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[CIShell-SVN] SF.net SVN: cishell:[907] trunk/core/org.cishell.algorithm.convertergraph
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From: <tan...@us...> - 2009-07-30 16:57:13
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Revision: 907
http://cishell.svn.sourceforge.net/cishell/?rev=907&view=rev
Author: tankchintan
Date: 2009-07-30 16:57:02 +0000 (Thu, 30 Jul 2009)
Log Message:
-----------
Converted the plugin to use jung/graph instead of nwb to resolve the dependency issue, since converter graph is inside the org.cishell package.
Modified Paths:
--------------
trunk/core/org.cishell.algorithm.convertergraph/META-INF/MANIFEST.MF
trunk/core/org.cishell.algorithm.convertergraph/OSGI-INF/algorithm.properties
trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/ConverterGraphAlgorithm.java
trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/ConverterGraphComputation.java
Removed Paths:
-------------
trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/ConverterGraphOutputGenerator.java
trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/Edge.java
trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/Node.java
Modified: trunk/core/org.cishell.algorithm.convertergraph/META-INF/MANIFEST.MF
===================================================================
--- trunk/core/org.cishell.algorithm.convertergraph/META-INF/MANIFEST.MF 2009-07-30 14:48:59 UTC (rev 906)
+++ trunk/core/org.cishell.algorithm.convertergraph/META-INF/MANIFEST.MF 2009-07-30 16:57:02 UTC (rev 907)
@@ -5,8 +5,14 @@
Bundle-Version: 1.0.0
Bundle-ClassPath: .
Bundle-Localization: plugin
-Import-Package: edu.iu.nwb.converter.nwb.common,
- edu.iu.nwb.util.nwbfile,
+Import-Package: edu.uci.ics.jung.graph,
+ edu.uci.ics.jung.graph.decorators,
+ edu.uci.ics.jung.graph.event,
+ edu.uci.ics.jung.graph.filters,
+ edu.uci.ics.jung.graph.filters.impl,
+ edu.uci.ics.jung.graph.impl,
+ edu.uci.ics.jung.graph.predicates,
+ edu.uci.ics.jung.utils,
org.cishell.framework,
org.cishell.framework.algorithm,
org.cishell.framework.data,
Modified: trunk/core/org.cishell.algorithm.convertergraph/OSGI-INF/algorithm.properties
===================================================================
--- trunk/core/org.cishell.algorithm.convertergraph/OSGI-INF/algorithm.properties 2009-07-30 14:48:59 UTC (rev 906)
+++ trunk/core/org.cishell.algorithm.convertergraph/OSGI-INF/algorithm.properties 2009-07-30 16:57:02 UTC (rev 907)
@@ -2,7 +2,7 @@
label=Converter Graph
description=Provides graph of all the converters in the tool.
in_data=null
-out_data=file:text/nwb
+out_data=edu.uci.ics.jung.graph.Graph
service.pid=org.cishell.algorithm.convertergraph.ConverterGraphAlgorithm
remoteable=true
written_in=Java
Modified: trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/ConverterGraphAlgorithm.java
===================================================================
--- trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/ConverterGraphAlgorithm.java 2009-07-30 14:48:59 UTC (rev 906)
+++ trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/ConverterGraphAlgorithm.java 2009-07-30 16:57:02 UTC (rev 907)
@@ -1,13 +1,6 @@
package org.cishell.algorithm.convertergraph;
-import java.io.File;
-import java.io.IOException;
import java.util.Dictionary;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
import org.cishell.framework.CIShellContext;
import org.cishell.framework.algorithm.Algorithm;
@@ -21,9 +14,11 @@
import org.osgi.framework.ServiceReference;
import org.osgi.service.log.LogService;
+import edu.uci.ics.jung.graph.Graph;
+
/**
* This plugin collects information about all the active converters in the tool and
- * outputs a NWB file having this Directed network. Also nodes corresponding to each
+ * outputs a JUNG Graph having this Directed network. Also nodes corresponding to each
* MIME/TYPE are weighted depending upon how many times they participate in a converter
* relationship.
*
@@ -35,7 +30,9 @@
private LogService logger;
private BundleContext bundleContext;
- private int nodeCount, edgeCount;
+ private Graph outputGraph;
+
+ private int nodeCount = 0, edgeCount = 0;
/**
* Construct with the appropriate parameters.
