/** * Downloads the given file specified via url to the given canonicalDestination. * * @param urlSource String * @param urlDestination String * @throws Exception */ @Override public void downloadFile(String urlSource, String urlDestination) throws Exception { // sanity check if (urlSource == null || urlSource.length() == 0 || urlDestination == null || urlDestination.length() == 0) { throw new IllegalArgumentException( "downloadFile(): urlSource or urlDestination argument is null..."); } // URLs for given parameters URL source = new URL(urlSource); URL destination = new URL(urlDestination); // we have a compressed file if (GzipUtils.isCompressedFilename(urlSource)) { // downlod to temp destination File tempDestinationFile = org.apache.commons.io.FileUtils.getFile( org.apache.commons.io.FileUtils.getTempDirectory(), new File(source.getFile()).getName()); if (LOG.isInfoEnabled()) { LOG.info("downloadFile(), " + urlSource + ", this may take a while..."); } org.apache.commons.io.FileUtils.copyURLToFile(source, tempDestinationFile); if (LOG.isInfoEnabled()) { LOG.info("downloadFile(), gunzip: we have compressed file, decompressing..."); } // decompress the file gunzip(tempDestinationFile.getCanonicalPath()); if (LOG.isInfoEnabled()) { LOG.info("downloadFile(), gunzip complete..."); } // move temp/decompressed file to final destination File destinationFile = new File(destination.getFile()); if (destinationFile.exists()) { org.apache.commons.io.FileUtils.forceDelete(destinationFile); } org.apache.commons.io.FileUtils.moveFile( org.apache.commons.io.FileUtils.getFile( GzipUtils.getUncompressedFilename(tempDestinationFile.getCanonicalPath())), destinationFile); // lets cleanup after ourselves - remove compressed file tempDestinationFile.delete(); } // uncompressed file, download directry to urlDestination else { if (LOG.isInfoEnabled()) { LOG.info("downloadFile(), " + urlSource + ", this may take a while..."); } org.apache.commons.io.FileUtils.copyURLToFile( source, org.apache.commons.io.FileUtils.getFile(destination.getFile())); } }
public static void init() { if (initialize) { logger.warn("配置文件已经加载,不需要在调用init()方法!"); return; } final Properties p = new Properties(); ResourceKit.loadFileInProperties(APPLICATION_PROP, p); if (checkNullOrEmpty(p)) { throw new IllegalArgumentException("Properties file can not be empty. " + APPLICATION_PROP); } final String configFolder = p.getProperty(GojaPropConst.APPCONFIGFOLDER); if (!Strings.isNullOrEmpty(configFolder)) { configFolderFile = new File(configFolder); if (!configFolderFile.exists()) { throw new RuntimeException( "The application config folder " + configFolder + " is not found!"); } configProps = PropKit.use(FileUtils.getFile(configFolderFile, "application.conf")).getProperties(); } else { configProps = p; } applicationMode = getApplicationModel(); security = getPropertyToBoolean(GojaPropConst.APPSECURITY, true); appSecurityConfig = getProperty(GojaPropConst.APPSECURITYCONFIG, "security.conf"); if (security) { // 如果启用了身份验证,如果配置文件不存在,系统无法启动 if (!Strings.isNullOrEmpty(configFolder)) { final File securityFile = FileUtils.getFile(configFolderFile, appSecurityConfig); if (!securityFile.exists()) { throw new RuntimeException( "The app security config file [ " + appSecurityConfig + "] not found in [" + configFolder + "]!"); } } } version = getProperty(GojaPropConst.APPVERSION, "V0.0.1"); appName = getProperty(GojaPropConst.APPNAME, "application"); appDomain = getProperty(GojaPropConst.APPDOMAIN, "http://127.0.0.1:8080/" + appName); defaultDBUrl = getProperty(GojaPropConst.DBURL); defaultDBUsername = getProperty(GojaPropConst.DBUSERNAME, "root"); defaultDBPassword = getProperty(GojaPropConst.DBPASSWORD, "123456"); defaultViewPath = GojaConfig.getProperty( GojaPropConst.APP_VIEWPATH, File.separator + "WEB-INF" + File.separator + "views"); String appScan = GojaConfig.getProperty(GojaPropConst.APP_SCAN, "app"); appScans = Func.COMMA_SPLITTER.splitToList(appScan); jsonMode = GojaConfig.getProperty(GojaPropConst.APP_JSON_MODE); api = GojaConfig.getPropertyToBoolean(GojaPropConst.APP_API, false); initialize = true; }
@AfterClass public static void tearDownAfterClass() throws Exception { System.out.println("Resetting fits.xml"); // Set the backup to the original fits.xml FileUtils.copyFile(FileUtils.getFile("xml/fits_back.xml"), FileUtils.getFile("xml/fits.xml")); // Remove the temp file FileUtils.deleteQuietly(FileUtils.getFile("xml/fits_back.xml")); }
@BeforeClass public static void setUpBeforeClass() throws Exception { System.out.println("Moving test fits.xml in"); // Copy fits.xml to fits_back.xml FileUtils.copyFile(FileUtils.getFile("xml/fits.xml"), FileUtils.getFile("xml/fits_back.xml")); // Copy in test fits.xml FileUtils.copyFile( FileUtils.getFile("testfiles/properties/fits_no_md5_audio.xml"), FileUtils.getFile("xml/fits.xml")); }
/** * Creates a staging file with contents from the given DataMatrix. * * @param portalMetadata PortalMetadata * @param cancerStudyMetadata CancerStudyMetadata * @param datatypeMetadata DatatypeMetadata * @param dataMatrix DataMatrix * @throws Exception */ @Override public void writeStagingFile( PortalMetadata portalMetadata, CancerStudyMetadata cancerStudyMetadata, DatatypeMetadata datatypeMetadata, DataMatrix dataMatrix) throws Exception { // staging file String stagingFilename = datatypeMetadata.getStagingFilename(); stagingFilename = stagingFilename.replaceAll( DatatypeMetadata.CANCER_STUDY_TAG, cancerStudyMetadata.toString()); File stagingFile = org.apache.commons.io.FileUtils.getFile( portalMetadata.getStagingDirectory(), cancerStudyMetadata.getStudyPath(), stagingFilename); if (LOG.isInfoEnabled()) { LOG.info("writingStagingFile(), staging file: " + stagingFile); } FileOutputStream out = org.apache.commons.io.FileUtils.openOutputStream(stagingFile, false); dataMatrix.write(out); IOUtils.closeQuietly(out); // meta file if (datatypeMetadata.requiresMetafile()) { if (LOG.isInfoEnabled()) { LOG.info("writingStagingFile(), creating metadata file for staging file: " + stagingFile); } writeMetadataFile(portalMetadata, cancerStudyMetadata, datatypeMetadata, dataMatrix); } }
@Override public void write(String path) throws IOException { File dir = FileUtils.getFile(path, "ensemble", getName()); if (!dir.isDirectory()) { dir.mkdirs(); } ObjectOutputStream oop = new ObjectOutputStream(new FileOutputStream(new File(dir, "similarityCoefficients"))); oop.writeObject(simlarityCoefficients); oop.flush(); oop.close(); oop = new ObjectOutputStream(new FileOutputStream(new File(dir, "mostSimilarCoefficients"))); oop.writeObject(mostSimilarCoefficients); oop.flush(); oop.close(); oop = new ObjectOutputStream(new FileOutputStream(new File(dir, "similarityInterpolator"))); oop.writeObject(similarityInterpolator); oop.flush(); oop.close(); oop = new ObjectOutputStream(new FileOutputStream(new File(dir, "mostSimilarInterpolator"))); oop.writeObject(mostSimilarInterpolator); oop.flush(); oop.close(); }
