List of usage examples for java.nio.file Files readAllLines
public static List<String> readAllLines(Path path) throws IOException
From source file:ostepu.cconfig.control.java
/** * ruft die existierende Konfiguration ab und gibt sie aus * * @param context der Kontext des Servlet * @param request die eingehende Anfrage * @param response das Antwortobjekt//from w w w . ja va 2 s . c om */ public static void getControl(ServletContext context, HttpServletRequest request, HttpServletResponse response) { PrintWriter out; try { out = response.getWriter(); } catch (IOException ex) { Logger.getLogger(control.class.getName()).log(Level.SEVERE, null, ex); response.setStatus(500); return; } Path cconfigPath = Paths.get(context.getRealPath("/data/CConfig.json")); try { if (Files.exists(cconfigPath)) { List<String> content = Files.readAllLines(cconfigPath); JsonElement obj = new JsonParser().parse(String.join("", content)); JsonObject newObject = obj.getAsJsonObject(); if (newObject.has("prefix")) { newObject.remove("prefix"); newObject.add("prefix", (JsonElement) new JsonPrimitive(context.getAttribute("prefix").toString())); } else { newObject.add("prefix", (JsonElement) new JsonPrimitive(context.getAttribute("prefix").toString())); } out.print(newObject.toString()); response.setStatus(200); } else { response.setStatus(404); out.print("[]"); } } catch (IOException ex) { Logger.getLogger(control.class.getName()).log(Level.SEVERE, null, ex); response.setStatus(500); } finally { out.close(); } }
From source file:org.moe.cli.manager.ExecutorManager.java
public static IExecutor getExecutorByParams(CommandLine request) throws IOException, InterruptedException, WrapNatJGenException { if (request.hasOption(OptionsHandler.HELP.getLongOpt())) { OptionsHandler.printHelp();/*from w ww. ja v a 2s .c o m*/ return null; } String packageName = request.hasOption(OptionsHandler.PACKAGE_NAME.getLongOpt()) ? request.getOptionValue(OptionsHandler.PACKAGE_NAME.getLongOpt()) : "org.moe"; String[] javaSource = request.getOptionValues(OptionsHandler.JAVA_SOURCE.getLongOpt()); String[] bundle = request.getOptionValues(OptionsHandler.BUNDLE.getLongOpt()); String ldFlags = null; if (request.hasOption(OptionsHandler.LD_FLAGS.getLongOpt())) { String ldFlagsPath = request.getOptionValue(OptionsHandler.LD_FLAGS.getLongOpt()); File ldFlagsFile = new File(ldFlagsPath); if (ldFlagsFile.exists()) { List<String> lines = Files.readAllLines(ldFlagsFile.toPath()); StringBuilder strbldr = new StringBuilder(); for (String line : lines) { strbldr.append(line); strbldr.append(";"); } ldFlags = strbldr.toString(); if (ldFlags.startsWith(" ")) ldFlags = ldFlags.substring(1); } } IExecutor executor = null; if (request.hasOption(OptionsHandler.FRAMEWORK.getLongOpt())) { String[] frameworks = request.getOptionValues(OptionsHandler.FRAMEWORK.getLongOpt()); String[] headers = request.getOptionValues(OptionsHandler.HEADERS.getLongOpt()); if (headers == null) { File frameworkFile = null; Set<String> headersContent = new HashSet<String>(); Set<String> frameworkNameSet = new HashSet<String>(); for (String framework : frameworks) { if ((framework == null) || framework.isEmpty()) { continue; } frameworkFile = new File(framework); if (!frameworkNameSet.contains(frameworkFile.getName())) { File headersFolder = new File(frameworkFile, "Headers"); if (headersFolder.exists()) { headersContent.add(headersFolder.getPath()); } else { System.err.println(String.format("Specify correct path in %s parameter", OptionsHandler.FRAMEWORK.getLongOpt())); return null; // TODO: Error throwing } } frameworkNameSet.add(frameworkFile.getName()); } headers = headersContent.toArray(new String[0]); } String outFile = request.getOptionValue(OptionsHandler.OUTPUT_FILE_PATH.getLongOpt()); if (outFile == null || !outFile.endsWith(".jar")) { System.err.println(String.format("Specify jar file in %s parameter", OptionsHandler.OUTPUT_FILE_PATH.getLongOpt())); return