statement>();
+		statements.add(statement);
+	}
+	
+	public void addStatements(Collection<Statement> newStatements) {
+		if (statements == null)
+			statements = new LinkedList<Statement>();
+		statements.addAll(newStatements);
+	}
+	
+	public void addStatements(Statement[] statements) {
+		addStatements(Arrays.asList(statements));
+	}
+
+	
+	
+	public void clearStatements() {
+		statements = new LinkedList<Statement>();
+	}
+	
+	// shift to frame-style
+	public void nestStatementsUnderNodes() {
+		for (Statement s : getStatements()) {
+			Node n = nodeMap.get(s.getNodeId());
+			if (n==null) {
+				n = new Node();
+				n.setId(s.getNodeId());
+				addNode(n);
+			}
+			n.addStatement(s);
+		}
+		clearStatements();
+	}
+	
+	// shift to axiom-style
+	public void nestStatementsUnderGraph() {
+		for (Node n : getNodes()) {
+			for (Statement s : n.getStatements()) {
+				addStatement(s);
+			}
+			n.clearStatements();
+		}
+	}
+
+	public void merge(Graph g2) {
+		addNodes(g2.getNodes());
+		addStatements(g2.getStatements());
+	}
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/model/LinkStatement.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/LinkStatement.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/LinkStatement.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -0,0 +1,48 @@
+package org.obd.model;
+
+public class LinkStatement extends Statement {
+
+	protected boolean appliesToAllInstancesOf;
+	protected boolean isExistential;
+	protected boolean isUniversal;
+	protected boolean hasIntersectionSemantics;
+	protected boolean hasUnionSemantics;
+	
+	public boolean isAppliesToAllInstancesOf() {
+		return appliesToAllInstancesOf;
+	}
+	public void setAppliesToAllInstancesOf(boolean appliesToAllInstancesOf) {
+		this.appliesToAllInstancesOf = appliesToAllInstancesOf;
+	}
+	public boolean isExistential() {
+		return isExistential;
+	}
+	public void setExistential(boolean isExistential) {
+		this.isExistential = isExistential;
+	}
+	public boolean isUniversal() {
+		return isUniversal;
+	}
+	public void setUniversal(boolean isUniversal) {
+		this.isUniversal = isUniversal;
+	}
+	public boolean isHasIntersectionSemantics() {
+		return hasIntersectionSemantics;
+	}
+	public void setHasIntersectionSemantics(boolean hasIntersectionSemantics) {
+		this.hasIntersectionSemantics = hasIntersectionSemantics;
+	}
+	public boolean isHasUnionSemantics() {
+		return hasUnionSemantics;
+	}
+	public void setHasUnionSemantics(boolean hasUnionSemantics) {
+		this.hasUnionSemantics = hasUnionSemantics;
+	}
+
+	public String toString() {
+		String s = super.toString();
+		if (this.hasIntersectionSemantics)
+			s = s + " [^]";
+		return s;
+	}
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/model/LiteralStatement.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/LiteralStatement.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/LiteralStatement.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -0,0 +1,27 @@
+package org.obd.model;
+
+public class LiteralStatement extends Statement {
+	protected String datatype;
+	protected Object value;
+	
+	public String getDatatype() {
+		return datatype;
+	}
+
+	public void setDatatype(String datatype) {
+		this.datatype = datatype;
+	}
+
+	public String getSValue() {
+		return (String)value;
+	}
+
+	public Object getValue() {
+		return value;
+	}
+
+	public void setValue(String value) {
+		this.value = value;
+	}
+
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/model/Node.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/Node.java	2007-12-09 07:00:44 UTC (rev 1298)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/Node.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -3,6 +3,7 @@
 import java.io.Serializable;
 import java.util.Collection;
 import java.util.HashSet;
+import java.util.LinkedList;
 
 public class Node implements Serializable {
 	/**
@@ -12,19 +13,13 @@
 	
 	protected String id;
 	protected String name;
-	protected String metatype;
 	protected Collection<Statement> statements;
 	protected String sourceId;
+	protected boolean isAnonymous;
 	
-	public String getMetatype() {
-		return metatype;
-	}
 
-	public void setMetatype(String metatype) {
-		this.metatype = metatype;
-	}
-
 	public Node() {
+		statements = new LinkedList<Statement>();
 	}
 
 	public String getId() {
@@ -43,9 +38,23 @@
 		this.name = name;
 	}
 
-	public Collection<Statement> getStatements() {
-		return statements;
+	// WSDL-friendly : use arrays
+	public Statement[] getStatements() {
+		return (Statement[])statements.toArray(new Statement[0]);
 	}
+	
+	public LinkStatement[] getIntersectionStatements() {
+		LinkedList<Statement> statements = new LinkedList<Statement>();
+		for (Statement s : getStatements()) {
+			if (s instanceof LinkStatement) {
+					LinkStatement ls = (LinkStatement)s;
+					if (ls.hasIntersectionSemantics)
+						statements.add(ls);
+			}
+		}
+		return (LinkStatement[])statements.toArray(new LinkStatement[0]);
+	}
+	
 
 	public void setStatements(Collection<Statement> statements) {
 		this.statements = statements;
@@ -56,6 +65,9 @@
 			statements = new HashSet<Statement>();
 		statements.add(statement);
 	}
+	public void clearStatements() {
+		statements = new LinkedList<Statement>();
+	}
 	
 	public String getSourceId() {
 		return sourceId;
@@ -64,5 +76,26 @@
 		this.sourceId = sourceId;
 	}
 
+	public boolean isAnonymous() {
+		return isAnonymous;
+	}
+
+	public void setAnonymous(boolean isAnonymous) {
+		this.isAnonymous = isAnonymous;
+	}
+
+
+	public String toString() {
+		String s = id + " \""+name+"\"";
+		if (isAnonymous)
+			s = " ANON:"+id;
+		if (sourceId != null)
+			s = s + " src:"+sourceId;
+		return s;
+	}
+
+
+
+
 	
 }

Added: obdapi/trunk/OBDAPI/src/org/obd/model/NodeAlias.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/NodeAlias.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/NodeAlias.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -0,0 +1,21 @@
+package org.obd.model;
+
+public class NodeAlias extends LiteralStatement {
+	public enum Scope { BROAD, NARROW, RELATED, EXACT }
+	
+	public String categoryId;
+	public Scope scope;
+	
+	public String getCategoryId() {
+		return categoryId;
+	}
+	public void setCategoryId(String categoryId) {
+		this.categoryId = categoryId;
+	}
+	public Scope getScope() {
+		return scope;
+	}
+	public void setScope(Scope scope) {
+		this.scope = scope;
+	}
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/model/Shard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/Shard.java	2007-12-09 07:00:44 UTC (rev 1298)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/Shard.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -4,18 +4,48 @@
 import java.util.HashSet;
 
 import org.obd.model.bridge.OBOBridge;
+import org.obd.model.stats.AggregateStatisticCollection;
 import org.obo.datamodel.IdentifiedObject;
 
 public interface Shard {
 	
+	public enum EntailmentUse {
+		USE_ASSERTED,
+		USE_IMPLIED,
+		FULL_TRANSITIVE_CLOSURE
+	}
+	public enum GraphExpansionAlgorithm {
+		MINIMAL,
+		INCLUDE_SUBGRAPH
+	}
+	
 	public Node getNode(String id);
 	public Collection<Node> getNodes();
 	public Collection<Node> getNodes(String sourceId);
-	public Collection<Statement> getStatements();
+	public Collection<Node> getSourceNodes();
+	
+	//public Statement getStatement(String id);
 	public Collection<Statement> getStatements(String sourceId);
+
+	public Collection<Statement> getAnnotationStatementsForAnnotatedEntity(String id, 
+			EntailmentUse entailment, GraphExpansionAlgorithm strategy);
+	public Graph getAnnotationGraphAroundNode(String id, 
+			EntailmentUse entailment, GraphExpansionAlgorithm gea);
+
 	public Collection<Statement> getStatementsForNode(String id);
-	public Collection<Statement> getStatementsForNode(String id, String sourceId);
-	public Collection<Statement> getStatementsForTarget(String id) throws Exception;
-	public Collection<Statement> getStatementsForTarget(String id, String sourceId) throws Exception;
-
+	public Collection<Statement> getStatementsForNodeWithSource(String id, String sourceId);
+	public Collection<Statement> getStatementsForTarget(String id);
+	public Collection<Statement> getStatementsForTargetWithSource(String id, String sourceId);
+	
+	public Collection<Statement> getStatements(String nodeId, 
+					String relationId, String targetId, String sourceId,
+					Boolean useImplied, Boolean isReified);
+	
+	public Collection<Statement> getSubjectStatements(String subjectId, 
+			String subjectRelationId, String targetRelationId, 
+			String nodeId, String targetId, 
+			String subjectSourceId, String nodeSourceId,
+			Boolean useImplied, Boolean isReified);
+	
+	public AggregateStatisticCollection getSummaryStatistics();
 }

Deleted: obdapi/trunk/OBDAPI/src/org/obd/model/Statement.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/Statement.java	2007-12-09 07:00:44 UTC (rev 1298)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/Statement.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -1,25 +0,0 @@
-package org.obd.model;
-
-public class Statement extends Node {
-	protected String nodeId;
-	protected String relationId;
-	protected String targetId;
-	public String getNodeId() {
-		return nodeId;
-	}
-	public void setNodeId(String nodeId) {
-		this.nodeId = nodeId;
-	}
-	public String getRelationId() {
-		return relationId;
-	}
-	public void setRelationId(String relationId) {
-		this.relationId = relationId;
-	}
-	public String getTargetId() {
-		return targetId;
-	}
-	public void setTargetId(String targetId) {
-		this.targetId = targetId;
-	}
-}

Added: obdapi/trunk/OBDAPI/src/org/obd/model/Statement.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/Statement.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/Statement.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -0,0 +1,62 @@
+package org.obd.model;
+
+/**
+ * @author cjm
+ *
+ */
+public class Statement extends Node {
+	protected String nodeId;
+	protected String relationId;
+	protected String targetId;
+	protected String positedByNodeId;
+	protected boolean isImplied;
+	
+	public boolean isImplied() {
+		return isImplied;
+	}
+	public void setImplied(boolean isImplied) {
+		this.isImplied = isImplied;
+	}
+	public String getPositedByNodeId() {
+		return positedByNodeId;
+	}
+	public void setPositedByNodeId(String positedByNodeId) {
+		this.positedByNodeId = positedByNodeId;
+	}
+	/**
+	 * @return the identifier of the node of which this statement is about
+	 */
+	public String getNodeId() {
+		return nodeId;
+	}
+	public void setNodeId(String nodeId) {
+		this.nodeId = nodeId;
+	}
+	/**
+	 * @return the identifier of the relation node used in this statement
+	 */
+	public String getRelationId() {
+		return relationId;
+	}
+	public void setRelationId(String relationId) {
+		this.relationId = relationId;
+	}
+	/**
+	 * @return the identifier of the relatum node
+	 */
+	public String getTargetId() {
+		return targetId;
+	}
+	public void setTargetId(String targetId) {
+		this.targetId = targetId;
+	}
+	
+	public String toString() {
+		String s = nodeId+" "+relationId+" "+targetId;
+		if (isImplied)
+			s = s + " [Implied]";
+		if (positedByNodeId != null)
+			s = s + "positedBy:"+positedByNodeId;
+		return s;
+	}
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBOBridge.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBOBridge.java	2007-12-09 07:00:44 UTC (rev 1298)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBOBridge.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -1,36 +1,87 @@
 package org.obd.model.bridge;
 
+import org.obd.model.LinkStatement;
+import org.obd.model.LiteralStatement;
 import org.obd.model.Node;
 import org.obd.model.Statement;
+import org.obo.annotation.datamodel.Annotation;
 import org.obo.datamodel.IdentifiedObject;
 import org.obo.datamodel.Link;
 import org.obo.datamodel.LinkedObject;
 import org.obo.datamodel.Namespace;
+import org.obo.datamodel.OBORestriction;
+import org.obo.datamodel.Synonym;
+import org.obo.datamodel.SynonymedObject;
+import org.obo.datamodel.impl.DanglingLinkImpl;
 
 public class OBOBridge {
 
+
+	
+	public static String namespace2src(Namespace ns) {
+		if (ns == null)
+			return null;
+		String src = ns.getID();
+		return "obo:"+src;
+	}
+	
+	public static Node namespace2srcNode(Namespace ns) {
+		Node n = new Node();
+		n.setId(namespace2src(ns));
+		return n;
+	}
+	
 	public static Node obj2node(IdentifiedObject io) {
+		if (io == null)
+			return null;
 		Node node = new Node();
 		node.setId(io.getID());
 		node.setName(io.getName());
-		node.setSourceId(io.getNamespace() == null ? "" : io.getNamespace().toString());
+		node.setSourceId(namespace2src(io.getNamespace()));
+		node.setAnonymous(io.isAnonymous());
 		for (Link link : ((LinkedObject)io).getParents() ) {
 			node.addStatement(link2statement(link));
 		}
+		if (io instanceof SynonymedObject) {
+			for (Synonym s : ((SynonymedObject)io).getSynonyms()) {
+				LiteralStatement ls = new LiteralStatement();
+				ls.setNodeId(node.getId());
+				ls.setValue(s.getText());
+				node.addStatement(ls);
+			}
+		}
 		return node;
 	}
 	
 	public static Statement link2statement(Link link) {
-		Statement s = new Statement();
+		LinkStatement s = new LinkStatement();
 		s.setNodeId(link.getChild().getID());
 		s.setRelationId(link.getType().getID());
 		s.setTargetId(link.getParent().getID());
-		Namespace src = link.getNamespace();
+		s.setImplied(link.isImplied());
+		if (link instanceof OBORestriction) {
+			OBORestriction rlink = (OBORestriction)link;
+			s.setAppliesToAllInstancesOf(true);
+			s.setHasIntersectionSemantics(rlink.completes());
+		}
+		String src = namespace2src(link.getNamespace());
 		if (src == null)
-			src = link.getChild().getNamespace();
+			src = namespace2src(link.getChild().getNamespace());
 		if (src != null)
-			s.setSourceId(src.getID());
+			s.setSourceId(src);
 		return s;
 	}
+	
+	public Statement annotation2statement(Annotation a) {
+		Link link = 
+			new DanglingLinkImpl(
+					a.getSubject() == null ? "" : a.getSubject().getID(),
+							a.getRelationship() == null ? "" :a.getRelationship().getID(),
+									a.getObject() == null ? "" : a.getObject().getID());
+		Statement s = OBOBridge.link2statement(link);
+		s.setPositedByNodeId(a.getID());
+		return s;
+		
+	}
 
 }

Modified: obdapi/trunk/OBDAPI/src/org/obd/model/impl/MultiShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/impl/MultiShard.java	2007-12-09 07:00:44 UTC (rev 1298)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/impl/MultiShard.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -3,17 +3,24 @@
 import java.util.Collection;
 import java.util.HashSet;
 
+import org.obd.model.Graph;
 import org.obd.model.Node;
 import org.obd.model.Shard;
 import org.obd.model.Statement;
+import org.obd.model.Shard.EntailmentUse;
+import org.obd.model.Shard.GraphExpansionAlgorithm;
+import org.obd.model.stats.AggregateStatistic;
+import org.obd.model.stats.AggregateStatisticCollection;
 
 public class MultiShard implements Shard {
 
 	Collection<Shard> shards = new HashSet<Shard>();
 
 	public Node getNode(String id) {
+		System.out.println("ms getNode: "+id);
 		for (Shard s : shards) {
 			Node n = s.getNode(id);
+			System.out.println(s+" "+n);
 			if (n != null)
 				return n;
 		}
@@ -34,12 +41,7 @@
 		return nodes;
 	}
 
-	public Collection<Statement> getStatements() {
-		HashSet<Statement> statements = new HashSet<Statement>();
-		for (Shard s : shards) 
-			statements.addAll(s.getStatements());
-		return statements;
-	}
+
 	
 	public Collection<Statement> getStatements(String sourceId) {
 		HashSet<Statement> statements = new HashSet<Statement>();
@@ -48,12 +50,18 @@
 		return statements;
 	}
 
-	public Collection<Statement> getStatementsForTarget(String id) throws Exception {
+	public Collection<Statement> getStatementsForTarget(String id)  {
 		HashSet<Statement> statements = new HashSet<Statement>();
 		for (Shard s : shards) 
 			statements.addAll(s.getStatementsForTarget(id));
 		return statements;
 	}
+	public Collection<Statement> getStatementsForTargetWithSource(String id, String sourceId) {
+		HashSet<Statement> statements = new HashSet<Statement>();
+		for (Shard s : shards) 
+			statements.addAll(s.getStatementsForTargetWithSource(id, sourceId));
+		return statements;
+	}
 
 	public Collection<Shard> getShards() {
 		return shards;
@@ -77,18 +85,65 @@
 		return statements;
 	}
 
-	public Collection<Statement> getStatementsForNode(String id, String sourceId) {
+	public Collection<Statement> getStatementsForNodeWithSource(String id, String sourceId) {
 		HashSet<Statement> statements = new HashSet<Statement>();
 		for (Shard s : shards) 
-			statements.addAll(s.getStatementsForNode(id, sourceId));
+			statements.addAll(s.getStatementsForNodeWithSource(id, sourceId));
 		return statements;
 	}
 
-	public Collection<Statement> getStatementsForTarget(String id, String sourceId) throws Exception {
+
+	public Collection<Statement> getStatements(String nodeId, String relationId, String targetId, String sourceId, Boolean useImplied, Boolean isReified) {
 		HashSet<Statement> statements = new HashSet<Statement>();
 		for (Shard s : shards) 
-			statements.addAll(s.getStatementsForTarget(id, sourceId));
+			statements.addAll(s.getStatements(nodeId, 
+					relationId,  targetId,  sourceId,  useImplied,  isReified));
 		return statements;
 	}
+
+	public Collection<Statement> getSubjectStatements(String subjectId, String subjectRelationId, String targetRelationId, String nodeId, String targetId, String subjectSourceId, String nodeSourceId, Boolean useImplied, Boolean isReified) {
+		HashSet<Statement> statements = new HashSet<Statement>();
+		for (Shard s : shards) 
+			statements.addAll(s.getSubjectStatements( subjectId, 
+					subjectRelationId,  targetRelationId,  nodeId,  targetId, 
+					subjectSourceId,  nodeSourceId,  useImplied,  isReified));
+
+		return statements;
+	}
+
+	public Collection<Statement> getAnnotationStatementsForAnnotatedEntity(String id, EntailmentUse entailment, GraphExpansionAlgorithm strategy) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	public Graph getAnnotationGraphAroundNode(String id, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
+		Graph g = new Graph();
+		for (Shard s : shards) 
+			g.merge(s.getAnnotationGraphAroundNode(id,  entailment,  gea));
+		return g;	
+		
+	}
+
+
+	public Collection<Node> getSourceNodes() {
+		HashSet<Node> nodes = new HashSet<Node>();
+		for (Shard s : shards) 
+			nodes.addAll(s.getSourceNodes());
+		return nodes;	
+	}
+
+	public AggregateStatisticCollection getSummaryStatistics() {
+		AggregateStatisticCollection combinedStats = new AggregateStatisticCollection();
+		for (Shard s : shards) {
+			AggregateStatisticCollection sc = s.getSummaryStatistics();
+			Collection<AggregateStatistic> stats;
+			if (sc != null) {
+				stats = sc.getStats();
+				combinedStats.getStats().addAll(stats);
+			}
+		}
+		return combinedStats;
+	}
+
 	
 }

Modified: obdapi/trunk/OBDAPI/src/org/obd/model/impl/OBDSQLShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/impl/OBDSQLShard.java	2007-12-09 07:00:44 UTC (rev 1298)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/impl/OBDSQLShard.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -1,108 +1,417 @@
 package org.obd.model.impl;
 
+import java.sql.ResultSet;
 import java.sql.SQLException;
+import java.util.Arrays;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.HashSet;
+import java.util.LinkedList;
 
+import org.bbop.rdbms.RelationalQuery;
+import org.bbop.rdbms.WhereClause;
+import org.bbop.rdbms.impl.SqlQueryImpl;
+import org.bbop.rdbms.impl.SqlWhereClauseImpl;
+import org.obd.model.Graph;
 import org.obd.model.Node;
 import org.obd.model.Shard;
 import org.obd.model.Statement;
 import org.obd.model.bridge.OBOBridge;
+import org.obd.model.stats.AggregateStatisticCollection;
+import org.obd.query.GraphQuery;
 import org.obo.annotation.datamodel.Annotation;
 import org.obo.dataadapter.OBDSQLDatabaseAdapter;
 import org.obo.dataadapter.OBOFileAdapter;
 import org.obo.dataadapter.OBDSQLDatabaseAdapter.OBDSQLDatabaseAdapterConfiguration;
+import org.obo.datamodel.IdentifiedObject;
 import org.obo.datamodel.Link;
 import org.obo.datamodel.LinkedObject;
 import org.obo.datamodel.OBOSession;
 import org.obo.datamodel.impl.DanglingLinkImpl;
+import org.obo.datamodel.impl.OBOSessionImpl;
 
+/**
+ * @author cjm
+ *
+ */
 public class OBDSQLShard implements Shard {
 	
-	OBOFileAdapter adapter = new OBOFileAdapter();
 	OBDSQLDatabaseAdapter obd = new OBDSQLDatabaseAdapter();
+	OBDSQLDatabaseAdapterConfiguration obdconfig = 
+		new OBDSQLDatabaseAdapter.OBDSQLDatabaseAdapterConfiguration();
 	
-	protected OBOSession session; // TODO: remove
+	protected OBOSession session =
+		new OBOSessionImpl(); // TODO: remove? need it for tracking namespaces etc
 	
 	public OBDSQLShard() throws SQLException, ClassNotFoundException {
 	}
-
-	public String getID() {
-		return "OBD-Query-Service"; // TODO: introspect metadata
-	}
 	
 	public void connect(String jdbcPath) throws SQLException, ClassNotFoundException {
-		OBDSQLDatabaseAdapterConfiguration obdconfig = 
-			new OBDSQLDatabaseAdapter.OBDSQLDatabaseAdapterConfiguration();
 		obdconfig.getReadPaths().add(jdbcPath);
 		obd = new OBDSQLDatabaseAdapter();
 		obd.setConfiguration(obdconfig);
 		obd.connect();
 	}
 
+	public String getID() {
+		return "OBD-Query-Service"; // TODO: introspect metadata
+	}
+	
 
-	public Collection<Statement> getStatementsForTarget(String id) throws Exception {
-		
+
+	public Node getNode(String id) {
+		RelationalQuery q = new SqlQueryImpl();
+		q.addTable("node_with_source");
+		WhereClause whereClause = q.getWhereClause();
+		whereClause.addEqualityConstraint("uid", id);
+		Node n = null;
+		try {
+			ResultSet rs = execute(q);
+			if (rs.next()) {
+				IdentifiedObject lo = obd.fetchObject(session, rs);
+				n = OBOBridge.obj2node(lo);
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return n;
+	}
+	
+	public Collection<Node> getNodes(String sourceId) {
+		Collection<Node> nodes = new LinkedList<Node>();
+		RelationalQuery q = new SqlQueryImpl();
+		q.addTable("node_with_source");
+		WhereClause whereClause = q.getWhereClause();
+		if (sourceId != null)
+			whereClause.addEqualityConstraint("source_uid", sourceId);
+		Node n = null;
+		try {
+			ResultSet rs = execute(q);
+			while (rs.next()) {
+				IdentifiedObject io = obd.fetchObject(session, rs);
+				nodes.add(OBOBridge.obj2node(io));
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return nodes;
+	}
+
+	public Collection<Node> getNodes() {
+		return getNodes(null);
+	}
+	
+	public Collection<Node> getSourceNodes() {
+		Collection<Node> nodes = new LinkedList<Node>();
+		RelationalQuery q = new SqlQueryImpl();
+		q.addTable("source_node");
+		WhereClause whereClause = q.getWhereClause();
+			Node n = null;
+		try {
+			ResultSet rs = execute(q);
+			while (rs.next()) {
+				IdentifiedObject io = obd.fetchObject(session, rs);
+				nodes.add(OBOBridge.obj2node(io));
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return nodes;
+	}
+
+	public Collection<Statement> getStatements() {
+		// TODO Auto-generated method stub
+		return new HashSet<Statement>();
+	}
+
+
+
+	public Collection<Statement> getStatements(String ns) {
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		if (ns != null) {
+			whereClause.addEqualityConstraint("source_uid",ns);
+		}
+		return getStatements(whereClause);
+	}
+	
+	public Collection<Statement> getStatements(WhereClause whereClause) {
 		HashSet<Statement> statements = new HashSet<Statement>();
-		for (Link link : obd.fetchLinksByObject(id)) {
-			statements.add(OBOBridge.link2statement(link));
+		try {
+			for (Link link : obd.fetchLinks(whereClause)) {
+				statements.add(OBOBridge.link2statement(link));
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
 		}
 		return statements;
+
 	}
 
-	public Collection<Statement> getAnnotationStatementsForTarget(String id) throws Exception {
-		LinkedObject obj = (LinkedObject)session.getObject(id); // TODO
+	
+	
+	public Collection<Statement> getStatementsForTarget(String id)  {
 		
 		HashSet<Statement> statements = new HashSet<Statement>();
-		for (Annotation a : obd.fetchAnnotationsByObject(session,obj)) {
-			Link link = 
-				new DanglingLinkImpl(
-						a.getSubject() == null ? "" : a.getSubject().getID(),
-								a.getRelationship() == null ? "" :a.getRelationship().getID(),
-										a.getObject() == null ? "" : a.getObject().getID());
-			statements.add(OBOBridge.link2statement(link));
+		try {
+			for (Link link : obd.fetchLinksByObject(id)) {
+				statements.add(OBOBridge.link2statement(link));
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
 		}
 		return statements;
 	}
+	
+	public Collection<Statement> getStatementsForTargetWithSource(String id, String sourceId) {
+		HashSet<Statement> statements = new HashSet<Statement>();
+		System.out.println("id="+id+" src="+sourceId);
+		try {
+			for (Link link : obd.fetchLinksByObject(id, sourceId)) {
+				statements.add(OBOBridge.link2statement(link));
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return statements;
+	}
 
-	public Node getNode(String id) {
-		// TODO Auto-generated method stub
-		return null;
+	/**
+	 * @param id
+	 * @return All statements whose target is subsumed by id
+	 * @throws Exception
+	 */
+	public Collection<Statement> getStatementsAround(String id) throws Exception {
+
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		whereClause.addConstraint("object_uid in "+
+				"(SELECT node_id FROM link_to_node WHERE object_uid ='"+id+"')");
+		return getStatements(whereClause);
 	}
+	
+	
 
-	public Collection<Node> getNodes() {
-		// TODO Auto-generated method stub
-		return new HashSet<Node>();
+
+	public Collection<Statement> getStatementsForNode(String id) {
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		whereClause.addEqualityConstraint("node_uid",id);
+		return getStatements(whereClause);
 	}
+	
+	public Collection<Statement> getStatementsForNode(String id, boolean useImplied) {
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		whereClause.addEqualityConstraint("node_uid",id);
+		if (!useImplied)
+			whereClause.addEqualityConstraint("is_inferred",false);
+		return getStatements(whereClause);
+	}
+	
 
-	public Collection<Statement> getStatements() {
-		// TODO Auto-generated method stub
-		return new HashSet<Statement>();
+	public Collection<Statement> getStatementsForNodeWithSource(String id, String ns) {
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		whereClause.addEqualityConstraint("node_uid",id);
+		if (ns != null) {
+			whereClause.addEqualityConstraint("source_uid",ns);
+		}
+		return getStatements(whereClause);
 	}
+	
+	public Collection<Statement> getStatements(String nodeId, 
+			String relationId, String targetId, String sourceId,
+			Boolean useImplied, Boolean isReified) {
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		if (nodeId != null)
+			whereClause.addEqualityConstraint("node_uid",nodeId);
+		if (relationId != null)
+			whereClause.addEqualityConstraint("pred_uid",relationId);
+		if (targetId != null)
+			whereClause.addEqualityConstraint("object_uid",targetId);
+		if (sourceId != null)
+			whereClause.addEqualityConstraint("source_uid",sourceId);
+		if (useImplied != null)
+			whereClause.addEqualityConstraint("is_inferred",useImplied);
+		if (isReified)
+			whereClause.addConstraint("reiflink_node_id IS NOT NULL");
+		return getStatements(whereClause);
+	}
+	
+	public Collection<Statement> getSubjectStatements(String subjectId, 
+			String subjectRelationId, String targetRelationId, 
+			String nodeId, String targetId, 
+			String subjectSourceId, String nodeSourceId,
+			Boolean useImplied, Boolean isReified) {
+		
+		System.out.println("getSubjectStatements "+subjectId+","+ 
+				subjectRelationId +","+ targetRelationId +"," + nodeId +","+ targetId + "," +
+				subjectSourceId + ","+ nodeSourceId +","+  useImplied +","+ isReified);
 
-	public Collection<Node> getNodes(String sourceId) {
-		// TODO Auto-generated method stub
-		return getNodes();
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		if (subjectId != null && !subjectId.equals(""))
+			whereClause.addEqualityConstraint("node_uid",subjectId);
+		if (subjectRelationId != null && !subjectRelationId.equals(""))
+			whereClause.addEqualityConstraint("pred_uid",subjectRelationId);
+		if (nodeId != null && !nodeId.equals(""))
+			whereClause.addEqualityConstraint("node_uid",nodeId);
+		if (subjectSourceId != null && !subjectSourceId.equals(""))
+			whereClause.addEqualityConstraint("source_uid",subjectSourceId);
+		if (isReified != null && isReified)
+			whereClause.addConstraint("reiflink_node_id IS NOT NULL");
+		
+		RelationalQuery subQuery = new SqlQueryImpl();
+		subQuery.getSelectClause().addColumn("node_uid");
+		subQuery.addTable("node_link_node_with_pred_and_source");
+		WhereClause subWhereClause = new SqlWhereClauseImpl();
+		subQuery.setWhereClause(subWhereClause);
+		
+		if (targetId != null && !targetId.equals(""))
+			subWhereClause.addEqualityConstraint("object_uid",targetId);
+		if (nodeSourceId != null && !nodeSourceId.equals(""))
+			subWhereClause.addEqualityConstraint("source_uid",nodeSourceId);
+		if (targetRelationId != null && !targetRelationId.equals(""))
+			subWhereClause.addEqualityConstraint("pred_uid",targetRelationId);
+		if (useImplied != null && !useImplied.equals(""))
+			subWhereClause.addEqualityConstraint("is_inferred",useImplied);
+		
+		whereClause.addInConstraint("object_uid", subQuery);
+		return getStatements(whereClause);
+
 	}
 
-	public Collection<Statement> getStatements(String sourceId) {
-		// TODO Auto-generated method stub
-		return getStatements();
+
+
+
+
+
+	
+
+
+	public Collection<Statement> getAnnotationStatementsForAnnotatedEntity(String id, EntailmentUse entailment, GraphExpansionAlgorithm strategy) {
+
+		// node_uid is the annotated entity - find everything about it -
+		// both additional metadata and annotation
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		whereClause.addEqualityConstraint("node_uid",id);
+		Collection<Statement> annots = getStatements(whereClause);
+		return annots;
 	}
 
-	public Collection<Statement> getStatementsForNode(String id) {
-		// TODO Auto-generated method stub
-		return new HashSet<Statement>();
+	public Graph getAnnotationGraphAroundNode(String id, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
+
+		// find graph around node, outwards
+		Collection<Statement> stmts;
+		if (gea == null || gea.equals(GraphExpansionAlgorithm.INCLUDE_SUBGRAPH)) {
+			 Graph sg = getSubgraph(id, entailment, gea);
+			 stmts = Arrays.asList(sg.getStatements());
+		}
+		else
+			stmts = new LinkedList<Statement>(); // TODO: minimal info?
+			 
+	
+		// find all annotations to id
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		if (true || entailment == null) {
+			// currently this is under-constrained
+			// will fetch the full graph;
+			//  G has_role* X and X R* Y, where Y is ground
+			/*
+			 * we actually want
+			 * G has_role X, X Rmd MD, X R* Y
+			 */
+			RelationalQuery subQuery = new SqlQueryImpl();
+			subQuery.getSelectClause().addColumn("node_uid");
+			subQuery.addTable("node_link_node_with_pred_and_source");
+			WhereClause subWhereClause = new SqlWhereClauseImpl();
+			subWhereClause.addEqualityConstraint("object_uid",id);			
+			subQuery.setWhereClause(subWhereClause);
+			
+			whereClause.addInConstraint("object_uid",subQuery);	
+			whereClause.addEqualityConstraint("is_inferred", false);
+		}
+		else {
+			// TODO: only works in annot links are inlcuded in deductive closure
+			whereClause.addEqualityConstraint("object_uid",id);
+		}
+		//whereClause.addConstraint("reiflink_node_id IS NOT NULL");
+		Collection<Statement> annots = getStatements(whereClause);
+		Graph g = new Graph(annots);
+		for (String nid : g.getReferencedNodeIds()) {
+			Node n = getNode(nid);
+			g.addNode(n);
+			Collection<Statement> mdLinks = getStatementsForNode(nid,false);
+			g.addStatements(mdLinks);
+		}
+		g.addStatements(stmts);
+		g.nestStatementsUnderNodes();
+		return g;
+
 	}
+	
+	public Graph getSubGraphUsingQuery(GraphQuery gq) {
 
-	public Collection<Statement> getStatementsForNode(String id, String sourceId) {
-		// TODO Auto-generated method stub
-		return getStatementsForNode(id);
+		WhereClause whereClause = new SqlWhereClauseImpl();
+
+		// node_uid is the ontology - find full DAG
+		whereClause.addEqualityConstraint("node_uid",gq.getNodeId());
+		Collection<Statement> stmts = getStatements(whereClause);
+		Graph g = new Graph(stmts);
+		return g;
 	}
+	
+	public Graph getSubgraph(String nodeId, EntailmentUse entailment,
+			GraphExpansionAlgorithm gea) {
 
-	public Collection<Statement> getStatementsForTarget(String id, String sourceId) throws Exception {
-		// TODO Auto-generated method stub
-		return getStatementsForTarget(id);
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		whereClause.addEqualityConstraint("node_uid",nodeId);
+		
+		RelationalQuery subQuery = new SqlQueryImpl();
+		subQuery.getSelectClause().addColumn("node_uid");
+		subQuery.addTable("node_link_node_with_pred_and_source");
+		WhereClause subWhereClause = new SqlWhereClauseImpl();
+		subQuery.setWhereClause(subWhereClause);
+		Collection<Statement> stmts = getStatements(whereClause);
+		Graph g = new Graph(stmts);
+		return g;
 	}
+	
+	public AggregateStatisticCollection getSummaryStatistics()  {
+		AggregateStatisticCollection sc = new AggregateStatisticCollection();
+		
+		RelationalQuery q = new SqlQueryImpl();
+		q.addTable("source_summary");		
+		ResultSet rs;
+		try {
+			rs = execute(q);
+			while (rs.next()) {
+				String src = rs.getString("uid");
+				Integer nc = rs.getInt("node_count");
+				sc.setCount("node", src, nc);
+				Integer lc = rs.getInt("link_count");
+				sc.setCount("link", src, lc);
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return sc;
+	}
+	
+	// UTIL
+	
+	public ResultSet execute(RelationalQuery q) throws SQLException {
+		ResultSet rs = q.execute(obd.getConnection());
+		return rs;
+	}
 
+
+
+	
+	
+	
+
+
 }

Modified: obdapi/trunk/OBDAPI/src/org/obd/model/impl/OBOSessionShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/impl/OBOSessionShard.java	2007-12-09 07:00:44 UTC (rev 1298)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/impl/OBOSessionShard.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -1,27 +1,27 @@
 package org.obd.model.impl;
 
-import java.sql.SQLException;
 import java.util.Collection;
+import java.util.HashMap;
 import java.util.HashSet;
+import java.util.LinkedList;
 import java.util.logging.Logger;
 
-import org.bbop.dataadapter.DataAdapterException;
+import org.obd.model.Graph;
 import org.obd.model.Node;
 import org.obd.model.Shard;
 import org.obd.model.Statement;
+import org.obd.model.Shard.EntailmentUse;
+import org.obd.model.Shard.GraphExpansionAlgorithm;
 import org.obd.model.bridge.OBOBridge;
-import org.obo.annotation.datamodel.Annotation;
-import org.obo.dataadapter.OBDSQLDatabaseAdapter;
-import org.obo.dataadapter.OBOAdapter;
+import org.obd.model.stats.AggregateStatisticCollection;
+import org.obd.model.stats.MeasuredEntity;
 import org.obo.dataadapter.OBOFileAdapter;
-import org.obo.dataadapter.OBDSQLDatabaseAdapter.OBDSQLDatabaseAdapterConfiguration;
 import org.obo.datamodel.DefinedObject;
 import org.obo.datamodel.IdentifiedObject;
 import org.obo.datamodel.Link;
 import org.obo.datamodel.LinkedObject;
 import org.obo.datamodel.Namespace;
 import org.obo.datamodel.OBOSession;
-import org.obo.datamodel.impl.DanglingLinkImpl;
 
 
 public class OBOSessionShard implements Shard {
@@ -81,16 +81,18 @@
 		HashSet<Statement> statements = new HashSet<Statement>();
 		LinkedObject obj = (LinkedObject)session.getObject(id);
 		System.out.println("obj="+obj);
-		for (Link link : obj.getParents()) {
-			System.out.println("p="+link);
-			Logger.getLogger("org.obd").info("p2s"+link);
-			statements.add(OBOBridge.link2statement(link));
+		if (obj != null ) {
+			for (Link link : obj.getParents()) {
+				System.out.println("p="+link);
+				Logger.getLogger("org.obd").info("p2s"+link);
+				statements.add(OBOBridge.link2statement(link));
+			}
 		}
 		return statements;
 	}
 	
 
-	public Collection<Statement> getStatementsForNode(String id, String sourceId) {
+	public Collection<Statement> getStatementsForNodeWithSource(String id, String sourceId) {
 		HashSet<Statement> statements = new HashSet<Statement>();
 		LinkedObject obj = (LinkedObject)session.getObject(id);
 		for (Link link : obj.getParents()) {
@@ -105,24 +107,27 @@
 	public Collection<Statement> getStatementsForTarget(String id) {
 		HashSet<Statement> statements = new HashSet<Statement>();
 		LinkedObject obj = (LinkedObject)session.getObject(id);
-		for (Link link : obj.getChildren()) {
-			statements.add(OBOBridge.link2statement(link));
+		if (obj != null) {
+			for (Link link : obj.getChildren()) {
+				statements.add(OBOBridge.link2statement(link));
+			}
 		}
 		return statements;
 	}
 	
-	public Collection<Statement> getStatementsForTarget(String id, String sourceId) {
+	public Collection<Statement> getStatementsForTargetWithSource(String id, String sourceId) {
 		HashSet<Statement> statements = new HashSet<Statement>();
 		LinkedObject obj = (LinkedObject)session.getObject(id);
-		for (Link link : obj.getChildren()) {
-			Statement s = OBOBridge.link2statement(link);
-			if (s.getSourceId().equals(sourceId))
-				statements.add(s);
+		if (obj != null) {
+			for (Link link : obj.getChildren()) {
+				Statement s = OBOBridge.link2statement(link);
+				if (s.getSourceId().equals(sourceId))
+					statements.add(s);
+			}
 		}
 		return statements;
 	}
 
-	
 	// simple types
 	public String getNodeName(String id) {
 		return session.getObject(id).getName();
@@ -132,6 +137,47 @@
 		return ((DefinedObject)session.getObject(id)).getDefinition();
 	}
 
+	public Collection<Node> getSourceNodes() {
+		Collection<Namespace> nsl = session.getNamespaces();
+		HashSet<Node> nodes = new HashSet<Node>();
+		for (Namespace ns : nsl)
+			nodes.add(OBOBridge.namespace2srcNode(ns));
+		return nodes;
+	}
+	
+	public AggregateStatisticCollection getSummaryStatistics() {
+		AggregateStatisticCollection stats = new AggregateStatisticCollection();
+		for (IdentifiedObject io : session.getObjects()) {
+			if (io.isBuiltIn())
+				continue;
+			String src = OBOBridge.namespace2src(io.getNamespace());
+			MeasuredEntity entity = stats.getMeasuredEntity("node",src);
+			stats.incrementCount(entity);
+			if (io instanceof LinkedObject) {
+				for (Link link : ((LinkedObject)io).getParents()) {
+					stats.incrementCount("link", src);
+				}
+			}
+		}
+		return stats;
+	}
 
-	
+	public Collection<Statement> getStatements(String nodeId, String relationId, String targetId, String sourceId, Boolean useImplied, Boolean isReified) {
+		return new LinkedList<Statement>();
+	}
+
+	public Collection<Statement> getSubjectStatements(String subjectId, String subjectRelationId, String targetRelationId, String nodeId, String targetId, String subjectSourceId, String nodeSourceId, Boolean useImplied, Boolean isReified) {
+		return new LinkedList<Statement>();
+	}
+
+	public Collection<Statement> getAnnotationStatementsForAnnotatedEntity(String id, EntailmentUse entailment, GraphExpansionAlgorithm strategy) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	public Graph getAnnotationGraphAroundNode(String id, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
+		return new Graph();
+	}
+
+
 }

