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

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

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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:edu.cornell.med.icb.goby.modes.TestReformatCompactReadsMode.java

/**
* Validates that reformating does not change quality score length by default.
* @throws IOException if there is a problem reading or writing to the files
*///from ww w . j a va 2s .c o m
@Test
public void reformatQualityScoreLength() throws IOException {
    final ReformatCompactReadsMode reformat = new ReformatCompactReadsMode();

    final String inputFilename = "test-data/compact-reads/with-meta-data-input.compact-reads";
    reformat.setInputFilenames(inputFilename);

    final String outputFilename = "test-results/with-meta-data-output-same.compact-reads";
    reformat.setOutputFile(outputFilename);
    reformat.execute();

    ReadsReader reader1 = new ReadsReader(inputFilename);
    for (Reads.ReadEntry it : reader1) {
        System.out.println(it.toString());
        System.out.println();
    }

    ReadsReader reader2 = new ReadsReader(outputFilename);
    for (Reads.ReadEntry it : reader2) {
        System.out.println(it.toString());
        System.out.println();
    }

    //    assertTrue(FileUtils.contentEquals(new File(inputFilename), new File(outputFilename)));

    final ReadsReader reader = new ReadsReader(FileUtils.openInputStream(new File(outputFilename)));
    assertTrue("There should be reads in this file", reader.hasNext());
    final Reads.ReadEntry entry = reader.next();
    assertEquals(12, entry.getQualityScores().size());

}

From source file:gov.nih.nci.caarray.application.project.FileUploadUtilsTest.java

@Test
public void testUnpackFiles_IOException() throws Exception {
    CaArrayFile mockFile = mock(CaArrayFile.class);
    InputStream input = FileUtils.openInputStream(File.createTempFile("aaa", "bbb"));
    IOUtils.closeQuietly(input);/* www. jav a  2s  . c o  m*/
    when(mockStorageFacade.openInputStream(any(URI.class), eq(false))).thenReturn(input);

    try {
        uploadUtils.unpackFiles(project, Lists.newArrayList(mockFile));
        fail("An InvalidFileException should have been thrown!");
    } catch (InvalidFileException e) {
        assertTrue(e.getCause() instanceof IOException);
    }
}

From source file:com.cts.ptms.carrier.ups.UPSHTTPClient.java

/**
 * This method to load the property file(s)
 *//*from w  w w  .  j  a  v  a  2 s  .  c  om*/
private void loadProperties() {
    try {
        File initialFile = new File(ShippingConstants.buildPropertiesPath);
        InputStream inputStream = FileUtils.openInputStream(initialFile);
        properties.load(inputStream);

    } catch (IOException e) {
        e.printStackTrace();
    }
}

From source file:com.buddycloud.mediaserver.business.dao.MediaDAO.java

protected Thumbnail getPreview(String entityId, String mediaId, Integer maxHeight, Integer maxWidth,
        String mediaDirectory)/*from   w ww.j a va2 s  . co  m*/
        throws MetadataSourceException, IOException, InvalidPreviewFormatException, MediaNotFoundException {
    File media = new File(mediaDirectory + File.separator + mediaId);

    if (!media.exists()) {
        throw new MediaNotFoundException(mediaId, entityId);
    }

    String previewId = dataSource.getPreviewId(mediaId, maxHeight, maxWidth);

    if (previewId != null) {
        File preview = new File(mediaDirectory + File.separator + previewId);

        if (!preview.exists()) {
            dataSource.deletePreview(previewId);
        } else {
            return new Thumbnail(dataSource.getPreviewMimeType(previewId),
                    IOUtils.toByteArray(FileUtils.openInputStream(preview)));
        }
    } else {
        // generate random id
        previewId = RandomStringUtils.randomAlphanumeric(20);
    }

    return buildNewPreview(media, mediaId, previewId, mediaDirectory, maxHeight, maxWidth);
}

From source file:key.secretkey.crypto.PgpHandler.java

public void decryptAndVerify(Intent data) {
    data.setAction(OpenPgpApi.ACTION_DECRYPT_VERIFY);

    findViewById(R.id.progress_bar).setVisibility(View.VISIBLE);

    try {//from ww w . j ava  2s  .c o m
        InputStream is = FileUtils.openInputStream(new File(getIntent().getExtras().getString("FILE_PATH")));

        ByteArrayOutputStream os = new ByteArrayOutputStream();

        OpenPgpApi api = new OpenPgpApi(this, mServiceConnection.getService());
        api.executeApiAsync(data, is, os, new PgpCallback(true, os, REQUEST_CODE_DECRYPT_AND_VERIFY));
    } catch (Exception e) {
        e.printStackTrace();
    }
}

