public void downloadInteractions(CyNetwork networkToMerge) {
String networkTitle = peName + ": Network";
CPathWebService webApi = CPathWebServiceImpl.getInstance();
CPathResponseFormat format;
CPathProperties config = CPathProperties.getInstance();
if (config.getDownloadMode() == CPathProperties.DOWNLOAD_FULL_BIOPAX) {
format = CPathResponseFormat.BIOPAX;
} else {
format = CPathResponseFormat.BINARY_SIF;
}
TaskManager taskManager = factory.getTaskManager();
ExecuteGetRecordByCPathIdTaskFactory taskFactory =
factory.createExecuteGetRecordByCPathIdTaskFactory(
webApi, ids, format, networkTitle, networkToMerge);
taskManager.execute(taskFactory.createTaskIterator());
}
/** 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);
}
}
/**
* Constructor.
*
* @param passedRecordList List of Records that Passed over Filter.
* @param peName Name of Physical Entity.
* @param bpContainer
*/
public DownloadDetails(
List<BasicRecordType> passedRecordList, String peName, CPath2Factory factory) {
super();
this.factory = factory;
this.peName = peName;
this.setTitle("Retrieval Confirmation");
this.setModal(true);
Container contentPane = getContentPane();
contentPane.setLayout(new BorderLayout());
GradientHeader header =
new GradientHeader("Confirm Retrieval: " + passedRecordList.size() + " records");
contentPane.add(header, BorderLayout.NORTH);
DefaultTableModel tableModel = new NonEditableTableModel();
Vector headerList = new Vector();
headerList.add("Name (if available)");
headerList.add("Type");
headerList.add("Data Source");
tableModel.setColumnIdentifiers(headerList);
tableModel.setRowCount(passedRecordList.size());
JTable table = new JTable(tableModel);
// Adjust width / height of viewport; fixes bug #1620.
Dimension d = table.getPreferredSize();
d.width = d.width * 2;
if (d.height > 200) {
d.height = 200;
}
table.setPreferredScrollableViewportSize(d);
table.setAutoCreateColumnsFromModel(true);
table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
ids = new long[passedRecordList.size()];
int i = 0;
for (BasicRecordType record : passedRecordList) {
if (record.getName().equalsIgnoreCase("N/A")) {
record.setName("---");
}
tableModel.setValueAt(record.getName(), i, 0);
tableModel.setValueAt(record.getEntityType(), i, 1);
if (record.getDataSource() != null) {
tableModel.setValueAt(record.getDataSource().getName(), i, 2);
} else {
tableModel.setValueAt("---", i, 3);
}
ids[i++] = record.getPrimaryId();
}
JScrollPane scrollPane = new JScrollPane(table);
scrollPane.setBorder(new EmptyBorder(5, 5, 5, 5));
contentPane.add(scrollPane, BorderLayout.CENTER);
JPanel buttonPanel = createButtonPanel(this);
mergePanel = factory.createMergePanel();
JPanel panel = new JPanel();
panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));
if (mergePanel != null) {
panel.add(mergePanel);
}
panel.add(buttonPanel);
contentPane.add(panel, BorderLayout.SOUTH);
pack();
setLocationRelativeTo(factory.getCySwingApplication().getJFrame());
}