List of usage examples for java.io File isDirectory
public boolean isDirectory()
From source file:fr.inria.edelweiss.kgdqp.core.CentralizedInferrencing.java
public static void main(String args[]) throws ParseException, EngineException, InterruptedException, IOException { List<String> endpoints = new ArrayList<String>(); String queryPath = null;// w w w . j av a 2s . com boolean rulesSelection = false; File rulesDir = null; File ontDir = null; ///////////////// Graph graph = Graph.create(); QueryProcess exec = QueryProcess.create(graph); Options options = new Options(); Option helpOpt = new Option("h", "help", false, "print this message"); // Option queryOpt = new Option("q", "query", true, "specify the sparql query file"); // Option endpointOpt = new Option("e", "endpoint", true, "a federated sparql endpoint URL"); Option versionOpt = new Option("v", "version", false, "print the version information and exit"); Option rulesOpt = new Option("r", "rulesDir", true, "directory containing the inference rules"); Option ontOpt = new Option("o", "ontologiesDir", true, "directory containing the ontologies for rules selection"); // Option locOpt = new Option("c", "centralized", false, "performs centralized inferences"); Option dataOpt = new Option("l", "load", true, "data file or directory to be loaded"); // Option selOpt = new Option("s", "rulesSelection", false, "if set to true, only the applicable rules are run"); // options.addOption(queryOpt); // options.addOption(endpointOpt); options.addOption(helpOpt); options.addOption(versionOpt); options.addOption(rulesOpt); options.addOption(ontOpt); // options.addOption(selOpt); // options.addOption(locOpt); options.addOption(dataOpt); String header = "Corese/KGRAM rule engine experiment command line interface"; String footer = "\nPlease report any issue to alban.gaignard@cnrs.fr, olivier.corby@inria.fr"; CommandLineParser parser = new BasicParser(); CommandLine cmd = parser.parse(options, args); if (cmd.hasOption("h")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("kgdqp", header, options, footer, true); System.exit(0); } if (cmd.hasOption("o")) { rulesSelection = true; String ontDirPath = cmd.getOptionValue("o"); ontDir = new File(ontDirPath); if (!ontDir.isDirectory()) { logger.warn(ontDirPath + " is not a valid directory path."); System.exit(0); } } if (!cmd.hasOption("r")) { logger.info("You must specify a path for inference rules directory !"); System.exit(0); } if (cmd.hasOption("l")) { String[] dataPaths = cmd.getOptionValues("l"); for (String path : dataPaths) { Load ld = Load.create(graph); ld.load(path); logger.info("Loaded " + path); } } if (cmd.hasOption("v")) { logger.info("version 3.0.4-SNAPSHOT"); System.exit(0); } String rulesDirPath = cmd.getOptionValue("r"); rulesDir = new File(rulesDirPath); if (!rulesDir.isDirectory()) { logger.warn(rulesDirPath + " is not a valid directory path."); System.exit(0); } // Local rules graph initialization Graph rulesG = Graph.create(); Load ld = Load.create(rulesG); if (rulesSelection) { // Ontology loading if (ontDir.isDirectory()) { for (File o : ontDir.listFiles()) { logger.info("Loading " + o.getAbsolutePath()); ld.load(o.getAbsolutePath()); } } } // Rules loading if (rulesDir.isDirectory()) { for (File r : rulesDir.listFiles()) { logger.info("Loading " + r.getAbsolutePath()); ld.load(r.getAbsolutePath()); } } // Rule engine initialization RuleEngine ruleEngine = RuleEngine.create(graph); ruleEngine.set(exec); ruleEngine.setOptimize(true); ruleEngine.setConstructResult(true); ruleEngine.setTrace(true); StopWatch sw = new StopWatch(); logger.info("Federated graph size : " + graph.size()); logger.info("Rules graph size : " + rulesG.size()); // Rule selection logger.info("Rules selection"); QueryProcess localKgram = QueryProcess.create(rulesG); ArrayList<String> applicableRules = new ArrayList<String>(); sw.start(); String rulesSelQuery = ""; if (rulesSelection) { rulesSelQuery = pertinentRulesQuery; } else { rulesSelQuery = allRulesQuery; } Mappings maps = localKgram.query(rulesSelQuery); logger.info("Rules selected in " + sw.getTime() + " ms"); logger.info("Applicable rules : " + maps.size()); // Selected rule loading for (Mapping map : maps) { IDatatype dt = (IDatatype) map.getValue("?res"); String rule = dt.getLabel(); //loading rule in the rule engine // logger.info("Adding rule : "); // System.out.println("-------"); // System.out.println(rule); // System.out.println(""); // if (! rule.toLowerCase().contains("sameas")) { applicableRules.add(rule); ruleEngine.addRule(rule); // } } // Rules application on distributed sparql endpoints logger.info("Rules application (" + applicableRules.size() + " rules)"); ExecutorService threadPool = Executors.newCachedThreadPool(); RuleEngineThread ruleThread = new RuleEngineThread(ruleEngine); sw.reset(); sw.start(); // ruleEngine.process(); threadPool.execute(ruleThread); threadPool.shutdown(); //monitoring loop while (!threadPool.isTerminated()) { // System.out.println("******************************"); // System.out.println(Util.jsonDqpCost(QueryProcessDQP.queryCounter, QueryProcessDQP.queryVolumeCounter, QueryProcessDQP.sourceCounter, QueryProcessDQP.sourceVolumeCounter)); // System.out.println("Rule engine running for " + sw.getTime() + " ms"); // System.out.println("Federated graph size : " + graph.size()); System.out.println(sw.getTime() + " , " + graph.size()); Thread.sleep(5000); } logger.info("Federated graph size : " + graph.size()); // logger.info(Util.jsonDqpCost(QueryProcessDQP.queryCounter, QueryProcessDQP.queryVolumeCounter, QueryProcessDQP.sourceCounter, QueryProcessDQP.sourceVolumeCounter)); // TripleFormat f = TripleFormat.create(graph, true); // f.write("/tmp/gAll.ttl"); }
From source file:de.huberlin.cuneiform.main.Main.java
public static void main(String[] args) throws ParseException, IOException, NotDerivableException, InterruptedException, JSONException { GnuParser gnuParser;/*from w ww. ja v a 2s .c o m*/ CommandLine cmdline; Options opt; String value; int platform; File outputDir; String[] fileList; StringBuffer buf; String line; String dagid; File logFile; opt = new Options(); opt.addOption("p", "platform", true, "The platform to perform the Cuneiform script's interpretation. " + "Possible platforms are: 'dot', 'local', and 'debug'. Default is 'local'."); opt.addOption("d", "directory", true, "The output directory, to put the interpretation intermediate and output result as well as the default location to store the log."); opt.addOption("c", "clean", false, "If set, the execution engine ignores all cached results and starts a clean workflow run."); opt.addOption("r", "runid", true, "If set, a custom id is set for this workflow run. By default a UUID string is used."); opt.addOption("f", "file", true, "Override the default location of the log file and use the specified filename instead. If the platform is 'dot', this option sets the name of the output dot-file."); opt.addOption("h", "help", false, "Print help text."); gnuParser = new GnuParser(); cmdline = gnuParser.parse(opt, args); if (cmdline.hasOption("help")) { System.out.println("CUNEIFORM - A Functional Workflow Language\n" + LABEL_VERSION); new HelpFormatter().printHelp("java -jar cuneiform.jar [OPTION]*", opt); return; } if (cmdline.hasOption("platform")) { value = cmdline.getOptionValue("platform"); if (value.equals("dot")) platform = PLATFORM_DOT; else if (value.equals("local")) platform = PLATFORM_LOCAL; else if (value.equals("debug")) platform = PLATFORM_DEBUG; else throw new RuntimeException("Specified platform '" + value + "' not recognized."); } else platform = PLATFORM_LOCAL; if (cmdline.hasOption('d')) { value = cmdline.getOptionValue('d'); } else value = "build"; outputDir = new File(value); if (outputDir.exists()) { if (!outputDir.isDirectory()) throw new IOException( "Output directory '" + outputDir.getAbsolutePath() + "' exists but is not a directory."); else if (cmdline.hasOption('c')) { FileUtils.deleteDirectory(outputDir); if (!outputDir.mkdirs()) throw new IOException( "Could not create output directory '" + outputDir.getAbsolutePath() + "'"); } } else if (!outputDir.mkdirs()) throw new IOException("Could not create output directory '" + outputDir.getAbsolutePath() + "'"); if (cmdline.hasOption('r')) dagid = cmdline.getOptionValue('r'); else dagid = UUID.randomUUID().toString(); if (cmdline.hasOption('f')) logFile = new File(cmdline.getOptionValue('f')); else logFile = null; fileList = cmdline.getArgs(); buf = new StringBuffer(); if (fileList.length == 0) { try (BufferedReader reader = new BufferedReader(new InputStreamReader(System.in))) { while ((line = reader.readLine()) != null) buf.append(line).append('\n'); } switch (platform) { case PLATFORM_DOT: createDot(buf.toString(), outputDir, logFile); break; case PLATFORM_LOCAL: runLocal(buf.toString(), outputDir, logFile, dagid); break; case PLATFORM_DEBUG: runDebug(buf.toString(), outputDir, logFile, dagid); break; default: throw new RuntimeException("Platform not recognized."); } } else switch (platform) { case PLATFORM_DOT: createDot(fileList, outputDir, logFile); break; case PLATFORM_LOCAL: runLocal(fileList, outputDir, logFile, dagid); break; case PLATFORM_DEBUG: runDebug(fileList, outputDir, logFile, dagid); break; default: throw new RuntimeException("Platform not recognized."); } }
From source file:fr.inria.edelweiss.kgdqp.core.CentralizedInferrencingNoSpin.java
public static void main(String args[]) throws ParseException, EngineException, InterruptedException, IOException, LoadException { List<String> endpoints = new ArrayList<String>(); String queryPath = null;/*from w ww . j av a 2s . c o m*/ boolean rulesSelection = false; File rulesDir = null; File ontDir = null; ///////////////// Graph graph = Graph.create(); QueryProcess exec = QueryProcess.create(graph); Options options = new Options(); Option helpOpt = new Option("h", "help", false, "print this message"); // Option queryOpt = new Option("q", "query", true, "specify the sparql query file"); // Option endpointOpt = new Option("e", "endpoint", true, "a federated sparql endpoint URL"); Option versionOpt = new Option("v", "version", false, "print the version information and exit"); Option rulesOpt = new Option("r", "rulesDir", true, "directory containing the inference rules"); Option ontOpt = new Option("o", "ontologiesDir", true, "directory containing the ontologies for rules selection"); // Option locOpt = new Option("c", "centralized", false, "performs centralized inferences"); Option dataOpt = new Option("l", "load", true, "data file or directory to be loaded"); // Option selOpt = new Option("s", "rulesSelection", false, "if set to true, only the applicable rules are run"); // options.addOption(queryOpt); // options.addOption(endpointOpt); options.addOption(helpOpt); options.addOption(versionOpt); options.addOption(rulesOpt); options.addOption(ontOpt); // options.addOption(selOpt); // options.addOption(locOpt); options.addOption(dataOpt); String header = "Corese/KGRAM rule engine experiment command line interface"; String footer = "\nPlease report any issue to alban.gaignard@cnrs.fr, olivier.corby@inria.fr"; CommandLineParser parser = new BasicParser(); CommandLine cmd = parser.parse(options, args); if (cmd.hasOption("h")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("kgdqp", header, options, footer, true); System.exit(0); } if (cmd.hasOption("o")) { rulesSelection = true; String ontDirPath = cmd.getOptionValue("o"); ontDir = new File(ontDirPath); if (!ontDir.isDirectory()) { logger.warn(ontDirPath + " is not a valid directory path."); System.exit(0); } } if (!cmd.hasOption("r")) { logger.info("You must specify a path for inference rules directory !"); System.exit(0); } if (cmd.hasOption("l")) { String[] dataPaths = cmd.getOptionValues("l"); for (String path : dataPaths) { Load ld = Load.create(graph); ld.load(path); logger.info("Loaded " + path); } } if (cmd.hasOption("v")) { logger.info("version 3.0.4-SNAPSHOT"); System.exit(0); } String rulesDirPath = cmd.getOptionValue("r"); rulesDir = new File(rulesDirPath); if (!rulesDir.isDirectory()) { logger.warn(rulesDirPath + " is not a valid directory path."); System.exit(0); } // Local rules graph initialization Graph rulesG = Graph.create(); Load ld = Load.create(rulesG); if (rulesSelection) { // Ontology loading if (ontDir.isDirectory()) { for (File o : ontDir.listFiles()) { logger.info("Loading " + o.getAbsolutePath()); ld.load(o.getAbsolutePath()); } } } // Rules loading if (rulesDir.isDirectory()) { for (File r : rulesDir.listFiles()) { if (r.getAbsolutePath().endsWith(".rq")) { logger.info("Loading " + r.getAbsolutePath()); // ld.load(r.getAbsolutePath()); // byte[] encoded = Files.readAllBytes(Paths.get(r.getAbsolutePath())); // String construct = new String(encoded, "UTF-8"); //StandardCharsets.UTF_8); FileInputStream f = new FileInputStream(r); QueryLoad ql = QueryLoad.create(); String construct = ql.read(f); f.close(); SPINProcess sp = SPINProcess.create(); String spinConstruct = sp.toSpin(construct); ld.load(new ByteArrayInputStream(spinConstruct.getBytes()), Load.TURTLE_FORMAT); logger.info("Rules graph size : " + rulesG.size()); } } } // Rule engine initialization RuleEngine ruleEngine = RuleEngine.create(graph); ruleEngine.set(exec); ruleEngine.setOptimize(true); ruleEngine.setConstructResult(true); ruleEngine.setTrace(true); StopWatch sw = new StopWatch(); logger.info("Federated graph size : " + graph.size()); logger.info("Rules graph size : " + rulesG.size()); // Rule selection logger.info("Rules selection"); QueryProcess localKgram = QueryProcess.create(rulesG); ArrayList<String> applicableRules = new ArrayList<String>(); sw.start(); String rulesSelQuery = ""; if (rulesSelection) { rulesSelQuery = pertinentRulesQuery; } else { rulesSelQuery = allRulesQuery; } Mappings maps = localKgram.query(rulesSelQuery); logger.info("Rules selected in " + sw.getTime() + " ms"); logger.info("Applicable rules : " + maps.size()); // Selected rule loading for (Mapping map : maps) { IDatatype dt = (IDatatype) map.getValue("?res"); String rule = dt.getLabel(); //loading rule in the rule engine // logger.info("Adding rule : "); // System.out.println("-------"); // System.out.println(rule); // System.out.println(""); // if (! rule.toLowerCase().contains("sameas")) { applicableRules.add(rule); ruleEngine.addRule(rule); // } } // Rules application on distributed sparql endpoints logger.info("Rules application (" + applicableRules.size() + " rules)"); ExecutorService threadPool = Executors.newCachedThreadPool(); RuleEngineThread ruleThread = new RuleEngineThread(ruleEngine); sw.reset(); sw.start(); // ruleEngine.process(); threadPool.execute(ruleThread); threadPool.shutdown(); //monitoring loop while (!threadPool.isTerminated()) { // System.out.println("******************************"); // System.out.println(Util.jsonDqpCost(QueryProcessDQP.queryCounter, QueryProcessDQP.queryVolumeCounter, QueryProcessDQP.sourceCounter, QueryProcessDQP.sourceVolumeCounter)); // System.out.println("Rule engine running for " + sw.getTime() + " ms"); // System.out.println("Federated graph size : " + graph.size()); System.out.println(sw.getTime() + " , " + graph.size()); Thread.sleep(5000); } logger.info("Federated graph size : " + graph.size()); // logger.info(Util.jsonDqpCost(QueryProcessDQP.queryCounter, QueryProcessDQP.queryVolumeCounter, QueryProcessDQP.sourceCounter, QueryProcessDQP.sourceVolumeCounter)); // TripleFormat f = TripleFormat.create(graph, true); // f.write("/tmp/gAll.ttl"); }
From source file:com.moviejukebox.MovieJukebox.java
public static void main(String[] args) throws Throwable { JukeboxStatistics.setTimeStart(System.currentTimeMillis()); // Create the log file name here, so we can change it later (because it's locked System.setProperty("file.name", LOG_FILENAME); PropertyConfigurator.configure("properties/log4j.properties"); LOG.info("Yet Another Movie Jukebox {}", GitRepositoryState.getVersion()); LOG.info("~~~ ~~~~~~~ ~~~~~ ~~~~~~~ {}", StringUtils.repeat("~", GitRepositoryState.getVersion().length())); LOG.info("https://github.com/YAMJ/yamj-v2"); LOG.info("Copyright (c) 2004-2016 YAMJ Members"); LOG.info(""); LOG.info("This software is licensed under the GNU General Public License v3+"); LOG.info("See this page: https://github.com/YAMJ/yamj-v2/wiki/License"); LOG.info(""); LOG.info(" Revision SHA: {} {}", GIT.getCommitId(), GIT.getDirty() ? "(Custom Build)" : ""); LOG.info(" Commit Date: {}", GIT.getCommitTime()); LOG.info(" Build Date: {}", GIT.getBuildTime()); LOG.info(""); LOG.info(" Java Version: {}", GitRepositoryState.getJavaVersion()); LOG.info(""); if (!SystemTools.validateInstallation()) { LOG.info("ABORTING."); return;// w w w . j a va2s . c o m } String movieLibraryRoot = null; String jukeboxRoot = null; Map<String, String> cmdLineProps = new LinkedHashMap<>(); try { for (int i = 0; i < args.length; i++) { String arg = args[i]; if ("-v".equalsIgnoreCase(arg)) { // We've printed the version, so quit now return; } else if ("-t".equalsIgnoreCase(arg)) { String pin = args[++i]; // load the apikeys.properties file if (!setPropertiesStreamName("./properties/apikeys.properties", Boolean.TRUE)) { return; } // authorize to Trakt.TV TraktTV.getInstance().initialize().authorizeWithPin(pin); // We've authorized access to Trakt.TV, so quit now return; } else if ("-o".equalsIgnoreCase(arg)) { jukeboxRoot = args[++i]; PropertiesUtil.setProperty("mjb.jukeboxRoot", jukeboxRoot); } else if ("-c".equalsIgnoreCase(arg)) { jukeboxClean = Boolean.TRUE; PropertiesUtil.setProperty("mjb.jukeboxClean", TRUE); } else if ("-k".equalsIgnoreCase(arg)) { setJukeboxPreserve(Boolean.TRUE); } else if ("-p".equalsIgnoreCase(arg)) { userPropertiesName = args[++i]; } else if ("-i".equalsIgnoreCase(arg)) { skipIndexGeneration = Boolean.TRUE; PropertiesUtil.setProperty("mjb.skipIndexGeneration", TRUE); } else if ("-h".equalsIgnoreCase(arg)) { skipHtmlGeneration = Boolean.TRUE; PropertiesUtil.setProperty("mjb.skipHtmlGeneration", Boolean.TRUE); } else if ("-dump".equalsIgnoreCase(arg)) { dumpLibraryStructure = Boolean.TRUE; } else if ("-memory".equalsIgnoreCase(arg)) { showMemory = Boolean.TRUE; PropertiesUtil.setProperty("mjb.showMemory", Boolean.TRUE); } else if (arg.startsWith("-D")) { String propLine = arg.length() > 2 ? arg.substring(2) : args[++i]; int propDiv = propLine.indexOf('='); if (-1 != propDiv) { cmdLineProps.put(propLine.substring(0, propDiv), propLine.substring(propDiv + 1)); } } else if (arg.startsWith("-")) { help(); return; } else { movieLibraryRoot = args[i]; } } } catch (Exception error) { LOG.error("Wrong arguments specified"); help(); return; } // Save the name of the properties file for use later setProperty("userPropertiesName", userPropertiesName); LOG.info("Processing started at {}", new Date()); LOG.info(""); // Load the moviejukebox-default.properties file if (!setPropertiesStreamName("./properties/moviejukebox-default.properties", Boolean.TRUE)) { return; } // Load the user properties file "moviejukebox.properties" // No need to abort if we don't find this file // Must be read before the skin, because this may contain an override skin setPropertiesStreamName(userPropertiesName, Boolean.FALSE); // Grab the skin from the command-line properties if (cmdLineProps.containsKey(SKIN_DIR)) { setProperty(SKIN_DIR, cmdLineProps.get(SKIN_DIR)); } // Load the skin.properties file if (!setPropertiesStreamName(getProperty(SKIN_DIR, SKIN_DEFAULT) + "/skin.properties", Boolean.TRUE)) { return; } // Load the skin-user.properties file (ignore the error) setPropertiesStreamName(getProperty(SKIN_DIR, SKIN_DEFAULT) + "/skin-user.properties", Boolean.FALSE); // Load the overlay.properties file (ignore the error) String overlayRoot = getProperty("mjb.overlay.dir", Movie.UNKNOWN); overlayRoot = (PropertiesUtil.getBooleanProperty("mjb.overlay.skinroot", Boolean.TRUE) ? (getProperty(SKIN_DIR, SKIN_DEFAULT) + File.separator) : "") + (StringTools.isValidString(overlayRoot) ? (overlayRoot + File.separator) : ""); setPropertiesStreamName(overlayRoot + "overlay.properties", Boolean.FALSE); // Load the apikeys.properties file if (!setPropertiesStreamName("./properties/apikeys.properties", Boolean.TRUE)) { return; } // This is needed to update the static reference for