Example usage for org.apache.commons.io FileUtils openInputStream

List of usage examples for org.apache.commons.io FileUtils openInputStream

  1. HOME
  2. Java
  3. org.apache.commons
  4. org.apache.commons.io.*
  5. FileUtils
  6. openInputStream

Introduction

In this page you can find the example usage for org.apache.commons.io FileUtils openInputStream.

Prototype

public static FileInputStream openInputStream(File file) throws IOException

Source Link

Document

Opens a FileInputStream for the specified file, providing better error messages than simply calling new FileInputStream(file).

Usage

From source file:org.artificer.test.server.atom.services.BatchResourceTest.java

/**
 * This also tests the zipPackage method of the {@link org.artificer.server.atom.services.BatchResource} class, but it is
 * more thorough.  It tests adding new content, updating existing content, etc.
 *///from   w ww .  j  av a 2 s.com
@Test
public void testZipPackage_Multi() throws Exception {
    ArtificerArchive archive = null;
    InputStream xsd1ContentStream = null;
    InputStream wsdlContentStream = null;
    File zipFile = null;
    InputStream zipStream = null;
    ClientRequest request = null;

    WsdlDocument wsdlDoc = createWsdlArtifact();
    XmlDocument xmlDoc = createXmlArtifact();

    String xsdUuid = null;
    String wsdlUuid = null;
    String xmlUuid = null;

    try {
        // Create a test s-ramp archive
        archive = new ArtificerArchive();

        // A new XSD document
        xsd1ContentStream = this.getClass().getResourceAsStream("/sample-files/xsd/PO.xsd");
        BaseArtifactType metaData = new XsdDocument();
        metaData.setArtifactType(BaseArtifactEnum.XSD_DOCUMENT);
        metaData.setUuid(UUID.randomUUID().toString()); // will be ignored
        metaData.setName("PO.xsd");
        archive.addEntry("schemas/PO.xsd", metaData, xsd1ContentStream);
        // Update an existing WSDL document (content and meta-data)
        wsdlContentStream = this.getClass().getResourceAsStream("/sample-files/wsdl/sample-updated.wsdl");
        metaData = wsdlDoc;
        metaData.setVersion("2.0");
        ArtificerModelUtils.setCustomProperty(metaData, "foo", "bar");
        archive.addEntry("wsdl/sample.wsdl", metaData, wsdlContentStream);
        // Update an existing XML document (meta-data only)
        metaData = xmlDoc;
        metaData.setVersion("3.0");
        ArtificerModelUtils.setCustomProperty(metaData, "far", "baz");
        archive.addEntry("core/PO.xml", metaData, null);

        zipFile = archive.pack();
        zipStream = FileUtils.openInputStream(zipFile);

        // Now POST the archive to the s-ramp repository (POST to /s-ramp as application/zip)
        request = clientRequest("/s-ramp");
        request.body(MediaType.APPLICATION_ZIP, zipStream);
        ClientResponse<MultipartInput> clientResponse = request.post(MultipartInput.class);

        // Process the response - it should be multipart/mixed with each part being
        // itself an http response with a code, content-id, and an s-ramp atom entry
        // body
        MultipartInput response = clientResponse.getEntity();
        List<InputPart> parts = response.getParts();
        Map<String, HttpResponseBean> respMap = new HashMap<String, HttpResponseBean>();
        for (InputPart part : parts) {
            String id = part.getHeaders().getFirst("Content-ID");
            HttpResponseBean rbean = part.getBody(HttpResponseBean.class, null);
            respMap.put(id, rbean);
        }

        // Should be three responses.
        Assert.assertEquals(3, respMap.size());
        Assert.assertTrue(respMap.keySet().contains("<schemas/PO.xsd@package>"));
        Assert.assertTrue(respMap.keySet().contains("<wsdl/sample.wsdl@package>"));
        Assert.assertTrue(respMap.keySet().contains("<core/PO.xml@package>"));

        // Assertions for artifact 1 (PO.xsd)
        HttpResponseBean httpResp = respMap.get("<schemas/PO.xsd@package>");
        Assert.assertEquals(201, httpResp.getCode());
        Assert.assertEquals("Created", httpResp.getStatus());
        Entry entry = (Entry) httpResp.getBody();
        BaseArtifactType artifact = ArtificerAtomUtils.unwrapSrampArtifact(entry);
        Assert.assertEquals("PO.xsd", artifact.getName());
        Assert.assertNull(artifact.getVersion());
        Long size = ((XsdDocument) artifact).getContentSize();
        Assert.assertTrue(size >= 2376L);
        xsdUuid = artifact.getUuid();

