List of usage examples for java.io File getName
public String getName()
From source file:io.apicurio.studio.tools.release.ReleaseTool.java
/** * Main method./*from w ww .j a v a 2 s. c om*/ * @param args */ public static void main(String[] args) throws Exception { Options options = new Options(); options.addOption("n", "release-name", true, "The name of the new release."); options.addOption("p", "prerelease", false, "Indicate that this is a pre-release."); options.addOption("t", "release-tag", true, "The tag name of the new release."); options.addOption("o", "previous-tag", true, "The tag name of the previous release."); options.addOption("g", "github-pat", true, "The GitHub PAT (for authentication/authorization)."); options.addOption("a", "artifact", true, "The binary release artifact (full path)."); options.addOption("d", "output-directory", true, "Where to store output file(s)."); CommandLineParser parser = new DefaultParser(); CommandLine cmd = parser.parse(options, args); if (!cmd.hasOption("n") || !cmd.hasOption("t") || !cmd.hasOption("o") || !cmd.hasOption("g") || !cmd.hasOption("a")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("release-studio", options); System.exit(1); } // Arguments (command line) String releaseName = cmd.getOptionValue("n"); boolean isPrerelease = cmd.hasOption("p"); String releaseTag = cmd.getOptionValue("t"); String oldReleaseTag = cmd.getOptionValue("o"); String githubPAT = cmd.getOptionValue("g"); String artifact = cmd.getOptionValue("a"); File outputDir = new File(""); if (cmd.hasOption("d")) { outputDir = new File(cmd.getOptionValue("d")); if (!outputDir.exists()) { outputDir.mkdirs(); } } File releaseArtifactFile = new File(artifact); File releaseArtifactSigFile = new File(artifact + ".asc"); String releaseArtifact = releaseArtifactFile.getName(); String releaseArtifactSig = releaseArtifactSigFile.getName(); if (!releaseArtifactFile.isFile()) { System.err.println("Missing file: " + releaseArtifactFile.getAbsolutePath()); System.exit(1); } if (!releaseArtifactSigFile.isFile()) { System.err.println("Missing file: " + releaseArtifactSigFile.getAbsolutePath()); System.exit(1); } System.out.println("========================================="); System.out.println("Creating Release: " + releaseTag); System.out.println("Previous Release: " + oldReleaseTag); System.out.println(" Name: " + releaseName); System.out.println(" Artifact: " + releaseArtifact); System.out.println(" Pre-Release: " + isPrerelease); System.out.println("========================================="); String releaseNotes = ""; // Step #1 - Generate Release Notes // * Grab info about the previous release (extract publish date) // * Query all Issues for ones closed since that date // * Generate Release Notes from the resulting Issues try { System.out.println("Getting info about release " + oldReleaseTag); HttpResponse<JsonNode> response = Unirest .get("https://api.github.com/repos/apicurio/apicurio-studio/releases/tags/v" + oldReleaseTag) .header("Accept", "application/json").header("Authorization", "token " + githubPAT).asJson(); if (response.getStatus() != 200) { throw new Exception("Failed to get old release info: " + response.getStatusText()); } JsonNode body = response.getBody(); String publishedDate = body.getObject().getString("published_at"); if (publishedDate == null) { throw new Exception("Could not find Published Date for previous release " + oldReleaseTag); } System.out.println("Release " + oldReleaseTag + " was published on " + publishedDate); List<JSONObject> issues = getIssuesForRelease(publishedDate, githubPAT); System.out.println("Found " + issues.size() + " issues closed in release " + releaseTag); System.out.println("Generating Release Notes"); releaseNotes = generateReleaseNotes(releaseName, releaseTag, issues); System.out.println("------------ Release Notes --------------"); System.out.println(releaseNotes); System.out.println("-----------------------------------------"); } catch (Exception e) { e.printStackTrace(); System.exit(1); } String assetUploadUrl = null; // Step #2 - Create a GitHub Release try { System.out.println("\nCreating GitHub Release " + releaseTag); JSONObject body = new JSONObject(); body.put("tag_name", "v" + releaseTag); body.put("name", releaseName); body.put("body", releaseNotes); body.put("prerelease", isPrerelease); HttpResponse<JsonNode> response = Unirest .post("https://api.github.com/repos/apicurio/apicurio-studio/releases") .header("Accept", "application/json").header("Content-Type", "application/json") .header("Authorization", "token " + githubPAT).body(body).asJson(); if (response.getStatus() != 201) { throw new Exception("Failed to create release in GitHub: " + response.getStatusText()); } assetUploadUrl = response.getBody().getObject().getString("upload_url"); if (assetUploadUrl == null || assetUploadUrl.trim().isEmpty()) { throw new Exception("Failed to get Asset Upload URL for newly created release!"); } } catch (Exception e) { e.printStackTrace(); System.exit(1); } // Step #3 - Upload Release Artifact (zip file) System.out.println("\nUploading Quickstart Artifact: " + releaseArtifact); try { String artifactUploadUrl = createUploadUrl(assetUploadUrl, releaseArtifact); byte[] artifactData = loadArtifactData(releaseArtifactFile); System.out.println("Uploading artifact asset: " + artifactUploadUrl); HttpResponse<JsonNode> response = Unirest.post(artifactUploadUrl).header("Accept", "application/json") .header("Content-Type", "application/zip").header("Authorization", "token " + githubPAT) .body(artifactData).asJson(); if (response.getStatus() != 201) { throw new Exception("Failed to upload asset: " + releaseArtifact, new Exception(response.getStatus() + "::" + response.getStatusText())); } Thread.sleep(1000); artifactUploadUrl = createUploadUrl(assetUploadUrl, releaseArtifactSig); artifactData = loadArtifactData(releaseArtifactSigFile); System.out.println("Uploading artifact asset: " + artifactUploadUrl); response = Unirest.post(artifactUploadUrl).header("Accept", "application/json") .header("Content-Type", "text/plain").header("Authorization", "token " + githubPAT) .body(artifactData).asJson(); if (response.getStatus() != 201) { throw new Exception("Failed to upload asset: " + releaseArtifactSig, new Exception(response.getStatus() + "::" + response.getStatusText())); } } catch (Exception e) { e.printStackTrace(); System.exit(1); } Thread.sleep(1000); // Step #4 - Download Latest Release JSON for inclusion in the project web site try { System.out.println("Getting info about the release."); HttpResponse<JsonNode> response = Unirest .get("https://api.github.com/repos/apicurio/apicurio-studio/releases/latest") .header("Accept", "application/json").asJson(); if (response.getStatus() != 200) { throw new Exception("Failed to get release info: " + response.getStatusText()); } JsonNode body = response.getBody(); String publishedDate = body.getObject().getString("published_at"); if (publishedDate == null) { throw new Exception("Could not find Published Date for release."); } String fname = publishedDate.replace(':', '-'); File outFile = new File(outputDir, fname + ".json"); System.out.println("Writing latest release info to: " + outFile.getAbsolutePath()); String output = body.getObject().toString(4); try (FileOutputStream fos = new FileOutputStream(outFile)) { fos.write(output.getBytes("UTF-8")); fos.flush(); } System.out.println("Release info successfully written."); } catch (Exception e) { e.printStackTrace(); System.exit(1); } System.out.println("========================================="); System.out.println("All Done!"); System.out.println("========================================="); }
From source file:de.tudarmstadt.ukp.experiments.argumentation.convincingness.sampling.Step4MTurkOutputCollector.java
@SuppressWarnings("unchecked") public static void main(String[] args) throws Exception { String inputDirWithArgumentPairs = args[0]; File[] resultFiles;// ww w . j a v a2s . c o m if (args[1].contains("*")) { File path = new File(args[1]); File directory = path.getParentFile(); String regex = path.getName().replaceAll("\\*", ""); List<File> files = new ArrayList<>(FileUtils.listFiles(directory, new String[] { regex }, false)); resultFiles = new File[files.size()]; for (int i = 0; i < files.size(); i++) { resultFiles[i] = files.get(i); } } else { // result file is a comma-separated list of CSV files from MTurk String[] split = args[1].split(","); resultFiles = new File[split.length]; for (int i = 0; i < split.length; i++) { resultFiles[i] = new File(split[i]); } } File outputDir = new File(args[2]); if (!outputDir.exists()) { if (!outputDir.mkdirs()) { throw new IOException("Cannot create directory " + outputDir); } } // error if output folder not empty to prevent any confusion by mixing files if (!FileUtils.listFiles(outputDir, null, false).isEmpty()) { throw new IllegalArgumentException("Output dir " + outputDir + " is not empty"); } // collected assignments with empty reason for rejections Set<String> assignmentsWithEmptyReason = new HashSet<>(); // parse with first line as header MTurkOutputReader mTurkOutputReader = new MTurkOutputReader(resultFiles); Collection<File> files = FileUtils.listFiles(new File(inputDirWithArgumentPairs), new String[] { "xml" }, false); if (files.isEmpty()) { throw new IOException("No xml files found in " + inputDirWithArgumentPairs); } // statistics: how many hits with how many assignments ; hit ID / assignments Map<String, Map<String, Integer>> assignmentsPerHits = new HashMap<>(); // collect accept/reject statistics for (Map<String, String> record : mTurkOutputReader) { boolean wasRejected = "Rejected".equals(record.get("assignmentstatus")); String hitID = record.get("hitid"); String hitTypeId = record.get("hittypeid"); if (!wasRejected) { // update statistics if (!assignmentsPerHits.containsKey(hitTypeId)) { assignmentsPerHits.put(hitTypeId, new HashMap<String, Integer>()); } if (!assignmentsPerHits.get(hitTypeId).containsKey(hitID)) { assignmentsPerHits.get(hitTypeId).put(hitID, 0); } assignmentsPerHits.get(hitTypeId).put(hitID, assignmentsPerHits.get(hitTypeId).get(hitID) + 1); } } // statistics: how many hits with how many assignments ; hit ID / assignments Map<String, Integer> approvedAssignmentsPerHit = new HashMap<>(); Map<String, Integer> rejectedAssignmentsPerHit = new HashMap<>(); // collect accept/reject statistics for (Map<String, String> record : mTurkOutputReader) { boolean approved = "Approved".equals(record.get("assignmentstatus")); boolean rejected = "Rejected".equals(record.get("assignmentstatus")); String hitID = record.get("hitid"); if (approved) { // update statistics if (!approvedAssignmentsPerHit.containsKey(hitID)) { approvedAssignmentsPerHit.put(hitID, 0); } approvedAssignmentsPerHit.put(hitID, approvedAssignmentsPerHit.get(hitID) + 1); } else if (rejected) { // update statistics if (!rejectedAssignmentsPerHit.containsKey(hitID)) { rejectedAssignmentsPerHit.put(hitID, 0); } rejectedAssignmentsPerHit.put(hitID, rejectedAssignmentsPerHit.get(hitID) + 1); } else { throw new IllegalStateException( "Unknown