the API Keys in the pattern formatter // because the formatter is initialised before the properties files are read FilteringLayout.addApiKeys(); // Load the rest of the command-line properties for (Map.Entry<String, String> propEntry : cmdLineProps.entrySet()) { setProperty(propEntry.getKey(), propEntry.getValue()); } // Read the information about the skin SkinProperties.readSkinVersion(); // Display the information about the skin SkinProperties.printSkinVersion(); StringBuilder properties = new StringBuilder("{"); for (Map.Entry<Object, Object> propEntry : PropertiesUtil.getEntrySet()) { properties.append(propEntry.getKey()); properties.append("="); properties.append(propEntry.getValue()); properties.append(","); } properties.replace(properties.length() - 1, properties.length(), "}"); // Print out the properties to the log file. LOG.debug("Properties: {}", properties.toString()); // Check for mjb.skipIndexGeneration and set as necessary // This duplicates the "-i" functionality, but allows you to have it in the property file skipIndexGeneration = PropertiesUtil.getBooleanProperty("mjb.skipIndexGeneration", Boolean.FALSE); if (PropertiesUtil.getBooleanProperty("mjb.people", Boolean.FALSE)) { peopleScan = Boolean.TRUE; peopleScrape = PropertiesUtil.getBooleanProperty("mjb.people.scrape", Boolean.TRUE); peopleMax = PropertiesUtil.getIntProperty("mjb.people.maxCount", 10); popularity = PropertiesUtil.getIntProperty("mjb.people.popularity", 5); // Issue 1947: Cast enhancement - option to save all related files to a specific folder peopleFolder = PropertiesUtil.getProperty("mjb.people.folder", ""); if (isNotValidString(peopleFolder)) { peopleFolder = ""; } else if (!peopleFolder.endsWith(File.separator)) { peopleFolder += File.separator; } StringTokenizer st = new StringTokenizer( PropertiesUtil.getProperty("photo.scanner.photoExtensions", "jpg,jpeg,gif,bmp,png"), ",;| "); while (st.hasMoreTokens()) { PHOTO_EXTENSIONS.add(st.nextToken()); } } // Check for mjb.skipHtmlGeneration and set as necessary // This duplicates the "-h" functionality, but allows you to have it in the property file skipHtmlGeneration = PropertiesUtil.getBooleanProperty("mjb.skipHtmlGeneration", Boolean.FALSE); // Look for the parameter in the properties file if it's not been set on the command line // This way we don't overwrite the setting if it's not found and defaults to FALSE showMemory = PropertiesUtil.getBooleanProperty("mjb.showMemory", Boolean.FALSE); // This duplicates the "-c" functionality, but allows you to have it in the property file jukeboxClean = PropertiesUtil.getBooleanProperty("mjb.jukeboxClean", Boolean.FALSE); MovieFilenameScanner.setSkipKeywords( tokenizeToArray(getProperty("filename.scanner.skip.keywords", ""), ",;| "), PropertiesUtil.getBooleanProperty("filename.scanner.skip.caseSensitive", Boolean.TRUE)); MovieFilenameScanner.setSkipRegexKeywords( tokenizeToArray(getProperty("filename.scanner.skip.keywords.regex", ""), ","), PropertiesUtil.getBooleanProperty("filename.scanner.skip.caseSensitive.regex", Boolean.TRUE)); MovieFilenameScanner.setExtrasKeywords( tokenizeToArray(getProperty("filename.extras.keywords", "trailer,extra,bonus"), ",;| ")); MovieFilenameScanner.setMovieVersionKeywords(tokenizeToArray( getProperty("filename.movie.versions.keywords", "remastered,directors cut,extended cut,final cut"), ",;|")); MovieFilenameScanner.setLanguageDetection( PropertiesUtil.getBooleanProperty("filename.scanner.language.detection", Boolean.TRUE)); final KeywordMap languages = PropertiesUtil.getKeywordMap("filename.scanner.language.keywords", null); if (!languages.isEmpty()) { MovieFilenameScanner.clearLanguages(); for (String lang : languages.getKeywords()) { String values = languages.get(lang); if (values != null) { MovieFilenameScanner.addLanguage(lang, values, values); } else { LOG.info("No values found for language code '{}'", lang); } } } final KeywordMap sourceKeywords = PropertiesUtil.getKeywordMap("filename.scanner.source.keywords", "HDTV,PDTV,DVDRip,DVDSCR,DSRip,CAM,R5,LINE,HD2DVD,DVD,DVD5,DVD9,HRHDTV,MVCD,VCD,TS,VHSRip,BluRay,HDDVD,D-THEATER,SDTV"); MovieFilenameScanner.setSourceKeywords(sourceKeywords.getKeywords(), sourceKeywords); String temp = getProperty("sorting.strip.prefixes"); if (temp != null) { StringTokenizer st = new StringTokenizer(temp, ","); while (st.hasMoreTokens()) { String token = st.nextToken().trim(); if (token.startsWith("\"") && token.endsWith("\"")) { token = token.substring(1, token.length() - 1); } Movie.addSortIgnorePrefixes(token.toLowerCase()); } } enableWatchScanner = PropertiesUtil.getBooleanProperty("watched.scanner.enable", Boolean.TRUE); enableWatchTraktTv = PropertiesUtil.getBooleanProperty("watched.trakttv.enable", Boolean.FALSE); enableCompleteMovies = PropertiesUtil.getBooleanProperty("complete.movies.enable", Boolean.TRUE); // Check to see if don't have a root, check the property file if (StringTools.isNotValidString(movieLibraryRoot)) { movieLibraryRoot = getProperty("mjb.libraryRoot"); if (StringTools.isValidString(movieLibraryRoot)) { LOG.info("Got libraryRoot from properties file: {}", movieLibraryRoot); } else { LOG.error("No library root found!"); help(); return; } } if (jukeboxRoot == null) { jukeboxRoot = getProperty("mjb.jukeboxRoot"); if (jukeboxRoot == null) { LOG.info("jukeboxRoot is null in properties file. Please fix this as it may cause errors."); } else { LOG.info("Got jukeboxRoot from properties file: {}", jukeboxRoot); } } File f = new File(movieLibraryRoot); if (f.exists() && f.isDirectory() && jukeboxRoot == null) { jukeboxRoot = movieLibraryRoot; } if (movieLibraryRoot == null) { help(); return; } if (jukeboxRoot == null) { LOG.info("Wrong arguments specified: you must define the jukeboxRoot property (-o) !"); help(); return; } if (!f.exists()) { LOG.error("Directory or library configuration file '{}', not found.", movieLibraryRoot); return; } FileTools.initUnsafeChars(); FileTools.initSubtitleExtensions(); // make canonical names jukeboxRoot = FileTools.getCanonicalPath(jukeboxRoot); movieLibraryRoot = FileTools.getCanonicalPath(movieLibraryRoot); MovieJukebox ml = new MovieJukebox(movieLibraryRoot, jukeboxRoot); if (dumpLibraryStructure) { LOG.warn( "WARNING !!! A dump of your library directory structure will be generated for debug purpose. !!! Library won't be built or updated"); ml.makeDumpStructure(); } else { ml.generateLibrary(); } // Now rename the log files renameLogFile(); if (ScanningLimit.isLimitReached()) { LOG.warn("Scanning limit of {} was reached, please re-run to complete processing.", ScanningLimit.getLimit()); System.exit(EXIT_SCAN_LIMIT); } else { System.exit(EXIT_NORMAL); } }
From source file:edu.duke.igsp.gkde.Main.java
public static void main(String[] argv) throws Exception { Options opts = new Options(); opts.addOption("s", true, "wiggle track step (default=1)"); opts.addOption("l", true, "feature length (default=600)"); opts.addOption("f", true, "fragment size (default=estimated from data)"); // opts.addOption("b", true, "bandwidth (default=200)"); // opts.addOption("w", true, "window (default=3800"); opts.addOption("wg", true, "wg threshold set (defualt = calculated)"); opts.addOption("c", true, "genomic total read weight (defualt = calculated)"); opts.addOption("h", false, "print usage"); opts.addOption(OptionBuilder.withArgName("input dir").hasArg() .withDescription("input directory (default=current directory)").isRequired(false).create("d")); opts.addOption(OptionBuilder.withArgName("output dir").hasArg() .withDescription("output directory (default=current directory)").isRequired(false).create("o")); opts.addOption(OptionBuilder.withArgName("background dir").hasArg() .withDescription("background directory (default=none)").isRequired(false).create("b")); opts.addOption(OptionBuilder.withArgName("ploidy dir").hasArg() .withDescription("ploidy/input directory (default=none)").isRequired(false).create("p")); opts.addOption(OptionBuilder.withArgName("wig | bed | npf").hasArg() .withDescription("output format (default wig)").isRequired(false).create("of")); opts.addOption(OptionBuilder.withArgName("dnase | chip | faire | atac").hasArg() .withDescription("input data").isRequired(true).create("in")); opts.addOption(OptionBuilder.withArgName("weight clip").hasArg() .withDescription("weight clip value (default none)").isRequired(false).create("wc")); opts.addOption("t", true, "threshold (standard deviations) (default=4.0)"); // opts.addOption("r", true, "background ratio (default=2.0)"); opts.addOption("v", false, "verbose output"); CommandLineParser parser = new GnuParser(); int fragment_size = -1; int fragment_offset = 0; long featureLength = 600l; // float thresh = 2; float threshold = KDEChromosome.Settings.DEFAULT_THRESHOLD; int step = 1; boolean showHelp = false; boolean verbose = false; String inputDirectory = null; String backgroundDirectory = null; String ploidyDirectory = null; String[] files = null;//from w w w . j a v a2 s. c o m String[] bgfiles = {}; String[] ipfiles = {}; String outputFormat = "wig"; String inputDataType = "dnase"; File outputDirectory = new File(System.getProperty("user.dir")); long bandwidth = 0l; long window = 0l; double ncuts = 0.0d; float temp_threshold = 0f; int weight_clip = 0; System.out.println("F-Seq Version 1.85"); try { CommandLine cmd = parser.parse(opts, argv); showHelp = (cmd.hasOption("h")); verbose = (cmd.hasOption("v")); if (cmd.hasOption("s")) step = Integer.parseInt(cmd.getOptionValue("s")); if (cmd.hasOption("f")) fragment_size = Integer.parseInt(cmd.getOptionValue("f")); if (cmd.hasOption("d")) //input directory inputDirectory = cmd.getOptionValue("d"); if (cmd.hasOption("b")) //background directory backgroundDirectory = cmd.getOptionValue("b"); if (cmd.hasOption("p")) //ploidy|input directory ploidyDirectory = cmd.getOptionValue("p"); if (cmd.hasOption("l")) // bandwidth featureLength = Long.parseLong(cmd.getOptionValue("l")); if (cmd.hasOption("of")) { // output format outputFormat = cmd.getOptionValue("of"); if (!outputFormat.equals("wig") && !outputFormat.equals("bed") && !outputFormat.equals("npf")) { System.out.println("Parameter error: output format must be 'wig' or 'bed'."); showHelp = true; } } if (cmd.hasOption("in")) { // input data type inputDataType = cmd.getOptionValue("in"); if (!inputDataType.equals("dnase") && !inputDataType.equals("chip") && !inputDataType.equals("faire") && !inputDataType.equals("atac")) { System.out.println( "Parameter error: input data type must be 'dnase', 'chip', 'faire', or 'atac'."); showHelp = true; } } if (cmd.hasOption("wc")) { // weight clip weight_clip = Integer.parseInt(cmd.getOptionValue("wc")); } if (cmd.hasOption("t")) { // threshold (standard deviations) threshold = Float.parseFloat(cmd.getOptionValue("t")); } if (cmd.hasOption("o")) { // output directory String out = cmd.getOptionValue("o"); outputDirectory = new File(out); if (!outputDirectory.exists() && !outputDirectory.isDirectory()) { System.out.println("Output directory '" + out + "' is not a valid directory."); showHelp = true; } } if (cmd.hasOption("wg")) temp_threshold = Float.parseFloat(cmd.getOptionValue("wg")); if (cmd.hasOption("c")) ncuts = Double.parseDouble(cmd.getOptionValue("c")); // TESTING ONLY // if(cmd.hasOption("w")) // window // window = Long.parseLong(cmd.getOptionValue("w")); //if(cmd.hasOption("b")) // window // bandwidth = Long.parseLong(cmd.getOptionValue("b")); files = cmd.getArgs(); // input files //bgfiles = cmd.getArgs(); // background files } catch (Exception e) { System.out.println("Error parsing arguments: " + e.getMessage()); e.printStackTrace(); showHelp = true; } if (showHelp || (inputDirectory == null && files.length == 0)) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("fseq [options]... [file(s)]...", opts); System.exit(1); } File[] pfiles = getFiles(inputDirectory, files); File[] background_files = getFiles(backgroundDirectory, bgfiles); File[] ploidy_files = getFiles(ploidyDirectory, ipfiles); KDEChromosome[] chrs = null; // assume all files are of the same type, if not we'll get parsing errors String path = pfiles[0].getPath(); String extension = path.substring(path.lastIndexOf('.')).toLowerCase(); System.out.println("Path: " + path + ", extension: " + extension); if (extension.equals(".bed")) { System.out.println("Parsing BED file."); chrs = BedReader.read(pfiles); } else if (extension.equals(".sam") || extension.equals(".bam")) { System.out.println("Parsing SAM/BAM file."); chrs = SamReader.read(pfiles, weight_clip); } //KDEChromosome[] input = BedReader.read(ifiles); //compute fragment offset if (fragment_size == -1) { fragment_size = wgShiftCalc(chrs); } fragment_offset = (int) (fragment_size / 2); if (ncuts == 0.0d) { for (int i = 0; i < chrs.length; ++i) { // computes the total read weight of all cuts on a chromosome ncuts += chrs[i].getTotalWeight(); } } KDEChromosome.Settings settings = null; if (bandwidth > 0 || window > 0) { settings = new KDEChromosome.Settings(bandwidth, window, threshold, fragment_offset, ncuts, inputDataType); } else { settings = new KDEChromosome.Settings(featureLength, threshold, fragment_offset, ncuts, inputDataType); } float wg_threshold = wgThreshold(settings, chrs); if (temp_threshold != 0f) { wg_threshold = temp_threshold; } //KDEChromosome.Settings bg_settings = null; //bg_settings = new KDEChromosome.Settings(featureLength*2, threshold, fragment_offset); //int background_size = 0; //int input_size = 0; //float bg_ratio = 0; //float sd = 0; if (verbose) { System.out.println("Settings: "); System.out.println("\twindow=" + (settings.window * 2)); System.out.println("\tbandwidth=" + (settings.bandwidth)); //System.out.println("\tfragment offset=" + (settings.offset)); System.out.println("\tthreshold = " + wg_threshold); System.out.println("\test. fragment size = " + fragment_size); System.out.println("\tsequence length = " + chrs[0].getSequenceLength()); } // if(backgroundDirectory != null) { // for(int i = 0; i < input.length; ++i) { // background_size += input[i].getLength(); // } // for(int i = 0; i < chrs.length; ++i) { // input_size += chrs[i].getLength(); // } // bg_ratio = (float)input_size/(float)background_size; // sd = computeSD(bg_settings, input); // //System.out.println("Sample Ratio: " + bg_ratio); // //System.out.println("Input Size: " + input_size); // //System.out.println("Background Size: " + background_size); // //System.out.println("Input standard deviation: " + (settings.threshold * (float)Math.sqrt((double)bg_ratio * (double)sd * (double)sd))); // //System.out.println("Data standard deviation: " + settings.threshold * computeSD(settings, chrs)); // } for (int i = 0; i < chrs.length; ++i) { if (chrs[i].getFirstPos() == chrs[i].getLastPos()) { System.out.println("Warning: " + chrs[i].getChromosome() + " has size zero. Skipping."); continue; } File ofile = Util.makeUniqueFileWithExtension(outputDirectory, chrs[i].getChromosome(), outputFormat); DensityWriter dw = null; if (outputFormat.equals("wig")) { dw = new WiggleDensityWriter(ofile, chrs[i].getChromosome(), chrs[i].getFirstPos(), step); } else { if (outputFormat.equals("npf")) { dw = new NpfDensityWriter(ofile, chrs[i].getChromosome(), chrs[i].getFirstPos(), step); } else { dw = new BedDensityWriter(ofile, chrs[i].getChromosome(), chrs[i].getFirstPos(), step); } } //Function takes all? or new function for each? // if(backgroundDirectory != null) { // boolean hit = false; // for(int j = 0; j < background_files.length; ++j) { // if(background_files[j].getName().equals(chrs[i].getChromosome() + ".bff")) { // System.out.println("Running background on Chromosome " + chrs[i].getChromosome()); // chrs[i].runBG(settings, dw, verbose, wg_threshold, background_files[j]); // hit = true; // } // } // if(!hit) // System.out.println("No background for Chromosome " + chrs[i].getChromosome()); // } else { // if(ploidyDirectory !=) // chrs[i].run(settings, dw, verbose, wg_threshold); // } chrs[i].run(settings, dw, verbose, wg_threshold, background_files, ploidy_files); dw.close(); } //kde.showGraph(); }
From source file:ch.kostceco.tools.kostval.KOSTVal.java
/** Die Eingabe besteht aus 2 oder 3 Parameter: [0] Validierungstyp [1] Pfad zur Val-File [2] * option: Verbose//from ww w. ja v a2 s .c o m * * @param args * @throws IOException */ @SuppressWarnings("unused") public static void main(String[] args) throws IOException { ApplicationContext context = new ClassPathXmlApplicationContext("classpath:config/applicationContext.xml"); // Zeitstempel Start java.util.Date nowStart = new java.util.Date(); java.text.SimpleDateFormat sdfStart = new java.text.SimpleDateFormat("dd.MM.yyyy HH:mm:ss"); String ausgabeStart = sdfStart.format(nowStart); /* TODO: siehe Bemerkung im applicationContext-services.xml bezglich Injection in der * Superklasse aller Impl-Klassen ValidationModuleImpl validationModuleImpl = * (ValidationModuleImpl) context.getBean("validationmoduleimpl"); */ KOSTVal kostval = (KOSTVal) context.getBean("kostval"); File configFile = new File("configuration" + File.separator + "kostval.conf.xml"); // Ueberprfung des Parameters (Log-Verzeichnis) String pathToLogfile = kostval.getConfigurationService().getPathToLogfile(); File directoryOfLogfile = new File(pathToLogfile); if (!directoryOfLogfile.exists()) { directoryOfLogfile.mkdir(); } // Im Logverzeichnis besteht kein Schreibrecht if (!directoryOfLogfile.canWrite()) { System.out.println( kostval.getTextResourceService().getText(ERROR_LOGDIRECTORY_NOTWRITABLE, directoryOfLogfile)); System.exit(1); } if (!directoryOfLogfile.isDirectory()) { System.out.println(kostval.getTextResourceService().getText(ERROR_LOGDIRECTORY_NODIRECTORY)); System.exit(1); } // Ist die Anzahl Parameter (mind. 2) korrekt? if (args.length < 2) { System.out.println(kostval.getTextResourceService().getText(ERROR_PARAMETER_USAGE)); System.exit(1); } File valDatei = new File(args[1]); File logDatei = null; logDatei = valDatei; // Informationen zum Arbeitsverzeichnis holen String pathToWorkDir = kostval.getConfigurationService().getPathToWorkDir(); /* Nicht vergessen in "src/main/resources/config/applicationContext-services.xml" beim * entsprechenden Modul die property anzugeben: <property name="configurationService" * ref="configurationService" /> */ // Informationen holen, welche Formate validiert werden sollen String pdfaValidation = kostval.getConfigurationService().pdfaValidation(); String siardValidation = kostval.getConfigurationService().siardValidation(); String tiffValidation = kostval.getConfigurationService().tiffValidation(); String jp2Validation = kostval.getConfigurationService().jp2Validation(); // Konfiguration des Loggings, ein File Logger wird zustzlich erstellt LogConfigurator logConfigurator = (LogConfigurator) context.getBean("logconfigurator"); String logFileName = logConfigurator.configure(directoryOfLogfile.getAbsolutePath(), logDatei.getName()); File logFile = new File(logFileName); // Ab hier kann ins log geschrieben werden... String formatValOn = ""; // ermitteln welche Formate validiert werden knnen respektive eingeschaltet sind if (pdfaValidation.equals("yes")) { formatValOn = "PDF/A"; if (tiffValidation.equals("yes")) { formatValOn = formatValOn + ", TIFF"; } if (jp2Validation.equals("yes")) { formatValOn = formatValOn + ", JP2"; } if (siardValidation.equals("yes")) { formatValOn = formatValOn + ", SIARD"; } } else if (tiffValidation.equals("yes")) { formatValOn = "TIFF"; if (jp2Validation.equals("yes")) { formatValOn = formatValOn + ", JP2"; } if (siardValidation.equals("yes")) { formatValOn = formatValOn + ", SIARD"; } } else if (jp2Validation.equals("yes")) { formatValOn = "JP2"; if (siardValidation.equals("yes")) { formatValOn = formatValOn + ", SIARD"; } } else if (siardValidation.equals("yes")) { formatValOn = "SIARD"; } LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_HEADER)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_START, ausgabeStart)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_END)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_FORMATON, formatValOn)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_INFO)); System.out.println("KOST-Val"); System.out.println(""); if (args[0].equals("--format") && formatValOn.equals("")) { // Formatvalidierung aber alle Formate ausgeschlossen LOGGER.logError(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_NOFILEENDINGS))); System.out.println(kostval.getTextResourceService().getText(ERROR_NOFILEENDINGS)); System.exit(1); } File xslOrig = new File("resources" + File.separator + "kost-val.xsl"); File xslCopy = new File(directoryOfLogfile.getAbsolutePath() + File.separator + "kost-val.xsl"); if (!xslCopy.exists()) { Util.copyFile(xslOrig, xslCopy); } File tmpDir = new File(pathToWorkDir); /* bestehendes Workverzeichnis Abbruch wenn nicht leer, da am Schluss das Workverzeichnis * gelscht wird und entsprechend bestehende Dateien gelscht werden knnen */ if (tmpDir.exists()) { if (tmpDir.isDirectory()) { // Get list of file in the directory. When its length is not zero the folder is not empty. String[] files = tmpDir.list(); if (files.length > 0) { LOGGER.logError(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_WORKDIRECTORY_EXISTS, pathToWorkDir))); System.out.println( kostval.getTextResourceService().getText(ERROR_WORKDIRECTORY_EXISTS, pathToWorkDir)); System.exit(1); } } } // Im Pfad keine Sonderzeichen xml-Validierung SIP 1d und SIARD C strzen ab String patternStr = "[^!