        // Assertions for artifact 2 (sample.wsdl)
        httpResp = respMap.get("<wsdl/sample.wsdl@package>");
        Assert.assertEquals(200, httpResp.getCode());
        Assert.assertEquals("OK", httpResp.getStatus());
        entry = (Entry) httpResp.getBody();
        artifact = ArtificerAtomUtils.unwrapSrampArtifact(entry);
        Assert.assertEquals("sample.wsdl", artifact.getName());
        Assert.assertEquals("2.0", artifact.getVersion());
        wsdlUuid = artifact.getUuid();

        // Assertions for artifact 3 (PO.xml)
        httpResp = respMap.get("<core/PO.xml@package>");
        Assert.assertEquals(200, httpResp.getCode());
        Assert.assertEquals("OK", httpResp.getStatus());
        entry = (Entry) httpResp.getBody();
        artifact = ArtificerAtomUtils.unwrapSrampArtifact(entry);
        Assert.assertEquals("PO.xml", artifact.getName());
        Assert.assertEquals("3.0", artifact.getVersion());
        xmlUuid = artifact.getUuid();
    } finally {
        IOUtils.closeQuietly(xsd1ContentStream);
        IOUtils.closeQuietly(wsdlContentStream);
        ArtificerArchive.closeQuietly(archive);
        IOUtils.closeQuietly(zipStream);
        FileUtils.deleteQuietly(zipFile);
    }

    // Verify by querying
    // Do a query using GET with query params
    Map<String, BaseArtifactType> artyMap = new HashMap<String, BaseArtifactType>();
    request = clientRequest("/s-ramp/xsd/XsdDocument");
    ClientResponse<Feed> response = request.get(Feed.class);
    Feed feed = response.getEntity();
    Assert.assertEquals(1, feed.getEntries().size());
    for (Entry entry : feed.getEntries()) {
        String uuid = entry.getId().toString().replace("urn:uuid:", "");
        request = clientRequest("/s-ramp/xsd/XsdDocument/" + uuid);
        BaseArtifactType artifact = ArtificerAtomUtils
                .unwrapSrampArtifact(request.get(Entry.class).getEntity());
        artyMap.put(artifact.getUuid(), artifact);
    }
    request = clientRequest("/s-ramp/wsdl/WsdlDocument");
    response = request.get(Feed.class);
    feed = response.getEntity();
    Assert.assertEquals(1, feed.getEntries().size());
    for (Entry entry : feed.getEntries()) {
        String uuid = entry.getId().toString().replace("urn:uuid:", "");
        request = clientRequest("/s-ramp/wsdl/WsdlDocument/" + uuid);
        BaseArtifactType artifact = ArtificerAtomUtils
                .unwrapSrampArtifact(request.get(Entry.class).getEntity());
        artyMap.put(artifact.getUuid(), artifact);
    }
    request = clientRequest("/s-ramp/core/XmlDocument");
    response = request.get(Feed.class);
    feed = response.getEntity();
    Assert.assertEquals(1, feed.getEntries().size());
    for (Entry entry : feed.getEntries()) {
        String uuid = entry.getId().toString().replace("urn:uuid:", "");
        request = clientRequest("/s-ramp/core/XmlDocument/" + uuid);
        BaseArtifactType artifact = ArtificerAtomUtils
                .unwrapSrampArtifact(request.get(Entry.class).getEntity());
        artyMap.put(artifact.getUuid(), artifact);
    }

    Assert.assertEquals(3, artyMap.size());

    // Assertions for artifact 1 (PO.xsd)
    BaseArtifactType artifact = artyMap.get(xsdUuid);
    Assert.assertEquals("PO.xsd", artifact.getName());
    Assert.assertNull(artifact.getVersion());

    // Assertions for artifact 2 (sample.wsdl)
    artifact = artyMap.get(wsdlUuid);
    Assert.assertEquals("sample.wsdl", artifact.getName());
    Assert.assertEquals("2.0", artifact.getVersion());

    // Assertions for artifact 3 (PO.xml)
    artifact = artyMap.get(xmlUuid);
    Assert.assertEquals("PO.xml", artifact.getName());
    Assert.assertEquals("3.0", artifact.getVersion());
}