Added: obdapi/trunk/OBDAPI/src/org/obd/model/stats/AggregateStatistic.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/stats/AggregateStatistic.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/stats/AggregateStatistic.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -0,0 +1,29 @@
+package org.obd.model.stats;
+
+import java.io.Serializable;
+
+public class AggregateStatistic implements Serializable {
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 1L;
+	
+	public enum AggregateType { COUNT, AVERAGE, MIN, MAX }
+	
+	protected AggregateType type;
+	protected MeasuredEntity measuredEntity;
+	
+	public AggregateStatistic(MeasuredEntity measuredEntity) {
+		super();
+		this.measuredEntity = measuredEntity;
+	}
+
+	public MeasuredEntity getMeasuredEntity() {
+		return measuredEntity;
+	}
+
+	public void setMeasuredEntity(MeasuredEntity measuredEntity) {
+		this.measuredEntity = measuredEntity;
+	}	
+	
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/model/stats/AggregateStatisticCollection.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/stats/AggregateStatisticCollection.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/stats/AggregateStatisticCollection.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -0,0 +1,83 @@
+package org.obd.model.stats;
+
+import java.io.Serializable;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+
+
+public class AggregateStatisticCollection implements Serializable {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 1L;
+	
+	protected String id;
+
+	protected HashMap<String,AggregateStatistic> statMap = 
+		new HashMap<String,AggregateStatistic>();
+	// for Axis2
+	protected Collection<AggregateStatistic> stats = 
+		new HashSet<AggregateStatistic>();
+
+	public AggregateStatisticCollection() {
+		super();
+	}
+
+	public void setCount(String type, String filter, Integer c) {
+		MeasuredEntity e = getMeasuredEntity(type, filter);
+		AggregateStatistic stat = getStat(e);
+		((CountStatistic)stat).setCount(c);
+	}
+	
+	public void incrementCount(MeasuredEntity entity) {
+		AggregateStatistic stat = getStat(entity);
+		((CountStatistic)stat).incrementCount();
+	}
+
+	public AggregateStatistic getStat(MeasuredEntity entity) {
+		AggregateStatistic stat = statMap.get(entity.toString());
+		if (stat == null) {
+			System.out.println("creating a new stat for "+entity);
+			stat = new CountStatistic(entity);
+			System.out.println("creating a new stat for "+entity+" / "+stat);
+			statMap.put(entity.toString(), stat);
+			stats.add(stat);
+		}
+		return stat;
+	}
+
+	public String getId() {
+		return id;
+	}
+
+	public void setId(String id) {
+		this.id = id;
+	}
+
+	public Collection<AggregateStatistic> getStats() {
+		return stats;
+	}
+	
+	
+	public void setStats(Collection<AggregateStatistic> stats) {
+		this.stats = stats;
+	}
+	
+	public void combine(AggregateStatisticCollection c) {
+		
+	}
+
+	// e.g. type=link entity=cell-ont
+	public void incrementCount(String type, String filter) {
+		MeasuredEntity entity = getMeasuredEntity(type,filter);
+		incrementCount(entity);
+	}
+	public MeasuredEntity getMeasuredEntity(String type, String filter) {
+		return new MeasuredEntity(type,filter);
+	}
+
+	
+		
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/model/stats/CountStatistic.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/stats/CountStatistic.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/stats/CountStatistic.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -0,0 +1,22 @@
+package org.obd.model.stats;
+
+public class CountStatistic extends AggregateStatistic {
+	public CountStatistic(MeasuredEntity measuredEntity) {
+		super(measuredEntity);
+		// TODO Auto-generated constructor stub
+	}
+
+	protected int count = 0;
+
+	public int getCount() {
+		return count;
+	}
+
+	public void setCount(int count) {
+		this.count = count;
+	}
+	
+	public void incrementCount() {
+		count++;
+	}
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/model/stats/MeasuredEntity.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/stats/MeasuredEntity.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/stats/MeasuredEntity.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -0,0 +1,38 @@
+package org.obd.model.stats;
+
+import java.io.Serializable;
+
+public class MeasuredEntity implements Serializable {
+	protected String type;
+	protected String filter;
+	
+	public MeasuredEntity(String type, String filter) {
+		this.type=type;
+		this.filter=filter;
+	}
+	public String getFilter() {
+		return filter;
+	}
+	public void setFilter(String filter) {
+		this.filter = filter;
+	}
+	public String getType() {
+		return type;
+	}
+	public void setType(String type) {
+		this.type = type;
+	}
+	
+	public boolean equals(MeasuredEntity e2) {
+		return e2.getType().equals(this.type) && e2.getFilter().equals(this.filter);
+	}
+	
+	public int hashCode() {
+		return this.toString().hashCode();
+	}
+
+	public String toString() {
+		return type + " by " + filter;
+	}
+	
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/model/stats/SummaryStatistics.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/stats/SummaryStatistics.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/stats/SummaryStatistics.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -0,0 +1,6 @@
+package org.obd.model.stats;
+
+public class SummaryStatistics {
+	protected String shardId;
+	
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/query/GraphQuery.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/GraphQuery.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/GraphQuery.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -0,0 +1,16 @@
+package org.obd.query;
+
+public class GraphQuery {
+	protected String nodeId;
+
+	public String getNodeId() {
+		return nodeId;
+	}
+
+	public void setNodeId(String nodeId) {
+		this.nodeId = nodeId;
+	}
+	
+	
+	
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/test/OBDQueryServiceTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/OBDQueryServiceTest.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/OBDQueryServiceTest.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -0,0 +1,76 @@
+package org.obd.test;
+
+import java.io.PrintStream;
+import java.util.logging.Logger;
+
+import org.bbop.io.AuditedPrintStream;
+import org.obd.model.Graph;
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.ws.OBDQueryService;
+import org.obo.datamodel.impl.DefaultLinkDatabase;
+import org.obo.reasoner.impl.ForwardChainingReasoner;
+import org.obo.test.OBDAnnotationSaveTest;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+public class OBDQueryServiceTest extends TestCase {
+
+	OBDQueryService service;
+	
+	
+	public OBDQueryServiceTest(String n) {
+		super(n);
+	}
+
+
+	public void setUp() throws Exception {
+		System.out.println("Setting up: " + this);
+		service = new OBDQueryService();
+		
+	}
+
+	public static Test suite() {
+		TestSuite suite = new TestSuite();
+		addTests(suite);
+		return suite;
+	}
+
+	public static void addTests(TestSuite suite) {
+		suite.addTest(new OBDQueryServiceTest("testQuery"));
+	}
+	
+	public void testQuery() {
+		String id = "GO:0006811";
+		Node node = 
+			service.getNode(id);
+		Logger.getLogger("org.obd.test").info("node="+node.getName());
+		assertTrue(node != null);
+		
+		for (Statement s : service.getStatementsForNode(id)) {
+			Logger.getLogger("org.obd.test").info("parentLink="+s);
+		}
+
+		for (Statement s : service.getStatementsForTarget(id)) {
+			Logger.getLogger("org.obd.test").info("childLink="+s);
+		}
+		
+		for (Statement s : service.getSubjectStatements(null, 
+				null, null, null, id, null, null, true, true)) {
+			Logger.getLogger("org.obd.test").info("annot="+s);
+		}
+		
+		Graph g = service.getAnnotationGraphAroundNode(id, null, null);
+		g.nestStatementsUnderNodes();
+		for (Node n : g.getNodes()) {
+			System.out.println(n);
+			for (Statement s : n.getStatements()) {
+				System.out.println("    "+s);
+			}	
+		}
+
+	}
+
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/ws/OBDQueryService.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/OBDQueryService.java	2007-12-09 07:00:44 UTC (rev 1298)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/OBDQueryService.java	2007-12-10 00:56:49 UTC (rev 1299)
@@ -1,44 +1,46 @@
 package org.obd.ws;
 
 import java.sql.SQLException;
+import java.util.Arrays;
 import java.util.Collection;
-import java.util.HashSet;
+import java.util.Collections;
 
 import org.bbop.dataadapter.DataAdapterException;
+import org.obd.model.Graph;
 import org.obd.model.Node;
 import org.obd.model.Shard;
 import org.obd.model.Statement;
+import org.obd.model.Shard.EntailmentUse;
+import org.obd.model.Shard.GraphExpansionAlgorithm;
 import org.obd.model.impl.MultiShard;
 import org.obd.model.impl.MutableOBOSessionShard;
 import org.obd.model.impl.OBDSQLShard;
-import org.obo.annotation.datamodel.Annotation;
-import org.obo.dataadapter.OBDSQLDatabaseAdapter;
-import org.obo.dataadapter.OBOAdapter;
-import org.obo.dataadapter.OBOFileAdapter;
-import org.obo.dataadapter.OBDSQLDatabaseAdapter.OBDSQLDatabaseAdapterConfiguration;
-import org.obo.datamodel.DefinedObject;
-import org.obo.datamodel.IdentifiedObject;
-import org.obo.datamodel.Link;
-import org.obo.datamodel.LinkedObject;
-import org.obo.datamodel.Namespace;
-import org.obo.datamodel.OBOSession;
-import org.obo.datamodel.impl.DanglingLinkImpl;
+import org.obd.model.stats.AggregateStatisticCollection;
 
 	
 
-public class OBDQueryService extends MultiShard implements Shard {
+public class OBDQueryService {
 	
 	//String jdbcPath = "jdbc:postgresql://spitz.lbl.gov:5432/obd_phenotype";
 	String defaultJdbcPath = "jdbc:postgresql://localhost:5432/obd_phenotype_full";
 	MultiShard shard;
 	
-	public OBDQueryService() throws SQLException, ClassNotFoundException, DataAdapterException {
+	
+	
+	public OBDQueryService() throws ClassNotFoundException, DataAdapterException {
 		shard = new MultiShard();
-		OBDSQLShard obd = new OBDSQLShard();
-		obd.connect(defaultJdbcPath);
+		
+		OBDSQLShard obd;
+		try {
+			obd = new OBDSQLShard();
+			obd.connect(defaultJdbcPath);
+			shard.addShard(obd);
+		} catch (SQLException e) {
+			e.printStackTrace();
+		}
+
 		MutableOBOSessionShard moss = new MutableOBOSessionShard();
-		moss.load("quality");
-		shard.addShard(obd);
+		moss.loadLocal("cell");
 		shard.addShard(moss);
 	}
 
@@ -47,45 +49,75 @@
 	}
 	
 	public Node getNode(String id) {
+		System.out.println("getNode: "+id);
 		return shard.getNode(id);
 	}
 	
 	// TODO - tidy this - make delegate calls match signature
 
-	public Collection<Node> getNodes() {
-		return shard.getNodes();
+	public Node[] getNodes() {
+		return (Node[])shard.getNodes().toArray(new Node[0]);
 	}
-	public Collection<Node> getNodesWithSource(String sourceId) {
-		return shard.getNodes(sourceId);
+	
+	public Node[]  getSourceNodes() {
+		return (Node[] )shard.getSourceNodes().toArray(new Node[0]);
 	}
+	public Node[] getNodesWithSource(String sourceId) {
+		return (Node[])shard.getNodes(sourceId).toArray(new Node[0]);
+	}
 
+	public Graph getGraph() {
+		return null;
+	}
 
-	public Collection<Statement> getStatements() {
-		return shard.getStatements();
+
+	
+	public Graph getAnnotationGraphAroundNode(String id, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
+		return shard.getAnnotationGraphAroundNode(id, entailment, gea);
 	}
-	public Collection<Statement> getStatementsWithSource(String sourceId) {
-		return shard.getStatements(sourceId);
+
+	public Statement getStatement(String id) {
+		//return shard.getStatements().iterator().next();
+		return null;
 	}
+	public Statement[] getStatementsWithSource(String sourceId) {
+		return (Statement[])shard.getStatements(sourceId).toArray(new Statement[0]);
+	}
 
 
-	public Collection<Statement> getStatementsForTarget(String id) throws Exception {
-		return shard.getStatementsForTarget(id);
+	public Statement[] getStatementsForTarget(String id) {
+		return (Statement[])shard.getStatementsForTarget(id).toArray(new Statement[0]);
 	}
-	public Collection<Statement> getStatementsForTargetWithSource(String id, String sourceId) throws Exception {
-		return shard.getStatementsForTarget(id, sourceId);
+	public Statement[] getStatementsForTargetWithSource(String id, String sourceId) throws Exception {
+		return (Statement[])shard.getStatementsForTargetWithSource(id, sourceId).toArray(new Statement[0]);
 	}
 
-
-	public Collection<Statement> getStatementsForNode(String id) {
-		return shard.getStatementsForNode(id);
+	
+	public  Statement[] getStatementsForNode(String id) {
+		return (Statement[])shard.getStatementsForNode(id).toArray(new Statement[0]);
 	}
-	public Collection<Statement> getStatementsForNodeWithSource(String id, String sourceId) {
+	public Statement[] getStatementsForNodeWithSource(String id, String sourceId) {
 		System.out.println("parentsFrom="+id);
-		return shard.getStatementsForNode(id, sourceId);
+		return (Statement[])shard.getStatementsForNodeWithSource(id, sourceId).toArray(new Statement[0]);
 	}
 
 
 
+	public AggregateStatisticCollection getSummaryStatistics() {
+		return shard.getSummaryStatistics();
+	}
+
+	public Statement[] getSubjectStatements(String subjectId, String subjectRelationId, String targetRelationId, String nodeId, String targetId, String subjectSourceId, String nodeSourceId, Boolean useImplied, Boolean isReified) {
+
+		System.out.println("getSubjectStatements "+subjectId+","+ 
+				subjectRelationId +","+ targetRelationId +"," + nodeId +","+ targetId + "," +
+				subjectSourceId + ","+ nodeSourceId +","+  useImplied +","+ isReified);
+
+		return (Statement[])shard.getSubjectStatements(subjectId, subjectRelationId, targetRelationId, nodeId, targetId, subjectSourceId, nodeSourceId, useImplied, isReified).toArray(new Statement[0]);
+	}
+
+
+
 	
 	
 	


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 1302
          http://obo.svn.sourceforge.net/obo/?rev=1302&view=rev
Author:   cmungall
Date:     2007-12-10 17:56:57 -0800 (Mon, 10 Dec 2007)

Log Message:
-----------


Modified Paths:
--------------
    obdapi/trunk/OBDAPI/src/org/obd/model/Graph.java
    obdapi/trunk/OBDAPI/src/org/obd/model/LinkStatement.java
    obdapi/trunk/OBDAPI/src/org/obd/model/LiteralStatement.java
    obdapi/trunk/OBDAPI/src/org/obd/model/Node.java
    obdapi/trunk/OBDAPI/src/org/obd/model/Statement.java
    obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBOBridge.java
    obdapi/trunk/OBDAPI/src/org/obd/query/GraphQuery.java
    obdapi/trunk/OBDAPI/src/org/obd/ws/OBDQueryService.java

Added Paths:
-----------
    obdapi/trunk/OBDAPI/src/org/obd/model/InstanceQuantifier.java
    obdapi/trunk/OBDAPI/src/org/obd/model/NestedCompositionalDescription.java
    obdapi/trunk/OBDAPI/src/org/obd/query/AtomicQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/ComparisonQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/QueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/Shard.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/AbstractShard.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/MutableOBOSessionShard.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBOSessionShard.java
    obdapi/trunk/OBDAPI/src/org/obd/test/AnnotationGraphTest.java
    obdapi/trunk/OBDAPI/src/org/obd/test/MiniTest.java
    obdapi/trunk/OBDAPI/src/org/obd/test/MultiNodeFetchTest.java
    obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java
    obdapi/trunk/OBDAPI/src/org/obd/test/SearchTest.java

Removed Paths:
-------------
    obdapi/trunk/OBDAPI/src/org/obd/model/Shard.java
    obdapi/trunk/OBDAPI/src/org/obd/model/impl/MultiShard.java
    obdapi/trunk/OBDAPI/src/org/obd/model/impl/MutableOBOSessionShard.java
    obdapi/trunk/OBDAPI/src/org/obd/model/impl/OBDSQLShard.java
    obdapi/trunk/OBDAPI/src/org/obd/model/impl/OBOSessionShard.java
    obdapi/trunk/OBDAPI/src/org/obd/test/OBDQueryServiceTest.java

Modified: obdapi/trunk/OBDAPI/src/org/obd/model/Graph.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/Graph.java	2007-12-10 20:13:17 UTC (rev 1301)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/Graph.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -48,6 +48,8 @@
 			nids.add(s.getNodeId());
 			nids.add(s.getTargetId());
 			nids.add(s.getRelationId());
+			if (s.getPositedByNodeId() != null)
+				nids.add(s.getPositedByNodeId());
 		}
 		return (String[]) nids.toArray(new String[0]);
 	}
@@ -62,7 +64,7 @@
 			nodeMap.put(n.getId(), n);
 	}
 	public void addNodes(Node[] nodeArr) {
-		LinkedList<Node> nodes = new LinkedList<Node>();
+		HashSet<Node> nodes = new HashSet<Node>();
 		nodes.addAll(Arrays.asList(nodeArr));
 		addNodes(nodes);
 	}
@@ -87,7 +89,7 @@
 	 * or not
 	 */
 	private Statement[] getAllStatements() {
-		LinkedList<Statement> statements = new LinkedList<Statement>();
+		HashSet<Statement> statements = new HashSet<Statement>();
 		statements.addAll(Arrays.asList(getStatements()));
 		for (Node n : getNodes()) {
 			statements.addAll(Arrays.asList(n.getStatements()));
@@ -108,7 +110,7 @@
 	
 	public void addStatements(Collection<Statement> newStatements) {
 		if (statements == null)
-			statements = new LinkedList<Statement>();
+			statements = new HashSet<Statement>();
 		statements.addAll(newStatements);
 	}
 	
@@ -119,7 +121,7 @@
 	
 	
 	public void clearStatements() {
-		statements = new LinkedList<Statement>();
+		statements = new HashSet<Statement>();
 	}
 	
 	// shift to frame-style

Added: obdapi/trunk/OBDAPI/src/org/obd/model/InstanceQuantifier.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/InstanceQuantifier.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/InstanceQuantifier.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -0,0 +1,36 @@
+package org.obd.model;
+
+public class InstanceQuantifier {
+
+	protected boolean isExistential;
+	protected boolean isUniversal;
+	protected int minCardinality;
+	protected int maxCardinality;
+	
+	public boolean isExistential() {
+		return isExistential;
+	}
+	public void setExistential(boolean isExistential) {
+		this.isExistential = isExistential;
+	}
+	public boolean isUniversal() {
+		return isUniversal;
+	}
+	public void setUniversal(boolean isUniversal) {
+		this.isUniversal = isUniversal;
+	}
+	public int getMaxCardinality() {
+		return maxCardinality;
+	}
+	public void setMaxCardinality(int maxCardinality) {
+		this.maxCardinality = maxCardinality;
+	}
+	public int getMinCardinality() {
+		return minCardinality;
+	}
+	public void setMinCardinality(int minCardinality) {
+		this.minCardinality = minCardinality;
+	}
+	
+	
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/model/LinkStatement.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/LinkStatement.java	2007-12-10 20:13:17 UTC (rev 1301)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/LinkStatement.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -3,11 +3,11 @@
 public class LinkStatement extends Statement {
 
 	protected boolean appliesToAllInstancesOf;
-	protected boolean isExistential;
-	protected boolean isUniversal;
 	protected boolean hasIntersectionSemantics;
 	protected boolean hasUnionSemantics;
+	protected InstanceQuantifier instanceQuantifier;
 	
+	
 	public boolean isAppliesToAllInstancesOf() {
 		return appliesToAllInstancesOf;
 	}
@@ -15,16 +15,26 @@
 		this.appliesToAllInstancesOf = appliesToAllInstancesOf;
 	}
 	public boolean isExistential() {
-		return isExistential;
+		if (instanceQuantifier == null)
+			return false;
+		else
+			return instanceQuantifier.isExistential();
 	}
 	public void setExistential(boolean isExistential) {
-		this.isExistential = isExistential;
+		if (instanceQuantifier == null)
+			instanceQuantifier = new InstanceQuantifier();
+		 instanceQuantifier.setExistential(isExistential);
 	}
 	public boolean isUniversal() {
-		return isUniversal;
+		if (instanceQuantifier == null)
+			return false;
+		else
+			return instanceQuantifier.isUniversal();
 	}
 	public void setUniversal(boolean isUniversal) {
-		this.isUniversal = isUniversal;
+		if (instanceQuantifier == null)
+			instanceQuantifier = new InstanceQuantifier();
+		 instanceQuantifier.setUniversal(isUniversal);
 	}
 	public boolean isHasIntersectionSemantics() {
 		return hasIntersectionSemantics;
@@ -45,4 +55,10 @@
 			s = s + " [^]";
 		return s;
 	}
+	public InstanceQuantifier getInstanceQuantifier() {
+		return instanceQuantifier;
+	}
+	public void setInstanceQuantifier(InstanceQuantifier instanceQuantifier) {
+		this.instanceQuantifier = instanceQuantifier;
+	}
 }

Modified: obdapi/trunk/OBDAPI/src/org/obd/model/LiteralStatement.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/LiteralStatement.java	2007-12-10 20:13:17 UTC (rev 1301)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/LiteralStatement.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -24,4 +24,10 @@
 		this.value = value;
 	}
 
+	public String toString() {
+		String s = super.toString();
+		s = s + " "+getValue();
+		return s;
+	}
+
 }

Added: obdapi/trunk/OBDAPI/src/org/obd/model/NestedCompositionalDescription.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/NestedCompositionalDescription.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/NestedCompositionalDescription.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -0,0 +1,18 @@
+package org.obd.model;
+
+import java.util.Collection;
+
+public class NestedCompositionalDescription {
+	public enum DescriptionType { INTERSECTION, UNION, COMPLEMENT, RESTRICTION, ATOM }
+
+	protected DescriptionType type;
+	protected Collection<NestedCompositionalDescription> children;
+	
+	public DescriptionType xxxgetType() {
+		if (children.size() == 0)
+			return DescriptionType.ATOM;
+		return null;
+	}
+	
+	
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/model/Node.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/Node.java	2007-12-10 20:13:17 UTC (rev 1301)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/Node.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -19,7 +19,7 @@
 	
 
 	public Node() {
-		statements = new LinkedList<Statement>();
+		statements = new HashSet<Statement>();
 	}
 
 	public String getId() {
@@ -65,6 +65,13 @@
 			statements = new HashSet<Statement>();
 		statements.add(statement);
 	}
+	
+	public void addStatements(Collection<Statement> newStatements) {
+		if (statements == null)
+			statements = new HashSet<Statement>();
+		statements.addAll(newStatements);
+	}
+
 	public void clearStatements() {
 		statements = new LinkedList<Statement>();
 	}
@@ -94,6 +101,9 @@
 		return s;
 	}
 
+	public int hashCode() {
+		return id.hashCode();
+	}
 
 
 

Deleted: obdapi/trunk/OBDAPI/src/org/obd/model/Shard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/Shard.java	2007-12-10 20:13:17 UTC (rev 1301)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/Shard.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -1,51 +0,0 @@
-package org.obd.model;
-
-import java.util.Collection;
-import java.util.HashSet;
-
-import org.obd.model.bridge.OBOBridge;
-import org.obd.model.stats.AggregateStatisticCollection;
-import org.obo.datamodel.IdentifiedObject;
-
-public interface Shard {
-	
-	public enum EntailmentUse {
-		USE_ASSERTED,
-		USE_IMPLIED,
-		FULL_TRANSITIVE_CLOSURE
-	}
-	public enum GraphExpansionAlgorithm {
-		MINIMAL,
-		INCLUDE_SUBGRAPH
-	}
-	
-	public Node getNode(String id);
-	public Collection<Node> getNodes();
-	public Collection<Node> getNodes(String sourceId);
-	public Collection<Node> getSourceNodes();
-	
-	//public Statement getStatement(String id);
-	public Collection<Statement> getStatements(String sourceId);
-
-	public Collection<Statement> getAnnotationStatementsForAnnotatedEntity(String id, 
-			EntailmentUse entailment, GraphExpansionAlgorithm strategy);
-	public Graph getAnnotationGraphAroundNode(String id, 
-			EntailmentUse entailment, GraphExpansionAlgorithm gea);
-
-	public Collection<Statement> getStatementsForNode(String id);
-	public Collection<Statement> getStatementsForNodeWithSource(String id, String sourceId);
-	public Collection<Statement> getStatementsForTarget(String id);
-	public Collection<Statement> getStatementsForTargetWithSource(String id, String sourceId);
-	
-	public Collection<Statement> getStatements(String nodeId, 
-					String relationId, String targetId, String sourceId,
-					Boolean useImplied, Boolean isReified);
-	
-	public Collection<Statement> getSubjectStatements(String subjectId, 
-			String subjectRelationId, String targetRelationId, 
-			String nodeId, String targetId, 
-			String subjectSourceId, String nodeSourceId,
-			Boolean useImplied, Boolean isReified);
-	
-	public AggregateStatisticCollection getSummaryStatistics();
-}

Modified: obdapi/trunk/OBDAPI/src/org/obd/model/Statement.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/Statement.java	2007-12-10 20:13:17 UTC (rev 1301)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/Statement.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -56,7 +56,12 @@
 		if (isImplied)
 			s = s + " [Implied]";
 		if (positedByNodeId != null)
-			s = s + "positedBy:"+positedByNodeId;
+			s = s + " positedBy:"+positedByNodeId;
 		return s;
 	}
+	
+	public int hashCode() {
+		return toString().hashCode();
+	}
+
 }

Modified: obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBOBridge.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBOBridge.java	2007-12-10 20:13:17 UTC (rev 1301)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBOBridge.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -3,8 +3,10 @@
 import org.obd.model.LinkStatement;
 import org.obd.model.LiteralStatement;
 import org.obd.model.Node;
+import org.obd.model.NodeAlias;
 import org.obd.model.Statement;
 import org.obo.annotation.datamodel.Annotation;
+import org.obo.datamodel.DefinedObject;
 import org.obo.datamodel.IdentifiedObject;
 import org.obo.datamodel.Link;
 import org.obo.datamodel.LinkedObject;
@@ -44,12 +46,22 @@
 		}
 		if (io instanceof SynonymedObject) {
 			for (Synonym s : ((SynonymedObject)io).getSynonyms()) {
-				LiteralStatement ls = new LiteralStatement();
+				LiteralStatement ls = new NodeAlias();
 				ls.setNodeId(node.getId());
 				ls.setValue(s.getText());
 				node.addStatement(ls);
 			}
 		}
+		if (io instanceof DefinedObject) {
+			String def = ((DefinedObject)io).getDefinition();
+			if (def != null) {
+				LiteralStatement ls = new LiteralStatement();
+				ls.setNodeId(node.getId());
+				ls.setValue(def);
+				ls.setRelationId("definition");
+				node.addStatement(ls);
+			}
+		}
 		return node;
 	}
 	

Deleted: obdapi/trunk/OBDAPI/src/org/obd/model/impl/MultiShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/impl/MultiShard.java	2007-12-10 20:13:17 UTC (rev 1301)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/impl/MultiShard.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -1,149 +0,0 @@
-package org.obd.model.impl;
-
-import java.util.Collection;
-import java.util.HashSet;
-
-import org.obd.model.Graph;
-import org.obd.model.Node;
-import org.obd.model.Shard;
-import org.obd.model.Statement;
-import org.obd.model.Shard.EntailmentUse;
-import org.obd.model.Shard.GraphExpansionAlgorithm;
-import org.obd.model.stats.AggregateStatistic;
-import org.obd.model.stats.AggregateStatisticCollection;
-
-public class MultiShard implements Shard {
-
-	Collection<Shard> shards = new HashSet<Shard>();
-
-	public Node getNode(String id) {
-		System.out.println("ms getNode: "+id);
-		for (Shard s : shards) {
-			Node n = s.getNode(id);
-			System.out.println(s+" "+n);
-			if (n != null)
-				return n;
-		}
-		return null;
-	}
-
-	public Collection<Node> getNodes() {
-		HashSet<Node> nodes = new HashSet<Node>();
-		for (Shard s : shards) 
-			nodes.addAll(s.getNodes());
-		return nodes;
-	}
-	
-	public Collection<Node> getNodes(String sourceId) {
-		HashSet<Node> nodes = new HashSet<Node>();
-		for (Shard s : shards) 
-			nodes.addAll(s.getNodes(sourceId));
-		return nodes;
-	}
-
-
-	
-	public Collection<Statement> getStatements(String sourceId) {
-		HashSet<Statement> statements = new HashSet<Statement>();
-		for (Shard s : shards) 
-			statements.addAll(s.getStatements(sourceId));
-		return statements;
-	}
-
-	public Collection<Statement> getStatementsForTarget(String id)  {
-		HashSet<Statement> statements = new HashSet<Statement>();
-		for (Shard s : shards) 
-			statements.addAll(s.getStatementsForTarget(id));
-		return statements;
-	}
-	public Collection<Statement> getStatementsForTargetWithSource(String id, String sourceId) {
-		HashSet<Statement> statements = new HashSet<Statement>();
-		for (Shard s : shards) 
-			statements.addAll(s.getStatementsForTargetWithSource(id, sourceId));
-		return statements;
-	}
-
-	public Collection<Shard> getShards() {
-		return shards;
-	}
-
-	public void setShards(Collection<Shard> shards) {
-		this.shards = shards;
-	}
-	
-	public void addShard(Shard shard) {
-		if (shards == null)
-			shards = new HashSet<Shard>();
-		shards.add(shard);
-	}
-
-	public Collection<Statement> getStatementsForNode(String id) {
-		HashSet<Statement> statements = new HashSet<Statement>();
-		System.out.println("getting parents for="+id);
-		for (Shard s : shards) 
-			statements.addAll(s.getStatementsForNode(id));
-		return statements;
-	}
-
-	public Collection<Statement> getStatementsForNodeWithSource(String id, String sourceId) {
-		HashSet<Statement> statements = new HashSet<Statement>();
-		for (Shard s : shards) 
-			statements.addAll(s.getStatementsForNodeWithSource(id, sourceId));
-		return statements;
-	}
-
-
-	public Collection<Statement> getStatements(String nodeId, String relationId, String targetId, String sourceId, Boolean useImplied, Boolean isReified) {
-		HashSet<Statement> statements = new HashSet<Statement>();
-		for (Shard s : shards) 
-			statements.addAll(s.getStatements(nodeId, 
-					relationId,  targetId,  sourceId,  useImplied,  isReified));
-		return statements;
-	}
-
-	public Collection<Statement> getSubjectStatements(String subjectId, String subjectRelationId, String targetRelationId, String nodeId, String targetId, String subjectSourceId, String nodeSourceId, Boolean useImplied, Boolean isReified) {
-		HashSet<Statement> statements = new HashSet<Statement>();
-		for (Shard s : shards) 
-			statements.addAll(s.getSubjectStatements( subjectId, 
-					subjectRelationId,  targetRelationId,  nodeId,  targetId, 
-					subjectSourceId,  nodeSourceId,  useImplied,  isReified));
-
-		return statements;
-	}
-
-	public Collection<Statement> getAnnotationStatementsForAnnotatedEntity(String id, EntailmentUse entailment, GraphExpansionAlgorithm strategy) {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	public Graph getAnnotationGraphAroundNode(String id, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
-		Graph g = new Graph();
-		for (Shard s : shards) 
-			g.merge(s.getAnnotationGraphAroundNode(id,  entailment,  gea));
-		return g;	
-		
-	}
-
-
-	public Collection<Node> getSourceNodes() {
-		HashSet<Node> nodes = new HashSet<Node>();
-		for (Shard s : shards) 
-			nodes.addAll(s.getSourceNodes());
-		return nodes;	
-	}
-
-	public AggregateStatisticCollection getSummaryStatistics() {
-		AggregateStatisticCollection combinedStats = new AggregateStatisticCollection();
-		for (Shard s : shards) {
-			AggregateStatisticCollection sc = s.getSummaryStatistics();
-			Collection<AggregateStatistic> stats;
-			if (sc != null) {
-				stats = sc.getStats();
-				combinedStats.getStats().addAll(stats);
-			}
-		}
-		return combinedStats;
-	}
-
-	
-}

Deleted: obdapi/trunk/OBDAPI/src/org/obd/model/impl/MutableOBOSessionShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/impl/MutableOBOSessionShard.java	2007-12-10 20:13:17 UTC (rev 1301)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/impl/MutableOBOSessionShard.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -1,29 +0,0 @@
-package org.obd.model.impl;
-
-import org.bbop.dataadapter.DataAdapterException;
-import org.obo.dataadapter.OBOAdapter;
-import org.obo.dataadapter.OBOFileAdapter;
-
-public class MutableOBOSessionShard extends OBOSessionShard {
-
-	public int loadLocal(String ontName) throws DataAdapterException {
-		String path = "/users/cjm/obo-all/"+ontName+"/"+ontName+".obo";
-		return loadFile(path);
-	}
-	public int load(String ontName) throws DataAdapterException {
-		String path = "http://purl.org/obo/obo-all/"+ontName+"/"+ontName+".obo";
-		return loadFile(path);
-	}
-	public int loadFile(String path) throws DataAdapterException {
-		OBOFileAdapter.OBOAdapterConfiguration config = new OBOFileAdapter.OBOAdapterConfiguration();
-		config.getReadPaths().add(path);
-		
-		config.setAllowDangling(true);
-		config.setBasicSave(false);
-		config.setFailFast(false);
-		session = adapter.doOperation(OBOAdapter.READ_ONTOLOGY, config,
-				null);
-		return session.getObjects().size();
-	}
-
-}

Deleted: obdapi/trunk/OBDAPI/src/org/obd/model/impl/OBDSQLShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/impl/OBDSQLShard.java	2007-12-10 20:13:17 UTC (rev 1301)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/impl/OBDSQLShard.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -1,417 +0,0 @@
-package org.obd.model.impl;
-
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.LinkedList;
-
-import org.bbop.rdbms.RelationalQuery;
-import org.bbop.rdbms.WhereClause;
-import org.bbop.rdbms.impl.SqlQueryImpl;
-import org.bbop.rdbms.impl.SqlWhereClauseImpl;
-import org.obd.model.Graph;
-import org.obd.model.Node;
-import org.obd.model.Shard;
-import org.obd.model.Statement;
-import org.obd.model.bridge.OBOBridge;
-import org.obd.model.stats.AggregateStatisticCollection;
-import org.obd.query.GraphQuery;
-import org.obo.annotation.datamodel.Annotation;
-import org.obo.dataadapter.OBDSQLDatabaseAdapter;
-import org.obo.dataadapter.OBOFileAdapter;
-import org.obo.dataadapter.OBDSQLDatabaseAdapter.OBDSQLDatabaseAdapterConfiguration;
-import org.obo.datamodel.IdentifiedObject;
-import org.obo.datamodel.Link;
-import org.obo.datamodel.LinkedObject;
-import org.obo.datamodel.OBOSession;
-import org.obo.datamodel.impl.DanglingLinkImpl;
-import org.obo.datamodel.impl.OBOSessionImpl;
-
-/**
- * @author cjm
- *
- */
-public class OBDSQLShard implements Shard {
-	
-	OBDSQLDatabaseAdapter obd = new OBDSQLDatabaseAdapter();
-	OBDSQLDatabaseAdapterConfiguration obdconfig = 
-		new OBDSQLDatabaseAdapter.OBDSQLDatabaseAdapterConfiguration();
-	
-	protected OBOSession session =
-		new OBOSessionImpl(); // TODO: remove? need it for tracking namespaces etc
-	
-	public OBDSQLShard() throws SQLException, ClassNotFoundException {
-	}
-	
-	public void connect(String jdbcPath) throws SQLException, ClassNotFoundException {
-		obdconfig.getReadPaths().add(jdbcPath);
-		obd = new OBDSQLDatabaseAdapter();
-		obd.setConfiguration(obdconfig);
-		obd.connect();
-	}
-
-	public String getID() {
-		return "OBD-Query-Service"; // TODO: introspect metadata
-	}
-	
-
-
-	public Node getNode(String id) {
-		RelationalQuery q = new SqlQueryImpl();
-		q.addTable("node_with_source");
-		WhereClause whereClause = q.getWhereClause();
-		whereClause.addEqualityConstraint("uid", id);
-		Node n = null;
-		try {
-			ResultSet rs = execute(q);
-			if (rs.next()) {
-				IdentifiedObject lo = obd.fetchObject(session, rs);
-				n = OBOBridge.obj2node(lo);
-			}
-		} catch (SQLException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-		return n;
-	}
-	
-	public Collection<Node> getNodes(String sourceId) {
-		Collection<Node> nodes = new LinkedList<Node>();
-		RelationalQuery q = new SqlQueryImpl();
-		q.addTable("node_with_source");
-		WhereClause whereClause = q.getWhereClause();
-		if (sourceId != null)
-			whereClause.addEqualityConstraint("source_uid", sourceId);
-		Node n = null;
-		try {
-			ResultSet rs = execute(q);
-			while (rs.next()) {
-				IdentifiedObject io = obd.fetchObject(session, rs);
-				nodes.add(OBOBridge.obj2node(io));
-			}
-		} catch (SQLException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-		return nodes;
-	}
-
-	public Collection<Node> getNodes() {
-		return getNodes(null);
-	}
-	
-	public Collection<Node> getSourceNodes() {
-		Collection<Node> nodes = new LinkedList<Node>();
-		RelationalQuery q = new SqlQueryImpl();
-		q.addTable("source_node");
-		WhereClause whereClause = q.getWhereClause();
-			Node n = null;
-		try {
-			ResultSet rs = execute(q);
-			while (rs.next()) {
-				IdentifiedObject io = obd.fetchObject(session, rs);
-				nodes.add(OBOBridge.obj2node(io));
-			}
-		} catch (SQLException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-		return nodes;
-	}
-
-	public Collection<Statement> getStatements() {
-		// TODO Auto-generated method stub
-		return new HashSet<Statement>();
-	}
-
-
-
-	public Collection<Statement> getStatements(String ns) {
-		WhereClause whereClause = new SqlWhereClauseImpl();
-		if (ns != null) {
-			whereClause.addEqualityConstraint("source_uid",ns);
-		}
-		return getStatements(whereClause);
-	}
-	
-	public Collection<Statement> getStatements(WhereClause whereClause) {
-		HashSet<Statement> statements = new HashSet<Statement>();
-		try {
-			for (Link link : obd.fetchLinks(whereClause)) {
-				statements.add(OBOBridge.link2statement(link));
-			}
-		} catch (SQLException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-		return statements;
-
-	}
-
-	
-	
-	public Collection<Statement> getStatementsForTarget(String id)  {
-		
-		HashSet<Statement> statements = new HashSet<Statement>();
-		try {
-			for (Link link : obd.fetchLinksByObject(id)) {
-				statements.add(OBOBridge.link2statement(link));
-			}
-		} catch (SQLException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-		return statements;
-	}
-	
-	public Collection<Statement> getStatementsForTargetWithSource(String id, String sourceId) {
-		HashSet<Statement> statements = new HashSet<Statement>();
-		System.out.println("id="+id+" src="+sourceId);
-		try {
-			for (Link link : obd.fetchLinksByObject(id, sourceId)) {
-				statements.add(OBOBridge.link2statement(link));
-			}
-		} catch (SQLException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-		return statements;
-	}
-
-	/**
-	 * @param id
-	 * @return All statements whose target is subsumed by id
-	 * @throws Exception
-	 */
-	public Collection<Statement> getStatementsAround(String id) throws Exception {
-
-		WhereClause whereClause = new SqlWhereClauseImpl();
-		whereClause.addConstraint("object_uid in "+
-				"(SELECT node_id FROM link_to_node WHERE object_uid ='"+id+"')");
-		return getStatements(whereClause);
-	}
-	
-	
-
-
-	public Collection<Statement> getStatementsForNode(String id) {
-		WhereClause whereClause = new SqlWhereClauseImpl();
-		whereClause.addEqualityConstraint("node_uid",id);
-		return getStatements(whereClause);
-	}
-	
-	public Collection<Statement> getStatementsForNode(String id, boolean useImplied) {
-		WhereClause whereClause = new SqlWhereClauseImpl();
-		whereClause.addEqualityConstraint("node_uid",id);
-		if (!useImplied)
-			whereClause.addEqualityConstraint("is_inferred",false);
-		return getStatements(whereClause);
-	}
-	
-
-	public Collection<Statement> getStatementsForNodeWithSource(String id, String ns) {
-		WhereClause whereClause = new SqlWhereClauseImpl();
-		whereClause.addEqualityConstraint("node_uid",id);
-		if (ns != null) {
-			whereClause.addEqualityConstraint("source_uid",ns);
-		}
-		return getStatements(whereClause);
-	}
-	
-	public Collection<Statement> getStatements(String nodeId, 
-			String relationId, String targetId, String sourceId,
-			Boolean useImplied, Boolean isReified) {
-		WhereClause whereClause = new SqlWhereClauseImpl();
-		if (nodeId != null)
-			whereClause.addEqualityConstraint("node_uid",nodeId);
-		if (relationId != null)
-			whereClause.addEqualityConstraint("pred_uid",relationId);
-		if (targetId != null)
-			whereClause.addEqualityConstraint("object_uid",targetId);
-		if (sourceId != null)
-			whereClause.addEqualityConstraint("source_uid",sourceId);
-		if (useImplied != null)
-			whereClause.addEqualityConstraint("is_inferred",useImplied);
-		if (isReified)
-			whereClause.addConstraint("reiflink_node_id IS NOT NULL");
-		return getStatements(whereClause);
-	}
-	
-	public Collection<Statement> getSubjectStatements(String subjectId, 
-			String subjectRelationId, String targetRelationId, 
-			String nodeId, String targetId, 
-			String subjectSourceId, String nodeSourceId,
-			Boolean useImplied, Boolean isReified) {
-		
-		System.out.println("getSubjectStatements "+subjectId+","+ 
-				subjectRelationId +","+ targetRelationId +"," + nodeId +","+ targetId + "," +
-				subjectSourceId + ","+ nodeSourceId +","+  useImplied +","+ isReified);
-
-		WhereClause whereClause = new SqlWhereClauseImpl();
-		if (subjectId != null && !subjectId.equals(""))
-			whereClause.addEqualityConstraint("node_uid",subjectId);
-		if (subjectRelationId != null && !subjectRelationId.equals(""))
-			whereClause.addEqualityConstraint("pred_uid",subjectRelationId);
-		if (nodeId != null && !nodeId.equals(""))
-			whereClause.addEqualityConstraint("node_uid",nodeId);
-		if (subjectSourceId != null && !subjectSourceId.equals(""))
-			whereClause.addEqualityConstraint("source_uid",subjectSourceId);
-		if (isReified != null && isReified)
-			whereClause.addConstraint("reiflink_node_id IS NOT NULL");
-		
-		RelationalQuery subQuery = new SqlQueryImpl();
-		subQuery.getSelectClause().addColumn("node_uid");
-		subQuery.addTable("node_link_node_with_pred_and_source");
-		WhereClause subWhereClause = new SqlWhereClauseImpl();
-		subQuery.setWhereClause(subWhereClause);
-		
-		if (targetId != null && !targetId.equals(""))
-			subWhereClause.addEqualityConstraint("object_uid",targetId);
-		if (nodeSourceId != null && !nodeSourceId.equals(""))
-			subWhereClause.addEqualityConstraint("source_uid",nodeSourceId);
-		if (targetRelationId != null && !targetRelationId.equals(""))
-			subWhereClause.addEqualityConstraint("pred_uid",targetRelationId);
-		if (useImplied != null && !useImplied.equals(""))
-			subWhereClause.addEqualityConstraint("is_inferred",useImplied);
-		
-		whereClause.addInConstraint("object_uid", subQuery);
-		return getStatements(whereClause);
-
-	}
-
-
-
-
-
-
-	
-
-
-	public Collection<Statement> getAnnotationStatementsForAnnotatedEntity(String id, EntailmentUse entailment, GraphExpansionAlgorithm strategy) {
-
-		// node_uid is the annotated entity - find everything about it -
-		// both additional metadata and annotation
-		WhereClause whereClause = new SqlWhereClauseImpl();
-		whereClause.addEqualityConstraint("node_uid",id);
-		Collection<Statement> annots = getStatements(whereClause);
-		return annots;
-	}
-
-	public Graph getAnnotationGraphAroundNode(String id, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
-
-		// find graph around node, outwards
-		Collection<Statement> stmts;
-		if (gea == null || gea.equals(GraphExpansionAlgorithm.INCLUDE_SUBGRAPH)) {
-			 Graph sg = getSubgraph(id, entailment, gea);
-			 stmts = Arrays.asList(sg.getStatements());
-		}
-		else
-			stmts = new LinkedList<Statement>(); // TODO: minimal info?
-			 
-	
-		// find all annotations to id
-		WhereClause whereClause = new SqlWhereClauseImpl();
-		if (true || entailment == null) {
-			// currently this is under-constrained
-			// will fetch the full graph;
-			//  G has_role* X and X R* Y, where Y is ground
-			/*
-			 * we actually want
-			 * G has_role X, X Rmd MD, X R* Y
-			 */
-			RelationalQuery subQuery = new SqlQueryImpl();
-			subQuery.getSelectClause().addColumn("node_uid");
-			subQuery.addTable("node_link_node_with_pred_and_source");
-			WhereClause subWhereClause = new SqlWhereClauseImpl();
-			subWhereClause.addEqualityConstraint("object_uid",id);			
-			subQuery.setWhereClause(subWhereClause);
-			
-			whereClause.addInConstraint("object_uid",subQuery);	
-			whereClause.addEqualityConstraint("is_inferred", false);
-		}
-		else {
-			// TODO: only works in annot links are inlcuded in deductive closure
-			whereClause.addEqualityConstraint("object_uid",id);
-		}
-		//whereClause.addConstraint("reiflink_node_id IS NOT NULL");
-		Collection<Statement> annots = getStatements(whereClause);
-		Graph g = new Graph(annots);
-		for (String nid : g.getReferencedNodeIds()) {
-			Node n = getNode(nid);
-			g.addNode(n);
-			Collection<Statement> mdLinks = getStatementsForNode(nid,false);
-			g.addStatements(mdLinks);
-		}
-		g.addStatements(stmts);
-		g.nestStatementsUnderNodes();
-		return g;
-
-	}
-	
-	public Graph getSubGraphUsingQuery(GraphQuery gq) {
-
-		WhereClause whereClause = new SqlWhereClauseImpl();
-
-		// node_uid is the ontology - find full DAG
-		whereClause.addEqualityConstraint("node_uid",gq.getNodeId());
-		Collection<Statement> stmts = getStatements(whereClause);
-		Graph g = new Graph(stmts);
-		return g;
-	}
-	
-	public Graph getSubgraph(String nodeId, EntailmentUse entailment,
-			GraphExpansionAlgorithm gea) {
-
-		WhereClause whereClause = new SqlWhereClauseImpl();
-		whereClause.addEqualityConstraint("node_uid",nodeId);
-		
-		RelationalQuery subQuery = new SqlQueryImpl();
-		subQuery.getSelectClause().addColumn("node_uid");
-		subQuery.addTable("node_link_node_with_pred_and_source");
-		WhereClause subWhereClause = new SqlWhereClauseImpl();
-		subQuery.setWhereClause(subWhereClause);
-		Collection<Statement> stmts = getStatements(whereClause);
-		Graph g = new Graph(stmts);
-		return g;
-	}
-	
-	public AggregateStatisticCollection getSummaryStatistics()  {
-		AggregateStatisticCollection sc = new AggregateStatisticCollection();
-		
-		RelationalQuery q = new SqlQueryImpl();
-		q.addTable("source_summary");		
-		ResultSet rs;
-		try {
-			rs = execute(q);
-			while (rs.next()) {
-				String src = rs.getString("uid");
-				Integer nc = rs.getInt("node_count");
-				sc.setCount("node", src, nc);
-				Integer lc = rs.getInt("link_count");
-				sc.setCount("link", src, lc);
-			}
-		} catch (SQLException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-		return sc;
-	}
-	
-	// UTIL
-	
-	public ResultSet execute(RelationalQuery q) throws SQLException {
-		ResultSet rs = q.execute(obd.getConnection());
-		return rs;
-	}
-
-
-
-	
-	
-	
-
-
-}

