private void extractNetworks(InputStream is, String entryName) throws Exception {
CyNetworkReader reader = networkReaderMgr.getReader(is, entryName);
reader.run(taskMonitor);
final CyNetwork[] netArray = reader.getNetworks();
for (final CyNetwork net : netArray) {
// Add its root-network to the lookup map first
final CyRootNetwork rootNet = rootNetworkManager.getRootNetwork(net);
if (!networkLookup.containsKey(rootNet.getSUID())) ;
networkLookup.put(rootNet.getSUID(), rootNet);
networkLookup.put(net.getSUID(), net);
networks.add(net); // Note: do NOT add the root-network to this set!
}
}
/** Executes Task. */
public void run(TaskMonitor taskMonitor) throws Exception {
taskMonitor.setTitle("Loading Network");
taskMonitor.setProgress(0);
taskMonitor.setStatusMessage("Reading in Network Data...");
try {
CyNetworkReaderManager readerManager = factory.getCyNetworkViewReaderManager();
CyNetworkReader reader = readerManager.getReader(url.toURI(), url.getFile());
if (reader == null) {
JOptionPane.showMessageDialog(
factory.getCySwingApplication().getJFrame(),
"Unable to connect to URL " + url,
"URL Connect Error",
JOptionPane.ERROR_MESSAGE);
return;
}
taskMonitor.setStatusMessage("Creating Cytoscape Network...");
reader.run(taskMonitor);
CyNetwork[] networks = reader.getNetworks();
CyNetwork cyNetwork = networks[0];
// TODO: Does CPath2 listen for this?
// Object[] ret_val = new Object[2];
// ret_val[0] = cyNetwork;
// ret_val[1] = url.toString();
//
// Cytoscape.firePropertyChange(Cytoscape.NETWORK_LOADED, null, ret_val);
if (cyNetwork != null) {
informUserOfGraphStats(cyNetwork, taskMonitor);
} else {
StringBuffer sb = new StringBuffer();
sb.append("Could not read network from: ");
sb.append(url);
sb.append("\nThis file may not be a valid file format.");
throw new IOException(sb.toString());
}
taskMonitor.setProgress(1.0);
} catch (Exception e) {
throw new Exception("Unable to load network.", e);
}
}
private void extractNetworkView(InputStream is, String entryName) throws Exception {
// Get the token which identifies the network
Matcher matcher = NETWORK_VIEW_PATTERN.matcher(entryName);
Long oldNetId = null;
if (matcher.matches()) {
String netViewToken = matcher.group(2);
matcher = NETWORK_VIEW_NAME_PATTERN.matcher(netViewToken);
if (matcher.matches()) {
try {
oldNetId = Long.valueOf(matcher.group(1));
} catch (NumberFormatException nfe) {
logger.error("Cannot extract network view SUID from: " + netViewToken);
}
}
}
if (oldNetId != null) {
final CyNetwork network = cache.getNetwork(oldNetId);
if (network != null && !cancelled) {
// Create the view
final CyNetworkReader reader = networkReaderMgr.getReader(is, entryName);
reader.run(taskMonitor);
final CyNetworkView view = reader.buildCyNetworkView(network);
networkViews.add(view);
// Get its visual style name
if (reader instanceof SessionXGMMLNetworkViewReader) {
final String vsName = ((SessionXGMMLNetworkViewReader) reader).getVisualStyleName();
if (vsName != null && !vsName.isEmpty()) this.visualStyleMap.put(view, vsName);
}
}
} else {
logger.error(
"The network view will cannot be recreated. The network view entry is invalid: "
+ entryName);
}
}
/*
* (non-Javadoc)
*
* @see cytoscape.util.SwingWorker#construct()
*/
@Override
public Object construct() {
progress = 0;
for (final File inputFile : inputFiles) {
// Make a new network in cytoscape from a filename in
// the network-directory
CyNetwork network = null;
try {
write(Messages.SM_LOADING + inputFile.getName() + " ... ");
if (!inputFile.isFile()) {
throw new RuntimeException();
}