state: " + record.get("assignmentstatus") + " HITID: " + hitID); } } // System.out.println("Approved: " + approvedAssignmentsPerHit); // System.out.println("Rejected: " + rejectedAssignmentsPerHit); System.out.println("Approved (values): " + new HashSet<>(approvedAssignmentsPerHit.values())); System.out.println("Rejected (values): " + new HashSet<>(rejectedAssignmentsPerHit.values())); // rejection statistics int totalRejected = 0; for (Map.Entry<String, Integer> rejectionEntry : rejectedAssignmentsPerHit.entrySet()) { totalRejected += rejectionEntry.getValue(); } System.out.println("Total rejections: " + totalRejected); /* // generate .success files for adding more annotations for (File resultFile : resultFiles) { String hitTypeID = mTurkOutputReader.getHitTypeIdForFile().get(resultFile); // assignments for that hittypeid (= file) Map<String, Integer> assignments = assignmentsPerHits.get(hitTypeID); prepareUpdateHITsFiles(assignments, hitTypeID, resultFile); } */ int totalSavedPairs = 0; // load all previously prepared argument pairs for (File file : files) { List<ArgumentPair> argumentPairs = (List<ArgumentPair>) XStreamTools.getXStream().fromXML(file); List<AnnotatedArgumentPair> annotatedArgumentPairs = new ArrayList<>(); for (ArgumentPair argumentPair : argumentPairs) { AnnotatedArgumentPair annotatedArgumentPair = new AnnotatedArgumentPair(argumentPair); // is there such an answer? String key = "Answer." + argumentPair.getId(); // iterate only if there is such column to save time if (mTurkOutputReader.getColumnNames().contains(key)) { // now find the results for (Map<String, String> record : mTurkOutputReader) { if (record.containsKey(key)) { // extract the values AnnotatedArgumentPair.MTurkAssignment assignment = new AnnotatedArgumentPair.MTurkAssignment(); boolean wasRejected = "Rejected".equals(record.get("assignmentstatus")); // only non-rejected (if required) if (!wasRejected) { String hitID = record.get("hitid"); String workerID = record.get("workerid"); String assignmentId = record.get("assignmentid"); try { assignment.setAssignmentAcceptTime( DATE_FORMAT.parse(record.get("assignmentaccepttime"))); assignment.setAssignmentSubmitTime( DATE_FORMAT.parse(record.get("assignmentsubmittime"))); assignment.setHitComment(record.get("Answer.feedback")); assignment.setHitID(hitID); assignment.setTurkID(workerID); assignment.setAssignmentId(assignmentId); // and answer specific fields String valueRaw = record.get(key); // so far the label has had format aXXX_aYYY_a1, aXXX_aYYY_a2, or aXXX_aYYY_equal // strip now only true label String label = valueRaw.split("_")[2]; assignment.setValue(label); String reason = record.get(key + "_reason"); // missing reason if (reason == null) { assignmentsWithEmptyReason.add(assignmentId); } else { assignment.setReason(reason); // get worker's stance String stanceRaw = record.get(key + "_stance"); if (stanceRaw != null) { // parse stance String stance = stanceRaw.split("_stance_")[1]; assignment.setWorkerStance(stance); } // we take maximal 5 assignments Collections.sort(annotatedArgumentPair.mTurkAssignments, new Comparator<AnnotatedArgumentPair.MTurkAssignment>() { @Override public int compare(AnnotatedArgumentPair.MTurkAssignment o1, AnnotatedArgumentPair.MTurkAssignment o2) { return o1.getAssignmentAcceptTime() .compareTo(o2.getAssignmentAcceptTime()); } }); if (annotatedArgumentPair.mTurkAssignments .size() < MAXIMUM_ASSIGNMENTS_PER_HIT) { annotatedArgumentPair.mTurkAssignments.add(assignment); } } } catch (IllegalArgumentException | NullPointerException ex) { System.err.println("Malformed annotations for HIT " + hitID + ", worker " + workerID + ", assignment " + assignmentId + "; " + ex.getMessage() + ", full record: " + record); } } } } } // and if there are some annotations, add it to the result set if (!annotatedArgumentPair.mTurkAssignments.isEmpty()) { annotatedArgumentPairs.add(annotatedArgumentPair); } } if (!annotatedArgumentPairs.isEmpty()) { File outputFile = new File(outputDir, file.getName()); XStreamTools.toXML(annotatedArgumentPairs, outputFile); System.out.println("Saved " + annotatedArgumentPairs.size() + " annotated pairs to " + outputFile); totalSavedPairs += annotatedArgumentPairs.size(); } } System.out.println("Total saved " + totalSavedPairs + " pairs"); // print assignments with empty reasons if (!assignmentsWithEmptyReason.isEmpty()) { System.out.println( "== Assignments with empty reason:\nassignmentIdToReject\tassignmentIdToRejectComment"); for (String assignmentId : assignmentsWithEmptyReason) { System.out.println( assignmentId + "\t\"Dear worker, you did not fill the required field with a reason.\""); } } }
From source file:gash.router.app.DemoApp.java
/** * sample application (client) use of our messaging service * * @param args// w w w. j av a 2 s.com */ public static void main(String[] args) { if (args.length == 0) { System.out.println("usage: <ip address> <port no>"); System.exit(1); } String ipAddress = args[0]; int port = Integer.parseInt(args[1]); Scanner s = new Scanner(System.in); boolean isExit = false; try { MessageClient mc = new MessageClient(ipAddress, port); DemoApp da = new DemoApp(mc); int choice = 0; while (true) { System.out.println( "Enter your option \n1. WRITE a file. \n2. READ a file. \n3. Update a File. \n4. Delete a File\n 5 Ping(Global)\n 6 Exit"); choice = s.nextInt(); switch (choice) { case 1: { System.out.println("Enter the full pathname of the file to be written "); String currFileName = s.next(); File file = new File(currFileName); if (file.exists()) { ArrayList<ByteString> chunkedFile = da.divideFileChunks(file); String name = file.getName(); int i = 0; String requestId = SupportMessageGenerator.generateRequestID(); for (ByteString string : chunkedFile) { mc.saveFile(name, string, chunkedFile.size(), i++, requestId); } } else { throw new FileNotFoundException("File does not exist in this path "); } } break; case 2: { System.out.println("Enter the file name to be read : "); String currFileName = s.next(); da.sendReadTasks(currFileName); //Thread.sleep(1000 * 100); } break; case 3: { System.out.println("Enter the full pathname of the file to be updated"); String currFileName = s.next(); File file = new File(currFileName); if (file.exists()) { ArrayList<ByteString> chunkedFile = da.divideFileChunks(file); String name = file.getName(); int i = 0; String requestId = SupportMessageGenerator.generateRequestID(); for (ByteString string : chunkedFile) { mc.updateFile(name, string, chunkedFile.size(), i++, requestId); } //Thread.sleep(10 * 1000); } else { throw new FileNotFoundException("File does not exist in this path "); } } break; case 4: System.out.println("Enter the file name to be deleted : "); String currFileName = s.next(); mc.deleteFile(currFileName); //Thread.sleep(1000 * 100); break; case 5: da.ping(1); break; case 6: isExit = true; break; default: break; } if (isExit) break; } } catch (Exception e) { e.printStackTrace(); } finally { CommConnection.getInstance().release(); if (s != null) s.close(); } }
From source file:mujava.cli.genmutes.java
public static void main(String[] args) throws Exception { // System.out.println("test"); genmutesCom jct = new genmutesCom(); String[] argv = { "-all", "-debug", "Flower" }; // development use, when release, // comment out this line JCommander jCommander = new JCommander(jct, args); // check session name if (jct.getParameters().size() > 1) { Util.Error("Has more parameters than needed."); return;//from w w w . java2s. co m } // set session name String sessionName = jct.getParameters().get(0); muJavaHomePath = Util.loadConfig(); // check if debug mode if (jct.isDebug()) { Util.debug = true; } // get all existing session name File folder = new File(muJavaHomePath); // check if the config file has defined the correct folder if (!folder.isDirectory()) { Util.Error("ERROR: cannot locate the folder specified in mujava.config"); return; } File[] listOfFiles = folder.listFiles(); // null checking // check the specified folder has files or not if (listOfFiles == null) { Util.Error("ERROR: no files in the muJava home folder: " + muJavaHomePath); return; } List<String> fileNameList = new ArrayList<>(); for (File file : listOfFiles) { fileNameList.add(file.getName()); } // check if session is already created. if (!fileNameList.contains(sessionName)) { Util.Error("Session does not exist."); return; } // get all files in the session String[] file_list = new String[1]; // if(jct.getD()) // { File sessionFolder = new File(muJavaHomePath + "/" + sessionName + "/src"); File[] listOfFilesInSession = sessionFolder.listFiles(); file_list = new String[listOfFilesInSession.length]; for (int i = 0; i < listOfFilesInSession.length; i++) { file_list[i] = listOfFilesInSession[i].getName(); } // get all mutation operators selected HashMap<String, List<String>> ops = new HashMap<String, List<String>>(); // used // for // add // random // percentage // and // maximum String[] paras = new String[] { "1", "0" }; if (jct.getAll()) // all is selected, add all operators { // if all is selected, all mutation operators are added ops.put("AORB", new ArrayList<String>(Arrays.asList(paras))); ops.put("AORS", new ArrayList<String>(Arrays.asList(paras))); ops.put("AOIU", new ArrayList<String>(Arrays.asList(paras))); ops.put("AOIS", new ArrayList<String>(Arrays.asList(paras))); ops.put("AODU", new ArrayList<String>(Arrays.asList(paras))); ops.put("AODS", new ArrayList<String>(Arrays.asList(paras))); ops.put("ROR", new ArrayList<String>(Arrays.asList(paras))); ops.put("COR", new ArrayList<String>(Arrays.asList(paras))); ops.put("COD", new ArrayList<String>(Arrays.asList(paras))); ops.put("COI", new ArrayList<String>(Arrays.asList(paras))); ops.put("SOR", new ArrayList<String>(Arrays.asList(paras))); ops.put("LOR", new ArrayList<String>(Arrays.asList(paras))); ops.put("LOI", new ArrayList<String>(Arrays.asList(paras))); ops.put("LOD", new ArrayList<String>(Arrays.asList(paras))); ops.put("ASRS", new ArrayList<String>(Arrays.asList(paras))); ops.put("SDL", new ArrayList<String>(Arrays.asList(paras))); ops.put("ODL", new ArrayList<String>(Arrays.asList(paras))); ops.put("VDL", new ArrayList<String>(Arrays.asList(paras))); ops.put("CDL", new ArrayList<String>(Arrays.asList(paras))); // ops.put("SDL", jct.getAll()); } else { // if not all, add selected ops to the list if (jct.getAORB()) { ops.put("AORB", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getAORS()) { ops.put("AORS", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getAOIU()) { ops.put("AOIU", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getAOIS()) { ops.put("AOIS", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getAODU()) { ops.put("AODU", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getAODS()) { ops.put("AODS", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getROR()) { ops.put("ROR", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getCOR()) { ops.put("COR", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getCOD()) { ops.put("COD", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getCOI()) { ops.put("COI", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getSOR()) { ops.put("SOR", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getLOR()) { ops.put("LOR", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getLOI()) { ops.put("LOI", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getLOD()) { ops.put("LOD", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getASRS()) { ops.put("ASRS", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getSDL()) { ops.put("SDL", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getVDL()) { ops.put("VDL", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getODL()) { ops.put("ODL", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getCDL()) { ops.put("CDL", new