Deleted: obdapi/trunk/OBDAPI/src/org/obd/model/impl/OBOSessionShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/impl/OBOSessionShard.java	2007-12-10 20:13:17 UTC (rev 1301)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/impl/OBOSessionShard.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -1,183 +0,0 @@
-package org.obd.model.impl;
-
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.logging.Logger;
-
-import org.obd.model.Graph;
-import org.obd.model.Node;
-import org.obd.model.Shard;
-import org.obd.model.Statement;
-import org.obd.model.Shard.EntailmentUse;
-import org.obd.model.Shard.GraphExpansionAlgorithm;
-import org.obd.model.bridge.OBOBridge;
-import org.obd.model.stats.AggregateStatisticCollection;
-import org.obd.model.stats.MeasuredEntity;
-import org.obo.dataadapter.OBOFileAdapter;
-import org.obo.datamodel.DefinedObject;
-import org.obo.datamodel.IdentifiedObject;
-import org.obo.datamodel.Link;
-import org.obo.datamodel.LinkedObject;
-import org.obo.datamodel.Namespace;
-import org.obo.datamodel.OBOSession;
-
-
-public class OBOSessionShard implements Shard {
-	OBOFileAdapter adapter = new OBOFileAdapter();
-	
-	protected OBOSession session;
-		
-	// node fetching
-	public Node getNode(String id) {
-		Node node = OBOBridge.obj2node(session.getObject(id));
-		//node.serial
-		return node;
-	}
-	
-	public Collection<Node> getNodes() {
-		HashSet<Node> nodes = new HashSet<Node>();
-		for (IdentifiedObject io : session.getObjects()) {
-			if (io.isBuiltIn())
-				continue;
-			nodes.add(OBOBridge.obj2node(io));
-		}
-		return nodes;
-	}
-	
-	public Collection<Node> getNodes(String sourceId) {
-		HashSet<Node> nodes = new HashSet<Node>();
-		for (IdentifiedObject io : session.getObjects()) {
-			if (io.isBuiltIn())
-				continue;
-			if (io.getNamespace() != null && io.getNamespace().getID().equals(sourceId))
-				nodes.add(OBOBridge.obj2node(io));
-		}
-		return nodes;
-	}
-
-	
-	// simple types
-	public Collection<String> getNodeIDs() {
-		HashSet<String> ids = new HashSet<String>();
-		for (IdentifiedObject io : session.getObjects()) {
-			ids.add(io.getID());
-		}
-		return ids;
-	}		
-
-	public Collection<Statement> getStatements() {
-		// TODO Auto-generated method stub
-		return new HashSet<Statement>();
-	}
-	
-	public Collection<Statement> getStatements(String sourceId) {
-		// TODO Auto-generated method stub
-		return new HashSet<Statement>();
-	}
-
-	public Collection<Statement> getStatementsForNode(String id) {
-		HashSet<Statement> statements = new HashSet<Statement>();
-		LinkedObject obj = (LinkedObject)session.getObject(id);
-		System.out.println("obj="+obj);
-		if (obj != null ) {
-			for (Link link : obj.getParents()) {
-				System.out.println("p="+link);
-				Logger.getLogger("org.obd").info("p2s"+link);
-				statements.add(OBOBridge.link2statement(link));
-			}
-		}
-		return statements;
-	}
-	
-
-	public Collection<Statement> getStatementsForNodeWithSource(String id, String sourceId) {
-		HashSet<Statement> statements = new HashSet<Statement>();
-		LinkedObject obj = (LinkedObject)session.getObject(id);
-		for (Link link : obj.getParents()) {
-			Statement s = OBOBridge.link2statement(link);
-			if (s.getSourceId().equals(sourceId))
-				statements.add(s);
-		}
-		return statements;
-	}
-
-
-	public Collection<Statement> getStatementsForTarget(String id) {
-		HashSet<Statement> statements = new HashSet<Statement>();
-		LinkedObject obj = (LinkedObject)session.getObject(id);
-		if (obj != null) {
-			for (Link link : obj.getChildren()) {
-				statements.add(OBOBridge.link2statement(link));
-			}
-		}
-		return statements;
-	}
-	
-	public Collection<Statement> getStatementsForTargetWithSource(String id, String sourceId) {
-		HashSet<Statement> statements = new HashSet<Statement>();
-		LinkedObject obj = (LinkedObject)session.getObject(id);
-		if (obj != null) {
-			for (Link link : obj.getChildren()) {
-				Statement s = OBOBridge.link2statement(link);
-				if (s.getSourceId().equals(sourceId))
-					statements.add(s);
-			}
-		}
-		return statements;
-	}
-
-	// simple types
-	public String getNodeName(String id) {
-		return session.getObject(id).getName();
-	}
-	
-	public String getNodeDef(String id) {
-		return ((DefinedObject)session.getObject(id)).getDefinition();
-	}
-
-	public Collection<Node> getSourceNodes() {
-		Collection<Namespace> nsl = session.getNamespaces();
-		HashSet<Node> nodes = new HashSet<Node>();
-		for (Namespace ns : nsl)
-			nodes.add(OBOBridge.namespace2srcNode(ns));
-		return nodes;
-	}
-	
-	public AggregateStatisticCollection getSummaryStatistics() {
-		AggregateStatisticCollection stats = new AggregateStatisticCollection();
-		for (IdentifiedObject io : session.getObjects()) {
-			if (io.isBuiltIn())
-				continue;
-			String src = OBOBridge.namespace2src(io.getNamespace());
-			MeasuredEntity entity = stats.getMeasuredEntity("node",src);
-			stats.incrementCount(entity);
-			if (io instanceof LinkedObject) {
-				for (Link link : ((LinkedObject)io).getParents()) {
-					stats.incrementCount("link", src);
-				}
-			}
-		}
-		return stats;
-	}
-
-	public Collection<Statement> getStatements(String nodeId, String relationId, String targetId, String sourceId, Boolean useImplied, Boolean isReified) {
-		return new LinkedList<Statement>();
-	}
-
-	public Collection<Statement> getSubjectStatements(String subjectId, String subjectRelationId, String targetRelationId, String nodeId, String targetId, String subjectSourceId, String nodeSourceId, Boolean useImplied, Boolean isReified) {
-		return new LinkedList<Statement>();
-	}
-
-	public Collection<Statement> getAnnotationStatementsForAnnotatedEntity(String id, EntailmentUse entailment, GraphExpansionAlgorithm strategy) {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	public Graph getAnnotationGraphAroundNode(String id, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
-		return new Graph();
-	}
-
-
-}

Added: obdapi/trunk/OBDAPI/src/org/obd/query/AtomicQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/AtomicQueryTerm.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/AtomicQueryTerm.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -0,0 +1,24 @@
+package org.obd.query;
+
+public class AtomicQueryTerm extends QueryTerm {
+
+	protected String value;
+
+	public AtomicQueryTerm(String value) {
+		super();
+		this.value = value;
+	}
+
+	public String getValue() {
+		return value;
+	}
+
+	public void setValue(String value) {
+		this.value = value;
+	}
+
+	public String toString() {
+		return getValue().toString();
+	}
+
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/query/ComparisonQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/ComparisonQueryTerm.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/ComparisonQueryTerm.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -0,0 +1,43 @@
+package org.obd.query;
+
+public class ComparisonQueryTerm extends QueryTerm {
+	public enum Operator {EQUALS, STARTS_WITH, CONTAINS}
+	
+	protected Operator operator;
+	protected QueryTerm value;	
+
+	public ComparisonQueryTerm(Operator operator, String valueAtom) {
+		super();
+		this.operator = operator;
+		this.value = new AtomicQueryTerm(valueAtom);
+	}
+	public ComparisonQueryTerm(Operator operator, QueryTerm value) {
+		super();
+		this.operator = operator;
+		this.value = value;
+	}
+
+	public Operator getOperator() {
+		return operator;
+	}
+
+	public void setOperator(Operator operator) {
+		this.operator = operator;
+	}
+
+	public QueryTerm getValue() {
+		return value;
+	}
+
+	public void setValue(QueryTerm value) {
+		this.value = value;
+	}
+	
+	public String toString() {
+		String s = operator.toString();
+		if (getValue() != null)
+			s = s + " "+getValue().toString();
+		return s;
+	}
+
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/GraphQuery.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/GraphQuery.java	2007-12-10 20:13:17 UTC (rev 1301)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/GraphQuery.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -12,5 +12,4 @@
 	}
 	
 	
-	
 }

Added: obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -0,0 +1,50 @@
+package org.obd.query;
+
+public class LinkQueryTerm extends QueryTerm {
+	protected QueryTerm target;
+	
+	
+	/**
+	 * Example: anything that is part of something that develops from the imaginal disc
+	 *   LinkStatementQueryTerm(partOf,
+	 *           new LinkStatementQueryTerm(developsFrom, 
+	 *                     new LiteralStatementQueryTerm(NAME, "imaginal disc")))
+	 *                     
+	 * @param relation
+	 * @param target
+	 */
+	public LinkQueryTerm(String relation, QueryTerm target) {
+		super();
+		this.relation = new AtomicQueryTerm(relation);
+		this.target = target;
+	}
+	public LinkQueryTerm(QueryTerm relation, QueryTerm target) {
+		super();
+		this.relation = relation;
+		this.target = target;
+	}
+
+	public LinkQueryTerm(String relationAtom, String targetAtom) {
+		super();
+		this.relation = new AtomicQueryTerm(relationAtom);
+		this.target = new AtomicQueryTerm(targetAtom);
+	}
+	
+	
+	public QueryTerm getTarget() {
+		return target;
+	}
+
+	public void setTarget(QueryTerm target) {
+		this.target = target;
+	}
+
+	public String toString() {
+		String s = getRelation().toString();
+		if (getTarget() != null)
+			s = s + " "+getTarget().toString();
+		return s;
+	}
+
+
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -0,0 +1,49 @@
+package org.obd.query;
+
+public class LiteralQueryTerm extends QueryTerm {
+	public enum AliasType {ID, PRIMARY_NAME, ALTERNATE_LABEL, ANY_LABEL }
+	
+	protected AliasType aliasType = AliasType.ID;
+	protected QueryTerm value;
+	
+	public LiteralQueryTerm(AliasType aliasType, String valueAtom) {
+		super();
+		this.value = new AtomicQueryTerm(valueAtom);;
+		this.aliasType = aliasType;
+	}
+	public LiteralQueryTerm(AliasType aliasType, QueryTerm value) {
+		super();
+		this.value = value;
+		this.aliasType = aliasType;
+	}
+	public LiteralQueryTerm(QueryTerm value) {
+		super();
+		this.value = value;
+	}
+	public LiteralQueryTerm(String valueAtom) {
+		super();
+		this.value = new AtomicQueryTerm(valueAtom);
+	}
+
+	public QueryTerm getValue() {
+		return value;
+	}
+
+	public void setValue(QueryTerm value) {
+		this.value = value;
+	}
+
+	public AliasType getAliasType() {
+		return aliasType;
+	}
+	public void setAliasType(AliasType aliasType) {
+		this.aliasType = aliasType;
+	}
+
+	public String toString() {
+		String s = " has "+getAliasType().toString();
+		if (getValue() != null)
+			s = s + " "+getValue().toString();
+		return s;
+	}
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/query/QueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/QueryTerm.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/QueryTerm.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -0,0 +1,46 @@
+package org.obd.query;
+
+public abstract class QueryTerm {
+	
+	protected QueryTerm relation;
+	protected QueryTerm source;
+	protected QueryTerm positedBy;
+	
+	public QueryTerm() {
+		super();
+	}
+	
+	public QueryTerm(QueryTerm relation, QueryTerm source, QueryTerm positedBy) {
+		super();
+		this.relation = relation;
+		this.source = source;
+		this.positedBy = positedBy;
+	}
+	public QueryTerm getPositedBy() {
+		return positedBy;
+	}
+	public void setPositedBy(QueryTerm positedBy) {
+		this.positedBy = positedBy;
+	}
+	public QueryTerm getSource() {
+		return source;
+	}
+	public void setSource(QueryTerm source) {
+		this.source = source;
+	}
+	public QueryTerm getRelation() {
+		return relation;
+	}
+	public void setRelation(QueryTerm relation) {
+		this.relation = relation;
+	}
+	
+	public String toString() {
+		String s = "";
+		if (positedBy != null)
+			s = s + positedBy.toString();
+		return s;
+	}
+
+		
+}

Copied: obdapi/trunk/OBDAPI/src/org/obd/query/Shard.java (from rev 1299, obdapi/trunk/OBDAPI/src/org/obd/model/Shard.java)
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/Shard.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/Shard.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -0,0 +1,173 @@
+package org.obd.query;
+
+import java.util.Collection;
+import java.util.HashSet;
+
+import org.obd.model.Graph;
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.model.bridge.OBOBridge;
+import org.obd.model.stats.AggregateStatisticCollection;
+import org.obo.datamodel.IdentifiedObject;
+
+
+/**
+ * @author cjm
+ *
+ */
+public interface Shard {
+	
+	public enum EntailmentUse {
+		USE_ASSERTED,
+		USE_IMPLIED,
+		FULL_TRANSITIVE_CLOSURE
+	}
+	public enum GraphExpansionAlgorithm {
+		MINIMAL,
+		INCLUDE_SUBGRAPH
+	}
+	
+	/**
+	 * @return Node with matching ID
+	 */
+	public Node getNode(String id);
+	public Collection<Node> getNodes();
+	
+	/**
+	 * @return all nodes with matching source
+	 */
+	public Collection<Node> getNodesBySource(String sourceId);
+	
+	/**
+	 * @param searchTerm
+	 * @return all matching Nodes
+	 */
+	public Collection<Node> getNodesBySearch(String searchTerm);
+
+	/**
+	 * @return all Nodes used as a source
+	 */
+	public Collection<Node> getSourceNodes();
+	
+	/**
+	 * @param ids
+	 * @param entailment
+	 * @param gea
+	 * @return all Nodes that are beneath each of the nodes with given ids
+	 */
+	public Collection<Node> getNodesBelowNodeSet(Collection<String> ids,
+			EntailmentUse entailment,
+			GraphExpansionAlgorithm gea);
+	
+	public Collection<Node> getNodesByQuery(QueryTerm queryTerm);
+	
+
+	/**
+	 * @param ids
+	 * @param entailment
+	 * @param gea
+	 * @return all annotated entities that have at least one annotation to each node
+	 * in the given set
+	 */
+	public Collection<Node> getAnnotatedEntitiesBelowNodeSet(Collection<String> ids,
+			EntailmentUse entailment,
+			GraphExpansionAlgorithm gea);
+
+	
+	//public Statement getStatement(String id);
+	
+	/**
+	 * @param sourceId
+	 * @return all statements matching this source
+	 */
+	public Collection<Statement> getStatements(String sourceId);
+	
+	public Collection<Statement> getStatementsByQuery(QueryTerm queryTerm);
+
+
+	/**
+	 * @param id
+	 * @param entailment
+	 * @param strategy
+	 * @return given an annotated entity (eg a genotype node), return all annotation
+	 * statements
+	 */
+	public Collection<Statement> getAnnotationStatementsForAnnotatedEntity(String id, 
+			EntailmentUse entailment, GraphExpansionAlgorithm strategy);
+	
+	/**
+	 * @param id
+	 * @param entailment
+	 * @param gea
+	 * @return given a node (eg a class in an ontology), return a graph centered
+	 * around this node, including annotation to nodes subsumed by this node
+	 */
+	public Graph getAnnotationGraphAroundNode(String id, 
+			EntailmentUse entailment, GraphExpansionAlgorithm gea);
+	
+	public Graph getGraphByQuery(QueryTerm queryTerm, 
+			EntailmentUse entailment, GraphExpansionAlgorithm gea);
+
+
+	/**
+	 * @param id
+	 * @return
+	 */
+	public Collection<Statement> getStatementsForNode(String id);
+	
+	/**
+	 * @param id
+	 * @param sourceId
+	 * @return
+	 */
+	public Collection<Statement> getStatementsForNodeWithSource(String id, String sourceId);
+	
+	/**
+	 * @param id
+	 * @return
+	 */
+	public Collection<Statement> getStatementsForTarget(String id);
+	
+	/**
+	 * @param id
+	 * @param sourceId
+	 * @return
+	 */
+	public Collection<Statement> getStatementsForTargetWithSource(String id, String sourceId);
+	
+	/**
+	 * @param nodeId
+	 * @param relationId
+	 * @param targetId
+	 * @param sourceId
+	 * @param useImplied
+	 * @param isReified
+	 * @return
+	 */
+	public Collection<Statement> getStatements(String nodeId, 
+					String relationId, String targetId, String sourceId,
+					Boolean useImplied, Boolean isReified);
+	
+	/**
+	 * @param subjectId
+	 * @param subjectRelationId
+	 * @param targetRelationId
+	 * @param nodeId
+	 * @param targetId
+	 * @param subjectSourceId
+	 * @param nodeSourceId
+	 * @param useImplied
+	 * @param isReified
+	 * @return
+	 */
+	public Collection<Statement> getSubjectStatements(String subjectId, 
+			String subjectRelationId, String targetRelationId, 
+			String nodeId, String targetId, 
+			String subjectSourceId, String nodeSourceId,
+			Boolean useImplied, Boolean isReified);
+	
+	/**
+	 * @return
+	 */
+	public AggregateStatisticCollection getSummaryStatistics();
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/query/impl/AbstractShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/AbstractShard.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/AbstractShard.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -0,0 +1,9 @@
+package org.obd.query.impl;
+
+import org.obd.query.Shard;
+
+
+public abstract class AbstractShard implements Shard {
+
+
+}

Copied: obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java (from rev 1299, obdapi/trunk/OBDAPI/src/org/obd/model/impl/MultiShard.java)
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -0,0 +1,192 @@
+package org.obd.query.impl;
+
+import java.util.Collection;
+import java.util.HashSet;
+
+import org.obd.model.Graph;
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.model.stats.AggregateStatistic;
+import org.obd.model.stats.AggregateStatisticCollection;
+import org.obd.query.QueryTerm;
+import org.obd.query.Shard;
+import org.obd.query.Shard.EntailmentUse;
+import org.obd.query.Shard.GraphExpansionAlgorithm;
+
+public class MultiShard implements Shard {
+
+	Collection<Shard> shards = new HashSet<Shard>();
+
+	public Node getNode(String id) {
+		System.out.println("ms getNode: "+id);
+		for (Shard s : shards) {
+			Node n = s.getNode(id);
+			System.out.println(s+" "+n);
+			if (n != null)
+				return n;
+		}
+		return null;
+	}
+
+	public Collection<Node> getNodes() {
+		HashSet<Node> nodes = new HashSet<Node>();
+		for (Shard s : shards) 
+			nodes.addAll(s.getNodes());
+		return nodes;
+	}
+	
+	public Collection<Node> getNodesBySource(String sourceId) {
+		HashSet<Node> nodes = new HashSet<Node>();
+		for (Shard s : shards) 
+			nodes.addAll(s.getNodesBySource(sourceId));
+		return nodes;
+	}
+	
+	public Collection<Node> getNodesBySearch(String searchTerm) {
+		HashSet<Node> nodes = new HashSet<Node>();
+		for (Shard s : shards) 
+			nodes.addAll(s.getNodesBySearch(searchTerm));
+		return nodes;
+	}
+	
+	public Collection<Node> getNodesBelowNodeSet(Collection<String> ids, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
+		HashSet<Node> nodes = new HashSet<Node>();
+		for (Shard s : shards) 
+			nodes.addAll(s.getNodesBelowNodeSet(ids, entailment, gea));
+		return nodes;
+	}
+
+
+
+	
+	public Collection<Statement> getStatements(String sourceId) {
+		HashSet<Statement> statements = new HashSet<Statement>();
+		for (Shard s : shards) 
+			statements.addAll(s.getStatements(sourceId));
+		return statements;
+	}
+
+	public Collection<Statement> getStatementsForTarget(String id)  {
+		HashSet<Statement> statements = new HashSet<Statement>();
+		for (Shard s : shards) 
+			statements.addAll(s.getStatementsForTarget(id));
+		return statements;
+	}
+	public Collection<Statement> getStatementsForTargetWithSource(String id, String sourceId) {
+		HashSet<Statement> statements = new HashSet<Statement>();
+		for (Shard s : shards) 
+			statements.addAll(s.getStatementsForTargetWithSource(id, sourceId));
+		return statements;
+	}
+
+	public Collection<Shard> getShards() {
+		return shards;
+	}
+
+	public void setShards(Collection<Shard> shards) {
+		this.shards = shards;
+	}
+	
+	public void addShard(Shard shard) {
+		if (shards == null)
+			shards = new HashSet<Shard>();
+		shards.add(shard);
+	}
+
+	public Collection<Statement> getStatementsForNode(String id) {
+		HashSet<Statement> statements = new HashSet<Statement>();
+		System.out.println("getting parents for="+id);
+		for (Shard s : shards) 
+			statements.addAll(s.getStatementsForNode(id));
+		return statements;
+	}
+
+	public Collection<Statement> getStatementsForNodeWithSource(String id, String sourceId) {
+		HashSet<Statement> statements = new HashSet<Statement>();
+		for (Shard s : shards) 
+			statements.addAll(s.getStatementsForNodeWithSource(id, sourceId));
+		return statements;
+	}
+
+
+	public Collection<Statement> getStatements(String nodeId, String relationId, String targetId, String sourceId, Boolean useImplied, Boolean isReified) {
+		HashSet<Statement> statements = new HashSet<Statement>();
+		for (Shard s : shards) 
+			statements.addAll(s.getStatements(nodeId, 
+					relationId,  targetId,  sourceId,  useImplied,  isReified));
+		return statements;
+	}
+
+	public Collection<Statement> getSubjectStatements(String subjectId, String subjectRelationId, String targetRelationId, String nodeId, String targetId, String subjectSourceId, String nodeSourceId, Boolean useImplied, Boolean isReified) {
+		HashSet<Statement> statements = new HashSet<Statement>();
+		for (Shard s : shards) 
+			statements.addAll(s.getSubjectStatements( subjectId, 
+					subjectRelationId,  targetRelationId,  nodeId,  targetId, 
+					subjectSourceId,  nodeSourceId,  useImplied,  isReified));
+
+		return statements;
+	}
+
+	public Collection<Statement> getAnnotationStatementsForAnnotatedEntity(String id, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
+		HashSet<Statement> statements = new HashSet<Statement>();
+		for (Shard s : shards) 
+			statements.addAll(s.getAnnotationStatementsForAnnotatedEntity( id,
+					entailment, gea));
+
+		return statements;
+	}
+
+	public Graph getAnnotationGraphAroundNode(String id, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
+		Graph g = new Graph();
+		for (Shard s : shards) 
+			g.merge(s.getAnnotationGraphAroundNode(id,  entailment,  gea));
+		return g;	
+		
+	}
+	
+	public Collection<Node> getAnnotatedEntitiesBelowNodeSet(Collection<String> ids, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
+		HashSet<Node> nodes = new HashSet<Node>();
+		for (Shard s : shards) 
+			nodes.addAll(s.getAnnotatedEntitiesBelowNodeSet(ids, entailment, gea));
+		return nodes;
+	}
+
+
+	public Collection<Node> getSourceNodes() {
+		HashSet<Node> nodes = new HashSet<Node>();
+		for (Shard s : shards) 
+			nodes.addAll(s.getSourceNodes());
+		return nodes;	
+	}
+
+	public AggregateStatisticCollection getSummaryStatistics() {
+		AggregateStatisticCollection combinedStats = new AggregateStatisticCollection();
+		for (Shard s : shards) {
+			AggregateStatisticCollection sc = s.getSummaryStatistics();
+			Collection<AggregateStatistic> stats;
+			if (sc != null) {
+				stats = sc.getStats();
+				combinedStats.getStats().addAll(stats);
+			}
+		}
+		return combinedStats;
+	}
+
+	public Collection<Node> getNodesByQuery(QueryTerm queryTerm) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	public Graph getGraphByQuery(QueryTerm queryTerm, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	public Collection<Statement> getStatementsByQuery(QueryTerm queryTerm) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+
+	
+}

Copied: obdapi/trunk/OBDAPI/src/org/obd/query/impl/MutableOBOSessionShard.java (from rev 1290, obdapi/trunk/OBDAPI/src/org/obd/model/impl/MutableOBOSessionShard.java)
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/MutableOBOSessionShard.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/MutableOBOSessionShard.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -0,0 +1,29 @@
+package org.obd.query.impl;
+
+import org.bbop.dataadapter.DataAdapterException;
+import org.obo.dataadapter.OBOAdapter;
+import org.obo.dataadapter.OBOFileAdapter;
+
+public class MutableOBOSessionShard extends OBOSessionShard {
+
+	public int loadLocal(String ontName) throws DataAdapterException {
+		String path = "/users/cjm/obo-all/"+ontName+"/"+ontName+".obo";
+		return loadFile(path);
+	}
+	public int load(String ontName) throws DataAdapterException {
+		String path = "http://purl.org/obo/obo-all/"+ontName+"/"+ontName+".obo";
+		return loadFile(path);
+	}
+	public int loadFile(String path) throws DataAdapterException {
+		OBOFileAdapter.OBOAdapterConfiguration config = new OBOFileAdapter.OBOAdapterConfiguration();
+		config.getReadPaths().add(path);
+		
+		config.setAllowDangling(true);
+		config.setBasicSave(false);
+		config.setFailFast(false);
+		session = adapter.doOperation(OBOAdapter.READ_ONTOLOGY, config,
+				null);
+		return session.getObjects().size();
+	}
+
+}

Copied: obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java (from rev 1299, obdapi/trunk/OBDAPI/src/org/obd/model/impl/OBDSQLShard.java)
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -0,0 +1,530 @@
+package org.obd.query.impl;
+
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
+
+import org.bbop.rdbms.RelationalQuery;
+import org.bbop.rdbms.WhereClause;
+import org.bbop.rdbms.impl.SqlQueryImpl;
+import org.bbop.rdbms.impl.SqlWhereClauseImpl;
+import org.obd.model.Graph;
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.model.bridge.OBOBridge;
+import org.obd.model.stats.AggregateStatisticCollection;
+import org.obd.query.GraphQuery;
+import org.obd.query.QueryTerm;
+import org.obd.query.Shard;
+import org.obo.annotation.datamodel.Annotation;
+import org.obo.dataadapter.OBDSQLDatabaseAdapter;
+import org.obo.dataadapter.OBOFileAdapter;
+import org.obo.dataadapter.OBDSQLDatabaseAdapter.OBDSQLDatabaseAdapterConfiguration;
+import org.obo.datamodel.IdentifiedObject;
+import org.obo.datamodel.Link;
+import org.obo.datamodel.LinkedObject;
+import org.obo.datamodel.OBOSession;
+import org.obo.datamodel.impl.DanglingLinkImpl;
+import org.obo.datamodel.impl.OBOSessionImpl;
+
+/**
+ * @author cjm
+ *
+ */
+public class OBDSQLShard implements Shard {
+	
+	OBDSQLDatabaseAdapter obd = new OBDSQLDatabaseAdapter();
+	OBDSQLDatabaseAdapterConfiguration obdconfig = 
+		new OBDSQLDatabaseAdapter.OBDSQLDatabaseAdapterConfiguration();
+	
+	protected OBOSession session =
+		new OBOSessionImpl(); // TODO: remove? need it for tracking namespaces etc
+	
+	public OBDSQLShard() throws SQLException, ClassNotFoundException {
+	}
+	
+	public void connect(String jdbcPath) throws SQLException, ClassNotFoundException {
+		obdconfig.getReadPaths().add(jdbcPath);
+		obd = new OBDSQLDatabaseAdapter();
+		obd.setConfiguration(obdconfig);
+		obd.connect();
+	}
+
+	public String getID() {
+		return "OBD-Query-Service"; // TODO: introspect metadata
+	}
+	
+
+
+	public Node getNode(String id) {
+		RelationalQuery q = new SqlQueryImpl();
+		q.addTable("node_with_source");
+		WhereClause whereClause = q.getWhereClause();
+		whereClause.addEqualityConstraint("uid", id);
+		Node n = null;
+		OBOSession tempSession = new OBOSessionImpl();
+		try {
+			ResultSet rs = execute(q);
+			if (rs.next()) {
+				IdentifiedObject lo = obd.fetchObject(tempSession, rs);
+				obd.fetchObjectInfo(tempSession, lo);
+				n = OBOBridge.obj2node(lo);
+				Collection<Statement> statements = getStatementsForNode(n.getId(),false);
+				n.addStatements(statements);
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return n;
+	}
+	
+	public Collection<Node> getNodesBySource(String sourceId) {
+		Collection<Node> nodes = new LinkedList<Node>();
+		RelationalQuery q = new SqlQueryImpl();
+		q.addTable("node_with_source");
+		WhereClause whereClause = q.getWhereClause();
+		if (sourceId != null)
+			whereClause.addEqualityConstraint("source_uid", sourceId);
+		Node n = null;
+		try {
+			ResultSet rs = execute(q);
+			while (rs.next()) {
+				IdentifiedObject io = obd.fetchObject(session, rs);
+				nodes.add(OBOBridge.obj2node(io));
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return nodes;
+	}
+	
+	public Collection<Node> getNodesBySearch(String searchTerm) {
+		RelationalQuery q = new SqlQueryImpl();
+		q.addTable("node_with_source");
+		WhereClause whereClause = q.getWhereClause();
+		whereClause.addOperatorConstraint("LIKE", "label", searchTerm);
+		return getNodes(q);
+	}
+	
+	public Collection<Node> getNodesBelowNodeSet(Collection<String> ids,
+			EntailmentUse entailment,
+			GraphExpansionAlgorithm gea){
+		return getNodesBelowNodeSet(ids, entailment, gea, "link_to_node");
+	}
+	
+	public Collection<Node> getNodesBelowNodeSet(Collection<String> ids,
+			EntailmentUse entailment,
+			GraphExpansionAlgorithm gea,
+			String linkTable){
+		RelationalQuery q = new SqlQueryImpl();
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		q.addTable("node_with_source", "node");
+		int num = 0;
+		for (String id : ids) {
+			String alias = "link"+num;
+			q.addTable(linkTable, alias);
+			num++;
+			whereClause.addEqualityConstraint(alias+".object_uid",id);
+			whereClause.addConstraint(alias+".node_id"+" = node.node_id");
+			q.setWhereClause(whereClause);
+		}
+		q.getSelectClause().addColumn("node.*");
+		q.getSelectClause().setDistinct(true);
+		return getNodes(q);
+	}
+	
+	public Collection<Node> getNodes(RelationalQuery q) {
+		OBOSession tempSession = new OBOSessionImpl();
+		Collection<Node> nodes = new LinkedList<Node>();
+		try {
+			ResultSet rs = execute(q);
+			while (rs.next()) {
+				IdentifiedObject lo = obd.fetchObject(tempSession, rs);
+				obd.fetchObjectInfo(tempSession, lo);
+				Node n = OBOBridge.obj2node(lo);
+				nodes.add(n);
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return nodes;	
+	}
+
+	
+	
+
+	public Collection<Node> getNodes() {
+		return getNodesBySource(null);
+	}
+	
+	public Collection<Node> getSourceNodes() {
+		Collection<Node> nodes = new LinkedList<Node>();
+		RelationalQuery q = new SqlQueryImpl();
+		q.addTable("source_node");
+		WhereClause whereClause = q.getWhereClause();
+			Node n = null;
+		try {
+			ResultSet rs = execute(q);
+			while (rs.next()) {
+				IdentifiedObject io = obd.fetchObject(session, rs);
+				nodes.add(OBOBridge.obj2node(io));
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return nodes;
+	}
+
+	public Collection<Statement> getStatements() {
+		// TODO Auto-generated method stub
+		return new HashSet<Statement>();
+	}
+
+
+
+	public Collection<Statement> getStatements(String ns) {
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		if (ns != null) {
+			whereClause.addEqualityConstraint("source_uid",ns);
+		}
+		return getStatements(whereClause);
+	}
+	
+	public Collection<Statement> getStatements(WhereClause whereClause) {
+		HashSet<Statement> statements = new HashSet<Statement>();
+		try {
+			RelationalQuery q = new SqlQueryImpl();
+			q.addTable("node_link_node_with_pred_and_source");
+			q.setWhereClause(whereClause);
+			ResultSet rs = execute(q);
+			
+			OBOSession tempSession = new OBOSessionImpl();
+			HashMap<String, Link> positsMap = new HashMap<String,Link>();
+			while (rs.next()) {
+				obd.includeLinkResultSetInSession(tempSession, rs, positsMap);
+			}
+			HashSet<Link> links = new HashSet<Link>();
+			for (IdentifiedObject io : tempSession.getObjects()) {
+				if (io instanceof LinkedObject && !io.isBuiltIn())
+					links.addAll(((LinkedObject)io).getParents());
+			}
+			HashMap<String,Statement> statementMap = new HashMap<String,Statement>();
+			for (Link link : links) {
+				Statement s = OBOBridge.link2statement(link);
+				statements.add(s);
+				statementMap.put(s.toString(), s);
+			}
+			// slighly convoluted way of making reverse links, from
+			// posited link to positing (annotation) node
+			for (IdentifiedObject io : tempSession.getObjects()) {
+				String nodeId = io.getID();
+				if (positsMap.containsKey(nodeId)) {
+					Statement sKey = OBOBridge.link2statement(positsMap.get(io.getID()));
+					Statement s = statementMap.get(sKey.toString());
+					s.setPositedByNodeId(nodeId);
+				}
+			}
+					
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return statements;
+
+	}
+	
+	public Collection<Statement> getStatementsForTarget(String id)  {
+		
+		HashSet<Statement> statements = new HashSet<Statement>();
+		try {
+			for (Link link : obd.fetchLinksByObject(id)) {
+				statements.add(OBOBridge.link2statement(link));
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return statements;
+	}
+	
+	public Collection<Statement> getStatementsForTargetWithSource(String id, String sourceId) {
+		HashSet<Statement> statements = new HashSet<Statement>();
+		System.out.println("id="+id+" src="+sourceId);
+		try {
+			for (Link link : obd.fetchLinksByObject(id, sourceId)) {
+				statements.add(OBOBridge.link2statement(link));
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return statements;
+	}
+
+	/**
+	 * @param id
+	 * @return All statements whose target is subsumed by id
+	 * @throws Exception
+	 */
+	public Collection<Statement> getStatementsAround(String id) throws Exception {
+
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		whereClause.addConstraint("object_uid in "+
+				"(SELECT node_id FROM link_to_node WHERE object_uid ='"+id+"')");
+		return getStatements(whereClause);
+	}
+	
+	
+
+
+	public Collection<Statement> getStatementsForNode(String id) {
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		whereClause.addEqualityConstraint("node_uid",id);
+		return getStatements(whereClause);
+	}
+	
+	public Collection<Statement> getStatementsForNode(String id, boolean useImplied) {
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		whereClause.addEqualityConstraint("node_uid",id);
+		if (!useImplied)
+			whereClause.addEqualityConstraint("is_inferred",false);
+		return getStatements(whereClause);
+	}
+	
+
+	public Collection<Statement> getStatementsForNodeWithSource(String id, String ns) {
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		whereClause.addEqualityConstraint("node_uid",id);
+		if (ns != null) {
+			whereClause.addEqualityConstraint("source_uid",ns);
+		}
+		return getStatements(whereClause);
+	}
+	
+
+	
+	public Collection<Statement> getStatements(String nodeId, 
+			String relationId, String targetId, String sourceId,
+			Boolean useImplied, Boolean isReified) {
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		if (nodeId != null)
+			whereClause.addEqualityConstraint("node_uid",nodeId);
+		if (relationId != null)
+			whereClause.addEqualityConstraint("pred_uid",relationId);
+		if (targetId != null)
+			whereClause.addEqualityConstraint("object_uid",targetId);
+		if (sourceId != null)
+			whereClause.addEqualityConstraint("source_uid",sourceId);
+		if (useImplied != null)
+			whereClause.addEqualityConstraint("is_inferred",useImplied);
+		if (isReified)
+			whereClause.addConstraint("reiflink_node_id IS NOT NULL");
+		return getStatements(whereClause);
+	}
+	
+	public Collection<Statement> getSubjectStatements(String subjectId, 
+			String subjectRelationId, String targetRelationId, 
+			String nodeId, String targetId, 
+			String subjectSourceId, String nodeSourceId,
+			Boolean useImplied, Boolean isReified) {
+		
+		System.out.println("getSubjectStatements "+subjectId+","+ 
+				subjectRelationId +","+ targetRelationId +"," + nodeId +","+ targetId + "," +
+				subjectSourceId + ","+ nodeSourceId +","+  useImplied +","+ isReified);
+
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		if (subjectId != null && !subjectId.equals(""))
+			whereClause.addEqualityConstraint("node_uid",subjectId);
+		if (subjectRelationId != null && !subjectRelationId.equals(""))
+			whereClause.addEqualityConstraint("pred_uid",subjectRelationId);
+		if (nodeId != null && !nodeId.equals(""))
+			whereClause.addEqualityConstraint("node_uid",nodeId);
+		if (subjectSourceId != null && !subjectSourceId.equals(""))
+			whereClause.addEqualityConstraint("source_uid",subjectSourceId);
+		if (isReified != null && isReified)
+			whereClause.addConstraint("reiflink_node_id IS NOT NULL");
+		
+		RelationalQuery subQuery = new SqlQueryImpl();
+		subQuery.getSelectClause().addColumn("node_uid");
+		subQuery.addTable("node_link_node_with_pred_and_source");
+		WhereClause subWhereClause = new SqlWhereClauseImpl();
+		subQuery.setWhereClause(subWhereClause);
+		
+		if (targetId != null && !targetId.equals(""))
+			subWhereClause.addEqualityConstraint("object_uid",targetId);
+		if (nodeSourceId != null && !nodeSourceId.equals(""))
+			subWhereClause.addEqualityConstraint("source_uid",nodeSourceId);
+		if (targetRelationId != null && !targetRelationId.equals(""))
+			subWhereClause.addEqualityConstraint("pred_uid",targetRelationId);
+		if (useImplied != null && !useImplied.equals(""))
+			subWhereClause.addEqualityConstraint("is_inferred",useImplied);
+		
+		whereClause.addInConstraint("object_uid", subQuery);
+		return getStatements(whereClause);
+
+	}
+
+
+
+
+
+
+	
+
+
+	public Collection<Statement> getAnnotationStatementsForAnnotatedEntity(String id, EntailmentUse entailment, GraphExpansionAlgorithm strategy) {
+
+		// node_uid is the annotated entity - find everything about it -
+		// both additional metadata and annotation
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		whereClause.addEqualityConstraint("node_uid",id);
+		Collection<Statement> annots = getStatements(whereClause);
+		return annots;
+	}
+
+	public Graph getAnnotationGraphAroundNode(String id, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
+
+		// find graph around node, outwards
+		Collection<Statement> stmts;
+		if (gea == null || gea.equals(GraphExpansionAlgorithm.INCLUDE_SUBGRAPH)) {
+			 Graph sg = getSubgraph(id, entailment, gea);
+			 stmts = Arrays.asList(sg.getStatements());
+		}
+		else
+			stmts = new LinkedList<Statement>(); // TODO: minimal info?
+			 
+	
+		// find all annotations to id
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		if (true || entailment == null) {
+			// currently this is under-constrained
+			// will fetch the full graph;
+			//  G has_role* X and X R* Y, where Y is ground
+			/*
+			 * we actually want
+			 * G has_role X, X Rmd MD, X R* Y
+			 */
+			RelationalQuery subsumedNodeQuery = new SqlQueryImpl();
+			subsumedNodeQuery.getSelectClause().addColumn("node_uid");
+			subsumedNodeQuery.addTable("node_link_node_with_pred_and_source");
+			WhereClause subWhereClause = new SqlWhereClauseImpl();
+			subWhereClause.addEqualityConstraint("object_uid",id);			
+			subsumedNodeQuery.setWhereClause(subWhereClause);
+			
+			whereClause.addInConstraint("object_uid",subsumedNodeQuery);	
+			whereClause.addEqualityConstraint("is_inferred", false);
+		}
+		else {
+			// TODO: only works in annot links are inlcuded in deductive closure
+			whereClause.addEqualityConstraint("object_uid",id);
+		}
+		//whereClause.addConstraint("reiflink_node_id IS NOT NULL");
+		Collection<Statement> annots = getStatements(whereClause);
+		Graph g = new Graph(annots);
+		for (String nid : g.getReferencedNodeIds()) {
+			Node n = getNode(nid);
+			g.addNode(n);
+			Collection<Statement> mdLinks = getStatementsForNode(nid,false);
+			g.addStatements(mdLinks);
+		}
+		g.addStatements(stmts);
+		g.nestStatementsUnderNodes();
+		return g;
+
+	}
+	
+	public Collection<Node> getAnnotatedEntitiesBelowNodeSet(Collection<String> ids,
+			EntailmentUse entailment,
+			GraphExpansionAlgorithm gea){
+		return getNodesBelowNodeSet(ids, entailment, gea,
+				"implied_annotation_link_to_node");
+	}
+	
+	public Graph getSubGraphUsingQuery(GraphQuery gq) {
+
+		WhereClause whereClause = new SqlWhereClauseImpl();
+
+		// node_uid is the ontology - find full DAG
+		whereClause.addEqualityConstraint("node_uid",gq.getNodeId());
+		Collection<Statement> stmts = getStatements(whereClause);
+		Graph g = new Graph(stmts);
+		return g;
+	}
+	
+	public Graph getSubgraph(String nodeId, EntailmentUse entailment,
+			GraphExpansionAlgorithm gea) {
+
+		WhereClause whereClause = new SqlWhereClauseImpl();
+		whereClause.addEqualityConstraint("node_uid",nodeId);
+		
+		RelationalQuery subQuery = new SqlQueryImpl();
+		subQuery.getSelectClause().addColumn("node_uid");
+		subQuery.addTable("node_link_node_with_pred_and_source");
+		WhereClause subWhereClause = new SqlWhereClauseImpl();
+		subQuery.setWhereClause(subWhereClause);
+		Collection<Statement> stmts = getStatements(whereClause);
+		Graph g = new Graph(stmts);
+		return g;
+	}
+	
+	public AggregateStatisticCollection getSummaryStatistics()  {
+		AggregateStatisticCollection sc = new AggregateStatisticCollection();
+		
+		RelationalQuery q = new SqlQueryImpl();
+		q.addTable("source_summary");		
+		ResultSet rs;
+		try {
+			rs = execute(q);
+			while (rs.next()) {
+				String src = rs.getString("uid");
+				Integer nc = rs.getInt("node_count");
+				sc.setCount("node", src, nc);
+				Integer lc = rs.getInt("link_count");
+				sc.setCount("link", src, lc);
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return sc;
+	}
+	
+	// UTIL
+	
+	public ResultSet execute(RelationalQuery q) throws SQLException {
+		ResultSet rs = q.execute(obd.getConnection());
+		return rs;
+	}
+
+	public Collection<Node> getNodesByQuery(QueryTerm queryTerm) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	public Graph getGraphByQuery(QueryTerm queryTerm, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	public Collection<Statement> getStatementsByQuery(QueryTerm queryTerm) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+
+
+	
+	
+	
+
+
+}

