List of usage examples for java.lang String replace
public String replace(CharSequence target, CharSequence replacement)
From source file:com.aistor.generate.Generate.java
public static void main(String[] args) throws Exception { // ========== ?? ==================== // ??????//from w ww .j a v a2s . c om // ?{packageName}/{moduleName}/{dao,entity,service,web}/{subModuleName}/{className} // packageName ????applicationContext.xmlsrping-mvc.xml?base-package?packagesToScan?4? String packageName = "com.aistor.modules"; String moduleName = "factory"; // ???sys String subModuleName = ""; // ????? String className = "product"; // ??user String classAuthor = "Zaric"; // Zaric String functionName = "?"; // ?? // ??? Boolean isEnable = false; // ========== ?? ==================== if (!isEnable) { logger.error("????isEnable = true"); return; } if (StringUtils.isBlank(moduleName) || StringUtils.isBlank(moduleName) || StringUtils.isBlank(className) || StringUtils.isBlank(functionName)) { logger.error("??????????????"); return; } // ? String separator = File.separator; String classPath = new DefaultResourceLoader().getResource("").getFile().getPath(); String templatePath = classPath.replace( separator + "webapp" + separator + "WEB-INF" + separator + "classes", separator + "java" + separator + "com" + separator + "aistor" + separator + "modules"); String javaPath = classPath.replace(separator + "webapp" + separator + "WEB-INF" + separator + "classes", separator + "java" + separator + (StringUtils.lowerCase(packageName)).replace(".", separator)); String viewPath = classPath.replace(separator + "classes", separator + "views"); // ??? Configuration cfg = new Configuration(); cfg.setDirectoryForTemplateLoading( new File(templatePath.replace("modules", "generate" + separator + "template"))); // ??? Map<String, String> model = Maps.newHashMap(); model.put("packageName", StringUtils.lowerCase(packageName)); model.put("moduleName", StringUtils.lowerCase(moduleName)); model.put("subModuleName", StringUtils.isNotBlank(subModuleName) ? "." + StringUtils.lowerCase(subModuleName) : ""); model.put("className", StringUtils.uncapitalize(className)); model.put("ClassName", StringUtils.capitalize(className)); model.put("classAuthor", StringUtils.isNotBlank(classAuthor) ? classAuthor : "Generate Tools"); model.put("classVersion", DateUtils.getDate()); model.put("functionName", functionName); model.put("tableName", model.get("moduleName") + (StringUtils.isNotBlank(subModuleName) ? "_" + StringUtils.lowerCase(subModuleName) : "") + "_" + model.get("className")); model.put("urlPrefix", model.get("moduleName") + (StringUtils.isNotBlank(subModuleName) ? "/" + StringUtils.lowerCase(subModuleName) : "") + "/" + model.get("className")); model.put("viewPrefix", StringUtils.substringAfterLast(model.get("packageName"), ".") + "/" + model.get("urlPrefix")); model.put("permissionPrefix", model.get("moduleName") + (StringUtils.isNotBlank(subModuleName) ? ":" + StringUtils.lowerCase(subModuleName) : "") + ":" + model.get("className")); // ? Entity Template template = cfg.getTemplate("entity.ftl"); String content = FreeMarkers.renderTemplate(template, model); String filePath = javaPath + separator + model.get("moduleName") + separator + "entity" + separator + StringUtils.lowerCase(subModuleName) + separator + model.get("ClassName") + ".java"; writeFile(content, filePath); logger.info(filePath); // ? Dao template = cfg.getTemplate("dao.ftl"); content = FreeMarkers.renderTemplate(template, model); filePath = javaPath + separator + model.get("moduleName") + separator + "dao" + separator + StringUtils.lowerCase(subModuleName) + separator + model.get("ClassName") + "Dao.java"; writeFile(content, filePath); logger.info(filePath); // ? Service template = cfg.getTemplate("service.ftl"); content = FreeMarkers.renderTemplate(template, model); filePath = javaPath + separator + model.get("moduleName") + separator + "service" + separator + StringUtils.lowerCase(subModuleName) + separator + model.get("ClassName") + "Service.java"; writeFile(content, filePath); logger.info(filePath); // ? Controller template = cfg.getTemplate("controller.ftl"); content = FreeMarkers.renderTemplate(template, model); filePath = javaPath + separator + model.get("moduleName") + separator + "web" + separator + StringUtils.lowerCase(subModuleName) + separator + model.get("ClassName") + "Controller.java"; writeFile(content, filePath); logger.info(filePath); // ? ViewForm template = cfg.getTemplate("viewForm.ftl"); content = FreeMarkers.renderTemplate(template, model); filePath = viewPath + separator + StringUtils.substringAfterLast(model.get("packageName"), ".") + separator + model.get("moduleName") + separator + StringUtils.lowerCase(subModuleName) + separator + model.get("className") + "Form.jsp"; writeFile(content, filePath); logger.info(filePath); // ? ViewList template = cfg.getTemplate("viewList.ftl"); content = FreeMarkers.renderTemplate(template, model); filePath = viewPath + separator + StringUtils.substringAfterLast(model.get("packageName"), ".") + separator + model.get("moduleName") + separator + StringUtils.lowerCase(subModuleName) + separator + model.get("className") + "List.jsp"; writeFile(content, filePath); logger.info(filePath); logger.info("????"); }
From source file:net.minecraftforge.fml.common.patcher.GenDiffSet.java
public static void main(String[] args) throws IOException { String sourceJar = args[0]; //Clean Vanilla jar minecraft.jar or minecraft_server.jar String targetDir = args[1]; //Directory containing obfed output classes, typically mcp/reobf/minecraft String deobfData = args[2]; //Path to FML's deobfusication_data.lzma String outputDir = args[3]; //Path to place generated .binpatch String killTarget = args[4]; //"true" if we should destroy the target file if it generated a successful .binpatch LogManager.getLogger("GENDIFF").log(Level.INFO, String.format("Creating patches at %s for %s from %s", outputDir, sourceJar, targetDir)); Delta delta = new Delta(); FMLDeobfuscatingRemapper remapper = FMLDeobfuscatingRemapper.INSTANCE; remapper.setupLoadOnly(deobfData, false); JarFile sourceZip = new JarFile(sourceJar); boolean kill = killTarget.equalsIgnoreCase("true"); File f = new File(outputDir); f.mkdirs();/*from ww w . ja v a2s. c o m*/ for (String name : remapper.getObfedClasses()) { // Logger.getLogger("GENDIFF").info(String.format("Evaluating path for data :%s",name)); String fileName = name; String jarName = name; if (RESERVED_NAMES.contains(name.toUpperCase(Locale.ENGLISH))) { fileName = "_" + name; } File targetFile = new File(targetDir, fileName.replace('/', File.separatorChar) + ".class"); jarName = jarName + ".class"; if (targetFile.exists()) { String sourceClassName = name.replace('/', '.'); String targetClassName = remapper.map(name).replace('/', '.'); JarEntry entry = sourceZip.getJarEntry(jarName); byte[] vanillaBytes = toByteArray(sourceZip, entry); byte[] patchedBytes = Files.toByteArray(targetFile); byte[] diff = delta.compute(vanillaBytes, patchedBytes); ByteArrayDataOutput diffOut = ByteStreams.newDataOutput(diff.length + 50); // Original name diffOut.writeUTF(name); // Source name diffOut.writeUTF(sourceClassName); // Target name diffOut.writeUTF(targetClassName); // exists at original diffOut.writeBoolean(entry != null); if (entry != null) { diffOut.writeInt(Hashing.adler32().hashBytes(vanillaBytes).asInt()); } // length of patch diffOut.writeInt(diff.length); // patch diffOut.write(diff); File target = new File(outputDir, targetClassName + ".binpatch"); target.getParentFile().mkdirs(); Files.write(diffOut.toByteArray(), target); Logger.getLogger("GENDIFF").info(String.format("Wrote patch for %s (%s) at %s", name, targetClassName, target.getAbsolutePath())); if (kill) { targetFile.delete(); Logger.getLogger("GENDIFF").info(String.format(" Deleted target: %s", targetFile.toString())); } } } sourceZip.close(); }
From source file:Satellite.java