ArrayList<String>(Arrays.asList(paras))); } } // add default option "all" if (ops.size() == 0) { ops.put("AORB", new ArrayList<String>(Arrays.asList(paras))); ops.put("AORS", new ArrayList<String>(Arrays.asList(paras))); ops.put("AOIU", new ArrayList<String>(Arrays.asList(paras))); ops.put("AOIS", new ArrayList<String>(Arrays.asList(paras))); ops.put("AODU", new ArrayList<String>(Arrays.asList(paras))); ops.put("AODS", new ArrayList<String>(Arrays.asList(paras))); ops.put("ROR", new ArrayList<String>(Arrays.asList(paras))); ops.put("COR", new ArrayList<String>(Arrays.asList(paras))); ops.put("COD", new ArrayList<String>(Arrays.asList(paras))); ops.put("COI", new ArrayList<String>(Arrays.asList(paras))); ops.put("SOR", new ArrayList<String>(Arrays.asList(paras))); ops.put("LOR", new ArrayList<String>(Arrays.asList(paras))); ops.put("LOI", new ArrayList<String>(Arrays.asList(paras))); ops.put("LOD", new ArrayList<String>(Arrays.asList(paras))); ops.put("ASRS", new ArrayList<String>(Arrays.asList(paras))); ops.put("SDL", new ArrayList<String>(Arrays.asList(paras))); ops.put("ODL", new ArrayList<String>(Arrays.asList(paras))); ops.put("VDL", new ArrayList<String>(Arrays.asList(paras))); ops.put("CDL", new ArrayList<String>(Arrays.asList(paras))); } // String[] tradional_ops = ops.toArray(new String[0]); // set system setJMutationStructureAndSession(sessionName); // MutationSystem.setJMutationStructureAndSession(sessionName); MutationSystem.recordInheritanceRelation(); // generate mutants generateMutants(file_list, ops); //System.exit(0); }
From source file:Inmemantlr.java
public static void main(String[] args) { LOGGER.info("Inmemantlr tool"); HelpFormatter hformatter = new HelpFormatter(); Options options = new Options(); // Binary arguments options.addOption("h", "print this message"); Option grmr = Option.builder().longOpt("grmrfiles").hasArgs().desc("comma-separated list of ANTLR files") .required(true).argName("grmrfiles").type(String.class).valueSeparator(',').build(); Option infiles = Option.builder().longOpt("infiles").hasArgs() .desc("comma-separated list of files to parse").required(true).argName("infiles").type(String.class) .valueSeparator(',').build(); Option utilfiles = Option.builder().longOpt("utilfiles").hasArgs() .desc("comma-separated list of utility files to be added for " + "compilation").required(false) .argName("utilfiles").type(String.class).valueSeparator(',').build(); Option odir = Option.builder().longOpt("outdir") .desc("output directory in which the dot files will be " + "created").required(false).hasArg(true) .argName("outdir").type(String.class).build(); options.addOption(infiles);//from www .ja v a2 s. c om options.addOption(grmr); options.addOption(utilfiles); options.addOption(odir); CommandLineParser parser = new DefaultParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); if (cmd.hasOption('h')) { hformatter.printHelp("java -jar inmemantlr.jar", options); System.exit(0); } } catch (ParseException e) { hformatter.printHelp("java -jar inmemantlr.jar", options); LOGGER.error(e.getMessage()); System.exit(-1); } // input files Set<File> ins = getFilesForOption(cmd, "infiles"); // grammar files Set<File> gs = getFilesForOption(cmd, "grmrfiles"); // utility files Set<File> uf = getFilesForOption(cmd, "utilfiles"); // output dir Set<File> od = getFilesForOption(cmd, "outdir"); if (od.size() > 1) { LOGGER.error("output directories must be less than or equal to 1"); System.exit(-1); } if (ins.size() <= 0) { LOGGER.error("no input files were specified"); System.exit(-1); } if (gs.size() <= 0) { LOGGER.error("no grammar files were specified"); System.exit(-1); } LOGGER.info("create generic parser"); GenericParser gp = null; try { gp = new GenericParser(gs.toArray(new File[gs.size()])); } catch (FileNotFoundException e) { LOGGER.error(e.getMessage()); System.exit(-1); } if (!uf.isEmpty()) { try { gp.addUtilityJavaFiles(uf.toArray(new String[uf.size()])); } catch (FileNotFoundException e) { LOGGER.error(e.getMessage()); System.exit(-1); } } LOGGER.info("create and add parse tree listener"); DefaultTreeListener dt = new DefaultTreeListener(); gp.setListener(dt); LOGGER.info("compile generic parser"); try { gp.compile(); } catch (CompilationException e) { LOGGER.error("cannot compile generic parser: {}", e.getMessage()); System.exit(-1); } String fpfx = ""; for (File of : od) { if (!of.exists() || !of.isDirectory()) { LOGGER.error("output directory does not exist or is not a " + "directory"); System.exit(-1); } fpfx = of.getAbsolutePath(); } Ast ast; for (File f : ins) { try { gp.parse(f); } catch (IllegalWorkflowException | FileNotFoundException e) { LOGGER.error(e.getMessage()); System.exit(-1); } ast = dt.getAst(); if (!fpfx.isEmpty()) { String of = fpfx + "/" + FilenameUtils.removeExtension(f.getName()) + ".dot"; LOGGER.info("write file {}", of); try { FileUtils.writeStringToFile(new File(of), ast.toDot(), "UTF-8"); } catch (IOException e) { LOGGER.error(e.getMessage()); System.exit(-1); } } else { LOGGER.info("Tree for {} \n {}", f.getName(), ast.toDot()); } } System.exit(0); }
