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Changeset 2402

Timestamp:

08/12/08 14:05:09 (3 months ago)

Author:

kelleyt

Message:

added progresstrackable to the extract x-type network algorithms. Need to create real .properties files for the extract author-paper network algorithm

Files:

Legend:

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: Added
: Removed
: Modified
: Copied
: Moved

trunk/plugins/analysis/edu.iu.nwb.analysis.extractcoauthorship/src/edu/iu/nwb/analysis/extractcoauthorship/algorithms/ExtractAlgorithm.java

r2246	r2402
10	10	import org.cishell.framework.algorithm.Algorithm;
11	11	import org.cishell.framework.algorithm.AlgorithmExecutionException;
	12	import org.cishell.framework.algorithm.ProgressMonitor;
	13	import org.cishell.framework.algorithm.ProgressTrackable;
12	14	import org.cishell.framework.data.BasicData;
13	15	import org.cishell.framework.data.Data;
…	…
16	18
17	19	import edu.iu.nwb.analysis.extractcoauthorship.metadata.SupportedFileTypes;
18		~~import edu.iu.nwb.analysis.extractcoauthorship.metadata.SupportedFileTypes.CitationFormat;~~
19	20	import edu.iu.nwb.analysis.extractnetfromtable.components.ExtractNetworkFromTable;
20	21	import edu.iu.nwb.analysis.extractnetfromtable.components.GraphContainer;
21	22	import edu.iu.nwb.analysis.extractnetfromtable.components.InvalidColumnNameException;
22	23
23		public class ExtractAlgorithm implements Algorithm, SupportedFileTypes {
	24	public class ExtractAlgorithm implements Algorithm, SupportedFileTypes,ProgressTrackable {
24	25	Data[] data;
25	26	Dictionary parameters;
26	27	CIShellContext ciContext;
27	28	LogService logger;
	29	ProgressMonitor progressMonitor;
	30
	31	public ProgressMonitor getProgressMonitor() {
	32	// TODO Auto-generated method stub
	33	return this.progressMonitor;
	34	}
	35
	36	public void setProgressMonitor(ProgressMonitor monitor) {
	37	this.progressMonitor = monitor;
	38
	39	}
28	40
29	41	public ExtractAlgorithm(Data[] dm, Dictionary parameters,
…	…
57	69	try{
58	70	String authorColumn = CitationFormat.getAuthorColumnByName(fileFormat);
59		GraphContainer gc = GraphContainer.initializeGraph(dataTable, authorColumn, authorColumn, false, metaData, this.logger);
	71	GraphContainer gc = GraphContainer.initializeGraph(dataTable, authorColumn, authorColumn, false, metaData, this.logger,this.progressMonitor);
60	72	final prefuse.data.Graph outputGraph = gc.buildGraph(authorColumn, authorColumn, "\|", this.logger);
61	73	final Data outputData1 = new BasicData(outputGraph,

trunk/plugins/analysis/edu.iu.nwb.analysis.extractcoauthorship/src/edu/iu/nwb/analysis/extractcoauthorship/algorithms/ExtractAlgorithmFactory.java

r2207	r2402
36	36
37	37	String[] supportedFormats = SupportedFileTypes.supportedFormats;
38
39		~~for(int i = 0; i < supportedFormats.length; i++){~~
40		~~System.out.println(supportedFormats[i]);~~
41		}
42	38
43	39	definition.addAttributeDefinition(ObjectClassDefinition.REQUIRED,

trunk/plugins/analysis/edu.iu.nwb.analysis.extractcoauthorship/src/edu/iu/nwb/analysis/extractcoauthorship/metadata/SupportedFileTypes.java

r2207	r2402
12	12
13	13	public class CitationFormat{
14		~~String name;~~
15		~~String authorColumn;~~
16	14	private static HashMap nameToColumn = new HashMap();
17	15
18	16	public CitationFormat(String name, String authorColumn){
19		this.name = name;
20		this.authorColumn = authorColumn;
21		CitationFormat.nameToColumn.put(this.name, this.authorColumn);
	17	CitationFormat.nameToColumn.put(name, authorColumn);
22	18	}
23	19
24		~~public String getName(){~~
25		~~return this.name;~~
26		}
27
28		~~public String getAuthorColumn(){~~
29		~~return this.authorColumn;~~
30		}
31
32	20	public static String getAuthorColumnByName(String name){
33	21	return CitationFormat.nameToColumn.get(name).toString();

trunk/plugins/analysis/edu.iu.nwb.analysis.extractdirectednetfromtable/src/edu/iu/nwb/analysis/extractdirectednetfromtable/algorithms/ExtractDirectedNetworkAlgorithm.java