@@ -51,123 +48,25 @@
public Data[] execute() throws AlgorithmExecutionException {
- try {
-
- /*
- * Get all the converter service references currently in service.
- * */
- ServiceReference[] allConverterServices = getAllConverters();
-
- /*
- * Process the references to create a network of weighted nodes & directed edges.
- * */
- ConverterGraphComputation converterGraphComputation =
- new ConverterGraphComputation(allConverterServices, logger);
-
- /*
- * Used to generate the output file containing the network.
- * */
- File outputNWBFile = createOutputGraphFile(converterGraphComputation);
-
- return prepareOutputMetadata(new BasicData(outputNWBFile, "file:text/nwb"));
+ /*
+ * Get all the converter service references currently in service.
+ * */
+ ServiceReference[] allConverterServices = getAllConverters();
- } catch (IOException e) {
- throw new AlgorithmExecutionException(e);
- }
- }
-
- /**
- * Call all the NWB File Handler processes in order to create a NWB file.
- * @param converterGraphComputation
- * @return
- * @throws IOException
- */
- private File createOutputGraphFile(
- ConverterGraphComputation converterGraphComputation)
- throws IOException {
-
- File outputNWBFile = File.createTempFile("nwb-", ".nwb");
-
- ConverterGraphOutputGenerator outputGenerator = new ConverterGraphOutputGenerator(
- converterGraphComputation, outputNWBFile);
-
- outputGenerator.addComment("Graph of all Converters in the Tool.");
-
- nodeCount = converterGraphComputation.nodes.size();
- outputGenerator.setNodeCount(nodeCount);
-
- outputGenerator.setNodeSchema(converterGraphComputation.nodeSchema);
-
- /*
- * Print all the node rows to the output file.
- * */
- setNodeTuples(converterGraphComputation, outputGenerator);
-
- edgeCount = converterGraphComputation.edges.size();
- outputGenerator.setDirectedEdgeCount(edgeCount);
-
- outputGenerator.setDirectedEdgeSchema(converterGraphComputation.edgeSchema);
-
- /*
- * Print all the edge rows to the output file.
- * */
- setDirectedEdgeTuples(converterGraphComputation, outputGenerator);
-
- outputGenerator.finishedParsing();
- outputGenerator.haltParsingNow();
- return outputNWBFile;
- }
-
- /**
- * Iterate through the nodes and print it into the output file.
- * @param converterGraphComputation
- * @param outputGenerator
- */
- private void setDirectedEdgeTuples(
- ConverterGraphComputation converterGraphComputation,
- ConverterGraphOutputGenerator outputGenerator) {
-
- for (Iterator edgeIterator = converterGraphComputation.edges.iterator();
- edgeIterator.hasNext();) {
+ /*
+ * Process the references to create a network of weighted nodes & directed edges.
+ * */
+ ConverterGraphComputation converterGraphComputation =
+ new ConverterGraphComputation(allConverterServices, logger);
- Edge edge = (Edge) edgeIterator.next();
- int sourceNode = edge.source;
- int targetNode = edge.target;
- final String converterName = edge.serviceShortPID;
- final String servicePID = edge.serviceCompletePID;
-
- outputGenerator.addDirectedEdge(sourceNode, targetNode, new HashMap() {{
- put("converter_name", converterName);
- put("service_pid", servicePID);
- }});
- }
+ /*
+ * Used to generate the output reference for graph containing the network.
+ * */
+ return prepareOutputMetadata(new BasicData(converterGraphComputation.getOutputGraph(),
+ Graph.class.getName()));
}
/**
- * @param converterGraphComputation
- * @param outputGenerator
- */
- private void setNodeTuples(
- ConverterGraphComputation converterGraphComputation,
- ConverterGraphOutputGenerator outputGenerator) {
-
- for (Iterator nodeIterator = converterGraphComputation.nodes.entrySet().iterator();
- nodeIterator.hasNext();) {
-
- Map.Entry node = (Entry) nodeIterator.next();
-
- int nodeID = ((Node) node.getValue()).id;
- final int strength = ((Node) node.getValue()).strength;
- String label = node.getKey().toString();
-
- outputGenerator.addNode(nodeID, label, new HashMap() {{
- put("strength", strength);
- }});
- }
- }
-
-
- /**
* Gets all the converter service references based on the LDAP query.