/** Program entry point. * @param args program arguments (unused here) *///www. j a va2s . c o m public static void main(String[] args) { try { // configure Orekit AutoconfigurationCustom.configureOrekit(); // Initial state definition : date, orbit AbsoluteDate targetDate = new AbsoluteDate(2015, 12, 15, 2, 54, 27.000, TimeScalesFactory.getUTC()); //*******/ double mu = 3.986004415e+14; // gravitation coefficient //*******/ Frame inertialFrame = FramesFactory.getEME2000(); // inertial frame for orbit definition //*******/ Vector3D position = new Vector3D(-6142438.668, 3492467.560, -25767.25680); //*******/ Vector3D velocity = new Vector3D(505.8479685, 942.7809215, 7435.922231); //*******/ PVCoordinates pvCoordinates = new PVCoordinates(position, velocity); //*******/ Orbit initialOrbit = new KeplerianOrbit(pvCoordinates, inertialFrame, initialDate, mu); String Line1 = "1 25544U 98067A 15348.82280235 .00015563 00000-0 23610-3 0 9996"; String Line2 = "2 25544 51.6445 262.5935 0007865 276.8969 187.2494 15.54770155976144"; TLE TLEdata = new TLE(Line1, Line2); // Propagator : consider a simple keplerian motion (could be more elaborate) Propagator TLEProp = TLEPropagator.selectExtrapolator(TLEdata); // // Earth and frame // Frame earthFrame = FramesFactory.getITRF(IERSConventions.IERS_2010, true); // BodyShape earth = new OneAxisEllipsoid(Constants.WGS84_EARTH_EQUATORIAL_RADIUS, // Constants.WGS84_EARTH_FLATTENING, // earthFrame); // // // Station // final double longitude = FastMath.toRadians(89.); // final double latitude = FastMath.toRadians(-8); // final double altitude = 0.; // final GeodeticPoint station1 = new GeodeticPoint(latitude, longitude, altitude); // final TopocentricFrame sta1Frame = new TopocentricFrame(earth, station1, "station1"); // // // Event definition // final double maxcheck = 60.0; // final double threshold = 0.001; // final double elevation = FastMath.toRadians(5.0); // final EventDetector sta1Visi = // new ElevationDetector(maxcheck, threshold, sta1Frame). // withConstantElevation(elevation). // withHandler(new VisibilityHandler()); // Add event to be detected //kepler.addEventDetector(sta1Visi); //Propagate from the initial date to the first raising or for the fixed duration //SpacecraftState finalState = kepler.propagate(initialDate.shiftedBy(1500.)); //System.out.println(" Final state : " + finalState.getDate().durationFrom(initialDate)); String stateVector = TLEProp.propagate(targetDate) .getPVCoordinates(FramesFactory.getITRF(IERSConventions.IERS_2010, true)).toString(); stateVector = stateVector.replace("{", "").replace("}", ""); //Removes brackets {} stateVector = stateVector.replace("(", "").replace(")", ""); //Removes parentheses () stateVector = stateVector.replace("P", "").replace("V", "").replace("A", ""); //Removes P, V, A stateVector = stateVector.replace(" ", ""); //Removes spaces String[] lineData = stateVector.split(","); String timeStamp = new String(lineData[0]); double[] position = new double[] { Double.parseDouble(lineData[1]), Double.parseDouble(lineData[2]), Double.parseDouble(lineData[3]) }; double[] velocity = new double[] { Double.parseDouble(lineData[4]), Double.parseDouble(lineData[5]), Double.parseDouble(lineData[6]) }; double[] acceleration = new double[] { Double.parseDouble(lineData[7]), Double.parseDouble(lineData[8]), Double.parseDouble(lineData[9]) }; position = Convert_To_Lat_Long(position); System.out.format("Latitude %.8f N%n", position[0]); System.out.format("Longitude %.8f E%n", position[1]); System.out.format("Altitude %.0f m %n", position[2]); } catch (OrekitException oe) { System.err.println(oe.getMessage()); } }
From source file:de.pniehus.odal.App.java
public static void main(String[] args) throws IOException { List<Filter> filters = new ArrayList<Filter>(); filters.add(new RegexFilter()); filters.add(new FileTypeFilter()); filters.add(new KeywordFilter()); filters.add(new BlacklistFilter()); Profile p = parseArgs(args, filters); String fileName = "log-" + new Date().toString().replace(":", "-") + ".txt"; fileName = fileName.replace(" ", "-"); File logPath = new File(p.getLogDirectory() + fileName); if (!logPath.getParentFile().isDirectory() && !logPath.getParentFile().mkdirs()) { logPath = new File(fileName); }//from ww w. j av a 2s. c o m if (logPath.getParentFile().canWrite() || logPath.getParentFile().setWritable(true)) { SimpleLoggingSetup.configureRootLogger(logPath.getAbsolutePath(), p.getLogLevel(), !p.isSilent()); } else { Logger root = Logger.getLogger(""); for (Handler h : root.getHandlers()) { // Removing default console handlers if (h instanceof ConsoleHandler) { root.removeHandler(h); } } ConsolePrintLogHandler