null; // TODO: Error throwing } executor = new ThirdPartyFrameworkLinkExecutor(packageName, frameworks, javaSource, headers, bundle, outFile, ldFlags); } else if (request.hasOption(OptionsHandler.LIBRARY.getLongOpt())) { String[] library = request.getOptionValues(OptionsHandler.LIBRARY.getLongOpt()); String[] headers = request.getOptionValues(OptionsHandler.HEADERS.getLongOpt()); if (headers == null) { System.err.println( String.format("Specify headers in %s parameter", OptionsHandler.HEADERS.getLongOpt())); return null; // TODO: Error throwing } String outFile = request.getOptionValue(OptionsHandler.OUTPUT_FILE_PATH.getLongOpt()); if (outFile == null || !outFile.endsWith(".jar")) { System.err.println(String.format("Specify jar file in %s parameter", OptionsHandler.OUTPUT_FILE_PATH.getLongOpt())); return null; // TODO: Error throwing } executor = new ThirdPartyLibraryLinkExecutor(packageName, library, javaSource, headers, bundle, outFile, ldFlags); } else if (request.hasOption(OptionsHandler.POD.getLongOpt())) { String pod = request.getOptionValue(OptionsHandler.POD.getLongOpt()); String outFile = request.getOptionValue(OptionsHandler.OUTPUT_FILE_PATH.getLongOpt()); if (outFile == null || !outFile.endsWith(".jar")) { System.err.println(String.format("Specify jar file in %s parameter", OptionsHandler.OUTPUT_FILE_PATH.getLongOpt())); return null; // TODO: Error throwing } String jpodSpecRepo = request.getOptionValue(OptionsHandler.JPOD_SPEC_REPO.getLongOpt()); executor = new CocoaPodsExecutor(pod, outFile, javaSource, jpodSpecRepo, packageName, Collections.emptySet()); } else if (request.hasOption(OptionsHandler.ALL_DEPENDENCIES.getLongOpt())) { String pod = request.getOptionValue(OptionsHandler.ALL_DEPENDENCIES.getLongOpt()); Utils.printDependencies(pod, new HashSet<String>()); } else { String pathToProject = request.getOptionValue(OptionsHandler.PATH_TO_PROJECT.getLongOpt()); String headers = request.getOptionValue(OptionsHandler.HEADERS.getLongOpt()); if (pathToProject == null) { System.err.println(String.format("Specify correct path in %s parameter", OptionsHandler.PATH_TO_PROJECT.getLongOpt())); return null; // TODO: Error throwing } if (headers == null) { System.err.println(String.format("Specify jar correct path in %s parameter", OptionsHandler.HEADERS.getLongOpt())); return null; // TODO: Error throwing } executor = new GenerateBindingExecutor(pathToProject, packageName, headers, request.hasOption(OptionsHandler.CREATE_FROM_PROTOTYPE.getLongOpt())); } return executor; }
From source file:com.edmunds.etm.tools.urltoken.util.OptionUtils.java
@SuppressWarnings("unchecked") public static List<String> parseValues(OptionSet options, OptionSpec<File> fileSpec) throws IOException { List<String> values; File file = options.valueOf(fileSpec); if (file != null) { values = Files.readAllLines(file.toPath()); } else {// ww w . java2 s. co m values = Lists.newArrayList(); } return values; }
From source file:org.opencb.opencga.storage.app.cli.client.executors.VariantQueryCommandUtils.java
public static Query parseBasicVariantQuery(StorageVariantCommandOptions.BasicVariantQueryOptions options, Query query) throws Exception { /*/*from ww w. j av a 2s. com*/ * Parse Variant parameters */ if (options.region != null && !options.region.isEmpty()) { query.put(REGION.key(), options.region); } else if (options.regionFile != null && !options.regionFile.isEmpty()) { Path gffPath = Paths.get(options.regionFile); FileUtils.checkFile(gffPath); String regionsFromFile = Files.readAllLines(gffPath).stream().map(line -> { String[] array = line.split("\t"); return new String(array[0].replace("chr", "") + ":" + array[3] + "-" + array[4]); }).collect(Collectors.joining(",")); query.put(REGION.key(), regionsFromFile); } addParam(query, ID, options.id); addParam(query, GENE, options.gene); addParam(query, TYPE, options.type); /** * Annotation parameters */ addParam(query, ANNOT_CONSEQUENCE_TYPE, options.consequenceType); addParam(query, ANNOT_POPULATION_ALTERNATE_FREQUENCY, options.populationFreqs); addParam(query, ANNOT_CONSERVATION, options.conservation); addParam(query, ANNOT_FUNCTIONAL_SCORE, options.functionalScore); addParam(query, ANNOT_PROTEIN_SUBSTITUTION, options.proteinSubstitution); /* * Stats parameters */ // if (options.stats != null && !options.stats.isEmpty()) { // Set<String> acceptedStatKeys = new HashSet<>(Arrays.asList(STATS_MAF.key(), // STATS_MGF.key(), // MISSING_ALLELES.key(), // MISSING_GENOTYPES.key())); // // for (String stat : options.stats.split(",")) { // int index = stat.indexOf("<"); // index = index >= 0 ? index : stat.indexOf("!"); // index = index >= 0 ? index : stat.indexOf("~"); // index = index >= 0 ? index : stat.indexOf("<"); // index = index >= 0 ? index : stat.indexOf(">"); // index = index >= 0 ? index : stat.indexOf("="); // if (index < 0) { // throw new UnsupportedOperationException("Unknown stat filter operation: " + stat); // } // String name = stat.substring(0, index); // String cond = stat.substring(index); // // if (acceptedStatKeys.contains(name)) { // query.put(name, cond); // } else { // throw new UnsupportedOperationException("Unknown stat filter name: " + name); // } // logger.info("Parsed stat filter: {} {}", name, cond); // } // } addParam(query, STATS_MAF, options.maf); return query; }
From source file:org.opencb.opencga.storage.app.cli.client.VariantQueryCommandUtils.java
public static Query parseQuery(CliOptionsParser.QueryVariantsCommandOptions queryVariantsOptions, List<String> studyNames) throws Exception { Query query = new Query(); /*/*from www . j av a2 s. com*/ * Parse Variant parameters */ if (queryVariantsOptions.region != null && !queryVariantsOptions.region.isEmpty()) { query.put(REGION.key(), queryVariantsOptions.region); } else if (queryVariantsOptions.regionFile != null && !queryVariantsOptions.regionFile.isEmpty()) { Path gffPath = Paths.get(queryVariantsOptions.regionFile); FileUtils.checkFile(gffPath); String regionsFromFile = Files.readAllLines(gffPath).stream().map(line -> { String[] array = line.split("\t"); return new String(array[0].replace("chr", "") + ":" + array[3] + "-" + array[4]); }).collect(Collectors.joining(",")); query.put(REGION.key(), regionsFromFile); } addParam(query, ID, queryVariantsOptions.id); addParam(query, GENE, queryVariantsOptions.gene); addParam(query, TYPE, queryVariantsOptions.type); List<String> studies = new LinkedList<>(); if (queryVariantsOptions.study != null && !queryVariantsOptions.study.isEmpty()) { query.put(STUDIES.key(), queryVariantsOptions.study); for (String study : queryVariantsOptions.study.split(",|;")) { if (!study.startsWith("!")) { studies.add(study); } } } // If the studies to be returned is empty then we return the studies being queried if (queryVariantsOptions.returnStudy != null && !queryVariantsOptions.returnStudy.isEmpty()) { // query.put(RETURNED_STUDIES.key(), Arrays.asList(queryVariantsOptions.returnStudy.split(","))); List<String> list = new ArrayList<>(); Collections.addAll(list, queryVariantsOptions.returnStudy.split(",")); query.put(RETURNED_STUDIES.key(), list); } else { if (!studies.isEmpty()) { query.put(RETURNED_STUDIES.key(), studies); } } addParam(query, FILES, queryVariantsOptions.file); addParam(query, GENOTYPE, queryVariantsOptions.sampleGenotype); addParam(query, RETURNED_SAMPLES, queryVariantsOptions.returnSample); addParam(query, UNKNOWN_GENOTYPE, queryVariantsOptions.unknownGenotype); /** * Annotation parameters */ addParam(query, ANNOT_CONSEQUENCE_TYPE, queryVariantsOptions.consequenceType); addParam(query, ANNOT_BIOTYPE, queryVariantsOptions.biotype); addParam(query, ANNOT_POPULATION_ALTERNATE_FREQUENCY, queryVariantsOptions.populationFreqs); addParam(query, ANNOT_POPULATION_MINOR_ALLELE_FREQUENCY, queryVariantsOptions.populationMaf); addParam(query, ANNOT_CONSERVATION, queryVariantsOptions.conservation); if (queryVariantsOptions.proteinSubstitution != null && !queryVariantsOptions.proteinSubstitution.isEmpty()) { String[] fields = queryVariantsOptions.proteinSubstitution.split(","); for (String field : fields) { String[] arr = field.replaceAll("==", " ").replaceAll(">=", " ").replaceAll("<=", " ") .replaceAll("=", " ").replaceAll("<", " ").replaceAll(">", " ").split(" "); if (arr != null && arr.length > 1) { switch (arr[0]) { case "sift": query.put(ANNOT_SIFT.key(), field.replaceAll("sift", "")); break; case "polyphen": query.put(ANNOT_POLYPHEN.key(), field.replaceAll("polyphen", "")); break; default: query.put(ANNOT_PROTEIN_SUBSTITUTION.key(), field.replaceAll(arr[0], "")); break; } } } } /* * Stats parameters */ if (queryVariantsOptions.stats != null && !queryVariantsOptions.stats.isEmpty()) { Set<String> acceptedStatKeys = new HashSet<>(Arrays.asList(STATS_MAF.key(), STATS_MGF.key(), MISSING_ALLELES.key(), MISSING_GENOTYPES.key())); for (String stat : queryVariantsOptions.stats.split(",")) { int index = stat.indexOf("<"); index = index >= 0 ? index : stat.indexOf("!"); index = index >= 0 ? index : stat.indexOf("~"); index = index >= 0 ? index : stat.indexOf("<"); index = index >= 0 ? index : stat.indexOf(">"); index = index >= 0 ? index : stat.indexOf("="); if (index < 0) { throw new UnsupportedOperationException("Unknown stat filter operation: " + stat); } String name = stat.substring(0, index); String cond = stat.substring(index); if (acceptedStatKeys.contains(name)) { query.put(name, cond); } else { throw new UnsupportedOperationException("Unknown stat filter name: " + name); } logger.info("Parsed stat filter: {} {}", name, cond); } } addParam(query, STATS_MAF, queryVariantsOptions.maf); addParam(query, STATS_MGF, queryVariantsOptions.mgf); addParam(query, MISSING_ALLELES, queryVariantsOptions.missingAlleleCount); addParam(query, MISSING_GENOTYPES, queryVariantsOptions.missingGenotypeCount); boolean returnVariants = !queryVariantsOptions.count && StringUtils.isEmpty(queryVariantsOptions.groupBy) && StringUtils.isEmpty(queryVariantsOptions.rank); String outputFormat = "vcf"; if (StringUtils.isNotEmpty(queryVariantsOptions.outputFormat)) { if (queryVariantsOptions.outputFormat.equals("json") || queryVariantsOptions.outputFormat.equals("json.gz")) { outputFormat = "json"; } } if (returnVariants && outputFormat.equalsIgnoreCase("vcf")) { int returnedStudiesSize = query.getAsStringList(RETURNED_STUDIES.key()).size(); if (returnedStudiesSize == 0 && studies.size() == 1) { query.put(RETURNED_STUDIES.key(), studies.get(0)); } else if (returnedStudiesSize == 0 && studyNames.size() != 1 //If there are no returned studies, and there are more than one // study || returnedStudiesSize > 1) { // Or is required more than one returned study throw new Exception( "Only one study is allowed when returning VCF, please use '--return-study' to select the returned " + "study. Available studies: [ " + String.join(", ", studyNames) + " ]"); } else { if (returnedStudiesSize == 0) { //If there were no returned studies, set the study existing one query.put(RETURNED_STUDIES.key(), studyNames.get(0)); } } } return query; }
From source file:org.springframework.cloud.stream.app.plugin.utils.SpringCloudStreamPluginUtils.java
public static void ignoreUnitTestGeneratedByInitializer(String generatedAppHome) throws IOException { Collection<File> files = FileUtils.listFiles(new File(generatedAppHome, "src/test/java"), null, true); Optional<File> first = files.stream().filter(f -> f.getName().endsWith("ApplicationTests.java")) .findFirst();//w ww.ja v a2s .com if (first.isPresent()) { StringBuilder sb = new StringBuilder(); File f1 = first.get(); Files.readAllLines(f1.toPath()).forEach(l -> { if (l.startsWith("import") && !sb.toString().contains("import org.junit.Ignore")) { sb.append("import org.junit.Ignore;\n"); } else if (l.startsWith("@RunWith") && !sb.toString().contains("@Ignore")) { sb.append("@Ignore\n"); } sb.append(l); sb.append("\n"); }); Files.write(f1.toPath(), sb.toString().getBytes()); } }