Copied: obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBOSessionShard.java (from rev 1299, obdapi/trunk/OBDAPI/src/org/obd/model/impl/OBOSessionShard.java)
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBOSessionShard.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBOSessionShard.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -0,0 +1,218 @@
+package org.obd.query.impl;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.logging.Logger;
+
+import org.obd.model.Graph;
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.model.bridge.OBOBridge;
+import org.obd.model.stats.AggregateStatisticCollection;
+import org.obd.model.stats.MeasuredEntity;
+import org.obd.query.QueryTerm;
+import org.obd.query.Shard;
+import org.obd.query.Shard.EntailmentUse;
+import org.obd.query.Shard.GraphExpansionAlgorithm;
+import org.obo.dataadapter.OBOFileAdapter;
+import org.obo.datamodel.DefinedObject;
+import org.obo.datamodel.IdentifiedObject;
+import org.obo.datamodel.Link;
+import org.obo.datamodel.LinkedObject;
+import org.obo.datamodel.Namespace;
+import org.obo.datamodel.OBOSession;
+
+
+public class OBOSessionShard implements Shard {
+	OBOFileAdapter adapter = new OBOFileAdapter();
+	
+	protected OBOSession session;
+		
+	// node fetching
+	public Node getNode(String id) {
+		Node node = OBOBridge.obj2node(session.getObject(id));
+		//node.serial
+		return node;
+	}
+	
+	public Collection<Node> getNodes() {
+		HashSet<Node> nodes = new HashSet<Node>();
+		for (IdentifiedObject io : session.getObjects()) {
+			if (io.isBuiltIn())
+				continue;
+			nodes.add(OBOBridge.obj2node(io));
+		}
+		return nodes;
+	}
+	
+	public Collection<Node> getNodesBySource(String sourceId) {
+		HashSet<Node> nodes = new HashSet<Node>();
+		for (IdentifiedObject io : session.getObjects()) {
+			if (io.isBuiltIn())
+				continue;
+			if (io.getNamespace() != null && io.getNamespace().getID().equals(sourceId))
+				nodes.add(OBOBridge.obj2node(io));
+		}
+		return nodes;
+	}
+	
+	public Collection<Node> getNodesBySearch(String searchTerm) {
+		// TODO Auto-generated method stub
+		return new HashSet<Node>();
+	}
+	
+	public Collection<Node> getNodesBelowNodeSet(Collection<String> ids, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
+		// TODO Auto-generated method stub
+		return new HashSet<Node>();
+	}
+
+	
+	// simple types
+	public Collection<String> getNodeIDs() {
+		HashSet<String> ids = new HashSet<String>();
+		for (IdentifiedObject io : session.getObjects()) {
+			ids.add(io.getID());
+		}
+		return ids;
+	}		
+
+	public Collection<Statement> getStatements() {
+		// TODO Auto-generated method stub
+		return new HashSet<Statement>();
+	}
+	
+	public Collection<Statement> getStatements(String sourceId) {
+		// TODO Auto-generated method stub
+		return new HashSet<Statement>();
+	}
+
+	public Collection<Statement> getStatementsForNode(String id) {
+		HashSet<Statement> statements = new HashSet<Statement>();
+		LinkedObject obj = (LinkedObject)session.getObject(id);
+		System.out.println("obj="+obj);
+		if (obj != null ) {
+			for (Link link : obj.getParents()) {
+				System.out.println("p="+link);
+				Logger.getLogger("org.obd").info("p2s"+link);
+				statements.add(OBOBridge.link2statement(link));
+			}
+		}
+		return statements;
+	}
+	
+
+	public Collection<Statement> getStatementsForNodeWithSource(String id, String sourceId) {
+		HashSet<Statement> statements = new HashSet<Statement>();
+		LinkedObject obj = (LinkedObject)session.getObject(id);
+		for (Link link : obj.getParents()) {
+			Statement s = OBOBridge.link2statement(link);
+			if (s.getSourceId().equals(sourceId))
+				statements.add(s);
+		}
+		return statements;
+	}
+
+
+	public Collection<Statement> getStatementsForTarget(String id) {
+		HashSet<Statement> statements = new HashSet<Statement>();
+		LinkedObject obj = (LinkedObject)session.getObject(id);
+		if (obj != null) {
+			for (Link link : obj.getChildren()) {
+				statements.add(OBOBridge.link2statement(link));
+			}
+		}
+		return statements;
+	}
+	
+	public Collection<Statement> getStatementsForTargetWithSource(String id, String sourceId) {
+		HashSet<Statement> statements = new HashSet<Statement>();
+		LinkedObject obj = (LinkedObject)session.getObject(id);
+		if (obj != null) {
+			for (Link link : obj.getChildren()) {
+				Statement s = OBOBridge.link2statement(link);
+				if (s.getSourceId().equals(sourceId))
+					statements.add(s);
+			}
+		}
+		return statements;
+	}
+
+	// simple types
+	public String getNodeName(String id) {
+		return session.getObject(id).getName();
+	}
+	
+	public String getNodeDef(String id) {
+		return ((DefinedObject)session.getObject(id)).getDefinition();
+	}
+
+	public Collection<Node> getSourceNodes() {
+		Collection<Namespace> nsl = session.getNamespaces();
+		HashSet<Node> nodes = new HashSet<Node>();
+		for (Namespace ns : nsl)
+			nodes.add(OBOBridge.namespace2srcNode(ns));
+		return nodes;
+	}
+	
+	public AggregateStatisticCollection getSummaryStatistics() {
+		AggregateStatisticCollection stats = new AggregateStatisticCollection();
+		for (IdentifiedObject io : session.getObjects()) {
+			if (io.isBuiltIn())
+				continue;
+			String src = OBOBridge.namespace2src(io.getNamespace());
+			MeasuredEntity entity = stats.getMeasuredEntity("node",src);
+			stats.incrementCount(entity);
+			if (io instanceof LinkedObject) {
+				for (Link link : ((LinkedObject)io).getParents()) {
+					stats.incrementCount("link", src);
+				}
+			}
+		}
+		return stats;
+	}
+
+	public Collection<Statement> getStatements(String nodeId, String relationId, String targetId, String sourceId, Boolean useImplied, Boolean isReified) {
+		return new LinkedList<Statement>();
+	}
+
+	public Collection<Statement> getSubjectStatements(String subjectId, String subjectRelationId, String targetRelationId, String nodeId, String targetId, String subjectSourceId, String nodeSourceId, Boolean useImplied, Boolean isReified) {
+		return new HashSet<Statement>();
+	}
+
+	public Collection<Statement> getAnnotationStatementsForAnnotatedEntity(String id, EntailmentUse entailment, GraphExpansionAlgorithm strategy) {
+		return new HashSet<Statement>();
+	}
+
+	public Graph getAnnotationGraphAroundNode(String id, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
+		return new Graph();
+	}
+	
+	public Collection<Node> getAnnotatedEntitiesBelowNodeSet(Collection<String> ids,
+			EntailmentUse entailment,
+			GraphExpansionAlgorithm gea){
+		return new LinkedList<Node>(); // TODO
+	}
+
+	public Collection<Node> getNodesByQuery(QueryTerm queryTerm) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	public Graph getGraphByQuery(QueryTerm queryTerm, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	public Collection<Statement> getStatementsByQuery(QueryTerm queryTerm) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+
+
+
+
+
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/test/AnnotationGraphTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/AnnotationGraphTest.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/AnnotationGraphTest.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -0,0 +1,55 @@
+package org.obd.test;
+
+import java.io.PrintStream;
+import java.util.logging.Logger;
+
+import org.bbop.io.AuditedPrintStream;
+import org.obd.model.Graph;
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.ws.OBDQueryService;
+import org.obo.datamodel.impl.DefaultLinkDatabase;
+import org.obo.reasoner.impl.ForwardChainingReasoner;
+import org.obo.test.OBDAnnotationSaveTest;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+public class AnnotationGraphTest extends TestCase {
+
+	OBDQueryService service;
+	
+	
+	public AnnotationGraphTest(String n) {
+		super(n);
+	}
+
+
+	public void setUp() throws Exception {
+		System.out.println("Setting up: " + this);
+		service = new OBDQueryService();
+		
+	}
+
+	public static Test suite() {
+		TestSuite suite = new TestSuite();
+		addTests(suite);
+		return suite;
+	}
+
+	public static void addTests(TestSuite suite) {
+		suite.addTest(new AnnotationGraphTest("testQuery"));
+	}
+	
+	public void testQuery() {
+		
+		
+		
+		for (Statement s : service.getAnnotationStatementsForAnnotatedEntity("ZFIN:ZDB-GENO-960809-7", null, null)) {
+			System.out.println(s);
+		}
+
+	}
+
+}

Copied: obdapi/trunk/OBDAPI/src/org/obd/test/MiniTest.java (from rev 1299, obdapi/trunk/OBDAPI/src/org/obd/test/OBDQueryServiceTest.java)
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/MiniTest.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/MiniTest.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -0,0 +1,61 @@
+package org.obd.test;
+
+import java.io.PrintStream;
+import java.util.logging.Logger;
+
+import org.bbop.io.AuditedPrintStream;
+import org.obd.model.Graph;
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.ws.OBDQueryService;
+import org.obo.datamodel.impl.DefaultLinkDatabase;
+import org.obo.reasoner.impl.ForwardChainingReasoner;
+import org.obo.test.OBDAnnotationSaveTest;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+public class MiniTest extends TestCase {
+
+	OBDQueryService service;
+	
+	
+	public MiniTest(String n) {
+		super(n);
+	}
+
+
+	public void setUp() throws Exception {
+		System.out.println("Setting up: " + this);
+		service = new OBDQueryService();
+		
+	}
+
+	public static Test suite() {
+		TestSuite suite = new TestSuite();
+		addTests(suite);
+		return suite;
+	}
+
+	public static void addTests(TestSuite suite) {
+		suite.addTest(new MiniTest("testQuery"));
+	}
+	
+	public void testQuery() {
+		Graph g= new Graph();
+		g.addStatement(testStatement());
+		g.addStatement(testStatement());
+		System.out.println("Len="+g.getStatements().length);
+
+	}
+	
+	public Statement testStatement() {
+		Statement s = new Statement();
+		s.setNodeId("x");
+		s.setRelationId("y");
+		s.setTargetId("z");
+		return s;
+	}
+
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/test/MultiNodeFetchTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/MultiNodeFetchTest.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/MultiNodeFetchTest.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -0,0 +1,67 @@
+package org.obd.test;
+
+import java.io.PrintStream;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.logging.Logger;
+
+import org.bbop.io.AuditedPrintStream;
+import org.obd.model.Graph;
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.ws.OBDQueryService;
+import org.obo.datamodel.impl.DefaultLinkDatabase;
+import org.obo.reasoner.impl.ForwardChainingReasoner;
+import org.obo.test.OBDAnnotationSaveTest;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+public class MultiNodeFetchTest extends TestCase {
+
+	OBDQueryService service;
+	
+	
+	public MultiNodeFetchTest(String n) {
+		super(n);
+	}
+
+
+	public void setUp() throws Exception {
+		System.out.println("Setting up: " + this);
+		service = new OBDQueryService();
+		
+	}
+
+	public static Test suite() {
+		TestSuite suite = new TestSuite();
+		addTests(suite);
+		return suite;
+	}
+
+	public static void addTests(TestSuite suite) {
+		suite.addTest(new MultiNodeFetchTest("testQuery"));
+	}
+	
+	public void testQuery() {
+		
+		// heart development & blood cell
+		String[] ids =
+		{"GO:0003007", "PATO:0000001"};
+		
+		for (Node n : service.getNodesBelowNodeSet(Arrays.asList(ids) , null, null)) {
+			System.out.println(n);
+		}
+
+		String[] ids2 =
+		{"GO:0003007", "CL:0000081"};
+
+		for (Node n : service.getAnnotatedEntitiesBelowNodeSet(Arrays.asList(ids2) , null, null)) {
+			System.out.println(n);
+		}
+
+		
+	}
+
+}

Deleted: obdapi/trunk/OBDAPI/src/org/obd/test/OBDQueryServiceTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/OBDQueryServiceTest.java	2007-12-10 20:13:17 UTC (rev 1301)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/OBDQueryServiceTest.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -1,76 +0,0 @@
-package org.obd.test;
-
-import java.io.PrintStream;
-import java.util.logging.Logger;
-
-import org.bbop.io.AuditedPrintStream;
-import org.obd.model.Graph;
-import org.obd.model.Node;
-import org.obd.model.Statement;
-import org.obd.ws.OBDQueryService;
-import org.obo.datamodel.impl.DefaultLinkDatabase;
-import org.obo.reasoner.impl.ForwardChainingReasoner;
-import org.obo.test.OBDAnnotationSaveTest;
-
-import junit.framework.Test;
-import junit.framework.TestCase;
-import junit.framework.TestSuite;
-
-public class OBDQueryServiceTest extends TestCase {
-
-	OBDQueryService service;
-	
-	
-	public OBDQueryServiceTest(String n) {
-		super(n);
-	}
-
-
-	public void setUp() throws Exception {
-		System.out.println("Setting up: " + this);
-		service = new OBDQueryService();
-		
-	}
-
-	public static Test suite() {
-		TestSuite suite = new TestSuite();
-		addTests(suite);
-		return suite;
-	}
-
-	public static void addTests(TestSuite suite) {
-		suite.addTest(new OBDQueryServiceTest("testQuery"));
-	}
-	
-	public void testQuery() {
-		String id = "GO:0006811";
-		Node node = 
-			service.getNode(id);
-		Logger.getLogger("org.obd.test").info("node="+node.getName());
-		assertTrue(node != null);
-		
-		for (Statement s : service.getStatementsForNode(id)) {
-			Logger.getLogger("org.obd.test").info("parentLink="+s);
-		}
-
-		for (Statement s : service.getStatementsForTarget(id)) {
-			Logger.getLogger("org.obd.test").info("childLink="+s);
-		}
-		
-		for (Statement s : service.getSubjectStatements(null, 
-				null, null, null, id, null, null, true, true)) {
-			Logger.getLogger("org.obd.test").info("annot="+s);
-		}
-		
-		Graph g = service.getAnnotationGraphAroundNode(id, null, null);
-		g.nestStatementsUnderNodes();
-		for (Node n : g.getNodes()) {
-			System.out.println(n);
-			for (Statement s : n.getStatements()) {
-				System.out.println("    "+s);
-			}	
-		}
-
-	}
-
-}

Added: obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -0,0 +1,69 @@
+package org.obd.test;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+import org.obd.model.Statement;
+import org.obd.query.ComparisonQueryTerm;
+import org.obd.query.LinkQueryTerm;
+import org.obd.query.LiteralQueryTerm;
+import org.obd.query.QueryTerm;
+import org.obd.query.ComparisonQueryTerm.Operator;
+import org.obd.query.LiteralQueryTerm.AliasType;
+import org.obd.ws.OBDQueryService;
+
+public class QueryTest extends TestCase {
+
+	OBDQueryService service;
+	
+	
+	public QueryTest(String n) {
+		super(n);
+	}
+
+
+	public void setUp() throws Exception {
+		System.out.println("Setting up: " + this);
+		service = new OBDQueryService();
+		
+	}
+
+	public static Test suite() {
+		TestSuite suite = new TestSuite();
+		addTests(suite);
+		return suite;
+	}
+
+	public static void addTests(TestSuite suite) {
+		suite.addTest(new QueryTest("testQuery"));
+	}
+	
+	public void testQuery() {
+		
+		QueryTerm qt;
+		
+		runQuery(new LiteralQueryTerm(AliasType.PRIMARY_NAME,
+				"apoptosis"));
+		runQuery(new LiteralQueryTerm(AliasType.ALTERNATE_LABEL,
+				new ComparisonQueryTerm(Operator.STARTS_WITH,
+				"apoptosis")));
+		
+		String partOf = "OBO_REL:part_of";
+		String developsFrom = "OBO_REL:developsFrom";
+		runQuery(new LinkQueryTerm(partOf, "GO:0005634"));
+		runQuery(new LinkQueryTerm(partOf, 
+				new LiteralQueryTerm(AliasType.ANY_LABEL, "nucleus")));
+		runQuery(new LinkQueryTerm(partOf, 
+				new LinkQueryTerm(developsFrom, "CL:1234567")));
+		
+		
+
+	}
+	
+	public void runQuery(QueryTerm qt) {
+		System.out.println("running Q: "+qt.toString());
+
+	}
+
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/test/SearchTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/SearchTest.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/SearchTest.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -0,0 +1,66 @@
+package org.obd.test;
+
+import java.io.PrintStream;
+import java.util.logging.Logger;
+
+import org.bbop.io.AuditedPrintStream;
+import org.obd.model.Graph;
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.ws.OBDQueryService;
+import org.obo.datamodel.impl.DefaultLinkDatabase;
+import org.obo.reasoner.impl.ForwardChainingReasoner;
+import org.obo.test.OBDAnnotationSaveTest;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+public class SearchTest extends TestCase {
+
+	OBDQueryService service;
+	
+	
+	public SearchTest(String n) {
+		super(n);
+	}
+
+
+	public void setUp() throws Exception {
+		System.out.println("Setting up: " + this);
+		service = new OBDQueryService();
+		
+	}
+
+	public static Test suite() {
+		TestSuite suite = new TestSuite();
+		addTests(suite);
+		return suite;
+	}
+
+	public static void addTests(TestSuite suite) {
+		suite.addTest(new SearchTest("testQuery"));
+	}
+	
+	public void testQuery() {
+		
+		for (Node n : service.getNodesBySearch("AB%")) {
+			System.out.println(n);
+			for (Statement s : n.getStatements()) {
+				System.out.println("    "+s);
+			}	
+			
+		}
+		
+		for (Node n : service.getNodesBySearch("apoptosis%")) {
+			System.out.println(n);
+			for (Statement s : n.getStatements()) {
+				System.out.println("    "+s);
+			}	
+			
+		}
+
+
+	}
+
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/ws/OBDQueryService.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/OBDQueryService.java	2007-12-10 20:13:17 UTC (rev 1301)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/OBDQueryService.java	2007-12-11 01:56:57 UTC (rev 1302)
@@ -8,14 +8,15 @@
 import org.bbop.dataadapter.DataAdapterException;
 import org.obd.model.Graph;
 import org.obd.model.Node;
-import org.obd.model.Shard;
 import org.obd.model.Statement;
-import org.obd.model.Shard.EntailmentUse;
-import org.obd.model.Shard.GraphExpansionAlgorithm;
-import org.obd.model.impl.MultiShard;
-import org.obd.model.impl.MutableOBOSessionShard;
-import org.obd.model.impl.OBDSQLShard;
 import org.obd.model.stats.AggregateStatisticCollection;
+import org.obd.query.QueryTerm;
+import org.obd.query.Shard;
+import org.obd.query.Shard.EntailmentUse;
+import org.obd.query.Shard.GraphExpansionAlgorithm;
+import org.obd.query.impl.MultiShard;
+import org.obd.query.impl.MutableOBOSessionShard;
+import org.obd.query.impl.OBDSQLShard;
 
 	
 
@@ -62,9 +63,20 @@
 	public Node[]  getSourceNodes() {
 		return (Node[] )shard.getSourceNodes().toArray(new Node[0]);
 	}
-	public Node[] getNodesWithSource(String sourceId) {
-		return (Node[])shard.getNodes(sourceId).toArray(new Node[0]);
+	
+	
+	public Node[] getNodesBySource(String sourceId) {
+		return (Node[])shard.getNodesBySource(sourceId).toArray(new Node[0]);
 	}
+	public Node[] getNodesBySearch(String searchTerm) {
+		return (Node[])shard.getNodesBySearch(searchTerm).toArray(new Node[0]);
+	}
+	
+	public Node[] getNodesBelowNodeSet(Collection<String> ids,
+			EntailmentUse entailment,
+			GraphExpansionAlgorithm gea) {
+		return (Node[])shard.getNodesBelowNodeSet(ids, entailment, gea).toArray(new Node[0]);		
+	}
 
 	public Graph getGraph() {
 		return null;
@@ -75,7 +87,35 @@
 	public Graph getAnnotationGraphAroundNode(String id, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
 		return shard.getAnnotationGraphAroundNode(id, entailment, gea);
 	}
+	
+	
 
+	public Statement[] getAnnotationStatementsForAnnotatedEntity(String id, EntailmentUse entailment, GraphExpansionAlgorithm strategy) {
+		return (Statement[] ) shard.
+		getAnnotationStatementsForAnnotatedEntity(id, entailment, strategy).
+		toArray(new Statement[0]);
+	}
+	
+	public Node[] getAnnotatedEntitiesBelowNodeSet(Collection<String> ids,
+			EntailmentUse entailment,
+			GraphExpansionAlgorithm gea) {
+		return (Node[])shard.getAnnotatedEntitiesBelowNodeSet(ids, entailment, gea).toArray(new Node[0]);		
+	}
+	
+	
+
+	public Graph getGraphByQuery(QueryTerm queryTerm, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
+		return shard.getGraphByQuery(queryTerm, entailment, gea);
+	}
+
+	public Node[] getNodesByQuery(QueryTerm queryTerm) {
+		return (Node[])shard.getNodesByQuery(queryTerm).toArray(new Node[0]);
+	}
+
+	public Statement[] getStatementsByQuery(QueryTerm queryTerm) {
+		return (Statement[])shard.getStatementsByQuery(queryTerm).toArray(new Statement[0]);
+	}
+
 	public Statement getStatement(String id) {
 		//return shard.getStatements().iterator().next();
 		return null;
@@ -118,6 +158,7 @@
 
 
 
+
 	
 	
 	


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 1311
          http://obo.svn.sourceforge.net/obo/?rev=1311&view=rev
Author:   cmungall
Date:     2007-12-12 15:19:14 -0800 (Wed, 12 Dec 2007)

Log Message:
-----------


Modified Paths:
--------------
    obdapi/trunk/OBDAPI/src/org/obd/query/ComparisonQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/AbstractShard.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java
    obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java

Added Paths:
-----------
    obdapi/trunk/OBDAPI/src/org/obd/query/BooleanQueryTerm.java

Added: obdapi/trunk/OBDAPI/src/org/obd/query/BooleanQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/BooleanQueryTerm.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/BooleanQueryTerm.java	2007-12-12 23:19:14 UTC (rev 1311)
@@ -0,0 +1,60 @@
+package org.obd.query;
+
+import java.util.Collection;
+import java.util.LinkedList;
+
+public class BooleanQueryTerm extends QueryTerm {
+
+	public enum BooleanOperator {AND, OR, XOR, NOT}
+	
+	protected BooleanOperator operator;
+	
+	protected Collection<QueryTerm> queryTerms = new LinkedList<QueryTerm>();
+
+	public BooleanQueryTerm(BooleanOperator operator, Collection<QueryTerm> queryTerms) {
+		super();
+		this.operator = operator;
+		this.queryTerms = queryTerms;
+	}
+
+	public BooleanQueryTerm(BooleanOperator operator, QueryTerm... queryTerms) {
+		super();
+		this.operator = operator;
+		for (QueryTerm qt : queryTerms) {
+			addQueryTerm(qt);
+		}
+	}
+
+	public void addQueryTerm(QueryTerm qt) {
+		queryTerms.add(qt);
+	}
+
+	public String toString() {
+		return queryTerms.toString();
+	}
+
+
+
+	public BooleanOperator getOperator() {
+		return operator;
+	}
+
+
+
+	public void setOperator(BooleanOperator operator) {
+		this.operator = operator;
+	}
+
+
+
+	public Collection<QueryTerm> getQueryTerms() {
+		return queryTerms;
+	}
+
+
+
+	public void setQueryTerms(Collection<QueryTerm> queryTerms) {
+		this.queryTerms = queryTerms;
+	}
+
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/ComparisonQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/ComparisonQueryTerm.java	2007-12-12 22:11:19 UTC (rev 1310)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/ComparisonQueryTerm.java	2007-12-12 23:19:14 UTC (rev 1311)
@@ -6,6 +6,16 @@
 	protected Operator operator;
 	protected QueryTerm value;	
 
+	public ComparisonQueryTerm(String valueAtom) {
+		super();
+		this.operator = Operator.EQUALS;
+		this.value = new AtomicQueryTerm(valueAtom);
+	}
+	public ComparisonQueryTerm(QueryTerm value) {
+		super();
+		this.operator = Operator.EQUALS;;
+		this.value = value;
+	}
 	public ComparisonQueryTerm(Operator operator, String valueAtom) {
 		super();
 		this.operator = operator;

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java	2007-12-12 22:11:19 UTC (rev 1310)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java	2007-12-12 23:19:14 UTC (rev 1311)
@@ -8,9 +8,10 @@
 	
 	public LiteralQueryTerm(AliasType aliasType, String valueAtom) {
 		super();
-		this.value = new AtomicQueryTerm(valueAtom);;
+		this.value = new ComparisonQueryTerm(new AtomicQueryTerm(valueAtom));
 		this.aliasType = aliasType;
 	}
+
 	public LiteralQueryTerm(AliasType aliasType, QueryTerm value) {
 		super();
 		this.value = value;

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/impl/AbstractShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/AbstractShard.java	2007-12-12 22:11:19 UTC (rev 1310)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/AbstractShard.java	2007-12-12 23:19:14 UTC (rev 1311)
@@ -1,9 +1,15 @@
 package org.obd.query.impl;
 
+import org.bbop.rdbms.RelationalQuery;
+import org.obd.query.QueryTerm;
 import org.obd.query.Shard;
 
 
 public abstract class AbstractShard implements Shard {
 
+	public String translateQuery(QueryTerm qt, RelationalQuery rq, 
+			String x) {
+		return "--";
+	}
 
 }

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java	2007-12-12 22:11:19 UTC (rev 1310)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java	2007-12-12 23:19:14 UTC (rev 1311)
@@ -173,8 +173,10 @@
 	}
 
 	public Collection<Node> getNodesByQuery(QueryTerm queryTerm) {
-		// TODO Auto-generated method stub
-		return null;
+		HashSet<Node> nodes = new HashSet<Node>();
+		for (Shard s : shards) 
+			nodes.addAll(s.getNodesByQuery(queryTerm));
+		return nodes;
 	}
 
 	public Graph getGraphByQuery(QueryTerm queryTerm, EntailmentUse entailment, GraphExpansionAlgorithm gea) {

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java	2007-12-12 22:11:19 UTC (rev 1310)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java	2007-12-12 23:19:14 UTC (rev 1311)
@@ -18,7 +18,12 @@
 import org.obd.model.Statement;
 import org.obd.model.bridge.OBOBridge;
 import org.obd.model.stats.AggregateStatisticCollection;
+import org.obd.query.AtomicQueryTerm;
+import org.obd.query.BooleanQueryTerm;
+import org.obd.query.ComparisonQueryTerm;
 import org.obd.query.GraphQuery;
+import org.obd.query.LinkQueryTerm;
+import org.obd.query.LiteralQueryTerm;
 import org.obd.query.QueryTerm;
 import org.obd.query.Shard;
 import org.obo.annotation.datamodel.Annotation;
@@ -36,7 +41,7 @@
  * @author cjm
  *
  */
-public class OBDSQLShard implements Shard {
+public class OBDSQLShard extends AbstractShard implements Shard {
 	
 	OBDSQLDatabaseAdapter obd = new OBDSQLDatabaseAdapter();
 	OBDSQLDatabaseAdapterConfiguration obdconfig = 
@@ -91,7 +96,6 @@
 		WhereClause whereClause = q.getWhereClause();
 		if (sourceId != null)
 			whereClause.addEqualityConstraint("source_uid", sourceId);
-		Node n = null;
 		try {
 			ResultSet rs = execute(q);
 			while (rs.next()) {
@@ -506,8 +510,19 @@
 	}
 
 	public Collection<Node> getNodesByQuery(QueryTerm queryTerm) {
-		// TODO Auto-generated method stub
-		return null;
+		RelationalQuery rq = translateQueryForNode(queryTerm);
+		Collection<Node> nodes = new LinkedList<Node>();
+		try {
+			ResultSet rs = execute(rq);
+			while (rs.next()) {
+				IdentifiedObject io = obd.fetchObject(session, rs);
+				nodes.add(OBOBridge.obj2node(io));
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return nodes;		
 	}
 
 	public Graph getGraphByQuery(QueryTerm queryTerm, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
@@ -519,9 +534,73 @@
 		// TODO Auto-generated method stub
 		return null;
 	}
+	
 
+	public RelationalQuery translateQueryForNode(QueryTerm qt) {
+		RelationalQuery rq = new SqlQueryImpl();
+		rq.addTable("node");
+		translateQuery(qt,rq,"node.node_id");
+		return rq;
+	}
+	// Example: "x" => 'x'
+	public String translateQuery(QueryTerm qt, RelationalQuery rq, 
+			String subjCol) {
 
+		WhereClause wc = rq.getWhereClause();
+		if (qt instanceof AtomicQueryTerm) {
+			String val = ((AtomicQueryTerm)qt).getValue();
+			if (subjCol == null) {
+			}
+			else {
+				wc.addEqualityConstraint(subjCol,val);
+			}
+			return val;
+		}
+		else if (qt instanceof BooleanQueryTerm) {
+			BooleanQueryTerm cqt = (BooleanQueryTerm)qt;
+			for (QueryTerm subquery : cqt.getQueryTerms()) {
+				String val = translateQuery(subquery, rq, subjCol);
+			}
+			return subjCol;
+		}
+		else if (qt instanceof ComparisonQueryTerm) {
+			ComparisonQueryTerm cqt = (ComparisonQueryTerm)qt;
+			String val = translateQuery(cqt.getValue(), rq, null);
+			if (subjCol != null)
+				wc.addOperatorConstraint(cqt.getOperator().toString(), subjCol, val);
+			return subjCol;
+		}
+		else if (qt instanceof LiteralQueryTerm) {
+			// Example: hasName(Contains("x")) => name like 'x%';
+			LiteralQueryTerm cqt = (LiteralQueryTerm)qt;
+			String tbl = "alias"; // TODO: table alias
+			// TODO: node.label
+			String rel = rq.addAutoAliasedTable(tbl);
+			if (subjCol != null)
+				wc.addConstraint(rel+".node_id = " + subjCol);
+			String field = cqt.getAliasType().toString();
+			// e.g. Contains("x") => tbl.label like 'x%'
+			String val = translateQuery(cqt.getValue(), rq, rel+".label");
+			return rel+".node_id";
+		}
+		else if (qt instanceof LinkQueryTerm) {
+			LinkQueryTerm cqt = (LinkQueryTerm)qt;
+			String tbl = "link"; 
+			String tblAlias = rq.addAutoAliasedTable(tbl);
+			if (subjCol != null)
+				wc.addConstraint(tblAlias+".node_id = " + subjCol);
+			String rel = translateQuery(cqt.getRelation(), rq, tblAlias+".predicate_id");
+			String target = translateQuery(cqt.getTarget(), rq, tblAlias+".object_id");
+			return subjCol;
+		}
+		else 
+			return null;  // TODO _ throw
+	}
+	
+	
 
+
+
 	
 	
 	

Modified: obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java	2007-12-12 22:11:19 UTC (rev 1310)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java	2007-12-12 23:19:14 UTC (rev 1311)
@@ -1,16 +1,22 @@
 package org.obd.test;
 
+import java.sql.SQLException;
+
 import junit.framework.Test;
 import junit.framework.TestCase;
 import junit.framework.TestSuite;
 
+import org.bbop.rdbms.RelationalQuery;
 import org.obd.model.Statement;
+import org.obd.query.BooleanQueryTerm;
 import org.obd.query.ComparisonQueryTerm;
 import org.obd.query.LinkQueryTerm;
 import org.obd.query.LiteralQueryTerm;
 import org.obd.query.QueryTerm;
+import org.obd.query.BooleanQueryTerm.BooleanOperator;
 import org.obd.query.ComparisonQueryTerm.Operator;
 import org.obd.query.LiteralQueryTerm.AliasType;
+import org.obd.query.impl.OBDSQLShard;
 import org.obd.ws.OBDQueryService;
 
 public class QueryTest extends TestCase {
@@ -39,7 +45,7 @@
 		suite.addTest(new QueryTest("testQuery"));
 	}
 	
-	public void testQuery() {
+	public void testQuery() throws SQLException, ClassNotFoundException {
 		
 		QueryTerm qt;
 		
@@ -56,13 +62,24 @@
 				new LiteralQueryTerm(AliasType.ANY_LABEL, "nucleus")));
 		runQuery(new LinkQueryTerm(partOf, 
 				new LinkQueryTerm(developsFrom, "CL:1234567")));
+		runQuery(new LinkQueryTerm(partOf, 
+				new BooleanQueryTerm( 
+						BooleanOperator.AND,
+						new LinkQueryTerm(partOf, "GO:0005634"),
+						new LinkQueryTerm(partOf, "GO:0005739")
+						)));
 		
 		
 
 	}
 	
-	public void runQuery(QueryTerm qt) {
+	public void runQuery(QueryTerm qt) throws SQLException, ClassNotFoundException {
 		System.out.println("running Q: "+qt.toString());
+		OBDSQLShard s = new OBDSQLShard();
+		RelationalQuery rq = s.translateQueryForNode(qt);
+		System.out.println(rq.toString());
+		for (Object v : rq.getPlaceHolderVals())
+			System.out.println(" "+v);
 
 	}
 


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Revision: 1328
          http://obo.svn.sourceforge.net/obo/?rev=1328&view=rev
Author:   cmungall
Date:     2007-12-19 19:05:16 -0800 (Wed, 19 Dec 2007)

Log Message:
-----------


Modified Paths:
--------------
    obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java
    obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java

Added Paths:
-----------
    obdapi/trunk/OBDAPI/src/org/obd/query/LabelQueryTerm.java

Removed Paths:
-------------
    obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java

Copied: obdapi/trunk/OBDAPI/src/org/obd/query/LabelQueryTerm.java (from rev 1311, obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java)
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/LabelQueryTerm.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/LabelQueryTerm.java	2007-12-20 03:05:16 UTC (rev 1328)
@@ -0,0 +1,50 @@
+package org.obd.query;
+
+public class LabelQueryTerm extends QueryTerm {
+	public enum AliasType {ID, PRIMARY_NAME, ALTERNATE_LABEL, ANY_LABEL }
+	
+	protected AliasType aliasType = AliasType.ID;
+	protected QueryTerm value;
+	
+	public LabelQueryTerm(AliasType aliasType, String valueAtom) {
+		super();
+		this.value = new ComparisonQueryTerm(new AtomicQueryTerm(valueAtom));
+		this.aliasType = aliasType;
+	}
+
+	public LabelQueryTerm(AliasType aliasType, QueryTerm value) {
+		super();
+		this.value = value;
+		this.aliasType = aliasType;
+	}
+	public LabelQueryTerm(QueryTerm value) {
+		super();
+		this.value = value;
+	}
+	public LabelQueryTerm(String valueAtom) {
+		super();
+		this.value = new ComparisonQueryTerm(new AtomicQueryTerm(valueAtom));
+	}
+
+	public QueryTerm getValue() {
+		return value;
+	}
+
+	public void setValue(QueryTerm value) {
+		this.value = value;
+	}
+
+	public AliasType getAliasType() {
+		return aliasType;
+	}
+	public void setAliasType(AliasType aliasType) {
+		this.aliasType = aliasType;
+	}
+
+	public String toString() {
+		String s = " has "+getAliasType().toString();
+		if (getValue() != null)
+			s = s + " "+getValue().toString();
+		return s;
+	}
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java	2007-12-19 23:44:51 UTC (rev 1327)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java	2007-12-20 03:05:16 UTC (rev 1328)
@@ -26,8 +26,10 @@
 
 	public LinkQueryTerm(String relationAtom, String targetAtom) {
 		super();
-		this.relation = new AtomicQueryTerm(relationAtom);
-		this.target = new AtomicQueryTerm(targetAtom);
+//		this.relation = new AtomicQueryTerm(relationAtom);
+		this.relation = new LabelQueryTerm(relationAtom);
+//		this.target = new AtomicQueryTerm(targetAtom);
+		this.target = new LabelQueryTerm(targetAtom);
 	}
 	
 	

Deleted: obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java	2007-12-19 23:44:51 UTC (rev 1327)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java	2007-12-20 03:05:16 UTC (rev 1328)
@@ -1,50 +0,0 @@
-package org.obd.query;
-
-public class LiteralQueryTerm extends QueryTerm {
-	public enum AliasType {ID, PRIMARY_NAME, ALTERNATE_LABEL, ANY_LABEL }
-	
-	protected AliasType aliasType = AliasType.ID;
-	protected QueryTerm value;
-	
-	public LiteralQueryTerm(AliasType aliasType, String valueAtom) {
-		super();
-		this.value = new ComparisonQueryTerm(new AtomicQueryTerm(valueAtom));
-		this.aliasType = aliasType;
-	}
-
-	public LiteralQueryTerm(AliasType aliasType, QueryTerm value) {
-		super();
-		this.value = value;
-		this.aliasType = aliasType;
-	}
-	public LiteralQueryTerm(QueryTerm value) {
-		super();
-		this.value = value;
-	}
-	public LiteralQueryTerm(String valueAtom) {
-		super();
-		this.value = new AtomicQueryTerm(valueAtom);
-	}
-
-	public QueryTerm getValue() {
-		return value;
-	}
-
-	public void setValue(QueryTerm value) {
-		this.value = value;
-	}
-
-	public AliasType getAliasType() {
-		return aliasType;
-	}
-	public void setAliasType(AliasType aliasType) {
-		this.aliasType = aliasType;
-	}
-
-	public String toString() {
-		String s = " has "+getAliasType().toString();
-		if (getValue() != null)
-			s = s + " "+getValue().toString();
-		return s;
-	}
-}

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java	2007-12-19 23:44:51 UTC (rev 1327)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java	2007-12-20 03:05:16 UTC (rev 1328)
@@ -23,10 +23,11 @@
 import org.obd.query.ComparisonQueryTerm;
 import org.obd.query.GraphQuery;
 import org.obd.query.LinkQueryTerm;
-import org.obd.query.LiteralQueryTerm;
+import org.obd.query.LabelQueryTerm;
 import org.obd.query.QueryTerm;
 import org.obd.query.Shard;
 import org.obd.query.ComparisonQueryTerm.Operator;
+import org.obd.query.LabelQueryTerm.AliasType;
 import org.obo.annotation.datamodel.Annotation;
 import org.obo.dataadapter.OBDSQLDatabaseAdapter;
 import org.obo.dataadapter.OBOFileAdapter;
@@ -543,7 +544,17 @@
 		translateQuery(qt,rq,"node.node_id");
 		return rq;
 	}
-	// Example: "x" => 'x'
+
+	/**
+	 * @param qt - OBD Query to be translated
+	 * @param rq - constructed Relation SQL Query
+	 * @param subjCol - column to use in where constraint. Can be null
+	 * @return DEPRECATED??
+	 * 
+	 * translates a query or part of a query to SQL.
+	 * Recursive.
+	 * Assumes 
+	 */
 	public String translateQuery(QueryTerm qt, RelationalQuery rq, 
 			String subjCol) {
 