cplh = new ConsolePrintLogHandler(); cplh.setFormatter(new ScribblerLogFormat(SimpleLoggingSetup.DEFAULT_DATE_FORMAT)); root.addHandler(cplh); System.out.println("Unable to create log: insufficient permissions!"); } Logger.getLogger("").setLevel(p.getLogLevel()); mainLogger = Logger.getLogger(App.class.getCanonicalName()); untrustedSSLSetup(); mainLogger.info("Successfully intitialized ODAL"); if (!p.isLogging()) mainLogger.setLevel(Level.OFF); if (p.isWindowsConsoleMode() && !p.isLogging()) { Logger root = Logger.getLogger(""); for (Handler h : root.getHandlers()) { if (h instanceof FileHandler) { root.removeHandler(h); // Removes FileHandler to allow console output through logging } } } OdalGui ogui = new OdalGui(p, filters); }
From source file:evalita.q4faq.baseline.Index.java
/** * @param args the command line arguments */// w w w .j a va2 s . c o m public static void main(String[] args) { try { if (args.length > 1) { Reader in = new FileReader(args[0]); IndexWriterConfig config = new IndexWriterConfig(Version.LATEST, new ItalianAnalyzer()); IndexWriter writer = new IndexWriter(FSDirectory.open(new File(args[1])), config); Iterable<CSVRecord> records = CSVFormat.EXCEL.withHeader().withDelimiter(';').parse(in); for (CSVRecord record : records) { int id = Integer.parseInt(record.get("id")); String question = record.get("question"); String answer = record.get("answer"); String tag = record.get("tag"); Document doc = new Document(); doc.add(new StringField("id", String.valueOf(id), Field.Store.YES)); doc.add(new TextField("question", question, Field.Store.NO)); doc.add(new TextField("answer", answer, Field.Store.NO)); doc.add(new TextField("tag", tag.replace(",", " "), Field.Store.NO)); writer.addDocument(doc); } writer.close(); } else { throw new IllegalArgumentException("Number of arguments not valid"); } } catch (IOException | IllegalArgumentException ex) { Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex); } }
From source file:com.ikanow.aleph2.analytics.spark.assets.SparkScalaInterpreterTopology.java
public static void main(String[] args) throws InstantiationException, IllegalAccessException, ClassNotFoundException { final SetOnce<IBucketLogger> logger = new SetOnce<>(); try {//w w w . j a va2 s . c o m final Tuple2<IAnalyticsContext, Optional<ProcessingTestSpecBean>> aleph2_tuple = SparkTechnologyUtils .initializeAleph2(args); final IAnalyticsContext context = aleph2_tuple._1(); final Optional<ProcessingTestSpecBean> test_spec = aleph2_tuple._2(); logger.set(context.getLogger(context.getBucket())); // Optional: make really really sure it exists after the specified timeout SparkTechnologyUtils.registerTestTimeout(test_spec, () -> { System.exit(0); }); //INFO: System.out.println("Starting SparkScalaInterpreterTopology logging=" + logger.optional().isPresent()); logger.optional().ifPresent(l -> { l.inefficientLog(Level.INFO, ErrorUtils.buildSuccessMessage("SparkScalaInterpreterTopology", "main", "Starting SparkScalaInterpreterTopology.{0}", Optionals.of(() -> context.getJob().get().name()).orElse("no_name"))); }); final SparkTopologyConfigBean job_config = BeanTemplateUtils .from(context.getJob().map(job -> job.config()).orElse(Collections.emptyMap()), SparkTopologyConfigBean.class) .get(); final String scala_script = Optional.ofNullable(job_config.script()).orElse(""); final String wrapper_script = IOUtils.toString( SparkScalaInterpreterTopology.class.getClassLoader().getResourceAsStream("ScriptRunner.scala"), "UTF-8"); final String to_compile = wrapper_script.replace("USER_SCRIPT", scala_script); final SparkCompilerService scs = new SparkCompilerService(); final Tuple2<ClassLoader, Object> o = scs.buildClass(to_compile, "ScriptRunner", logger.optional()); Thread.currentThread().setContextClassLoader(o._1()); test_spec.ifPresent(spec -> System.out .println("OPTIONS: test_spec = " + BeanTemplateUtils.toJson(spec).toString())); SparkConf spark_context = new SparkConf().setAppName("SparkPassthroughTopology"); final long streaming_batch_interval = (long) spark_context .getInt(SparkTopologyConfigBean.STREAMING_BATCH_INTERVAL, 10); // MAIN PROCESSING final Method m = o._2().getClass().getMethod("runScript", SparkScriptEngine.class); //DEBUG //final boolean test_mode = test_spec.isPresent(); // (serializable thing i can pass into the map) boolean is_streaming = context.getJob().map(j -> j.analytic_type()) .map(t -> MasterEnrichmentType.streaming == t).orElse(false); final Either<JavaSparkContext, JavaStreamingContext> jsc = Lambdas.get(() -> { return is_streaming ? Either.