@Test
/** Single SBMLTestCase: Can be read and is network created ? */
public void testSingleTestCase() throws Exception {
logger.info(String.format("SBMLTestCase: %s", resource));
final NetworkTestSupport nts = new NetworkTestSupport();
final CyNetworkFactory networkFactory = nts.getNetworkFactory();
final CyNetworkViewFactory viewFactory = null;
TaskMonitor taskMonitor = null;
// read SBML
String[] tokens = resource.split("/");
String fileName = tokens[2];
InputStream instream = getClass().getResourceAsStream(resource);
CyNetwork[] networks;
try {
// Reader can be tested without service adapter,
SBMLReaderTask readerTask =
new SBMLReaderTask(instream, fileName, networkFactory, null, null);
readerTask.run(taskMonitor);
networks = readerTask.getNetworks();
assertFalse(readerTask.getError());
} catch (Throwable t) {
networks = null;
t.printStackTrace();
}
// Networks could be read
assertNotNull(networks);
assertTrue(networks.length >= 1);
}
@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);
}
@Before
public void setUp() throws Exception {
taskMonitor = mock(TaskMonitor.class);
CyLayoutAlgorithm def = mock(CyLayoutAlgorithm.class);
Object context = new Object();
when(def.createLayoutContext()).thenReturn(context);
when(def.getDefaultLayoutContext()).thenReturn(context);
when(def.createTaskIterator(
Mockito.any(CyNetworkView.class),
Mockito.any(Object.class),
Mockito.anySet(),
Mockito.any(String.class)))
.thenReturn(new TaskIterator(new SimpleTask()));
layouts = mock(CyLayoutAlgorithmManager.class);
when(layouts.getDefaultLayout()).thenReturn(def);
NetworkTestSupport nts = new NetworkTestSupport();
netFactory = nts.getNetworkFactory();
networkManager = nts.getNetworkManager();
rootNetworkManager = nts.getRootNetworkFactory();
cyApplicationManager = mock(CyApplicationManager.class);
properties = new Properties();
CyProperty<Properties> cyProperties =
new SimpleCyProperty<Properties>(
"Test", properties, Properties.class, SavePolicy.DO_NOT_SAVE);
NetworkViewTestSupport nvts = new NetworkViewTestSupport();
setViewThreshold(DEF_THRESHOLD);
viewFactory = nvts.getNetworkViewFactory();
readUtil = new ReadUtils(new StreamUtilImpl(cyProperties));
}