From source file:com.buddycloud.mediaserver.business.dao.MediaDAO.java

protected String getFileShaChecksum(File file) {
    try {//from w  w  w  .  j av a  2  s  .  c o m
        return DigestUtils.shaHex(FileUtils.openInputStream(file));
    } catch (IOException e) {
        LOGGER.error("Error during media SHA1 checksum generation.", e);
    }

    return null;
}

From source file:key.secretkey.crypto.PgpHandler.java

public void edit(Intent data) {
    // exactly same as decrypt, only we want a different callback
    data.setAction(OpenPgpApi.ACTION_DECRYPT_VERIFY);

    findViewById(R.id.progress_bar).setVisibility(View.VISIBLE);

    try {/*from   w w  w .  j  av a 2 s.  c o m*/
        InputStream is = FileUtils.openInputStream(new File(getIntent().getExtras().getString("FILE_PATH")));

        ByteArrayOutputStream os = new ByteArrayOutputStream();

        OpenPgpApi api = new OpenPgpApi(this, mServiceConnection.getService());
        api.executeApiAsync(data, is, os, new PgpCallback(true, os, REQUEST_CODE_EDIT));
    } catch (Exception e) {
        e.printStackTrace();
    }
}

From source file:edu.ku.brc.specify.utilapps.sp5utils.Sp5Forms.java

@SuppressWarnings({ "unchecked" })
private void openXML() {
    FileDialog fileDlg = new FileDialog((Frame) UIRegistry.getTopWindow(), "", FileDialog.LOAD);

    fileDlg.setFilenameFilter(new FilenameFilter() {
        @Override// w w  w  . j a va2  s  . c o m
        public boolean accept(File dir, String name) {
            return name.toLowerCase().endsWith(".xml");
        }
    });
    fileDlg.setVisible(true);

    String fileName = fileDlg.getFile();
    if (fileName != null) {
        File iFile = new File(fileDlg.getDirectory() + File.separator + fileName);

        XStream xstream = new XStream();
        FormInfo.configXStream(xstream);
        FormFieldInfo.configXStream(xstream);

        try {
            forms = (Vector<FormInfo>) xstream.fromXML(FileUtils.openInputStream(iFile));
            formsTable.setModel(new FormCellModel(forms));

        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}

From source file:com.vmware.photon.controller.deployer.xenon.workflow.BatchCreateManagementWorkflowService.java

private void generateCertificate(DeploymentService.State deploymentState) {
    if (!deploymentState.oAuthEnabled) {
        sendStageProgressPatch(TaskStage.STARTED, TaskState.SubStage.CREATE_VMS);
        return;/*ww  w.  j  a v a 2s. c o m*/
    }

    List<String> command = new ArrayList<>();
    command.add("./" + GENERATE_CERTIFICATE_SCRIPT_NAME);
    command.add(deploymentState.oAuthServerAddress);
    command.add(deploymentState.oAuthPassword);
    command.add(deploymentState.oAuthTenantName);
    command.add(PhotonControllerXenonHost.KEYSTORE_FILE);
    command.add(PhotonControllerXenonHost.KEYSTORE_PASSWORD);

    DeployerContext deployerContext = HostUtils.getDeployerContext(this);
    File scriptLogFile = new File(deployerContext.getScriptLogDirectory(),
            GENERATE_CERTIFICATE_SCRIPT_NAME + ".log");

    ScriptRunner scriptRunner = new ScriptRunner.Builder(command, deployerContext.getScriptTimeoutSec())
            .directory(deployerContext.getScriptDirectory())
            .redirectOutput(ProcessBuilder.Redirect.to(scriptLogFile)).build();

    ListenableFutureTask<Integer> futureTask = ListenableFutureTask.create(scriptRunner);
    HostUtils.getListeningExecutorService(this).submit(futureTask);

    Futures.addCallback(futureTask, new FutureCallback<Integer>() {
        @Override
        public void onSuccess(@javax.validation.constraints.NotNull Integer result) {
            try {
                if (result != 0) {
                    logScriptErrorAndFail(result, scriptLogFile);
                } else {
                    // Set the inInstaller flag to true which would allow us to override the xenon service client to talk
                    // to the auth enabled newly deployed management plane using https with two way SSL.
                    ((PhotonControllerXenonHost) getHost()).setInInstaller(true);

                    // need to switch the ssl context for the thrift clients to use
                    // the generated certs to be able to talk to the authenticated
                    // agents
                    try {
                        SSLContext sslContext = SSLContext.getInstance(KeyStoreUtils.THRIFT_PROTOCOL);
                        TrustManagerFactory tmf = null;

                        tmf = TrustManagerFactory.getInstance(TrustManagerFactory.getDefaultAlgorithm());
                        KeyStore keyStore = KeyStore.getInstance("JKS");
                        InputStream in = FileUtils
                                .openInputStream(new File(PhotonControllerXenonHost.KEYSTORE_FILE));
                        keyStore.load(in, PhotonControllerXenonHost.KEYSTORE_PASSWORD.toCharArray());
                        tmf.init(keyStore);
                        sslContext.init(null, tmf.getTrustManagers(), null);
                        ((PhotonControllerXenonHost) getHost()).regenerateThriftClients(sslContext);