@@ -576,15 +587,31 @@
 			}
 			return subjCol;
 		}
-		else if (qt instanceof LiteralQueryTerm) {
+		else if (qt instanceof LabelQueryTerm) {
 			// Example: hasName(Contains("x")) => name like 'x%';
-			LiteralQueryTerm cqt = (LiteralQueryTerm)qt;
+			LabelQueryTerm cqt = (LabelQueryTerm)qt;
+			AliasType alias = cqt.getAliasType();
+			if (alias.equals(AliasType.ID)) {
+				String rel = rq.addAutoAliasedTable("node");
+				translateQuery(cqt.getValue(), rq, rel+".node_uid");
+				if (subjCol != null)
+					wc.addConstraint(rel+".node_id = " + subjCol);
+				return rel+".node_id";
+			}
+			if (alias.equals(AliasType.PRIMARY_NAME)) {
+				String rel = rq.addAutoAliasedTable("node");
+				translateQuery(cqt.getValue(), rq, rel+".label");
+				if (subjCol != null)
+					wc.addConstraint(rel+".node_id = " + subjCol);
+				return rel+".node_idxx";
+			}
+				
 			String tbl = "alias"; // TODO: table alias
 			// TODO: node.label
 			String rel = rq.addAutoAliasedTable(tbl);
 			if (subjCol != null)
 				wc.addConstraint(rel+".node_id = " + subjCol);
-			String field = cqt.getAliasType().toString();
+			String field = alias.toString();
 			// e.g. Contains("x") => tbl.label like 'x%'
 			String val = translateQuery(cqt.getValue(), rq, rel+".label");
 			return rel+".node_id";

Modified: obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java	2007-12-19 23:44:51 UTC (rev 1327)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java	2007-12-20 03:05:16 UTC (rev 1328)
@@ -11,11 +11,11 @@
 import org.obd.query.BooleanQueryTerm;
 import org.obd.query.ComparisonQueryTerm;
 import org.obd.query.LinkQueryTerm;
-import org.obd.query.LiteralQueryTerm;
+import org.obd.query.LabelQueryTerm;
 import org.obd.query.QueryTerm;
 import org.obd.query.BooleanQueryTerm.BooleanOperator;
 import org.obd.query.ComparisonQueryTerm.Operator;
-import org.obd.query.LiteralQueryTerm.AliasType;
+import org.obd.query.LabelQueryTerm.AliasType;
 import org.obd.query.impl.OBDSQLShard;
 import org.obd.ws.OBDQueryService;
 
@@ -46,12 +46,10 @@
 	}
 	
 	public void testQuery() throws SQLException, ClassNotFoundException {
-		
-		QueryTerm qt;
-		
-		runQuery(new LiteralQueryTerm(AliasType.PRIMARY_NAME,
+				
+		runQuery(new LabelQueryTerm(AliasType.PRIMARY_NAME,
 				"apoptosis"));
-		runQuery(new LiteralQueryTerm(AliasType.ALTERNATE_LABEL,
+		runQuery(new LabelQueryTerm(AliasType.ALTERNATE_LABEL,
 				new ComparisonQueryTerm(Operator.STARTS_WITH,
 				"apoptosis")));
 		
@@ -59,7 +57,7 @@
 		String developsFrom = "OBO_REL:developsFrom";
 		runQuery(new LinkQueryTerm(partOf, "GO:0005634"));
 		runQuery(new LinkQueryTerm(partOf, 
-				new LiteralQueryTerm(AliasType.ANY_LABEL, "nucleus")));
+				new LabelQueryTerm(AliasType.ANY_LABEL, "nucleus")));
 		runQuery(new LinkQueryTerm(partOf, 
 				new LinkQueryTerm(developsFrom, "CL:1234567")));
 		runQuery(new LinkQueryTerm(partOf, 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 1333
          http://obo.svn.sourceforge.net/obo/?rev=1333&view=rev
Author:   cmungall
Date:     2007-12-20 11:10:26 -0800 (Thu, 20 Dec 2007)

Log Message:
-----------


Modified Paths:
--------------
    obdapi/trunk/OBDAPI/src/org/obd/model/Graph.java
    obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBOBridge.java
    obdapi/trunk/OBDAPI/src/org/obd/query/BooleanQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/Shard.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java

Added Paths:
-----------
    obdapi/trunk/OBDAPI/src/org/obd/query/BooleanIntersectionQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/test/ExecuteQueryTest.java

Modified: obdapi/trunk/OBDAPI/src/org/obd/model/Graph.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/Graph.java	2007-12-20 18:20:33 UTC (rev 1332)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/Graph.java	2007-12-20 19:10:26 UTC (rev 1333)
@@ -30,6 +30,7 @@
 		super();
 		setStatements(statements);
 	}
+	
 
 	public Graph(Collection<Node> nodes, Collection<Statement> statements) {
 		super();
@@ -149,6 +150,8 @@
 	}
 
 	public void merge(Graph g2) {
+		if (g2==null)
+			return;
 		addNodes(g2.getNodes());
 		addStatements(g2.getStatements());
 	}

Modified: obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBOBridge.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBOBridge.java	2007-12-20 18:20:33 UTC (rev 1332)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBOBridge.java	2007-12-20 19:10:26 UTC (rev 1333)
@@ -54,7 +54,7 @@
 		}
 		if (io instanceof DefinedObject) {
 			String def = ((DefinedObject)io).getDefinition();
-			if (def != null) {
+			if (def != null && !def.equals("")) {
 				LiteralStatement ls = new LiteralStatement();
 				ls.setNodeId(node.getId());
 				ls.setValue(def);

Added: obdapi/trunk/OBDAPI/src/org/obd/query/BooleanIntersectionQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/BooleanIntersectionQueryTerm.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/BooleanIntersectionQueryTerm.java	2007-12-20 19:10:26 UTC (rev 1333)
@@ -0,0 +1,37 @@
+package org.obd.query;
+
+import java.util.Collection;
+import java.util.LinkedList;
+
+public class BooleanIntersectionQueryTerm extends BooleanQueryTerm {
+
+		
+	public BooleanIntersectionQueryTerm(Collection<QueryTerm> queryTerms) {
+		super();
+		this.queryTerms = queryTerms;
+	}
+
+	public BooleanIntersectionQueryTerm(QueryTerm... queryTerms) {
+		super();
+		for (QueryTerm qt : queryTerms) {
+			addQueryTerm(qt);
+		}
+	}
+
+	public BooleanOperator getOperator() {
+		return BooleanOperator.AND;
+	}
+
+	public void setOperator(BooleanOperator operator) {
+		this.operator = operator;
+	}
+
+	public Collection<QueryTerm> getQueryTerms() {
+		return queryTerms;
+	}
+
+	public void setQueryTerms(Collection<QueryTerm> queryTerms) {
+		this.queryTerms = queryTerms;
+	}
+
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/BooleanQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/BooleanQueryTerm.java	2007-12-20 18:20:33 UTC (rev 1332)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/BooleanQueryTerm.java	2007-12-20 19:10:26 UTC (rev 1333)
@@ -11,6 +11,22 @@
 	
 	protected Collection<QueryTerm> queryTerms = new LinkedList<QueryTerm>();
 
+	public BooleanQueryTerm() {
+		super();
+	}
+	
+	public BooleanQueryTerm(Collection<QueryTerm> queryTerms) {
+		super();
+		this.queryTerms = queryTerms;
+	}
+
+	public BooleanQueryTerm(QueryTerm... queryTerms) {
+		super();
+		for (QueryTerm qt : queryTerms) {
+			addQueryTerm(qt);
+		}
+	}
+
 	public BooleanQueryTerm(BooleanOperator operator, Collection<QueryTerm> queryTerms) {
 		super();
 		this.operator = operator;

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java	2007-12-20 18:20:33 UTC (rev 1332)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java	2007-12-20 19:10:26 UTC (rev 1333)
@@ -13,9 +13,10 @@
 	 * @param relation
 	 * @param target
 	 */
-	public LinkQueryTerm(String relation, QueryTerm target) {
+	public LinkQueryTerm(String relationAtom, QueryTerm target) {
 		super();
-		this.relation = new AtomicQueryTerm(relation);
+		//this.relation = new AtomicQueryTerm(relation);
+		this.relation = new LabelQueryTerm(relationAtom);
 		this.target = target;
 	}
 	public LinkQueryTerm(QueryTerm relation, QueryTerm target) {
@@ -42,10 +43,10 @@
 	}
 
 	public String toString() {
-		String s = getRelation().toString();
+		String s = "Link["+getRelation().toString();
 		if (getTarget() != null)
 			s = s + " "+getTarget().toString();
-		return s;
+		return s+"]";
 	}
 
 

Added: obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java	2007-12-20 19:10:26 UTC (rev 1333)
@@ -0,0 +1,41 @@
+package org.obd.query;
+
+public class LiteralQueryTerm extends QueryTerm {
+	protected QueryTerm value;
+	
+	public LiteralQueryTerm(QueryTerm relation, String valueAtom) {
+		super();
+		this.value = new ComparisonQueryTerm(new AtomicQueryTerm(valueAtom));
+		setRelation(relation);
+	}
+
+	public LiteralQueryTerm(String relationAtom, QueryTerm value) {
+		super();
+		this.value = value;
+		setRelation(new ComparisonQueryTerm(new AtomicQueryTerm(relationAtom)));
+	}
+	public LiteralQueryTerm(QueryTerm value) {
+		super();
+		this.value = value;
+	}
+	public LiteralQueryTerm(String valueAtom) {
+		super();
+		this.value = new ComparisonQueryTerm(new AtomicQueryTerm(valueAtom));
+	}
+
+	public QueryTerm getValue() {
+		return value;
+	}
+
+	public void setValue(QueryTerm value) {
+		this.value = value;
+	}
+
+
+	public String toString() {
+		String s = " has "+getRelation().toString();
+		if (getValue() != null)
+			s = s + " "+getValue().toString();
+		return s;
+	}
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/Shard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/Shard.java	2007-12-20 18:20:33 UTC (rev 1332)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/Shard.java	2007-12-20 19:10:26 UTC (rev 1333)
@@ -1,14 +1,11 @@
 package org.obd.query;
 
 import java.util.Collection;
-import java.util.HashSet;
 
 import org.obd.model.Graph;
 import org.obd.model.Node;
 import org.obd.model.Statement;
-import org.obd.model.bridge.OBOBridge;
 import org.obd.model.stats.AggregateStatisticCollection;
-import org.obo.datamodel.IdentifiedObject;
 
 
 /**

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java	2007-12-20 18:20:33 UTC (rev 1332)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java	2007-12-20 19:10:26 UTC (rev 1333)
@@ -180,13 +180,18 @@
 	}
 
 	public Graph getGraphByQuery(QueryTerm queryTerm, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
-		// TODO Auto-generated method stub
-		return null;
+		Graph g = new Graph();
+		for (Shard s : shards) 
+			g.merge(s.getGraphByQuery(queryTerm,  entailment,  gea));
+		return g;	
 	}
 
 	public Collection<Statement> getStatementsByQuery(QueryTerm queryTerm) {
-		// TODO Auto-generated method stub
-		return null;
+		HashSet<Statement> statements = new HashSet<Statement>();
+		for (Shard s : shards) 
+			statements.addAll(s.getStatementsByQuery(queryTerm));
+
+		return statements;
 	}
 
 

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java	2007-12-20 18:20:33 UTC (rev 1332)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java	2007-12-20 19:10:26 UTC (rev 1333)
@@ -528,8 +528,10 @@
 	}
 
 	public Graph getGraphByQuery(QueryTerm queryTerm, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
-		// TODO Auto-generated method stub
-		return null;
+		Collection<Node> nodes = getNodesByQuery(queryTerm);
+		Graph g = new Graph();
+		g.setNodes(nodes);
+		return g;		
 	}
 
 	public Collection<Statement> getStatementsByQuery(QueryTerm queryTerm) {
@@ -540,10 +542,12 @@
 
 	public RelationalQuery translateQueryForNode(QueryTerm qt) {
 		RelationalQuery rq = new SqlQueryImpl();
-		rq.addTable("node");
-		translateQuery(qt,rq,"node.node_id");
+		rq.addTable("node_with_source");
+		translateQuery(qt,rq,"node_with_source.node_id");
+		rq.setSelectClause("node_with_source.*");
 		return rq;
 	}
+	
 
 	/**
 	 * @param qt - OBD Query to be translated
@@ -593,7 +597,7 @@
 			AliasType alias = cqt.getAliasType();
 			if (alias.equals(AliasType.ID)) {
 				String rel = rq.addAutoAliasedTable("node");
-				translateQuery(cqt.getValue(), rq, rel+".node_uid");
+				translateQuery(cqt.getValue(), rq, rel+".uid");
 				if (subjCol != null)
 					wc.addConstraint(rel+".node_id = " + subjCol);
 				return rel+".node_id";
@@ -605,6 +609,9 @@
 					wc.addConstraint(rel+".node_id = " + subjCol);
 				return rel+".node_idxx";
 			}
+			if (alias.equals(AliasType.ANY_LABEL)) {
+				// TODO: OR query
+			}
 				
 			String tbl = "alias"; // TODO: table alias
 			// TODO: node.label

Added: obdapi/trunk/OBDAPI/src/org/obd/test/ExecuteQueryTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/ExecuteQueryTest.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/ExecuteQueryTest.java	2007-12-20 19:10:26 UTC (rev 1333)
@@ -0,0 +1,47 @@
+package org.obd.test;
+
+import java.sql.SQLException;
+
+import junit.framework.Test;
+import junit.framework.TestSuite;
+
+import org.bbop.rdbms.RelationalQuery;
+import org.obd.model.Graph;
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.query.QueryTerm;
+import org.obd.query.impl.OBDSQLShard;
+
+public class ExecuteQueryTest extends QueryTest {
+
+	public ExecuteQueryTest(String n) {
+		super(n);
+		// TODO Auto-generated constructor stub
+	}
+	
+	public void runQuery(QueryTerm qt) throws SQLException, ClassNotFoundException {
+		System.out.println("exec Q: "+qt.toString());
+		Graph g = service.getGraphByQuery(qt, null, null);
+		g.nestStatementsUnderNodes();
+		for (Node n : g.getNodes()) {
+			System.out.println(n);
+			for (Statement s : n.getStatements()) {
+				System.out.println("    "+s);
+			}	
+		}
+
+	}
+	
+	public static Test suite() {
+		TestSuite suite = new TestSuite();
+		addTests(suite);
+		return suite;
+	}
+
+
+	public static void addTests(TestSuite suite) {
+		suite.addTest(new ExecuteQueryTest("testQuery"));
+	}
+
+
+}


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 1335
          http://obo.svn.sourceforge.net/obo/?rev=1335&view=rev
Author:   cmungall
Date:     2008-01-02 16:18:24 -0800 (Wed, 02 Jan 2008)

Log Message:
-----------


Modified Paths:
--------------
    obdapi/trunk/OBDAPI/src/org/obd/query/Shard.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/AbstractShard.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBOSessionShard.java
    obdapi/trunk/OBDAPI/src/org/obd/test/SearchTest.java
    obdapi/trunk/OBDAPI/src/org/obd/ws/OBDQueryService.java

Added Paths:
-----------
    obdapi/trunk/OBDAPI/src/org/obd/model/stats/ScoredNode.java
    obdapi/trunk/OBDAPI/src/org/obd/test/SimilarityTest.java

Added: obdapi/trunk/OBDAPI/src/org/obd/model/stats/ScoredNode.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/stats/ScoredNode.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/stats/ScoredNode.java	2008-01-03 00:18:24 UTC (rev 1335)
@@ -0,0 +1,53 @@
+package org.obd.model.stats;
+
+import org.obd.model.Node;
+
+public class ScoredNode implements Comparable {
+	protected String nodeId;
+	protected double score;
+	
+	public ScoredNode() {
+		super();
+	}
+	
+	public ScoredNode(String nodeId) {
+		super();
+		this.nodeId = nodeId;
+	}
+
+	public ScoredNode(String nodeId, double score) {
+		super();
+		this.nodeId = nodeId;
+		this.score = score;
+	}
+
+	public double getScore() {
+		return score;
+	}
+	public void setScore(double score) {
+		this.score = score;
+	}
+	
+
+	public String getNodeId() {
+		return nodeId;
+	}
+
+	public void setNodeId(String nodeId) {
+		this.nodeId = nodeId;
+	}
+
+	public int hashCode() {
+		return nodeId.hashCode();
+	}
+
+	public String toString() {
+		return nodeId + " ["+score+"]";
+	}
+
+	public int compareTo(Object sn)  throws ClassCastException  {
+	    if (!(sn instanceof ScoredNode))
+	        throw new ClassCastException("A ScoredNode object expected.");
+		return score > ((ScoredNode)sn).getScore()  ? 1 : -1;
+	}
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/Shard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/Shard.java	2007-12-22 16:14:04 UTC (rev 1334)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/Shard.java	2008-01-03 00:18:24 UTC (rev 1335)
@@ -1,11 +1,13 @@
 package org.obd.query;
 
 import java.util.Collection;
+import java.util.List;
 
 import org.obd.model.Graph;
 import org.obd.model.Node;
 import org.obd.model.Statement;
 import org.obd.model.stats.AggregateStatisticCollection;
+import org.obd.model.stats.ScoredNode;
 
 
 /**
@@ -167,4 +169,13 @@
 	 * @return
 	 */
 	public AggregateStatisticCollection getSummaryStatistics();
+	
+	/**
+	 * @param nodeId
+	 * @return all comparable nodes with similarity p-value
+	 */
+	public List<ScoredNode> getSimilarNodes(String nodeId);
+	
+	public int getAnnotatedNodeCount();
+
 }

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/impl/AbstractShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/AbstractShard.java	2007-12-22 16:14:04 UTC (rev 1334)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/AbstractShard.java	2008-01-03 00:18:24 UTC (rev 1335)
@@ -1,6 +1,16 @@
 package org.obd.query.impl;
 
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.List;
+
 import org.bbop.rdbms.RelationalQuery;
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.model.stats.ScoredNode;
 import org.obd.query.QueryTerm;
 import org.obd.query.Shard;
 
@@ -11,5 +21,43 @@
 			String x) {
 		return "--";
 	}
+	
+	public List<ScoredNode> getSimilarNodes(String nodeId) {
+		int totalNodes = this.getAnnotatedNodeCount();
+		List<ScoredNode> scoredNodes = new LinkedList<ScoredNode>();
+		HashMap<String, Double> nodePvalMap = new HashMap<String,Double>();
+		Collection<Statement> stmts = 
+			getAnnotationStatementsForAnnotatedEntity(nodeId, null, null);
+		HashSet<String> annotClassIds = new HashSet<String>();
+		for (Statement stmt : stmts) {
+			// TODO : don't count redundant ones
+			// E.g. annot to Eye and Organ should only count for Organ
+			annotClassIds.add(stmt.getTargetId());
+		}
+		/*
+		 * multiply all probabilities together
+		 * note: this biases things in favour of multiple annotations
+		 */
+		for (String annotClassId : annotClassIds) {
+			 Collection<Node> nodes = 
+				 getAnnotatedEntitiesBelowNodeSet(Collections.singleton(annotClassId)
+				, null, null);
+			 double p = ((float)nodes.size()) / totalNodes;
+			 System.out.println(nodes.size()+"/"+totalNodes+" p="+p);
+			 for (Node n : nodes) {
+				 String nid = n.getId();
+				 if (nodePvalMap.containsKey(nid)) {
+					 nodePvalMap.put(nid, p * nodePvalMap.get(nid));
+				 }
+				 else {
+					 nodePvalMap.put(nid, p);
+				 }
+			 }
+		}
+		for (String nid : nodePvalMap.keySet())
+			scoredNodes.add(new ScoredNode(nid,nodePvalMap.get(nid)));
+		Collections.sort(scoredNodes);
+		return scoredNodes;
+	}
 
 }

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java	2007-12-22 16:14:04 UTC (rev 1334)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java	2008-01-03 00:18:24 UTC (rev 1335)
@@ -1,13 +1,17 @@
 package org.obd.query.impl;
 
 import java.util.Collection;
+import java.util.Collections;
 import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.List;
 
 import org.obd.model.Graph;
 import org.obd.model.Node;
 import org.obd.model.Statement;
 import org.obd.model.stats.AggregateStatistic;
 import org.obd.model.stats.AggregateStatisticCollection;
+import org.obd.model.stats.ScoredNode;
 import org.obd.query.QueryTerm;
 import org.obd.query.Shard;
 import org.obd.query.Shard.EntailmentUse;
@@ -194,6 +198,20 @@
 		return statements;
 	}
 
+	public int getAnnotatedNodeCount() {
+		// TODO Auto-generated method stub
+		return 0;
+	}
 
+	public List<ScoredNode> getSimilarNodes(String nodeId) {
+		List<ScoredNode> scoredNodes = new LinkedList<ScoredNode>();
+		for (Shard s : shards) {
+			// TODO: combine p-vals
+			scoredNodes.addAll(s.getSimilarNodes(nodeId));
+		}
+		return scoredNodes;
+	}
+
+
 	
 }

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java	2007-12-22 16:14:04 UTC (rev 1334)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java	2008-01-03 00:18:24 UTC (rev 1335)
@@ -389,10 +389,12 @@
 
 	public Collection<Statement> getAnnotationStatementsForAnnotatedEntity(String id, EntailmentUse entailment, GraphExpansionAlgorithm strategy) {
 
-		// node_uid is the annotated entity - find everything about it -
-		// both additional metadata and annotation
+		// node_uid is the annotated entity 
 		WhereClause whereClause = new SqlWhereClauseImpl();
 		whereClause.addEqualityConstraint("node_uid",id);
+		whereClause.addConstraint("is_inferred='f'");
+		whereClause.addConstraint("reiflink_node_id IS NOT NULL");
+		
 		Collection<Statement> annots = getStatements(whereClause);
 		return annots;
 	}
@@ -575,7 +577,9 @@
 		else if (qt instanceof BooleanQueryTerm) {
 			BooleanQueryTerm cqt = (BooleanQueryTerm)qt;
 			for (QueryTerm subquery : cqt.getQueryTerms()) {
-				String val = translateQuery(subquery, rq, subjCol);
+				RelationalQuery subrq = new SqlQueryImpl();
+				translateQuery(subquery, rq, "node_id");
+				wc.addInConstraint(subjCol, subrq);
 			}
 			return subjCol;
 		}
@@ -636,6 +640,24 @@
 		else 
 			return null;  // TODO _ throw
 	}
+
+	public int getAnnotatedNodeCount() {
+		RelationalQuery q = new SqlQueryImpl();
+		q.addTable("annotated_entity");
+		q.setSelectClause("count(node_id) AS c");
+		ResultSet rs;
+		int n = 0;
+		try {
+			rs = execute(q);
+			if (rs.next()) {
+				n = rs.getInt("c");
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return n;
+	}
 	
 	
 

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBOSessionShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBOSessionShard.java	2007-12-22 16:14:04 UTC (rev 1334)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBOSessionShard.java	2008-01-03 00:18:24 UTC (rev 1335)
@@ -25,7 +25,7 @@
 import org.obo.datamodel.OBOSession;
 
 
-public class OBOSessionShard implements Shard {
+public class OBOSessionShard extends AbstractShard implements Shard {
 	OBOFileAdapter adapter = new OBOFileAdapter();
 	
 	protected OBOSession session;
@@ -210,9 +210,14 @@
 		return null;
 	}
 
+	public int getAnnotatedNodeCount() {
+		// TODO Auto-generated method stub
+		return 0;
+	}
 
 
 
 
 
+
 }

Modified: obdapi/trunk/OBDAPI/src/org/obd/test/SearchTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/SearchTest.java	2007-12-22 16:14:04 UTC (rev 1334)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/SearchTest.java	2008-01-03 00:18:24 UTC (rev 1335)
@@ -1,21 +1,13 @@
 package org.obd.test;
 
-import java.io.PrintStream;
-import java.util.logging.Logger;
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
 
-import org.bbop.io.AuditedPrintStream;
-import org.obd.model.Graph;
 import org.obd.model.Node;
 import org.obd.model.Statement;
 import org.obd.ws.OBDQueryService;
-import org.obo.datamodel.impl.DefaultLinkDatabase;
-import org.obo.reasoner.impl.ForwardChainingReasoner;
-import org.obo.test.OBDAnnotationSaveTest;
 
-import junit.framework.Test;
-import junit.framework.TestCase;
-import junit.framework.TestSuite;
-
 public class SearchTest extends TestCase {
 
 	OBDQueryService service;

Added: obdapi/trunk/OBDAPI/src/org/obd/test/SimilarityTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/SimilarityTest.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/SimilarityTest.java	2008-01-03 00:18:24 UTC (rev 1335)
@@ -0,0 +1,57 @@
+package org.obd.test;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.LinkedList;
+import java.util.List;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.model.stats.ScoredNode;
+import org.obd.ws.OBDQueryService;
+
+public class SimilarityTest extends TestCase {
+
+	OBDQueryService service;
+	
+	
+	public SimilarityTest(String n) {
+		super(n);
+	}
+
+
+	public void setUp() throws Exception {
+		System.out.println("Setting up: " + this);
+		service = new OBDQueryService();
+		
+	}
+
+	public static Test suite() {
+		TestSuite suite = new TestSuite();
+		addTests(suite);
+		return suite;
+	}
+
+	public static void addTests(TestSuite suite) {
+		suite.addTest(new SimilarityTest("testQuery"));
+	}
+	
+	public void testQuery() {
+		
+		// OMIM:601653.0014
+		
+		List<ScoredNode> sns = 
+			Arrays.asList(service.getSimilarNodes("Eya1<tm1Rilm>/Eya1<tm1Rilm>"));
+		Collections.sort(sns);
+		for (ScoredNode sn : sns) {
+			System.out.println(sn);
+		}
+		
+
+	}
+
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/ws/OBDQueryService.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/OBDQueryService.java	2007-12-22 16:14:04 UTC (rev 1334)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/OBDQueryService.java	2008-01-03 00:18:24 UTC (rev 1335)
@@ -10,6 +10,7 @@
 import org.obd.model.Node;
 import org.obd.model.Statement;
 import org.obd.model.stats.AggregateStatisticCollection;
+import org.obd.model.stats.ScoredNode;
 import org.obd.query.QueryTerm;
 import org.obd.query.Shard;
 import org.obd.query.Shard.EntailmentUse;
@@ -23,11 +24,13 @@
 public class OBDQueryService {
 	
 	//String jdbcPath = "jdbc:postgresql://spitz.lbl.gov:5432/obd_phenotype";
-	String defaultJdbcPath = "jdbc:postgresql://localhost:5432/obd_phenotype_full";
+	//String defaultJdbcPath = "jdbc:postgresql://localhost:5432/obd_phenotype_full";
+	String defaultJdbcPath = "jdbc:postgresql://localhost:5432/obd_phenotype_mouse";
 	MultiShard shard;
 	
 	
 	
+
 	public OBDQueryService() throws ClassNotFoundException, DataAdapterException {
 		shard = new MultiShard();
 		
@@ -156,10 +159,8 @@
 		return (Statement[])shard.getSubjectStatements(subjectId, subjectRelationId, targetRelationId, nodeId, targetId, subjectSourceId, nodeSourceId, useImplied, isReified).toArray(new Statement[0]);
 	}
 
-
-
-
+	public ScoredNode[] getSimilarNodes(String nodeId) {
+		return (ScoredNode[])shard.getSimilarNodes(nodeId).toArray(new ScoredNode[0]);
+	}	
 	
-	
-	
 }


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 1346
          http://obo.svn.sourceforge.net/obo/?rev=1346&view=rev
Author:   cmungall
Date:     2008-01-04 17:27:45 -0800 (Fri, 04 Jan 2008)

Log Message:
-----------


Modified Paths:
--------------
    obdapi/trunk/OBDAPI/src/org/obd/model/Graph.java
    obdapi/trunk/OBDAPI/src/org/obd/model/Node.java
    obdapi/trunk/OBDAPI/src/org/obd/model/Statement.java
    obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBOBridge.java
    obdapi/trunk/OBDAPI/src/org/obd/query/ComparisonQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/LabelQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/QueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/Shard.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/AbstractShard.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBOSessionShard.java
    obdapi/trunk/OBDAPI/src/org/obd/test/AnnotationGraphTest.java
    obdapi/trunk/OBDAPI/src/org/obd/test/ExecuteQueryTest.java
    obdapi/trunk/OBDAPI/src/org/obd/test/MiniTest.java
    obdapi/trunk/OBDAPI/src/org/obd/test/MultiNodeFetchTest.java
    obdapi/trunk/OBDAPI/src/org/obd/test/OBDQueryServiceTest.java
    obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java
    obdapi/trunk/OBDAPI/src/org/obd/test/SearchTest.java
    obdapi/trunk/OBDAPI/src/org/obd/ws/OBDQueryService.java

Added Paths:
-----------
    obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBDJSONBridge.java
    obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBDXMLBridge.java
    obdapi/trunk/OBDAPI/src/org/obd/query/AnnotationLinkQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/CoAnnotatedQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/ExistentialQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/test/AllTests.java
    obdapi/trunk/OBDAPI/src/org/obd/ws/GraphResource.java
    obdapi/trunk/OBDAPI/src/org/obd/ws/HomeResource.java
    obdapi/trunk/OBDAPI/src/org/obd/ws/NodeResource.java
    obdapi/trunk/OBDAPI/src/org/obd/ws/NodesBySearchResource.java
    obdapi/trunk/OBDAPI/src/org/obd/ws/OBDResource.java
    obdapi/trunk/OBDAPI/src/org/obd/ws/OBDRestApplication.java
    obdapi/trunk/OBDAPI/src/org/obd/ws/ShardMetadataResource.java
    obdapi/trunk/OBDAPI/src/org/obd/ws/StatementsResource.java

Modified: obdapi/trunk/OBDAPI/src/org/obd/model/Graph.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/Graph.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/Graph.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -98,7 +98,8 @@
 		return (Statement[])statements.toArray(new Statement[0]);
 	}
 	public void setStatements(Collection<Statement> statements) {
-		this.statements = statements;
+		clearStatements();
+		this.statements.addAll(statements);
 	}
 	
 

Modified: obdapi/trunk/OBDAPI/src/org/obd/model/Node.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/Node.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/Node.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -12,7 +12,7 @@
 	private static final long serialVersionUID = 1L;
 	
 	protected String id;
-	protected String name;
+	protected String label;
 	protected Collection<Statement> statements;
 	protected String sourceId;
 	protected boolean isAnonymous;
@@ -30,12 +30,12 @@
 		this.id = id;
 	}
 
-	public String getName() {
-		return name;
+	public String getLabel() {
+		return label;
 	}
 
-	public void setName(String name) {
-		this.name = name;
+	public void setLabel(String name) {
+		this.label = name;
 	}
 
 	// WSDL-friendly : use arrays
@@ -93,13 +93,14 @@
 
 
 	public String toString() {
-		String s = id + " \""+name+"\"";
+		String s = id + " \""+label+"\"";
 		if (isAnonymous)
 			s = " ANON:"+id;
 		if (sourceId != null)
 			s = s + " src:"+sourceId;
 		return s;
 	}
+	
 
 	public int hashCode() {
 		return id.hashCode();

Modified: obdapi/trunk/OBDAPI/src/org/obd/model/Statement.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/Statement.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/Statement.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -1,21 +1,23 @@
 package org.obd.model;
 
+import java.io.Serializable;
+
 /**
  * @author cjm
  *
  */
-public class Statement extends Node {
+public class Statement extends Node implements Serializable {
 	protected String nodeId;
 	protected String relationId;
 	protected String targetId;
 	protected String positedByNodeId;
-	protected boolean isImplied;
+	protected boolean isInferred;
 	
-	public boolean isImplied() {
-		return isImplied;
+	public boolean isInferred() {
+		return isInferred;
 	}
-	public void setImplied(boolean isImplied) {
-		this.isImplied = isImplied;
+	public void setInferred(boolean isImplied) {
+		this.isInferred = isImplied;
 	}
 	public String getPositedByNodeId() {
 		return positedByNodeId;
@@ -53,10 +55,12 @@
 	
 	public String toString() {
 		String s = nodeId+" "+relationId+" "+targetId;
-		if (isImplied)
+		if (isInferred)
 			s = s + " [Implied]";
 		if (positedByNodeId != null)
 			s = s + " positedBy:"+positedByNodeId;
+		if (sourceId != null)
+			s = s + " source:"+sourceId;
 		return s;
 	}
 	

Added: obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBDJSONBridge.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBDJSONBridge.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBDJSONBridge.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -0,0 +1,135 @@
+package org.obd.model.bridge;
+
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+
+import org.json.JSONArray;
+import org.json.JSONException;
+import org.json.JSONObject;
+import org.obd.model.Graph;
+import org.obd.model.LinkStatement;
+import org.obd.model.LiteralStatement;
+import org.obd.model.Node;
+import org.obd.model.NodeAlias;
+import org.obd.model.Statement;
+import org.obd.model.stats.AggregateStatistic;
+import org.obd.model.stats.AggregateStatisticCollection;
+import org.obd.model.stats.CountStatistic;
+
+
+public class OBDJSONBridge {
+
+
+	
+	public static JSONObject toJSON(Collection<Statement> coll) {
+		JSONObject jsonObj = new JSONObject();
+		try {
+			JSONArray a = new JSONArray();
+			for (Statement s : coll) {
+				a.put(toJSON(s));
+			}
+			jsonObj.put("statements", a);
+
+		} catch (JSONException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}	
+		return jsonObj;
+	}
+	
+	public static JSONObject nodesToJSON(Collection<Node> coll) {
+		JSONObject jsonObj = new JSONObject();
+		try {
+			JSONArray a = new JSONArray();
+			for (Node d : coll) {
+				a.put(toJSON(d));
+			}
+			jsonObj.put("nodes", a);
+
+		} catch (JSONException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}	
+		return jsonObj;
+	}
+
+	
+	public static JSONObject toJSON(Graph g) {
+		JSONObject jsonObj = toJSON(Arrays.asList(g.getStatements()));
+		JSONArray a = new JSONArray();
+		for (Node n : g.getNodes()) {
+			a.put(toJSON(n));		
+		}
+		try {
+			jsonObj.put("nodes", a);
+		} catch (JSONException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return jsonObj;
+	}
+	public static JSONObject toJSON(Node node) {
+		JSONObject jsonObj = new JSONObject();
+		if (node instanceof LinkStatement) {
+			LinkStatement link = (LinkStatement)node;
+			toJSON(link, jsonObj);
+			try {
+				jsonObj.put("appliesToAllInstancesOf", new Boolean(link.isAppliesToAllInstancesOf()));
+
+				} catch (NumberFormatException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			} catch (JSONException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+			
+		}
+		try {
+			jsonObj.put("id",  node.getId());
+			jsonObj.put("label", node.getLabel());
+		} catch (JSONException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return jsonObj;
+	}
+	
+
+	public static Object toJSON(AggregateStatisticCollection stats) {
+		JSONObject o = new JSONObject();
+		for (AggregateStatistic s : stats.getStats() ) {
+			if (s instanceof CountStatistic) {
+				CountStatistic c = (CountStatistic)s;
+				try {
+					o.put(s.getMeasuredEntity().toString(), 
+							new Integer(c.getCount()));
+				} catch (JSONException e) {
+					// TODO Auto-generated catch block
+					e.printStackTrace();
+				}
+			}
+			
+		}
+		return o;
+	}
+
+
+	
+	public static void toJSON(Statement s, JSONObject jsonObj) {
+		try {
+			jsonObj.put("node", s.getNodeId());
+			jsonObj.put("relation", s.getRelationId());
+			jsonObj.put("target", s.getTargetId());
+		} catch (NumberFormatException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		} catch (JSONException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+	}
+	
+
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBDXMLBridge.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBDXMLBridge.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBDXMLBridge.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -0,0 +1,39 @@
+package org.obd.model.bridge;
+
+import org.obd.model.LinkStatement;
+import org.obd.model.LiteralStatement;
+import org.obd.model.Node;
+import org.obd.model.NodeAlias;
+import org.obd.model.Statement;
+
+
+public class OBDXMLBridge {
+
+
+	
+	public static String toXML(Node node) {
+		// TODO: use JAXB/XMLBeans
+		StringBuilder sb = new StringBuilder();
+		sb.append("<Node id=\""+node.getId()+"\">");
+		sb.append("  <label>"+node.getLabel()+"</label>");
+		sb.append("</Node>");
+		return sb.toString();
+	}
+	
+	public static String toXML(LinkStatement link) {
+		// TODO: use JAXB/XMLBeans
+		StringBuilder sb = new StringBuilder();
+		sb.append("<LinkStatement>");
+		sb.append(toInnerXML(link));
+		sb.append("</LinkStatement>");
+		return sb.toString();
+	}
+	
+	public static String toInnerXML(Statement s) {
+		StringBuilder sb = new StringBuilder();
+		sb.append("  <subject about=\""+s.getNodeId()+"\"/>");
+		return sb.toString();
+	}
+	
+
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBOBridge.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBOBridge.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/model/bridge/OBOBridge.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -38,7 +38,7 @@
 			return null;
 		Node node = new Node();
 		node.setId(io.getID());
-		node.setName(io.getName());
+		node.setLabel(io.getName());
 		node.setSourceId(namespace2src(io.getNamespace()));
 		node.setAnonymous(io.isAnonymous());
 		for (Link link : ((LinkedObject)io).getParents() ) {
@@ -70,7 +70,7 @@
 		s.setNodeId(link.getChild().getID());
 		s.setRelationId(link.getType().getID());
 		s.setTargetId(link.getParent().getID());
-		s.setImplied(link.isImplied());
+		s.setInferred(link.isImplied());
 		if (link instanceof OBORestriction) {
 			OBORestriction rlink = (OBORestriction)link;
 			s.setAppliesToAllInstancesOf(true);

Added: obdapi/trunk/OBDAPI/src/org/obd/query/AnnotationLinkQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/AnnotationLinkQueryTerm.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/AnnotationLinkQueryTerm.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -0,0 +1,15 @@
+package org.obd.query;
+
+public class AnnotationLinkQueryTerm extends LinkQueryTerm {
+
+	public AnnotationLinkQueryTerm(QueryTerm target) {
+		super(target);
+		// TODO Auto-generated constructor stub
+	}
+
+	public AnnotationLinkQueryTerm(String targetAtom) {
+		super(targetAtom);
+		// TODO Auto-generated constructor stub
+	}
+
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/query/CoAnnotatedQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/CoAnnotatedQueryTerm.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/CoAnnotatedQueryTerm.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -0,0 +1,15 @@
+package org.obd.query;
+
+public class CoAnnotatedQueryTerm extends LinkQueryTerm {
+
+	public CoAnnotatedQueryTerm(QueryTerm target) {
+		super(target);
+		// TODO Auto-generated constructor stub
+	}
+
+	public CoAnnotatedQueryTerm(String targetAtom) {
+		super(targetAtom);
+		// TODO Auto-generated constructor stub
+	}
+
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/ComparisonQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/ComparisonQueryTerm.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/ComparisonQueryTerm.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -10,6 +10,7 @@
 		GREATER_THAN_OR_EQUAL_TO(">"),
 		NOT_EQUAL_TO("!="),
 		
+		CONTAINS("contains"),
 		STARTS_WITH("starts_with");
 		
 		String s;

Added: obdapi/trunk/OBDAPI/src/org/obd/query/ExistentialQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/ExistentialQueryTerm.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/ExistentialQueryTerm.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -0,0 +1,9 @@
+package org.obd.query;
+
+public class ExistentialQueryTerm extends QueryTerm {
+
+	public ExistentialQueryTerm() {
+		super();
+	}
+
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/LabelQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/LabelQueryTerm.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/LabelQueryTerm.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -1,14 +1,15 @@
 package org.obd.query;
 
 public class LabelQueryTerm extends QueryTerm {
-	public enum AliasType {ID, PRIMARY_NAME, ALTERNATE_LABEL, ANY_LABEL }
+	public enum AliasType {ID, INTERNAL_ID, PRIMARY_NAME, ALTERNATE_LABEL, ANY_LABEL }
 	
 	protected AliasType aliasType = AliasType.ID;
 	protected QueryTerm value;
 	
 	public LabelQueryTerm(AliasType aliasType, String valueAtom) {
 		super();
-		this.value = new ComparisonQueryTerm(new AtomicQueryTerm(valueAtom));
+		this.value = 
+			new ComparisonQueryTerm(valueAtom);
 		this.aliasType = aliasType;
 	}
 

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -24,6 +24,10 @@
 		this.relation = relation;
 		this.target = target;
 	}
+	public LinkQueryTerm(QueryTerm target) {
+		super();
+		this.target = target;
+	}
 
 	public LinkQueryTerm(String relationAtom, String targetAtom) {
 		super();
@@ -33,6 +37,13 @@
 		this.target = new LabelQueryTerm(targetAtom);
 	}
 	
+	public LinkQueryTerm(String targetAtom) {
+		super();
+		this.target = new LabelQueryTerm(targetAtom);
+	}
+	public LinkQueryTerm() {
+		super();
+	}
 	
 	public QueryTerm getTarget() {
 		return target;
@@ -41,9 +52,12 @@
 	public void setTarget(QueryTerm target) {
 		this.target = target;
 	}
-
+	public void setTarget(String nodeAtom) {
+		this.target = new LabelQueryTerm(nodeAtom);
+	}
+	
 	public String toString() {
-		String s = "Link["+getRelation().toString();
+		String s = "Link["+getRelation();
 		if (getTarget() != null)
 			s = s + " "+getTarget().toString();
 		return s+"]";

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/LiteralQueryTerm.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -22,6 +22,10 @@
 		super();
 		this.value = new ComparisonQueryTerm(new AtomicQueryTerm(valueAtom));
 	}
+	
+	public LiteralQueryTerm() {
+		super();
+	}
 
 	public QueryTerm getValue() {
 		return value;
@@ -33,7 +37,7 @@
 
 
 	public String toString() {
-		String s = " has "+getRelation().toString();
+		String s = " has "+getRelation();
 		if (getValue() != null)
 			s = s + " "+getValue().toString();
 		return s;