From source file:org.artificer.ui.server.servlets.ArtifactUploadServlet.java

/**
 * Uploads a single artifact to the S-RAMP repository.
 * @param artifactType// w w w  . j  av  a  2 s . co m
 * @param fileName
 * @param tempFile
 * @param responseParams
 * @throws Exception
 */
private void uploadSingleArtifact(String artifactType, String fileName, File tempFile,
        Map<String, String> responseParams) throws Exception {
    InputStream contentStream = null;
    try {
        contentStream = FileUtils.openInputStream(tempFile);
        BaseArtifactType artifact;
        if (artifactType != null) {
            artifact = ArtificerApiClientAccessor.getClient().uploadArtifact(ArtifactType.valueOf(artifactType),
                    contentStream, fileName);
        } else {
            artifact = ArtificerApiClientAccessor.getClient().uploadArtifact(contentStream, fileName);
        }
        ArtifactType responseArtifactType = ArtifactType.valueOf(artifact);
        responseParams.put("model", responseArtifactType.getModel());
        responseParams.put("type", responseArtifactType.getType());
        responseParams.put("uuid", artifact.getUuid());
    } finally {
        IOUtils.closeQuietly(contentStream);
    }
}

From source file:org.artificer.ui.server.servlets.OntologyUploadServlet.java

/**
 * Uploads a single ontology to the S-RAMP repository.
 * @param tempFile//from ww  w. j  a  v a2s  . c  o m
 * @param responseParams
 * @throws Exception
 */
private void uploadSingleOntology(File tempFile, Map<String, String> responseParams) throws Exception {
    InputStream contentStream = null;
    try {
        contentStream = FileUtils.openInputStream(tempFile);
        RDF ontology = ArtificerApiClientAccessor.getClient().uploadOntology(contentStream);

        if (ontology.getOtherAttributes() != null) {
            responseParams.put("namespace", ontology.getOtherAttributes()
                    .get(new QName("http://www.w3.org/XML/1998/namespace", "base")));
            QName uuid = new QName(ArtificerConstants.SRAMP_NS, "uuid");
            if (ontology.getOtherAttributes().get(uuid) != null) {
                responseParams.put("uuid", ontology.getOtherAttributes().get(uuid));
            }
        }

        responseParams.put("id", ontology.getOntology().getID());
        responseParams.put("label", ontology.getOntology().getLabel());
        responseParams.put("comment", ontology.getOntology().getComment());
    } finally {
        IOUtils.closeQuietly(contentStream);
    }
}

From source file:org.bdval.BDVModel.java

/**
 * Loads a BDVal model from disk. BDVal models are generated with the
 * {@link org.bdval.DiscoverAndValidate} tools (BDVal).
 *
 * @param options specific options to use when loading the model
 * @throws IOException            if there is a problem accessing the model
 * @throws ClassNotFoundException if the type of the model is not recognized
 *///from w  w  w  .  j a v a  2  s.c  om
public void load(final DAVOptions options) throws IOException, ClassNotFoundException {
    final boolean zipExists = new File(zipFilename).exists();
    if (LOG.isDebugEnabled()) {
        LOG.debug("model zip file exists: " + BooleanUtils.toStringYesNo(zipExists));
    }
    properties.clear();
    properties.setDelimiterParsingDisabled(true);
    // check to see if a zip file exists - if it doesn't we assume it's an old binary format
    if (zipModel && zipExists) {
        LOG.info("Reading model from filename: " + zipFilename);

        final ZipFile zipFile = new ZipFile(zipFilename);
        try {
            final ZipEntry propertyEntry = zipFile.getEntry(FilenameUtils.getName(modelPropertiesFilename));
            // load properties
            properties.clear();
            properties.addAll(loadProperties(zipFile.getInputStream(propertyEntry), options));

