Examples with DefaultInputSupplier eu.esdihumboldt.hale.common.core.io.supplier.DefaultInputSupplier used on opensource projects

Example 31 with DefaultInputSupplier

use of eu.esdihumboldt.hale.common.core.io.supplier.DefaultInputSupplier in project hale by halestudio.

the class AbstractBaseAlignmentLoader method generatePrefixMapping.

/**
 * Function to fill the prefixMapping and alignmentToInfo maps.
 *
 * @param addBase the URI of the new base alignment to add
 * @param projectLocation the project location or <code>null</code>
 * @param existingBases the map of existing bases
 * @param prefixMapping gets filled with a mapping from local to global
 *            prefixes
 * @param alignmentToInfo gets filled with a mapping from base alignment
 *            representations to prefixes and URIs
 * @param reporter the reporter
 * @return whether newBase actually is a new base and the add process should
 *         continue
 */
private boolean generatePrefixMapping(URI addBase, URI projectLocation, Map<String, URI> existingBases, Map<A, Map<String, String>> prefixMapping, Map<A, AlignmentInfo> alignmentToInfo, IOReporter reporter) {
    // Project location may be null if the project wasn't saved yet
    // Then, it still is okay, if all bases are absolute.
    URI currentAbsolute = projectLocation;
    URI usedAddBaseURI = addBase;
    URI absoluteAddBaseURI = resolve(currentAbsolute, usedAddBaseURI);
    // set of already seen URIs
    Set<URI> knownURIs = new HashSet<URI>();
    // reverse map of base
    Map<URI, String> uriToPrefix = new HashMap<URI, String>();
    // create URI to prefix map and known URIs
    for (Entry<String, URI> baseEntry : existingBases.entrySet()) {
        // make sure to use absolute URIs here for comparison
        URI absoluteBase = resolve(currentAbsolute, baseEntry.getValue());
        knownURIs.add(absoluteBase);
        uriToPrefix.put(absoluteBase, baseEntry.getKey());
    }
    if (uriToPrefix.containsKey(absoluteAddBaseURI)) {
        reporter.info(new IOMessageImpl("The base alignment (" + addBase + ") is already included.", null));
        return false;
    }
    Set<String> existingPrefixes = new HashSet<String>(existingBases.keySet());
    String newPrefix = generatePrefix(existingPrefixes);
    existingPrefixes.add(newPrefix);
    uriToPrefix.put(absoluteAddBaseURI, newPrefix);
    /*
		 * XXX Adding a base alignment could only use a PathUpdate for the
		 * movement of the base alignment which is not known in the current
		 * project. Maybe could try the one of the current project either way?
		 */
    // find all alignments to load (also missing ones) and load the beans
    LinkedList<URIPair> queue = new LinkedList<URIPair>();
    queue.add(new URIPair(absoluteAddBaseURI, usedAddBaseURI));
    while (!queue.isEmpty()) {
        URIPair baseURI = queue.pollFirst();
        A baseA;
        try {
            baseA = loadAlignment(new DefaultInputSupplier(baseURI.absoluteURI).getInput(), reporter);
        } catch (IOException e) {
            reporter.error(new IOMessageImpl("Couldn't load an included base alignment (" + baseURI.absoluteURI + ").", e));
            reporter.setSuccess(false);
            return false;
        }
        // add to alignment info map
        alignmentToInfo.put(baseA, new AlignmentInfo(uriToPrefix.get(baseURI.absoluteURI), baseURI));
        prefixMapping.put(baseA, new HashMap<String, String>());
        // load "missing" base alignments, too, add prefix mapping
        for (Entry<String, URI> baseEntry : getBases(baseA).entrySet()) {
            // rawURI may be relative
            URI rawURI = baseEntry.getValue();
            URI absoluteURI = baseURI.absoluteURI.resolve(rawURI);
            URI usedURI = absoluteURI;
            // and rawURI are relative, continue using a relative URI.
            if (!usedAddBaseURI.isAbsolute() && !baseURI.usedURI.isAbsolute() && !rawURI.isAbsolute()) {
                usedURI = IOUtils.getRelativePath(absoluteURI, currentAbsolute);
            }
            // check whether this base alignment is missing
            if (!knownURIs.contains(absoluteURI)) {
                reporter.info(new IOMessageImpl("A base alignment referenced another base alignment (" + absoluteURI + ") that was not yet known. It is now included, too.", null));
                queue.add(new URIPair(absoluteURI, usedURI));
                knownURIs.add(absoluteURI);
                String prefix = generatePrefix(existingPrefixes);
                existingPrefixes.add(prefix);
                uriToPrefix.put(absoluteURI, prefix);
            }
            // add prefix mapping
            prefixMapping.get(baseA).put(baseEntry.getKey(), uriToPrefix.get(absoluteURI));
        }
    }
    return true;
}

