Examples with NetworkTestSupport org.cytoscape.model.NetworkTestSupport used on opensource projects

Example 1 with NetworkTestSupport

use of org.cytoscape.model.NetworkTestSupport in project cytoscape-impl by cytoscape.

the class CloneNetworkTaskFactoryTest method testObserver.

@Test
public void testObserver() throws Exception {
    NetworkViewTestSupport viewSupport = new NetworkViewTestSupport();
    NetworkTestSupport networkSupport = new NetworkTestSupport();
    CyNetworkManager networkMgr = Mockito.mock(CyNetworkManager.class);
    CyNetworkViewManager networkViewMgr = Mockito.mock(CyNetworkViewManager.class);
    VisualMappingManager vmm = Mockito.mock(VisualMappingManager.class);
    CyNetworkFactory netFactory = networkSupport.getNetworkFactory();
    CyNetworkViewFactory netViewFactory = viewSupport.getNetworkViewFactory();
    CyNetworkNaming naming = Mockito.mock(CyNetworkNaming.class);
    CyApplicationManager appMgr = Mockito.mock(CyApplicationManager.class);
    CyNetworkTableManager netTableMgr = Mockito.mock(CyNetworkTableManager.class);
    CyRootNetworkManager rootNetMgr = new CyRootNetworkManagerImpl();
    CyGroupManager groupMgr = Mockito.mock(CyGroupManager.class);
    CyGroupFactory groupFactory = Mockito.mock(CyGroupFactory.class);
    RenderingEngineManager renderingEngineMgr = Mockito.mock(RenderingEngineManager.class);
    CyNetworkViewFactory nullNetworkViewFactory = new NullCyNetworkViewFactory();
    CyServiceRegistrar serviceRegistrar = Mockito.mock(CyServiceRegistrar.class);
    CloneNetworkTaskFactoryImpl factory = new CloneNetworkTaskFactoryImpl(networkMgr, networkViewMgr, vmm, netFactory, netViewFactory, naming, appMgr, netTableMgr, rootNetMgr, groupMgr, groupFactory, renderingEngineMgr, nullNetworkViewFactory, serviceRegistrar);
    CyNetwork network = netFactory.createNetwork();
    TaskObserver observer = Mockito.mock(TaskObserver.class);
    TaskIterator iterator = factory.createTaskIterator(network);
    TaskMonitor taskMonitor = Mockito.mock(TaskMonitor.class);
    while (iterator.hasNext()) {
        Task t = iterator.next();
        t.run(taskMonitor);
        if (t instanceof ObservableTask)
            observer.taskFinished((ObservableTask) t);
    }
    Mockito.verify(observer, Mockito.times(1)).taskFinished(Mockito.any(ObservableTask.class));
}

Example 2 with NetworkTestSupport

use of org.cytoscape.model.NetworkTestSupport in project cytoscape-impl by cytoscape.

the class NewNetworkSelectedNodesEdgesTaskFactoryTest method testObserver.

@Test
public void testObserver() throws Exception {
    NetworkViewTestSupport viewSupport = new NetworkViewTestSupport();
    NetworkTestSupport networkSupport = new NetworkTestSupport();
    CyNetworkFactory networkFactory = networkSupport.getNetworkFactory();
    UndoSupport undoSupport = mock(UndoSupport.class);
    CyRootNetworkManager crnf = new CyRootNetworkManagerImpl();
    CyNetworkViewFactory cnvf = viewSupport.getNetworkViewFactory();
    CyNetworkManager netmgr = mock(CyNetworkManager.class);
    CyNetworkViewManager networkViewManager = mock(CyNetworkViewManager.class);
    CyNetworkNaming naming = mock(CyNetworkNaming.class);
    VisualMappingManager vmm = mock(VisualMappingManager.class);
    CyApplicationManager appManager = mock(CyApplicationManager.class);
    CyEventHelper eventHelper = mock(CyEventHelper.class);
    CyGroupManager groupMgr = mock(CyGroupManager.class);
    RenderingEngineManager renderingEngineMgr = mock(RenderingEngineManager.class);
    CyLayoutAlgorithm defLayout = mock(CyLayoutAlgorithm.class);
    CyLayoutAlgorithmManager layoutMgr = mock(CyLayoutAlgorithmManager.class);
    when(layoutMgr.getDefaultLayout()).thenReturn(defLayout);
    CyServiceRegistrar serviceRegistrar = mock(CyServiceRegistrar.class);
    when(serviceRegistrar.getService(CyLayoutAlgorithmManager.class)).thenReturn(layoutMgr);
    NewNetworkSelectedNodesEdgesTaskFactoryImpl factory = new NewNetworkSelectedNodesEdgesTaskFactoryImpl(undoSupport, crnf, cnvf, netmgr, networkViewManager, naming, vmm, appManager, eventHelper, groupMgr, renderingEngineMgr, serviceRegistrar);
    CyNetwork network = networkFactory.createNetwork();
    CyNode node = network.addNode();
    network.getRow(node).set(CyNetwork.SELECTED, true);
    TaskObserver observer = mock(TaskObserver.class);
    TaskMonitor taskMonitor = mock(TaskMonitor.class);
    TaskIterator iterator = factory.createTaskIterator(network);
    while (iterator.hasNext()) {
        Task t = iterator.next();
        t.run(taskMonitor);
        if (t instanceof ObservableTask)
            observer.taskFinished((ObservableTask) t);
    }
    verify(observer, times(1)).taskFinished(any(ObservableTask.class));
}

Example 3 with NetworkTestSupport

use of org.cytoscape.model.NetworkTestSupport in project cytoscape-impl by cytoscape.

the class AbstractGroupTaskTest method setUp.

