List of usage examples for org.apache.commons.io FileUtils readLines
public static List readLines(File file) throws IOException
From source file:ml.shifu.shifu.core.pmml.PMMLTranslatorTest.java
private void compareScore(File test, File control, String scoreName, String sep, Double errorRange) throws Exception { List<String> testData = FileUtils.readLines(test); List<String> controlData = FileUtils.readLines(control); String[] testSchema = testData.get(0).trim().split(sep); String[] controlSchema = controlData.get(0).trim().split(sep); for (int row = 1; row < controlData.size(); row++) { Map<String, Object> ctx = new HashMap<String, Object>(); Map<String, Object> controlCtx = new HashMap<String, Object>(); String[] testRowValue = testData.get(row).split(sep, testSchema.length); for (int index = 0; index < testSchema.length; index++) { ctx.put(testSchema[index], testRowValue[index]); }/*from www .j av a 2 s . c om*/ String[] controlRowValue = controlData.get(row).split(sep, controlSchema.length); for (int index = 0; index < controlSchema.length; index++) { controlCtx.put(controlSchema[index], controlRowValue[index]); } Double controlScore = Double.valueOf((String) controlCtx.get(scoreName)); Double testScore = Double.valueOf((String) ctx.get(scoreName)); Assert.assertEquals(controlScore, testScore, errorRange); } }
From source file:com.gargoylesoftware.htmlunit.source.BrowserVersionFeaturesSource.java
private void generate(final File dir, final String toSearchFor, final BrowserVersion[] versions) throws IOException { final File propertiesFolder = new File(root_, "src/main/resources/com/gargoylesoftware/htmlunit/javascript/configuration"); final File featuresFile = new File(root_, "src/main/java/com/gargoylesoftware/htmlunit/BrowserVersionFeatures.java"); for (final File f : dir.listFiles()) { if (f.isDirectory()) { if (!".svn".equals(f.getName())) { generate(f, toSearchFor, versions); }/* w w w. j a v a 2s. c o m*/ } else if (!"JavaScriptConfiguration.java".equals(f.getName())) { final List<String> lines = FileUtils.readLines(f); boolean modified = false; for (int i = 0; i < lines.size(); i++) { String line = lines.get(i); if (line.contains(toSearchFor)) { line = line.replace(toSearchFor, ".hasFeature(BrowserVersionFeatures." + GENERATED_PREFIX + generatedNext_ + ")"); lines.set(i, line); modified = true; final List<String> featuresLines = FileUtils.readLines(featuresFile); featuresLines.add(featuresLines.size() - 4, ""); featuresLines.add(featuresLines.size() - 4, " /** Was originally " + toSearchFor + ". */"); featuresLines.add(featuresLines.size() - 4, " " + GENERATED_PREFIX + generatedNext_ + ","); FileUtils.writeLines(featuresFile, featuresLines); for (final File file : propertiesFolder.listFiles(new FileFilter() { public boolean accept(final File pathname) { for (final BrowserVersion version : versions) { if (pathname.getName().equals(version.getNickname() + ".properties")) { return true; } } return false; } })) { final List<String> features = FileUtils.readLines(file); features.add(GENERATED_PREFIX + generatedNext_); Collections.sort(features); FileUtils.writeLines(file, features); } generatedNext_++; } } if (modified) { FileUtils.writeLines(f, lines); } } } }
From source file:de.tudarmstadt.ukp.dkpro.core.io.ditop.DiTopWriterTest.java