r2245	r2402
7	7	import org.cishell.framework.algorithm.Algorithm;
8	8	import org.cishell.framework.algorithm.AlgorithmExecutionException;
	9	import org.cishell.framework.algorithm.ProgressMonitor;
	10	import org.cishell.framework.algorithm.ProgressTrackable;
9	11	import org.cishell.framework.data.BasicData;
10	12	import org.cishell.framework.data.Data;
…	…
17	19	import edu.iu.nwb.analysis.extractnetfromtable.components.PropertyHandler;
18	20
19		public class ExtractDirectedNetworkAlgorithm implements Algorithm {
	21	public class ExtractDirectedNetworkAlgorithm implements Algorithm, ProgressTrackable {
20	22	Data[] data;
21	23	Dictionary parameters;
22	24	CIShellContext context;
23	25	LogService logger;
	26	ProgressMonitor progressMonitor;
24	27
25		public ExtractDirectedNetworkAlgorithm(Data[] data, Dictionary parameters, CIShellContext context) {
	28
	29
	30	public ProgressMonitor getProgressMonitor() {
	31	// TODO Auto-generated method stub
	32	return this.progressMonitor;
	33	}
	34
	35	public void setProgressMonitor(ProgressMonitor monitor) {
	36	this.progressMonitor = monitor;
	37	}
	38
	39	public ExtractDirectedNetworkAlgorithm(Data[] data, Dictionary parameters, CIShellContext context) {
26	40	this.data = data;
27	41	this.parameters = parameters;
…	…
49	63
50	64	try{
51		GraphContainer gc = GraphContainer.initializeGraph(dataTable, sourceColumn, targetColumn, true,functions, this.logger);
	65	GraphContainer gc = GraphContainer.initializeGraph(dataTable, sourceColumn, targetColumn, true,functions, this.logger,this.progressMonitor);
52	66	Graph directedNetwork = gc.buildGraph(sourceColumn, targetColumn, split, this.logger);
53	67

trunk/plugins/analysis/edu.iu.nwb.analysis.extractnetfromtable/src/edu/iu/nwb/analysis/extractnetfromtable/components/GraphContainer.java