#\\$%\\(\\)\\+,\\-_\\.=@\\[\\]\\{\\}\\~:\\\\a-zA-Z0-9 ]"; Pattern pattern = Pattern.compile(patternStr); String name = tmpDir.getAbsolutePath(); String[] pathElements = name.split("/"); for (int i = 0; i < pathElements.length; i++) { String element = pathElements[i]; Matcher matcher = pattern.matcher(element); boolean matchFound = matcher.find(); if (matchFound) { LOGGER.logError(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name))); System.out.println(kostval.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name)); System.exit(1); } } // die Anwendung muss mindestens unter Java 6 laufen String javaRuntimeVersion = System.getProperty("java.vm.version"); if (javaRuntimeVersion.compareTo("1.6.0") < 0) { LOGGER.logError(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_WRONG_JRE))); System.out.println(kostval.getTextResourceService().getText(ERROR_WRONG_JRE)); System.exit(1); } // bestehendes Workverzeichnis wieder anlegen if (!tmpDir.exists()) { tmpDir.mkdir(); } // Im workverzeichnis besteht kein Schreibrecht if (!tmpDir.canWrite()) { LOGGER.logError(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_WORKDIRECTORY_NOTWRITABLE, tmpDir))); System.out.println(kostval.getTextResourceService().getText(ERROR_WORKDIRECTORY_NOTWRITABLE, tmpDir)); System.exit(1); } /* Vorberitung fr eine allfllige Festhaltung bei unterschiedlichen PDFA-Validierungsresultaten * in einer PDF_Diagnosedatei sowie Zhler der SIP-Dateiformate */ String diaPath = kostval.getConfigurationService().getPathToDiagnose(); // Im diaverzeichnis besteht kein Schreibrecht File diaDir = new File(diaPath); if (!diaDir.exists()) { diaDir.mkdir(); } if (!diaDir.canWrite()) { LOGGER.logError(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_DIADIRECTORY_NOTWRITABLE, diaDir))); System.out.println(kostval.getTextResourceService().getText(ERROR_DIADIRECTORY_NOTWRITABLE, diaDir)); System.exit(1); } File xmlDiaOrig = new File("resources" + File.separator + "KaD-Diagnosedaten.kost-val.xml"); File xmlDiaCopy = new File(diaPath + File.separator + "KaD-Diagnosedaten.kost-val.xml"); if (!xmlDiaCopy.exists()) { Util.copyFile(xmlDiaOrig, xmlDiaCopy); } File xslDiaOrig = new File("resources" + File.separator + "kost-val_KaDdia.xsl"); File xslDiaCopy = new File(diaPath + File.separator + "kost-val_KaDdia.xsl"); if (!xslDiaCopy.exists()) { Util.copyFile(xslDiaOrig, xslDiaCopy); } /* Ueberprfung des optionalen Parameters (2 -v --> im Verbose-mode werden die originalen Logs * nicht gelscht (PDFTron, Jhove & Co.) */ boolean verbose = false; if (args.length > 2) { if (!(args[2].equals("-v"))) { LOGGER.logError(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_PARAMETER_OPTIONAL_1))); System.out.println(kostval.getTextResourceService().getText(ERROR_PARAMETER_OPTIONAL_1)); System.exit(1); } else { verbose = true; } } /* Initialisierung TIFF-Modul B (JHove-Validierung) berprfen der Konfiguration: existiert die * jhove.conf am angebenen Ort? */ String jhoveConf = kostval.getConfigurationService().getPathToJhoveConfiguration(); File fJhoveConf = new File(jhoveConf); if (!fJhoveConf.exists() || !fJhoveConf.getName().equals("jhove.conf")) { LOGGER.logError(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_JHOVECONF_MISSING))); System.out.println(kostval.getTextResourceService().getText(ERROR_JHOVECONF_MISSING)); System.exit(1); } // Im Pfad keine Sonderzeichen xml-Validierung SIP 1d und SIARD C strzen ab name = valDatei.getAbsolutePath(); pathElements = name.split("/"); for (int i = 0; i < pathElements.length; i++) { String element = pathElements[i]; Matcher matcher = pattern.matcher(element); boolean matchFound = matcher.find(); if (matchFound) { LOGGER.logError(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name))); System.out.println(kostval.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name)); System.exit(1); } } // Ueberprfung des Parameters (Val-Datei): existiert die Datei? if (!valDatei.exists()) { LOGGER.logError(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_VALFILE_FILENOTEXISTING))); System.out.println(kostval.getTextResourceService().getText(ERROR_VALFILE_FILENOTEXISTING)); System.exit(1); } if (args[0].equals("--format")) { LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_FORMAT1)); Integer countNio = 0; Integer countSummaryNio = 0; Integer count = 0; Integer pdfaCountIo = 0; Integer pdfaCountNio = 0; Integer siardCountIo = 0; Integer siardCountNio = 0; Integer tiffCountIo = 0; Integer tiffCountNio = 0; Integer jp2CountIo = 0; Integer jp2CountNio = 0; // TODO: Formatvalidierung an einer Datei --> erledigt --> nur Marker if (!valDatei.isDirectory()) { boolean valFile = valFile(valDatei, logFileName, directoryOfLogfile, verbose); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_FORMAT2)); // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_LOGEND)); // Zeitstempel End java.util.Date nowEnd = new java.util.Date(); java.text.SimpleDateFormat sdfEnd = new java.text.SimpleDateFormat("dd.MM.yyyy HH:mm:ss"); String ausgabeEnd = sdfEnd.format(nowEnd); ausgabeEnd = "<End>" + ausgabeEnd + "</End>"; Util.valEnd(ausgabeEnd, logFile); Util.amp(logFile); // Die Konfiguration hereinkopieren try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(false); factory.setExpandEntityReferences(false); Document docConfig = factory.newDocumentBuilder().parse(configFile); NodeList list = docConfig.getElementsByTagName("configuration"); Element element = (Element) list.item(0); Document docLog = factory.newDocumentBuilder().parse(logFile); Node dup = docLog.importNode(element, true); docLog.getDocumentElement().appendChild(dup); FileWriter writer = new FileWriter(logFile); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ElementToStream(docLog.getDocumentElement(), baos); String stringDoc2 = new String(baos.toByteArray()); writer.write(stringDoc2); writer.close(); // Der Header wird dabei leider verschossen, wieder zurck ndern String newstring = kostval.getTextResourceService().getText(MESSAGE_XML_HEADER); String oldstring = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><KOSTValLog>"; Util.oldnewstring(oldstring, newstring, logFile); } catch (Exception e) { LOGGER.logError("<Error>" + kostval.getTextResourceService().getText(ERROR_XML_UNKNOWN, e.getMessage())); System.out.println("Exception: " + e.getMessage()); } if (valFile) { // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } // Validierte Datei valide System.exit(0); } else { // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } // Fehler in Validierte Datei --> invalide System.exit(2); } } else { // TODO: Formatvalidierung ber ein Ordner --> erledigt --> nur Marker Map<String, File> fileMap = Util.getFileMap(valDatei, false); Set<String> fileMapKeys = fileMap.keySet(); for (Iterator<String> iterator = fileMapKeys.iterator(); iterator.hasNext();) { String entryName = iterator.next(); File newFile = fileMap.get(entryName); if (!newFile.isDirectory()) { valDatei = newFile; count = count + 1; // Ausgabe Dateizhler Ersichtlich das KOST-Val Dateien durchsucht System.out.print(count + " "); System.out.print("\r"); if (((valDatei.getAbsolutePath().toLowerCase().endsWith(".jp2"))) && jp2Validation.equals("yes")) { boolean valFile = valFile(valDatei, logFileName, directoryOfLogfile, verbose); // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } if (valFile) { jp2CountIo = jp2CountIo + 1; // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } } else { jp2CountNio = jp2CountNio + 1; // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } } } else if (((valDatei.getAbsolutePath().toLowerCase().endsWith(".tiff") || valDatei.getAbsolutePath().toLowerCase().endsWith(".tif"))) && tiffValidation.equals("yes")) { boolean valFile = valFile(valDatei, logFileName, directoryOfLogfile, verbose); // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } if (valFile) { tiffCountIo = tiffCountIo + 1; // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } } else { tiffCountNio = tiffCountNio + 1; // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } } } else if ((valDatei.getAbsolutePath().toLowerCase().endsWith(".siard")) && siardValidation.equals("yes")) { boolean valFile = valFile(valDatei, logFileName, directoryOfLogfile, verbose); // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } if (valFile) { siardCountIo = siardCountIo + 1; // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } } else { siardCountNio = siardCountNio + 1; // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } } } else if (((valDatei.getAbsolutePath().toLowerCase().endsWith(".pdf") || valDatei.getAbsolutePath().toLowerCase().endsWith(".pdfa"))) && pdfaValidation.equals("yes")) { boolean valFile = valFile(valDatei, logFileName, directoryOfLogfile, verbose); // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } if (valFile) { pdfaCountIo = pdfaCountIo + 1; // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } } else { pdfaCountNio = pdfaCountNio + 1; // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } } } else { countNio = countNio + 1; } } } System.out.print(" "); System.out.print("\r"); if (countNio.equals(count)) { // keine Dateien Validiert LOGGER.logError( kostval.getTextResourceService().getText(ERROR_INCORRECTFILEENDINGS, formatValOn)); System.out.println( kostval.getTextResourceService().getText(ERROR_INCORRECTFILEENDINGS, formatValOn)); } LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_FORMAT2)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_LOGEND)); // Zeitstempel End java.util.Date nowEnd = new java.util.Date(); java.text.SimpleDateFormat sdfEnd = new java.text.SimpleDateFormat("dd.MM.yyyy HH:mm:ss"); String ausgabeEnd = sdfEnd.format(nowEnd); ausgabeEnd = "<End>" + ausgabeEnd + "</End>"; Util.valEnd(ausgabeEnd, logFile); Util.amp(logFile); // Die Konfiguration hereinkopieren try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(false); factory.setExpandEntityReferences(false); Document docConfig = factory.newDocumentBuilder().parse(configFile); NodeList list = docConfig.getElementsByTagName("configuration"); Element element = (Element) list.item(0); Document docLog = factory.newDocumentBuilder().parse(logFile); Node dup = docLog.importNode(element, true); docLog.getDocumentElement().appendChild(dup); FileWriter writer = new FileWriter(logFile); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ElementToStream(docLog.getDocumentElement(), baos); String stringDoc2 = new String(baos.toByteArray()); writer.write(stringDoc2); writer.close(); // Der Header wird dabei leider verschossen, wieder zurck ndern String newstring = kostval.getTextResourceService().getText(MESSAGE_XML_HEADER); String oldstring = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><KOSTValLog>"; Util.oldnewstring(oldstring, newstring, logFile); } catch (Exception e) { LOGGER.logError("<Error>" + kostval.getTextResourceService().getText(ERROR_XML_UNKNOWN, e.getMessage())); System.out.println("Exception: " + e.getMessage()); } countSummaryNio = pdfaCountNio + siardCountNio + tiffCountNio + jp2CountNio; if (countNio.equals(count)) { // keine Dateien Validiert bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } System.exit(1); } else if (countSummaryNio == 0) { // bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } // alle Validierten Dateien valide System.exit(0); } else { // bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } // Fehler in Validierten Dateien --> invalide System.exit(2); } if (tmpDir.exists()) { Util.deleteDir(tmpDir); tmpDir.deleteOnExit(); } } LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_FORMAT2)); } else if (args[0].equals("--sip")) { LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_FORMAT1)); // TODO: Sipvalidierung --> erledigt --> nur Marker boolean validFormat = false; File originalSipFile = valDatei; File unSipFile = valDatei; File outputFile3c = null; String fileName3c = null; File tmpDirZip = null; // zuerst eine Formatvalidierung ber den Content dies ist analog aufgebaut wie --format Integer countNio = 0; Integer countSummaryNio = 0; Integer countSummaryIo = 0; Integer count = 0; Integer pdfaCountIo = 0; Integer pdfaCountNio = 0; Integer siardCountIo = 0; Integer siardCountNio = 0; Integer tiffCountIo = 0; Integer tiffCountNio = 0; Integer jp2CountIo = 0; Integer jp2CountNio = 0; if (!valDatei.isDirectory()) { Boolean zip = false; // Eine ZIP Datei muss mit PK.. beginnen if ((valDatei.getAbsolutePath().toLowerCase().endsWith(".zip") || valDatei.getAbsolutePath().toLowerCase().endsWith(".zip64"))) { FileReader fr = null; try { fr = new FileReader(valDatei); BufferedReader read = new BufferedReader(fr); // Hex 03 in Char umwandeln String str3 = "03"; int i3 = Integer.parseInt(str3, 16); char c3 = (char) i3; // Hex 04 in Char umwandeln String str4 = "04"; int i4 = Integer.parseInt(str4, 16); char c4 = (char) i4; // auslesen der ersten 4 Zeichen der Datei int length; int i; char[] buffer = new char[4]; length = read.read(buffer); for (i = 0; i != length; i++) ; // die beiden charArrays (soll und ist) mit einander vergleichen char[] charArray1 = buffer; char[] charArray2 = new char[] { 'P', 'K', c3, c4 }; if (Arrays.equals(charArray1, charArray2)) { // hchstwahrscheinlich ein ZIP da es mit 504B0304 respektive PK.. beginnt zip = true; } } catch (Exception e) { LOGGER.logError("<Error>" + kostval.getTextResourceService().getText(ERROR_XML_UNKNOWN, e.getMessage())); System.out.println("Exception: " + e.getMessage()); } } // wenn die Datei kein Directory ist, muss sie mit zip oder zip64 enden if ((!(valDatei.getAbsolutePath().toLowerCase().endsWith(".zip") || valDatei.getAbsolutePath().toLowerCase().endsWith(".zip64"))) || zip == false) { // Abbruch! D.h. Sip message beginnen, Meldung und Beenden ab hier bis System.exit( 1 ); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_FORMAT2)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_SIP1)); valDatei = originalSipFile; LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALTYPE, kostval.getTextResourceService().getText(MESSAGE_SIPVALIDATION))); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALFILE, valDatei.getAbsolutePath())); System.out.println(kostval.getTextResourceService().getText(MESSAGE_SIPVALIDATION)); System.out.println(valDatei.getAbsolutePath()); // die eigentliche Fehlermeldung LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_MODUL_Aa_SIP) + kostval.getTextResourceService().getText(ERROR_XML_AA_INCORRECTFILEENDING)); System.out.println(kostval.getTextResourceService().getText(ERROR_XML_AA_INCORRECTFILEENDING)); // Fehler im Validierten SIP --> invalide & Abbruch LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_INVALID)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_CLOSE)); System.out.println("Invalid"); System.out.println(""); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_SIP2)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_LOGEND)); // Zeitstempel End java.util.Date nowEnd = new java.util.Date(); java.text.SimpleDateFormat sdfEnd = new java.text.SimpleDateFormat("dd.MM.yyyy HH:mm:ss"); String ausgabeEnd = sdfEnd.format(nowEnd); ausgabeEnd = "<End>" + ausgabeEnd + "</End>"; Util.valEnd(ausgabeEnd, logFile); Util.amp(logFile); // Die Konfiguration hereinkopieren try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(false); factory.setExpandEntityReferences(false); Document docConfig = factory.newDocumentBuilder().parse(configFile); NodeList list = docConfig.getElementsByTagName("configuration"); Element element = (Element) list.item(0); Document docLog = factory.newDocumentBuilder().parse(logFile); Node dup = docLog.importNode(element, true); docLog.getDocumentElement().appendChild(dup); FileWriter writer = new FileWriter(logFile); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ElementToStream(docLog.getDocumentElement(), baos); String stringDoc2 = new String(baos.toByteArray()); writer.write(stringDoc2); writer.close(); // Der Header wird dabei leider verschossen, wieder zurck ndern String newstring = kostval.getTextResourceService().getText(MESSAGE_XML_HEADER); String oldstring = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><KOSTValLog>"; Util.oldnewstring(oldstring, newstring, logFile); } catch (Exception e) { LOGGER.logError("<Error>" + kostval.getTextResourceService().getText(ERROR_XML_UNKNOWN, e.getMessage())); System.out.println("Exception: " + e.getMessage()); } // bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } System.exit(1); } else { // geziptes SIP --> in temp dir entzipen String toplevelDir = valDatei.getName(); int lastDotIdx = toplevelDir.lastIndexOf("."); toplevelDir = toplevelDir.substring(0, lastDotIdx); tmpDirZip = new File( tmpDir.getAbsolutePath() + File.separator + "ZIP" + File.separator + toplevelDir); try { Zip64Archiver.unzip(valDatei.getAbsolutePath(), tmpDirZip.getAbsolutePath()); } catch (Exception e) { try { Zip64Archiver.unzip64(valDatei, tmpDirZip); } catch (Exception e1) { // Abbruch! D.h. Sip message beginnen, Meldung und Beenden ab hier bis System.exit LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_FORMAT2)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_SIP1)); valDatei = originalSipFile; LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALTYPE, kostval.getTextResourceService().getText(MESSAGE_SIPVALIDATION))); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALFILE, valDatei.getAbsolutePath())); System.out.println(kostval.getTextResourceService().getText(MESSAGE_SIPVALIDATION)); System.out.println(valDatei.getAbsolutePath()); // die eigentliche Fehlermeldung LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_MODUL_Aa_SIP) + kostval.getTextResourceService().getText(ERROR_XML_AA_CANNOTEXTRACTZIP)); System.out.println( kostval.getTextResourceService().getText(ERROR_XML_AA_CANNOTEXTRACTZIP)); // Fehler im Validierten SIP --> invalide & Abbruch LOGGER.logError( kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_INVALID)); LOGGER.logError( kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_CLOSE)); System.out.println("Invalid"); System.out.println(""); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_SIP2)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_LOGEND)); // Zeitstempel End java.util.Date nowEnd = new java.util.Date(); java.text.SimpleDateFormat sdfEnd = new java.text.SimpleDateFormat( "dd.MM.yyyy HH:mm:ss"); String ausgabeEnd = sdfEnd.format(nowEnd); ausgabeEnd = "<End>" + ausgabeEnd + "</End>"; Util.valEnd(ausgabeEnd, logFile); Util.amp(logFile); // Die Konfiguration hereinkopieren try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(false); factory.setExpandEntityReferences(false); Document docConfig = factory.newDocumentBuilder().parse(configFile); NodeList list = docConfig.getElementsByTagName("configuration"); Element element = (Element) list.item(0); Document docLog = factory.newDocumentBuilder().parse(logFile); Node dup = docLog.importNode(element, true); docLog.getDocumentElement().appendChild(dup); FileWriter writer = new FileWriter(logFile); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ElementToStream(docLog.getDocumentElement(), baos); String stringDoc2 = new