/** * Creates a staging file for mutation data (and meta file) with contents from the given * DataMatrix. This is called when the mutation file needs to be run through the Oncotator and * Mutation Assessor Tools. * * @param portalMetadata PortalMetadata * @param cancerStudy CancerStudyMetadata * @param datatypeMetadata DatatypeMetadata * @param dataMatrix DataMatrix * @throws Exception */ @Override public void writeMutationStagingFile( PortalMetadata portalMetadata, CancerStudyMetadata cancerStudyMetadata, DatatypeMetadata datatypeMetadata, DataMatrix dataMatrix) throws Exception { // we only have data matrix at this point, we need to create a temp with its contents File oncotatorInputFile = org.apache.commons.io.FileUtils.getFile( org.apache.commons.io.FileUtils.getTempDirectory(), "oncotatorInputFile"); FileOutputStream out = org.apache.commons.io.FileUtils.openOutputStream(oncotatorInputFile); dataMatrix.write(out); IOUtils.closeQuietly(out); // output should be the path/name of staging file String stagingFilename = datatypeMetadata.getStagingFilename(); stagingFilename = stagingFilename.replaceAll( DatatypeMetadata.CANCER_STUDY_TAG, cancerStudyMetadata.toString()); File stagingFile = org.apache.commons.io.FileUtils.getFile( portalMetadata.getStagingDirectory(), cancerStudyMetadata.getStudyPath(), stagingFilename); // call oncotateAF oncotateMAF( FileUtils.FILE_URL_PREFIX + oncotatorInputFile.getCanonicalPath(), FileUtils.FILE_URL_PREFIX + stagingFile.getCanonicalPath()); // clean up if (oncotatorInputFile.exists()) { org.apache.commons.io.FileUtils.forceDelete(oncotatorInputFile); } // meta file if (datatypeMetadata.requiresMetafile()) { if (LOG.isInfoEnabled()) { LOG.info( "writingMutationStagingFile(), creating metadata file for staging file: " + stagingFile); } writeMetadataFile(portalMetadata, cancerStudyMetadata, datatypeMetadata, dataMatrix); } }
/** * Unpacks file into temporary directory * * @param inputStream InputStream representing archive file * @param originalFileName Name of the archive * @return Directory to which the archive was unpacked * @throws IOException * @throws ZipException */ private File unpackArchive(InputStream inputStream, String originalFileName) throws IOException, ZipException { String randomDirectoryName = RandomStringUtils.randomAlphanumeric(8); File directoryForUnpacking = FileUtils.getFile(FileUtils.getTempDirectoryPath(), randomDirectoryName); FileUtils.forceMkdir(directoryForUnpacking); File zipFileDownloaded = FileUtils.getFile(FileUtils.getTempDirectoryPath(), originalFileName); try (OutputStream os = new FileOutputStream(zipFileDownloaded)) { IOUtils.copy(inputStream, os); } ZipFile zipFile = new ZipFile(zipFileDownloaded); zipFile.extractAll(directoryForUnpacking.toString()); FileUtils.forceDelete(zipFileDownloaded); return directoryForUnpacking; }
public File createInfile(int fileId) { if (infile != null) { cleanUp(); } infile = FileUtils.getFile(Integer.toString(fileId) + ".txt"); return infile; }
/** * Creates (or overwrites) the given file with the given contents. Filename is canonical * path/filename. * * @param filename String * @param fileContent String * @return File * @throws Exception */ @Override public File createFileWithContents(String filename, String fileContent) throws Exception { File file = org.apache.commons.io.FileUtils.getFile(filename); org.apache.commons.io.FileUtils.writeStringToFile(file, fileContent, false); // outta here return file; }
/** * Load an MEI file. * * @param filename A path to an MEI file to load * @return an {@link MeiDocument} representing the MEI file. */ public static MeiDocument loadFile(String filename) { try { File fp = FileUtils.getFile(filename); MeiXmlReader loader = new MeiXmlReader(fp); return loader.readDocument(); } catch (FileNotFoundException e) { throw new MeiXmlReadException("Cannot find file " + filename); } }