<JavaSparkContext, JavaStreamingContext>right(new JavaStreamingContext( spark_context, Durations.seconds(streaming_batch_interval))) : Either.<JavaSparkContext, JavaStreamingContext>left(new JavaSparkContext(spark_context)); }); try { final JavaSparkContext jsc_batch = jsc.either(l -> l, r -> r.sparkContext()); final Multimap<String, JavaPairRDD<Object, Tuple2<Long, IBatchRecord>>> inputs = SparkTechnologyUtils .buildBatchSparkInputs(context, test_spec, jsc_batch, Collections.emptySet()); final Multimap<String, JavaPairDStream<String, Tuple2<Long, IBatchRecord>>> streaming_inputs = jsc .<Multimap<String, JavaPairDStream<String, Tuple2<Long, IBatchRecord>>>>either( l -> HashMultimap .<String, JavaPairDStream<String, Tuple2<Long, IBatchRecord>>>create(), r -> SparkTechnologyUtils.buildStreamingSparkInputs(context, test_spec, r, Collections.emptySet())); final SparkScriptEngine script_engine_bridge = new SparkScriptEngine(context, inputs, streaming_inputs, test_spec, jsc_batch, jsc.either(l -> null, r -> r), job_config); // Add driver and generated JARs to path: jsc_batch.addJar(LiveInjector.findPathJar(o._2().getClass())); m.invoke(o._2(), script_engine_bridge); jsc.either(l -> { l.stop(); return null; }, r -> { r.stop(); return null; }); logger.optional().ifPresent(l -> { l.inefficientLog(Level.INFO, ErrorUtils.buildSuccessMessage("SparkScalaInterpreterTopology", "main", "Stopping SparkScalaInterpreterTopology.{0}", Optionals.of(() -> context.getJob().get().name()).orElse("no_name"))); }); //INFO: System.out.println("Finished interpreter"); } finally { jsc.either(l -> { l.close(); return null; }, r -> { r.close(); return null; }); } logger.optional().ifPresent(Lambdas.wrap_consumer_u(l -> l.flush().get(10, TimeUnit.SECONDS))); } catch (Throwable t) { logger.optional().ifPresent(l -> { l.inefficientLog(Level.ERROR, ErrorUtils.buildSuccessMessage("SparkScalaInterpreterTopology", "main", ErrorUtils.getLongForm("Error executing SparkScalaInterpreterTopology.unknown: {0}", t))); }); System.out.println(ErrorUtils.getLongForm("ERROR: {0}", t)); logger.optional().ifPresent(Lambdas.wrap_consumer_u(l -> l.flush().get(10, TimeUnit.SECONDS))); System.exit(-1); } }
From source file:com.jiangyifen.ec2.globaldata.license.LicenseManagerMain.java
/** * ?License//www . j a va 2s. c o m * * @param args */ public static void main(String[] args) { // Mac ? // String mac="00-50-56-C0-00-08"; // jrh 160 String mac = "C8:1F:66:B9:26:96"; mac = "00-50-56-C0-00-08"; mac = "90-B1-1C-82-D7-1F"; mac = mac.replace(":", "-"); // String date = "2015-08-25 00:00:00"; // ??? String count = "35"; System.out.println(generateLicense(mac, date, count)); System.out.println(); System.out.println(); jrh_license_test(); }
From source file:com.alexoree.jenkins.Main.java
public static void main(String[] args) throws Exception { // create Options object Options options = new Options(); options.addOption("t", false, "throttle the downloads, waits 5 seconds in between each d/l"); // automatically generate the help statement HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("jenkins-sync", options); CommandLineParser parser = new DefaultParser(); CommandLine cmd = parser.parse(options, args); boolean throttle = cmd.hasOption("t"); String plugins = "https://updates.jenkins-ci.org/latest/"; List<String> ps = new ArrayList<String>(); Document doc = Jsoup.connect(plugins).get(); for (Element file : doc.select("td a")) { //System.out.println(file.attr("href")); if (file.attr("href").endsWith(".hpi") || file.attr("href").endsWith(".war")) { ps.add(file.attr("href")); }/*from ww w .ja va2s . c o m*/ } File root = new File("."); //https://updates.jenkins-ci.org/latest/AdaptivePlugin.hpi new File("./latest").mkdirs(); //output zip file String zipFile = "jenkinsSync.zip"; // create byte buffer byte[] buffer = new byte[1024]; FileOutputStream