Example 32 with DefaultInputSupplier

use of eu.esdihumboldt.hale.common.core.io.supplier.DefaultInputSupplier in project hale by halestudio.

the class OMLReaderTest method loadAlignment.

private static Alignment loadAlignment(URI sourceSchemaLocation, URI targetSchemaLocation, final URI alignmentLocation) throws IOProviderConfigurationException, IOException {
    // load source schema
    Schema source = readXMLSchema(new DefaultInputSupplier(sourceSchemaLocation));
    // load target schema
    Schema target = readXMLSchema(new DefaultInputSupplier(targetSchemaLocation));
    OmlReader reader = new OmlReader();
    reader.setSourceSchema(source);
    reader.setTargetSchema(target);
    reader.setSource(new DefaultInputSupplier(alignmentLocation));
    reader.validate();
    IOReport report = reader.execute(null);
    assertTrue(report.isSuccess());
    return reader.getAlignment();
}

Example 33 with DefaultInputSupplier

use of eu.esdihumboldt.hale.common.core.io.supplier.DefaultInputSupplier in project hale by halestudio.

the class URILink method createDefaultSelectionAdapter.

// create the the SelectionAdapter for the UriLink
private SelectionAdapter createDefaultSelectionAdapter(final URI uri) {
    return new SelectionAdapter() {

        private URI removeFragment(URI uri) throws URISyntaxException {
            String uristring = uri.toString();
            uristring = uristring.substring(0, uristring.indexOf("#"));
            return new URI(uristring);
        }

        // the URI has to be an existing file on the local drive or on a
        // server
        @Override
        public void widgetSelected(SelectionEvent e) {
            URI newuri = uri;
            try {
                // online resource
                if (uri.getScheme().equals("http") || uri.getScheme().equals("https")) {
                    try {
                        Desktop.getDesktop().browse(uri);
                    } catch (IOException e1) {
                        MessageDialog.openWarning(Display.getCurrent().getActiveShell(), "Opening Error", "No default application set!");
                    }
                    return;
                }
                if (uri.toString().contains("#")) {
                    newuri = removeFragment(uri);
                }
                // local resource or bundle resource
                if (DefaultInputSupplier.SCHEME_LOCAL.equals(newuri.getScheme()) || "bundleentry".equals(newuri.getScheme())) {
                    // cannot be opened by system
                    // so copy resource to temporary file
                    String name = newuri.getPath();
                    int index = name.lastIndexOf('/');
                    if (index >= 0) {
                        name = name.substring(index + 1);
                    }
                    if (!name.isEmpty()) {
                        File tmpFile = Files.createTempFile("resource", name).toFile();
                        try (OutputStream out = new FileIOSupplier(tmpFile).getOutput();
                            InputStream in = new DefaultInputSupplier(newuri).getInput()) {
                            ByteStreams.copy(in, out);
                        }
                        tmpFile.deleteOnExit();
                        newuri = tmpFile.toURI();
                    }
                }
                // try creating a file
                File file = new File(newuri);
                if (file.exists()) {
                    try {
                        Desktop.getDesktop().open(file);
                    } catch (IOException e2) {
                        try {
                            Desktop.getDesktop().browse(newuri);
                        } catch (IOException e1) {
                            MessageDialog.openWarning(Display.getCurrent().getActiveShell(), "Opening Error", "No default application set!");
                        }
                    }
                } else {
                    try {
                        Desktop.getDesktop().browse(newuri);
                    } catch (IOException e1) {
                        MessageDialog.openWarning(Display.getCurrent().getActiveShell(), "Opening Error", "No default application set!");
                    }
                }
            } catch (Exception e1) {
            // ignore
            }
        }
    };
}