@Test public void testSimple() throws UIMAException, IOException { int expectedNDocuments = 2; CollectionReaderDescription reader = createReaderDescription(TextReader.class, TextReader.PARAM_SOURCE_LOCATION, CAS_DIR, TextReader.PARAM_PATTERNS, CAS_FILE_PATTERN, TextReader.PARAM_LANGUAGE, LANGUAGE); AnalysisEngineDescription segmenter = createEngineDescription(BreakIteratorSegmenter.class); AnalysisEngineDescription inferencer = createEngineDescription(MalletTopicModelInferencer.class, MalletTopicModelInferencer.PARAM_MODEL_LOCATION, MODEL_FILE); AnalysisEngineDescription ditopwriter = createEngineDescription(DiTopWriter.class, DiTopWriter.PARAM_TARGET_LOCATION, TARGET_DITOP, DiTopWriter.PARAM_MODEL_LOCATION, MODEL_FILE, DiTopWriter.PARAM_CORPUS_NAME, DITOP_CORPUSNAME); SimplePipeline.runPipeline(reader, segmenter, inferencer, ditopwriter); /* test whether target files and dirs exist */ File contentDir = new File(TARGET_DITOP, DITOP_CORPUSNAME + "_" + N_TOPICS); File topicsFile = new File(contentDir, "topics.csv"); File topicTermT15File = new File(contentDir, "topicTerm-T15.txt"); File topicTermFile = new File(contentDir, "topicTerm.txt"); File topicTermMatrixFile = new File(contentDir, "topicTermMatrix.txt"); assertTrue(new File(TARGET_DITOP, "config.all").exists()); assertTrue(contentDir.isDirectory()); assertTrue(topicTermT15File.exists()); assertTrue(topicTermFile.exists());/*from ww w . ja v a 2 s . co m*/ assertTrue(topicTermMatrixFile.exists()); assertTrue(topicsFile.exists()); /* check that file lengths are correct */ assertEquals(expectedNDocuments + 1, FileUtils.readLines(topicsFile).size()); assertEquals(N_TOPICS, FileUtils.readLines(topicTermT15File).size()); assertEquals(N_TOPICS, FileUtils.readLines(topicTermFile).size()); assertEquals(N_TOPICS, FileUtils.readLines(topicTermMatrixFile).size()); }
From source file:es.uvigo.ei.sing.adops.datatypes.BatchProject.java
public BatchProject(File folder) throws IllegalStateException { this.folder = folder; this.deleted = false; this.running = false; this.propertiesFile = new File(this.folder, BatchProject.CONFIGURATION_FILE); this.configuration = new Configuration(Configuration.getSystemConfiguration(), this.propertiesFile); if (this.hasAbsoluteFastaPaths()) { this.fastaFiles = filenamesToFiles(this.configuration.getFastaFile()); } else {/*from w w w.j a v a 2 s. c o m*/ final List<File> fastaList = new LinkedList<>(); try { for (String fastaFilename : FileUtils.readLines(new File(this.folder, "fasta.names"))) { fastaList.add(new File(this.folder, fastaFilename)); } this.fastaFiles = fastaList.toArray(new File[fastaList.size()]); } catch (IOException e) { throw new IllegalStateException("Missing 'fasta.names' file", e); } } Arrays.sort(this.fastaFiles); this.getOutput(); // Forces output loading }
From source file:edu.ku.brc.specify.tools.datamodelgenerator.DataDict.java
/** * @param query// w w w . j a v a 2s . c om */ @SuppressWarnings("unchecked") public void processSpecify5Schema() { File file = new File("src/edu/ku/brc/specify/tools/datamodelgenerator/Specify5Tables.txt"); try { TableDef tableDef = null; Vector<FieldDef> fields = null; boolean processingTable = false; for (String line : (List<String>) FileUtils.readLines(file)) { if (processingTable) { if (line.startsWith(") ON [")) { processingTable = false; } else { String[] tokens = StringUtils.split(line, "[]"); //System.out.println(line); String notNull = tokens[4]; FieldDef fieldDef = new FieldDef(tokens[1], tokens[3], "", notNull != null && notNull.indexOf("NOT NULL") > -1 ? "true" : "false", ""); fields.add(fieldDef); tokens = StringUtils.split(line, "()"); if (tokens.length > 1) { fieldDef.setLength(tokens[1]); } } } else if (line.startsWith("CREATE TABLE")) { String[] tokens = StringUtils.split(line, "[]"); tableDef = new TableDef(tokens[3], ""); sp5Tables.add(tableDef); fields = tableDef.getFields(); processingTable = true; } } } catch (IOException ex) { edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount(); edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(DataDict.class, ex); System.err.println(file.getAbsolutePath()); ex.printStackTrace(); } catch (Exception ex) { edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount(); edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(DataDict.class, ex); ex.printStackTrace(); } }