                        KeyStoreUtils.acceptAllCerts(KeyStoreUtils.THRIFT_PROTOCOL);
                    } catch (Throwable t) {
                        ServiceUtils.logSevere(BatchCreateManagementWorkflowService.this,
                                "Regenerating the SSL Context for thrift failed, ignoring to make tests pass, it fail later");
                        ServiceUtils.logSevere(BatchCreateManagementWorkflowService.this, t);
                    }
                    sendStageProgressPatch(TaskStage.STARTED, TaskState.SubStage.CREATE_VMS);
                }
            } catch (Throwable t) {
                failTask(t);
            }
        }

        @Override
        public void onFailure(Throwable throwable) {
            failTask(throwable);
        }
    });
}

From source file:eu.cloud4soa.soa.ApplicationDeployment.java

@Override
public InputStream dumpDatabase(String applicationInstanceUriId, String paaSInstanceUriId,
        String dbStorageComponentUriId) throws SOAException {
    InputStream inputStream = null;
    logger.debug("received applicationInstanceUriId: " + applicationInstanceUriId);
    logger.debug("received paaSInstanceUriId: " + paaSInstanceUriId);
    logger.debug("received dbStorageComponentUriId: " + dbStorageComponentUriId);

    logger.debug("call applicationProfilesRepository.getApplicationInstance(applicationInstanceUriId)");

    ApplicationInstance applicationInstance;
    try {//from   www  .ja  v  a 2 s .c  om
        applicationInstance = applicationProfilesRepository.getApplicationInstance(applicationInstanceUriId);
    } catch (RepositoryException ex) {
        throw new SOAException(Response.Status.INTERNAL_SERVER_ERROR, ex.getMessage());
    }

    logger.debug("retrieved applicationInstance: " + applicationInstance);
    PaaSInstance paaSInstance;
    try {
        paaSInstance = paaSOfferingProfilesRepository.getPaaSInstance(paaSInstanceUriId);
    } catch (RepositoryException ex) {
        throw new SOAException(Response.Status.INTERNAL_SERVER_ERROR, ex.getMessage());
    }
    logger.debug("retrived paaSInstance: " + paaSInstance);

    //check if the application is deployed (The application should be stopped or not deployed during the db initialization)
    if (applicationInstance.getPaaSOfferingDeploymentName() != null) {
        if (applicationInstance.getStatus().compareTo(StatusType.Stopped) != 0)
            throw new SOAException(Response.Status.BAD_REQUEST,
                    "The selected application is deployed and running.");
    }

    String dbUrl = null;
    String dbName = null;
    String dbUser = null;
    String dbPassword = null;
    String dbType = null;

    List<SoftwareComponentInstance> softwareComponents = applicationInstance.getSoftwareComponents();

    for (SoftwareComponentInstance softwareComponentInstance : softwareComponents) {
        String uriId = softwareComponentInstance.getUriId();
        if (softwareComponentInstance instanceof DBStorageComponentInstance
                && uriId.equals(dbStorageComponentUriId)) {
            logger.debug("found DBStorageComponent having dbStorageComponentUriId: " + dbStorageComponentUriId);
            DBStorageComponentInstance dbStorageComponentInstance = (DBStorageComponentInstance) softwareComponentInstance;

            //check if the db is already created
            if (dbStorageComponentInstance.getDeploymentLocationUriId() == null) {
                throw new SOAException(Response.Status.BAD_REQUEST, "The selected db has to be created first.");
            }

            dbName = dbStorageComponentInstance.getDbname();
            dbUser = dbStorageComponentInstance.getDbuser();
            dbPassword = dbStorageComponentInstance.getDbpassword();
            dbType = dbStorageComponentInstance.getRelatedhwcategoryInstance().getTitle();

            UserPaaSCredentials userCredentialsForPaaS = userManagementAndSecurityModule
                    .readUserCredentialsForPaaS(applicationInstance.getOwnerUriId(), paaSInstance.getUriId());
            File dumpFile;
            try {
                dumpFile = File.createTempFile(dbName + "_" + "dump", ".sql");
            } catch (IOException ex) {
                String error = "Impossible to dump database: " + dbName
                        + " since the temp file cannot be created - cause: " + ex.getMessage();
                logger.error(error);
                throw new SOAException(Response.Status.INTERNAL_SERVER_ERROR,
                        "Error in dumping the DB: " + dbName);
            }
            try {
                executionManagementServiceModule.downloadDataBase(applicationInstance,
                        userCredentialsForPaaS.getPublicKey(), userCredentialsForPaaS.getSecretKey(), dbName,
                        dbUser, dbPassword, dbType, dumpFile.getAbsolutePath());
                inputStream = FileUtils.openInputStream(dumpFile);
            } catch (IOException ex) {
                String error = "Impossible to dump database: " + dbName
                        + " since the temp file cannot be read - cause: " + ex.getMessage();
                logger.error(error);
                throw new SOAException(Response.Status.INTERNAL_SERVER_ERROR,
                        "Error in dumping the DB: " + dbName);
            } catch (Cloud4SoaException ex) {
                String error = "Impossible to dump database: " + dbName + " cause: " + ex.getMessage();
                logger.error(error);
                throw new SOAException(Response.Status.INTERNAL_SERVER_ERROR,
                        "Error in dumping the DB: " + dbName);
            }
        }
    }

    return inputStream;
}