public File getInfile(int fileId) { if (infile == null) { infile = FileUtils.getFile(Integer.toString(fileId) + ".txt"); if (!infile.exists()) { infile = null; } } return infile; }
/** * This method takes care to not load the metric itself, and just deal in names. Once the metric * is loaded, it has already accessed its data files. * * @throws ConfigurationException */ public void deleteDataDirectories() throws ConfigurationException { for (String name : getSubmetrics(metricName)) { File dir = FileUtils.getFile(srDir, name, language.getLangCode()); if (dir.exists()) { LOG.info("deleting metric directory " + dir); FileUtils.deleteQuietly(dir); } } }
/** * Creates a temporary file with the given contents. * * @param filename String * @param fileContent String * @return File * @throws Exception */ @Override public File createTmpFileWithContents(String filename, String fileContent) throws Exception { File tmpFile = org.apache.commons.io.FileUtils.getFile( org.apache.commons.io.FileUtils.getTempDirectoryPath(), filename); org.apache.commons.io.FileUtils.writeStringToFile(tmpFile, fileContent, false); return tmpFile; }
/** * Returns an override file (if it exists) for the given portal & cancer study. The override in * this case is the override file that a DataMatrix is created from. * * <p>Null is returned if an override file is not found. * * @param portalMetadata PortalMetadata * @param cancerStudyMetadata CancerStudyMetadata * @param filename String * @return File * @throws Exception */ @Override public File getOverrideFile( PortalMetadata portalMetadata, CancerStudyMetadata cancerStudyMetadata, String filename) throws Exception { File overrideFile = org.apache.commons.io.FileUtils.getFile( portalMetadata.getOverrideDirectory(), cancerStudyMetadata.getStudyPath(), filename); return (overrideFile.exists()) ? overrideFile : null; }
public static URI createNeoGraphURI(URI uri) { if (NeoURI.FILE_SCHEME.equals(uri.scheme())) { return createNeoGraphURI(FileUtils.getFile(uri.toFileString())); } else if (NEO_GRAPH_SCHEME.equals(uri.scheme())) { return NeoURI.createNeoURI(uri); } else { throw new IllegalArgumentException( MessageFormat.format("Can not create NeoGraphURI from the URI scheme {0}", uri.scheme())); } }
public LoadButtonAndSheetHandler() { File sheet = FileUtils.getFile( ConfigurationSettings.getPreviewDir(), "companions", "compact_companion.htm"); //$NON-NLS-1$ //$NON-NLS-2$ this.sheetSupport = new HtmlSheetSupport(infoPane, sheet.getAbsolutePath()); this.selectedRow = -1; this.selectionModel = companionsTable.getSelectionModel(); this.frame = (PCGenFrame) JOptionPane.getFrameForComponent(CompanionInfoTab.this); }
private static File getXMLTemplate(CharacterFacade character) { File template = FileUtils.getFile( ConfigurationSettings.getSystemsDir(), "gameModes", character.getDataSet().getGameMode().getName(), "base.xml.ftl"); if (!template.exists()) { template = new File(ConfigurationSettings.getOutputSheetsDir(), "base.xml.ftl"); } return template; }
@Test // SONAR-6184 public void testDuplicationFix() throws IOException { analyzeProject(projectDir, PROJECT_KEY, true); verifyDuplicationMeasures(PROJECT_KEY + ":module1", 1, 27, 1, 45); verifyDuplicationMeasures(PROJECT_KEY + ":module2", 1, 27, 1, 75); // remove File1 from module1 File f1 = FileUtils.getFile(projectDir, "module1", "src", "main", "xoo", "sample", "File1.xoo"); File f1m = FileUtils.getFile( projectDir, "module2", "src", "main", "xoo", "sample", "File1.xoo.measures"); f1.delete(); f1m.delete(); // duplication should be 0 analyzeProject(projectDir, PROJECT_KEY, false); verifyDuplicationMeasures(PROJECT_KEY + ":module1", 0, 0, 0, 0); verifyDuplicationMeasures(PROJECT_KEY + ":module2", 0, 0, 0, 0); }