From source file:com.recomdata.transmart.data.export.util.SftpClient.java
public static void main(String[] args) { //File outputFile = new File("./latestGet.log"); try {//w w w . j a va2 s . c o m SftpClient sftpClient = new SftpClient("factbookdev", "SvcCOPSSH", "C:/Users/smunikuntla/Downloads/SaiMunikuntla12.ppk", "22", ""); sftpClient.putFile(new File("C:/Users/smunikuntla/Downloads/camelinaction-src.zip")); //sftpClient.getFile("server1.log", outputFile); File jobZipFile = null; File tempFile = null; /*StringTokenizer st = new StringTokenizer("ftp://SvcCOPSSH:@factbookdev:22/camelinaction-src.zip", "/"); String token = null; while (st.hasMoreTokens()) { token = st.nextToken(); }*/ tempFile = new File("ftp://SvcCOPSSH:@factbookdev:22/camelinaction-src.zip"); jobZipFile = new File(tempFile.getName()); sftpClient.getFile("camelinaction-src.zip", jobZipFile); sftpClient.close(); } catch (Exception e) { e.printStackTrace(); } }
From source file:net.itransformers.idiscover.core.DiscoveryManager.java
public static void main(String[] args) throws Exception, IllegalAccessException, JAXBException { Map<String, String> params = CmdLineParser.parseCmdLine(args); if (params == null) { printUsage("mibDir"); return;//from w w w . j a v a 2 s . c om } final String fileName = params.get("-f"); if (fileName == null) { printUsage("fileName"); return; } File file = new File(fileName); DiscoveryManager manager = createDiscoveryManager(file.getParentFile(), file.getName(), "network", true); String mode = params.get("-d"); if (mode == null) { //Set default snmpDiscovery mode to discover network!!! mode = "network"; } Map<String, String> resourceSelectionParams = new HashMap<String, String>(); resourceSelectionParams.put("protocol", "SNMP"); ResourceType snmp = manager.discoveryResource.returnResourceByParam(resourceSelectionParams); Map<String, String> snmpConnParams = new HashMap<String, String>(); snmpConnParams = manager.discoveryResource.getParamMap(snmp, "snmp"); String host = params.get("-h"); IPv4Address initialIPaddress = new IPv4Address(host, null); snmpConnParams.put("status", "initial"); String mibDir = params.get("-m"); snmpConnParams.put("mibDir", mibDir); snmpConnParams.get("port"); Resource resource = new Resource(initialIPaddress, null, Integer.parseInt(snmpConnParams.get("port")), snmpConnParams); if (resource == null) ; String[] discoveryTypes = new String[] { "PHYSICAL", "NEXT_HOP", "OSPF", "ISIS", "BGP", "RIP", "ADDITIONAL", "IPV6" }; // DiscovererFactory.init(new SimulSnmpWalker(resource, new File("logs.log"))); // DiscovererFactory.init(); // Discoverer discoverer = new SnmpWalker(resource); NetworkType network = manager.discoverNetwork(resource, mode, discoveryTypes); for (DiscoveredDeviceData data : network.getDiscoveredDevice()) { System.out.println(data.getName() + "\n"); for (ObjectType object : data.getObject()) { for (ObjectType innterObject : object.getObject()) { System.out.println(innterObject.getObjectType()); } } } // List<DiscoveredDeviceData> discoveredDeviceDatas = network.getDiscoveredDevice(); // for (DiscoveredDeviceData discoveredDeviceData : discoveredDeviceDatas) { // discoveredDeviceData.getName(); // ParametersType parameters = discoveredDeviceData.getParameters(); // List<ParameterType> paras = parameters.getParameter(); // for (ParameterType para : paras) { // // } // // } }
From source file:it.univpm.deit.semedia.musicuri.utils.experimental.LambdaCalculator.java
public static void main(String[] args) throws Exception { //***************************************************************************** //************************* F I L E I N P U T *************************** //***************************************************************************** if ((args.length == 1) && (new File(args[0]).exists())) { // get the file's canonical path File givenHandle = new File(args[0]); String queryAudioCanonicalPath = givenHandle.getCanonicalPath(); System.out.println("Input: " + queryAudioCanonicalPath); //PerformanceStatistic tempStat; SummaryStatistics lambdaSummary = SummaryStatistics.newInstance(); if (givenHandle.isDirectory()) { File[] list = givenHandle.listFiles(); if (list.length == 0) { System.out.println("Directory is empty"); return; } else { ArrayList allStats = new ArrayList(); File currentFile; for (int i = 0; i < list.length; i++) { currentFile = list[i]; try { if (Toolset.isSupportedAudioFile(currentFile)) { System.out.println("\nCalculating optimal lambda : " + currentFile.getName()); lambdaSummary.addValue(getBestLambda(new MusicURIQuery(currentFile))); }/*from w ww . j a v a 2 s . c o m*/ } catch (Exception e) { e.printStackTrace(); } } // System.out.println("\n\nStatistics for Test Case: " + queryAudioCanonicalPath); // mergeStatistics(allStats); } } if (givenHandle.isFile()) { if (Toolset.isSupportedAudioFile(givenHandle)) { // tempStat = getBestLambda (new MusicURIQuery(givenHandle)); // if (tempStat!=null) // { // //tempStat.printStatistics(); // ArrayList allStats = new ArrayList(); // allStats.add(tempStat); // mergeStatistics(allStats); // } // else // System.out.println("Error in identification "); } } } //end if else { System.err.println("LambdaCalculator"); System.err.println("Usage: java tester.LambdaCalculator {directory}"); } }
From source file:ca.uqac.info.monitor.BeepBeepMonitor.java