* @return
*/
@@ -199,8 +98,10 @@
* @param outNWBData
*/
private Data[] prepareOutputMetadata(Data outNWBData) {
+
outNWBData.getMetadata().put(DataProperty.LABEL, "Converter Graph having "
- + nodeCount + " nodes & " + edgeCount + " edges.");
+ + ((Graph) outNWBData.getData()).numVertices() + " nodes & "
+ + ((Graph) outNWBData.getData()).numEdges() + " edges.");
outNWBData.getMetadata().put(DataProperty.TYPE, DataProperty.NETWORK_TYPE);
return new Data[]{outNWBData};
}
Modified: trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/ConverterGraphComputation.java
===================================================================
--- trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/ConverterGraphComputation.java 2009-07-30 14:48:59 UTC (rev 906)
+++ trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/ConverterGraphComputation.java 2009-07-30 16:57:02 UTC (rev 907)
@@ -3,41 +3,44 @@
*/
package org.cishell.algorithm.convertergraph;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Set;
import org.osgi.framework.ServiceReference;
import org.osgi.service.log.LogService;
-import edu.iu.nwb.util.nwbfile.NWBFileProperty;
+import edu.uci.ics.jung.graph.Edge;
+import edu.uci.ics.jung.graph.Graph;
+import edu.uci.ics.jung.graph.Vertex;
+import edu.uci.ics.jung.graph.impl.DirectedSparseEdge;
+import edu.uci.ics.jung.graph.impl.DirectedSparseGraph;
+import edu.uci.ics.jung.graph.impl.DirectedSparseVertex;
+import edu.uci.ics.jung.utils.UserDataContainer;
/**
* The algorithm is used for getting information about current converters is,
* 1. Get all the service references for converters in the system.
- * 2. Create Node Schema to be used when constructing the NWB file. In this case
- * it will be,
+ * 2. Node Schema to be used is,
* id*int, label*string, strength*int
- * 3. Create Edge Schema to be used when constructing the NWB file. In this case
- * it will be,
+ * 3. Edge Schema to be used is,
* source*int, target*int, converter_name*string, service_pid*string
* 4. Iterate over all the converter service reference one at a time.
* 5. For collecting information for Nodes do,
* (a). Get node label using service properties in_data & out_data.
- * (b). Check to see if this node is already present in the nodes map.
+ * (b). Check to see if this node is already present in the nodeLabels set.
* (c). If it is present then just update the strength of node by incrementing
* that node's strength by 1.
* (d). Else create a new node. Provide it a default strength of 1 and update
- * the node count.
+ * the node count. Also create an entry in the nodeLabels for future
+ * reference.
* 6. For collecting information about Edges do,
- * (a). Get the respective source & target node ids from the recently updates
- * respective nodes.
+ * (a). Get the respective source & target node references from the recently updated
+ * nodes.
* (b). Get the service_pid by using service property service.pid.
* (c). Get the converter_name by extracting the last block from service_pid.
- * 7. These information is then passed on to {@link ConverterGraphOutputGenerator}
- * for printing it into a NWB file.
+ * 7. Since the graph is being created during the processing of each node & edge
+ * it just needs to be referenced on the UI. This is done by outputting the metadata.
*
* @author cdtank
*
@@ -47,12 +50,17 @@
private LogService logger;
private ServiceReference[] allConverterServices;
- public Map nodes = new HashMap();
- public LinkedHashMap nodeSchema = new LinkedHashMap();
+ private Set nodeLabels = new HashSet();
- public List edges = new ArrayList();
- public LinkedHashMap edgeSchema = new LinkedHashMap();
+ private Graph outputGraph;
+ /**
+ * @return the outputGraph
+ */
+ public Graph getOutputGraph() {
+ return outputGraph;
+ }
+
private int nodeCount;
public ConverterGraphComputation(ServiceReference[] allConverterServices,
@@ -61,38 +69,14 @@
this.nodeCount = 0;
this.logger = logger;
this.allConverterServices = allConverterServices;
+ this.outputGraph = new DirectedSparseGraph();
/*
- * Side affects nodeSchema
- * */
- createNodeSchema();
-
- /*
- * Side affects edgeSchema
- * */
- createEdgeSchema();
-
- /*
* Side affects nodes & edges
* */
processServiceReferences();
}
- private void createNodeSchema() {
- nodeSchema.put("id", NWBFileProperty.TYPE_INT);
- nodeSchema.put("label", NWBFileProperty.TYPE_STRING);
- nodeSchema.put("strength", NWBFileProperty.TYPE_INT);
- }
-
- private void createEdgeSchema() {
- edgeSchema.put("source", NWBFileProperty.TYPE_INT);
- edgeSchema.put("target", NWBFileProperty.TYPE_INT);
- edgeSchema.put("converter_name", NWBFileProperty.TYPE_STRING);
- edgeSchema.put("service_pid", NWBFileProperty.TYPE_STRING);
- }
-
-
-
/*
* Iterate over all the converter service references and process the
* information to get nodes & edges.