fos = new FileOutputStream(zipFile); ZipOutputStream zos = new ZipOutputStream(fos); //download the plugins for (int i = 0; i < ps.size(); i++) { System.out.println("[" + i + "/" + ps.size() + "] downloading " + plugins + ps.get(i)); String outputFile = download(root.getAbsolutePath() + "/latest/" + ps.get(i), plugins + ps.get(i)); FileInputStream fis = new FileInputStream(outputFile); // begin writing a new ZIP entry, positions the stream to the start of the entry data zos.putNextEntry(new ZipEntry(outputFile.replace(root.getAbsolutePath(), "") .replace("updates.jenkins-ci.org/", "").replace("https:/", ""))); int length; while ((length = fis.read(buffer)) > 0) { zos.write(buffer, 0, length); } zos.closeEntry(); fis.close(); if (throttle) Thread.sleep(WAIT); new File(root.getAbsolutePath() + "/latest/" + ps.get(i)).deleteOnExit(); } //download the json metadata plugins = "https://updates.jenkins-ci.org/"; ps = new ArrayList<String>(); doc = Jsoup.connect(plugins).get(); for (Element file : doc.select("td a")) { //System.out.println(file.attr("href")); if (file.attr("href").endsWith(".json")) { ps.add(file.attr("href")); } } for (int i = 0; i < ps.size(); i++) { download(root.getAbsolutePath() + "/" + ps.get(i), plugins + ps.get(i)); FileInputStream fis = new FileInputStream(root.getAbsolutePath() + "/" + ps.get(i)); // begin writing a new ZIP entry, positions the stream to the start of the entry data zos.putNextEntry(new ZipEntry(plugins + ps.get(i))); int length; while ((length = fis.read(buffer)) > 0) { zos.write(buffer, 0, length); } zos.closeEntry(); fis.close(); new File(root.getAbsolutePath() + "/" + ps.get(i)).deleteOnExit(); if (throttle) Thread.sleep(WAIT); } // close the ZipOutputStream zos.close(); }
From source file:com.almende.eve.deploy.Boot.java
/** * The default agent booter. It takes an EVE yaml file and creates all * agents mentioned in the "agents" section. * /*from w w w. j a va 2 s .com*/ * @param args * Single argument: args[0] -> Eve yaml */ public static void main(final String[] args) { if (args.length == 0) { LOG.warning("Missing argument pointing to yaml file:"); LOG.warning("Usage: java -jar <jarfile> eve.yaml"); return; } final ClassLoader cl = new ClassLoader() { @Override protected Class<?> findClass(final String name) throws ClassNotFoundException { Class<?> result = null; try { result = super.findClass(name); } catch (ClassNotFoundException cne) { } if (result == null) { FileInputStream fi = null; try { String path = name.replace('.', '/'); fi = new FileInputStream(System.getProperty("user.dir") + "/" + path + ".class"); byte[] classBytes = new byte[fi.available()]; fi.read(classBytes); fi.close(); return defineClass(name, classBytes, 0, classBytes.length); } catch (Exception e) { LOG.log(Level.WARNING, "Failed to load class:", e); } } if (result == null) { throw new ClassNotFoundException(name); } return result; } }; String configFileName = args[0]; try { InputStream is = new FileInputStream(new File(configFileName)); boot(is, cl); } catch (FileNotFoundException e) { LOG.log(Level.WARNING, "Couldn't find configfile:" + configFileName, e); return; } }
From source file:Pathway2RDFv2.java
public static void main(String[] args) throws ParserConfigurationException, SAXException, IOException, ServiceException, ClassNotFoundException, IDMapperException, ParseException { int softwareVersion = 0; int schemaVersion = 0; int latestRevision = 0; BioDataSource.init();//from w w w .jav a2 s . c o m Class.forName("org.bridgedb.rdb.IDMapperRdb"); File dir = new File("/Users/andra/Downloads/bridge"); File[] bridgeDbFiles = dir.listFiles(); IDMapperStack mapper = new IDMapperStack(); for (File bridgeDbFile : bridgeDbFiles) { System.out.println(bridgeDbFile.getAbsolutePath()); mapper.addIDMapper("idmapper-pgdb:" + bridgeDbFile.getAbsolutePath()); } Model bridgeDbmodel = ModelFactory.createDefaultModel(); InputStream in = new FileInputStream("/tmp/BioDataSource.ttl"); bridgeDbmodel.read(in, "", "TURTLE"); WikiPathwaysClient client = new WikiPathwaysClient( new URL("http://www.wikipathways.org/wpi/webservice/webservice.php")); basicCalls.printMemoryStatus(); //Map wikipathway organisms to NCBI organisms