String(baos.toByteArray()); writer.write(stringDoc2); writer.close(); // Der Header wird dabei leider verschossen, wieder zurck ndern String newstring = kostval.getTextResourceService().getText(MESSAGE_XML_HEADER); String oldstring = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><KOSTValLog>"; Util.oldnewstring(oldstring, newstring, logFile); } catch (Exception e2) { LOGGER.logError("<Error>" + kostval.getTextResourceService() .getText(ERROR_XML_UNKNOWN, e2.getMessage())); System.out.println("Exception: " + e2.getMessage()); } // bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } System.exit(1); } } valDatei = tmpDirZip; File toplevelfolder = new File( valDatei.getAbsolutePath() + File.separator + valDatei.getName()); if (toplevelfolder.exists()) { valDatei = toplevelfolder; } unSipFile = valDatei; } } else { // SIP ist ein Ordner valDatei bleibt unverndert } // Vorgngige Formatvalidierung (Schritt 3c) Map<String, File> fileMap = Util.getFileMap(valDatei, false); Set<String> fileMapKeys = fileMap.keySet(); int pdf = 0; int tiff = 0; int siard = 0; int txt = 0; int csv = 0; int xml = 0; int xsd = 0; int wave = 0; int mp3 = 0; int jp2 = 0; int jpx = 0; int jpeg = 0; int png = 0; int dng = 0; int svg = 0; int mpeg2 = 0; int mp4 = 0; int xls = 0; int odt = 0; int ods = 0; int odp = 0; int other = 0; for (Iterator<String> iterator = fileMapKeys.iterator(); iterator.hasNext();) { String entryName = iterator.next(); File newFile = fileMap.get(entryName); if (!newFile.isDirectory() && newFile.getAbsolutePath().contains(File.separator + "content" + File.separator)) { valDatei = newFile; count = count + 1; // Ausgabe Dateizhler Ersichtlich das KOST-Val Dateien durchsucht System.out.print(count + " "); System.out.print("\r"); String extension = valDatei.getName(); int lastIndexOf = extension.lastIndexOf("."); if (lastIndexOf == -1) { // empty extension extension = "other"; } else { extension = extension.substring(lastIndexOf); } if (extension.equalsIgnoreCase(".pdf") || extension.equalsIgnoreCase(".pdfa")) { pdf = pdf + 1; } else if (extension.equalsIgnoreCase(".tiff") || extension.equalsIgnoreCase(".tif")) { tiff = tiff + 1; } else if (extension.equalsIgnoreCase(".siard")) { siard = siard + 1; } else if (extension.equalsIgnoreCase(".txt")) { txt = txt + 1; } else if (extension.equalsIgnoreCase(".csv")) { csv = csv + 1; } else if (extension.equalsIgnoreCase(".xml")) { xml = xml + 1; } else if (extension.equalsIgnoreCase(".xsd")) { xsd = xsd + 1; } else if (extension.equalsIgnoreCase(".wav")) { wave = wave + 1; } else if (extension.equalsIgnoreCase(".mp3")) { mp3 = mp3 + 1; } else if (extension.equalsIgnoreCase(".jp2")) { jp2 = jp2 + 1; } else if (extension.equalsIgnoreCase(".jpx") || extension.equalsIgnoreCase(".jpf")) { jpx = jpx + 1; } else if (extension.equalsIgnoreCase(".jpe") || extension.equalsIgnoreCase(".jpeg") || extension.equalsIgnoreCase(".jpg")) { jpeg = jpeg + 1; } else if (extension.equalsIgnoreCase(".png")) { png = png + 1; } else if (extension.equalsIgnoreCase(".dng")) { dng = dng + 1; } else if (extension.equalsIgnoreCase(".svg")) { svg = svg + 1; } else if (extension.equalsIgnoreCase(".mpeg") || extension.equalsIgnoreCase(".mpg")) { mpeg2 = mpeg2 + 1; } else if (extension.equalsIgnoreCase(".f4a") || extension.equalsIgnoreCase(".f4v") || extension.equalsIgnoreCase(".m4a") || extension.equalsIgnoreCase(".m4v") || extension.equalsIgnoreCase(".mp4")) { mp4 = mp4 + 1; } else if (extension.equalsIgnoreCase(".xls") || extension.equalsIgnoreCase(".xlw") || extension.equalsIgnoreCase(".xlsx")) { xls = xls + 1; } else if (extension.equalsIgnoreCase(".odt") || extension.equalsIgnoreCase(".ott")) { odt = odt + 1; } else if (extension.equalsIgnoreCase(".ods") || extension.equalsIgnoreCase(".ots")) { ods = ods + 1; } else if (extension.equalsIgnoreCase(".odp") || extension.equalsIgnoreCase(".otp")) { odp = odp + 1; } else { other = other + 1; } if (((valDatei.getAbsolutePath().toLowerCase().endsWith(".jp2"))) && jp2Validation.equals("yes")) { boolean valFile = valFile(valDatei, logFileName, directoryOfLogfile, verbose); if (valFile) { jp2CountIo = jp2CountIo + 1; } else { jp2CountNio = jp2CountNio + 1; } } else if (((valDatei.getAbsolutePath().toLowerCase().endsWith(".tiff") || valDatei.getAbsolutePath().toLowerCase().endsWith(".tif"))) && tiffValidation.equals("yes")) { boolean valFile = valFile(valDatei, logFileName, directoryOfLogfile, verbose); if (valFile) { tiffCountIo = tiffCountIo + 1; } else { tiffCountNio = tiffCountNio + 1; } } else if ((valDatei.getAbsolutePath().toLowerCase().endsWith(".siard")) && siardValidation.equals("yes")) { // Arbeitsverzeichnis zum Entpacken des Archivs erstellen String pathToWorkDirSiard = kostval.getConfigurationService().getPathToWorkDir(); File tmpDirSiard = new File(pathToWorkDirSiard + File.separator + "SIARD"); if (tmpDirSiard.exists()) { Util.deleteDir(tmpDirSiard); } if (!tmpDirSiard.exists()) { tmpDirSiard.mkdir(); } boolean valFile = valFile(valDatei, logFileName, directoryOfLogfile, verbose); if (valFile) { siardCountIo = siardCountIo + 1; } else { siardCountNio = siardCountNio + 1; } } else if (((valDatei.getAbsolutePath().toLowerCase().endsWith(".pdf") || valDatei.getAbsolutePath().toLowerCase().endsWith(".pdfa"))) && pdfaValidation.equals("yes")) { boolean valFile = valFile(valDatei, logFileName, directoryOfLogfile, verbose); if (valFile) { pdfaCountIo = pdfaCountIo + 1; } else { pdfaCountNio = pdfaCountNio + 1; } } else { countNio = countNio + 1; } } } countSummaryNio = pdfaCountNio + siardCountNio + tiffCountNio + jp2CountNio; countSummaryIo = pdfaCountIo + siardCountIo + tiffCountIo + jp2CountIo; int countSummaryIoP = 100 / count * countSummaryIo; int countSummaryNioP = 100 / count * countSummaryNio; int countNioP = 100 / count * countNio; String summary3c = kostval.getTextResourceService().getText(MESSAGE_XML_SUMMARY_3C, count, countSummaryIo, countSummaryNio, countNio, countSummaryIoP, countSummaryNioP, countNioP); if (countSummaryNio == 0) { // alle Validierten Dateien valide validFormat = true; fileName3c = "3c_Valide.txt"; } else { // Fehler in Validierten Dateien --> invalide validFormat = false; fileName3c = "3c_Invalide.txt"; } // outputFile3c = new File( directoryOfLogfile + fileName3c ); outputFile3c = new File(pathToWorkDir + File.separator + fileName3c); try { outputFile3c.createNewFile(); } catch (IOException e) { e.printStackTrace(); } if (countNio == count) { // keine Dateien Validiert LOGGER.logError(kostval.getTextResourceService().getText(ERROR_INCORRECTFILEENDINGS, formatValOn)); System.out .println(kostval.getTextResourceService().getText(ERROR_INCORRECTFILEENDINGS, formatValOn)); } LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_FORMAT2)); // Start Normale SIP-Validierung mit auswertung Format-Val. im 3c LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_SIP1)); valDatei = unSipFile; LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALTYPE, kostval.getTextResourceService().getText(MESSAGE_SIPVALIDATION))); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALFILE, originalSipFile.getAbsolutePath())); System.out.println(kostval.getTextResourceService().getText(MESSAGE_SIPVALIDATION)); System.out.println(originalSipFile.getAbsolutePath()); Controllersip controller = (Controllersip) context.getBean("controllersip"); boolean okMandatory = false; okMandatory = controller.executeMandatory(valDatei, directoryOfLogfile); boolean ok = false; /* die Validierungen 1a - 1d sind obligatorisch, wenn sie bestanden wurden, knnen die * restlichen Validierungen, welche nicht zum Abbruch der Applikation fhren, ausgefhrt * werden. * * 1a wurde bereits getestet (vor der Formatvalidierung entsprechend fngt der Controller mit * 1b an */ if (okMandatory) { ok = controller.executeOptional(valDatei, directoryOfLogfile); } // Formatvalidierung validFormat ok = (ok && okMandatory && validFormat); if (ok) { // Validiertes SIP valide LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_VALID)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_CLOSE)); System.out.println("Valid"); System.out.println(""); } else { // Fehler im Validierten SIP --> invalide LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_INVALID)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_CLOSE)); System.out.println("Invalid"); System.out.println(""); } // ggf. Fehlermeldung 3c ergnzen Util.val3c(summary3c, logFile ); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_SIP2)); LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_LOGEND)); // Zeitstempel End java.util.Date nowEnd = new java.util.Date(); java.text.SimpleDateFormat sdfEnd = new java.text.SimpleDateFormat("dd.MM.yyyy HH:mm:ss"); String ausgabeEnd = sdfEnd.format(nowEnd); ausgabeEnd = "<End>" + ausgabeEnd + "</End>"; Util.valEnd(ausgabeEnd, logFile); Util.val3c(summary3c, logFile); Util.amp(logFile); // Die Konfiguration hereinkopieren try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(false); factory.setExpandEntityReferences(false); Document docConfig = factory.newDocumentBuilder().parse(configFile); NodeList list = docConfig.getElementsByTagName("configuration"); Element element = (Element) list.item(0); Document docLog = factory.newDocumentBuilder().parse(logFile); Node dup = docLog.importNode(element, true); docLog.getDocumentElement().appendChild(dup); FileWriter writer = new FileWriter(logFile); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ElementToStream(docLog.getDocumentElement(), baos); String stringDoc2 = new String(baos.toByteArray()); writer.write(stringDoc2); writer.close(); // Der Header wird dabei leider verschossen, wieder zurck ndern String newstring = kostval.getTextResourceService().getText(MESSAGE_XML_HEADER); String oldstring = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><KOSTValLog>"; Util.oldnewstring(oldstring, newstring, logFile); } catch (Exception e) { LOGGER.logError( "<Error>" + kostval.getTextResourceService().getText(ERROR_XML_UNKNOWN, e.getMessage())); System.out.println("Exception: " + e.getMessage()); } // bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } StringBuffer command = new StringBuffer("rd " + tmpDir.getAbsolutePath() + " /s /q"); try { // KaD-Diagnose-Datei mit den neusten Anzahl Dateien pro KaD-Format Updaten DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance(); DocumentBuilder dBuilder = dbFactory.newDocumentBuilder(); Document doc = dBuilder.parse(xmlDiaCopy); doc.getDocumentElement().normalize(); NodeList nList = doc.getElementsByTagName("KOSTVal_FFCounter"); for (int temp = 0; temp < nList.getLength(); temp++) { Node nNode = nList.item(temp); if (nNode.getNodeType() == Node.ELEMENT_NODE) { Element eElement = (Element) nNode; if (pdf > 0) { String pdfNodeString = eElement.getElementsByTagName("pdf").item(0).getTextContent(); int pdfNodeValue = Integer.parseInt(pdfNodeString); pdf = pdf + pdfNodeValue; Util.kadDia("<pdf>" + pdfNodeValue + "</pdf>", "<pdf>" + pdf + "</pdf>", xmlDiaCopy); } if (tiff > 0) { String tiffNodeString = eElement.getElementsByTagName("tiff").item(0).getTextContent(); int tiffNodeValue = Integer.parseInt(tiffNodeString); tiff = tiff + tiffNodeValue; Util.kadDia("<tiff>" + tiffNodeValue + "</tiff>", "<tiff>" + tiff + "</tiff>", xmlDiaCopy); } if (siard > 0) { String siardNodeString = eElement.getElementsByTagName("siard").item(0) .getTextContent(); int siardNodeValue = Integer.parseInt(siardNodeString); siard = siard + siardNodeValue; Util.kadDia("<siard>" + siardNodeValue + "</siard>", "<siard>" + siard + "</siard>", xmlDiaCopy); } if (txt > 0) { String txtNodeString = eElement.getElementsByTagName("txt").item(0).getTextContent(); int txtNodeValue = Integer.parseInt(txtNodeString); txt = txt + txtNodeValue; Util.kadDia("<txt>" + txtNodeValue + "</txt>", "<txt>" + txt + "</txt>", xmlDiaCopy); } if (csv > 0) { String csvNodeString = eElement.getElementsByTagName("csv").item(0).getTextContent(); int csvNodeValue = Integer.parseInt(csvNodeString); csv = csv + csvNodeValue; Util.kadDia("<csv>" + csvNodeValue + "</csv>", "<csv>" + csv + "</csv>", xmlDiaCopy); } if (xml > 0) { String xmlNodeString = eElement.getElementsByTagName("xml").item(0).getTextContent(); int xmlNodeValue = Integer.parseInt(xmlNodeString); xml = xml + xmlNodeValue; Util.kadDia("<xml>" + xmlNodeValue + "</xml>", "<xml>" + xml + "</xml>", xmlDiaCopy); } if (xsd > 0) { String xsdNodeString = eElement.getElementsByTagName("xsd").item(0).getTextContent(); int xsdNodeValue = Integer.parseInt(xsdNodeString); xsd = xsd + xsdNodeValue; Util.kadDia("<xsd>" + xsdNodeValue + "</xsd>", "<xsd>" + xsd + "</xsd>", xmlDiaCopy); } if (wave > 0) { String waveNodeString = eElement.getElementsByTagName("wave").item(0).getTextContent(); int waveNodeValue = Integer.parseInt(waveNodeString); wave = wave + waveNodeValue; Util.kadDia("<wave>" + waveNodeValue + "</wave>", "<wave>" + wave + "</wave>", xmlDiaCopy); } if (mp3 > 0) { String mp3NodeString = eElement.getElementsByTagName("mp3").item(0).getTextContent(); int mp3NodeValue = Integer.parseInt(mp3NodeString); mp3 = mp3 + mp3NodeValue; Util.kadDia("<mp3>" + mp3NodeValue + "</mp3>", "<mp3>" + mp3 + "</mp3>", xmlDiaCopy); } if (jp2 > 0) { String jp2NodeString = eElement.getElementsByTagName("jp2").item(0).getTextContent(); int jp2NodeValue = Integer.parseInt(jp2NodeString); jp2 = jp2 + jp2NodeValue; Util.kadDia("<jp2>" + jp2NodeValue + "</jp2>", "<jp2>" + jp2 + "</jp2>", xmlDiaCopy); } if (jpx > 0) { String jpxNodeString = eElement.getElementsByTagName("jpx").item(0).getTextContent(); int jpxNodeValue = Integer.parseInt(jpxNodeString); jpx = jpx + jpxNodeValue; Util.kadDia("<jpx>" + jpxNodeValue + "</jpx>", "<jpx>" + jpx + "</jpx>", xmlDiaCopy); } if (jpeg > 0) { String jpegNodeString = eElement.getElementsByTagName("jpeg").item(0).getTextContent(); int jpegNodeValue = Integer.parseInt(jpegNodeString); jpeg = jpeg + jpegNodeValue; Util.kadDia("<jpeg>" + jpegNodeValue + "</jpeg>", "<jpeg>" + jpeg + "</jpeg>", xmlDiaCopy); } if (png > 0) { String pngNodeString = eElement.getElementsByTagName("png").item(0).getTextContent(); int pngNodeValue = Integer.parseInt(pngNodeString); png = png + pngNodeValue; Util.kadDia("<png>" + pngNodeValue + "</png>", "<png>" + png + "</png>", xmlDiaCopy); } if (dng > 0) { String dngNodeString = eElement.getElementsByTagName("dng").item(0).getTextContent(); int dngNodeValue = Integer.parseInt(dngNodeString); dng = dng + dngNodeValue; Util.kadDia("<dng>" + dngNodeValue + "</dng>", "<dng>" + dng + "</dng>", xmlDiaCopy); } if (svg > 0) { String svgNodeString = eElement.getElementsByTagName("svg").item(0).getTextContent(); int svgNodeValue = Integer.parseInt(svgNodeString); svg = svg + svgNodeValue; Util.kadDia("<svg>" + svgNodeValue + "</svg>", "<svg>" + svg + "</svg>", xmlDiaCopy); } if (mpeg2 > 0) { String mpeg2NodeString = eElement.getElementsByTagName("mpeg2").item(0) .getTextContent(); int mpeg2NodeValue = Integer.parseInt(mpeg2NodeString); mpeg2 = mpeg2 + mpeg2NodeValue; Util.kadDia("<mpeg2>" + mpeg2NodeValue + "</mpeg2>", "<mpeg2>" + mpeg2 + "</mpeg2>", xmlDiaCopy); } if (mp4 > 0) { String mp4NodeString = eElement.getElementsByTagName("mp4").item(0).getTextContent(); int mp4NodeValue = Integer.parseInt(mp4NodeString); mp4 = mp4 + mp4NodeValue; Util.kadDia("<mp4>" + mp4NodeValue + "</mp4>", "<mp4>" + mp4 + "</mp4>", xmlDiaCopy); } if (xls > 0) { String xlsNodeString = eElement.getElementsByTagName("xls").item(0).getTextContent(); int xlsNodeValue = Integer.parseInt(xlsNodeString); xls = xls + xlsNodeValue; Util.kadDia("<xls>" + xlsNodeValue + "</xls>", "<xls>" + xls + "</xls>", xmlDiaCopy); } if (odt > 0) { String odtNodeString = eElement.getElementsByTagName("odt").item(0).getTextContent(); int odtNodeValue = Integer.parseInt(odtNodeString); odt = odt + odtNodeValue; Util.kadDia("<odt>" + odtNodeValue + "</odt>", "<odt>" + odt + "</odt>", xmlDiaCopy); } if (ods > 0) { String odsNodeString = eElement.getElementsByTagName("ods").item(0).getTextContent(); int odsNodeValue = Integer.parseInt(odsNodeString); ods = ods + odsNodeValue; Util.kadDia("<ods>" + odsNodeValue + "</ods>", "<ods>" + ods + "</ods>", xmlDiaCopy); } if (odp > 0) { String odpNodeString = eElement.getElementsByTagName("odp").item(0).getTextContent(); int odpNodeValue = Integer.parseInt(odpNodeString); odp = odp + odpNodeValue; Util.kadDia("<odp>" + odpNodeValue + "</odp>", "<odp>" + odp + "</odp>", xmlDiaCopy); } if (other > 0) { String otherNodeString = eElement.getElementsByTagName("other").item(0) .getTextContent(); int otherNodeValue = Integer.parseInt(otherNodeString); other = other + otherNodeValue; Util.kadDia("<other>" + otherNodeValue + "</other>", "<other>" + other + "</other>", xmlDiaCopy); } } } } catch (Exception e) { e.printStackTrace(); } if (ok) { // bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } if (tmpDir.exists()) { Runtime rt = Runtime.getRuntime(); Process proc = rt.exec(command.toString()); } System.exit(0); } else { // bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } if (tmpDir.exists()) { Runtime rt = Runtime.getRuntime(); Process proc = rt.exec(command.toString()); } System.exit(2); } LOGGER.logError(kostval.getTextResourceService().getText(MESSAGE_XML_SIP2)); } else { /* Ueberprfung des Parameters (Val-Typ): format / sip args[0] ist nicht "--format" oder * "--sip" --> INVALIDE */ LOGGER.logError(kostval.getTextResourceService().getText(ERROR_IOE, kostval.getTextResourceService().getText(ERROR_PARAMETER_USAGE))); System.out.println(kostval.getTextResourceService().getText(ERROR_PARAMETER_USAGE)); if (tmpDir.exists()) { Util.deleteDir(tmpDir); tmpDir.deleteOnExit(); } System.exit(1); } }
From source file:ch.kostceco.tools.siardexcerpt.SIARDexcerpt.java