@@ -103,7 +87,7 @@
converterCount < allConverterServices.length;
converterCount++) {
- int sourceNodeID, targetNodeID;
+ Vertex sourceNode, targetNode;
ServiceReference currentConverterServiceReference =
allConverterServices[converterCount];
@@ -113,47 +97,61 @@
String targetNodeKey =
(String) currentConverterServiceReference.getProperty("out_data");
- if (nodes.containsKey(sourceNodeKey)) {
- sourceNodeID = updateNode(sourceNodeKey);
+ if (nodeLabels.contains(sourceNodeKey)) {
+ sourceNode = updateNode(sourceNodeKey);
} else {
- sourceNodeID = createNode(sourceNodeKey);
+ sourceNode = createNode(sourceNodeKey);
}
- if (nodes.containsKey(targetNodeKey)) {
- targetNodeID = updateNode(targetNodeKey);
+ if (nodeLabels.contains(targetNodeKey)) {
+ targetNode = updateNode(targetNodeKey);
} else {
- targetNodeID = createNode(targetNodeKey);
+ targetNode = createNode(targetNodeKey);
}
- createEdge(sourceNodeID, targetNodeID, currentConverterServiceReference);
+ createEdge(sourceNode, targetNode, currentConverterServiceReference);
}
}
- private int updateNode(String currentNodeKey) {
- int sourceNodeID;
- Node sourceNodeValue = (Node) nodes.get(currentNodeKey);
- sourceNodeID = sourceNodeValue.id;
- sourceNodeValue.strength += 1;
- return sourceNodeID;
+ private Vertex updateNode(String currentNodeKey) {
+
+ for (Iterator nodeIterator = outputGraph.getVertices().iterator();
+ nodeIterator.hasNext();) {
+ Vertex currentVertex = (Vertex) nodeIterator.next();
+ if (currentVertex.getUserDatum("label").toString()
+ .equalsIgnoreCase(currentNodeKey)) {
+ int currentVertexStrength =
+ ((Integer) currentVertex.getUserDatum("strength")).intValue();
+ currentVertex.setUserDatum("strength", ++currentVertexStrength,
+ new UserDataContainer.CopyAction.Shared());
+ return currentVertex;
+ }
+ }
+ return new DirectedSparseVertex();
}
- private int createNode(String nodeKey) {
+ private Vertex createNode(String nodeKey) {
nodeCount++;
- Node nodeValue = new Node();
- nodeValue.id = nodeCount;
- nodeValue.strength = 1;
- nodes.put(nodeKey, nodeValue);
- return nodeCount;
+ Vertex node = new DirectedSparseVertex();
+
+ node.addUserDatum("id", nodeCount, new UserDataContainer.CopyAction.Shared());
+ node.addUserDatum("strength", 1, new UserDataContainer.CopyAction.Shared());
+ node.addUserDatum("label", nodeKey, new UserDataContainer.CopyAction.Shared());
+
+ outputGraph.addVertex(node);
+ nodeLabels.add(nodeKey);
+
+ return node;
}
/**
* Create an edge based on source id, target id & other information.
- * @param sourceNodeID
- * @param targetNodeID
+ * @param sourceNode
+ * @param targetNode
* @param currentConverterServiceReference
*/
- private void createEdge(int sourceNodeID, int targetNodeID,
+ private void createEdge(Vertex sourceNode, Vertex targetNode,
ServiceReference currentConverterServiceReference) {
String serviceCompletePID =
(String) currentConverterServiceReference.getProperty("service.pid");
@@ -166,15 +164,16 @@
String serviceShortPID = serviceCompletePID.substring(startIndexForConverterName);
/*
- * Build the actual edge tuple.