From source file:org.omegat.MainTest.java
public static void testConsoleTranslate() throws Exception { // Create project properties ProjectProperties props = new ProjectProperties(tmpDir.toFile()); // Create project internal directories props.autocreateDirectories();// w w w .j av a2 s.c o m // Create version-controlled glossary file props.getWritableGlossaryFile().getAsFile().createNewFile(); ProjectFileStorage.writeProjectFile(props); String fileName = "foo.txt"; List<String> fileContent = Arrays.asList("Foo"); Path srcFile = tmpDir.resolve(OConsts.DEFAULT_SOURCE).resolve(fileName); Files.write(srcFile, fileContent); Main.main(new String[] { "--mode=console-translate", tmpDir.toString() }); Path trgFile = tmpDir.resolve(OConsts.DEFAULT_TARGET).resolve(fileName); assertTrue(trgFile.toFile().isFile()); assertEquals(fileContent, Files.readAllLines(trgFile)); }
From source file:fi.johannes.kata.ocr.utils.files.ExistingFileConnection.java
public List<String> readLines() throws IOException { return Files.readAllLines(p); }
From source file:org.elasticsearch.qa.die_with_dignity.DieWithDignityIT.java
public void testDieWithDignity() throws Exception { // deleting the PID file prevents stopping the cluster from failing since it occurs if and only if the PID file exists final Path pidFile = PathUtils.get(System.getProperty("pidfile")); final List<String> pidFileLines = Files.readAllLines(pidFile); assertThat(pidFileLines, hasSize(1)); final int pid = Integer.parseInt(pidFileLines.get(0)); Files.delete(pidFile);//from w w w . j ava2s. c o m IOException e = expectThrows(IOException.class, () -> client().performRequest(new Request("GET", "/_die_with_dignity"))); Matcher<IOException> failureMatcher = instanceOf(ConnectionClosedException.class); if (Constants.WINDOWS) { /* * If the other side closes the connection while we're waiting to fill our buffer * we can get IOException with the message below. It seems to only come up on * Windows and it *feels* like it could be a ConnectionClosedException but * upstream does not consider this a bug: * https://issues.apache.org/jira/browse/HTTPASYNC-134 * * So we catch it here and consider it "ok". */ failureMatcher = either(failureMatcher).or( hasToString(containsString("An existing connection was forcibly closed by the remote host"))); } assertThat(e, failureMatcher); // the Elasticsearch process should die and disappear from the output of jps assertBusy(() -> { final String jpsPath = PathUtils.get(System.getProperty("runtime.java.home"), "bin/jps").toString(); final Process process = new ProcessBuilder().command(jpsPath).start(); assertThat(process.waitFor(), equalTo(0)); try (InputStream is = process.getInputStream(); BufferedReader in = new BufferedReader(new InputStreamReader(is, "UTF-8"))) { String line; while ((line = in.readLine()) != null) { final int currentPid = Integer.parseInt(line.split("\\s+")[0]); assertThat(line, pid, not(equalTo(currentPid))); } } }); // parse the logs and ensure that Elasticsearch died with the expected cause final List<String> lines = Files.readAllLines(PathUtils.get(System.getProperty("log"))); final Iterator<String> it = lines.iterator(); boolean fatalErrorOnTheNetworkLayer = false; boolean fatalErrorInThreadExiting = false; while (it.hasNext() && (fatalErrorOnTheNetworkLayer == false || fatalErrorInThreadExiting == false)) { final String line = it.next(); if (line.contains("fatal error on the network layer")) { fatalErrorOnTheNetworkLayer = true; } else if (line.matches(".*\\[ERROR\\]\\[o.e.b.ElasticsearchUncaughtExceptionHandler\\] \\[node-0\\]" + " fatal error in thread \\[Thread-\\d+\\], exiting$")) { fatalErrorInThreadExiting = true; assertTrue(it.hasNext()); assertThat(it.next(), equalTo("java.lang.OutOfMemoryError: die with dignity")); } } assertTrue(fatalErrorOnTheNetworkLayer); assertTrue(fatalErrorInThreadExiting); }