/** Die Eingabe besteht aus mind 3 Parameter: [0] Pfad zur SIARD-Datei oder Verzeichnis [1] * configfile [2] Modul/*from w w w.j a va2s.co m*/ * * bersicht der Module: --init --search --extract sowie --finish * * bei --search kommen danach noch die Suchtexte und bei --extract die Schlssel * * @param args * @throws IOException */ public static void main(String[] args) throws IOException { ApplicationContext context = new ClassPathXmlApplicationContext("classpath:config/applicationContext.xml"); /** SIARDexcerpt: Aufbau des Tools * * 1) init: Config Kopieren und ggf SIARD-Datei ins Workverzeichnis entpacken * * 2) search: gemss config die Tabelle mit Suchtext befragen und Ausgabe des Resultates * * 3) extract: mit den Keys anhand der config einen Records herausziehen und anzeigen * * 4) finish: Config-Kopie sowie Workverzeichnis lschen */ /* TODO: siehe Bemerkung im applicationContext-services.xml bezglich Injection in der * Superklasse aller Impl-Klassen ValidationModuleImpl validationModuleImpl = * (ValidationModuleImpl) context.getBean("validationmoduleimpl"); */ SIARDexcerpt siardexcerpt = (SIARDexcerpt) context.getBean("siardexcerpt"); // Ist die Anzahl Parameter (mind 3) korrekt? if (args.length < 3) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_PARAMETER_USAGE)); System.exit(1); } String module = new String(args[2]); File siardDatei = new File(args[0]); File configFile = new File(args[1]); /* arg 1 gibt den Pfad zur configdatei an. Da dieser in ConfigurationServiceImpl hartcodiert * ist, wird diese nach "configuration/SIARDexcerpt.conf.xml" kopiert. */ File configFileHard = new File("configuration" + File.separator + "SIARDexcerpt.conf.xml"); // excerpt ist der Standardwert wird aber anhand der config dann gesetzt File directoryOfOutput = new File("excerpt"); // temp_SIARDexcerpt ist der Standardwert wird aber anhand der config dann gesetzt File tmpDir = new File("temp_SIARDexcerpt"); boolean okA = false; boolean okB = false; boolean okC = false; // die Anwendung muss mindestens unter Java 6 laufen String javaRuntimeVersion = System.getProperty("java.vm.version"); if (javaRuntimeVersion.compareTo("1.6.0") < 0) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_WRONG_JRE)); System.exit(1); } if (module.equalsIgnoreCase("--init")) { /** 1) init: Config Kopieren und ggf SIARD-Datei ins Workverzeichnis entpacken * * a) config muss existieren und SIARDexcerpt.conf.xml noch nicht * * b) Excerptverzeichnis mit schreibrechte und ggf anlegen * * c) Workverzeichnis muss leer sein und mit schreibrechte * * d) SIARD-Datei entpacken * * e) Struktur-Check SIARD-Verzeichnis * * TODO: Erledigt */ System.out.println("SIARDexcerpt: init"); /** a) config muss existieren und SIARDexcerpt.conf.xml noch nicht */ if (!configFile.exists()) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_CONFIGFILE_FILENOTEXISTING, configFile.getAbsolutePath())); System.exit(1); } if (configFileHard.exists()) { System.out .println(siardexcerpt.getTextResourceService().getText(ERROR_CONFIGFILEHARD_FILEEXISTING)); System.exit(1); } Util.copyFile(configFile, configFileHard); /** b) Excerptverzeichnis mit schreibrechte und ggf anlegen */ String pathToOutput = siardexcerpt.getConfigurationService().getPathToOutput(); directoryOfOutput = new File(pathToOutput); if (!directoryOfOutput.exists()) { directoryOfOutput.mkdir(); } // Im Logverzeichnis besteht kein Schreibrecht if (!directoryOfOutput.canWrite()) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_LOGDIRECTORY_NOTWRITABLE, directoryOfOutput)); // Lschen des configFileHard, falls eines angelegt wurde if (configFileHard.exists()) { Util.deleteDir(configFileHard); } System.exit(1); } if (!directoryOfOutput.isDirectory()) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_LOGDIRECTORY_NODIRECTORY)); // Lschen des configFileHard, falls eines angelegt wurde if (configFileHard.exists()) { Util.deleteDir(configFileHard); } System.exit(1); } /** c) Workverzeichnis muss leer sein und mit schreibrechte */ String pathToWorkDir = siardexcerpt.getConfigurationService().getPathToWorkDir(); tmpDir = new File(pathToWorkDir); /* bestehendes Workverzeichnis Abbruch wenn nicht leer, da am Schluss das Workverzeichnis * gelscht wird und entsprechend bestehende Dateien gelscht werden knnen */ if (tmpDir.exists()) { if (tmpDir.isDirectory()) { // Get list of file in the directory. When its length is not zero the folder is not empty. String[] files = tmpDir.list(); if (files.length > 0) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_WORKDIRECTORY_EXISTS, pathToWorkDir)); // Lschen des configFileHard, falls eines angelegt wurde if (configFileHard.exists()) { Util.deleteDir(configFileHard); } System.exit(1); } } } if (!tmpDir.exists()) { tmpDir.mkdir(); } // Im Workverzeichnis besteht kein Schreibrecht if (!tmpDir.canWrite()) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_WORKDIRECTORY_NOTWRITABLE, pathToWorkDir)); // Lschen des configFileHard, falls eines angelegt wurde if (configFileHard.exists()) { Util.deleteDir(configFileHard); } System.exit(1); } /** d) SIARD-Datei entpacken */ if (!siardDatei.exists()) { // SIARD-Datei existiert nicht System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_SIARDFILE_FILENOTEXISTING, siardDatei.getAbsolutePath())); // Lschen des configFileHard, falls eines angelegt wurde if (configFileHard.exists()) { Util.deleteDir(configFileHard); } System.exit(1); } if (!siardDatei.isDirectory()) { /* SIARD-Datei ist eine Datei * * Die Datei muss ins Workverzeichnis extrahiert werden. Dies erfolgt im Modul A. * * danach der Pfad zu SIARD-Datei dorthin zeigen lassen */ Controllerexcerpt controllerexcerpt = (Controllerexcerpt) context.getBean("controllerexcerpt"); File siardDateiNew = new File(pathToWorkDir + File.separator + siardDatei.getName()); okA = controllerexcerpt.executeA(siardDatei, siardDateiNew, ""); if (!okA) { // SIARD Datei konte nicht entpackt werden System.out.println(MESSAGE_XML_MODUL_A); System.out.println(ERROR_XML_A_CANNOTEXTRACTZIP); // Lschen des Arbeitsverzeichnisses und configFileHard, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } if (configFileHard.exists()) { Util.deleteDir(configFileHard); } // Fehler Extraktion --> invalide System.exit(2); } else { @SuppressWarnings("unused") File siardDateiOld = siardDatei; siardDatei = siardDateiNew; } } else { /* SIARD-Datei entpackt oder Datei war bereits ein Verzeichnis. * * Gerade bei grsseren SIARD-Dateien ist es sinnvoll an einer Stelle das ausgepackte SIARD * zu haben, damit diese nicht immer noch extrahiert werden muss */ } /** e) Struktur-Check SIARD-Verzeichnis */ File content = new File(siardDatei.getAbsolutePath() + File.separator + "content"); File header = new File(siardDatei.getAbsolutePath() + File.separator + "header"); File xsd = new File( siardDatei.getAbsolutePath() + File.separator + "header" + File.separator + "metadata.xsd"); File metadata = new File( siardDatei.getAbsolutePath() + File.separator + "header" + File.separator + "metadata.xml"); if (!content.exists() || !header.exists() || !xsd.exists() || !metadata.exists()) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_XML_B_STRUCTURE)); // Lschen des Arbeitsverzeichnisses und configFileHard, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } if (configFileHard.exists()) { Util.deleteDir(configFileHard); } // Fehler Extraktion --> invalide System.exit(2); } else { // Struktur sieht plausibel aus, extraktion kann starten } } // End init if (module.equalsIgnoreCase("--search")) { /** 2) search: gemss config die Tabelle mit Suchtext befragen und Ausgabe des Resultates * * a) Ist die Anzahl Parameter (mind 4) korrekt? arg4 = Suchtext * * b) Suchtext einlesen * * c) search.xml vorbereiten (Header) und xsl in Output kopieren * * d) grep ausfhren * * e) Suchergebnis speichern und anzeigen (via GUI) * * TODO: Noch offen */ System.out.println("SIARDexcerpt: search"); String pathToOutput = siardexcerpt.getConfigurationService().getPathToOutput(); directoryOfOutput = new File(pathToOutput); if (!directoryOfOutput.exists()) { directoryOfOutput.mkdir(); } /** a) Ist die Anzahl Parameter (mind 4) korrekt? arg4 = Suchtext */ if (args.length < 4) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_PARAMETER_USAGE)); System.exit(1); } if (!siardDatei.isDirectory()) { File siardDateiNew = new File(tmpDir.getAbsolutePath() + File.separator + siardDatei.getName()); if (!siardDateiNew.exists()) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_NOINIT)); System.exit(1); } else { siardDatei = siardDateiNew; } } /** b) Suchtext einlesen */ String searchString = new String(args[3]); /** c) search.xml vorbereiten (Header) und xsl in Output kopieren */ // Zeitstempel der Datenextraktion java.util.Date nowStartS = new java.util.Date(); java.text.SimpleDateFormat sdfStartS = new java.text.SimpleDateFormat("dd.MM.yyyy HH:mm:ss"); String ausgabeStartS = sdfStartS.format(nowStartS); /* Der SearchString kann zeichen enthalten, welche nicht im Dateinamen vorkommen drfen. * Entsprechend werden diese normalisiert */ String searchStringFilename = searchString.replaceAll("/", "_"); searchStringFilename = searchStringFilename.replaceAll(">", "_"); searchStringFilename = searchStringFilename.replaceAll("<", "_"); searchStringFilename = searchStringFilename.replace(".*", "_"); searchStringFilename = searchStringFilename.replaceAll("___", "_"); searchStringFilename = searchStringFilename.replaceAll("__", "_"); String outDateiNameS = siardDatei.getName() + "_" + searchStringFilename + "_SIARDsearch.xml"; outDateiNameS = outDateiNameS.replaceAll("__", "_"); // Informationen zum Archiv holen String archiveS = siardexcerpt.getConfigurationService().getArchive(); // Konfiguration des Outputs, ein File Logger wird zustzlich erstellt LogConfigurator logConfiguratorS = (LogConfigurator) context.getBean("logconfigurator"); String outFileNameS = logConfiguratorS.configure(directoryOfOutput.getAbsolutePath(), outDateiNameS); File outFileSearch = new File(outFileNameS); // Ab hier kann ins Output geschrieben werden... // Informationen zum XSL holen String pathToXSLS = siardexcerpt.getConfigurationService().getPathToXSLsearch(); File xslOrigS = new File(pathToXSLS); File xslCopyS = new File(directoryOfOutput.getAbsolutePath() + File.separator + xslOrigS.getName()); if (!xslCopyS.exists()) { Util.copyFile(xslOrigS, xslCopyS); } LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_HEADER, xslCopyS.getName())); LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_START, ausgabeStartS)); LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_ARCHIVE, archiveS)); LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_INFO)); /** d) search: dies ist in einem eigenen Modul realisiert */ Controllerexcerpt controllerexcerptS = (Controllerexcerpt) context.getBean("controllerexcerpt"); okB = controllerexcerptS.executeB(siardDatei, outFileSearch, searchString); /** e) Ausgabe und exitcode */ if (!okB) { // Suche konnte nicht erfolgen LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_MODUL_B)); LOGGER.logError(siardexcerpt.getTextResourceService().getText(ERROR_XML_B_CANNOTSEARCHRECORD)); LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_LOGEND)); System.out.println(MESSAGE_XML_MODUL_B); System.out.println(ERROR_XML_B_CANNOTSEARCHRECORD); System.out.println(""); // Lschen des Arbeitsverzeichnisses und configFileHard erfolgt erst bei schritt 4 finish // Fehler Extraktion --> invalide System.exit(2); } else { // Suche konnte durchgefhrt werden LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_LOGEND)); // Lschen des Arbeitsverzeichnisses und configFileHard erfolgt erst bei schritt 4 finish // Record konnte extrahiert werden System.exit(0); } } // End search if (module.equalsIgnoreCase("--excerpt")) { /** 3) extract: mit den Keys anhand der config einen Records herausziehen und anzeigen * * a) Ist die Anzahl Parameter (mind 4) korrekt? arg4 = Suchtext * * b) extract.xml vorbereiten (Header) und xsl in Output kopieren * * c) extraktion: dies ist in einem eigenen Modul realisiert * * d) Ausgabe und exitcode * * TODO: Erledigt */ System.out.println("SIARDexcerpt: extract"); String pathToOutput = siardexcerpt.getConfigurationService().getPathToOutput(); directoryOfOutput = new File(pathToOutput); if (!directoryOfOutput.exists()) { directoryOfOutput.mkdir(); } /** a) Ist die Anzahl Parameter (mind 4) korrekt? arg4 = Suchtext */ if (args.length < 4) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_PARAMETER_USAGE)); System.exit(1); } if (!siardDatei.isDirectory()) { File siardDateiNew = new File(tmpDir.getAbsolutePath() + File.separator + siardDatei.getName()); if (!siardDateiNew.exists()) { System.out.println(siardexcerpt.getTextResourceService().getText(ERROR_NOINIT)); System.exit(1); } else { siardDatei = siardDateiNew; } } /** b) extract.xml vorbereiten (Header) und xsl in Output kopieren */ // Zeitstempel der Datenextraktion java.util.Date nowStart = new java.util.Date(); java.text.SimpleDateFormat sdfStart = new java.text.SimpleDateFormat("dd.MM.yyyy HH:mm:ss"); String ausgabeStart = sdfStart.format(nowStart); String excerptString = new String(args[3]); String outDateiName = siardDatei.getName() + "_" + excerptString + "_SIARDexcerpt.xml"; // Informationen zum Archiv holen String archive = siardexcerpt.getConfigurationService().getArchive(); // Konfiguration des Outputs, ein File Logger wird zustzlich erstellt LogConfigurator logConfigurator = (LogConfigurator) context.getBean("logconfigurator"); String outFileName = logConfigurator.configure(directoryOfOutput.getAbsolutePath(), outDateiName); File outFile = new File(outFileName); // Ab hier kann ins Output geschrieben werden... // Informationen zum XSL holen String pathToXSL = siardexcerpt.getConfigurationService().getPathToXSL(); File xslOrig = new File(pathToXSL); File xslCopy = new File(directoryOfOutput.getAbsolutePath() + File.separator + xslOrig.getName()); if (!xslCopy.exists()) { Util.copyFile(xslOrig, xslCopy); } LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_HEADER, xslCopy.getName())); LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_START, ausgabeStart)); LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_ARCHIVE, archive)); LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_INFO)); /** c) extraktion: dies ist in einem eigenen Modul realisiert */ Controllerexcerpt controllerexcerpt = (Controllerexcerpt) context.getBean("controllerexcerpt"); okC = controllerexcerpt.executeC(siardDatei, outFile, excerptString); /** d) Ausgabe und exitcode */ if (!okC) { // Record konnte nicht extrahiert werden LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_MODUL_C)); LOGGER.logError(siardexcerpt.getTextResourceService().getText(ERROR_XML_C_CANNOTEXTRACTRECORD)); LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_LOGEND)); System.out.println(MESSAGE_XML_MODUL_C); System.out.println(ERROR_XML_C_CANNOTEXTRACTRECORD); System.out.println(""); // Lschen des Arbeitsverzeichnisses und configFileHard erfolgt erst bei schritt 4 finish // Fehler Extraktion --> invalide System.exit(2); } else { // Record konnte extrahiert werden LOGGER.logError(siardexcerpt.getTextResourceService().getText(MESSAGE_XML_LOGEND)); // Lschen des Arbeitsverzeichnisses und configFileHard erfolgt erst bei schritt 4 finish // Record konnte extrahiert werden System.exit(0); } } // End extract if (module.equalsIgnoreCase("--finish")) { /** 4) finish: Config-Kopie sowie Workverzeichnis lschen * * TODO: Erledigt */ System.out.println("SIARDexcerpt: finish"); // Lschen des Arbeitsverzeichnisses und confiFileHard, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } if (configFileHard.exists()) { Util.deleteDir(configFileHard); } } // End finish }
From source file:com.github.wshackle.java4cpp.J4CppMain.java
public static void main(String[] args) throws IOException, ClassNotFoundException { main_completed = false;/* w w w. j av a 2 s . c om*/ Options options = new Options(); options.addOption(Option.builder("?").desc("Print this message").longOpt("help").build()); options.addOption(Option.builder("n").hasArg().desc("C++ namespace for newly generated classes.") .longOpt("namespace").build()); options.addOption( Option.builder("c").hasArgs().desc("Single Java class to extract.").longOpt("classes").build()); options.addOption( Option.builder("p").hasArgs().desc("Java Package prefix to extract").longOpt("packages").build()); options.addOption(Option.builder("o").hasArg().desc("Output C++ source file.").longOpt("output").build()); options.addOption(Option.builder("j").hasArg().desc("Input jar file").longOpt("jar").build()); options.addOption(Option.builder("h").hasArg().desc("Output C++ header file.").longOpt("header").build()); options.addOption(Option.builder("l").hasArg() .desc("Maximum limit on classes to extract from jars.[default=200]").longOpt("limit").build()); options.addOption(Option.builder("v").desc("enable verbose output").longOpt("verbose").build()); options.addOption(Option.builder().hasArg().desc("Classes per output file.[default=10]") .longOpt(CLASSESPEROUTPUT).build()); options.addOption(Option.builder().hasArgs().desc( "Comma seperated list of nativeclass=javaclass native where nativeclass will be generated as an extension/implementation of the java class.") .longOpt("natives").build()); options.addOption(Option.builder().hasArg() .desc("library name for System.loadLibrary(...) for native extension classes") .longOpt("loadlibname").build()); String output = null; String header = null; String jar = null; Set<String> classnamesToFind = null; Set<String> packageprefixes = null; String loadlibname = null; Map<String, String> nativesNameMap = null; Map<String, Class> nativesClassMap = null; int limit = DEFAULT_LIMIT; int classes_per_file = 10; List<Class> classes = new ArrayList<>(); String limitstring = Integer.toString(limit); try { // parse the command line arguments System.out.println("args = " + Arrays.toString(args)); CommandLine line = new DefaultParser().parse(options, args); loadlibname = line.getOptionValue("loadlibname"); verbose = line.hasOption("verbose"); if (line.hasOption(CLASSESPEROUTPUT)) { String cpoStr = line.getOptionValue(CLASSESPEROUTPUT); try { int cpoI = Integer.valueOf(cpoStr); classes_per_file = cpoI; } catch (Exception e) { System.err.println("Option for " + CLASSESPEROUTPUT + "=\"" + cpoStr + "\""); printHelpAndExit(options, args); } } if (line.hasOption("natives")) { String natives[] = line.getOptionValues("natives"); if (verbose) { System.out.println("natives = " + Arrays.toString(natives)); } nativesNameMap = new HashMap<>(); nativesClassMap = new HashMap<>(); for (int i = 0; i < natives.length; i++) { int eq_index = natives[i].indexOf('='); String nativeClassName = natives[i].substring(0, eq_index).trim(); String javaClassName = natives[i].substring(eq_index + 1).trim(); Class javaClass = null; try { javaClass = Class.forName(javaClassName); } catch (ClassNotFoundException e) { //e.printStackTrace(); System.err.println("Class for " + javaClassName + " not found. (It may be found later in jar if specified.)"); } nativesNameMap.put(javaClassName, nativeClassName); if (javaClass != null) { nativesClassMap.put(nativeClassName, javaClass); if (!classes.contains(javaClass)) { classes.add(javaClass); } } } } // // validate that block-size has been set // if (line.hasOption("block-size")) { // // print the value of block-size // if(verbose) System.out.println(line.getOptionValue("block-size")); // } jar = line.getOptionValue("jar", jar); if (verbose) { System.out.println("jar = " + jar); } if (null != jar) { if (jar.startsWith("~/")) { jar = new File(new File(getHomeDir()), jar.substring(2)).getCanonicalPath(); } if (jar.startsWith("./")) { jar = new File(new File(getCurrentDir()), jar.substring(2)).getCanonicalPath(); } if (jar.startsWith("../")) { jar = new File(new File(getCurrentDir()).getParentFile(), jar.substring(3)).getCanonicalPath(); } } if (line.hasOption("classes")) { classnamesToFind = new HashSet<String>(); String classStrings[] = line.getOptionValues("classes"); if (verbose) { System.out.println("classStrings = " + Arrays.toString(classStrings)); } classnamesToFind.addAll(Arrays.asList(classStrings)); if (verbose) { System.out.println("classnamesToFind = " + classnamesToFind); } } // if (!line.hasOption("namespace")) { // if (classname != null && classname.length() > 0) { // namespace = classname.toLowerCase().replace(".", "_"); // } else if (jar != null && jar.length() > 0) { // int lastSep = jar.lastIndexOf(File.separator); // int start = Math.max(0, lastSep + 1); // int period = jar.indexOf('.', start + 1); // int end = Math.max(start + 1, period); // namespace = jar.substring(start, end).toLowerCase(); // namespace = namespace.replace(" ", "_"); // if (namespace.indexOf("-") > 0) { // namespace = namespace.substring(0, namespace.indexOf("-")); // } // } // } namespace = line.getOptionValue("namespace", namespace); if (verbose) { System.out.println("namespace = " + namespace); } if (null != namespace) { output = namespace + ".cpp"; } output = line.getOptionValue("output", output); if (verbose) { System.out.println("output = " + output); } if (null != output) { if (output.startsWith("~/")) { output = System.getProperty("user.home") + output.substring(1); } header = output.substring(0, output.lastIndexOf('.')) + ".h"; } else { output = "out.cpp"; } header = line.getOptionValue("header", header); if (verbose) { System.out.println("header = " + header); } if (null != header) { if (header.startsWith("~/")) { header = System.getProperty("user.home") + header.substring(1); } } else { header = "out.h"; } if (line.hasOption("packages")) { packageprefixes = new HashSet<String>(); packageprefixes.addAll(Arrays.asList(line.getOptionValues("packages"))); } if (line.hasOption("limit")) { limitstring = line.getOptionValue("limit", Integer.toString(DEFAULT_LIMIT)); limit = Integer.valueOf(limitstring); } if (line.hasOption("help")) { printHelpAndExit(options, args); } } catch (ParseException exp) { if (verbose) { System.out.println("Unexpected exception:" + exp.getMessage()); } printHelpAndExit(options, args); } Set<Class> excludedClasses = new HashSet<>(); Set<String> foundClassNames = new HashSet<>(); excludedClasses.add(Object.class); excludedClasses.add(String.class); excludedClasses.add(void.class); excludedClasses.add(Void.class); excludedClasses.add(Class.class); excludedClasses.add(Enum.class); Set<String> packagesSet = new TreeSet<>(); List<URL> urlsList = new ArrayList<>(); String cp = System.getProperty("java.class.path"); if (verbose) { System.out.println("System.getProperty(\"java.class.path\") = " + cp); } if (null != cp) { for (String cpe : cp.split(File.pathSeparator)) { if (verbose) { System.out.println("class path element = " + cpe); } File f = new File(cpe); if (f.isDirectory()) { urlsList.add(new URL("file:" + f.getCanonicalPath() + File.separator)); } else if (cpe.endsWith(".jar")) { urlsList.add(new URL("jar:file:" + f.getCanonicalPath() + "!