@Before
public void setUp() {
    MockitoAnnotations.initMocks(this);
    support = new NetworkTestSupport();
    network = support.getNetwork();
    CyRootNetworkManager rootNetworkManager = new CyRootNetworkManagerImpl();
    rootNetwork = rootNetworkManager.getRootNetwork(network);
    when(registrar.getService(VisualMappingManager.class)).thenReturn(vmMgr);
    when(registrar.getService(CyNetworkViewManager.class)).thenReturn(netViewMgr);
    when(registrar.getService(CyEventHelper.class)).thenReturn(eventHelper);
    final LockedVisualPropertiesManager lvpCache = new LockedVisualPropertiesManager(registrar);
    groupManager = new CyGroupManagerImpl(registrar);
    groupFactory = new CyGroupFactoryImpl(groupManager, lvpCache);
    group1 = groupFactory.createGroup(network, true);
    rootNetwork.getRow(group1.getGroupNode(), CyRootNetwork.SHARED_ATTRS).set(CyRootNetwork.SHARED_NAME, "group1");
    group2 = groupFactory.createGroup(network, true);
    rootNetwork.getRow(group2.getGroupNode(), CyRootNetwork.SHARED_ATTRS).set(CyRootNetwork.SHARED_NAME, "group2");
    task = new AbstractGroupTask() {

        @Override
        public void run(TaskMonitor taskMonitor) throws Exception {
        }
    };
    task.net = network;
    task.groupMgr = groupManager;
}

Example 4 with NetworkTestSupport

use of org.cytoscape.model.NetworkTestSupport in project cytoscape-impl by cytoscape.

the class GeneAssociationReaderTest method setUp.

@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);
}

Example 5 with NetworkTestSupport

use of org.cytoscape.model.NetworkTestSupport in project cytoscape-impl by cytoscape.

the class StringToModelTest method testNodeListParsing.

// TODO still need to test SUID
@Test
public void testNodeListParsing() {
    NetworkTestSupport networkTestSupport = new NetworkTestSupport();
    CyNetwork network = networkTestSupport.getNetwork();
    CyNode n1 = network.addNode();
    CyNode n2 = network.addNode();
    CyNode n3 = network.addNode();
    CyNode n4 = network.addNode();
    CyNode n5 = network.addNode();
    CyNode n6 = network.addNode();
    CyNode n7 = network.addNode();
    network.getRow(n1).set("name", "node 1");
    network.getRow(n2).set("name", "node 2");
    network.getRow(n3).set("name", "node,3");
    network.getRow(n4).set("name", "node:4");
    network.getRow(n5).set("name", "node:5,5");
    network.getRow(n6).set("name", "node\\:6");
    network.getRow(n7).set("name", "name:7");
    StringToModel stringToModel = new StringToModelImpl(serviceRegistrar);
    List<CyNode> nodes;
    nodes = stringToModel.getNodeList(network, "node 1,node 2");
    assertEquals(2, nodes.size());
    assertTrue(nodes.contains(n1));
    assertTrue(nodes.contains(n2));
    nodes = stringToModel.getNodeList(network, "name:node 1,name:node 2");
    assertEquals(2, nodes.size());
    assertTrue(nodes.contains(n1));
    assertTrue(nodes.contains(n2));
    nodes = stringToModel.getNodeList(network, "name:node\\,3,name:node 1,name:node 2");
    assertEquals(3, nodes.size());
    assertTrue(nodes.contains(n1));
    assertTrue(nodes.contains(n2));
    assertTrue(nodes.contains(n3));
    nodes = stringToModel.getNodeList(network, "name:node\\:4,name:node 1,name:node 2");
    assertEquals(3, nodes.size());
    assertTrue(nodes.contains(n1));
    assertTrue(nodes.contains(n2));
    assertTrue(nodes.contains(n4));
    nodes = stringToModel.getNodeList(network, "name:node\\:5\\,5");
    assertEquals(1, nodes.size());
    assertTrue(nodes.contains(n5));
    nodes = stringToModel.getNodeList(network, "node\\\\:6");
    assertEquals(1, nodes.size());
    assertTrue(nodes.contains(n6));
    // shouldn't need to escape colons after the first colon
    nodes = stringToModel.getNodeList(network, "name:node:4");
    assertEquals(1, nodes.size());
    assertTrue(nodes.contains(n4));
}