Example 34 with DefaultInputSupplier

use of eu.esdihumboldt.hale.common.core.io.supplier.DefaultInputSupplier in project hale by halestudio.

the class ProjectParser method load.

private void load(URI source, String actionId, String msgCT, String msgIO, @SuppressWarnings("rawtypes") Class clazz) {
    // create IOConfiguration for source data
    IOConfiguration conf = new IOConfiguration();
    // populate IOConfiguration
    // set action ID
    conf.setActionId(actionId);
    // find provider
    File file;
    try {
        file = new File(source);
    } catch (IllegalArgumentException e) {
        file = null;
    }
    @SuppressWarnings("unchecked") IContentType ct = HaleIO.findContentType(clazz, new DefaultInputSupplier(source), (file == null) ? (null) : (file.getAbsolutePath()));
    if (ct == null) {
        report.error(new IOMessageImpl(msgCT, null, -1, -1, source));
        return;
    }
    @SuppressWarnings("unchecked") IOProviderDescriptor srf = HaleIO.findIOProviderFactory(clazz, ct, null);
    if (srf == null) {
        report.error(new IOMessageImpl(msgIO, null, -1, -1, source));
        return;
    }
    conf.setProviderId(srf.getIdentifier());
    // provider configuration
    // source
    conf.getProviderConfiguration().put(AbstractImportProvider.PARAM_SOURCE, Value.of(source.toString()));
    // content type
    conf.getProviderConfiguration().put(AbstractImportProvider.PARAM_CONTENT_TYPE, Value.of(ct.getId()));
    // no dependencies needed
    // add configuration to project
    project.getResources().add(conf);
}

Example 35 with DefaultInputSupplier

use of eu.esdihumboldt.hale.common.core.io.supplier.DefaultInputSupplier in project hale by halestudio.

the class ValidatorConfigurationReaderImpl method execute.

/**
 * @see eu.esdihumboldt.hale.common.core.io.impl.AbstractIOProvider#execute(eu.esdihumboldt.hale.common.core.io.ProgressIndicator,
 *      eu.esdihumboldt.hale.common.core.io.report.IOReporter)
 */
@Override
protected IOReport execute(ProgressIndicator progress, IOReporter reporter) throws IOProviderConfigurationException, IOException {
    progress.begin("Loading validator configuration.", ProgressIndicator.UNKNOWN);
    final URI sourceLocation = getSource().getLocation();
    if (sourceLocation == null) {
        throw new IOProviderConfigurationException("No source location provided when trying to read validator configuration.");
    }
    final DefaultInputSupplier validationRuleInputSupplier = new DefaultInputSupplier(sourceLocation);
    final InputStream validationRuleInput = validationRuleInputSupplier.getInput();
    if (validationRuleInput == null) {
        throw new IOProviderConfigurationException("Cannot read validator configuration.");
    }
    try {
        // XXX UTF 8 encoding is assumed here. The actual encoding should be
        // detected or be configurable
        configuration = new ValidatorConfiguration(IOUtils.toString(validationRuleInput, StandardCharsets.UTF_8), sourceLocation, getContentType());
        reporter.setSuccess(true);
    } catch (Exception e) {
        throw new IOProviderConfigurationException(MessageFormat.format("Could not read validation rule from '{0}': {1}", sourceLocation.toString(), e.getMessage()), e);
    } finally {
        IOUtils.closeQuietly(validationRuleInput);
    }
    progress.setCurrentTask("Validation rule loaded.");
    return reporter;
}