HashMap<String, String> organismTaxonomy = wpRelatedCalls.getOrganismsTaxonomyMapping(); //HashMap<String, String> miriamSources = new HashMap<String, String>(); // HashMap<String, Str ing> miriamLinks = basicCalls.getMiriamUriBridgeDb(); //Document wikiPathwaysDom = basicCalls.openXmlFile(args[0]); Document wikiPathwaysDom = basicCalls.openXmlFile("/tmp/WpGPML.xml"); //initiate the Jena model to be populated Model model = ModelFactory.createDefaultModel(); Model voidModel = ModelFactory.createDefaultModel(); voidModel.setNsPrefix("xsd", XSD.getURI()); voidModel.setNsPrefix("void", Void.getURI()); voidModel.setNsPrefix("wprdf", "http://rdf.wikipathways.org/"); voidModel.setNsPrefix("pav", Pav.getURI()); voidModel.setNsPrefix("prov", Prov.getURI()); voidModel.setNsPrefix("dcterms", DCTerms.getURI()); voidModel.setNsPrefix("biopax", Biopax_level3.getURI()); voidModel.setNsPrefix("gpml", Gpml.getURI()); voidModel.setNsPrefix("wp", Wp.getURI()); voidModel.setNsPrefix("foaf", FOAF.getURI()); voidModel.setNsPrefix("hmdb", "http://identifiers.org/hmdb/"); voidModel.setNsPrefix("freq", Freq.getURI()); voidModel.setNsPrefix("dc", DC.getURI()); setModelPrefix(model); //Populate void.ttl Calendar now = Calendar.getInstance(); Literal nowLiteral = voidModel.createTypedLiteral(now); Literal titleLiteral = voidModel.createLiteral("WikiPathways-RDF VoID Description", "en"); Literal descriptionLiteral = voidModel .createLiteral("This is the VoID description for a WikiPathwyas-RDF dataset.", "en"); Resource voidBase = voidModel.createResource("http://rdf.wikipathways.org/"); Resource identifiersOrg = voidModel.createResource("http://identifiers.org"); Resource wpHomeBase = voidModel.createResource("http://www.wikipathways.org/"); Resource authorResource = voidModel .createResource("http://semantics.bigcat.unimaas.nl/figshare/search_author.php?author=waagmeester"); Resource apiResource = voidModel .createResource("http://www.wikipathways.org/wpi/webservice/webservice.php"); Resource mainDatadump = voidModel.createResource("http://rdf.wikipathways.org/wpContent.ttl.gz"); Resource license = voidModel.createResource("http://creativecommons.org/licenses/by/3.0/"); Resource instituteResource = voidModel.createResource("http://dbpedia.org/page/Maastricht_University"); voidBase.addProperty(RDF.type, Void.Dataset); voidBase.addProperty(DCTerms.title, titleLiteral); voidBase.addProperty(DCTerms.description, descriptionLiteral); voidBase.addProperty(FOAF.homepage, wpHomeBase); voidBase.addProperty(DCTerms.license, license); voidBase.addProperty(Void.uriSpace, voidBase); voidBase.addProperty(Void.uriSpace, identifiersOrg); voidBase.addProperty(Pav.importedBy, authorResource); voidBase.addProperty(Pav.importedFrom, apiResource); voidBase.addProperty(Pav.importedOn, nowLiteral); voidBase.addProperty(Void.dataDump, mainDatadump); voidBase.addProperty(Voag.frequencyOfChange, Freq.Irregular); voidBase.addProperty(Pav.createdBy, authorResource); voidBase.addProperty(Pav.createdAt, instituteResource); voidBase.addLiteral(Pav.createdOn, nowLiteral); voidBase.addProperty(DCTerms.subject, Biopax_level3.Pathway); voidBase.addProperty(Void.exampleResource, voidModel.createResource("http://identifiers.org/ncbigene/2678")); voidBase.addProperty(Void.exampleResource, voidModel.createResource("http://identifiers.org/pubmed/15215856")); voidBase.addProperty(Void.exampleResource, voidModel.createResource("http://identifiers.org/hmdb/HMDB02005")); voidBase.addProperty(Void.exampleResource, voidModel.createResource("http://rdf.wikipathways.org/WP15")); voidBase.addProperty(Void.exampleResource, voidModel.createResource("http://identifiers.org/obo.chebi/17242")); for (String organism : organismTaxonomy.values()) { voidBase.addProperty(DCTerms.subject, voidModel.createResource("http://dbpedia.org/page/" + organism.replace(" ", "_"))); } voidBase.addProperty(Void.vocabulary, Biopax_level3.NAMESPACE); voidBase.addProperty(Void.vocabulary, voidModel.createResource(Wp.getURI())); voidBase.addProperty(Void.vocabulary, voidModel.createResource(Gpml.getURI())); voidBase.addProperty(Void.vocabulary, FOAF.NAMESPACE); voidBase.addProperty(Void.vocabulary, Pav.NAMESPACE); //Custom Properties