From source file:com.iyonger.apm.web.service.ScriptValidationService.java
@Override public String validate(User user, IFileEntry scriptIEntry, boolean useScriptInSVN, String hostString) { FileEntry scriptEntry = TypeConvertUtils.cast(scriptIEntry); try {//from ww w . j a v a 2 s. c o m checkNotNull(scriptEntry, "scriptEntity should be not null"); checkNotEmpty(scriptEntry.getPath(), "scriptEntity path should be provided"); if (!useScriptInSVN) { checkNotEmpty(scriptEntry.getContent(), "scriptEntity content should be provided"); } checkNotNull(user, "user should be provided"); // String result = checkSyntaxErrors(scriptEntry.getContent()); ScriptHandler handler = scriptHandlerFactory.getHandler(scriptEntry); if (config.getControllerProperties().getPropertyBoolean(PROP_CONTROLLER_VALIDATION_SYNTAX_CHECK)) { String result = handler.checkSyntaxErrors(scriptEntry.getPath(), scriptEntry.getContent()); LOGGER.info("Perform Syntax Check by {} for {}", user.getUserId(), scriptEntry.getPath()); if (result != null) { return result; } } File scriptDirectory = config.getHome().getScriptDirectory(user); FileUtils.deleteDirectory(scriptDirectory); Preconditions.checkTrue(scriptDirectory.mkdirs(), "Script directory {} creation is failed."); ProcessingResultPrintStream processingResult = new ProcessingResultPrintStream( new ByteArrayOutputStream()); handler.prepareDist(0L, user, scriptEntry, scriptDirectory, config.getControllerProperties(), processingResult); if (!processingResult.isSuccess()) { return new String(processingResult.getLogByteArray()); } File scriptFile = new File(scriptDirectory, FilenameUtils.getName(scriptEntry.getPath())); if (useScriptInSVN) { fileEntryService.writeContentTo(user, scriptEntry.getPath(), scriptDirectory); } else { FileUtils.writeStringToFile(scriptFile, scriptEntry.getContent(), StringUtils.defaultIfBlank(scriptEntry.getEncoding(), "UTF-8")); } File doValidate = localScriptTestDriveService.doValidate(scriptDirectory, scriptFile, new Condition(), config.isSecurityEnabled(), hostString, getTimeout()); List<String> readLines = FileUtils.readLines(doValidate); StringBuilder output = new StringBuilder(); String path = config.getHome().getDirectory().getAbsolutePath(); for (String each : readLines) { if (!each.startsWith("*sys-package-mgr")) { each = each.replace(path, "${NGRINDER_HOME}"); output.append(each).append("\n"); } } return output.toString(); } catch (Exception e) { throw processException(e); } }
From source file:gov.nih.nci.caarray.magetab.splitter.SdrfSplitterTest.java
/** * linesToAdd are added in sequential order. This <em>modifies</em> the lines * in place. So to add 2 lines before the header and 1 after, the keys should be * (0, 1, 3), because that will add two lines (moving the header down), then add after * the header./* w ww. ja v a 2 s . c o m*/ */ private Function<File, File> getTransform(final SortedMap<Integer, String> linesToAdd) { Function<File, File> transform = new Function<File, File>() { @Override public File apply(File input) { try { @SuppressWarnings("unchecked") List<String> lines = FileUtils.readLines(input); for (Integer i : linesToAdd.keySet()) { lines.add(i, linesToAdd.get(i)); } File revisedSdrf = File.createTempFile("test", ".sdrf"); FileUtils.writeLines(revisedSdrf, lines); return revisedSdrf; } catch (IOException ioe) { throw new RuntimeException(ioe); } } }; return transform; }
From source file:de.nbi.ontology.test.OntologyMatchTest.java