            // the platform is more than one entry in the zip, so here we pass the whole zip
            trainingPlatform = options.trainingPlatform = loadPlatform(zipFile);

            if (isConsensusModel()) {
                int index = 0;
                final ObjectList<String> modelJurorFilePrefixes = new ObjectArrayList<String>();
                String nextFilename;
                while ((nextFilename = (String) properties
                        .getProperty("bdval.consensus.model." + Integer.toString(index))) != null) {
                    modelJurorFilePrefixes.add(nextFilename);
                    index++;
                }

                delegate = new ConsensusBDVModel(modelFilenamePrefix,
                        modelJurorFilePrefixes.toArray(new String[modelJurorFilePrefixes.size()]));
                delegate.load(options);
                setGeneList(convertTrainingPlatformToGeneList(options));
                return;
            } else {
                probesetScaleMeanMap = options.probesetScaleMeanMap = loadMeansMap(
                        zipFile.getInputStream(zipFile.getEntry(FilenameUtils.getName(meansMapFilename))));
                probesetScaleRangeMap = options.probesetScaleRangeMap = loadRangeMap(
                        zipFile.getInputStream(zipFile.getEntry(FilenameUtils.getName(rangeMapFilename))));
                setGeneList(convertTrainingPlatformToGeneList(options));
            }

            final String modelParameters = properties.getString("training.classifier.parameters");

            LOG.info("Loading model " + modelFilename);
            final InputStream modelStream = zipFile
                    .getInputStream(zipFile.getEntry(FilenameUtils.getName(modelFilename)));
            helper = ClassificationModel.load(modelStream, modelParameters);
            LOG.info("Model loaded.");

            options.classiferClass = helper.classifier.getClass();
            // we don't have a way to inspect the saved model for parameters used during training:
            options.classifierParameters = ClassificationModel.splitModelParameters(modelParameters);
        } finally {
            try {
                zipFile.close();
            } catch (IOException e) { // NOPMD
                // ignore since there is not much we can do anyway
            }
        }
    } else {
        final File propertyFile = new File(modelFilenamePrefix + "." + ModelFileExtension.props.toString());
        LOG.debug("Loading properties from " + propertyFile.getAbsolutePath());
        final Properties properties = loadProperties(FileUtils.openInputStream(propertyFile), options);

        trainingPlatform = options.trainingPlatform = (GEOPlatformIndexed) BinIO.loadObject(platformFilename);

        if (isConsensusModel()) {
            int index = 0;
            final ObjectList<String> modelJurorFilePrefixes = new ObjectArrayList<String>();
            String nextFilename = null;
            while ((nextFilename = (String) properties
                    .getProperty("bdval.consensus.model." + Integer.toString(index))) != null) {
                modelJurorFilePrefixes.add(nextFilename);
                index++;
            }

            delegate = new ConsensusBDVModel(modelFilenamePrefix,
                    modelJurorFilePrefixes.toArray(new String[modelJurorFilePrefixes.size()]));
            delegate.load(options);
            setGeneList(convertTrainingPlatformToGeneList(options));
            return;
        } else {
            probesetScaleMeanMap = options.probesetScaleMeanMap = (Object2DoubleMap<MutableString>) BinIO
                    .loadObject(modelFilenamePrefix + ".means");
            if (LOG.isDebugEnabled()) {
                LOG.debug("Number of entries in means map = " + probesetScaleMeanMap.size());
            }
            probesetScaleRangeMap = options.probesetScaleRangeMap = (Object2DoubleMap<MutableString>) BinIO
                    .loadObject(modelFilenamePrefix + ".ranges");
            if (LOG.isDebugEnabled()) {
                LOG.debug("Number of entries in range map = " + probesetScaleRangeMap.size());
            }
            setGeneList(convertTrainingPlatformToGeneList(options));
        }

        final String modelParameters = properties.getString("training.classifier.parameters");

        LOG.info("Loading model " + modelFilename);
        helper = ClassificationModel.load(modelFilename, modelParameters);
        LOG.info("Model loaded.");

        options.classiferClass = helper.classifier.getClass();
        // we don't have a way to inspect the saved model for parameters used during training:
        options.classifierParameters = ClassificationModel.splitModelParameters(modelParameters);
    }
}

From source file:org.bdval.ConsensusBDVModel.java

/**
 * @param options specific options to use when loading the properties
 * @throws IOException if there is a problem accessing the properties
 *//*  w w w  .  j a va2s. c o m*/
private void loadProperties(final DAVOptions options) throws IOException {
    final boolean zipExists = new File(zipFilename).exists();
    if (LOG.isDebugEnabled()) {
        LOG.debug("model zip file exists: " + BooleanUtils.toStringYesNo(zipExists));
    }

    properties.clear();