public static void main(String[] args) { int verbosity = 1, slowdown = 0, tcp_port = 0; boolean show_stats = false, to_stdout = false; String trace_filename = "", pipe_filename = "", event_name = "message"; final MonitorFactory mf = new MonitorFactory(); // In case we open a socket ServerSocket m_serverSocket = null; Socket m_connection = null;//from ww w . j a v a2s. co m // Parse command line arguments Options options = setupOptions(); CommandLine c_line = setupCommandLine(args, options); assert c_line != null; if (c_line.hasOption("verbosity")) { verbosity = Integer.parseInt(c_line.getOptionValue("verbosity")); } if (verbosity > 0) { showHeader(); } if (c_line.hasOption("version")) { System.err.println("(C) 2008-2013 Sylvain Hall et al., Universit du Qubec Chicoutimi"); System.err.println("This program comes with ABSOLUTELY NO WARRANTY."); System.err.println("This is a free software, and you are welcome to redistribute it"); System.err.println("under certain conditions. See the file COPYING for details.\n"); System.exit(ERR_OK); } if (c_line.hasOption("h")) { showUsage(options); System.exit(ERR_OK); } if (c_line.hasOption("version")) { System.exit(ERR_OK); } if (c_line.hasOption("slowdown")) { slowdown = Integer.parseInt(c_line.getOptionValue("slowdown")); if (verbosity > 0) System.err.println("Slowdown factor: " + slowdown + " ms"); } if (c_line.hasOption("stats")) { show_stats = true; } if (c_line.hasOption("csv")) { // Will output data in CSV format to stdout to_stdout = true; } if (c_line.hasOption("eventname")) { // Set event name event_name = c_line.getOptionValue("eventname"); } if (c_line.hasOption("t")) { // Read events from a trace trace_filename = c_line.getOptionValue("t"); } if (c_line.hasOption("p")) { // Read events from a pipe pipe_filename = c_line.getOptionValue("p"); } if (c_line.hasOption("k")) { // Read events from a TCP port tcp_port = Integer.parseInt(c_line.getOptionValue("k")); } if (!trace_filename.isEmpty() && !pipe_filename.isEmpty()) { System.err.println("ERROR: you must specify at most one of trace file or named pipe"); showUsage(options); System.exit(ERR_ARGUMENTS); } @SuppressWarnings("unchecked") List<String> remaining_args = c_line.getArgList(); if (remaining_args.isEmpty()) { System.err.println("ERROR: no input formula specified"); showUsage(options); System.exit(ERR_ARGUMENTS); } // Instantiate the event notifier boolean notify = (verbosity > 0); EventNotifier en = new EventNotifier(notify); en.m_slowdown = slowdown; en.m_csvToStdout = to_stdout; // Create one monitor for each input file and add it to the notifier for (String formula_filename : remaining_args) { try { String formula_contents = FileReadWrite.readFile(formula_filename); Operator op = Operator.parseFromString(formula_contents); op.accept(mf); Monitor mon = mf.getMonitor(); Map<String, String> metadata = getMetadata(formula_contents); metadata.put("Filename", formula_filename); en.addMonitor(mon, metadata); } catch (IOException e) { e.printStackTrace(); System.exit(ERR_IO); } catch (Operator.ParseException e) { System.err.println("Error parsing input formula"); System.exit(ERR_PARSE); } } // Read trace and iterate // Opens file PipeReader pr = null; try { if (!pipe_filename.isEmpty()) { // We tell the pipe reader we read a pipe File f = new File(pipe_filename); if (verbosity > 0) System.err.println("Reading from pipe named " + f.getName()); pr = new PipeReader(new FileInputStream(f), en, false); } else if (!trace_filename.isEmpty()) { // We tell the pipe reader we read a regular file File f = new File(trace_filename); if (verbosity > 0) System.err.println("Reading from file " + f.getName()); pr = new PipeReader(new FileInputStream(f), en, true); } else if (tcp_port > 0) { // We tell the pipe reader we read from a socket if (verbosity > 0) System.err.println("Reading from TCP port " + tcp_port); m_serverSocket = new ServerSocket(tcp_port); m_connection = m_serverSocket.accept(); pr = new PipeReader(m_connection.getInputStream(), en, false); } else { // We tell the pipe reader we read from standard input if (verbosity > 0) System.err.println("Reading from standard input"); pr = new PipeReader(System.in, en, false); } } catch (FileNotFoundException ex) { // We print both trace and pipe since one of them must be empty System.err.println("ERROR: file not found " + trace_filename + pipe_filename); System.exit(ERR_IO); } catch (IOException e) { // Caused by socket error e.printStackTrace(); System.exit(ERR_IO); } pr.setSeparator("<" + event_name + ">", "</" + event_name + ">"); // Check parameters for the event notifier if (c_line.hasOption("no-trigger")) { en.m_notifyOnVerdict = false; } else { en.m_notifyOnVerdict = true; } if (c_line.hasOption("mirror")) { en.m_mirrorEventsOnStdout = true; } // Start event notifier en.reset(); Thread th = new Thread(pr); long clock_start = System.nanoTime(); th.start(); try { th.join(); // Wait for thread to finish } catch (InterruptedException e1) { // Thread is finished } if (tcp_port > 0 && m_serverSocket != null) { // We opened a socket; now we close it try { m_serverSocket.close(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } } long clock_end = System.nanoTime(); int ret_code = pr.getReturnCode(); switch (ret_code) { case PipeReader.ERR_EOF: if (verbosity > 0) System.err.println("\nEnd of file reached"); break; case PipeReader.ERR_EOT: if (verbosity > 0) System.err.println("\nEOT received on pipe: closing"); break; case PipeReader.ERR_OK: // Do nothing break; default: // An error System.err.println("Runtime error"); System.exit(ERR_RUNTIME); break; } if (show_stats) { if (verbosity > 0) { System.out.println("Messages: " + en.m_numEvents); System.out.println("Time: " + (int) (en.m_totalTime / 1000000f) + " ms"); System.out.println("Clock time: " + (int) ((clock_end - clock_start) / 1000000f) + " ms"); System.out.println("Max heap: " + (int) (en.heapSize / 1048576f) + " MB"); } else { // If stats are asked but verbosity = 0, only show time value // (both monitor and wall clock) System.out.print((int) (en.m_totalTime / 1000000f)); System.out.print(","); System.out.print((int) ((clock_end - clock_start) / 1000000f)); } } System.exit(ERR_OK); }