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/QueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/QueryTerm.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/QueryTerm.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -2,9 +2,11 @@
 
 public abstract class QueryTerm {
 	
+	protected QueryTerm node;
 	protected QueryTerm relation;
 	protected QueryTerm source;
 	protected QueryTerm positedBy;
+	protected Boolean isInferred;
 	
 	public QueryTerm() {
 		super();
@@ -28,12 +30,32 @@
 	public void setSource(QueryTerm source) {
 		this.source = source;
 	}
-	public QueryTerm getRelation() {
+
+	public QueryTerm getNode() {
+		return node;
+	}
+	public void setNode(QueryTerm node) {
+		this.node = node;
+	}
+	public void setNode(String nodeAtom) {
+		this.node = new LabelQueryTerm(nodeAtom);
+	}
+public QueryTerm getRelation() {
 		return relation;
 	}
 	public void setRelation(QueryTerm relation) {
 		this.relation = relation;
 	}
+	public void setRelation(String relationAtom) {
+		this.relation = new LabelQueryTerm(relationAtom);
+	}
+
+	public Boolean isInferred() {
+		return isInferred;
+	}
+	public void setInferred(Boolean isInferred) {
+		this.isInferred = isInferred;
+	}
 	
 	public String toString() {
 		String s = "";

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/Shard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/Shard.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/Shard.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -42,7 +42,11 @@
 	 * @return all matching Nodes
 	 */
 	public Collection<Node> getNodesBySearch(String searchTerm);
+	
+	public Collection<Node> getNodesBySearch(String searchTerm,
+			ComparisonQueryTerm.Operator op);
 
+
 	/**
 	 * @return all Nodes used as a source
 	 */
@@ -97,6 +101,16 @@
 	/**
 	 * @param id
 	 * @param entailment
+	 * @param strategy
+	 * @return given an node (eg a class node from an ontology), return all annotation
+	 * statements
+	 */
+	public Collection<Statement> getAnnotationStatementsForNode(String id, 
+			EntailmentUse entailment, GraphExpansionAlgorithm strategy);
+	
+	/**
+	 * @param id
+	 * @param entailment
 	 * @param gea
 	 * @return given a node (eg a class in an ontology), return a graph centered
 	 * around this node, including annotation to nodes subsumed by this node
@@ -171,6 +185,14 @@
 	public AggregateStatisticCollection getSummaryStatistics();
 	
 	/**
+	 * given an annotated entity node (e.g. a PMID or a genotype ID)
+	 * this will return all similar nodes attached to a score for that node.
+	 * The similarity is determined by finding other annotated entities with
+	 * similar annotation profiles.
+	 * 
+	 * The score is an uncorrected p-value (low values close to zero indicate
+	 * high degree of similarity).
+	 * 
 	 * @param nodeId
 	 * @return all comparable nodes with similarity p-value
 	 */

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/impl/AbstractShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/AbstractShard.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/AbstractShard.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -13,6 +13,7 @@
 import org.obd.model.stats.ScoredNode;
 import org.obd.query.QueryTerm;
 import org.obd.query.Shard;
+import org.obd.query.Shard.EntailmentUse;
 
 
 public abstract class AbstractShard implements Shard {
@@ -56,8 +57,14 @@
 		}
 		for (String nid : nodePvalMap.keySet())
 			scoredNodes.add(new ScoredNode(nid,nodePvalMap.get(nid)));
+//			scoredNodes.add(new ScoredNode(nid,pvalToScore(nodePvalMap.get(nid))));
 		Collections.sort(scoredNodes);
 		return scoredNodes;
 	}
+	
+	protected static double pvalToScore(double p) {
+		return Math.log(p)/Math.log(2);
+	}
+	
 
 }

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/MultiShard.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -12,6 +12,7 @@
 import org.obd.model.stats.AggregateStatistic;
 import org.obd.model.stats.AggregateStatisticCollection;
 import org.obd.model.stats.ScoredNode;
+import org.obd.query.ComparisonQueryTerm;
 import org.obd.query.QueryTerm;
 import org.obd.query.Shard;
 import org.obd.query.Shard.EntailmentUse;
@@ -52,6 +53,13 @@
 			nodes.addAll(s.getNodesBySearch(searchTerm));
 		return nodes;
 	}
+	public Collection<Node> getNodesBySearch(String searchTerm,
+			ComparisonQueryTerm.Operator op) {
+		HashSet<Node> nodes = new HashSet<Node>();
+		for (Shard s : shards) 
+			nodes.addAll(s.getNodesBySearch(searchTerm,op));
+		return nodes;
+	}
 	
 	public Collection<Node> getNodesBelowNodeSet(Collection<String> ids, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
 		HashSet<Node> nodes = new HashSet<Node>();
@@ -139,7 +147,16 @@
 
 		return statements;
 	}
+	
+	public Collection<Statement> getAnnotationStatementsForNode(String id, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
+		HashSet<Statement> statements = new HashSet<Statement>();
+		for (Shard s : shards) 
+			statements.addAll(s.getAnnotationStatementsForNode( id,
+					entailment, gea));
 
+		return statements;
+	}
+
 	public Graph getAnnotationGraphAroundNode(String id, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
 		Graph g = new Graph();
 		for (Shard s : shards) 

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -8,8 +8,10 @@
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.LinkedList;
+import java.util.List;
 
 import org.bbop.rdbms.RelationalQuery;
+import org.bbop.rdbms.SelectClause;
 import org.bbop.rdbms.WhereClause;
 import org.bbop.rdbms.impl.SqlQueryImpl;
 import org.bbop.rdbms.impl.SqlWhereClauseImpl;
@@ -18,16 +20,22 @@
 import org.obd.model.Statement;
 import org.obd.model.bridge.OBOBridge;
 import org.obd.model.stats.AggregateStatisticCollection;
+import org.obd.model.stats.ScoredNode;
+import org.obd.query.AnnotationLinkQueryTerm;
 import org.obd.query.AtomicQueryTerm;
 import org.obd.query.BooleanQueryTerm;
+import org.obd.query.CoAnnotatedQueryTerm;
 import org.obd.query.ComparisonQueryTerm;
+import org.obd.query.ExistentialQueryTerm;
 import org.obd.query.GraphQuery;
 import org.obd.query.LinkQueryTerm;
 import org.obd.query.LabelQueryTerm;
+import org.obd.query.LiteralQueryTerm;
 import org.obd.query.QueryTerm;
 import org.obd.query.Shard;
 import org.obd.query.ComparisonQueryTerm.Operator;
 import org.obd.query.LabelQueryTerm.AliasType;
+import org.obd.query.Shard.EntailmentUse;
 import org.obo.annotation.datamodel.Annotation;
 import org.obo.dataadapter.OBDSQLDatabaseAdapter;
 import org.obo.dataadapter.OBOFileAdapter;
@@ -52,6 +60,8 @@
 	protected OBOSession session =
 		new OBOSessionImpl(); // TODO: remove? need it for tracking namespaces etc
 	
+	HashMap<Integer,String> iid2nodeId = new HashMap<Integer,String>();
+	
 	public OBDSQLShard() throws SQLException, ClassNotFoundException {
 	}
 	
@@ -119,6 +129,14 @@
 		return getNodes(q);
 	}
 	
+	public Collection<Node> getNodesBySearch(String searchTerm,
+			ComparisonQueryTerm.Operator op) {
+		LabelQueryTerm q = 
+			 new LabelQueryTerm(AliasType.ANY_LABEL,
+					 new ComparisonQueryTerm(op, searchTerm));
+		return getNodesByQuery(q);
+	}
+	
 	public Collection<Node> getNodesBelowNodeSet(Collection<String> ids,
 			EntailmentUse entailment,
 			GraphExpansionAlgorithm gea){
@@ -236,7 +254,10 @@
 				if (positsMap.containsKey(nodeId)) {
 					Statement sKey = OBOBridge.link2statement(positsMap.get(io.getID()));
 					Statement s = statementMap.get(sKey.toString());
-					s.setPositedByNodeId(nodeId);
+					if (s != null)
+						s.setPositedByNodeId(nodeId);
+					else
+						System.err.println("no stmt: "+sKey);
 				}
 			}
 					
@@ -299,6 +320,13 @@
 	}
 	
 	public Collection<Statement> getStatementsForNode(String id, boolean useImplied) {
+	  LinkQueryTerm q = new LinkQueryTerm();
+	  q.setNode(id);
+	  if (useImplied)
+		  q.setInferred(true);
+	  return getStatementsByQuery(q);
+	}
+	public Collection<Statement> old___getStatementsForNode(String id, boolean useImplied) {
 		WhereClause whereClause = new SqlWhereClauseImpl();
 		whereClause.addEqualityConstraint("node_uid",id);
 		if (!useImplied)
@@ -398,7 +426,12 @@
 		Collection<Statement> annots = getStatements(whereClause);
 		return annots;
 	}
+	
+	public Collection<Statement> getAnnotationStatementsForNode(String id, EntailmentUse entailment, GraphExpansionAlgorithm strategy) {
 
+		return getStatementsByQuery(new AnnotationLinkQueryTerm(id));
+ 	}
+
 	public Graph getAnnotationGraphAroundNode(String id, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
 
 		// find graph around node, outwards
@@ -409,34 +442,9 @@
 		}
 		else
 			stmts = new LinkedList<Statement>(); // TODO: minimal info?
-			 
-	
-		// find all annotations to id
-		WhereClause whereClause = new SqlWhereClauseImpl();
-		if (true || entailment == null) {
-			// currently this is under-constrained
-			// will fetch the full graph;
-			//  G has_role* X and X R* Y, where Y is ground
-			/*
-			 * we actually want
-			 * G has_role X, X Rmd MD, X R* Y
-			 */
-			RelationalQuery subsumedNodeQuery = new SqlQueryImpl();
-			subsumedNodeQuery.getSelectClause().addColumn("node_uid");
-			subsumedNodeQuery.addTable("node_link_node_with_pred_and_source");
-			WhereClause subWhereClause = new SqlWhereClauseImpl();
-			subWhereClause.addEqualityConstraint("object_uid",id);			
-			subsumedNodeQuery.setWhereClause(subWhereClause);
-			
-			whereClause.addInConstraint("object_uid",subsumedNodeQuery);	
-			whereClause.addEqualityConstraint("is_inferred", false);
-		}
-		else {
-			// TODO: only works in annot links are inlcuded in deductive closure
-			whereClause.addEqualityConstraint("object_uid",id);
-		}
-		//whereClause.addConstraint("reiflink_node_id IS NOT NULL");
-		Collection<Statement> annots = getStatements(whereClause);
+		
+		Collection<Statement> annots = 
+			getAnnotationStatementsForNode(id, entailment, null);
 		Graph g = new Graph(annots);
 		for (String nid : g.getReferencedNodeIds()) {
 			Node n = getNode(nid);
@@ -450,6 +458,10 @@
 
 	}
 	
+	
+
+	
+	
 	public Collection<Node> getAnnotatedEntitiesBelowNodeSet(Collection<String> ids,
 			EntailmentUse entailment,
 			GraphExpansionAlgorithm gea){
@@ -530,32 +542,159 @@
 	}
 
 	public Graph getGraphByQuery(QueryTerm queryTerm, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
-		Collection<Node> nodes = getNodesByQuery(queryTerm);
-		Graph g = new Graph();
-		g.setNodes(nodes);
-		return g;		
+
+		Collection<Statement> stmts = 
+			getStatementsByQuery(queryTerm);
+		Graph g = new Graph(stmts);
+		for (String nid : g.getReferencedNodeIds()) {
+			Node n = getNode(nid);
+			g.addNode(n);
+			Collection<Statement> mdLinks = getStatementsForNode(nid,false);
+			g.addStatements(mdLinks);
+		}
+		g.addStatements(stmts);
+		g.nestStatementsUnderNodes();
+		return g;
 	}
 
 	public Collection<Statement> getStatementsByQuery(QueryTerm queryTerm) {
-		// TODO Auto-generated method stub
-		return null;
+		RelationalQuery rq = translateQueryForLink(queryTerm);
+		Collection<Statement> statements = new LinkedList<Statement>();
+		try {
+			ResultSet rs = execute(rq);
+			while (rs.next()) {
+				Statement s = new Statement();
+				s.setNodeId(rs.getString("node_uid"));
+				s.setRelationId(rs.getString("predicate_uid"));
+				s.setTargetId(rs.getString("object_uid"));
+				s.setPositedByNodeId(rs.getString("annotation_node_uid"));
+				s.setInferred(rs.getBoolean("is_inferred"));
+				setSourceId(s,rs.getInt("source_id"));
+				statements.add(s);
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return statements;		
 	}
 	
 
+	public void setSourceId(Statement s, Integer iid) {
+		String sourceId = null;
+		if (iid == null)
+			return;
+		if (iid == 0)
+			return;
+		if (iid2nodeId.containsKey(iid)) {
+			sourceId = iid2nodeId.get(iid);
+		}
+		else {
+			// TODO: make this more general
+			RelationalQuery rq = new SqlQueryImpl();
+			rq.addTable("node");
+			rq.setSelectClause("uid");
+			rq.getWhereClause().addEqualityConstraint("node_id", iid);
+			ResultSet rs;
+			try {
+				rs = execute(rq);
+				if (rs.next()) {
+					sourceId = rs.getString("uid");
+				}
+			} catch (SQLException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+		}
+		if (sourceId != null)
+			s.setSourceId(sourceId);
+	}
+	
+
 	public RelationalQuery translateQueryForNode(QueryTerm qt) {
 		RelationalQuery rq = new SqlQueryImpl();
 		rq.addTable("node_with_source");
 		translateQuery(qt,rq,"node_with_source.node_id");
 		rq.setSelectClause("node_with_source.*");
+		rq.getSelectClause().setDistinct(true);
 		return rq;
 	}
 	
+	public RelationalQuery translateQueryForLiteral(QueryTerm qt) {
+		RelationalQuery rq = new SqlQueryImpl();
 
+		String linkTableAlias = translateQuery(qt,rq,null);
+		SelectClause selectClause = rq.getSelectClause();
+		selectClause.setDistinct(true);
+		selectClause.addColumn(linkTableAlias+".*");
+		WhereClause wc = rq.getWhereClause();
+		// TODO: optimize. No need to join if we query on node
+		rq.addTable("node AS snode");
+		wc.addConstraint("snode.node_id = " + linkTableAlias+".node_id");
+		selectClause.addColumn("snode.uid AS node_uid");
+		rq.addTable("node AS rnode");
+		wc.addConstraint("rnode.node_id = " + linkTableAlias+".predicate_id");
+		selectClause.addColumn("rnode.uid AS predicate_uid");
+		
+		if (qt instanceof AnnotationLinkQueryTerm) {
+			rq.addTable("node AS anode");
+			wc.addConstraint("anode.node_id = " + linkTableAlias+".reiflink_node_id");
+			selectClause.addColumn("anode.uid AS annotation_node_uid");
+		}
+		else {
+			selectClause.addColumn("NULL as annotation_node_uid");
+		}
+		
+		//rq.addTable("node");
+		return rq;
+	}
+	
+	public RelationalQuery translateQueryForLink(QueryTerm qt) {
+		RelationalQuery rq = new SqlQueryImpl();
+
+		if (!(qt instanceof LinkQueryTerm)) {
+			// it only makes sense to return links for link queries;
+			// a query to for example LiteralQuery("apoptosis") should
+			// be wrapped such that links with this node are returned
+			LinkQueryTerm outerq = new LinkQueryTerm();
+			outerq.setNode(qt);
+			return translateQueryForLink(outerq);
+		}
+		String linkTableAlias = translateQuery(qt,rq,null);
+		SelectClause selectClause = rq.getSelectClause();
+		selectClause.setDistinct(true);
+		selectClause.addColumn(linkTableAlias+".*");
+		WhereClause wc = rq.getWhereClause();
+		// TODO: optimize. No need to join if we query on node
+		rq.addTable("node AS snode");
+		wc.addConstraint("snode.node_id = " + linkTableAlias+".node_id");
+		selectClause.addColumn("snode.uid AS node_uid");
+		rq.addTable("node AS rnode");
+		wc.addConstraint("rnode.node_id = " + linkTableAlias+".predicate_id");
+		selectClause.addColumn("rnode.uid AS predicate_uid");
+		rq.addTable("node AS tnode");
+		wc.addConstraint("tnode.node_id = " + linkTableAlias+".object_id");
+		selectClause.addColumn("tnode.uid AS object_uid");
+		
+		if (qt instanceof AnnotationLinkQueryTerm) {
+			rq.addTable("node AS anode");
+			wc.addConstraint("anode.node_id = " + linkTableAlias+".reiflink_node_id");
+			selectClause.addColumn("anode.uid AS annotation_node_uid");
+		}
+		else {
+			selectClause.addColumn("NULL as annotation_node_uid");
+		}
+		
+		//rq.addTable("node");
+		return rq;
+	}
+	
+
 	/**
 	 * @param qt - OBD Query to be translated
 	 * @param rq - constructed Relation SQL Query
 	 * @param subjCol - column to use in where constraint. Can be null
-	 * @return DEPRECATED??
+	 * @return tableName
 	 * 
 	 * translates a query or part of a query to SQL.
 	 * Recursive.
@@ -574,6 +713,14 @@
 			}
 			return val;
 		}
+		else if (qt instanceof ExistentialQueryTerm) {
+			if (subjCol == null) {
+			}
+			else {
+				wc.addConstraint(subjCol+" IS NOT NULL");
+			}
+			return subjCol;
+		}
 		else if (qt instanceof BooleanQueryTerm) {
 			BooleanQueryTerm cqt = (BooleanQueryTerm)qt;
 			for (QueryTerm subquery : cqt.getQueryTerms()) {
@@ -590,10 +737,12 @@
 			if (subjCol != null) {
 				if (op.equals(Operator.STARTS_WITH))
 					wc.addOperatorConstraint("LIKE", subjCol, val+"%"); // TODO: before?
+				else if (op.equals(Operator.CONTAINS))
+					wc.addOperatorConstraint("LIKE", subjCol, "%"+val+"%"); // TODO: before?
 				else 
 					wc.addOperatorConstraint(cqt.getOperator().toString(), subjCol, val);
 			}
-			return subjCol;
+			return "x";
 		}
 		else if (qt instanceof LabelQueryTerm) {
 			// Example: hasName(Contains("x")) => name like 'x%';
@@ -604,28 +753,69 @@
 				translateQuery(cqt.getValue(), rq, rel+".uid");
 				if (subjCol != null)
 					wc.addConstraint(rel+".node_id = " + subjCol);
-				return rel+".node_id";
+				return rel;
 			}
+			if (alias.equals(AliasType.INTERNAL_ID)) {
+				String rel = rq.addAutoAliasedTable("node");
+				translateQuery(cqt.getValue(), rq, rel+".node_id");
+				if (subjCol != null)
+					wc.addConstraint(rel+".node_id = " + subjCol);
+				return rel;
+			}
 			if (alias.equals(AliasType.PRIMARY_NAME)) {
 				String rel = rq.addAutoAliasedTable("node");
 				translateQuery(cqt.getValue(), rq, rel+".label");
 				if (subjCol != null)
 					wc.addConstraint(rel+".node_id = " + subjCol);
-				return rel+".node_idxx";
+				return rel;
 			}
 			if (alias.equals(AliasType.ANY_LABEL)) {
-				// TODO: OR query
+				String tbl = "node_label"; // TODO: table alias
+				// TODO: node.label
+				String rel = rq.addAutoAliasedTable(tbl);
+				if (subjCol != null)
+					wc.addConstraint(rel+".node_id = " + subjCol);
+				String field = alias.toString();
+				// e.g. Contains("x") => tbl.label like 'x%'
+				String val = translateQuery(cqt.getValue(), rq, rel+".label");
+				return rel;
 			}
-				
-			String tbl = "alias"; // TODO: table alias
-			// TODO: node.label
-			String rel = rq.addAutoAliasedTable(tbl);
+			else {	
+				String tbl = "alias"; // TODO: table alias
+				// TODO: node.label
+				String rel = rq.addAutoAliasedTable(tbl);
+				if (subjCol != null)
+					wc.addConstraint(rel+".node_id = " + subjCol);
+				String field = alias.toString();
+				// e.g. Contains("x") => tbl.label like 'x%'
+				String val = translateQuery(cqt.getValue(), rq, rel+".label");
+				return rel;
+			}
+		}
+		else if (qt instanceof AnnotationLinkQueryTerm) {
+			AnnotationLinkQueryTerm cqt = (AnnotationLinkQueryTerm)qt;
+			// TODO: allow inner link query to have a relation
+			LinkQueryTerm newqt =
+				new LinkQueryTerm(new LinkQueryTerm(cqt.getTarget()));
+			newqt.setPositedBy(new ExistentialQueryTerm());
+			newqt.setInferred(false);
+			return
+			 translateQuery(newqt,rq,subjCol);
+		}
+		else if (qt instanceof CoAnnotatedQueryTerm) {
+			CoAnnotatedQueryTerm cqt = (CoAnnotatedQueryTerm)qt;
+			// TODO: allow inner link query to have a relation
+			String tbl = "co_annotated_to_pair";
+			if (cqt.isInferred() != null && !cqt.isInferred())
+				tbl = "co_annotated_to_pair_asserted";
+			String tblAlias = rq.addAutoAliasedTable(tbl);
+			rq.getSelectClause().addColumn(tblAlias+".node_count");
 			if (subjCol != null)
-				wc.addConstraint(rel+".node_id = " + subjCol);
-			String field = alias.toString();
-			// e.g. Contains("x") => tbl.label like 'x%'
-			String val = translateQuery(cqt.getValue(), rq, rel+".label");
-			return rel+".node_id";
+				wc.addConstraint(tblAlias+".node_id = " + subjCol);
+			String nodeTbl = translateQuery(cqt.getNode(), rq, tblAlias+".object1_id");
+			String targetTbl = translateQuery(cqt.getTarget(), rq, tblAlias+".object2_id");
+			// returns the name of the link table alias used in this query
+			return tblAlias;
 		}
 		else if (qt instanceof LinkQueryTerm) {
 			LinkQueryTerm cqt = (LinkQueryTerm)qt;
@@ -633,10 +823,30 @@
 			String tblAlias = rq.addAutoAliasedTable(tbl);
 			if (subjCol != null)
 				wc.addConstraint(tblAlias+".node_id = " + subjCol);
-			String rel = translateQuery(cqt.getRelation(), rq, tblAlias+".predicate_id");
-			String target = translateQuery(cqt.getTarget(), rq, tblAlias+".object_id");
-			return subjCol;
+			if (cqt.isInferred() != null)
+				wc.addEqualityConstraint(tblAlias+".is_inferred",cqt.isInferred());
+			String nodeTbl = translateQuery(cqt.getNode(), rq, tblAlias+".node_id");
+			String relTbl = translateQuery(cqt.getRelation(), rq, tblAlias+".predicate_id");
+			String targetTbl = translateQuery(cqt.getTarget(), rq, tblAlias+".object_id");
+			String positsNodeTbl = translateQuery(cqt.getPositedBy(), rq, tblAlias+".reiflink_node_id");
+			// returns the name of the link table alias used in this query
+			return tblAlias;
 		}
+		else if (qt instanceof LiteralQueryTerm) { // TODO: DRY
+			LiteralQueryTerm cqt = (LiteralQueryTerm)qt;
+			String tbl = "node_literal"; 
+			String tblAlias = rq.addAutoAliasedTable(tbl);
+			if (subjCol != null)
+				wc.addConstraint(tblAlias+".node_id = " + subjCol);
+			if (cqt.isInferred() != null)
+				wc.addEqualityConstraint(tblAlias+".is_inferred",cqt.isInferred());
+			String nodeTbl = translateQuery(cqt.getNode(), rq, tblAlias+".node_id");
+			String relTbl = translateQuery(cqt.getRelation(), rq, tblAlias+".predicate_id");
+			//String valTbl = translateQuery(cqt.getValue()), rq, tblAlias+".object_id");
+			String positsNodeTbl = translateQuery(cqt.getPositedBy(), rq, tblAlias+".reiflink_node_id");
+			// returns the name of the link table alias used in this query
+			return tblAlias;
+		}
 		else 
 			return null;  // TODO _ throw
 	}
@@ -659,13 +869,10 @@
 		return n;
 	}
 	
-	
+	public List<ScoredNode> getCoAnnotatedNodes(String nodeId, EntailmentUse entailment) {
+		List<ScoredNode> sns = new LinkedList<ScoredNode>();
+		
+		return sns;
+	}
+}
 
-
-
-	
-	
-	
-
-
-}

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBOSessionShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBOSessionShard.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBOSessionShard.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -14,6 +14,7 @@
 import org.obd.model.stats.MeasuredEntity;
 import org.obd.query.QueryTerm;
 import org.obd.query.Shard;
+import org.obd.query.ComparisonQueryTerm.Operator;
 import org.obd.query.Shard.EntailmentUse;
 import org.obd.query.Shard.GraphExpansionAlgorithm;
 import org.obo.dataadapter.OBOFileAdapter;
@@ -63,6 +64,12 @@
 		return new HashSet<Node>();
 	}
 	
+	public Collection<Node> getNodesBySearch(String searchTerm, Operator op) {
+		// TODO Auto-generated method stub
+		return new HashSet<Node>();
+	}
+	
+	
 	public Collection<Node> getNodesBelowNodeSet(Collection<String> ids, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
 		// TODO Auto-generated method stub
 		return new HashSet<Node>();
@@ -184,6 +191,10 @@
 	public Collection<Statement> getAnnotationStatementsForAnnotatedEntity(String id, EntailmentUse entailment, GraphExpansionAlgorithm strategy) {
 		return new HashSet<Statement>();
 	}
+	public Collection<Statement> getAnnotationStatementsForNode(String id, EntailmentUse entailment, GraphExpansionAlgorithm strategy) {
+		return new HashSet<Statement>();
+	}
+	
 
 	public Graph getAnnotationGraphAroundNode(String id, EntailmentUse entailment, GraphExpansionAlgorithm gea) {
 		return new Graph();
@@ -206,8 +217,7 @@
 	}
 
 	public Collection<Statement> getStatementsByQuery(QueryTerm queryTerm) {
-		// TODO Auto-generated method stub
-		return null;
+		return new LinkedList<Statement>();
 	}
 
 	public int getAnnotatedNodeCount() {
@@ -220,4 +230,6 @@
 
 
 
+
+
 }

Added: obdapi/trunk/OBDAPI/src/org/obd/test/AllTests.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/AllTests.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/AllTests.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -0,0 +1,30 @@
+package org.obd.test;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+
+
+public class AllTests extends TestCase {
+
+	protected AllTests(String name) {
+		super(name);
+	}
+	
+	public static Test suite() {
+		TestSuite out = new TestSuite();
+
+		out.addTestSuite(AnnotationGraphTest.class);
+		out.addTestSuite(ExecuteQueryTest.class);
+		out.addTestSuite(MiniTest.class);
+		out.addTestSuite(MultiNodeFetchTest.class);
+		out.addTestSuite(OBDQueryServiceTest.class);
+		out.addTestSuite(QueryTest.class);
+		out.addTestSuite(SearchTest.class);
+		out.addTestSuite(SimilarityTest.class);
+
+		return out;
+	}
+
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/test/AnnotationGraphTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/AnnotationGraphTest.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/AnnotationGraphTest.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -1,21 +1,15 @@
 package org.obd.test;
 
-import java.io.PrintStream;
-import java.util.logging.Logger;
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
 
-import org.bbop.io.AuditedPrintStream;
 import org.obd.model.Graph;
 import org.obd.model.Node;
 import org.obd.model.Statement;
+import org.obd.query.LinkQueryTerm;
 import org.obd.ws.OBDQueryService;
-import org.obo.datamodel.impl.DefaultLinkDatabase;
-import org.obo.reasoner.impl.ForwardChainingReasoner;
-import org.obo.test.OBDAnnotationSaveTest;
 
-import junit.framework.Test;
-import junit.framework.TestCase;
-import junit.framework.TestSuite;
-
 public class AnnotationGraphTest extends TestCase {
 
 	OBDQueryService service;
@@ -44,12 +38,36 @@
 	
 	public void testQuery() {
 		
+		for (Statement s : service.getAnnotationStatementsForAnnotatedEntity("ZFIN:ZDB-GENO-960809-7", null, null)) {
+			System.out.println(s);
+		}
 		
+		printGraph(service.getAnnotationGraphAroundNode("FMA:54448", null, null));
 		
-		for (Statement s : service.getAnnotationStatementsForAnnotatedEntity("ZFIN:ZDB-GENO-960809-7", null, null)) {
+		printGraph(service.getAnnotationGraphAroundNode("CL:0000148", null, null));
+
+		LinkQueryTerm lq = new LinkQueryTerm();
+    	lq.setRelation("OBO_REL:is_a");
+    	lq.setNode("CL:0000148");
+    	Statement[] stmts = service.getStatementsByQuery(lq);
+    	int n = 0;
+		for (Statement s : stmts) {
 			System.out.println(s);
+			if (s.isInferred())
+				n++;
 		}
+		assertTrue(n>0);
+	}
 
+	public static void printGraph(Graph g) {
+		for (Node n : g.getNodes()) {
+			System.out.println("nodes="+n);
+			for (Statement s : n.getStatements()) {
+				System.out.println("    "+s);
+			}	
+		}
+		assertTrue(g.getNodes().length > 0);
 	}
 
+
 }

Modified: obdapi/trunk/OBDAPI/src/org/obd/test/ExecuteQueryTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/ExecuteQueryTest.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/ExecuteQueryTest.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -19,7 +19,7 @@
 		// TODO Auto-generated constructor stub
 	}
 	
-	public void runQuery(QueryTerm qt) throws SQLException, ClassNotFoundException {
+	public void runNodeQuery(QueryTerm qt) throws SQLException, ClassNotFoundException {
 		System.out.println("exec Q: "+qt.toString());
 		Graph g = service.getGraphByQuery(qt, null, null);
 		g.nestStatementsUnderNodes();
@@ -29,8 +29,26 @@
 				System.out.println("    "+s);
 			}	
 		}
+		assertTrue(g.getNodes().length > 0);
+		
+	}
+	
+	public void runLinkQuery(QueryTerm qt) throws SQLException, ClassNotFoundException {
+		System.out.println("exec Q: "+qt.toString());
+		Statement[] stmts = service.getStatementsByQuery(qt);
+		for (Statement s : stmts)
+			System.out.println(" "+s);
+		assertTrue(stmts.length > 0);
+	}
 
+	public void runLiteralQuery(QueryTerm qt) throws SQLException, ClassNotFoundException {
+		System.out.println("exec Q: "+qt.toString());
+		Statement[] stmts = service.getStatementsByQuery(qt);
+		for (Statement s : stmts)
+			System.out.println(" "+s);
+		assertTrue(stmts.length > 0);
 	}
+
 	
 	public static Test suite() {
 		TestSuite suite = new TestSuite();

Modified: obdapi/trunk/OBDAPI/src/org/obd/test/MiniTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/MiniTest.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/MiniTest.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -1,21 +1,15 @@
 package org.obd.test;
 
-import java.io.PrintStream;
-import java.util.logging.Logger;
+import java.util.HashSet;
 
-import org.bbop.io.AuditedPrintStream;
-import org.obd.model.Graph;
-import org.obd.model.Node;
-import org.obd.model.Statement;
-import org.obd.ws.OBDQueryService;
-import org.obo.datamodel.impl.DefaultLinkDatabase;
-import org.obo.reasoner.impl.ForwardChainingReasoner;
-import org.obo.test.OBDAnnotationSaveTest;
-
 import junit.framework.Test;
 import junit.framework.TestCase;
 import junit.framework.TestSuite;
 
+import org.obd.model.Graph;
+import org.obd.model.Statement;
+import org.obd.ws.OBDQueryService;
+
 public class MiniTest extends TestCase {
 
 	OBDQueryService service;
@@ -47,6 +41,10 @@
 		g.addStatement(testStatement());
 		g.addStatement(testStatement());
 		System.out.println("Len="+g.getStatements().length);
+		HashSet<Statement> set = new HashSet<Statement>();
+		set.add(testStatement());
+		set.add(testStatement());
+		System.out.println("Set Len="+set.size());
 
 	}
 	
@@ -55,6 +53,7 @@
 		s.setNodeId("x");
 		s.setRelationId("y");
 		s.setTargetId("z");
+		System.out.println(s);
 		return s;
 	}
 

Modified: obdapi/trunk/OBDAPI/src/org/obd/test/MultiNodeFetchTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/MultiNodeFetchTest.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/MultiNodeFetchTest.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -1,23 +1,14 @@
 package org.obd.test;
 
-import java.io.PrintStream;
 import java.util.Arrays;
-import java.util.Collections;
-import java.util.logging.Logger;
 
-import org.bbop.io.AuditedPrintStream;
-import org.obd.model.Graph;
-import org.obd.model.Node;
-import org.obd.model.Statement;
-import org.obd.ws.OBDQueryService;
-import org.obo.datamodel.impl.DefaultLinkDatabase;
-import org.obo.reasoner.impl.ForwardChainingReasoner;
-import org.obo.test.OBDAnnotationSaveTest;
-
 import junit.framework.Test;
 import junit.framework.TestCase;
 import junit.framework.TestSuite;
 
+import org.obd.model.Node;
+import org.obd.ws.OBDQueryService;
+
 public class MultiNodeFetchTest extends TestCase {
 
 	OBDQueryService service;

Modified: obdapi/trunk/OBDAPI/src/org/obd/test/OBDQueryServiceTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/OBDQueryServiceTest.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/OBDQueryServiceTest.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -41,7 +41,7 @@
 		String id = "GO:0006811";
 		Node node = 
 			service.getNode(id);
-		Logger.getLogger("org.obd.test").info("node="+node.getName());
+		Logger.getLogger("org.obd.test").info("node="+node.getLabel());
 		assertTrue(node != null);
 		
 		for (Statement s : service.getStatementsForNode(id)) {

Modified: obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -8,10 +8,12 @@
 
 import org.bbop.rdbms.RelationalQuery;
 import org.obd.model.Statement;
+import org.obd.query.AnnotationLinkQueryTerm;
 import org.obd.query.BooleanQueryTerm;
 import org.obd.query.ComparisonQueryTerm;
 import org.obd.query.LinkQueryTerm;
 import org.obd.query.LabelQueryTerm;
+import org.obd.query.LiteralQueryTerm;
 import org.obd.query.QueryTerm;
 import org.obd.query.BooleanQueryTerm.BooleanOperator;
 import org.obd.query.ComparisonQueryTerm.Operator;
@@ -47,31 +49,40 @@
 	
 	public void testQuery() throws SQLException, ClassNotFoundException {
 				
-		runQuery(new LabelQueryTerm(AliasType.PRIMARY_NAME,
+		String partOf = "OBO_REL:part_of";
+		String developsFrom = "OBO_REL:developsFrom";
+		
+		runNodeQuery(new LinkQueryTerm(partOf, 
+				new LabelQueryTerm(AliasType.ANY_LABEL, "nucleus")));
+		runNodeQuery(new LabelQueryTerm(AliasType.PRIMARY_NAME,
 				"apoptosis"));
-		runQuery(new LabelQueryTerm(AliasType.ALTERNATE_LABEL,
+		runNodeQuery(new LabelQueryTerm(AliasType.ALTERNATE_LABEL,
 				new ComparisonQueryTerm(Operator.STARTS_WITH,
 				"apoptosis")));
 		
-		String partOf = "OBO_REL:part_of";
-		String developsFrom = "OBO_REL:developsFrom";
-		runQuery(new LinkQueryTerm(partOf, "GO:0005634"));
-		runQuery(new LinkQueryTerm(partOf, 
-				new LabelQueryTerm(AliasType.ANY_LABEL, "nucleus")));
-		runQuery(new LinkQueryTerm(partOf, 
+		runNodeQuery(new LinkQueryTerm(partOf, "GO:0005634"));
+		runNodeQuery(new LinkQueryTerm(partOf, 
 				new LinkQueryTerm(developsFrom, "CL:1234567")));
-		runQuery(new LinkQueryTerm(partOf, 
+		runNodeQuery(new LinkQueryTerm(partOf, 
 				new BooleanQueryTerm( 
 						BooleanOperator.AND,
 						new LinkQueryTerm(partOf, "GO:0005634"),
 						new LinkQueryTerm(partOf, "GO:0005739")
 						)));
+		runLinkQuery(new LinkQueryTerm(partOf, "GO:0031595")); // nuclear proteasome complex
 		
+		// annotations
+		 AnnotationLinkQueryTerm oq = new AnnotationLinkQueryTerm("FMA:54448");
+		runLinkQuery(oq);
 		
+		LiteralQueryTerm litq = new LiteralQueryTerm();
+		litq.setNode("MP:0008246");
+		runLiteralQuery(litq);
+		
 
 	}
 	
-	public void runQuery(QueryTerm qt) throws SQLException, ClassNotFoundException {
+	public void runNodeQuery(QueryTerm qt) throws SQLException, ClassNotFoundException {
 		System.out.println("running Q: "+qt.toString());
 		OBDSQLShard s = new OBDSQLShard();
 		RelationalQuery rq = s.translateQueryForNode(qt);
@@ -81,4 +92,22 @@
 
 	}
 
+	public void runLinkQuery(QueryTerm qt) throws SQLException, ClassNotFoundException {
+		System.out.println("running Q: "+qt.toString());
+		OBDSQLShard s = new OBDSQLShard();
+		RelationalQuery rq = s.translateQueryForLink(qt);
+		System.out.println(rq.toString());
+		for (Object v : rq.getPlaceHolderVals())
+			System.out.println(" "+v);
+
+	}
+	public void runLiteralQuery(QueryTerm qt) throws SQLException, ClassNotFoundException {
+		System.out.println("running Q: "+qt.toString());
+		OBDSQLShard s = new OBDSQLShard();
+		RelationalQuery rq = s.translateQueryForLiteral(qt);
+		System.out.println(rq.toString());
+		for (Object v : rq.getPlaceHolderVals())
+			System.out.println(" "+v);
+	}
+
 }

Modified: obdapi/trunk/OBDAPI/src/org/obd/test/SearchTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/SearchTest.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/SearchTest.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -6,6 +6,7 @@
 
 import org.obd.model.Node;
 import org.obd.model.Statement;
+import org.obd.query.ComparisonQueryTerm.Operator;
 import org.obd.ws.OBDQueryService;
 
 public class SearchTest extends TestCase {
@@ -52,6 +53,7 @@
 			
 		}
 
+	
 
 	}
 

Added: obdapi/trunk/OBDAPI/src/org/obd/ws/GraphResource.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/GraphResource.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/GraphResource.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -0,0 +1,112 @@
+
+package org.obd.ws;
+
+import org.obd.model.Graph;
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.model.bridge.OBDJSONBridge;
+import org.obd.query.AtomicQueryTerm;
+import org.obd.query.LinkQueryTerm;
+import org.obd.query.QueryTerm;
+import org.obd.query.Shard;
+import org.restlet.Context;
+import org.restlet.data.MediaType;
+import org.restlet.data.Request;
+import org.restlet.data.Response;
+import org.restlet.resource.Representation;
+import org.restlet.resource.Resource;
+import org.restlet.resource.StringRepresentation;
+import org.restlet.resource.Variant;
+
+/**
+ * Resource for a graph
+ * 
+ * @author cjm
+ */
+public class GraphResource extends NodeResource {
+
+ 
+    /**
+     * Constructor.
+     * 
+     * @param context
+     *                The parent context.
+     * @param request
+     *                The request to handle.
+     * @param response
+     *                The response to return.
+     */
+    public GraphResource(Context context, Request request, Response response) {
+        super(context, request, response);
+    }
+
+ 
+    /**
+     * Returns the parent OBDRestApplication.
+     * 
+     * @return the parent OBDRestApplication.
+     */
+    public OBDRestApplication getOBDRestApplication() {
+        return (OBDRestApplication) getContext().getAttributes().get(OBDRestApplication.KEY);
+    }
+
+    /**
+     * Returns the database container.
+     * 
+     * @return the database container.
+     */
+    public Shard getShard() {
+        return getOBDRestApplication().getShard();
+    }
+
+    @Override
+    public Representation getRepresentation(Variant variant) {
+        Representation result = null;
+
+        LinkQueryTerm q = new LinkQueryTerm();
+        q.setNode(getNodeId());
+        Graph graph = getShard().getGraphByQuery(q, null, null);
+  
+        if (format == null) {
+        	format = "";
+        }
+    
+        if (format.equals("json")) {
+             result = new StringRepresentation(OBDJSONBridge.toJSON(graph).toString());
+          }
+        else {
+        	// Creates a text representation
+        	StringBuilder sb = new StringBuilder();
+         	sb.append("<pre>");
+         	sb.append("------------\n");
+        	sb.append("Graph details\n");
+        	sb.append("------------\n\n");
+        	
+        	for (Node n : graph.getNodes()) {
+        		sb.append(href(n));
+        		sb.append("  ");
+        		sb.append(n.getLabel());
+      			sb.append("\n");
+      			for (Statement s : n.getStatements()) {
+        			sb.append("  ");
+        			sb.append(hrefStatement(s));
+        			sb.append("\n");
+        		}
+        	}
+  			sb.append("\n");
+  			 
+          	sb.append("------------\n");
+        	sb.append("Statements at graph level:\n");
+        	sb.append("------------\n\n");
+        	for (Statement s : graph.getStatements()) {
+        		sb.append(hrefStatement(s));
+        		sb.append("\n");
+        	}
+         	sb.append("</pre>");
+         	 
+        	result = new StringRepresentation(sb, MediaType.TEXT_HTML);
+        }
+        return result;
+    }
+
+  }