/")); } } } cp = System.getenv("CLASSPATH"); if (verbose) { System.out.println("System.getenv(\"CLASSPATH\") = " + cp); } if (null != cp) { for (String cpe : cp.split(File.pathSeparator)) { if (verbose) { System.out.println("class path element = " + cpe); } File f = new File(cpe); if (f.isDirectory()) { urlsList.add(new URL("file:" + f.getCanonicalPath() + File.separator)); } else if (cpe.endsWith(".jar")) { urlsList.add(new URL("jar:file:" + f.getCanonicalPath() + "!/")); } } } if (verbose) { System.out.println("urlsList = " + urlsList); } if (null != jar && jar.length() > 0) { Path jarPath = FileSystems.getDefault().getPath(jar); ZipInputStream zip = new ZipInputStream(Files.newInputStream(jarPath, StandardOpenOption.READ)); URL jarUrl = new URL("jar:file:" + jarPath.toFile().getCanonicalPath() + "!/"); urlsList.add(jarUrl); URL[] urls = urlsList.toArray(new URL[urlsList.size()]); if (verbose) { System.out.println("urls = " + Arrays.toString(urls)); } URLClassLoader cl = URLClassLoader.newInstance(urls); for (ZipEntry entry = zip.getNextEntry(); entry != null; entry = zip.getNextEntry()) { // This ZipEntry represents a class. Now, what class does it represent? String entryName = entry.getName(); if (verbose) { System.out.println("entryName = " + entryName); } if (!entry.isDirectory() && entryName.endsWith(".class")) { if (entryName.indexOf('$') >= 0) { continue; } String classFileName = entry.getName().replace('/', '.'); String className = classFileName.substring(0, classFileName.length() - ".class".length()); if (classnamesToFind != null && classnamesToFind.size() > 0 && !classnamesToFind.contains(className)) { if (verbose) { System.out.println("skipping className=" + className + " because it does not found in=" + classnamesToFind); } continue; } try { Class clss = cl.loadClass(className); if (null != nativesClassMap && null != nativesNameMap && nativesNameMap.containsKey(className)) { nativesClassMap.put(nativesNameMap.get(className), clss); if (!classes.contains(clss)) { classes.add(clss); } } if (packageprefixes != null && packageprefixes.size() > 0) { if (null == clss.getPackage()) { continue; } final String pkgName = clss.getPackage().getName(); boolean matchFound = false; for (String prefix : packageprefixes) { if (pkgName.startsWith(prefix)) { matchFound = true; break; } } if (!matchFound) { continue; } } Package p = clss.getPackage(); if (null != p) { packagesSet.add(clss.getPackage().getName()); } if (!classes.contains(clss) && isAddableClass(clss, excludedClasses)) { if (null != classnamesToFind && classnamesToFind.contains(className) && !foundClassNames.contains(className)) { foundClassNames.add(className); if (verbose) { System.out.println("foundClassNames = " + foundClassNames); } } // if(verbose) System.out.println("clss = " + clss); classes.add(clss); // Class superClass = clss.getSuperclass(); // while (null != superClass // && !classes.contains(superClass) // && isAddableClass(superClass, excludedClasses)) { // classes.add(superClass); // superClass = superClass.getSuperclass(); // } } } catch (ClassNotFoundException | NoClassDefFoundError ex) { System.err.println( "Caught " + ex.getClass().getName() + ":" + ex.getMessage() + " for className=" + className + ", entryName=" + entryName + ", jarPath=" + jarPath); } } } } if (null != classnamesToFind) { if (verbose) { System.out.println("Checking classnames arguments"); } for (String classname : classnamesToFind) { if (verbose) { System.out.println("classname = " + classname); } if (foundClassNames.contains(classname)) { if (verbose) { System.out.println("foundClassNames.contains(" + classname + ")"); } continue; } try { if (classes.contains(Class.forName(classname))) { if (verbose) { System.out.println("Classes list already contains: " + classname); } continue; } } catch (Exception e) { } if (null != classname && classname.length() > 0) { urlsList.add(new URL("file://" + System.getProperty("user.dir") + "/")); URL[] urls = urlsList.toArray(new URL[urlsList.size()]); if (verbose) { System.out.println("urls = " + Arrays.toString(urls)); } URLClassLoader cl = URLClassLoader.newInstance(urls); Class c = null; try { c = cl.loadClass(classname); } catch (ClassNotFoundException e) { System.err.println("Class " + classname + " not found "); } if (verbose) { System.out.println("c = " + c); } if (null == c) { try { c = ClassLoader.getSystemClassLoader().loadClass(classname); } catch (ClassNotFoundException e) { if (verbose) { System.out.println("System ClassLoader failed to find " + classname); } } } if (null != c) { classes.add(c); } else { System.err.println("Class " + classname + " not found"); } } } if (verbose) { System.out.println("Finished checking classnames arguments"); } } if (classes == null || classes.size() < 1) { if (null == nativesClassMap || nativesClassMap.keySet().size() < 1) { System.err.println("No Classes specified or found."); System.exit(1); } } if (verbose) { System.out.println("Classes found = " + classes.size()); } if (classes.size() > limit) { System.err.println("limit=" + limit); System.err.println( "Too many classes please use -c or -p options to limit classes or -l to increase limit."); if (verbose) { System.out.println("packagesSet = " + packagesSet); } System.exit(1); } List<Class> newClasses = new ArrayList<Class>(); for (Class clss : classes) { Class superClass = clss.getSuperclass(); while (null != superClass && !classes.contains(superClass) && !newClasses.contains(superClass) && isAddableClass(superClass, excludedClasses)) { newClasses.add(superClass); superClass = superClass.getSuperclass(); } try { Field fa[] = clss.getDeclaredFields(); for (Field f : fa) { if (Modifier.isPublic(f.getModifiers())) { Class fClass = f.getType(); if (!classes.contains(fClass) && !newClasses.contains(fClass) && isAddableClass(fClass, excludedClasses)) { newClasses.add(fClass); } } } } catch (NoClassDefFoundError e) { e.printStackTrace(); } for (Method m : clss.getDeclaredMethods()) { if (m.isSynthetic()) { continue; } if (!Modifier.isPublic(m.getModifiers()) || Modifier.isAbstract(m.getModifiers())) { continue; } Class retType = m.getReturnType(); if (verbose) { System.out.println("Checking dependancies for Method = " + m); } if (!classes.contains(retType) && !newClasses.contains(retType) && isAddableClass(retType, excludedClasses)) { newClasses.add(retType); superClass = retType.getSuperclass(); while (null != superClass && !classes.contains(superClass) && !newClasses.contains(superClass) && isAddableClass(superClass, excludedClasses)) { newClasses.add(superClass); superClass = superClass.getSuperclass(); } } for (Class paramType : m.getParameterTypes()) { if (!classes.contains(paramType) && !newClasses.contains(paramType) && isAddableClass(paramType, excludedClasses)) { newClasses.add(paramType); superClass = paramType.getSuperclass(); while (null != superClass && !classes.contains(superClass) && !newClasses.contains(superClass) && !excludedClasses.contains(superClass)) { newClasses.add(superClass); superClass = superClass.getSuperclass(); } } } } } if (null != nativesClassMap) { for (Class clss : nativesClassMap.values()) { if (null != clss) { Class superClass = clss.getSuperclass(); while (null != superClass && !classes.contains(superClass) && !newClasses.contains(superClass) && !excludedClasses.contains(superClass)) { newClasses.add(superClass); superClass = superClass.getSuperclass(); } } } } if (verbose) { System.out.println("Dependency classes needed = " + newClasses.size()); } classes.addAll(newClasses); List<Class> newOrderClasses = new ArrayList<>(); for (Class clss : classes) { if (newOrderClasses.contains(clss)) { continue; } Class superClass = clss.getSuperclass(); Stack<Class> stack = new Stack<>(); while (null != superClass && !newOrderClasses.contains(superClass) && !superClass.equals(java.lang.Object.class)) { stack.push(superClass); superClass = superClass.getSuperclass(); } while (!stack.empty()) { newOrderClasses.add(stack.pop()); } newOrderClasses.add(clss); } classes = newOrderClasses; if (verbose) { System.out.println("Total number of classes = " + classes.size()); System.out.println("classes = " + classes); } String forward_header = header.substring(0, header.lastIndexOf('.')) + "_fwd.h"; Map<String, String> map = new HashMap<>(); map.put(JAR, jar != null ? jar : ""); map.put("%CLASSPATH_PREFIX%", getCurrentDir() + ((jar != null) ? (File.pathSeparator + ((new File(jar).getCanonicalPath()).replace("\\", "\\\\"))) : "")); map.put("%FORWARD_HEADER%", forward_header); map.put("%HEADER%", header); map.put("%PATH_SEPERATOR%", File.pathSeparator); String tabs = ""; String headerDefine = forward_header.substring(Math.max(0, forward_header.indexOf(File.separator))) .replace(".", "_"); map.put(HEADER_DEFINE, headerDefine); map.put(NAMESPACE, namespace); if (null != nativesClassMap) { for (Entry<String, Class> e : nativesClassMap.entrySet()) { final Class javaClass = e.getValue(); final String nativeClassName = e.getKey(); try (PrintWriter pw = new PrintWriter(new FileWriter(nativeClassName + ".java"))) { if (javaClass.isInterface()) { pw.println("public class " + nativeClassName + " implements " + javaClass.getCanonicalName() + ", AutoCloseable{"); } else { pw.println("public class " + nativeClassName + " extends " + javaClass.getCanonicalName() + " implements AutoCloseable{"); } if (null != loadlibname && loadlibname.length() > 0) { pw.println(TAB_STRING + "static {"); pw.println(TAB_STRING + TAB_STRING + "System.loadLibrary(\"" + loadlibname + "\");"); pw.println(TAB_STRING + "}"); pw.println(); } pw.println(TAB_STRING + "public " + nativeClassName + "() {"); pw.println(TAB_STRING + "}"); pw.println(); pw.println(TAB_STRING + "private long nativeAddress=0;"); pw.println(TAB_STRING + "private boolean nativeDeleteOnClose=false;"); pw.println(); pw.println(TAB_STRING + "protected " + nativeClassName + "(final long nativeAddress) {"); pw.println(TAB_STRING + TAB_STRING + "this.nativeAddress = nativeAddress;"); pw.println(TAB_STRING + "}"); pw.println(TAB_STRING + "private native void nativeDelete();"); pw.println(); pw.println(TAB_STRING + "@Override"); pw.println(TAB_STRING + "public synchronized void close() {"); // pw.println(TAB_STRING + TAB_STRING + "if(nativeAddress != 0 && nativeDeleteOnClose) {"); pw.println(TAB_STRING + TAB_STRING + "nativeDelete();"); // pw.println(TAB_STRING + TAB_STRING + "}"); // pw.println(TAB_STRING + TAB_STRING + "nativeAddress=0;"); // pw.println(TAB_STRING + TAB_STRING + "nativeDeleteOnClose=false;"); pw.println(TAB_STRING + "}"); pw.println(); pw.println(TAB_STRING + "protected void finalizer() {"); pw.println(TAB_STRING + TAB_STRING + "close();"); pw.println(TAB_STRING + "}"); pw.println(); Method ma[] = javaClass.getDeclaredMethods(); for (Method m : ma) { int modifiers = m.getModifiers(); if (Modifier.isAbstract(modifiers) && Modifier.isPublic(modifiers) && !Modifier.isStatic(modifiers) // && !m.isDefault() && !m.isSynthetic()) { pw.println(); pw.println(TAB_STRING + "@Override"); String params = ""; for (int i = 0; i < m.getParameterTypes().length; i++) { params += m.getParameterTypes()[i].getCanonicalName() + " param" + i; if (i < m.getParameterTypes().length - 1) { params += ","; } } pw.println(TAB_STRING + "native public " + m.getReturnType().getCanonicalName() + " " + m.getName() + "(" + params + ");"); // + IntStream.range(0, m.getParameterTypes().length) // .mapToObj(i -> m.getParameterTypes()[i].getCanonicalName() + " param" + i) // .collect(Collectors.joining(",")) + ");"); } } pw.println("}"); } } } try (PrintWriter pw = new PrintWriter(new FileWriter(forward_header))) { tabs = ""; processTemplate(pw, map, "header_fwd_template_start.h", tabs); Class lastClass = null; for (int class_index = 0; class_index < classes.size(); class_index++) { Class clss = classes.get(class_index); String clssOnlyName = getCppClassName(clss); tabs = openClassNamespace(clss, pw, tabs, lastClass); tabs += TAB_STRING; pw.println(tabs + "class " + clssOnlyName + ";"); tabs = tabs.substring(0, tabs.length() - 1); Class nextClass = (class_index < (classes.size() - 1)) ? classes.get(class_index + 1) : null; tabs = closeClassNamespace(clss, pw, tabs, nextClass); lastClass = clss; } processTemplate(pw, map, "header_fwd_template_end.h", tabs); } headerDefine = header.substring(Math.max(0, header.indexOf(File.separator))).replace(".", "_"); map.put(HEADER_DEFINE, headerDefine); map.put(NAMESPACE, namespace); if (classes_per_file < 1) { classes_per_file = classes.size(); } final int num_class_segments = (classes.size() > 1) ? ((classes.size() + classes_per_file - 1) / classes_per_file) : 1; String fmt = "%d"; if (num_class_segments > 10) { fmt = "%02d"; } if (num_class_segments > 100) { fmt = "%03d"; } String header_file_base = header; if (header_file_base.endsWith(".h")) { header_file_base = header_file_base.substring(0, header_file_base.length() - 2); } else if (header_file_base.endsWith(".hh")) { header_file_base = header_file_base.substring(0, header_file_base.length() - 3); } else if (header_file_base.endsWith(".hpp")) { header_file_base = header_file_base.substring(0, header_file_base.length() - 4); } try (PrintWriter pw = new PrintWriter(new FileWriter(header))) { tabs = ""; processTemplate(pw, map, HEADER_TEMPLATE_STARTH, tabs); for (int segment_index = 0; segment_index < num_class_segments; segment_index++) { String header_segment_file = header_file_base + String.format(fmt, segment_index) + ".h"; pw.println("#include \"" + header_segment_file + "\""); } if (null != nativesClassMap) { tabs = TAB_STRING; for (Entry<String, Class> e : nativesClassMap.entrySet()) { final Class javaClass = e.getValue(); final String nativeClassName = e.getKey(); pw.println(); pw.println(tabs + "class " + nativeClassName + "Context;"); pw.println(); map.put(CLASS_NAME, nativeClassName); map.put("%BASE_CLASS_FULL_NAME%", "::" + namespace + "::" + getModifiedClassName(javaClass).replace(".", "::")); map.put(OBJECT_CLASS_FULL_NAME, "::" + namespace + "::java::lang::Object"); processTemplate(pw, map, HEADER_CLASS_STARTH, tabs); tabs += TAB_STRING; pw.println(tabs + nativeClassName + "Context *context;"); pw.println(tabs + nativeClassName + "();"); pw.println(tabs + "~" + nativeClassName + "();"); Method methods[] = javaClass.getDeclaredMethods(); for (int j = 0; j < methods.length; j++) { Method method = methods[j]; int modifiers = method.getModifiers(); if (!Modifier.isPublic(modifiers)) { continue; } if (Modifier.isAbstract(modifiers) && Modifier.isPublic(modifiers) && !Modifier.isStatic(modifiers) // && !method.isDefault() && !method.isSynthetic()) { pw.println(tabs + getNativeMethodCppDeclaration(method, javaClass)); } } pw.println(tabs + "void initContext(" + nativeClassName + "Context *ctx,bool isref);"); pw.println(tabs + "void deleteContext();"); tabs = tabs.substring(TAB_STRING.length()); pw.println(tabs + "}; // end class " + nativeClassName); } } tabs = ""; processTemplate(pw, map, HEADER_TEMPLATE_ENDH, tabs); } for (int segment_index = 0; segment_index < num_class_segments; segment_index++) { String header_segment_file = header_file_base + String.format(fmt, segment_index) + ".h"; try (PrintWriter pw = new PrintWriter(new FileWriter(header_segment_file))) { tabs = ""; //processTemplate(pw, map, HEADER_TEMPLATE_STARTH, tabs); pw.println("// Never include this file (" + header_segment_file + ") directly. include " + header + " instead."); pw.println(); Class lastClass = null; final int start_segment_index = segment_index * classes_per_file; final int end_segment_index = Math.min(segment_index * classes_per_file + classes_per_file, classes.size()); List<Class> classesSegList = classes.subList(start_segment_index, end_segment_index); pw.println(); pw.println(tabs + "// start_segment_index = " + start_segment_index); pw.println(tabs + "// start_segment_index = " + end_segment_index); pw.println(tabs + "// segment_index = " + segment_index); pw.println(tabs + "// classesSegList=" + classesSegList); pw.println(); for (int class_index = 0; class_index < classesSegList.size(); class_index++) { Class clss = classesSegList.get(class_index); pw.println(); pw.println(tabs + "// class_index = " + class_index + " clss=" + clss); pw.println(); String clssName = clss.getCanonicalName(); tabs = openClassNamespace(clss, pw, tabs, lastClass); String clssOnlyName = getCppClassName(clss); map.put(CLASS_NAME, clssOnlyName); map.put("%BASE_CLASS_FULL_NAME%", classToCppBase(clss)); map.put(OBJECT_CLASS_FULL_NAME, getCppRelativeName(Object.class, clss)); tabs += TAB_STRING; processTemplate(pw, map, HEADER_CLASS_STARTH, tabs); tabs += TAB_STRING; Constructor constructors[] = clss.getDeclaredConstructors(); if (!hasNoArgConstructor(constructors)) { if (Modifier.isAbstract(clss.getModifiers()) || clss.isInterface()) { pw.println(tabs + "protected:"); pw.println(tabs + clssOnlyName + "() {};"); pw.println(tabs + "public:"); } else { if (constructors.length > 0) { pw.println(tabs + "protected:"); } pw.println(tabs + clssOnlyName + "();"); if (constructors.length > 0) { pw.println(tabs + "public:"); } } } for (Constructor c : constructors) { if (c.getParameterTypes().length == 0 && Modifier.isProtected(c.getModifiers())) { pw.println(tabs + "protected:"); pw.println(tabs + clssOnlyName + "();"); pw.println(tabs + "public:"); } if (checkConstructor(c, clss, classes)) { continue; } if (c.getParameterTypes().length == 1 && clss.isAssignableFrom(c.getParameterTypes()[0])) { continue; } if (!Modifier.isPublic(c.getModifiers())) { continue; } if (c.getParameterTypes().length == 1) { if (c.getParameterTypes()[0].getName().equals(clss.getName())) { // if(verbose) System.out.println("skipping constructor."); continue; } } if (!checkParameters(c.getParameterTypes(), classes)) { continue; } pw.println( tabs + clssOnlyName + getCppParamDeclarations(c.getParameterTypes(), clss) + ";"); if (isConstructorToMakeEasy(c, clss)) { pw.println(tabs + clssOnlyName + getEasyCallCppParamDeclarations(c.getParameterTypes(), clss) + ";"); } } pw.println(tabs + "~" + clssOnlyName + "();"); Field fa[] = clss.getDeclaredFields(); for (int findex = 0; findex < fa.length; findex++) { Field field = fa[findex]; if (addGetterMethod(field, clss, classes)) { pw.println(tabs + getCppFieldGetterDeclaration(field, clss)); } if (addSetterMethod(field, clss, classes)) { pw.println(tabs + getCppFieldSetterDeclaration(field, clss)); } } Method methods[] = clss.getDeclaredMethods(); for (int j = 0; j < methods.length; j++) { Method method = methods[j]; if (!checkMethod(method, classes)) { continue; } if ((method.getModifiers() & Modifier.PUBLIC) == Modifier.PUBLIC) { pw.println(tabs + getCppDeclaration(method, clss)); } if (isArrayStringMethod(method)) { pw.println(tabs + getCppModifiers(method.getModifiers()) + getCppType(method.getReturnType(), clss) + " " + fixMethodName(method) + "(int argc,const char **argv);"); } if (isMethodToMakeEasy(method)) { pw.println(tabs + getEasyCallCppDeclaration(method, clss)); } } tabs = tabs.substring(TAB_STRING.length()); pw.println(tabs + "}; // end class " + clssOnlyName); tabs = tabs.substring(0, tabs.length() - 1); Class nextClass = (class_index < (classesSegList.size() - 1)) ? classesSegList.get(class_index + 1) : null; tabs = closeClassNamespace(clss, pw, tabs, nextClass); pw.println(); lastClass = clss; } //processTemplate(pw, map, HEADER_TEMPLATE_ENDH, tabs); } } for (int segment_index = 0; segment_index < num_class_segments; segment_index++) { String output_segment_file = output; if (output_segment_file.endsWith(".cpp")) { output_segment_file = output_segment_file.substring(0, output_segment_file.length() - 4); } else if (output_segment_file.endsWith(".cc")) { output_segment_file = output_segment_file.substring(0, output_segment_file.length() - 3); } output_segment_file += "" + String.format(fmt, segment_index) + ".cpp"; try (PrintWriter pw = new PrintWriter(new FileWriter(output_segment_file))) { tabs = ""; if (segment_index < 1) { processTemplate(pw, map, "cpp_template_start_first.cpp", tabs); } else { processTemplate(pw, map, CPP_TEMPLATE_STARTCPP, tabs); } final int start_segment_index = segment_index * classes_per_file; final int end_segment_index = Math.min(segment_index * classes_per_file + classes_per_file, classes.size()); List<Class> classesSegList = classes.subList(start_segment_index, end_segment_index); pw.println(); pw.println(tabs + "// start_segment_index = " + start_segment_index); pw.println(tabs + "// start_segment_index = " + end_segment_index); pw.println(tabs + "// segment_index = " + segment_index); pw.println(tabs + "// classesSegList=" + classesSegList); pw.println(); Class lastClass = null; for (int class_index = 0; class_index < classesSegList.size(); class_index++) { Class clss = classesSegList.get(class_index); pw.println(); pw.println(tabs + "// class_index = " + class_index + " clss=" + clss); pw.println(); String clssName = clss.getCanonicalName(); tabs = openClassNamespace(clss, pw, tabs, lastClass); String clssOnlyName = getCppClassName(clss); map.put(CLASS_NAME, clssOnlyName); map.put("%BASE_CLASS_FULL_NAME%", classToCppBase(clss)); map.put(FULL_CLASS_NAME, clssName); String fcjs = classToJNISignature(clss); fcjs = fcjs.substring(1, fcjs.length() - 1); map.put(FULL_CLASS_JNI_SIGNATURE, fcjs); if (verbose) { System.out.println("fcjs = " + fcjs); } map.put(OBJECT_CLASS_FULL_NAME, getCppRelativeName(Object.class, clss)); map.put("%INITIALIZE_CONTEXT%", ""); map.put("%INITIALIZE_CONTEXT_REF%", ""); processTemplate(pw, map, CPP_START_CLASSCPP, tabs); Constructor constructors[] = clss.getDeclaredConstructors(); if (!hasNoArgConstructor(constructors)) { if (!Modifier.isAbstract(clss.getModifiers()) && !clss.isInterface()) { pw.println(tabs + clssOnlyName + "::" + clssOnlyName + "() : " + classToCppBase(clss) + "((jobject)NULL,false) {"); map.put(JNI_SIGNATURE, "()V"); map.put(CONSTRUCTOR_ARGS, ""); processTemplate(pw, map, CPP_NEWCPP, tabs); pw.println(tabs + "}"); pw.println(); } } for (Constructor c : constructors) { if (checkConstructor(c, clss, classes)) { continue; } Class[] paramClasses = c.getParameterTypes(); pw.println(tabs + clssOnlyName + "::" + clssOnlyName + getCppParamDeclarations(paramClasses, clss) + " : " + classToCppBase(clss) + "((jobject)NULL,false) {"); tabs = tabs + TAB_STRING; map.put(JNI_SIGNATURE, "(" + getJNIParamSignature(paramClasses) + ")V"); map.put(CONSTRUCTOR_ARGS, (paramClasses.length > 0 ? "," : "") + getCppParamNames(paramClasses)); processTemplate(pw, map, CPP_NEWCPP, tabs); tabs = tabs.substring(0, tabs.length() - 1); pw.println(tabs + "}"); pw.println(); if (isConstructorToMakeEasy(c, clss)) { pw.println(tabs + clssOnlyName + "::" + clssOnlyName + getEasyCallCppParamDeclarations(c.getParameterTypes(), clss) + " : " + classToCppBase(clss) + "((jobject)NULL,false) {"); processTemplate(pw, map, "cpp_start_easy_constructor.cpp", tabs); for (int paramIndex = 0; paramIndex < paramClasses.length; paramIndex++) { Class paramClasse = paramClasses[paramIndex]; String parmName = getParamNameIn(paramClasse, paramIndex); if (isString(paramClasse)) { pw.println(tabs + "jstring " + parmName + " = env->NewStringUTF(easyArg_" + paramIndex + ");"); } else if (isPrimitiveArray(paramClasse)) { String callString = getMethodCallString(paramClasse.getComponentType()); pw.println(tabs + getCppArrayType(paramClasse.getComponentType()) + " " + classToParamNameDecl(paramClasse, paramIndex) + "= env->New" + callString + "Array(easyArg_" + paramIndex + "_length);"); pw.println(tabs + "env->Set" + callString + "ArrayRegion(" + classToParamNameDecl(paramClasse, paramIndex) + ",0,easyArg_" + paramIndex + "_length,easyArg_" + paramIndex + ");"); } else { pw.println(tabs + getCppType(paramClasse, clss) + " " + classToParamNameDecl(paramClasse, paramIndex) + "= easyArg_" + paramIndex + ";"); } } processTemplate(pw, map, "cpp_new_easy_internals.cpp", tabs); for (int paramIndex = 0; paramIndex < paramClasses.length; paramIndex++) { Class paramClasse = paramClasses[paramIndex]; String parmName = getParamNameIn(paramClasse, paramIndex); if (isString(paramClasse)) { pw.println(tabs + "jobjectRefType ref_" + paramIndex + " = env->GetObjectRefType(" + parmName + ");"); pw.println(tabs + "if(ref_" + paramIndex + " == JNIGlobalRefType) {"); pw.println(tabs + TAB_STRING + "env->DeleteGlobalRef(" + parmName + ");"); pw.println(tabs + "}"); } else if (isPrimitiveArray(paramClasse)) { String callString = getMethodCallString(paramClasse.getComponentType()); pw.println(tabs + "env->Get" + callString + "ArrayRegion(" + classToParamNameDecl(paramClasse, paramIndex) + ",0,easyArg_" + paramIndex + "_length,easyArg_" + paramIndex + ");"); pw.println(tabs + "jobjectRefType ref_" + paramIndex + " = env->GetObjectRefType(" + parmName + ");"); pw.println(tabs + "if(ref_" + paramIndex + " == JNIGlobalRefType) {"); pw.println(tabs + TAB_STRING + "env->DeleteGlobalRef(" + parmName + ");"); pw.println(tabs + "}"); } else { } } processTemplate(pw, map, "cpp_end_easy_constructor.cpp", tabs); pw.println(tabs + "}"); } } pw.println(); pw.println(tabs + "// Destructor for " + clssName); pw.println(tabs + clssOnlyName + "::~" + clssOnlyName + "() {"); pw.println(tabs + "\t// Place-holder for later extensibility."); pw.println(tabs + "}"); pw.println(); Field fa[] = clss.getDeclaredFields(); for (int findex = 0; findex < fa.length; findex++) { Field field = fa[findex]; if (addGetterMethod(field, clss, classes)) { pw.println(); pw.println(tabs + "// Field getter for " + field.getName()); pw.println(getCppFieldGetterDefinitionStart(tabs, clssOnlyName, field, clss)); map.put("%FIELD_NAME%", field.getName()); map.put(JNI_SIGNATURE, classToJNISignature(field.getType())); Class returnClass = field.getType(); map.put(METHOD_ONFAIL, getOnFailString(returnClass, clss)); map.put(METHOD_ARGS, ""); map.put("%METHOD_RETURN%", isVoid(returnClass) ? "" : "return"); map.put("%METHOD_CALL_TYPE%", getMethodCallString(returnClass)); map.put("%METHOD_RETURN_TYPE%", getCppType(returnClass, clss)); map.put("%RETURN_VAR_DECLARE%", getMethodReturnVarDeclare(returnClass)); String retStore = isVoid(returnClass) ? "" : "retVal= (" + getMethodReturnVarType(returnClass) + ") "; map.put("%METHOD_RETURN_STORE%", retStore); map.put("%METHOD_RETURN_GET%", getMethodReturnGet(tabs, returnClass, clss)); if (Modifier.isStatic(field.getModifiers())) { processTemplate(pw, map, "cpp_static_getfield.cpp", tabs); } else { processTemplate(pw, map, "cpp_getfield.cpp", tabs); } pw.println(tabs + "}"); } if (addSetterMethod(field, clss, classes)) { pw.println(); pw.println(tabs + "// Field setter for " + field.getName()); pw.println(getCppFieldSetterDefinitionStart(tabs, clssOnlyName, field, clss)); map.put("%FIELD_NAME%", field.getName()); map.put(JNI_SIGNATURE, classToJNISignature(field.getType())); Class returnClass = void.class; map.put(METHOD_ONFAIL, getOnFailString(returnClass, clss)); Class[] paramClasses = new Class[] { field.getType() }; String methodArgs = getCppParamNames(paramClasses); map.put(METHOD_ARGS, (paramClasses.length > 0 ? "," : "") + methodArgs); map.put("%METHOD_RETURN%", isVoid(returnClass) ? "" : "return"); map.put("%METHOD_CALL_TYPE%", getMethodCallString(field.getType())); map.put("%METHOD_RETURN_TYPE%", getCppType(returnClass, clss)); map.put("%RETURN_VAR_DECLARE%", getMethodReturnVarDeclare(returnClass)); String retStore = isVoid(returnClass) ? "" : "retVal= (" + getMethodReturnVarType(returnClass) + ") "; map.put("%METHOD_RETURN_STORE%", retStore); map.put("%METHOD_RETURN_GET%", getMethodReturnGet(tabs, returnClass, clss)); if (Modifier.isStatic(field.getModifiers())) { processTemplate(pw, map, "cpp_static_setfield.cpp", tabs); } else { processTemplate(pw, map, "cpp_setfield.cpp", tabs); } pw.println(tabs + "}"); } } Method methods[] = clss.getDeclaredMethods(); for (int j = 0; j < methods.length; j++) { Method method = methods[j]; if (checkMethod(method, classes)) { pw.println(); pw.println(getCppMethodDefinitionStart(tabs, clssOnlyName, method, clss)); map.put(METHOD_NAME, method.getName()); if (fixMethodName(method).contains("equals2")) { if (verbose) { System.out.println("debug me"); } } map.put("%JAVA_METHOD_NAME%", method.getName()); Class[] paramClasses = method.getParameterTypes(); String methodArgs = getCppParamNames(paramClasses); map.put(METHOD_ARGS, (paramClasses.length > 0 ? "," : "") + methodArgs); Class returnClass = method.getReturnType(); map.put(JNI_SIGNATURE, "(" + getJNIParamSignature(paramClasses) + ")" + classToJNISignature(returnClass)); map.put(METHOD_ONFAIL, getOnFailString(returnClass, clss)); map.put("%METHOD_RETURN%", isVoid(returnClass) ? "" : "return"); map.put("%METHOD_CALL_TYPE%", getMethodCallString(returnClass)); map.put("%METHOD_RETURN_TYPE%", getCppType(returnClass, clss)); map.put("%RETURN_VAR_DECLARE%", getMethodReturnVarDeclare(returnClass)); String retStore = isVoid(returnClass) ? "" : "retVal= (" + getMethodReturnVarType(returnClass) + ") "; map.put("%METHOD_RETURN_STORE%", retStore); map.put("%METHOD_RETURN_GET%", getMethodReturnGet(tabs, returnClass, clss)); tabs += TAB_STRING; if (!Modifier.isStatic(method.getModifiers())) { processTemplate(pw, map, CPP_METHODCPP, tabs); } else { processTemplate(pw, map, CPP_STATIC_METHODCPP, tabs); } tabs = tabs.substring(0, tabs.length() - TAB_STRING.length()); pw.println(tabs + "}"); if (isArrayStringMethod(method)) { map.put(METHOD_RETURN_STORE, isVoid(returnClass) ? "" : getCppType(returnClass, clss) + " returnVal="); map.put(METHOD_RETURN_GET, isVoid(returnClass) ? "return ;" : "return returnVal;"); processTemplate(pw, map, CPP_EASY_STRING_ARRAY_METHODCPP, tabs); } else if (isMethodToMakeEasy(method)) { pw.println(); pw.println(tabs + "// Easy call alternative for " + method.getName()); pw.println(getEasyCallCppMethodDefinitionStart(tabs, clssOnlyName, method, clss)); tabs += TAB_STRING; map.put("%RETURN_VAR_DECLARE%", getMethodReturnVarDeclareOut(returnClass, clss)); processTemplate(pw, map, "cpp_start_easy_method.cpp", tabs); for (int paramIndex = 0; paramIndex < paramClasses.length; paramIndex++) { Class paramClasse = paramClasses[paramIndex]; String parmName = getParamNameIn(paramClasse, paramIndex); if (isString(paramClasse)) { pw.println(tabs + "jstring " + parmName + " = env->NewStringUTF(easyArg_" + paramIndex + ");"); } else if (isPrimitiveArray(paramClasse)) { String callString = getMethodCallString(paramClasse.getComponentType()); pw.println(tabs + getCppArrayType(paramClasse.getComponentType()) + " " + classToParamNameDecl(paramClasse, paramIndex) + "= env->New" + callString + "Array(easyArg_" + paramIndex + "_length);"); pw.println(tabs + "env->Set" + callString + "ArrayRegion(" + classToParamNameDecl(paramClasse, paramIndex) + ",0,easyArg_" + paramIndex + "_length,easyArg_" + paramIndex + ");"); } else { pw.println(tabs + getCppType(paramClasse, clss) + " " + classToParamNameDecl(paramClasse, paramIndex) + "= easyArg_" + paramIndex + ";"); } } String methodArgsIn = getCppParamNamesIn(paramClasses); String retStoreOut = isVoid(returnClass) ? "" : "retVal= (" + getMethodReturnOutVarType(returnClass, clss) + ") "; pw.println(tabs + retStoreOut + fixMethodName(method) + "(" + methodArgsIn + ");"); for (int paramIndex = 0; paramIndex < paramClasses.length; paramIndex++) { Class paramClasse = paramClasses[paramIndex]; String parmName = getParamNameIn(paramClasse, paramIndex); if (isString(paramClasse)) { pw.println(tabs + "jobjectRefType ref_" + paramIndex + " = env->GetObjectRefType(" + parmName + ");"); pw.println(tabs + "if(ref_" + paramIndex + " == JNIGlobalRefType) {"); pw.println(tabs + TAB_STRING + "env->DeleteGlobalRef(" + parmName + ");"); pw.println(tabs + "}"); } else if (isPrimitiveArray(paramClasse)) { String callString = getMethodCallString(paramClasse.getComponentType()); pw.println(tabs + "env->Get" + callString + "ArrayRegion(" + classToParamNameDecl(paramClasse, paramIndex) + ",0,easyArg_" + paramIndex + "_length,easyArg_" + paramIndex + ");"); pw.println(tabs + "jobjectRefType ref_" + paramIndex + " = env->GetObjectRefType(" + parmName + ");"); pw.println(tabs + "if(ref_" + paramIndex + " == JNIGlobalRefType) {"); pw.println(tabs + TAB_STRING + "env->DeleteGlobalRef(" + parmName + ");"); pw.println(tabs + "}"); } else { } } processTemplate(pw, map, "cpp_end_easy_method.cpp", tabs); if (!isVoid(returnClass)) { pw.println(tabs + "return retVal;"); } tabs = tabs.substring(TAB_STRING.length()); pw.println(tabs + "}"); pw.println(); } } } processTemplate(pw, map, CPP_END_CLASSCPP, tabs); tabs = tabs.substring(0, tabs.length() - 1); Class nextClass = (class_index < (classesSegList.size() - 1)) ? classesSegList.get(class_index + 1) : null; tabs = closeClassNamespace(clss, pw, tabs, nextClass); lastClass = clss; } if (segment_index < 1) { if (null != nativesClassMap) { for (Entry<String, Class> e : nativesClassMap.entrySet()) { final Class javaClass = e.getValue(); final String nativeClassName = e.getKey(); map.put(CLASS_NAME, nativeClassName); map.put(FULL_CLASS_NAME, nativeClassName); map.put(FULL_CLASS_JNI_SIGNATURE, nativeClassName); map.put("%BASE_CLASS_FULL_NAME%", "::" + namespace + "::" + getModifiedClassName(javaClass).replace(".", "::")); map.put(OBJECT_CLASS_FULL_NAME, "::" + namespace + "::java::lang::Object"); map.put("%INITIALIZE_CONTEXT%", "context=NULL; initContext(NULL,false);"); map.put("%INITIALIZE_CONTEXT_REF%", "context=NULL; initContext(objref.context,true);"); tabs += TAB_STRING; processTemplate(pw, map, CPP_START_CLASSCPP, tabs); pw.println(); pw.println(tabs + nativeClassName + "::" + nativeClassName + "() : " + getModifiedClassName(javaClass).replace(".", "::") + "((jobject)NULL,false) {"); tabs += TAB_STRING; pw.println(tabs + "context=NULL;"); pw.println(tabs + "initContext(NULL,false);"); map.put(JNI_SIGNATURE, "()V"); map.put(CONSTRUCTOR_ARGS, ""); processTemplate(pw, map, "cpp_new_native.cpp", tabs); tabs = tabs.substring(TAB_STRING.length()); pw.println(tabs + "}"); pw.println(); pw.println(tabs + "// Destructor for " + nativeClassName); pw.println(tabs + nativeClassName + "::~" + nativeClassName + "() {"); pw.println(tabs + TAB_STRING + "if(NULL != context) {"); pw.println(tabs + TAB_STRING + TAB_STRING + "deleteContext();"); pw.println(tabs + TAB_STRING + "}"); pw.println(tabs + TAB_STRING + "context=NULL;"); pw.println(tabs + "}"); pw.println(); // pw.println(tabs + "public:"); // pw.println(tabs + nativeClassName + "();"); // pw.println(tabs + "~" + nativeClassName + "();"); tabs = tabs.substring(TAB_STRING.length()); // Method methods[] = javaClass.getDeclaredMethods(); // for (int j = 0; j < methods.length; j++) { // Method method = methods[j]; // int modifiers = method.getModifiers(); // if (!Modifier.isPublic(modifiers)) { // continue; // } // pw.println(tabs + getCppDeclaration(method, javaClass)); // } // pw.println(tabs + "}; // end class " + nativeClassName); processTemplate(pw, map, CPP_END_CLASSCPP, tabs); } } processTemplate(pw, map, "cpp_template_end_first.cpp", tabs); tabs = ""; if (null != nativesClassMap) { pw.println("using namespace " + namespace + ";"); pw.println("#ifdef __cplusplus"); pw.println("extern \"C\" {"); pw.println("#endif"); int max_method_count = 0; tabs = ""; for (Entry<String, Class> e : nativesClassMap.entrySet()) { final Class javaClass = e.getValue(); final String nativeClassName = e.getKey(); map.put(CLASS_NAME, nativeClassName); map.put(FULL_CLASS_NAME, nativeClassName); map.put("%BASE_CLASS_FULL_NAME%", "::" + namespace + "::" + getModifiedClassName(javaClass).replace(".", "::")); map.put(OBJECT_CLASS_FULL_NAME, "::" + namespace + "::java::lang::Object"); map.put(FULL_CLASS_JNI_SIGNATURE, nativeClassName); map.put(METHOD_ONFAIL, "return;"); Method methods[] = javaClass.getDeclaredMethods(); if (max_method_count < methods.length) { max_method_count = methods.length; } for (int j = 0; j < methods.length; j++) { Method method = methods[j]; int modifiers = method.getModifiers(); if (!Modifier.isPublic(modifiers)) { continue; } if (Modifier.isAbstract(modifiers) && Modifier.isPublic(modifiers) && !Modifier.isStatic(modifiers) // && !method.isDefault() && !method.isSynthetic()) { Class[] paramClasses = method.getParameterTypes(); String methodArgs = getCppParamNames(paramClasses); map.put(METHOD_ARGS, methodArgs); map.put(METHOD_NAME, method.getName()); Class returnClass = method.getReturnType(); String retStore = isVoid(returnClass) ? "" : "retVal= (" + getMethodReturnVarType(returnClass) + ") "; map.put(METHOD_ONFAIL, getOnFailString(returnClass, javaClass)); map.put("%RETURN_VAR_DECLARE%", getMethodReturnVarDeclare(returnClass)); map.put("%METHOD_RETURN_STORE%", retStore); map.put("%METHOD_RETURN_GET%", getMethodReturnGet(tabs, returnClass, javaClass)); pw.println(); String paramDecls = getCppParamDeclarations(paramClasses, javaClass); String argsToAdd = method.getParameterTypes().length > 0 ? "," + paramDecls.substring(1, paramDecls.length() - 1) : ""; pw.println("JNIEXPORT " + getCppType(returnClass, javaClass) + " JNICALL Java_" + nativeClassName + "_" + method.getName() + "(JNIEnv *env, jobject jthis" + argsToAdd + ") {"); tabs = TAB_STRING; processTemplate(pw, map, "cpp_native_wrap.cpp", tabs); tabs = tabs.substring(TAB_STRING.length()); pw.println("}"); pw.println(); } } pw.println("JNIEXPORT void JNICALL Java_" + nativeClassName + "_nativeDelete(JNIEnv *env, jobject jthis) {"); tabs += TAB_STRING; map.put(METHOD_ONFAIL, getOnFailString(void.class, javaClass)); processTemplate(pw, map, "cpp_native_delete.cpp", tabs); tabs = tabs.substring(TAB_STRING.length()); pw.println(tabs + "}"); pw.println(); } pw.println("#ifdef __cplusplus"); pw.println("} // end extern \"C\""); pw.println("#endif"); map.put("%MAX_METHOD_COUNT%", Integer.toString(max_method_count + 1)); processTemplate(pw, map, "cpp_start_register_native.cpp", tabs); for (Entry<String, Class> e : nativesClassMap.entrySet()) { final Class javaClass = e.getValue(); final String nativeClassName = e.getKey(); map.put(CLASS_NAME, nativeClassName); map.put(FULL_CLASS_NAME, nativeClassName); map.put("%BASE_CLASS_FULL_NAME%", "::" + namespace + "::" + getModifiedClassName(javaClass).replace(".", "::")); map.put(OBJECT_CLASS_FULL_NAME, "::" + namespace + "::java::lang::Object"); processTemplate(pw, map, "cpp_start_register_native_class.cpp", tabs); tabs += TAB_STRING; Method methods[] = javaClass.getDeclaredMethods(); int method_number = 0; for (int j = 0; j < methods.length; j++) { Method method = methods[j]; int modifiers = method.getModifiers(); if (!Modifier.isPublic(modifiers)) { continue; } if (Modifier.isAbstract(modifiers) && Modifier.isPublic(modifiers) && !Modifier.isStatic(modifiers) // && !method.isDefault() && !method.isSynthetic()) { map.put("%METHOD_NUMBER%", Integer.toString(method_number)); map.put(METHOD_NAME, method.getName()); map.put(JNI_SIGNATURE, "(" + getJNIParamSignature(method.getParameterTypes()) + ")" + classToJNISignature(method.getReturnType())); processTemplate(pw, map, "cpp_register_native_item.cpp", tabs); method_number++; } } map.put("%METHOD_NUMBER%", Integer.toString(method_number)); map.put(METHOD_NAME, "nativeDelete"); map.put(JNI_SIGNATURE, "()V"); processTemplate(pw, map, "cpp_register_native_item.cpp", tabs); map.put("%NUM_NATIVE_METHODS%", Integer.toString(method_number)); processTemplate(pw, map, "cpp_end_register_native_class.cpp", tabs); tabs = tabs.substring(TAB_STRING.length()); } processTemplate(pw, map, "cpp_end_register_native.cpp", tabs); } else { pw.println("// No Native classes : registerNativMethods not needed."); pw.println("static void registerNativeMethods(JNIEnv *env) {}"); } } else { processTemplate(pw, map, CPP_TEMPLATE_ENDCPP, tabs); } } if (null != nativesClassMap) { tabs = ""; for (Entry<String, Class> e : nativesClassMap.entrySet()) { String nativeClassName = e.getKey(); File nativeClassHeaderFile = new File( namespace.toLowerCase() + "_" + nativeClassName.toLowerCase() + ".h"); map.put("%NATIVE_CLASS_HEADER%", nativeClassHeaderFile.getName()); map.put(CLASS_NAME, nativeClassName); if (nativeClassHeaderFile.exists()) { if (verbose) { System.out.println("skipping " + nativeClassHeaderFile.getCanonicalPath() + " since it already exists."); } } else { try (PrintWriter pw = new PrintWriter(new FileWriter(nativeClassHeaderFile))) { processTemplate(pw, map, "header_native_imp.h", tabs); } } File nativeClassCppFile = new File( namespace.toLowerCase() + "_" + nativeClassName.toLowerCase() + ".cpp"); if (nativeClassCppFile.exists()) { if (verbose) { System.out.println("skipping " + nativeClassCppFile.getCanonicalPath() + " since it already exists."); } } else { try (PrintWriter pw = new PrintWriter(new FileWriter(nativeClassCppFile))) { processTemplate(pw, map, "cpp_native_imp_start.cpp", tabs); Class javaClass = e.getValue(); Method methods[] = javaClass.getDeclaredMethods(); int method_number = 0; for (int j = 0; j < methods.length; j++) { Method method = methods[j]; int modifiers = method.getModifiers(); if (!Modifier.isPublic(modifiers)) { continue; } if (Modifier.isAbstract(modifiers) && Modifier.isPublic(modifiers) && !Modifier.isStatic(modifiers) // && !method.isDefault() && !method.isSynthetic()) { Class[] paramClasses = method.getParameterTypes(); // String methodArgs = getCppParamNames(paramClasses); String paramDecls = getCppParamDeclarations(paramClasses, javaClass); String methodArgs = method.getParameterTypes().length > 0 ? paramDecls.substring(1, paramDecls.length() - 1) : ""; map.put(METHOD_ARGS, methodArgs); map.put(METHOD_NAME, method.getName()); Class returnClass = method.getReturnType(); String retStore = isVoid(returnClass) ? "" : "retVal= (" + getMethodReturnVarType(returnClass) + ") "; map.put(METHOD_ONFAIL, getOnFailString(returnClass, javaClass)); map.put("%RETURN_TYPE%", getCppType(returnClass, javaClass)); map.put("%RETURN_VAR_DECLARE%", getMethodReturnVarDeclare(returnClass)); map.put("%METHOD_RETURN_STORE%", retStore); map.put("%METHOD_RETURN_GET%", getMethodReturnGet(tabs, returnClass, javaClass)); processTemplate(pw, map, "cpp_native_imp_stub.cpp", tabs); } } processTemplate(pw, map, "cpp_native_imp_end.cpp", tabs); } } } } } main_completed = true; }