From source file:edu.msu.cme.rdp.alignment.errorcheck.CompareErrorType.java
public static void main(String[] args) throws IOException { Options options = new Options(); options.addOption("s", "stem", true, "Output stem (default <query_nucl.fasta>)"); final SeqReader queryReader; final List<Sequence> refSeqList; final PrintStream alignOutStream; final CompareErrorType errorProcessor; Sequence seq;//from w ww . jav a2s . co m Map<String, PAObject> matchMap = new HashMap(); try { CommandLine line = new PosixParser().parse(options, args); String stem; args = line.getArgs(); if (args.length != 2 && args.length != 3) { throw new Exception("Unexpected number of arguments"); } File refFile = new File(args[0]); File queryFile = new File(args[1]); if (line.hasOption("stem")) { stem = line.getOptionValue("stem"); } else { stem = queryFile.getName(); } File alignOutFile = new File(stem + "_alignments.txt"); File mismatchOutFile = new File(stem + "_mismatches.txt"); File indelOutFile = new File(stem + "_indels.txt"); File qualOutFile = null; refSeqList = SequenceReader.readFully(refFile); if (args.length == 3) { queryReader = new QSeqReader(queryFile, new File(args[2])); } else { queryReader = new SequenceReader(queryFile); } seq = queryReader.readNextSequence(); if (seq instanceof QSequence) { qualOutFile = new File(stem + "_qual.txt"); } errorProcessor = new CompareErrorType(mismatchOutFile, indelOutFile, qualOutFile); alignOutStream = new PrintStream(alignOutFile); System.err.println("Starting CompareErrorType"); System.err.println("* Time: " + new Date()); System.err.println("* Reference File: " + refFile); System.err.println("* Query File: " + queryFile); if (args.length == 3) { System.err.println("* Qual File: " + args[2]); } System.err.println("* Query format: " + queryReader.getFormat()); System.err.println("* Alignment Output: " + alignOutFile); System.err.println("* Mismatches Output: " + mismatchOutFile); System.err.println("* Alignment Output: " + indelOutFile); if (qualOutFile != null) { System.err.println("* Quality Output: " + qualOutFile); } } catch (Exception e) { new HelpFormatter().printHelp( "CompareErrorType [options] <ref_nucl> (<query_nucl> | <query_nucl.fasta> <query_nucl.qual>)", options); System.err.println("ERROR: " + e.getMessage()); throw new RuntimeException(e); //System.exit(1); //return; } //ScoringMatrix scoringMatrix = ScoringMatrix.getDefaultNuclMatrix(); // use a simple scoring function, match score 0, mismatch -1, gap opening -1, gap extension -1. ScoringMatrix scoringMatrix = new ScoringMatrix( ScoringMatrix.class.getResourceAsStream("/data/simple_scoringmatrix.txt"), -1, -1); do { try { PairwiseAlignment bestResult = null; Sequence bestSeq = null; boolean bestReversed = false; String querySeqStr = seq.getSeqString().toLowerCase(); String reversedQuery = IUBUtilities.reverseComplement(querySeqStr); PAObject bestMatch = null; //checking if sequence has been seen before if (matchMap.containsKey(seq.getSeqString())) { bestMatch = matchMap.get(seq.getSeqString()); } else { for (Sequence refSeq : refSeqList) { String refSeqStr = refSeq.getSeqString().toLowerCase(); PairwiseAlignment result = PairwiseAligner.align(refSeqStr, querySeqStr, scoringMatrix, AlignmentMode.global); PairwiseAlignment reversedResult = PairwiseAligner.align(refSeqStr, IUBUtilities.reverseComplement(querySeqStr), scoringMatrix, AlignmentMode.global); PairwiseAlignment currBest = (result.getScore() > reversedResult.getScore()) ? result : reversedResult; if (bestResult == null || currBest.getScore() > bestResult.getScore()) { bestResult = currBest; bestSeq = refSeq; if (currBest == reversedResult) { bestReversed = true; } else { bestReversed = false; } } //Since this is a new sequence, make a new PAObject to put into the map to compare against later bestMatch = new PAObject(bestResult, bestReversed, bestSeq); matchMap.put(seq.getSeqString(), bestMatch); } } int refStart = bestMatch.getPA().getStarti(); int refEnd = bestMatch.getPA().getEndi(); bestSeq = bestMatch.getRefSeq(); bestReversed = bestMatch.getReversed(); bestResult = bestMatch.getPA(); //output information alignOutStream.println(">\t" + seq.getSeqName() + "\t" + bestSeq.getSeqName() + "\t" + seq.getSeqString().length() + "\t" + refStart + "\t" + refEnd + "\t" + bestResult.getScore() + "\t" + ((bestReversed) ? "\treversed" : "")); alignOutStream.println(bestResult.getAlignedSeqj() + "\n"); alignOutStream.println(bestResult.getAlignedSeqi() + "\n"); //seqi is reference seq, seqj is the refseq errorProcessor.processSequence(seq, bestResult.getAlignedSeqj(), bestSeq.getSeqName(), bestResult.getAlignedSeqi(), refStart, bestReversed); } catch (Exception e) { throw new RuntimeException("Failed while processing seq " + seq.getSeqName(), e); } } while ((seq = queryReader.readNextSequence()) != null); queryReader.close(); alignOutStream.close(); errorProcessor.close(); }