    // check to see if a zip file exists - if it doesn't we assume it's an old binary format
    if (zipModel && zipExists) {
        LOG.info("Reading model from filename: " + zipFilename);

        final ZipFile zipFile = new ZipFile(zipFilename);
        try {
            final ZipEntry propertyEntry = zipFile.getEntry(FilenameUtils.getName(modelPropertiesFilename));
            // load properties
            properties.clear();
            properties.addAll(loadProperties(zipFile.getInputStream(propertyEntry), options));
        } finally {
            try {
                zipFile.close();
            } catch (IOException e) { // NOPMD
                // ignore since there is not much we can do anyway
            }
        }
    } else {
        final File propertyFile = new File(modelFilenamePrefix + "." + ModelFileExtension.props.toString());
        if (propertyFile.exists() && propertyFile.canRead()) {
            LOG.debug("Loading properties from " + propertyFile.getAbsolutePath());
            properties.addAll(loadProperties(FileUtils.openInputStream(propertyFile), options));
        }
    }
}

From source file:org.bdval.DAVMode.java

/**
 * Reads data from a file and stores it into a {@link edu.mssm.crover.tables.Table}.
 *
 * @param fileName Name of the file to read
 * @return A table that contains data read from the input file
 * @throws SyntaxErrorException       if there is an error in the file
 * @throws IOException                if the input file cannot be read
 * @throws UnsupportedFormatException if the file format is not recognized
 *///  ww  w  .j av  a  2  s .  c  om
protected Table readInputFile(final String fileName)
        throws IOException, SyntaxErrorException, UnsupportedFormatException {
    System.out.print("Reading input " + fileName + "... ");
    final Table table;
    Reader reader = null;
    try {
        // get a reader object for the file and store the file extension
        final InputStream inputStream = FileUtils.openInputStream(new File(fileName));
        String fileExtension = FilenameUtils.getExtension(fileName);
        if ("gz".equalsIgnoreCase(fileExtension)) {
            reader = new InputStreamReader(new GZIPInputStream(inputStream));
            // strip the ".gz" to get the "real" extension
            fileExtension = FilenameUtils.getExtension(FilenameUtils.getBaseName(fileName));
        } else {
            reader = new InputStreamReader(inputStream);
        }

        if ("soft".equalsIgnoreCase(fileExtension)) {
            if (fileName.contains("GDS")) { // GEO dataset
                final TableReader tableReader = new GeoDataSetReader();
                table = tableReader.read(reader);
            } else if (fileName.contains("GSE")) { // GEO series
                table = readGeoSeries(reader);
            } else {
                throw new UnsupportedFormatException(fileName);
            }
        } else if ("res".equalsIgnoreCase(fileExtension)) {
            final TableReader tableReader = new WhiteheadResReader();
            table = tableReader.read(reader);
        } else if ("tmm".equalsIgnoreCase(fileExtension)) {
            final TableReader tableReader = new ColumbiaTmmReader();
            table = tableReader.read(reader);
        } else if ("iconix".equalsIgnoreCase(fileExtension)) {
            final TableReader tableReader = new IconixReader();
            table = tableReader.read(reader);
        } else if ("cologne".equalsIgnoreCase(fileExtension)) {
            final TableReader tableReader = new CologneReader();
            table = tableReader.read(reader);
        } else {
            throw new UnsupportedFormatException(fileName);
        }

        if (table == null) {
            System.err.println("The input file could not be read. ");
            System.exit(1);
        }
        System.out.println("done");
    } finally {
        IOUtils.closeQuietly(reader);
    }
    return table;
}

From source file:org.broadinstitute.gatk.utils.runtime.ProcessController.java

/**
 * Executes a command line program with the settings and waits for it to return,
 * processing the output on a background thread.
 *
 * @param settings Settings to be run./*  w ww .jav  a2s  .  c  o  m*/
 * @return The output of the command.
 */
public ProcessOutput exec(ProcessSettings settings) {
    if (destroyed)
        throw new IllegalStateException("This controller was destroyed");

    ProcessBuilder builder = new ProcessBuilder(settings.getCommand());
    builder.directory(settings.getDirectory());

    Map<String, String> settingsEnvironment = settings.getEnvironment();
    if (settingsEnvironment != null) {
        Map<String, String> builderEnvironment = builder.environment();
        builderEnvironment.clear();
        builderEnvironment.putAll(settingsEnvironment);
    }

    builder.redirectErrorStream(settings.isRedirectErrorStream());

    StreamOutput stdout = null;
    StreamOutput stderr = null;

    // Start the process running.