public static void main(String[] args) throws IOException { String workDir = "E:/dev_workspace/tmp/workspace/duc2007"; String idfFilename = "duc2007.idf"; final double TOTAL_PAGE_COUNT = 30000000000.0D; Map<String, Double> idfValues = new HashMap<String, Double>(); File idfFIle = FileUtils.getFile(workDir + "/" + DIR_IDF_FILE, idfFilename); log.info("Loading idf value file[" + idfFIle.getAbsolutePath() + "]"); LineIterator lineIterator = null; try { lineIterator = FileUtils.lineIterator(idfFIle, DEFAULT_CHARSET.toString()); while (lineIterator.hasNext()) { String line = lineIterator.nextLine(); String[] strs = line.split("###"); if (strs.length != 2) { log.warn("Line[" + line + "] format is illegal, ignore it!"); continue; } idfValues.put(strs[0].trim(), Long.parseLong(strs[1]) / TOTAL_PAGE_COUNT); } log.info("Load idf value file[" + idfFIle.getAbsolutePath() + "] finished!"); } catch (IOException e) { log.error("Load idf value file[" + idfFIle.getAbsolutePath() + "] error!", e); throw e; } finally { if (lineIterator != null) { lineIterator.close(); } } String question = "Describe the legal battle between various recording artists and members of the record industry and the Internet music site Napster. What support, or lack thereof, have the litigants received?"; EhCacheUtil ehCacheUtil = new EhCacheUtil("db_cache_vec", "lab"); SummaryBuilderByVector summaryBuilder = new SummaryBuilderByVector( workDir, "0", "D0714D.txt", 10, idfValues, question, ehCacheUtil, 1.0f, 1.6f); ExecutorService es = Executors.newSingleThreadExecutor(); Future<Boolean> future = es.submit(summaryBuilder); try { future.get(); } catch (InterruptedException | ExecutionException e) { e.printStackTrace(); } es.shutdown(); EhCacheUtil.close(); }
/** * If it exists, moves an override file into the proper location in the given portals staging area * * @param portalMetadata PortalMetadata * @param cancerStudyMetadata CancerStudyMetadata * @param overrideFilename String * @param stagingFilename String * @throws Exception */ @Override public void applyOverride( PortalMetadata portalMetadata, CancerStudyMetadata cancerStudyMetadata, String overrideFilename, String stagingFilename) throws Exception { // check for override file File overrideFile = org.apache.commons.io.FileUtils.getFile( portalMetadata.getOverrideDirectory(), cancerStudyMetadata.getStudyPath(), overrideFilename); if (overrideFile.exists()) { File stagingFile = org.apache.commons.io.FileUtils.getFile( portalMetadata.getStagingDirectory(), cancerStudyMetadata.getStudyPath(), stagingFilename); if (LOG.isInfoEnabled()) { LOG.info( "applyOverride(), override file exists for " + stagingFile.getCanonicalPath() + ": " + overrideFile.getCanonicalPath()); } // copy override file to staging area if (overrideFile.isFile()) { org.apache.commons.io.FileUtils.copyFile(overrideFile, stagingFile); } else { org.apache.commons.io.FileUtils.copyDirectory(overrideFile, stagingFile); } } }
