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

Example 6 with CyFileFilter

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

the class SessionWriterImpl method zipProperties.

/**
 * Writes the cytoscape.props file to the session zip.
 */
private void zipProperties() throws Exception {
    for (CyProperty<?> cyProps : session.getProperties()) {
        if (cancelled)
            return;
        String filename = null;
        CyFileFilter filter = null;
        Class<?> type = cyProps.getPropertyType();
        if (Bookmarks.class.isAssignableFrom(type)) {
            filename = BOOKMARKS_FILE;
            filter = bookmarksFilter;
        } else if (Properties.class.isAssignableFrom(type)) {
            filename = cyProps.getName() + PROPERTIES_EXT;
            filter = propertiesFilter;
        } else {
            // filename = cyProps.getName();
            // TODO: how to get the file extension and the file filter for unknown CyProperty types?
            logger.error("Cannot save CyProperty \"" + cyProps.getName() + "\": type \"" + type + "\" is not supported");
            continue;
        }
        zos.putNextEntry(new ZipEntry(sessionDir + PROPERTIES_FOLDER + filename));
        CyWriter propertiesWriter = propertyWriterMgr.getWriter(cyProps.getProperties(), filter, zos);
        propertiesWriter.run(taskMonitor);
        zos.closeEntry();
        propertiesWriter = null;
    }
}

Example 7 with CyFileFilter

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

the class SupportedFileTypesManager method getSupportedFileTypes.

private List<FileChooserFilter> getSupportedFileTypes(final DataCategory category, final Set<CyFileFilterProvider> factories) {
    List<FileChooserFilter> types = new ArrayList<FileChooserFilter>();
    Set<String> allExtensions = new HashSet<String>();
    for (final CyFileFilterProvider factory : factories) {
        CyFileFilter filter = factory.getFileFilter();
        // this is a hack to exclude internal session table format
        if (filter.getExtensions().contains("cytable") || filter.getDataCategory() != category)
            continue;
        String description = filter.getDescription();
        Set<String> filterExtensions = filter.getExtensions();
        String[] extensions = new String[filterExtensions.size()];
        int index = 0;
        for (String extension : filterExtensions) {
            allExtensions.add(extension);
            extensions[index] = extension;
            index++;
        }
        types.add(new FileChooserFilter(description, extensions));
    }
    if (types.isEmpty())
        return types;
    Collections.sort(types, new Comparator<FileChooserFilter>() {

        @Override
        public int compare(FileChooserFilter o1, FileChooserFilter o2) {
            return o1.getDescription().compareTo(o2.getDescription());
        }
    });
    String description = String.format("All %1$s files", category.getDisplayName().toLowerCase());
    types.add(new FileChooserFilter(description, new ArrayList<String>(allExtensions).toArray(new String[allExtensions.size()])));
    return types;
}

Example 8 with CyFileFilter

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

the class AbstractCyWriter method addOrReplaceExtension.

/**
 * Adds or replaces the extension of the given File with one suitable for the selected export file format
 * @param file The input file
 * @return a File with an extension suitable for the selected export file format
 */
protected final File addOrReplaceExtension(final File file) {
    final CyFileFilter filter = getFileFilter(getExportFileFormat());
    if (filter == null)
        return file;
    final Iterator<String> extensions = filter.getExtensions().iterator();
    if (!extensions.hasNext())
        return file;
    final String filterExtension = extensions.next();
    String fileName = file.getAbsolutePath();
    final String fileExtension = FilenameUtils.getExtension(fileName);
    if (!filterExtension.trim().equals(fileExtension.trim()))
        fileName = FilenameUtils.removeExtension(fileName) + "." + filterExtension;
    return new File(fileName);
}

Example 9 with CyFileFilter

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

the class AbstractCyWriter method fileExtensionIsOk.

/**
 * Returns whether the given File's extension is acceptable for the selected file format
 * @param file The input file
 * @return true if the extension is accepted for the selected file format, and false otherwise
 */
protected final boolean fileExtensionIsOk(final File file) {
    final String exportFileFormat = getExportFileFormat();
    if (exportFileFormat == null)
        return true;
    final CyFileFilter filter = getFileFilter(exportFileFormat);
    if (filter == null)
        return true;
    return filter.getExtensions().contains(FilenameUtils.getExtension(file.getName()));
}

Example 10 with CyFileFilter

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

the class CySessionWriter method run.

/**
 * The method that will actually write the specified session to the specified
 * file.
 * @param tm The {@link org.cytoscape.work.TaskMonitor} provided by the TaskManager execution environment.
 */
@Override
public final void run(final TaskMonitor tm) throws Exception {
    final CySessionWriterManager writerMgr = serviceRegistrar.getService(CySessionWriterManager.class);
    final List<CyFileFilter> filters = writerMgr.getAvailableWriterFilters();
    if (filters == null || filters.size() < 1)
        throw new NullPointerException("No Session file filters found");
    if (filters.size() > 1)
        throw new IllegalArgumentException("Found too many session filters.");
    String filepath = outputFile.getAbsolutePath();
    if (!filepath.toLowerCase().endsWith(".cys")) {
        filepath += ".cys";
        outputFile = new File(filepath);
    }
    if (!canWrite(outputFile)) {
        throw new IOException("Session not saved. Cytoscape does not have write permission to save the session at \"" + outputFile.getParentFile().getAbsolutePath() + "\". Choose another folder or change the folder permissions.");
    }
    // Write to a temporary file first, to prevent the original file from being damaged, in case there is any error
    createTempFile();
    try {
        writer = writerMgr.getWriter(session, filters.get(0), tmpFile);
        if (writer == null)
            throw new NullPointerException("No CyWriter found for specified file type.");
        writer.run(tm);
    } catch (final Exception e) {
        deleteFile(tmpFile);
        throw e;
    }
    if (cancelled) {
        deleteFile(tmpFile);
        return;
    }
    // If the main task is successfully executed, this task will move the temp file to the actual output path
    replaceOutputFile();
}