@Before
public void setUp() throws Exception {
NetworkTestSupport netSupport = new NetworkTestSupport();
TableTestSupport tableSupport = new TableTestSupport();
CyNetworkFactory cyNetworkFactory = netSupport.getNetworkFactory();
tableFactory = tableSupport.getTableFactory();
tableManager = mock(CyTableManager.class);
dag = cyNetworkFactory.createNetwork();
tm = mock(TaskMonitor.class);
serviceRegistrar = mock(CyServiceRegistrar.class);
when(serviceRegistrar.getService(CyTableFactory.class)).thenReturn(tableFactory);
when(serviceRegistrar.getService(CyTableManager.class)).thenReturn(tableManager);
}
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
parentTaskMonitor = taskMonitor;
long start = System.currentTimeMillis();
taskMonitor.setProgress(0.01d);
taskMonitor.setTitle("Loading PSI-MI 2.5.x XML File ");
taskMonitor.setStatusMessage("Loading data file in PSI-MI 2.5 XML format.");
// support to add network into existing collection
this.initNodeMap();
PsimiXmlReader reader = new PsimiXmlReader();
EntrySet result = reader.read(inputStream);
taskMonitor.setProgress(0.4d);
taskMonitor.setStatusMessage("Data Loaded. Mapping Data to Network...");
if (cancelFlag) {
inputStream.close();
reader = null;
result = null;
return;
}
// network = cyNetworkFactory.createNetwork();
String networkCollectionName = this.rootNetworkList.getSelectedValue().toString();
if (networkCollectionName.equalsIgnoreCase(CRERATE_NEW_COLLECTION_STRING)) {
// This is a new network collection, create a root network and a subnetwork, which is a base
// subnetwork
network = cyNetworkFactory.createNetwork();
} else {
// Add a new subNetwork to the given collection
network = this.name2RootMap.get(networkCollectionName).addSubNetwork();
}
mapper = new PSIMI25EntryMapper(network, result);
mapper.map();
taskMonitor.setProgress(1.0d);
logger.info(
"PSI-MI XML Data Import finihsed in " + (System.currentTimeMillis() - start) + " msec.");
}