    try {
        synchronized (toCapture) {
            process = builder.start();
        }
        running.add(this);
    } catch (IOException e) {
        String message = String.format("Unable to start command: %s\nReason: %s",
                StringUtils.join(builder.command(), " "), e.getMessage());
        throw new ReviewedGATKException(message);
    }

    int exitCode;

    try {
        // Notify the background threads to start capturing.
        synchronized (toCapture) {
            toCapture.put(ProcessStream.Stdout, new CapturedStreamOutput(settings.getStdoutSettings(),
                    process.getInputStream(), System.out));
            toCapture.put(ProcessStream.Stderr, new CapturedStreamOutput(settings.getStderrSettings(),
                    process.getErrorStream(), System.err));
            toCapture.notifyAll();
        }

        // Write stdin content
        InputStreamSettings stdinSettings = settings.getStdinSettings();
        Set<StreamLocation> streamLocations = stdinSettings.getStreamLocations();
        if (!streamLocations.isEmpty()) {
            try {
                OutputStream stdinStream = process.getOutputStream();
                for (StreamLocation location : streamLocations) {
                    InputStream inputStream;
                    switch (location) {
                    case Buffer:
                        inputStream = new ByteArrayInputStream(stdinSettings.getInputBuffer());
                        break;
                    case File:
                        try {
                            inputStream = FileUtils.openInputStream(stdinSettings.getInputFile());
                        } catch (IOException e) {
                            throw new UserException.BadInput(e.getMessage());
                        }
                        break;
                    case Standard:
                        inputStream = System.in;
                        break;
                    default:
                        throw new ReviewedGATKException("Unexpected stream location: " + location);
                    }
                    try {
                        IOUtils.copy(inputStream, stdinStream);
                    } finally {
                        if (location != StreamLocation.Standard)
                            IOUtils.closeQuietly(inputStream);
                    }
                }
                stdinStream.flush();
            } catch (IOException e) {
                throw new ReviewedGATKException(
                        "Error writing to stdin on command: " + StringUtils.join(builder.command(), " "), e);
            }
        }

        // Wait for the process to complete.
        try {
            process.getOutputStream().close();
            process.waitFor();
        } catch (IOException e) {
            throw new ReviewedGATKException(
                    "Unable to close stdin on command: " + StringUtils.join(builder.command(), " "), e);
        } catch (InterruptedException e) {
            throw new ReviewedGATKException("Process interrupted", e);
        } finally {
            while (!destroyed && stdout == null || stderr == null) {
                synchronized (fromCapture) {
                    if (fromCapture.containsKey(ProcessStream.Stdout))
                        stdout = fromCapture.remove(ProcessStream.Stdout);
                    if (fromCapture.containsKey(ProcessStream.Stderr))
                        stderr = fromCapture.remove(ProcessStream.Stderr);
                    try {
                        if (stdout == null || stderr == null)
                            fromCapture.wait();
                    } catch (InterruptedException e) {
                        // Log the error, ignore the interrupt and wait patiently
                        // for the OutputCaptures to (via finally) return their
                        // stdout and stderr.
                        logger.error(e);
                    }
                }
            }

            if (destroyed) {
                if (stdout == null)
                    stdout = StreamOutput.EMPTY;
                if (stderr == null)
                    stderr = StreamOutput.EMPTY;
            }
        }
    } finally {
        synchronized (toCapture) {
            exitCode = process.exitValue();
            process = null;
        }
        running.remove(this);
    }

    return new ProcessOutput(exitCode, stdout, stderr);
}

From source file:org.broadinstitute.sting.gatk.report.GATKReportParser.java

public void parse(File file) throws IOException {
    InputStream stream = FileUtils.openInputStream(file);
    try {//from  w  w  w.  j ava 2 s .c o  m
        parse(stream);
    } finally {
        IOUtils.closeQuietly(stream);
    }
}

From source file:org.broadinstitute.sting.utils.runtime.ProcessController.java

/**
 * Executes a command line program with the settings and waits for it to return,
 * processing the output on a background thread.
 *
 * @param settings Settings to be run.// ww  w .  j  ava2s . c  om
 * @return The output of the command.
 */
public ProcessOutput exec(ProcessSettings settings) {
    if (destroyed)
        throw new IllegalStateException("This controller was destroyed");

    ProcessBuilder builder = new ProcessBuilder(settings.getCommand());
    builder.directory(settings.getDirectory());

