Examples with CyFileFilter org.cytoscape.io.CyFileFilter used on opensource projects

Example 1 with CyFileFilter

use of org.cytoscape.io.CyFileFilter in project cytoscape-impl by cytoscape.

the class GenericReaderManager method getReader.

public R getReader(InputStream stream, String inputName) {
    try {
        if (!stream.markSupported()) {
            stream = new BufferedInputStream(stream);
            stream.mark(1025);
        }
        for (T factory : factories) {
            CyFileFilter cff = factory.getFileFilter();
            // of the first 2KB rather than the stream itself.
            if (cff.accepts(CopyInputStream.copyKBytes(stream, 1), category)) {
                // logger.debug("successfully matched READER " + factory);
                return (R) factory.createTaskIterator(stream, inputName).next();
            }
        }
    } catch (IOException ioe) {
        userLogger.warn("Error setting input stream", ioe);
    }
    userLogger.warn("No reader found for input stream");
    return null;
}

Example 2 with CyFileFilter

use of org.cytoscape.io.CyFileFilter in project cytoscape-impl by cytoscape.

the class GenericReaderManager method getReader.

/**
 * Gets the GraphReader that is capable of reading the specified file.
 *
 * @param uri
 *            URI of file to be read.
 * @return GraphReader capable of reading the specified file. Null if file
 *         cannot be read.
 */
public R getReader(final URI uri, final String inputName) {
    // Data location is always required.
    if (uri == null) {
        throw new NullPointerException("Data source URI is null");
    }
    // This is the default reader, which accepts files with no extension.
    // Usually, this is ImportNetworkTableReaderFactory (Manual table
    // import)
    T defaultFactory = null;
    final List<T> factoryList = new ArrayList<T>();
    final Map<String, T> factoryTable = new HashMap<String, T>();
    // Pick compatible reader factories.
    for (final T factory : factories) {
        final CyFileFilter cff = factory.getFileFilter();
        // Got "Accepted" flag. Need to check it's default or not.
        if (cff.accepts(uri, category)) {
            logger.info("Filter returns Accepted.  Need to check priority: " + factory);
            if (factory.getClass().toString().contains(DEFAULT_READER_FACTORY_CLASS)) {
                defaultFactory = factory;
            } else {
                factoryList.add(factory);
                for (final String extension : cff.getExtensions()) {
                    factoryTable.put(extension, factory);
                }
            }
        }
    }
    T chosenFactory = null;
    // No compatible factory is available.
    if (factoryTable.isEmpty() && defaultFactory == null) {
        userLogger.warn("No reader found for uri: " + uri.toString());
        throw new IllegalStateException("Don't know how to read " + uri.toString());
    } else if (factoryList.size() == 1) {
        // There is only one compatible reader factory.  Use it:
        chosenFactory = factoryList.get(0);
    } else {
        if (factoryList.isEmpty() && defaultFactory != null) {
            // There is only one factory
            chosenFactory = defaultFactory;
        } else {
            // Well, we cannot decide which one is correct.  Try to use ext...
            String extension = FilenameUtils.getExtension(uri.toString());
            if (factoryTable.containsKey(extension))
                chosenFactory = factoryTable.get(extension);
            else {
                if (factoryTable.containsKey(""))
                    chosenFactory = factoryTable.get("");
                else {
                    userLogger.warn("Can't figure out how to read: " + uri.toString() + " from extension");
                    throw new IllegalStateException("Can't figure out how to read " + uri.toString() + " from extension");
                }
            }
        }
    }
    try {
        logger.info("Successfully found compatible ReaderFactory " + chosenFactory);
        // This returns strean using proxy if it exists.
        final InputStream stream = streamUtil.getInputStream(uri.toURL());
        return (R) chosenFactory.createTaskIterator(stream, inputName).next();
    } catch (FileNotFoundException e) {
        throw new IllegalStateException("File '" + inputName + "' not found:", e);
    } catch (IOException e) {
        userLogger.warn("Error opening stream to URI: " + uri.toString(), e);
        throw new IllegalStateException("Could not open stream for reader.", e);
    }
}

Example 3 with CyFileFilter

use of org.cytoscape.io.CyFileFilter in project cytoscape-impl by cytoscape.

the class CyNetworkViewWriterTest method setUp.