String baseUri = "http://rdf.wikipathways.org/"; NodeList pathwayElements = wikiPathwaysDom.getElementsByTagName("Pathway"); //BioDataSource.init(); for (int i = 0; i < pathwayElements.getLength(); i++) { Model pathwayModel = createPathwayModel(); String wpId = pathwayElements.item(i).getAttributes().getNamedItem("identifier").getTextContent(); String revision = pathwayElements.item(i).getAttributes().getNamedItem("revision").getTextContent(); String pathwayOrganism = ""; if (pathwayElements.item(i).getAttributes().getNamedItem("Organism") != null) pathwayOrganism = pathwayElements.item(i).getAttributes().getNamedItem("Organism").getTextContent() .trim(); if (Integer.valueOf(revision) > latestRevision) { latestRevision = Integer.valueOf(revision); } File f = new File("/tmp/" + args[0] + "/" + wpId + "_r" + revision + ".ttl"); System.out.println(f.getName()); if (!f.exists()) { Resource voidPwResource = wpRelatedCalls.addVoidTriples(voidModel, voidBase, pathwayElements.item(i), client); Resource pwResource = wpRelatedCalls.addPathwayLevelTriple(pathwayModel, pathwayElements.item(i), organismTaxonomy); // Get the comments NodeList commentElements = ((Element) pathwayElements.item(i)).getElementsByTagName("Comment"); wpRelatedCalls.addCommentTriples(pathwayModel, pwResource, commentElements, wpId, revision); // Get the Groups NodeList groupElements = ((Element) pathwayElements.item(i)).getElementsByTagName("Group"); for (int n = 0; n < groupElements.getLength(); n++) { wpRelatedCalls.addGroupTriples(pathwayModel, pwResource, groupElements.item(n), wpId, revision); } // Get all the Datanodes NodeList dataNodesElement = ((Element) pathwayElements.item(i)).getElementsByTagName("DataNode"); for (int j = 0; j < dataNodesElement.getLength(); j++) { wpRelatedCalls.addDataNodeTriples(pathwayModel, pwResource, dataNodesElement.item(j), wpId, revision, bridgeDbmodel, mapper); } // Get all the lines NodeList linesElement = ((Element) pathwayElements.item(i)).getElementsByTagName("Line"); for (int k = 0; k < linesElement.getLength(); k++) { wpRelatedCalls.addLineTriples(pathwayModel, pwResource, linesElement.item(k), wpId, revision); } //Get all the labels NodeList labelsElement = ((Element) pathwayElements.item(i)).getElementsByTagName("Label"); for (int l = 0; l < labelsElement.getLength(); l++) { wpRelatedCalls.addLabelTriples(pathwayModel, pwResource, labelsElement.item(l), wpId, revision); } NodeList referenceElements = ((Element) pathwayElements.item(i)) .getElementsByTagName("bp:PublicationXref"); for (int m = 0; m < referenceElements.getLength(); m++) { wpRelatedCalls.addReferenceTriples(pathwayModel, pwResource, referenceElements.item(m), wpId, revision); } NodeList referenceElements2 = ((Element) pathwayElements.item(i)) .getElementsByTagName("bp:publicationXref"); for (int m = 0; m < referenceElements2.getLength(); m++) { wpRelatedCalls.addReferenceTriples(pathwayModel, pwResource, referenceElements2.item(m), wpId, revision); } NodeList referenceElements3 = ((Element) pathwayElements.item(i)) .getElementsByTagName("bp:PublicationXRef"); for (int m = 0; m < referenceElements3.getLength(); m++) { wpRelatedCalls.addReferenceTriples(pathwayModel, pwResource, referenceElements3.item(m), wpId, revision); } NodeList ontologyElements = ((Element) pathwayElements.item(i)) .getElementsByTagName("bp:openControlledVocabulary"); for (int n = 0; n < ontologyElements.getLength(); n++) { wpRelatedCalls.addPathwayOntologyTriples(pathwayModel, pwResource, ontologyElements.item(n)); } System.out.println(wpId); basicCalls.saveRDF2File(pathwayModel, "/tmp/" + args[0] + "/" + wpId + "_r" + revision + ".ttl", "TURTLE"); model.add(pathwayModel); pathwayModel.removeAll(); } } Date myDate = new Date(); SimpleDateFormat sdf = new SimpleDateFormat("yyyyMMdd"); String myDateString = sdf.format(myDate); FileUtils.writeStringToFile(new File("latestVersion.txt"), "v" + schemaVersion + "." + softwareVersion + "." + latestRevision + "_" + myDateString); basicCalls.saveRDF2File(model, "/tmp/wpContent_v" + schemaVersion + "." + softwareVersion + "." + latestRevision + "_" + myDateString + ".ttl", "TURTLE"); basicCalls.saveRDF2File(voidModel, "/tmp/void.ttl", "TURTLE"); }