    Map<String, String> settingsEnvironment = settings.getEnvironment();
    if (settingsEnvironment != null) {
        Map<String, String> builderEnvironment = builder.environment();
        builderEnvironment.clear();
        builderEnvironment.putAll(settingsEnvironment);
    }

    builder.redirectErrorStream(settings.isRedirectErrorStream());

    StreamOutput stdout = null;
    StreamOutput stderr = null;

    // Start the process running.

    try {
        synchronized (toCapture) {
            process = builder.start();
        }
        running.add(this);
    } catch (IOException e) {
        throw new ReviewedStingException(
                "Unable to start command: " + StringUtils.join(builder.command(), " "));
    }

    int exitCode;

    try {
        // Notify the background threads to start capturing.
        synchronized (toCapture) {
            toCapture.put(ProcessStream.Stdout, new CapturedStreamOutput(settings.getStdoutSettings(),
                    process.getInputStream(), System.out));
            toCapture.put(ProcessStream.Stderr, new CapturedStreamOutput(settings.getStderrSettings(),
                    process.getErrorStream(), System.err));
            toCapture.notifyAll();
        }

        // Write stdin content
        InputStreamSettings stdinSettings = settings.getStdinSettings();
        Set<StreamLocation> streamLocations = stdinSettings.getStreamLocations();
        if (!streamLocations.isEmpty()) {
            try {
                OutputStream stdinStream = process.getOutputStream();
                for (StreamLocation location : streamLocations) {
                    InputStream inputStream;
                    switch (location) {
                    case Buffer:
                        inputStream = new ByteArrayInputStream(stdinSettings.getInputBuffer());
                        break;
                    case File:
                        try {
                            inputStream = FileUtils.openInputStream(stdinSettings.getInputFile());
                        } catch (IOException e) {
                            throw new UserException.BadInput(e.getMessage());
                        }
                        break;
                    case Standard:
                        inputStream = System.in;
                        break;
                    default:
                        throw new ReviewedStingException("Unexpected stream location: " + location);
                    }
                    try {
                        IOUtils.copy(inputStream, stdinStream);
                    } finally {
                        if (location != StreamLocation.Standard)
                            IOUtils.closeQuietly(inputStream);
                    }
                }
                stdinStream.flush();
            } catch (IOException e) {
                throw new ReviewedStingException(
                        "Error writing to stdin on command: " + StringUtils.join(builder.command(), " "), e);
            }
        }

        // Wait for the process to complete.
        try {
            process.getOutputStream().close();
            process.waitFor();
        } catch (IOException e) {
            throw new ReviewedStingException(
                    "Unable to close stdin on command: " + StringUtils.join(builder.command(), " "), e);
        } catch (InterruptedException e) {
            throw new ReviewedStingException("Process interrupted", e);
        } finally {
            while (!destroyed && stdout == null || stderr == null) {
                synchronized (fromCapture) {
                    if (fromCapture.containsKey(ProcessStream.Stdout))
                        stdout = fromCapture.remove(ProcessStream.Stdout);
                    if (fromCapture.containsKey(ProcessStream.Stderr))
                        stderr = fromCapture.remove(ProcessStream.Stderr);
                    try {
                        if (stdout == null || stderr == null)
                            fromCapture.wait();
                    } catch (InterruptedException e) {
                        // Log the error, ignore the interrupt and wait patiently
                        // for the OutputCaptures to (via finally) return their
                        // stdout and stderr.
                        logger.error(e);
                    }
                }
            }

            if (destroyed) {
                if (stdout == null)
                    stdout = StreamOutput.EMPTY;
                if (stderr == null)
                    stderr = StreamOutput.EMPTY;
            }
        }
    } finally {
        synchronized (toCapture) {
            exitCode = process.exitValue();
            process = null;
        }
        running.remove(this);
    }

    return new ProcessOutput(exitCode, stdout, stderr);
}

From source file:org.carewebframework.help.chm.maven.ChmSource.java

/**
 * Wraps a chm file as an IResourceIterator.
 * // w  ww . j  av a2  s. c o  m
 * @param chmFile The chm file.
 */
public ChmSource(String chmFile) {
    try (InputStream inp = FileUtils.openInputStream(new File(chmFile));) {
        chmExtractor = new ChmExtractor(inp);
        entries = buildEntryList();
        iterator = entries.iterator();
    } catch (Exception e) {
        throw new RuntimeException(e);
    }
}