CyNetworkReader reader =
cyNetworkViewReaderMgr.getReader(inputFile.toURI(), inputFile.getName());
try {
// TODO Use the Task's task monitor
reader.run(new SampleTaskMonitor());
} catch (Exception ex) {
return null;
}
network = reader.getNetworks()[0];
network.getRow(network).set(CyNetwork.NAME, inputFile.getName());
} catch (RuntimeException e) {
writeLine(Messages.SM_READERROR);
reports.add(new NetworkAnalysisReport(inputFile, null, AnalysisError.NETWORK_NOT_OPENED));
progress += PROGRESS_PER_NET;
continue;
}
// Get all possible interpretations for the network
NetworkInspection inspection = null;
try {
inspection = CyNetworkUtils.inspectNetwork(network);
} catch (IllegalArgumentException e) {
writeLine(Messages.SM_DONE);
reports.add(new NetworkAnalysisReport(inputFile, null, AnalysisError.NETWORK_EMPTY));
unloadNetwork(inputFile, network);
continue;
} catch (NullPointerException e) {
reports.add(new NetworkAnalysisReport(inputFile, null, AnalysisError.NETWORK_FILE_INVALID));
progress += PROGRESS_PER_NET;
continue;
}
final NetworkInterpretation[] interprs =
filterInterpretations(getInterpretations(inspection));
final int intCount = interprs.length;
final int advance = PROGRESS_PER_NET / intCount;
// Run NetworkAnalyzer on all accepted interpretations
writeLine(Messages.SM_DONE);
for (int j = 0; j < intCount; progress += advance, ++j) {
if (cancelled) {
writeLine(Messages.SM_ANALYSISC);
return null;
}
// Run the analysis for an interpretation
final NetworkInterpretation interpretation = interprs[j];
try {
if (interpretation.isDirected()) {
analyzer = new DirNetworkAnalyzer(network, null, interpretation);
} else {
analyzer = new UndirNetworkAnalyzer(network, null, interpretation);
}
writeLine(
Messages.DI_ANALYZINGINTERP1 + (j + 1) + Messages.DI_ANALYZINGINTERP2 + intCount);
final int maxProgress = analyzer.getMaxProgress();
scale = (double) advance / (double) maxProgress;
analyzing = true;
subProgress = 0;
analyzer.computeAll();
analyzing = false;
if (cancelled) {
writeLine(Messages.SM_ANALYSISC);
return null;
}
final NetworkStats stats = analyzer.getStats();
synchronized (this) {
analyzer = null;
}
final String networkName = network.getRow(network).get("name", String.class);
stats.setTitle(networkName + interpretation.getInterpretSuffix());
final String extendedName = networkName + createID(interpretation);
try {
if (SettingsSerializer.getPluginSettings().getUseNodeAttributes()) {
if (!saveNodeAttributes(
network, interpretation.isDirected(), outputDir, extendedName)) {
writeLine(Messages.SM_ATTRIBUTESNOTSAVED);
}
}
File netstatFile = new File(outputDir, extendedName + ".netstats");
StatsSerializer.save(stats, netstatFile);
writeLine(Messages.SM_RESULTSSAVED);
reports.add(new NetworkAnalysisReport(inputFile, interpretation, netstatFile));
} catch (SecurityException ex) {
writeError(Messages.SM_SAVEERROR);
reports.add(
new NetworkAnalysisReport(
inputFile, interpretation, AnalysisError.OUTPUT_NOT_CREATED));
} catch (FileNotFoundException ex) {
writeError(Messages.SM_SAVEERROR);
reports.add(
new NetworkAnalysisReport(
inputFile, interpretation, AnalysisError.OUTPUT_NOT_CREATED));
} catch (IOException e) {
writeError(Messages.SM_SAVEERROR);
reports.add(
new NetworkAnalysisReport(
inputFile, interpretation, AnalysisError.OUTPUT_IO_ERROR));
}
if (cancelled) {
writeLine(Messages.SM_ANALYSISC);
return null;
}
} catch (Exception e) {
reports.add(
new NetworkAnalysisReport(inputFile, interpretation, AnalysisError.INTERNAL_ERROR));
}
}
unloadNetwork(inputFile, network);
}
return null;
}