r2251	r2402
8	8	import java.util.regex.Pattern;
9	9
	10	import org.cishell.framework.algorithm.ProgressMonitor;
10	11	import org.osgi.service.log.LogService;
11	12
…	…
22	23	private AggregateFunctionMappings nodeMap;
23	24	private AggregateFunctionMappings edgeMap;
	25	private ProgressMonitor progMonitor = null;
24	26
25	27	public GraphContainer(Graph g, Table t, AggregateFunctionMappings nodeFunctionMap, AggregateFunctionMappings edgeFunctionMap){
…	…
30	32	}
31	33
	34	public GraphContainer(Graph g, Table t, AggregateFunctionMappings nodeFunctionMap, AggregateFunctionMappings edgeFunctionMap, ProgressMonitor pm){
	35	this.graph = g;
	36	this.table = t;
	37	this.nodeMap = nodeFunctionMap;
	38	this.edgeMap = edgeFunctionMap;
	39	this.progMonitor = pm;
	40	}
	41
32	42	public Graph buildGraph(String sourceColumnName, String targetColumnName, String splitString, LogService log){
33	43	if(this.graph.isDirected()){
…	…
37	47	}
38	48	}
39
	49
40	50	private Graph buildUndirectedGraph(String sourceColumnName, String targetColumnName, String splitString, LogService log){
41	51	boolean dupValues = false;
42	52	final HashMap dupValuesErrorMessages = new HashMap();
43
44
45
	53	int rows = this.table.getRowCount();
	54	int count = 0;
	55
	56	if(this.progMonitor != null){
	57	this.progMonitor.start(ProgressMonitor.WORK_TRACKABLE, rows);
	58	}
	59
46	60	for (Iterator it = this.table.rows(); it.hasNext();){
47	61	Node node1 = null;
…	…
65	79	if(seenObject.add(objects[j])){ //no duplicate nodes.
66	80	node2 = NodeContainer.mutateNode(objects[j], this.graph, this.table, row, this.nodeMap, AggregateFunctionMappings.SOURCEANDTARGET);
67
	81
68	82	}
69	83	//create or modify an edge as necessary
…	…
87	101	//ExtractNetworkFromTable.printNoValueToExtractError(title, columnName, this.log);
88	102	}
	103	count = count+1;
	104	if(this.progMonitor != null)
	105	this.progMonitor.worked(count);
	106
89	107	}
90	108	for(Iterator dupIter = dupValuesErrorMessages.keySet().iterator(); dupIter.hasNext();){
91	109	log.log(LogService.LOG_WARNING, (String)dupValuesErrorMessages.get(dupIter.next()));
92	110	}
93
	111
94	112	return this.graph;
95	113	}
96
	114
97	115	private Graph buildDirectedGraph(String sourceColumnName, String targetColumnName, String splitString, LogService log){
98	116	final Pattern p = Pattern.compile("\\Q" + splitString + "\\E");
…	…
102	120	Node node1;
103	121	Node node2;
	122
	123	int rows = this.table.getRowCount();
	124	int count = 0;
	125
	126	if(this.progMonitor != null){
	127	this.progMonitor.start(ProgressMonitor.WORK_TRACKABLE, rows);
	128	}
	129
104	130	for (Iterator it = this.table.rows(); it.hasNext();){
105	131
…	…
119	145	if(seenSource.add(sources[i])){
120	146	node1 = NodeContainer.mutateNode(sources[i],this.graph,this.table,row,this.nodeMap,AggregateFunctionMappings.SOURCE);
121		seenTarget = new HashSet();
122
	147	seenTarget = new HashSet();
	148
123	149	for (int j = 0; j < targets.length; j++) {
124		if(seenTarget.add(targets[j])){
125		node2 = NodeContainer.mutateNode(targets[j],this.graph,this.table,row,this.nodeMap,AggregateFunctionMappings.TARGET);
126
127		EdgeContainer.mutateEdge(node1,node2,this.graph,this.table,row,this.edgeMap);
	150	if(seenTarget.add(targets[j])){
	151	node2 = NodeContainer.mutateNode(targets[j],this.graph,this.table,row,this.nodeMap,AggregateFunctionMappings.TARGET);
	152
	153	EdgeContainer.mutateEdge(node1,node2,this.graph,this.table,row,this.edgeMap);
128	154	}
129	155	}
130	156	}
131	157	}
132		}
133		else{
	158	}
	159	else{
134	160	//String title = (String)pdt.get(row,pdt.getColumnNumber("TI"));
135	161	String title = "unknown";
136	162	//ExtractNetworkFromTable.printNoValueToExtractError(title, sourceColumnName, log);
137	163	}
	164	count = count+1;
	165	if(this.progMonitor != null)
	166	this.progMonitor.worked(count);
138	167	}
139	168	for(Iterator dupIter = dupValuesErrorMessages.keySet().iterator(); dupIter.hasNext();){
…	…
144	173	return this.graph;
145	174	}
146
	175
147	176	public static GraphContainer initializeGraph(Table pdt,String sourceColumnName, String targetColumnName, boolean isDirected,Properties p, LogService log) throws InvalidColumnNameException{
148	177
…	…
151	180	if(inputSchema.getColumnIndex(sourceColumnName) < 0)
152	181	throw new InvalidColumnNameException(sourceColumnName + " was not a column in this table.\n");
153
	182
154	183	if(inputSchema.getColumnIndex(targetColumnName) < 0)
155	184	throw new InvalidColumnNameException(targetColumnName + " was not a column in this table.\n");
…	…
157	186	Schema nodeSchema = createNodeSchema();
158	187	Schema edgeSchema = createEdgeSchema();
159
	188
160	189	AggregateFunctionMappings nodeAggregateFunctionMap = new AggregateFunctionMappings();
161	190	AggregateFunctionMappings edgeAggregateFunctionMap = new AggregateFunctionMappings();
162
	191
163	192	AggregateFunctionMappings.parseProperties(inputSchema, nodeSchema, edgeSchema, p,
164	193	nodeAggregateFunctionMap, edgeAggregateFunctionMap, log);
…	…
166	195	Graph outputGraph = new Graph(nodeSchema.instantiate(),
167	196	edgeSchema.instantiate(), isDirected);
168
169
	197
	198
170	199
171	200	return new GraphContainer(outputGraph,pdt,nodeAggregateFunctionMap,edgeAggregateFunctionMap);
	201
	202	}
	203
	204	public static GraphContainer initializeGraph(Table pdt,String sourceColumnName, String targetColumnName, boolean isDirected,Properties p, LogService log, ProgressMonitor pm) throws InvalidColumnNameException{
	205
	206	final Schema inputSchema = pdt.getSchema();
	207
	208	if(inputSchema.getColumnIndex(sourceColumnName) < 0)
	209	throw new InvalidColumnNameException(sourceColumnName + " was not a column in this table.\n");
	210
	211	if(inputSchema.getColumnIndex(targetColumnName) < 0)
	212	throw new InvalidColumnNameException(targetColumnName + " was not a column in this table.\n");
	213
	214	Schema nodeSchema = createNodeSchema();
	215	Schema edgeSchema = createEdgeSchema();
	216
	217	AggregateFunctionMappings nodeAggregateFunctionMap = new AggregateFunctionMappings();
	218	AggregateFunctionMappings edgeAggregateFunctionMap = new AggregateFunctionMappings();
	219
	220	AggregateFunctionMappings.parseProperties(inputSchema, nodeSchema, edgeSchema, p,
	221	nodeAggregateFunctionMap, edgeAggregateFunctionMap, log);
	222
	223	Graph outputGraph = new Graph(nodeSchema.instantiate(),
	224	edgeSchema.instantiate(), isDirected);
	225
	226
	227
	228	return new GraphContainer(outputGraph,pdt,nodeAggregateFunctionMap,edgeAggregateFunctionMap,pm);
172	229
173	230	}

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