From source file:com.diversityarrays.dal.server.DalServer.java
public static void main(String[] args) { String host = null;/*from ww w .ja v a 2 s .co m*/ int port = DalServerUtil.DEFAULT_DAL_SERVER_PORT; int inactiveMins = DalServerUtil.DEFAULT_MAX_INACTIVE_MINUTES; File docRoot = null; String serviceName = null; for (int i = 0; i < args.length; ++i) { String argi = args[i]; if (argi.startsWith("-")) { if ("--".equals(argi)) { break; } if ("-version".equals(argi)) { System.out.println(DAL_SERVER_VERSION); System.exit(0); } if ("-help".equals(argi)) { giveHelpThenExit(0); } if ("-docroot".equals(argi)) { if (++i >= args.length || args[i].startsWith("-")) { fatal("missing value for " + argi); } docRoot = new File(args[i]); } else if ("-sqllog".equals(argi)) { SqlUtil.logger = Logger.getLogger(SqlUtil.class.getName()); } else if ("-expire".equals(argi)) { if (++i >= args.length || args[i].startsWith("-")) { fatal("missing value for " + argi); } try { inactiveMins = Integer.parseInt(args[i], 10); if (inactiveMins <= 0) { fatal("invalid minutes: " + args[i]); } } catch (NumberFormatException e) { fatal("invalid minutes: " + args[i]); } } else if ("-localhost".equals(argi)) { host = "localhost"; } else if ("-port".equals(argi)) { if (++i >= args.length || args[i].startsWith("-")) { fatal("missing value for " + argi); } try { port = Integer.parseInt(args[i], 10); if (port < 0 || port > 65535) { fatal("invalid port number: " + args[i]); } } catch (NumberFormatException e) { fatal("invalid port number: " + args[i]); } } else { fatal("invalid option: " + argi); } } else { if (serviceName != null) { fatal("multiple serviceNames not supported: " + argi); } serviceName = argi; } } final DalServerPreferences preferences = new DalServerPreferences( Preferences.userNodeForPackage(DalServer.class)); if (docRoot == null) { docRoot = preferences.getWebRoot(new File(System.getProperty("user.dir"), "www")); } DalServer server = null; if (serviceName != null && docRoot.isDirectory()) { try { DalDatabase db = createDalDatabase(serviceName, preferences); if (db.isInitialiseRequired()) { Closure<String> progress = new Closure<String>() { @Override public void execute(String msg) { System.out.println("Database Initialisation: " + msg); } }; db.initialise(progress); } server = create(preferences, host, port, docRoot, db); } catch (NoServiceException e) { throw new RuntimeException(e); } catch (DalDbException e) { throw new RuntimeException(e); } } Image serverIconImage = null; InputStream imageIs = DalServer.class.getResourceAsStream("dalserver-24.png"); if (imageIs != null) { try { serverIconImage = ImageIO.read(imageIs); if (Util.isMacOS()) { try { MacApplication macapp = new MacApplication(null); macapp.setDockIconImage(serverIconImage); } catch (MacApplicationException e) { System.err.println(e.getMessage()); } } } catch (IOException ignore) { } } if (server != null) { server.setMaxInactiveMinutes(inactiveMins); } else { AskServerParams asker = new AskServerParams(serverIconImage, null, "DAL Server Start", docRoot, preferences); GuiUtil.centreOnScreen(asker); asker.setVisible(true); if (asker.cancelled) { System.exit(0); } host = asker.dalServerHostName; port = asker.dalServerPort; inactiveMins = asker.maxInactiveMinutes; server = create(preferences, host, port, asker.wwwRoot, asker.dalDatabase); // server.setUseSimpleDatabase(asker.useSimpleDatabase); } final DalServer f_server = server; final File f_wwwRoot = docRoot; final Image f_serverIconImage = serverIconImage; SwingUtilities.invokeLater(new Runnable() { @Override public void run() { DalServerFactory factory = new DalServerFactory() { @Override public DalServer create(String hostName, int port, File wwwRoot, DalDatabase dalDatabase) { return DalServer.create(preferences, hostName, port, wwwRoot, dalDatabase); } }; ServerGui gui = new ServerGui(f_serverIconImage, f_server, factory, f_wwwRoot, preferences); gui.setVisible(true); } }); }
From source file:tuit.java
@SuppressWarnings("ConstantConditions") public static void main(String[] args) { System.out.println(licence);/*from w ww .j av a 2s . co m*/ //Declare variables File inputFile; File outputFile; File tmpDir; File blastnExecutable; File properties; File blastOutputFile = null; // TUITPropertiesLoader tuitPropertiesLoader; TUITProperties tuitProperties; // String[] parameters = null; // Connection connection = null; MySQL_Connector mySQL_connector; // Map<Ranks, TUITCutoffSet> cutoffMap; // BLASTIdentifier blastIdentifier = null; // RamDb ramDb = null; CommandLineParser parser = new GnuParser(); Options options = new Options(); options.addOption(tuit.IN, "input<file>", true, "Input file (currently fasta-formatted only)"); options.addOption(tuit.OUT, "output<file>", true, "Output file (in " + tuit.TUIT_EXT + " format)"); options.addOption(tuit.P, "prop<file>", true, "Properties file (XML formatted)"); options.addOption(tuit.V, "verbose", false, "Enable verbose output"); options.addOption(tuit.B, "blast_output<file>", true, "Perform on a pre-BLASTed output"); options.addOption(tuit.DEPLOY, "deploy", false, "Deploy the taxonomic databases"); options.addOption(tuit.UPDATE, "update", false, "Update the taxonomic databases"); options.addOption(tuit.USE_DB, "usedb", false, "Use RDBMS instead of RAM-based taxonomy"); Option option = new Option(tuit.REDUCE, "reduce", true, "Pack identical (100% similar sequences) records in the given sample file"); option.setArgs(Option.UNLIMITED_VALUES); options.addOption(option); option = new Option(tuit.COMBINE, "combine", true, "Combine a set of given reduction files into an HMP Tree-compatible taxonomy"); option.setArgs(Option.UNLIMITED_VALUES); options.addOption(option); options.addOption(tuit.NORMALIZE, "normalize", false, "If used in combination with -combine ensures that the values are normalized by the root value"); HelpFormatter formatter = new HelpFormatter(); try { //Get TUIT directory final File tuitDir = new File( new File(tuit.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath()) .getParent()); final File ramDbFile = new File(tuitDir, tuit.RAM_DB); //Setup logger Log.getInstance().setLogName("tuit.log"); //Read command line final CommandLine commandLine = parser.parse(options, args, true); //Check if the REDUCE option is on if (commandLine.hasOption(tuit.REDUCE)) { final String[] fileList = commandLine.getOptionValues(tuit.REDUCE); for (String s : fileList) { final Path path = Paths.get(s); Log.getInstance().log(Level.INFO, "Processing " + path.toString() + "..."); final NucleotideFastaSequenceReductor nucleotideFastaSequenceReductor = NucleotideFastaSequenceReductor .fromPath(path); ReductorFileOperator.save(nucleotideFastaSequenceReductor, path.resolveSibling(path.getFileName().toString() + ".rdc")); } Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } //Check if COMBINE is on if (commandLine.hasOption(tuit.COMBINE)) { final boolean normalize = commandLine.hasOption(tuit.NORMALIZE); final String[] fileList = commandLine.getOptionValues(tuit.COMBINE); //TODO: implement a test for format here final List<TreeFormatter.TreeFormatterFormat.HMPTreesOutput> hmpTreesOutputs = new ArrayList<>(); final TreeFormatter treeFormatter = TreeFormatter .newInstance(new TreeFormatter.TuitLineTreeFormatterFormat()); for (String s : fileList) { final Path path = Paths.get(s); Log.getInstance().log(Level.INFO, "Merging " + path.toString() + "..."); treeFormatter.loadFromPath(path); final TreeFormatter.TreeFormatterFormat.HMPTreesOutput output = TreeFormatter.TreeFormatterFormat.HMPTreesOutput .newInstance(treeFormatter.toHMPTree(normalize), s.substring(0, s.indexOf("."))); hmpTreesOutputs.add(output); treeFormatter.erase(); } final Path destination; if (commandLine.hasOption(OUT)) { destination = Paths.get(commandLine.getOptionValue(tuit.OUT)); } else { destination = Paths.get("merge.tcf"); } CombinatorFileOperator.save(hmpTreesOutputs, treeFormatter, destination); Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } if (!commandLine.hasOption(tuit.P)) { throw new ParseException("No properties file option found, exiting."); } else { properties = new File(commandLine.getOptionValue(tuit.P)); } //Load properties tuitPropertiesLoader = TUITPropertiesLoader.newInstanceFromFile(properties); tuitProperties = tuitPropertiesLoader.getTuitProperties(); //Create tmp directory and blastn executable tmpDir = new File(tuitProperties.getTMPDir().getPath()); blastnExecutable = new File(tuitProperties.getBLASTNPath().getPath()); //Check for deploy if (commandLine.hasOption(tuit.DEPLOY)) { if (commandLine.hasOption(tuit.USE_DB)) { NCBITablesDeployer.fastDeployNCBIDatabasesFromNCBI(connection, tmpDir); } else { NCBITablesDeployer.fastDeployNCBIRamDatabaseFromNCBI(tmpDir, ramDbFile); } Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } //Check for update if (commandLine.hasOption(tuit.UPDATE)) { if (commandLine.hasOption(tuit.USE_DB)) { NCBITablesDeployer.updateDatabasesFromNCBI(connection, tmpDir); } else { //No need to specify a different way to update the database other than just deploy in case of the RAM database NCBITablesDeployer.fastDeployNCBIRamDatabaseFromNCBI(tmpDir, ramDbFile); } Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } //Connect to the database if (commandLine.hasOption(tuit.USE_DB)) { mySQL_connector = MySQL_Connector.newDefaultInstance( "jdbc:mysql://" + tuitProperties.getDBConnection().getUrl().trim() + "/", tuitProperties.getDBConnection().getLogin().trim(), tuitProperties.getDBConnection().getPassword().trim()); mySQL_connector.connectToDatabase(); connection = mySQL_connector.getConnection(); } else { //Probe for ram database if (ramDbFile.exists() && ramDbFile.canRead()) { Log.getInstance().log(Level.INFO, "Loading RAM taxonomic map..."); try { ramDb = RamDb.loadSelfFromFile(ramDbFile); } catch (IOException ie) { if (ie instanceof java.io.InvalidClassException) throw new IOException("The RAM-based taxonomic database needs to be updated."); } } else { Log.getInstance().log(Level.SEVERE, "The RAM database either has not been deployed, or is not accessible." + "Please use the --deploy option and check permissions on the TUIT directory. " + "If you were looking to use the RDBMS as a taxonomic reference, plese use the -usedb option."); return; } } if (commandLine.hasOption(tuit.B)) { blastOutputFile = new File(commandLine.getOptionValue(tuit.B)); if (!blastOutputFile.exists() || !blastOutputFile.canRead()) { throw new Exception("BLAST output file either does not exist, or is not readable."); } else if (blastOutputFile.isDirectory()) { throw new Exception("BLAST output file points to a directory."); } } //Check vital parameters if (!commandLine.hasOption(tuit.IN)) { throw new ParseException("No input file option found, exiting."); } else { inputFile = new File(commandLine.getOptionValue(tuit.IN)); Log.getInstance().setLogName(inputFile.getName().split("\\.")[0] + ".tuit.log"); } //Correct the output file option if needed if (!commandLine.hasOption(tuit.OUT)) { outputFile = new File((inputFile.getPath()).split("\\.")[0] + tuit.TUIT_EXT); } else { outputFile = new File(commandLine.getOptionValue(tuit.OUT)); } //Adjust the output level if (commandLine.hasOption(tuit.V)) { Log.getInstance().setLevel(Level.FINE); Log.getInstance().log(Level.INFO, "Using verbose output for the log"); } else { Log.getInstance().setLevel(Level.INFO); } //Try all files if (inputFile != null) { if (!inputFile.exists() || !inputFile.canRead()) { throw new Exception("Input file either does not exist, or is not readable."); } else if (inputFile.isDirectory()) { throw new Exception("Input file points to a directory."); } } if (!properties.exists() || !properties.canRead()) { throw new Exception("Properties file either does not exist, or is not readable."); } else if (properties.isDirectory()) { throw new Exception("Properties file points to a directory."); } //Create blast parameters final StringBuilder stringBuilder = new StringBuilder(); for (Database database : tuitProperties.getBLASTNParameters().getDatabase()) { stringBuilder.append(database.getUse()); stringBuilder.append(" ");//Gonna insert an extra space for the last database } String remote; String entrez_query; if (tuitProperties.getBLASTNParameters().getRemote().getDelegate().equals("yes")) { remote = "-remote"; entrez_query = "-entrez_query"; parameters = new String[] { "-db", stringBuilder.toString(), remote, entrez_query, tuitProperties.getBLASTNParameters().getEntrezQuery().getValue(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue() }; } else { if (!commandLine.hasOption(tuit.B)) { if (tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase() .startsWith("NOT") || tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase() .startsWith("ALL")) { parameters = new String[] { "-db", stringBuilder.toString(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue(), "-negative_gilist", TUITFileOperatorHelper.restrictToEntrez(tmpDir, tuitProperties.getBLASTNParameters().getEntrezQuery().getValue() .toUpperCase().replace("NOT", "OR")) .getAbsolutePath(), "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() }; } else if (tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase() .equals("")) { parameters = new String[] { "-db", stringBuilder.toString(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue(), "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() }; } else { parameters = new String[] { "-db", stringBuilder.toString(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue(), /*"-gilist", TUITFileOperatorHelper.restrictToEntrez( tmpDir, tuitProperties.getBLASTNParameters().getEntrezQuery().getValue()).getAbsolutePath(),*/ //TODO remove comment!!!!! "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() }; } } } //Prepare a cutoff Map if (tuitProperties.getSpecificationParameters() != null && tuitProperties.getSpecificationParameters().size() > 0) { cutoffMap = new HashMap<Ranks, TUITCutoffSet>(tuitProperties.getSpecificationParameters().size()); for (SpecificationParameters specificationParameters : tuitProperties .getSpecificationParameters()) { cutoffMap.put(Ranks.valueOf(specificationParameters.getCutoffSet().getRank()), TUITCutoffSet.newDefaultInstance( Double.parseDouble( specificationParameters.getCutoffSet().getPIdentCutoff().getValue()), Double.parseDouble(specificationParameters.getCutoffSet() .getQueryCoverageCutoff().getValue()), Double.parseDouble( specificationParameters.getCutoffSet().getAlpha().getValue()))); } } else { cutoffMap = new HashMap<Ranks, TUITCutoffSet>(); } final TUITFileOperatorHelper.OutputFormat format; if (tuitProperties.getBLASTNParameters().getOutputFormat().getFormat().equals("rdp")) { format = TUITFileOperatorHelper.OutputFormat.RDP_FIXRANK; } else { format = TUITFileOperatorHelper.OutputFormat.TUIT; } try (TUITFileOperator<NucleotideFasta> nucleotideFastaTUITFileOperator = NucleotideFastaTUITFileOperator .newInstance(format, cutoffMap);) { nucleotideFastaTUITFileOperator.setInputFile(inputFile); nucleotideFastaTUITFileOperator.setOutputFile(outputFile); final String cleanupString = tuitProperties.getBLASTNParameters().getKeepBLASTOuts().getKeep(); final boolean cleanup; if (cleanupString.equals("no")) { Log.getInstance().log(Level.INFO, "Temporary BLAST files will be deleted."); cleanup = true; } else { Log.getInstance().log(Level.INFO, "Temporary BLAST files will be kept."); cleanup = false; } //Create blast identifier ExecutorService executorService = Executors.newSingleThreadExecutor(); if (commandLine.hasOption(tuit.USE_DB)) { if (blastOutputFile == null) { blastIdentifier = TUITBLASTIdentifierDB.newInstanceFromFileOperator(tmpDir, blastnExecutable, parameters, nucleotideFastaTUITFileOperator, connection, cutoffMap, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup); } else { try { blastIdentifier = TUITBLASTIdentifierDB.newInstanceFromBLASTOutput( nucleotideFastaTUITFileOperator, connection, cutoffMap, blastOutputFile, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup); } catch (JAXBException e) { Log.getInstance().log(Level.SEVERE, "Error reading " + blastOutputFile.getName() + ", please check input. The file must be XML formatted."); } catch (Exception e) { e.printStackTrace(); } } } else { if (blastOutputFile == null) { blastIdentifier = TUITBLASTIdentifierRAM.newInstanceFromFileOperator(tmpDir, blastnExecutable, parameters, nucleotideFastaTUITFileOperator, cutoffMap, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup, ramDb); } else { try { blastIdentifier = TUITBLASTIdentifierRAM.newInstanceFromBLASTOutput( nucleotideFastaTUITFileOperator, cutoffMap, blastOutputFile, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup, ramDb); } catch (JAXBException e) { Log.getInstance().log(Level.SEVERE, "Error reading " + blastOutputFile.getName() + ", please check input. The file must be XML formatted."); } catch (Exception e) { e.printStackTrace(); } } } Future<?> runnableFuture = executorService.submit(blastIdentifier); runnableFuture.get(); executorService.shutdown(); } } catch (ParseException pe) { Log.getInstance().log(Level.SEVERE, (pe.getMessage())); formatter.printHelp("tuit", options); } catch (SAXException saxe) { Log.getInstance().log(Level.SEVERE, saxe.getMessage()); } catch (FileNotFoundException fnfe) { Log.getInstance().log(Level.SEVERE, fnfe.getMessage()); } catch (TUITPropertyBadFormatException tpbfe) { Log.getInstance().log(Level.SEVERE, tpbfe.getMessage()); } catch (ClassCastException cce) { Log.getInstance().log(Level.SEVERE, cce.getMessage()); } catch (JAXBException jaxbee) { Log.getInstance().log(Level.SEVERE, "The properties file is not well formatted. Please ensure that the XML is consistent with the io.properties.dtd schema."); } catch (ClassNotFoundException cnfe) { //Probably won't happen unless the library deleted from the .jar Log.getInstance().log(Level.SEVERE, cnfe.getMessage()); //cnfe.printStackTrace(); } catch (SQLException sqle) { Log.getInstance().log(Level.SEVERE, "A database communication error occurred with the following message:\n" + sqle.getMessage()); //sqle.printStackTrace(); if (sqle.getMessage().contains("Access denied for user")) { Log.getInstance().log(Level.SEVERE, "Please use standard database login: " + NCBITablesDeployer.login + " and password: " + NCBITablesDeployer.password); } } catch (Exception e) { Log.getInstance().log(Level.SEVERE, e.getMessage()); e.printStackTrace(); } finally { if (connection != null) { try { connection.close(); } catch (SQLException sqle) { Log.getInstance().log(Level.SEVERE, "Problem closing the database connection: " + sqle); } } Log.getInstance().log(Level.FINE, "Task done, exiting..."); } }