+ * Build the actual edge & attach it to the graph.
* */
- Edge edge = new Edge();
- edge.source = sourceNodeID;
- edge.target = targetNodeID;
- edge.serviceShortPID = serviceShortPID;
- edge.serviceCompletePID = serviceCompletePID;
+ Edge edge = new DirectedSparseEdge(sourceNode, targetNode);
- edges.add(edge);
+ edge.addUserDatum("converter_name", serviceShortPID,
+ new UserDataContainer.CopyAction.Shared());
+ edge.addUserDatum("service_pid", serviceCompletePID,
+ new UserDataContainer.CopyAction.Shared());
+
+ outputGraph.addEdge(edge);
}
}
Deleted: trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/ConverterGraphOutputGenerator.java
===================================================================
--- trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/ConverterGraphOutputGenerator.java 2009-07-30 14:48:59 UTC (rev 906)
+++ trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/ConverterGraphOutputGenerator.java 2009-07-30 16:57:02 UTC (rev 907)
@@ -1,62 +0,0 @@
-package org.cishell.algorithm.convertergraph;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.LinkedHashMap;
-import java.util.Map;
-
-import edu.iu.nwb.util.nwbfile.NWBFileParserHandler;
-import edu.iu.nwb.util.nwbfile.NWBFileWriter;
-
-public class ConverterGraphOutputGenerator implements NWBFileParserHandler {
-
- private NWBFileWriter output;
-
- public ConverterGraphOutputGenerator(ConverterGraphComputation converterGraphComputation,
- File outputNWBFile) throws IOException {
- output = new NWBFileWriter(outputNWBFile);
- }
-
- public void setNodeCount(int numberOfNodes) {
- output.setNodeCount(numberOfNodes);
- }
-
- public void setNodeSchema(LinkedHashMap schema) {
- output.setNodeSchema(schema);
- }
-
- public void addNode(int id, String label, Map attributes) {
- output.addNode(id, label, attributes);
- }
-
- public void addDirectedEdge(int sourceNode, int targetNode, Map attributes) {
- output.addDirectedEdge(sourceNode, targetNode, attributes);
- }
- public void addUndirectedEdge(int node1, int node2, Map attributes) {
- output.addUndirectedEdge(node1, node2, attributes);
- }
- public void setDirectedEdgeCount(int numberOfEdges) {
- output.setDirectedEdgeCount(numberOfEdges);
- }
- public void setDirectedEdgeSchema(LinkedHashMap schema) {
- output.setDirectedEdgeSchema(schema);
- }
- public void setUndirectedEdgeCount(int numberOfEdges) {
- output.setUndirectedEdgeCount(numberOfEdges);
- }
- public void setUndirectedEdgeSchema(LinkedHashMap schema) {
- output.setUndirectedEdgeSchema(schema);
- }
-
- public void addComment(String comment) {
- output.addComment(comment);
- }
-
- public void finishedParsing() {
- output.finishedParsing();
- }
-
- public boolean haltParsingNow() {
- return false;
- }
-}
Deleted: trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/Edge.java
===================================================================
--- trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/Edge.java 2009-07-30 14:48:59 UTC (rev 906)
+++ trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/Edge.java 2009-07-30 16:57:02 UTC (rev 907)
@@ -1,8 +0,0 @@
-package org.cishell.algorithm.convertergraph;
-
-public class Edge {
- public int source;
- public int target;
- public String serviceShortPID;
- public String serviceCompletePID;
-}
\ No newline at end of file
Deleted: trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/Node.java
===================================================================
--- trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/Node.java 2009-07-30 14:48:59 UTC (rev 906)
+++ trunk/core/org.cishell.algorithm.convertergraph/src/org/cishell/algorithm/convertergraph/Node.java 2009-07-30 16:57:02 UTC (rev 907)
@@ -1,13 +0,0 @@
-/**
- *
- */
-package org.cishell.algorithm.convertergraph;
-
-/**
- * @author cdtank
- *
- */
-public class Node {
- public int id;
- public int strength;
-}
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