@Test // SONAR-6184 public void testGhostDuplication() throws IOException { analyzeProject(projectDir, PROJECT_KEY, true); verifyDuplicationMeasures(PROJECT_KEY + ":module1", 1, 27, 1, 45); verifyDuplicationMeasures(PROJECT_KEY + ":module2", 1, 27, 1, 75); // move File2 from module1 to module2 File src = FileUtils.getFile(projectDir, "module1", "src", "main", "xoo", "sample", "File2.xoo"); File dst = FileUtils.getFile(projectDir, "module2", "src", "main", "xoo", "sample", "File2.xoo"); FileUtils.moveFile(src, dst); src = new File(src.getParentFile(), "File2.xoo.measures"); dst = new File(dst.getParentFile(), "File2.xoo.measures"); FileUtils.moveFile(src, dst); // duplication should remain unchanged (except for % of duplication) analyzeProject(projectDir, PROJECT_KEY, false); verifyDuplicationMeasures(PROJECT_KEY + ":module1", 1, 27, 1, 75); verifyDuplicationMeasures(PROJECT_KEY + ":module2", 1, 27, 1, 45); }
/** * Method which writes the cancer study metadata file. * * @param portalMetadata PortalMetadata * @param cancerStudyMetadata CancerStudyMetadata * @param numCases int * @throws Exception */ @Override public void writeCancerStudyMetadataFile( PortalMetadata portalMetadata, CancerStudyMetadata cancerStudyMetadata, int numCases) throws Exception { File metaFile = org.apache.commons.io.FileUtils.getFile( portalMetadata.getStagingDirectory(), cancerStudyMetadata.getStudyPath(), cancerStudyMetadata.getCancerStudyMetadataFilename()); if (LOG.isInfoEnabled()) { LOG.info("writeMetadataFile(), meta file: " + metaFile); } PrintWriter writer = new PrintWriter(org.apache.commons.io.FileUtils.openOutputStream(metaFile, false)); writer.print("type_of_cancer: " + cancerStudyMetadata.getTumorType() + "\n"); writer.print("cancer_study_identifier: " + cancerStudyMetadata + "\n"); String name = (cancerStudyMetadata.getName().length() > 0) ? cancerStudyMetadata.getName() : cancerStudyMetadata.getTumorTypeMetadata().getName(); name = name.replaceAll( CancerStudyMetadata.TUMOR_TYPE_NAME_TAG, cancerStudyMetadata.getTumorTypeMetadata().getName()); writer.print("name: " + name + "\n"); String description = cancerStudyMetadata.getDescription(); description = description.replaceAll(CancerStudyMetadata.NUM_CASES_TAG, Integer.toString(numCases)); description = description.replaceAll( CancerStudyMetadata.TUMOR_TYPE_TAG, cancerStudyMetadata.getTumorTypeMetadata().getType()); description = description.replaceAll( CancerStudyMetadata.TUMOR_TYPE_NAME_TAG, cancerStudyMetadata.getTumorTypeMetadata().getName()); writer.print("description: " + description + "\n"); if (cancerStudyMetadata.getCitation().length() > 0) { writer.print("citation: " + cancerStudyMetadata.getCitation() + "\n"); } if (cancerStudyMetadata.getPMID().length() > 0) { writer.print("pmid: " + cancerStudyMetadata.getPMID() + "\n"); } writer.flush(); writer.close(); }
/** * Method which writes a metadata file for the given DatatypeMetadata. DataMatrix may be null. * * @param portalMetadata PortalMetadata * @param cancerStudyMetadata CancerStudyMetadata * @param datatypeMetadata DatatypeMetadata * @param dataMatrix DataMatrix * @throws Exception */ @Override public void writeMetadataFile( PortalMetadata portalMetadata, CancerStudyMetadata cancerStudyMetadata, DatatypeMetadata datatypeMetadata, DataMatrix dataMatrix) throws Exception { File metaFile = org.apache.commons.io.FileUtils.getFile( portalMetadata.getStagingDirectory(), cancerStudyMetadata.getStudyPath(), datatypeMetadata.getMetaFilename()); if (LOG.isInfoEnabled()) { LOG.info("writeMetadataFile(), meta file: " + metaFile); } PrintWriter writer = new PrintWriter(org.apache.commons.io.FileUtils.openOutputStream(metaFile, false)); writer.print("cancer_study_identifier: " + cancerStudyMetadata + "\n"); writer.print( "genetic_alteration_type: " + datatypeMetadata.getMetaGeneticAlterationType() + "\n"); String stableID = datatypeMetadata.getMetaStableID(); stableID = stableID.replaceAll(DatatypeMetadata.CANCER_STUDY_TAG, cancerStudyMetadata.toString()); writer.print("stable_id: " + stableID + "\n"); writer.print( "show_profile_in_analysis_tab: " + datatypeMetadata.getMetaShowProfileInAnalysisTab() + "\n"); String profileDescription = datatypeMetadata.getMetaProfileDescription(); if (dataMatrix != null) { profileDescription = profileDescription.replaceAll( DatatypeMetadata.NUM_GENES_TAG, Integer.toString(dataMatrix.getGeneIDs().size())); profileDescription = profileDescription.replaceAll( DatatypeMetadata.NUM_CASES_TAG, Integer.toString(dataMatrix.getCaseIDs().size())); } profileDescription = profileDescription.replaceAll( DatatypeMetadata.TUMOR_TYPE_TAG, cancerStudyMetadata.getTumorType()); writer.print("profile_description: " + profileDescription + "\n"); writer.print("profile_name: " + datatypeMetadata.getMetaProfileName() + "\n"); writer.flush(); writer.close(); }
private Optional<Consumer<String>> getOutputMethod(final String fileName) { Consumer<String> out; if (outputFile != null) { final String outputName = fileName.replace(".xml", ".java"); final File outFile = FileUtils.getFile(this.outputFile, outputName); out = (sourceCode) -> { try (FileWriter fw = new FileWriter(outFile)) { System.out.println("gm.compiler :: writing " + fileName + " to " + outFile.getPath()); fw.write(sourceCode); } catch (Exception ex) { Logger.getAnonymousLogger().log(Level.SEVERE, null, ex); } }; } else { out = this.outputMethod; } return Optional.ofNullable(out); }
/** * Runs all MAFs for the given dataaSourcesMetadata through the Oncotator and OMA tools. * * @param dataSourcesMetadata DataSourcesMetadata * @throws Exception */ @Override public void oncotateAllMAFs(DataSourcesMetadata dataSourcesMetadata) throws Exception { // iterate over datasource download directory and process all MAFs String[] extensions = new String[] {DatatypeMetadata.MAF_FILE_EXT}; for (File maf : listFiles(new File(dataSourcesMetadata.getDownloadDirectory()), extensions, true)) { // create temp for given maf File oncotatorInputFile = org.apache.commons.io.FileUtils.getFile( org.apache.commons.io.FileUtils.getTempDirectory(), "oncotatorInputFile"); org.apache.commons.io.FileUtils.copyFile(maf, oncotatorInputFile); // input is tmp file we just created, we want output to go into the original maf oncotateMAF( FileUtils.FILE_URL_PREFIX + oncotatorInputFile.getCanonicalPath(), FileUtils.FILE_URL_PREFIX + maf.getCanonicalPath()); // clean up org.apache.commons.io.FileUtils.forceDelete(oncotatorInputFile); } }
public static void main(String args[]) throws IOException { String outputDir = DEFAULT_DIR; String resources[] = DEFAULT_RESOURCES; if (args.length == 0) { // use default settings } else if (args.length == 1) { usage(); return; } else { resources = ArrayUtils.subarray(args, 1, args.length); } if (!new File(outputDir).isDirectory()) { System.err.println("Output directory '" + outputDir + "' does not exist"); usage(); return; } for (String resource : resources) { File dest = FileUtils.getFile(outputDir, resource); InputStream is = ResourceInstaller.class.getResourceAsStream(resource); if (is == null) { System.err.println("Couldn't find resource " + resource); usage(); return; } if (dest.isFile()) { File backup = new File(dest + ".backup"); System.err.println("backing up " + dest + " to " + backup); FileUtils.deleteQuietly(backup); FileUtils.moveFile(dest, backup); } FileUtils.copyInputStreamToFile(is, dest); System.err.println("creating file " + dest.getAbsolutePath() + " from resources"); is.close(); if (dest.getName().toLowerCase().endsWith(".sh")) { dest.setExecutable(true); } } }