@Before
public void setUp() throws Exception {
    writerManager = mock(CyNetworkViewWriterManager.class);
    cyApplicationManager = mock(CyApplicationManager.class);
    view = viewSupport.getNetworkView();
    final List<CyFileFilter> filters = new ArrayList<CyFileFilter>();
    final CyFileFilter dummyFilter = mock(CyFileFilter.class);
    filters.add(dummyFilter);
    when(dummyFilter.getDescription()).thenReturn("dummy description");
    when(dummyFilter.getExtensions()).thenReturn(Collections.singleton("dummy"));
    when(writerManager.getAvailableWriterFilters()).thenReturn(filters);
    final CyNetworkViewWriter writer = new CyNetworkViewWriter(writerManager, cyApplicationManager, view);
    this.cyWriter = writer;
    when(writerManager.getWriter(eq(view), eq(dummyFilter), any(File.class))).thenReturn(writer, writer);
}

Example 4 with CyFileFilter

use of org.cytoscape.io.CyFileFilter in project cytoscape-impl by cytoscape.

the class ViewWriterTest method setUp.

@Before
@SuppressWarnings("rawtypes")
public void setUp() throws Exception {
    final PresentationWriterManager viewWriterMgr = mock(PresentationWriterManager.class);
    final CyApplicationManager applicationManager = mock(CyApplicationManager.class);
    final RenderingEngineManager engineManager = mock(RenderingEngineManager.class);
    final CyNetworkView view = mock(CyNetworkView.class);
    final CyNetwork network = mock(CyNetwork.class);
    final CyRow row = mock(CyRow.class);
    final RenderingEngine re = mock(RenderingEngine.class);
    final CyServiceRegistrar serviceRegistrar = mock(CyServiceRegistrar.class);
    when(serviceRegistrar.getService(CyApplicationManager.class)).thenReturn(applicationManager);
    when(serviceRegistrar.getService(RenderingEngineManager.class)).thenReturn(engineManager);
    when(serviceRegistrar.getService(PresentationWriterManager.class)).thenReturn(viewWriterMgr);
    fileFilter = mock(CyFileFilter.class);
    when(fileFilter.getDescription()).thenReturn("A dummy filter");
    when(fileFilter.getExtensions()).thenReturn(Collections.singleton("dummy"));
    final List<CyFileFilter> filters = new ArrayList<>();
    filters.add(fileFilter);
    when(viewWriterMgr.getAvailableWriterFilters()).thenReturn(filters);
    when(view.getModel()).thenReturn(network);
    when(network.getRow(network)).thenReturn(row);
    cyWriter = new ViewWriter(view, re, serviceRegistrar);
    final CyWriter aWriter = mock(CyWriter.class);
    when(viewWriterMgr.getWriter(eq(view), eq(re), eq(fileFilter), argThat(new AnyOutputStreamMatcher()))).thenReturn(aWriter);
}

Example 5 with CyFileFilter

use of org.cytoscape.io.CyFileFilter in project cytoscape-impl by cytoscape.

the class ExportNetworkImageTaskFactoryTest method setUp.

@Before
@SuppressWarnings({ "rawtypes", "unchecked" })
public void setUp() throws Exception {
    final CyFileFilter dummyFilter = mock(CyFileFilter.class);
    final RenderingEngine engine = mock(RenderingEngine.class);
    final List<CyFileFilter> filters = new ArrayList<>();
    filters.add(dummyFilter);
    when(dummyFilter.getDescription()).thenReturn("dummy description");
    when(dummyFilter.getExtensions()).thenReturn(Collections.singleton("dummy"));
    when(viewWriterMgr.getAvailableWriterFilters()).thenReturn(filters);
    when(applicationManager.getCurrentRenderingEngine()).thenReturn(engine);
    when(serviceRegistrar.getService(CyApplicationManager.class)).thenReturn(applicationManager);
    when(serviceRegistrar.getService(RenderingEngineManager.class)).thenReturn(engineManager);
    when(serviceRegistrar.getService(PresentationWriterManager.class)).thenReturn(viewWriterMgr);
}