Added: obdapi/trunk/OBDAPI/src/org/obd/ws/HomeResource.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/HomeResource.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/HomeResource.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -0,0 +1,139 @@
+
+package org.obd.ws;
+
+
+import org.restlet.Context;
+import org.restlet.data.MediaType;
+import org.restlet.data.Request;
+import org.restlet.data.Response;
+import org.restlet.resource.Representation;
+import org.restlet.resource.StringRepresentation;
+import org.restlet.resource.Variant;
+
+/**
+ * Resource for a node
+ */
+public class HomeResource extends OBDResource {
+
+  
+	/**
+     * Constructor.
+     * 
+     * @param context
+     *                The parent context.
+     * @param request
+     *                The request to handle.
+     * @param response
+     *                The response to return.
+     */
+    public HomeResource(Context context, Request request, Response response) {
+        super(context, request, response);
+        getVariants().add(new Variant(MediaType.TEXT_PLAIN));
+    }
+
+ 
+    @Override
+    public Representation getRepresentation(Variant variant) {
+        Representation result = null;
+        
+        StringBuilder sb = new StringBuilder();
+        sb.append("<pre>");
+        sb.append("------------\n");
+        sb.append("OBD\n");
+        sb.append("------------\n\n");
+        sb.append("This is the RESTful interface to an OBD shard\n");
+        sb.append("All resources in this shard should be accessible via a URL\n");
+        sb.append("For metadata on this shard see: "+example("/html/metadata/")+" (slow)\n");
+        sb.append("\n");
+        sb.append("\n");
+              
+        sb.append("GET Patterns Implemented:\n");
+        sb.append("~~~~~~~~~~~~~~~~~~~~\n\n");
+              
+        sb.append("  {format}/nodes/{id}\n");
+        sb.append("     A Node : can be class instance or relation\n");
+        sb.append("     Example: "+example("/html/nodes/CL:0000148")+"\n");
+        sb.append("     Example: "+example("/json/nodes/MP:0001306")+"\n");
+        sb.append("     TODO: concatenate multiple using +\n");
+        sb.append("\n");
+               
+        sb.append("  {format}/nodes/{id}/statements\n");
+        sb.append("     All statements concerning a node\n");
+        sb.append("     presently statements in which this node is subj OR obj (may change)\n");
+        sb.append("     TODO: separate resource for by-subj, by-obj\n");
+        sb.append("     Example: "+example("/html/nodes/CL:0000148/statements")+"\n");
+        sb.append("     Example: "+example("/json/nodes/MP:0001306/statements")+"\n");
+        sb.append("\n");
+        
+        sb.append("  {format}/nodes/{id}/statements/{relation}\n");
+        sb.append("     All statements concerning a node filtered by relation\n");
+        sb.append("     Example: "+example("/html/nodes/CL:0000148/statements/OBO_REL:is_a")+"\n");
+        sb.append("     Example: "+example("/html/nodes/CL:0000148/statements/develops_from")+"\n");
+        sb.append("\n");
+               
+        sb.append("  {format}/nodes/{id}/graph\n");
+        sb.append("     Graph around node; deductive closure to roots\n");
+        sb.append("     Example: "+example("/json/nodes/MP:0001306/graph")+"\n");
+        sb.append("\n");
+        sb.append("  {format}/nodes/{id}/annotation-graph\n");
+        sb.append("     Graph around annotations to node\n");             
+        sb.append("     TODO\n");
+        sb.append("     Example: "+example("/json/nodes/MP:0001306/annotation-graph")+"\n");
+        sb.append("\n");
+       
+        sb.append("  {format}/nodes-by-search/{searchTerm}\n");
+        sb.append("     Matching nodes (defaults to exact match)\n");
+        sb.append("     Example: "+example("/html/nodes-by-search/eye")+"\n");
+        sb.append("     Example: "+example("/html/nodes-by-search/Eye")+"\n");
+        sb.append("     Example: "+example("/html/nodes-by-search/cell")+"\n");
+        sb.append("\n");
+        
+        sb.append("  {format}/nodes-by-search/{searchTerm}/{comparisonOperator}\n");
+        sb.append("     Matching nodes; operator = starts_with OR contains\n");
+        sb.append("     Example: "+example("/html/nodes-by-search/eye/starts_with")+"\n");
+        sb.append("     Example: "+example("/html/nodes-by-search/eye/contains")+"\n");
+        sb.append("\n");
+        
+        sb.append("  {format}/nodes-by-search/{searchTerm}/{comparisonOperator}/{synType}   -- TODO\n");
+        sb.append("     TODO\n");
+        sb.append("\n");
+        
+        sb.append("  {format}/summary   -- TODO\n");
+        sb.append("  {format}/source/{id}   -- TODO\n");
+        sb.append("  {format}/source/{id}/nodes   -- TODO\n");
+        sb.append("  {format}/source/{id}/graph   -- TODO\n");
+        sb.append("  {format}/source/{id}/summary   -- TODO\n");
+        sb.append("  {format}/relation/{id}   -- TODO\n");
+        sb.append("  {format}/nodes-by-query/{obdQuery}   -- TODO\n");
+        sb.append("  {format}/nodes-by-query/{obdQuery}/graph   -- TODO\n");
+        sb.append("  {format}/hits-by-co-annotated/{id}   -- TODO\n");
+        sb.append("  {format}/hits-by-semantic-similarity/{id}   -- TODO\n");
+        sb.append("\n");
+        
+        sb.append("\n");
+        
+        sb.append("Formats:\n");
+        sb.append("~~~~~~~~~~~~~~~~~~~~\n\n");
+        sb.append(" - html : ultra basic information on resource\n");
+        sb.append(" - json : OBD-JSON (not finalized)\n");
+        sb.append(" - obdxml : TODO - next \n");
+        sb.append(" - owl : TODO - after (uses OWLAPI so various surface forms available)\n");
+        sb.append(" - obo : TODO - after \n");
+        sb.append("\n");
+        
+        sb.append("PUT Patterns:\n");
+        sb.append("~~~~~~~~~~~~~~~~~~~~\n\n");
+        sb.append(" class enrichment\n");
+        sb.append("\n");
+              
+                
+        sb.append("<pre>");
+        result = new StringRepresentation(sb, MediaType.TEXT_HTML);
+        return result;
+    }
+    
+    public String example(String path) {
+    	return "<a href=\""+path+"\">"+path+"</a>";
+    }
+
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/ws/NodeResource.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/NodeResource.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/NodeResource.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -0,0 +1,157 @@
+/*
+ * Copyright 2005-2007 Noelios Consulting.
+ * 
+ * The contents of this file are subject to the terms of the Common Development
+ * and Distribution License (the "License"). You may not use this file except in
+ * compliance with the License.
+ * 
+ * You can obtain a copy of the license at
+ * http://www.opensource.org/licenses/cddl1.txt See the License for the specific
+ * language governing permissions and limitations under the License.
+ * 
+ * When distributing Covered Code, include this CDDL HEADER in each file and
+ * include the License file at http://www.opensource.org/licenses/cddl1.txt If
+ * applicable, add the following below this CDDL HEADER, with the fields
+ * enclosed by brackets "[]" replaced with your own identifying information:
+ * Portions Copyright [yyyy] [name of copyright owner]
+ */
+
+package org.obd.ws;
+
+
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.model.bridge.OBDJSONBridge;
+import org.obd.query.Shard;
+import org.restlet.Context;
+import org.restlet.data.MediaType;
+import org.restlet.data.Request;
+import org.restlet.data.Response;
+import org.restlet.resource.Representation;
+import org.restlet.resource.Resource;
+import org.restlet.resource.StringRepresentation;
+import org.restlet.resource.Variant;
+
+/**
+ * Resource for a node
+ */
+public class NodeResource extends OBDResource {
+
+    private Node node;
+    private String nodeId;
+	protected String format;
+
+    public String getFormat() {
+		return format;
+	}
+
+
+	public void setFormat(String format) {
+		this.format = format;
+	}
+
+
+	/**
+     * Constructor.
+     * 
+     * @param context
+     *                The parent context.
+     * @param request
+     *                The request to handle.
+     * @param response
+     *                The response to return.
+     */
+    public NodeResource(Context context, Request request, Response response) {
+        super(context, request, response);
+        this.nodeId = (String) request.getAttributes().get("id");
+        //format = request.getResourceRef().getQueryAsForm().getFirstValue("format");
+        format = (String) request.getAttributes().get("format");
+  
+        this.node = findNode();
+
+        if (node != null) {
+            getVariants().add(new Variant(MediaType.TEXT_PLAIN));
+        }
+    }
+
+ 
+    /**
+     * Finds the associated node.
+     * 
+     * @return The node found or null.
+     */
+    public Node findNode() {
+        Node result = null;
+
+        if (nodeId != null) {       	
+        	result = getShard().getNode(nodeId);    	
+        }
+
+        return result;
+    }
+
+ 
+    @Override
+    public Representation getRepresentation(Variant variant) {
+        Representation result = null;
+        
+        if (format == null) {
+        	format = "";
+        }
+    
+        if (format.equals("json")) {
+            result = new StringRepresentation(OBDJSONBridge.toJSON(this.node).toString());
+        }
+         else {
+          	// Creates a text representation
+        	StringBuilder sb = new StringBuilder();
+        	sb.append("<pre>");
+          	sb.append("------------\n");
+          	sb.append("Node details\n");
+        	sb.append("------------\n\n");
+        	sb.append("Id:  ").append(href(node)).append('\n');
+          	sb.append("Label: ").append(this.node.getLabel()).append("\n");
+          	sb.append("Source: ").append(this.node.getSourceId()).append("\n\n");
+           	sb.append("Statements: ").append(hrefStatementsFor(node.getId())).append("\n\n");
+           	sb.append("Graph: ").append(hrefGraph(node.getId())).append("\n\n");
+           	sb.append("<pre>");
+          	result = new StringRepresentation(sb, MediaType.TEXT_HTML);
+        }
+        return result;
+    }
+    
+ 
+
+    /**
+     * Returns the associated node.
+     * 
+     * @return The associated node.
+     */
+    public Node getNode() {
+        return this.node;
+    }
+
+  
+    /**
+     * Sets the associated node.
+     * 
+     * @param node
+     *                The node to set.
+     */
+    public void setNode(Node node) {
+        this.node = node;
+    }
+
+
+	public String getNodeId() {
+		return nodeId;
+	}
+
+
+	public void setNodeId(String nodeId) {
+		this.nodeId = nodeId;
+	}
+    
+    
+
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/ws/NodesBySearchResource.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/NodesBySearchResource.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/NodesBySearchResource.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -0,0 +1,130 @@
+
+
+package org.obd.ws;
+
+
+import java.util.Collection;
+import java.util.LinkedList;
+
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.model.bridge.OBDJSONBridge;
+import org.obd.query.ComparisonQueryTerm;
+import org.obd.query.Shard;
+import org.obd.query.ComparisonQueryTerm.Operator;
+import org.restlet.Context;
+import org.restlet.data.MediaType;
+import org.restlet.data.Request;
+import org.restlet.data.Response;
+import org.restlet.resource.Representation;
+import org.restlet.resource.Resource;
+import org.restlet.resource.StringRepresentation;
+import org.restlet.resource.Variant;
+
+/**
+ * Resource for a node
+ */
+public class NodesBySearchResource extends OBDResource {
+
+    private Collection<Node> nodes;
+	protected String format;
+	protected String searchTerm;
+	protected String operatorString;
+
+    public String getFormat() {
+		return format;
+	}
+
+
+	public void setFormat(String format) {
+		this.format = format;
+	}
+
+
+	/**
+     * Constructor.
+     * 
+     * @param context
+     *                The parent context.
+     * @param request
+     *                The request to handle.
+     * @param response
+     *                The response to return.
+     */
+    public NodesBySearchResource(Context context, Request request, Response response) {
+        super(context, request, response);
+        this.searchTerm = (String) request.getAttributes().get("term");
+        this.operatorString = (String) request.getAttributes().get("operator");
+        //format = request.getResourceRef().getQueryAsForm().getFirstValue("format");
+        format = (String) request.getAttributes().get("format");
+  
+        this.nodes = findNodes();
+        getVariants().add(new Variant(MediaType.TEXT_PLAIN));
+    }
+
+ 
+    /**
+     * Finds the associated node.
+     * 
+     * @return The node found or null.
+     */
+    public Collection<Node> findNodes() {
+        nodes = new LinkedList<Node>();
+
+        if (searchTerm != null) { 
+        	Operator op = null;
+        	if (operatorString != null) {
+        		for (Operator currOp : Operator.values()) {
+        			System.out.println(currOp.toString());
+        			if (currOp.toString().equals(operatorString))
+        				op = currOp;
+        		}
+        	}
+        	if (op == null)
+           		nodes = getShard().getNodesBySearch(searchTerm);
+        	else
+        		nodes = getShard().getNodesBySearch(searchTerm, op);
+        }
+
+        return nodes;
+    }
+
+ 
+    @Override
+    public Representation getRepresentation(Variant variant) {
+        Representation result = null;
+        
+        if (format == null) {
+        	format = "";
+        }
+    
+        if (format.equals("json")) {
+            result = new StringRepresentation(OBDJSONBridge.nodesToJSON(nodes).toString());
+        }
+        else {
+          	// Creates a text representation
+        	StringBuilder sb = new StringBuilder();
+        	sb.append("<pre>");
+          	sb.append("------------\n");
+          	sb.append("Node list\n");
+           	sb.append("------------\n\n");
+         	sb.append("<table>\n");
+         	for (Node node : nodes) {
+         		sb.append("<tr>");
+         		sb.append("<td>"+href(node)+"</td>");
+        		sb.append("<td>"+node.getLabel()+"</td>");
+        		sb.append("<td>"+node.getSourceId()+"</td>");
+        		sb.append("</tr>");
+         		
+         	}
+         	sb.append("</table>\n");
+         	                   	
+         	result = new StringRepresentation(sb, MediaType.TEXT_HTML);
+        }
+        return result;
+    }
+    
+ 
+    
+
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/ws/OBDQueryService.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/OBDQueryService.java	2008-01-04 20:29:21 UTC (rev 1345)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/OBDQueryService.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -98,6 +98,11 @@
 		getAnnotationStatementsForAnnotatedEntity(id, entailment, strategy).
 		toArray(new Statement[0]);
 	}
+	public Statement[] getAnnotationStatementsForNode(String id, EntailmentUse entailment, GraphExpansionAlgorithm strategy) {
+		return (Statement[] ) shard.
+		getAnnotationStatementsForNode(id, entailment, strategy).
+		toArray(new Statement[0]);
+	}
 	
 	public Node[] getAnnotatedEntitiesBelowNodeSet(Collection<String> ids,
 			EntailmentUse entailment,

Added: obdapi/trunk/OBDAPI/src/org/obd/ws/OBDResource.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/OBDResource.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/OBDResource.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -0,0 +1,82 @@
+
+package org.obd.ws;
+
+
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.query.Shard;
+import org.restlet.Context;
+import org.restlet.data.Request;
+import org.restlet.data.Response;
+import org.restlet.resource.Resource;
+
+/**
+ * Resource for a node
+ */
+public abstract class OBDResource extends Resource {
+
+  
+    public OBDResource(Context context, Request request, Response response) {
+    	super(context, request, response);
+    }
+
+	/**
+     * Returns the parent OBDRestApplication.
+     * 
+     * @return the parent OBDRestApplication.
+     */
+    public OBDRestApplication getOBDRestApplication() {
+        return (OBDRestApplication) getContext().getAttributes().get(OBDRestApplication.KEY);
+    }
+
+    /**
+     * Returns the database container.
+     * 
+     * @return the database container.
+     */
+    public Shard getShard() {
+        return getOBDRestApplication().getShard();
+    }
+
+     
+    public String href(Node node) {
+    	String id = node.getId();
+    	return href(id);
+    }
+    public String href(String id) {
+    	return "<a href=\"/html/nodes/"+id+"\">"+id+"</a>";
+    }
+    public String hrefNodesBySearch(String n) {
+    	return "<a href=\"/html/nodes-by-search/"+n+"\">"+n+"</a>";
+    }
+    public String hrefStatementsFor(String id) {
+    	return "<a href=\"/html/nodes/"+id+"/statements\">"+id+"</a>";
+    }
+    
+    public String hrefStatement(Statement s) {
+    	StringBuilder sb = new StringBuilder();
+    	sb.append(href(s.getNodeId()));
+    	sb.append(" --[ ");
+       	sb.append(href(s.getRelationId()));
+    	sb.append("]--> ");
+      	sb.append(href(s.getTargetId()));
+      	if (s.isInferred())
+      		sb.append(" [Implied]");
+     	if (s.getSourceId() != null)
+      		sb.append(" [source:"+s.getSourceId()+"]");
+     	if (s.getPositedByNodeId() != null)
+      		sb.append(" [source:"+s.getPositedByNodeId()+"]");
+         	
+    	return sb.toString();
+    }
+
+
+    
+    public String hrefGraph(String id) {
+    	return "<a href=\"/html/nodes/"+id+"/graph\">"+id+"</a>";
+    }
+
+
+     
+
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/ws/OBDRestApplication.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/OBDRestApplication.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/OBDRestApplication.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -0,0 +1,114 @@
+package org.obd.ws;
+
+import java.sql.SQLException;
+
+import org.apache.commons.lang.StringUtils;
+import org.obd.query.Shard;
+import org.obd.query.impl.MultiShard;
+import org.obd.query.impl.MutableOBOSessionShard;
+import org.obd.query.impl.OBDSQLShard;
+import org.restlet.Application;
+import org.restlet.Component;
+import org.restlet.Context;
+import org.restlet.Restlet;
+import org.restlet.Router;
+import org.restlet.data.MediaType;
+import org.restlet.data.Protocol;
+import org.restlet.data.Request;
+import org.restlet.data.Response;
+import org.restlet.resource.StringRepresentation;
+
+public class OBDRestApplication extends Application {
+
+	static String defaultJdbcPath = "jdbc:postgresql://localhost:5432/obd_phenotype_mouse";
+	protected Shard shard;
+
+    public static void main(String[] args) throws Exception {
+        // Create a component
+        Component component = new Component();
+        component.getServers().add(Protocol.HTTP, 8182);
+        component.getClients().add(Protocol.FILE);
+
+        OBDRestApplication application = new OBDRestApplication(
+                component.getContext());
+        
+        // TODO: configurable
+        // for now we hardcode a multishard wrapping an obosession
+        // and a SQL shard
+        MultiShard multiShard = new MultiShard();
+		try {
+			OBDSQLShard obd = new OBDSQLShard();
+			obd.connect(defaultJdbcPath);
+			multiShard.addShard(obd);
+		} catch (SQLException e) {
+			e.printStackTrace();
+		}
+
+		MutableOBOSessionShard moss = new MutableOBOSessionShard();
+		moss.loadLocal("cell");
+		multiShard.addShard(moss);
+
+		application.setShard(multiShard);
+
+        // Attach the application to the component and start it
+        component.getDefaultHost().attach("", application);
+        
+        component.start();
+    }
+
+    public OBDRestApplication() {
+        super();
+    }
+
+    public OBDRestApplication(Context context) {
+        super(context);
+    }
+
+    @Override
+    public Restlet createRoot() {
+        Router router = new Router(getContext());
+
+        // Add a route for the top-level resource
+        
+        router.attach("/", HomeResource.class).
+           getTemplate().setMatchingMode(org.restlet.util.Template.MODE_EQUALS);
+        router.attach("", HomeResource.class);
+        router.attach("/help", HomeResource.class);
+        router.attach("/help/", HomeResource.class);
+        router.attach("/help/{id}", HomeResource.class);
+        
+        router.attach("/{format}/help/", HomeResource.class);
+
+        router.attach("/{format}/metadata/", ShardMetadataResource.class);
+
+       
+        // Add a route for node resources
+        router.attach("/{format}/nodes/{id}", NodeResource.class);
+
+        // Add a route for statements-by-node resources
+        router.attach("/{format}/nodes/{id}/statements", StatementsResource.class);
+        router.attach("/{format}/nodes/{id}/statements/{relation}", StatementsResource.class);
+
+        // Add a route for graph-by-node resources
+        router.attach("/{format}/nodes/{id}/graph", GraphResource.class);
+
+        // Add a route for node resources
+        router.attach("/{format}/nodes-by-search/{term}", NodesBySearchResource.class);
+        router.attach("/{format}/nodes-by-search/{term}/{operator}", NodesBySearchResource.class);
+
+   
+        return router;
+    }
+
+
+
+	public Shard getShard() {
+		return shard;
+	}
+
+	public void setShard(Shard shard) {
+		this.shard = shard;
+	}
+
+}
+

Added: obdapi/trunk/OBDAPI/src/org/obd/ws/ShardMetadataResource.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/ShardMetadataResource.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/ShardMetadataResource.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -0,0 +1,111 @@
+
+
+package org.obd.ws;
+
+
+import java.util.Collection;
+import java.util.LinkedList;
+
+import org.json.JSONException;
+import org.obd.model.Node;
+import org.obd.model.bridge.OBDJSONBridge;
+import org.obd.model.stats.AggregateStatistic;
+import org.obd.model.stats.AggregateStatisticCollection;
+import org.obd.model.stats.CountStatistic;
+import org.obd.query.ComparisonQueryTerm.Operator;
+import org.restlet.Context;
+import org.restlet.data.MediaType;
+import org.restlet.data.Request;
+import org.restlet.data.Response;
+import org.restlet.resource.Representation;
+import org.restlet.resource.StringRepresentation;
+import org.restlet.resource.Variant;
+
+/**
+ * Resource for a node
+ */
+public class ShardMetadataResource extends OBDResource {
+
+	protected AggregateStatisticCollection stats;
+ 	protected String format;
+
+    public String getFormat() {
+		return format;
+	}
+
+
+	public void setFormat(String format) {
+		this.format = format;
+	}
+
+
+	/**
+     * Constructor.
+     * 
+     * @param context
+     *                The parent context.
+     * @param request
+     *                The request to handle.
+     * @param response
+     *                The response to return.
+     */
+    public ShardMetadataResource(Context context, Request request, Response response) {
+        super(context, request, response);
+        format = (String) request.getAttributes().get("format");
+        getStats();
+        getVariants().add(new Variant(MediaType.TEXT_PLAIN));
+    }
+
+ 
+    /**
+     * Finds the associated node.
+     * 
+     * @return The node found or null.
+     */
+    public AggregateStatisticCollection getStats() {
+ 
+    	stats = getShard().getSummaryStatistics();
+   
+        return stats;
+    }
+
+ 
+    @Override
+    public Representation getRepresentation(Variant variant) {
+        Representation result = null;
+        
+        if (format == null) {
+        	format = "";
+        }
+    
+        if (format.equals("json")) {
+            result = new StringRepresentation(OBDJSONBridge.toJSON(stats).toString());
+        }
+        else {
+          	// Creates a text representation
+        	StringBuilder sb = new StringBuilder();
+        	sb.append("<pre>");
+          	sb.append("------------\n");
+          	sb.append("OBD Shard Information\n");
+           	sb.append("------------\n\n");
+         	sb.append("<table>\n");
+        	for (AggregateStatistic s : stats.getStats() ) {
+    			if (s instanceof CountStatistic) {
+    				CountStatistic c = (CountStatistic)s;
+    				sb.append(s.getMeasuredEntity().toString()+" = "+
+    						c.getCount());
+    				sb.append("\n");
+    			}
+        	}
+         	sb.append("</pre>");
+            
+         	                   	
+         	result = new StringRepresentation(sb, MediaType.TEXT_HTML);
+        }
+        return result;
+    }
+    
+ 
+    
+
+}

Added: obdapi/trunk/OBDAPI/src/org/obd/ws/StatementsResource.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/StatementsResource.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/StatementsResource.java	2008-01-05 01:27:45 UTC (rev 1346)
@@ -0,0 +1,111 @@
+
+
+package org.obd.ws;
+
+import java.util.Collection;
+
+import org.obd.model.Statement;
+import org.obd.model.bridge.OBDJSONBridge;
+import org.obd.query.LinkQueryTerm;
+import org.restlet.Context;
+import org.restlet.data.MediaType;
+import org.restlet.data.Reference;
+import org.restlet.data.ReferenceList;
+import org.restlet.data.Request;
+import org.restlet.data.Response;
+import org.restlet.resource.Representation;
+import org.restlet.resource.StringRepresentation;
+import org.restlet.resource.Variant;
+
+/**
+ * Resource for a node
+ * 
+ * @author cjm
+ */
+public class StatementsResource extends NodeResource {
+	
+	protected String relationId;
+
+    /**
+     * Constructor.
+     * 
+     * @param context
+     *            The parent context.
+     * @param request
+     *            The request to handle.
+     * @param response
+     *            The response to return.
+     */
+    public StatementsResource(Context context, Request request, Response response) {
+        super(context, request, response);
+        relationId = (String) request.getAttributes().get("relation");
+        getVariants().clear();
+        if (getNode() != null) {
+            getVariants().add(new Variant(MediaType.TEXT_HTML));
+        }
+    }
+
+    @Override
+    public Representation getRepresentation(Variant variant) {
+        Representation result = null;
+
+        
+        Collection<Statement> stmts;
+        
+        if (relationId == null) {
+        	// TODO: include other refs?
+        	stmts =	getShard().getStatementsForNode(getNodeId());
+        	stmts.addAll(getShard().getStatementsForTarget((getNodeId())));
+        }
+        else {
+        	LinkQueryTerm lq = new LinkQueryTerm();
+        	lq.setRelation(relationId);
+        	lq.setNode(getNodeId());
+        	stmts = getShard().getStatementsByQuery(lq);
+        	lq = new LinkQueryTerm();
+        	lq.setRelation(relationId);
+        	lq.setTarget(getNodeId());
+        	stmts.addAll(getShard().getStatementsByQuery(lq));
+        }
+        
+        if (format == null) {
+        	format = "";
+        }
+    
+        if (format.equals("json")) {
+             result = new StringRepresentation(OBDJSONBridge.toJSON(stmts).toString());
+            return result;
+     
+        }
+        else {
+        	//if (variant.getMediaType().equals(MediaType.TEXT_HTML)) {
+          	StringBuilder sb = new StringBuilder();
+           	sb.append("<pre>");
+           	sb.append("------------\n");
+        	sb.append("Statements\n");
+        	sb.append("------------\n\n");
+          	 
+        	for (Statement s : stmts) {
+        		sb.append(hrefStatement(s));
+        		sb.append("\n");
+             }
+         	sb.append("</pre>");
+         	result = new StringRepresentation(sb, MediaType.TEXT_HTML);
+        }
+
+        return result;
+    }
+    
+     @Override
+    public void handleGet() {
+        // Make sure that the Uri ends with a "/" without changing the query.
+        Reference ref = getRequest().getResourceRef();
+        if (!ref.getPath().endsWith("/")) {
+            ref.setPath(ref.getPath() + "/");
+            getResponse().redirectPermanent(ref);
+        } else {
+            super.handleGet();
+        }
+    }
+
+}


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 1356
          http://obo.svn.sourceforge.net/obo/?rev=1356&view=rev
Author:   cmungall
Date:     2008-01-07 17:47:34 -0800 (Mon, 07 Jan 2008)

Log Message:
-----------


Modified Paths:
--------------
    obdapi/trunk/OBDAPI/src/org/obd/query/ComparisonQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/QueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBOSessionShard.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/WrappedOBDRestShard.java
    obdapi/trunk/OBDAPI/src/org/obd/test/CompositionalDescriptionTest.java
    obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java
    obdapi/trunk/OBDAPI/src/org/obd/ws/HomeResource.java
    obdapi/trunk/OBDAPI/src/org/obd/ws/NodeResource.java
    obdapi/trunk/OBDAPI/src/org/obd/ws/NodesBySearchResource.java
    obdapi/trunk/OBDAPI/src/org/obd/ws/OBDRestApplication.java
    obdapi/trunk/OBDAPI/src/org/obd/ws/StatementsResource.java

Added Paths:
-----------
    obdapi/trunk/OBDAPI/src/org/obd/test/QueryBySourceTest.java
    obdapi/trunk/OBDAPI/src/org/obd/ws/StatementsBySearchResource.java

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/ComparisonQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/ComparisonQueryTerm.java	2008-01-07 20:03:33 UTC (rev 1355)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/ComparisonQueryTerm.java	2008-01-08 01:47:34 UTC (rev 1356)
@@ -10,6 +10,7 @@
 		GREATER_THAN_OR_EQUAL_TO(">"),
 		NOT_EQUAL_TO("!="),
 		
+		MATCHES("matches"),
 		CONTAINS("contains"),
 		STARTS_WITH("starts_with");
 		

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java	2008-01-07 20:03:33 UTC (rev 1355)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/LinkQueryTerm.java	2008-01-08 01:47:34 UTC (rev 1356)
@@ -1,9 +1,7 @@
 package org.obd.query;
 
 public class LinkQueryTerm extends QueryTerm {
-	public enum Aspect {SELF, RELATION, TARGET, SOURCE, POSITED_BY};
 	protected QueryTerm target;
-	protected Aspect aspect = Aspect.SELF;
 	protected boolean isDescriptionLink = false;
 	
 	/**
@@ -69,12 +67,6 @@
 			this.target = new LabelQueryTerm(nodeAtom);
 	}
 	
-	public Aspect getAspect() {
-		return aspect;
-	}
-	public void setAspect(Aspect aspect) {
-		this.aspect = aspect;
-	}
 	public boolean isDescriptionLink() {
 		return isDescriptionLink;
 	}

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/QueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/QueryTerm.java	2008-01-07 20:03:33 UTC (rev 1355)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/QueryTerm.java	2008-01-08 01:47:34 UTC (rev 1356)
@@ -1,12 +1,18 @@
 package org.obd.query;
 
+import org.obd.query.QueryTerm.Aspect;
+
 public abstract class QueryTerm {
 	
+	public enum Aspect {SELF, RELATION, TARGET, SOURCE, POSITED_BY};
+
 	protected QueryTerm node;
 	protected QueryTerm relation;
 	protected QueryTerm source;
 	protected QueryTerm positedBy;
 	protected Boolean isInferred;
+	protected Aspect aspect = Aspect.SELF;
+
 	
 	public QueryTerm() {
 		super();
@@ -62,6 +68,13 @@
 	public void setInferred(Boolean isInferred) {
 		this.isInferred = isInferred;
 	}
+	public Aspect getAspect() {
+		return aspect;
+	}
+	public void setAspect(Aspect aspect) {
+		this.aspect = aspect;
+	}
+
 	
 	public String toString() {
 		String s = "";

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java	2008-01-07 20:03:33 UTC (rev 1355)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java	2008-01-08 01:47:34 UTC (rev 1356)
@@ -37,7 +37,7 @@
 import org.obd.query.Shard;
 import org.obd.query.ComparisonQueryTerm.Operator;
 import org.obd.query.LabelQueryTerm.AliasType;
-import org.obd.query.LinkQueryTerm.Aspect;
+import org.obd.query.QueryTerm.Aspect;
 import org.obo.dataadapter.OBDSQLDatabaseAdapter;
 import org.obo.dataadapter.OBDSQLDatabaseAdapter.OBDSQLDatabaseAdapterConfiguration;
 import org.obo.datamodel.IdentifiedObject;
@@ -765,6 +765,20 @@
 			String subjCol) {
 
 		WhereClause wc = rq.getWhereClause();
+		String aspectCol = null;
+		if (subjCol != null && qt != null) {
+			aspectCol = "node_id";
+			Aspect aspect = qt.getAspect();
+			if (aspect.equals(Aspect.TARGET))
+				aspectCol = "object_id";
+			else if (aspect.equals(Aspect.RELATION))
+				aspectCol = "predicate_id";
+			else if (aspect.equals(Aspect.SOURCE))
+				aspectCol = "source_id";
+			else if (aspect.equals(Aspect.POSITED_BY))
+				aspectCol = "reiflink_node_id";
+		}
+
 		if (qt instanceof AtomicQueryTerm) {
 			String val = ((AtomicQueryTerm)qt).getValue();
 			if (subjCol == null) {
@@ -786,7 +800,9 @@
 			BooleanQueryTerm cqt = (BooleanQueryTerm)qt;
 			for (QueryTerm subquery : cqt.getQueryTerms()) {
 				RelationalQuery subrq = new SqlQueryImpl();
-				translateQuery(subquery, rq, "node_id");
+				//translateQuery(subquery, subrq, "link.node_id");
+				String subTbl = translateQuery(subquery, subrq, null);
+				subrq.setSelectClause(subTbl+".node_id");
 				wc.addInConstraint(subjCol, subrq);
 			}
 			return subjCol;
@@ -800,6 +816,8 @@
 					wc.addOperatorConstraint("LIKE", subjCol, val+"%"); // TODO: before?
 				else if (op.equals(Operator.CONTAINS))
 					wc.addOperatorConstraint("LIKE", subjCol, "%"+val+"%"); // TODO: before?
+				else if (op.equals(Operator.MATCHES))
+					wc.addOperatorConstraint("LIKE", subjCol, val); // TODO: before?
 				else 
 					wc.addOperatorConstraint(cqt.getOperator().toString(), subjCol, val);
 			}
@@ -820,7 +838,7 @@
 				String rel = rq.addAutoAliasedTable("node");
 				translateQuery(cqt.getValue(), rq, rel+".node_id");
 				if (subjCol != null)
-					wc.addConstraint(rel+".node_id = " + subjCol);
+					wc.addConstraint(rel+"." + aspectCol + " = " + subjCol);
 				return rel;
 			}
 			if (alias.equals(AliasType.PRIMARY_NAME)) {
@@ -885,17 +903,7 @@
 			String tbl = "link"; 
 			String tblAlias = rq.addAutoAliasedTable(tbl);
 			if (subjCol != null) {
-				String col = "node_id";
-				Aspect aspect = cqt.getAspect();
-				if (aspect.equals(Aspect.TARGET))
-					col = "object_id";
-				else if (aspect.equals(Aspect.RELATION))
-					col = "predicate_id";
-				else if (aspect.equals(Aspect.SOURCE))
-					col = "source_id";
-				else if (aspect.equals(Aspect.POSITED_BY))
-					col = "reiflink_node_id";
-				wc.addConstraint(tblAlias+"."+col+" = " + subjCol);
+				wc.addConstraint(tblAlias+"."+aspectCol+" = " + subjCol);
 			}
 			if (cqt.isInferred() != null)
 				wc.addEqualityConstraint(tblAlias+".is_inferred",cqt.isInferred());
@@ -904,6 +912,7 @@
 			String nodeTbl = translateQuery(cqt.getNode(), rq, tblAlias+".node_id");
 			String relTbl = translateQuery(cqt.getRelation(), rq, tblAlias+".predicate_id");
 			String targetTbl = translateQuery(cqt.getTarget(), rq, tblAlias+".object_id");
+			String sourceTbl = translateQuery(cqt.getSource(), rq, tblAlias+".source_id");
 			String positsNodeTbl = translateQuery(cqt.getPositedBy(), rq, tblAlias+".reiflink_node_id");
 			// returns the name of the link table alias used in this query
 			return tblAlias;

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBOSessionShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBOSessionShard.java	2008-01-07 20:03:33 UTC (rev 1355)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBOSessionShard.java	2008-01-08 01:47:34 UTC (rev 1356)
@@ -209,7 +209,7 @@
 
 	public Collection<Node> getNodesByQuery(QueryTerm queryTerm) {
 		// TODO Auto-generated method stub
-		return null;
+		return new HashSet<Node>();
 	}
 
 	public Graph getGraphByQuery(QueryTerm queryTerm, EntailmentUse entailment, GraphExpansionAlgorithm gea) {

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/impl/WrappedOBDRestShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/WrappedOBDRestShard.java	2008-01-07 20:03:33 UTC (rev 1355)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/WrappedOBDRestShard.java	2008-01-08 01:47:34 UTC (rev 1356)
@@ -37,7 +37,7 @@
 import org.obd.query.Shard;
 import org.obd.query.ComparisonQueryTerm.Operator;
 import org.obd.query.LabelQueryTerm.AliasType;
-import org.obd.query.LinkQueryTerm.Aspect;
+import org.obd.query.QueryTerm.Aspect;
 import org.obd.query.Shard.EntailmentUse;
 import org.obo.annotation.datamodel.Annotation;
 import org.obo.dataadapter.OBDSQLDatabaseAdapter;

Modified: obdapi/trunk/OBDAPI/src/org/obd/test/CompositionalDescriptionTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/CompositionalDescriptionTest.java	2008-01-07 20:03:33 UTC (rev 1355)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/CompositionalDescriptionTest.java	2008-01-08 01:47:34 UTC (rev 1356)
@@ -1,5 +1,7 @@
 package org.obd.test;
 
+import java.util.Collection;
+
 import junit.framework.Test;
 import junit.framework.TestCase;
 import junit.framework.TestSuite;
@@ -55,14 +57,13 @@
 		System.out.println("desc2="+desc);
 		assertFalse(desc.toString().contains("SOME MA:0000060"));
 		assertTrue(desc.toString().contains("SOME MA:0000236"));
-		
-
 		System.out.println("again, full expression:");
 		
 		desc = shard.getCompositionalDescription(id, true);
 		System.out.println("desc3="+desc);
 		assertTrue(desc.toString().contains("SOME MA:0000060"));
-
+		
+	
 	}
 
 

Added: obdapi/trunk/OBDAPI/src/org/obd/test/QueryBySourceTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/QueryBySourceTest.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/QueryBySourceTest.java	2008-01-08 01:47:34 UTC (rev 1356)
@@ -0,0 +1,131 @@
+package org.obd.test;
+
+import java.util.Collection;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+import org.obd.model.CompositionalDescription;
+import org.obd.model.Graph;
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.query.AtomicQueryTerm;
+import org.obd.query.BooleanQueryTerm;
+import org.obd.query.LabelQueryTerm;
+import org.obd.query.LinkQueryTerm;
+import org.obd.query.QueryTerm;
+import org.obd.query.BooleanQueryTerm.BooleanOperator;
+import org.obd.query.QueryTerm.Aspect;
+import org.obd.query.impl.MultiShard;
+import org.obd.ws.OBDQueryService;
+
+public class QueryBySourceTest extends AbstractOBDTest {
+
+	OBDQueryService service;
+	
+	
+	public QueryBySourceTest(String n) {
+		super(n);
+	}
+
+
+	public void setUp() throws Exception {
+		System.out.println("Setting up: " + this);
+		service = new OBDQueryService();
+		
+	}
+
+	public static Test suite() {
+		TestSuite suite = new TestSuite();
+		addTests(suite);
+		return suite;
+	}
+
+	public static void addTests(TestSuite suite) {
+		suite.addTest(new QueryBySourceTest("testQuery"));
+		suite.addTest(new QueryBySourceTest("testNodeQuery"));
+		suite.addTest(new QueryBySourceTest("testFetchGenotypesAnnotatedByAll"));
+		suite.addTest(new QueryBySourceTest("testFetchGenesAnnotatedByAll"));
+	}
+	
+	public void testQuery() {
+		
+		MultiShard shard = service.getShard();
+
+		String src = "omim_phenotype_bbop";
+		LinkQueryTerm q = new LinkQueryTerm();
+		q.setSource(src);
+		Collection<Statement> stmts = shard.getStatementsByQuery(q);
+		for (Statement s : stmts)
+			System.out.println(s);
+
+	}
+	
+	public void testNodeQuery() {
+		
+		MultiShard shard = service.getShard();
+
+		String src = "omim_phenotype_bbop";
+		LinkQueryTerm q = new LinkQueryTerm();
+		q.setSource(src);
+		Collection<Node> nodes = shard.getNodesByQuery(q);
+		for (Node n : nodes)
+			System.out.println(n);
+
+	}
+	
+	public void testFetchGenotypesAnnotatedByAll() {
+		
+		MultiShard shard = service.getShard();
+
+		String[] srcs = {"omim_phenotype_bbop",
+				"omim_phenotype_zfin",
+				"omim_phenotype_fb"};
+		BooleanQueryTerm bq = new BooleanQueryTerm();
+		bq.setOperator(BooleanOperator.AND);
+		for (String src : srcs) {
+			QueryTerm q = new LinkQueryTerm();
+			q.setSource(src);
+			//q.setAspect(Aspect.SOURCE);
+			bq.addQueryTerm(q);
+		}
+		Collection<Node> nodes = shard.getNodesByQuery(bq);
+		for (Node n : nodes)
+			System.out.println(n);
+
+	
+	}	
+	
+	
+	// link(node=and(link(src=a) link(src=b) link(src=c)))/TARGET
+	public void testFetchGenesAnnotatedByAll() {
+		
+		MultiShard shard = service.getShard();
+
+		String[] srcs = {"omim_phenotype_bbop",
+				"omim_phenotype_zfin",
+				"omim_phenotype_fb"};
+		BooleanQueryTerm bq = new BooleanQueryTerm();
+		bq.setOperator(BooleanOperator.AND);
+		for (String src : srcs) {
+			QueryTerm q = new LinkQueryTerm();
+			q.setSource(src);
+			bq.addQueryTerm(q);
+		}
+		LinkQueryTerm lq = new LinkQueryTerm();
+		lq.setNode(bq);
+		lq.setRelation("OBO_REL:variant_of");
+		lq.setAspect(Aspect.TARGET);
+		Collection<Node> nodes = shard.getNodesByQuery(lq);
+		for (Node n : nodes)
+			System.out.println(n);
+
+	
+	}	
+	
+	
+
+
+
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java	2008-01-07 20:03:33 UTC (rev 1355)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java	2008-01-08 01:47:34 UTC (rev 1356)
@@ -18,7 +18,7 @@
 import org.obd.query.BooleanQueryTerm.BooleanOperator;
 import org.obd.query.ComparisonQueryTerm.Operator;
 import org.obd.query.LabelQueryTerm.AliasType;
-import org.obd.query.LinkQueryTerm.Aspect;
+import org.obd.query.QueryTerm.Aspect;
 import org.obd.query.impl.OBDSQLShard;
 import org.obd.ws.OBDQueryService;
 

Modified: obdapi/trunk/OBDAPI/src/org/obd/ws/HomeResource.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/HomeResource.java	2008-01-07 20:03:33 UTC (rev 1355)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/HomeResource.java	2008-01-08 01:47:34 UTC (rev 1356)
@@ -56,7 +56,7 @@
         sb.append("     Example: "+example("/json/nodes/MP:0001306")+"\n");
         sb.append("     Example: "+example("/json/nodes/entrezgene:2138")+"\n");
         sb.append("     Example: "+example("/json/nodes/OMIM:601653.0008")+"\n");
-        sb.append("     Example: "+example("/html/nodes/PATO:0000963^OBO_REL:inheres_in(FMA:58238")+"\n");
+        sb.append("     Example: "+example("/html/nodes/PATO:0000963^OBO_REL:inheres_in(FMA:58238)")+"\n");
         sb.append("     TODO: concatenate multiple using +\n");
         sb.append("\n");
                
@@ -83,7 +83,8 @@
         sb.append("     Example: "+example("/json/nodes/entrezgene:2138/statements/all")+"\n");
         sb.append("     Example: "+example("/json/nodes/MP:0005099/statements/all")+"\n");
         sb.append("     Example: "+example("/json/nodes/MP:0002877/statements/annotations")+"\n");
-               
+        sb.append("     Example: "+example("/html/nodes/omim_phenotype_fb/statements/source/")+"\n");
+                      
         sb.append("\n");
                
         sb.append("  {format}/nodes/{id}/graph\n");
@@ -103,24 +104,26 @@
         sb.append("     Example: "+example("/json/nodes/MP:0001306/annotation-graph")+"\n");
         sb.append("\n");
        