/** * Create a case list file from the given case list metadata file. * * @param portalMetadata PortalMetadata * @param cancerStudyMetadata CancerStudyMetadata * @param caseListMetadata CaseListMetadata * @param caseList String[] * @throws Exception */ @Override public void writeCaseListFile( PortalMetadata portalMetadata, CancerStudyMetadata cancerStudyMetadata, CaseListMetadata caseListMetadata, String[] caseList) throws Exception { File caseListFile = org.apache.commons.io.FileUtils.getFile( portalMetadata.getStagingDirectory(), cancerStudyMetadata.getStudyPath(), "case_lists", caseListMetadata.getCaseListFilename()); if (LOG.isInfoEnabled()) { LOG.info("writeCaseListFile(), case list file: " + caseListFile.getCanonicalPath()); } PrintWriter writer = new PrintWriter(org.apache.commons.io.FileUtils.openOutputStream(caseListFile, false)); writer.print("cancer_study_identifier: " + cancerStudyMetadata + "\n"); String stableID = caseListMetadata.getMetaStableID(); stableID = stableID.replaceAll(DatatypeMetadata.CANCER_STUDY_TAG, cancerStudyMetadata.toString()); writer.print("stable_id: " + stableID + "\n"); writer.print("case_list_name: " + caseListMetadata.getMetaCaseListName() + "\n"); String caseListDescription = caseListMetadata.getMetaCaseListDescription(); caseListDescription = caseListDescription.replaceAll( DatatypeMetadata.NUM_CASES_TAG, Integer.toString(caseList.length)); writer.print("case_list_description: " + caseListDescription + "\n"); writer.print("case_list_category: " + caseListMetadata.getMetaCaseListCategory() + "\n"); writer.print("case_list_ids: "); for (String caseID : caseList) { writer.print(caseID + Converter.VALUE_DELIMITER); } writer.println(); writer.flush(); writer.close(); }
@Override public ConnectionState execute(Connection connection, ApplicationConfiguration configuration) { if (connection.getInputQueue().hasAny()) { String path = connection.getInputQueue().pop(); if (path.isEmpty()) { return connectionStateProvider.get(AdministrationMenu.class); } File file = FileUtils.getFile(path); if (file.exists()) { ImportConfiguration importConfiguration = new ImportConfiguration(); importConfiguration.setFile(file); databaseImportLauncher.launchWith(importConfiguration); return connectionStateProvider.get(AdministrationMenu.class); } else { String text = textMaker.getText( TextName.FileNotFound, connection.getLocale(), ImmutableMap.of("file path", path)); connection.getOutputQueue().push(text); return connectionStateProvider.get(ImportPathPrompt.class); } } return this; }
@Override public void read(String path) throws IOException { File dir = FileUtils.getFile(path, "ensemble", getName()); if (!dir.isDirectory()) { return; } try { ObjectInputStream oip = new ObjectInputStream(new FileInputStream(new File(dir, "similarityCoefficients"))); this.simlarityCoefficients = (TDoubleArrayList) oip.readObject(); oip.close(); oip = new ObjectInputStream(new FileInputStream(new File(dir, "mostSimilarCoefficients"))); this.mostSimilarCoefficients = (TDoubleArrayList) oip.readObject(); oip.close(); oip = new ObjectInputStream(new FileInputStream(new File(dir, "similarityInterpolator"))); this.similarityInterpolator = (Interpolator) oip.readObject(); oip.close(); oip = new ObjectInputStream(new FileInputStream(new File(dir, "mostSimilarInterpolator"))); this.mostSimilarInterpolator = (Interpolator) oip.readObject(); oip.close(); } catch (ClassNotFoundException e) { throw new IOException("Malformed coefficient file(s)", e); } }