/** * Test, if terms are properly match to concept labels. The a list of terms * contains a term in each line./* www . ja va 2 s .c o m*/ * * @param inFile * a list of terms * @throws IOException */ @SuppressWarnings("unchecked") @Test(dataProviderClass = TestFileProvider.class, dataProvider = "parentTestFiles", groups = { "functest" }) public void parents(File inFile) throws IOException { log.info("Processing " + inFile.getName()); String basename = FilenameUtils.removeExtension(inFile.getAbsolutePath()); File outFile = new File(basename + ".out"); File resFile = new File(basename + ".res"); List<String> terms = FileUtils.readLines(inFile); PrintWriter w = new PrintWriter(new FileWriter(outFile)); for (String term : terms) { OntClass clazz = index.getModel().getOntClass(term); log.trace("** matching " + term); w.println(index.getParents(clazz)); } w.flush(); w.close(); Assert.assertTrue(FileUtils.contentEquals(outFile, resFile)); }
From source file:de.tudarmstadt.ukp.dkpro.core.mallet.lda.io.MalletLdaTopicProportionsWriterTest.java
@Test public void testMultipleTargets() throws IOException, UIMAException { File targetDir = testContext.getTestOutputFolder(); File expectedFile0 = new File(targetDir, "dummy1.txt.topics"); File expectedFile1 = new File(targetDir, "dummy2.txt.topics"); int expectedLines = 1; String expectedLine0Regex = "dummy1.txt\t(0\\.[0-9]{4}\\t){9}0\\.[0-9]{4}"; String expectedLine1Regex = "dummy2.txt\t(0\\.[0-9]{4}\\t){9}0\\.[0-9]{4}"; File modelFile = new File(testContext.getTestOutputFolder(), "model"); MalletLdaUtil.trainModel(modelFile); CollectionReaderDescription reader = createReaderDescription(TextReader.class, TextReader.PARAM_SOURCE_LOCATION, MalletLdaUtil.CAS_DIR, TextReader.PARAM_PATTERNS, MalletLdaUtil.CAS_FILE_PATTERN, TextReader.PARAM_LANGUAGE, MalletLdaUtil.LANGUAGE); AnalysisEngineDescription segmenter = createEngineDescription(BreakIteratorSegmenter.class); AnalysisEngineDescription inferencer = createEngineDescription(MalletLdaTopicModelInferencer.class, MalletLdaTopicModelInferencer.PARAM_MODEL_LOCATION, modelFile); AnalysisEngineDescription writer = createEngineDescription(MalletLdaTopicProportionsWriter.class, MalletLdaTopicProportionsWriter.PARAM_TARGET_LOCATION, targetDir, MalletLdaTopicProportionsWriter.PARAM_OVERWRITE, true, MalletLdaTopicProportionsWriter.PARAM_SINGULAR_TARGET, false, MalletLdaTopicProportionsWriter.PARAM_WRITE_DOCID, true); SimplePipeline.runPipeline(reader, segmenter, inferencer, writer); assertTrue(expectedFile0.exists());/*from ww w . j av a 2 s .c o m*/ assertTrue(expectedFile1.exists()); List<String> lines = FileUtils.readLines(expectedFile0); assertTrue(lines.get(0).matches(expectedLine0Regex)); assertEquals(expectedLines, lines.size()); lines = FileUtils.readLines(expectedFile1); assertEquals(expectedLines, lines.size()); assertTrue(lines.get(0).matches(expectedLine1Regex)); }
From source file:com.etas.jenkins.plugins.CreateTextFile.CreateFileBuilderTest.java
@Test public void testAppendToEndFile() throws InterruptedException, IOException, Exception { EnvironmentVariablesNodeProperty prop = new EnvironmentVariablesNodeProperty(); EnvVars envVars = prop.getEnvVars(); envVars.put("FILE_NAME", "ExistingFile.txt"); envVars.put("LINE2", "Line2"); j.jenkins.getGlobalNodeProperties().add(prop); FreeStyleProject project = j.createFreeStyleProject(); project.getBuildersList().add(new TestBuilder() { @Override/*from w ww . ja v a 2s. c o m*/ public boolean perform(AbstractBuild<?, ?> build, Launcher launcher, BuildListener listener) throws InterruptedException, IOException { build.getWorkspace().child("ExistingFile.txt").write("LINE1", "UTF-8"); return true; } }); CreateFileBuilder builder = new CreateFileBuilder("${WORKSPACE}" + "/" + "${FILE_NAME}", "${LINE2}", "appendToEnd", true); project.getBuildersList().add(builder); FreeStyleBuild build = project.scheduleBuild2(0).get(); String filePath = build.getWorkspace().child("ExistingFile.txt").getRemote(); String firstLine = (String) FileUtils.readLines(new File(filePath)).get(0); String secondLine = (String) FileUtils.readLines(new File(filePath)).get(2); assertTrue(firstLine.equals("LINE1")); assertTrue(secondLine.equals("Line2")); }