-        sb.append("  {format}/nodes-by-search/{searchTerm}\n");
+        sb.append("  {format}/search/{searchTerm}\n");
         sb.append("     Matching nodes (defaults to exact match)\n");
-        sb.append("     Example: "+example("/html/nodes-by-search/eye")+"\n");
-        sb.append("     Example: "+example("/html/nodes-by-search/Eye")+"\n");
-        sb.append("     Example: "+example("/html/nodes-by-search/eya1")+"\n");
-        sb.append("     Example: "+example("/html/nodes-by-search/cell")+"\n");
+        sb.append("     Example: "+example("/html/search/matches/eye")+"\n");
+        sb.append("     Example: "+example("/html/search/matches/Eye")+"\n");
+        sb.append("     Example: "+example("/html/search/matches/eya1")+"\n");
+        sb.append("     Example: "+example("/html/search/matches/EYA1")+"\n");
+        sb.append("     Example: "+example("/html/search/matches/EYA1+SHH")+"\n"); // TODO: quote phrases
+        sb.append("     Example: "+example("/html/search/matches/cell")+"\n");
         sb.append("\n");
         
-        sb.append("  {format}/nodes-by-search/{searchTerm}/{comparisonOperator}\n");
+        sb.append("  {format}/search/{searchTerm}/{comparisonOperator}\n");
         sb.append("     Matching nodes; operator = starts_with OR contains\n");
-        sb.append("     Example: "+example("/html/nodes-by-search/eye/melanocyte/contains")+"\n");
-        sb.append("     Example: "+example("/html/nodes-by-search/eye/starts_with")+"\n");
-        sb.append("     Example: "+example("/html/nodes-by-search/eye/contains")+"\n");
-        sb.append("     Example: "+example("/html/nodes-by-search/eya/starts_with")+"\n");
-        sb.append("     Example: "+example("/html/nodes-by-search/OMIM:601653/starts_with")+"\n");
+        sb.append("     Example: "+example("/html/search/eye/contains/melanocyte")+"\n");
+        sb.append("     Example: "+example("/html/search/starts_with/eye")+"\n");
+        sb.append("     Example: "+example("/html/search/contains/eye")+"\n");
+        sb.append("     Example: "+example("/html/search/starts_with/eya")+"\n");
+        sb.append("     Example: "+example("/html/search/starts_with/OMIM:601653")+"\n");
        sb.append("\n");
         
-        sb.append("  {format}/nodes-by-search/{searchTerm}/{comparisonOperator}/{synType}   -- TODO\n");
+        sb.append("  {format}/search/{searchTerm}/{comparisonOperator}/{synType}   -- TODO\n");
         sb.append("     TODO\n");
         sb.append("\n");
  

Modified: obdapi/trunk/OBDAPI/src/org/obd/ws/NodeResource.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/NodeResource.java	2008-01-07 20:03:33 UTC (rev 1355)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/NodeResource.java	2008-01-08 01:47:34 UTC (rev 1356)
@@ -2,6 +2,9 @@
 package org.obd.ws;
 
 
+import java.util.Collection;
+import java.util.HashSet;
+
 import org.obd.model.Node;
 import org.obd.model.Statement;
 import org.obd.model.bridge.OBDJSONBridge;
@@ -48,7 +51,8 @@
     public NodeResource(Context context, Request request, Response response) {
         super(context, request, response);
         this.nodeId = (String) request.getAttributes().get("id");
-        this.nodeId = Reference.decode(nodeId);
+        if (nodeId != null)
+        	this.nodeId = Reference.decode(nodeId);
         //format = request.getResourceRef().getQueryAsForm().getFirstValue("format");
         format = (String) request.getAttributes().get("format");
   
@@ -74,6 +78,14 @@
 
         return result;
     }
+    
+    public Collection<Node> findNodes() {
+    	HashSet<Node> nodes = new HashSet<Node>();
+    	Node n = findNode();
+    	if (n!= null)
+    		nodes.add(n);
+    	return nodes;
+    }
 
  
     @Override

Modified: obdapi/trunk/OBDAPI/src/org/obd/ws/NodesBySearchResource.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/NodesBySearchResource.java	2008-01-07 20:03:33 UTC (rev 1355)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/NodesBySearchResource.java	2008-01-08 01:47:34 UTC (rev 1356)
@@ -11,6 +11,7 @@
 import org.obd.query.ComparisonQueryTerm.Operator;
 import org.restlet.Context;
 import org.restlet.data.MediaType;
+import org.restlet.data.Reference;
 import org.restlet.data.Request;
 import org.restlet.data.Response;
 import org.restlet.resource.Representation;
@@ -20,9 +21,9 @@
 /**
  * Resource for a node
  */
-public class NodesBySearchResource extends OBDResource {
+public class NodesBySearchResource extends NodeResource {
 
-    private Collection<Node> nodes;
+    protected Collection<Node> nodes;
 	protected String format;
 	protected String searchTerm;
 	protected String operatorString;
@@ -50,6 +51,7 @@
     public NodesBySearchResource(Context context, Request request, Response response) {
         super(context, request, response);
         this.searchTerm = (String) request.getAttributes().get("term");
+        this.searchTerm = Reference.decode(searchTerm);
         this.operatorString = (String) request.getAttributes().get("operator");
         //format = request.getResourceRef().getQueryAsForm().getFirstValue("format");
         format = (String) request.getAttributes().get("format");
@@ -76,10 +78,13 @@
         				op = currOp;
         		}
         	}
-        	if (op == null)
-           		nodes = getShard().getNodesBySearch(searchTerm);
-        	else
-        		nodes = getShard().getNodesBySearch(searchTerm, op);
+        	String[] searchTerms = searchTerm.split("\\s");
+        	for (String s : searchTerms) {
+        		if (op == null)
+        			nodes.addAll(getShard().getNodesBySearch(s));
+        		else
+        			nodes.addAll(getShard().getNodesBySearch(s, op));
+        	}
         }
 
         return nodes;

Modified: obdapi/trunk/OBDAPI/src/org/obd/ws/OBDRestApplication.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/OBDRestApplication.java	2008-01-07 20:03:33 UTC (rev 1355)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/OBDRestApplication.java	2008-01-08 01:47:34 UTC (rev 1356)
@@ -117,8 +117,9 @@
         router.attach("/{format}/sources/{id}/annotations", SourceResource.class);
                       
         // Add a route for node resources
-        router.attach("/{format}/nodes-by-search/{term}", NodesBySearchResource.class);
-        router.attach("/{format}/nodes-by-search/{term}/{operator}", NodesBySearchResource.class);
+        router.attach("/{format}/search/{operator}/{term}", NodesBySearchResource.class);
+        router.attach("/{format}/search/{operator}/{term}/statements", StatementsBySearchResource.class);
+        router.attach("/{format}/search/{operator}/{term}/statements/{aspect}", StatementsBySearchResource.class);
 
    
         return router;

Added: obdapi/trunk/OBDAPI/src/org/obd/ws/StatementsBySearchResource.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/StatementsBySearchResource.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/StatementsBySearchResource.java	2008-01-08 01:47:34 UTC (rev 1356)
@@ -0,0 +1,128 @@
+
+
+package org.obd.ws;
+
+import java.util.Collection;
+import java.util.HashSet;
+
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.model.bridge.OBDJSONBridge;
+import org.obd.query.AnnotationLinkQueryTerm;
+import org.obd.query.LinkQueryTerm;
+import org.restlet.Context;
+import org.restlet.data.MediaType;
+import org.restlet.data.Reference;
+import org.restlet.data.ReferenceList;
+import org.restlet.data.Request;
+import org.restlet.data.Response;
+import org.restlet.resource.Representation;
+import org.restlet.resource.StringRepresentation;
+import org.restlet.resource.Variant;
+
+/**
+ * Resource for a node
+ * 
+ * @author cjm
+ */
+public class StatementsBySearchResource extends NodesBySearchResource {
+	
+	protected String relationId;
+	protected String aspect;
+
+    /**
+     * Constructor.
+     * 
+     * @param context
+     *            The parent context.
+     * @param request
+     *            The request to handle.
+     * @param response
+     *            The response to return.
+     */
+    public StatementsBySearchResource(Context context, Request request, Response response) {
+        super(context, request, response);
+        aspect = (String) request.getAttributes().get("aspect");
+        
+      }
+
+    @Override
+    public Representation getRepresentation(Variant variant) {
+    	Representation result = null;
+
+    	nodes = findNodes();
+
+    	Collection<Statement> stmts =
+    		new HashSet<Statement>();
+
+    	if (aspect == null || aspect.equals(""))
+    		aspect = "about";
+    	for (Node node : nodes) {
+    		String nodeId = node.getId();
+    		LinkQueryTerm lq = new LinkQueryTerm();
+    		if (relationId != null)
+    			lq.setRelation(relationId);
+    		if (aspect.equals("annotations")) {
+    			lq = new AnnotationLinkQueryTerm(nodeId);
+    		}
+    		else {
+    			if (aspect.equals("about") || aspect.equals("all"))
+    				lq.setNode(nodeId);
+    			else if (aspect.equals("to"))
+    				lq.setTarget(nodeId);
+    			else if (aspect.equals("from"))
+    				lq.setSource(nodeId);
+    			else
+    				lq.setNode(nodeId);
+    		}
+
+    		stmts.addAll(getShard().getStatementsByQuery(lq));
+
+    		if (aspect.equals("all")) {
+    			lq = new LinkQueryTerm();
+    			lq.setRelation(relationId);
+    			lq.setTarget(nodeId);
+    			stmts.addAll(getShard().getStatementsByQuery(lq));
+    		}
+    	}
+    	if (format == null) {
+    		format = "";
+    	}
+
+    	if (format.equals("json")) {
+    		result = new StringRepresentation(OBDJSONBridge.toJSON(stmts).toString());
+    		return result;
+
+    	}
+    	else {
+    		//if (variant.getMediaType().equals(MediaType.TEXT_HTML)) {
+    		StringBuilder sb = new StringBuilder();
+    		sb.append("<pre>");
+    		sb.append("------------\n");
+    		sb.append("Statements\n");
+    		sb.append("------------\n\n");
+
+    		for (Statement s : stmts) {
+    			sb.append(hrefStatement(s));
+    			sb.append("\n");
+    		}
+    		sb.append("</pre>");
+    		result = new StringRepresentation(sb, MediaType.TEXT_HTML);
+    	}
+
+    	return result;
+    }
+    
+     @Override
+    public void handleGet() {
+        // Make sure that the Uri ends with a "/" without changing the query.
+        Reference ref = getRequest().getResourceRef();
+        if (!ref.getPath().endsWith("/")) {
+            ref.setPath(ref.getPath() + "/");
+            getResponse().redirectPermanent(ref);
+        } else {
+            super.handleGet();
+        }
+    }
+
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/ws/StatementsResource.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/StatementsResource.java	2008-01-07 20:03:33 UTC (rev 1355)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/StatementsResource.java	2008-01-08 01:47:34 UTC (rev 1356)
@@ -69,7 +69,7 @@
         		lq.setNode(getNodeId());
         	else if (aspect.equals("to"))
         		lq.setTarget(getNodeId());
-        	else if (aspect.equals("from"))
+        	else if (aspect.equals("source"))
         		lq.setSource(getNodeId());
         	else
         		lq.setNode(getNodeId());


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 1408
          http://obo.svn.sourceforge.net/obo/?rev=1408&view=rev
Author:   cmungall
Date:     2008-01-24 17:16:00 -0800 (Thu, 24 Jan 2008)

Log Message:
-----------


Modified Paths:
--------------
    obdapi/trunk/OBDAPI/src/org/obd/query/QueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java
    obdapi/trunk/OBDAPI/src/org/obd/test/AggregateQueryTest.java
    obdapi/trunk/OBDAPI/src/org/obd/test/ExecuteQueryTest.java
    obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java
    obdapi/trunk/OBDAPI/src/org/obd/ws/pages/UseCase16.ftl
    obdapi/trunk/OBDAPI/src/org/obd/ws/pages/UseCase7.ftl

Added Paths:
-----------
    obdapi/trunk/OBDAPI/src/org/obd/query/SourceQueryTerm.java
    obdapi/trunk/OBDAPI/src/org/obd/test/DisplayQueryTest.java

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/QueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/QueryTerm.java	2008-01-24 23:08:36 UTC (rev 1407)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/QueryTerm.java	2008-01-25 01:16:00 UTC (rev 1408)
@@ -13,6 +13,7 @@
 	protected Boolean isInferred;
 	protected Boolean isAnnotation;
 	protected Aspect aspect = Aspect.SELF;
+	protected String queryAlias;
 
 	
 	public QueryTerm() {
@@ -84,8 +85,15 @@
 	public void setAspect(Aspect aspect) {
 		this.aspect = aspect;
 	}
+	
+	public String getQueryAlias() {
+		return queryAlias;
+	}
 
-	
+	public void setQueryAlias(String queryAlias) {
+		this.queryAlias = queryAlias;
+	}
+
 	public String toString() {
 		String s = "";
 		if (positedBy != null)

Added: obdapi/trunk/OBDAPI/src/org/obd/query/SourceQueryTerm.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/SourceQueryTerm.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/SourceQueryTerm.java	2008-01-25 01:16:00 UTC (rev 1408)
@@ -0,0 +1,25 @@
+package org.obd.query;
+
+public class SourceQueryTerm extends QueryTerm {
+	protected QueryTerm target;
+	
+
+	public SourceQueryTerm(QueryTerm target) {
+		super();
+		this.target = target;
+	}
+	public SourceQueryTerm(String targetAtom) {
+		super();
+		this.target = new LabelQueryTerm(targetAtom);
+	}
+
+	public QueryTerm getTarget() {
+		return target;
+	}
+
+	public void setTarget(QueryTerm target) {
+		this.target = target;
+	}
+
+	
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java	2008-01-24 23:08:36 UTC (rev 1407)
+++ obdapi/trunk/OBDAPI/src/org/obd/query/impl/OBDSQLShard.java	2008-01-25 01:16:00 UTC (rev 1408)
@@ -10,6 +10,7 @@
 import java.util.LinkedList;
 import java.util.logging.Logger;
 
+import org.bbop.rdbms.GroupByClause;
 import org.bbop.rdbms.RelationalQuery;
 import org.bbop.rdbms.SelectClause;
 import org.bbop.rdbms.WhereClause;
@@ -35,6 +36,8 @@
 import org.obd.query.LiteralQueryTerm;
 import org.obd.query.QueryTerm;
 import org.obd.query.Shard;
+import org.obd.query.SourceQueryTerm;
+import org.obd.query.BooleanQueryTerm.BooleanOperator;
 import org.obd.query.ComparisonQueryTerm.Operator;
 import org.obd.query.LabelQueryTerm.AliasType;
 import org.obd.query.QueryTerm.Aspect;
@@ -504,9 +507,52 @@
 	 * perform an aggregate query; e.g. count all nodes;
 	 * avg all nodes; optionally partitioned; eg by source of node
 	 * 
+	 * Example:
+	 * gnaqr(null, COUNT, {LinkQueryTerm()/SOURCE}
+	 * 
 	 * @param queryTerm
 	 * @return
 	 */
+	public Integer getNodeAggregateQueryResults(QueryTerm queryTerm,
+			AggregateType aggType, Collection<QueryTerm> groupByQueryTerms) {
+		RelationalQuery rq = new SqlQueryImpl();
+		String tbl = translateQuery(queryTerm,rq,null);
+		
+		// GROUP BY a,b,c
+		// group by term can be a link eg to source
+		GroupByClause groupByClause = rq.getGroupByClause();
+		for (QueryTerm groupBy : groupByQueryTerms) {
+			String groupByTbl = translateQuery(groupBy,rq,tbl+".node_id");
+			groupByClause.addColumn(groupByTbl+".uid");
+		}
+		
+		if (aggType.equals(AggregateType.COUNT))
+			rq.setSelectClause("COUNT(DISTINCT "+tbl+".node_id) AS agg");
+		else if (aggType.equals(AggregateType.AVERAGE))
+			rq.setSelectClause("AVG("+tbl+".node_id) AS agg");
+		else 
+			rq.setSelectClause(aggType+"("+tbl+".node_id) AS agg");
+
+		Integer num = null;
+		try {
+			ResultSet rs = execute(rq);
+			if (rs.next()) {
+				num = rs.getInt("agg");
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return num;		
+	}
+	
+	/**
+	 * perform an aggregate query; e.g. count all nodes;
+	 * avg all nodes; optionally partitioned; eg by source of node
+	 * 
+	 * @param queryTerm
+	 * @return
+	 */
 	public Integer getLinkAggregateQueryResults(QueryTerm queryTerm,
 			AggregateType aggType) {
 		// TODO: DRY
@@ -683,9 +729,10 @@
 	 * @param subjCol - column to use in where constraint. Can be null
 	 * @return tableName
 	 * 
-	 * translates a query or part of a query to SQL.
-	 * Recursive.
-	 * Assumes 
+	 * Recursively translates a query or part of a query to SQL.
+	 * 
+	 * 
+	 *  
 	 */
 	public String translateQuery(QueryTerm qt, RelationalQuery rq, 
 			String subjCol) {
@@ -724,13 +771,26 @@
 		}
 		else if (qt instanceof BooleanQueryTerm) {
 			BooleanQueryTerm cqt = (BooleanQueryTerm)qt;
+			WhereClause booleanWhereClause = wc;
+			
+			// constraints are conjunctive by default.
+			// if a disjunctive query is required we add a sub-clause
+			if (cqt.getOperator().equals(BooleanOperator.OR)) {
+				booleanWhereClause =
+					new SqlWhereClauseImpl();
+			}
 			for (QueryTerm subquery : cqt.getQueryTerms()) {
 				RelationalQuery subrq = new SqlQueryImpl();
 				//translateQuery(subquery, subrq, "link.node_id");
 				String subTbl = translateQuery(subquery, subrq, null);
 				subrq.setSelectClause(subTbl+".node_id");
-				wc.addInConstraint(subjCol, subrq);
+				booleanWhereClause.addInConstraint(subjCol, subrq);
 			}
+			
+			// make sure placeholders go in the right order..
+			if (cqt.getOperator().equals(BooleanOperator.OR)) {
+				wc.addDisjunctiveConstraints(booleanWhereClause);
+			}
 			return subjCol;
 		}
 		else if (qt instanceof ComparisonQueryTerm) {
@@ -757,7 +817,7 @@
 				String rel = rq.addAutoAliasedTable("node");
 				translateQuery(cqt.getValue(), rq, rel+".uid");
 				if (subjCol != null)
-					wc.addConstraint(rel+".node_id = " + subjCol);
+					wc.addConstraint(rel+"." + aspectCol + " = " + subjCol);
 				return rel;
 			}
 			if (alias.equals(AliasType.INTERNAL_ID)) {
@@ -800,6 +860,12 @@
 		else if (qt instanceof AnnotationLinkQueryTerm) {
 			AnnotationLinkQueryTerm cqt = (AnnotationLinkQueryTerm)qt;
 			// TODO: allow inner link query to have a relation
+			
+			// We want to return annotations of R(X,Y) if R'(Y,Z),
+			// where Z is the class of interest and X is the annotated entity.
+			// R(X,Y) is asserted.
+			// We do this with a nested link query
+			// newqt = Link(inf=f,positedBy=NOT_NULL,target=Link(target=COI))
 			LinkQueryTerm newqt =
 				new LinkQueryTerm(new LinkQueryTerm(cqt.getTarget()));
 
@@ -825,6 +891,7 @@
 			return tblAlias;
 		}
 		else if (qt instanceof LinkQueryTerm) {
+			// Example: LQ(partOf,x) => link * node[r]{po} * node[p]{x}
 			LinkQueryTerm cqt = (LinkQueryTerm)qt;
 			String tbl = "link"; 
 			String tblAlias = rq.addAutoAliasedTable(tbl);
@@ -864,6 +931,18 @@
 			// returns the name of the link table alias used in this query
 			return tblAlias;
 		}
+		else if (qt instanceof SourceQueryTerm) { // Source Query
+			SourceQueryTerm cqt = (SourceQueryTerm)qt;
+			
+			String tbl = "node";
+			String tblAlias = rq.addAutoAliasedTable(tbl);
+			if (subjCol != null)
+				wc.addConstraint(tblAlias+".node_id = " + subjCol);
+				
+			String nodeTbl = translateQuery(cqt.getNode(), rq, tblAlias+".node_id");
+			String targetTbl = translateQuery(cqt.getTarget(), rq, tblAlias+".source_id");
+			return tblAlias;
+		}
 		else 
 			return null;  // TODO _ throw
 	}

Modified: obdapi/trunk/OBDAPI/src/org/obd/test/AggregateQueryTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/AggregateQueryTest.java	2008-01-24 23:08:36 UTC (rev 1407)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/AggregateQueryTest.java	2008-01-25 01:16:00 UTC (rev 1408)
@@ -1,6 +1,7 @@
 package org.obd.test;
 
 import java.util.Collection;
+import java.util.LinkedList;
 
 import junit.framework.Test;
 import junit.framework.TestSuite;
@@ -10,9 +11,11 @@
 import org.obd.model.Statement;
 import org.obd.model.stats.AggregateStatistic.AggregateType;
 import org.obd.query.AnnotationLinkQueryTerm;
+import org.obd.query.AtomicQueryTerm;
 import org.obd.query.LinkQueryTerm;
 import org.obd.query.QueryTerm;
 import org.obd.query.QueryTerm.Aspect;
+import org.obd.query.impl.OBDSQLShard;
 
 public class AggregateQueryTest extends AbstractOBDTest {
 
@@ -41,6 +44,10 @@
 		runQuery(new AnnotationLinkQueryTerm(id), 
 				AggregateType.COUNT,
 				"number of entities that are annotated to "+id);
+	
+		QueryTerm sqt = new LinkQueryTerm("cell");
+		sqt.setAspect(Aspect.SOURCE);
+		runQuery(sqt, AggregateType.COUNT, "number of terms in cell ontology");
 		
 		LinkQueryTerm qt = new LinkQueryTerm();
 		qt.setNode(id);
@@ -54,7 +61,19 @@
 			shard.getNodeAggregateQueryResults(qt,at);
 		System.out.println(msg+" NODES: "+num);
 		assertTrue(num>0);
+
+		/*
+		Collection<QueryTerm> groups = new LinkedList<QueryTerm>();
+		QueryTerm sq = new LinkQueryTerm();
+		sq.setAspect(Aspect.SOURCE);
+		groups.add(sq);
 		num = 
+			((OBDSQLShard)shard).getNodeAggregateQueryResults(qt,AggregateType.COUNT,groups);
+		System.out.println(msg+" NODES BY : "+num);
+		assertTrue(num>0);
+		*/
+		
+		num = 
 			shard.getLinkAggregateQueryResults(qt,at);
 		System.out.println(msg+" LINKS: "+num);
 		assertTrue(num>0);

Added: obdapi/trunk/OBDAPI/src/org/obd/test/DisplayQueryTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/DisplayQueryTest.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/DisplayQueryTest.java	2008-01-25 01:16:00 UTC (rev 1408)
@@ -0,0 +1,89 @@
+package org.obd.test;
+
+import java.sql.SQLException;
+import java.util.Collection;
+
+import junit.framework.Test;
+import junit.framework.TestSuite;
+
+import org.obd.model.Graph;
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.query.QueryTerm;
+
+public class DisplayQueryTest extends QueryTest {
+
+	public DisplayQueryTest(String n) {
+		super(n);
+		// TODO Auto-generated constructor stub
+	}
+	
+	public Graph runNodeQuery(QueryTerm qt, String nid) throws SQLException, ClassNotFoundException {
+		System.out.println("exec Q: "+qt.toString());
+		Collection<Node> nodes = shard.getNodesByQuery(qt);
+		boolean matchFound = false;
+		for (Node n : nodes) {
+			System.out.println(n);
+			if (nid == null || n.getId().equals(nid))
+				matchFound = true;
+		}
+		assertTrue(nodes.size() > 0);
+		assertTrue(matchFound);
+		Graph g = new Graph();
+		g.setNodes(nodes);
+		return g;
+	}
+	
+	public Graph old__runNodeQuery(QueryTerm qt) throws SQLException, ClassNotFoundException {
+		System.out.println("exec Q: "+qt.toString());
+		Graph g = shard.getGraphByQuery(qt, null, null);
+		g.nestStatementsUnderNodes();
+		for (Node n : g.getNodes()) {
+			System.out.println(n);
+			for (Statement s : n.getStatements()) {
+				System.out.println("    "+s);
+			}	
+		}
+		assertTrue(g.getNodes().length > 0);
+		return g;
+	}
+	
+
+	
+	public Graph runLinkQuery(QueryTerm qt, Statement matchStmt) throws SQLException, ClassNotFoundException {
+		System.out.println("exec Q: "+qt.toString());
+		 Collection<Statement> stmts = shard.getStatementsByQuery(qt);
+		 boolean matchFound = false;
+		for (Statement s : stmts) {
+			System.out.println(" "+s);
+			if (matchStmt == null || s.equals(matchStmt) )
+				matchFound = true;
+		}
+		assertTrue(stmts.size() > 0);
+		assertTrue(matchFound);
+		return new Graph(stmts);
+	}
+
+	public Graph runLiteralQuery(QueryTerm qt) throws SQLException, ClassNotFoundException {
+		System.out.println("exec Q: "+qt.toString());
+		Collection<Statement> stmts = shard.getStatementsByQuery(qt);
+		for (Statement s : stmts)
+			System.out.println(" "+s);
+		assertTrue(stmts.size() > 0);
+		return new Graph(stmts);
+	}
+
+	
+	public static Test suite() {
+		TestSuite suite = new TestSuite();
+		addTests(suite);
+		return suite;
+	}
+
+
+	public static void addTests(TestSuite suite) {
+		suite.addTest(new DisplayQueryTest("testQuery"));
+	}
+
+
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/test/ExecuteQueryTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/ExecuteQueryTest.java	2008-01-24 23:08:36 UTC (rev 1407)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/ExecuteQueryTest.java	2008-01-25 01:16:00 UTC (rev 1408)
@@ -20,6 +20,33 @@
 	
 	public Graph runNodeQuery(QueryTerm qt) throws SQLException, ClassNotFoundException {
 		System.out.println("exec Q: "+qt.toString());
+		Collection<Node> nodes = shard.getNodesByQuery(qt);
+		for (Node n : nodes) {
+			System.out.println(n);
+		}
+		assertTrue(nodes.size() > 0);
+		Graph g = new Graph();
+		g.setNodes(nodes);
+		return g;
+	}
+	public Graph runNodeQuery(QueryTerm qt, String nid) throws SQLException, ClassNotFoundException {
+		System.out.println("exec Q: "+qt.toString());
+		Collection<Node> nodes = shard.getNodesByQuery(qt);
+		boolean matchFound = false;
+		for (Node n : nodes) {
+			System.out.println(n);
+			if (nid == null || n.getId().equals(nid))
+				matchFound = true;
+		}
+		assertTrue(nodes.size() > 0);
+		assertTrue(matchFound);
+		Graph g = new Graph();
+		g.setNodes(nodes);
+		return g;
+	}
+	
+	public Graph old__runNodeQuery(QueryTerm qt) throws SQLException, ClassNotFoundException {
+		System.out.println("exec Q: "+qt.toString());
 		Graph g = shard.getGraphByQuery(qt, null, null);
 		g.nestStatementsUnderNodes();
 		for (Node n : g.getNodes()) {
@@ -32,14 +59,30 @@
 		return g;
 	}
 	
+
 	public Graph runLinkQuery(QueryTerm qt) throws SQLException, ClassNotFoundException {
 		System.out.println("exec Q: "+qt.toString());
 		 Collection<Statement> stmts = shard.getStatementsByQuery(qt);
-		for (Statement s : stmts)
+			for (Statement s : stmts) {
 			System.out.println(" "+s);
+		}
 		assertTrue(stmts.size() > 0);
 		return new Graph(stmts);
 	}
+	public Graph runLinkQuery(QueryTerm qt, Statement matchStmt) throws SQLException, ClassNotFoundException {
+		System.out.println("exec Q: "+qt.toString());
+		 Collection<Statement> stmts = shard.getStatementsByQuery(qt);
+		 boolean matchFound = false;
+		for (Statement s : stmts) {
+			System.out.println(" "+s);
+			if (matchStmt == null || s.toString().equals(matchStmt.toString()) ) {
+				matchFound = true;
+			}
+		}
+		assertTrue(stmts.size() > 0);
+		assertTrue(matchFound);
+		return new Graph(stmts);
+	}
 
 	public Graph runLiteralQuery(QueryTerm qt) throws SQLException, ClassNotFoundException {
 		System.out.println("exec Q: "+qt.toString());

Modified: obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java	2008-01-24 23:08:36 UTC (rev 1407)
+++ obdapi/trunk/OBDAPI/src/org/obd/test/QueryTest.java	2008-01-25 01:16:00 UTC (rev 1408)
@@ -1,5 +1,6 @@
 package org.obd.test;
 
+
 import java.sql.SQLException;
 
 import junit.framework.Test;
@@ -7,13 +8,17 @@
 
 import org.bbop.rdbms.RelationalQuery;
 import org.obd.model.Graph;
+import org.obd.model.LinkStatement;
+import org.obd.model.Statement;
 import org.obd.query.AnnotationLinkQueryTerm;
+import org.obd.query.AtomicQueryTerm;
 import org.obd.query.BooleanQueryTerm;
 import org.obd.query.ComparisonQueryTerm;
 import org.obd.query.LabelQueryTerm;
 import org.obd.query.LinkQueryTerm;
 import org.obd.query.LiteralQueryTerm;
 import org.obd.query.QueryTerm;
+import org.obd.query.SourceQueryTerm;
 import org.obd.query.BooleanQueryTerm.BooleanOperator;
 import org.obd.query.ComparisonQueryTerm.Operator;
 import org.obd.query.LabelQueryTerm.AliasType;
@@ -39,62 +44,203 @@
 	}
 	
 	public void testQuery() throws SQLException, ClassNotFoundException {
-				
+
+		/**
+		 * core set of relations to use to test
+		 */
+		String isA = "OBO_REL:is_a";
 		String partOf = "OBO_REL:part_of";
-		String developsFrom = "OBO_REL:develops_from";
+		String developsFrom = "develops_from";
+
+
+		/**
+		 * which is the source of the COI?
+		 * 
+		 * Label(COI)/SOURCE
+		 */
+		if (true) {
+			QueryTerm srcqt = new LabelQueryTerm("FMA:7088");
+			srcqt.setAspect(Aspect.SOURCE);
+			runNodeQuery(srcqt, "fma");
+		}
+
+		/**
+		 * complex boolean queries
+		 */
+		if (true) {
+
+			/**
+			 * all classes that are subsumed (subclass/isa children) of
+			 * heart OR kidney
+			 */
+			QueryTerm heartOrKidneyQuery =
+				new BooleanQueryTerm( 
+						BooleanOperator.OR,
+						new LinkQueryTerm(isA, "FMA:7088"),
+						new LinkQueryTerm(isA, "FMA:7203"));
+
+			/*
+
+		 QueryTerm heartOrKidneyQuery =
+			new BooleanQueryTerm( 
+					BooleanOperator.OR,
+					new LinkQueryTerm(isA, 
+							new LabelQueryTerm(AliasType.PRIMARY_NAME,"heart")),
+					new LinkQueryTerm(isA, 
+							new LabelQueryTerm(AliasType.PRIMARY_NAME,"kidney")));
+			 */
+
+			runNodeQuery(heartOrKidneyQuery, "FMA:7205"); // left kidney
+
+			QueryTerm sizeOfHeartOrKidneyQuery =
+				new BooleanQueryTerm(
+						BooleanOperator.AND,
+						new LinkQueryTerm(isA,"PATO:0000117"),
+						new LinkQueryTerm(heartOrKidneyQuery));
+
+			runNodeQuery(new AnnotationLinkQueryTerm(sizeOfHeartOrKidneyQuery));
+		}
+
+		/*
+		 * all entities that are part of the nucleus
+		 */
+		if (true) {
+			LinkQueryTerm partOfNucleusQuery = new LinkQueryTerm(partOf, 
+					new LabelQueryTerm(AliasType.ANY_LABEL, "nucleus"));
+			
+			// find the entities themselves
+			runNodeQuery(partOfNucleusQuery);
+			
+			// anything annotated to part-of-nucleus
+			runLinkQuery(new AnnotationLinkQueryTerm(partOfNucleusQuery));
+		}
 		
-		LinkQueryTerm iq = new LinkQueryTerm();
-		iq.setNode("MP:0008324");
-		iq.setAspect(Aspect.TARGET);
-		LinkQueryTerm q = new LinkQueryTerm();
-		q.setInferred(false);
-		q.setNode(iq);
-		runLinkQuery(q);
+		/*
+		 * label queries:
+		 * find all entities with a primary name "eya1"
+		 * (e.g. the eyes absent gene)
+		 * 
+		 */
+		if (true) {
+			LabelQueryTerm labelQuery =
+				new LabelQueryTerm(AliasType.PRIMARY_NAME,
+				"eya1");
+			
+			// matching entities
+			runNodeQuery(labelQuery);		
+			System.exit(0);
+		}
 		
-		runNodeQuery(new LinkQueryTerm(partOf, 
-				new LabelQueryTerm(AliasType.ANY_LABEL, "nucleus")));
-		runNodeQuery(new LabelQueryTerm(AliasType.PRIMARY_NAME,
-				"apoptosis"));
 		runNodeQuery(new LabelQueryTerm(AliasType.ALTERNATE_LABEL,
 				new ComparisonQueryTerm(Operator.STARTS_WITH,
 				"apoptosis")));
-		
+
 		runNodeQuery(new LinkQueryTerm(partOf, "GO:0005634"));
-		runNodeQuery(new LinkQueryTerm(partOf, 
-				new LinkQueryTerm(developsFrom, "CL:1234567")));
-		runNodeQuery(new LinkQueryTerm(partOf, 
-				new BooleanQueryTerm( 
-						BooleanOperator.AND,
-						new LinkQueryTerm(partOf, "GO:0005634"),
-						new LinkQueryTerm(partOf, "GO:0005739")
-						)));
+
+		/*
+		 * find all entities that are part of something that develops from
+		 * the visual primordium
+		 */
+		runNodeQuery(new LinkQueryTerm("part_of", 
+				new LinkQueryTerm("develops_from", "FBbt:00001059")));
+		/*
+		 * all entities that are undifferentiated and trace their
+		 * developmental lineage back to a neurectodermal cell
+		 */
+		QueryTerm cellQuery =
+			new BooleanQueryTerm( 
+					BooleanOperator.AND,
+					new LinkQueryTerm(isA, "CL:0000055"), // non-terminally differentiated cell
+					new LinkQueryTerm(developsFrom, "CL:0000133") // neurectodermal cell
+			);
+		runNodeQuery(cellQuery);
+
+		/*
+		 * all annotations to entities that are undifferentiated and trace their
+		 * developmental lineage back to a neurectodermal cell
+		 */
+		runNodeQuery(new AnnotationLinkQueryTerm(cellQuery));
+
 		runLinkQuery(new LinkQueryTerm(partOf, "GO:0031595")); // nuclear proteasome complex
-		
+
 		// annotations
-		 AnnotationLinkQueryTerm oq = new AnnotationLinkQueryTerm("FMA:54448");
+		AnnotationLinkQueryTerm oq = new AnnotationLinkQueryTerm("FMA:54448");
 		runLinkQuery(oq);
-		
+
 		LiteralQueryTerm litq = new LiteralQueryTerm();
 		litq.setNode("MP:0008246");
 		runLiteralQuery(litq);
-		
-		
 
+		/**
+		 * Finding asserted links in which the link node is subsumed by the COI
+		 * 
+		 * Link(inf=f,node=Link(target=COI))
+		 * 
+		 * link(A,B),implied_link(A,C)
+		 * 
+		 * similar semantics to annotation query
+		 */
+		if (true) {
+			LinkQueryTerm iq = new LinkQueryTerm();
+			iq.setTarget("FMA:7088"); // Heart
+			iq.setQueryAlias("");
+			LinkQueryTerm q1 = new LinkQueryTerm();
+			q1.setInferred(false);
+			q1.setNode(iq);
+			Statement match = new LinkStatement("FMA:9290", "OBO_REL:is_a", "FMA:9721");
+			runLinkQuery(q1, match);
+		}
+
+
+		/**
+		 * Finding asserted links in which the link target subsumes the COI
+		 * [atypical use case]
+		 * 
+		 * Link(inf=f,node=Link(node=COI)/TARGET)
+		 * 
+		 * The aspect (here /TARGET) indicates the context of the
+		 * link query term is such that the target of the link should be used in
+		 * the join to the outer query
+		 * 
+		 * link(A,B),link(C,B)
+		 */
+		if (true) {
+			LinkQueryTerm iq = new LinkQueryTerm();
+			iq.setNode("MP:0008324"); // abnormal melanotroph morphology
+			//iq.setTarget("MP:0008324"); // abnormal melanotroph morphology
+			iq.setAspect(Aspect.TARGET); 
+			iq.setQueryAlias("");
+			LinkQueryTerm q = new LinkQueryTerm();
+			q.setInferred(false);
+			q.setNode(iq);
+			runLinkQuery(q, 
+					new LinkStatement("CL:0000151", "OBO_REL:is_a", "CL:0000144"));
+		}
+
+
+
 	}
 	
 	public Graph runNodeQuery(QueryTerm qt) throws SQLException, ClassNotFoundException {
-		System.out.println("running Q: "+qt.toString());
+		return runNodeQuery(qt,null);
+	}
+	
+	public Graph runNodeQuery(QueryTerm qt, String nid) throws SQLException, ClassNotFoundException {
+		System.out.println("running Q: "+qt.toString()+" Expect: "+nid);
 		OBDSQLShard s = new OBDSQLShard();
 		RelationalQuery rq = s.translateQueryForNode(qt);
 		System.out.println(rq.toString());
 		for (Object v : rq.getPlaceHolderVals())
 			System.out.println(" "+v);
 		return null;
-
 	}
 
 
 	public Graph runLinkQuery(QueryTerm qt) throws SQLException, ClassNotFoundException {
+		return runLinkQuery(qt, null);
+	}
+	
+	public Graph runLinkQuery(QueryTerm qt, Statement stmt) throws SQLException, ClassNotFoundException {
 		System.out.println("running Q: "+qt.toString());
 		OBDSQLShard s = new OBDSQLShard();
 		RelationalQuery rq = s.translateQueryForLink(qt);

Modified: obdapi/trunk/OBDAPI/src/org/obd/ws/pages/UseCase16.ftl
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/pages/UseCase16.ftl	2008-01-24 23:08:36 UTC (rev 1407)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/pages/UseCase16.ftl	2008-01-25 01:16:00 UTC (rev 1408)
@@ -1,6 +1,6 @@
 <#include "PageMacros.ftl"> 
 
-<@page title="Use Case 7: Find similar entities based on annotation profile">
+<@page title="Use Case 16: Aggregate queries">
 
 <@section title="See Also">
 <p>
@@ -8,36 +8,32 @@
 </@section>
 <@section title="Goal">
 <p>
-To obtain similar entities to an entity of interest based on an annotation profile. For example,
-a researcher may be viewing a information on a gene that is implicated in a disease of interested
-(for example, a neurological disease). The gene may be associated with various phenotypes
-observed from a variety of methods at a variety of scales - from the permeability of mitochondrial
-cristae in a certain cell types to organismal/behavioural phenotypes. The goal is to
-find similar entities with similar profiles - these entities may be genes, genotypes, trials,
-individuals in trials, annotated images, publications.
-</p>
-<p>
- It is unlikely that profiles will match identically - the goal is to find a match
- similar to a subset of statistically significant ontological attributes, taking into account
- relations between these attributes. Think match.com or amazon book recommendation, with ontologies
  </p>
  
 </@section>
 
 <@section title="Summary">
 <p>
-The user arrives at an EOI (entity of interest) in BioPortal via search or browsing annotations; see
-<@usecase id="5"/>
-for example they may have arrived at a page showing the <@hrefSearch term="shh"/> (sonic hedgehpog) gene through annotations
-to the ontology class for the disease/phenotype "holoprosencephaly". They see that shh has a long list
-of annotations associated, directly or indirectly. Rather than explore each individually they
-instead choose to find similar entities based on the whole profile.
+<ul>
+<li>
+Total number of annotations for that class (incl or excl closure)
+</li>
+<li>
+Total number of annotations, group by annotations source (ie the organisation submitting the annotation)
+
+</li>
+<li>
+Average number of annotations by annotations source
+</li>
+<li>
+Average number of annotations by ontology and annotations source
+</li>
+<li>
+Total number of annotations by ontology, evidence and species
+</li>
+
+</ul>
 </p>
-<p>
-When they select this option, they see a list of entities together with minimal metadata (type, label, ID)
-plus match/similarity scores. These can be expanded to see the full list of annotations, possibly with
-the similar annotations highlighted.
-<p/>
 
 </@section>
 
@@ -51,10 +47,10 @@
 The following in sequence
 <ul>
 <li>
-User selects EOI within BioPortal (perhaps via some shopping cart)
+User selects COI within BioPortal
 </li>
 <li>
-User asks for all similar entities
+BioPortal shows aggregate statistic
 </li>
 </ul>
 </p>
@@ -64,17 +60,9 @@
 <@section title="Course of events">
 <ul>
 <li>
-User select EOI within BioPortal (perhaps via some shopping cart)
+User select COI within BioPortal
 </li>
 <li>
-User asks for all similar entities
-</li>
-<li>
-presentation layer makes query to OBD REST. URLs loos like:
-   <ul>
-   <li> <@obdurl path="/html/nodes/OMIM:601653.0008/blast"/>an OMIM allele record for eya1</li>
-   <li> <@obdurl path="/html/nodes/ZFIN:ZDB-GENO-980202-1557/blast"/> similar to this eya1 genotype in zfin</li>
-</li>
 </ul>
 </@section>
 

Modified: obdapi/trunk/OBDAPI/src/org/obd/ws/pages/UseCase7.ftl
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/ws/pages/UseCase7.ftl	2008-01-24 23:08:36 UTC (rev 1407)
+++ obdapi/trunk/OBDAPI/src/org/obd/ws/pages/UseCase7.ftl	2008-01-25 01:16:00 UTC (rev 1408)
@@ -1,6 +1,6 @@
 <#include "PageMacros.ftl"> 
 
-<@page title="Use Case 16: Aggregate queries">
+<@page title="Use Case 7: Find similar entities based on annotation profile">
 
 <@section title="See Also">
 <p>
@@ -8,6 +8,18 @@
 </@section>
 <@section title="Goal">
 <p>
+To obtain similar entities to an entity of interest based on an annotation profile. For example,
+a researcher may be viewing a information on a gene that is implicated in a disease of interested
+(for example, a neurological disease). The gene may be associated with various phenotypes
+observed from a variety of methods at a variety of scales - from the permeability of mitochondrial
+cristae in a certain cell types to organismal/behavioural phenotypes. The goal is to
+find similar entities with similar profiles - these entities may be genes, genotypes, trials,
+individuals in trials, annotated images, publications.
+</p>
+<p>
+ It is unlikely that profiles will match identically - the goal is to find a match
+ similar to a subset of statistically significant ontological attributes, taking into account
+ relations between these attributes. Think match.com or amazon book recommendation, with ontologies
  </p>
  
 </@section>


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