List of usage examples for java.util.regex Pattern DOTALL
int DOTALL
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From source file:org.craftercms.profile.services.ProfileServiceIT.java
@Test public void testCreateAndVerifyProfile() throws Exception { GreenMail mailServer = new GreenMail(ServerSetupTest.SMTP); mailServer.start();/*w ww. ja v a 2s .c o m*/ tenantService.verifyNewProfiles(DEFAULT_TENANT, true); Profile profile = profileService.createProfile(DEFAULT_TENANT, AVASQUEZ_USERNAME, AVASQUEZ_PASSWORD1, AVASQUEZ_EMAIL1, true, AVASQUEZ_ROLES1, null, VERIFICATION_URL); try { assertNotNull(profile); assertNotNull(profile.getId()); assertEquals(AVASQUEZ_USERNAME, profile.getUsername()); assertNull(profile.getPassword()); assertEquals(AVASQUEZ_EMAIL1, profile.getEmail()); assertFalse(profile.isVerified()); assertFalse(profile.isEnabled()); assertNotNull(profile.getCreatedOn()); assertNotNull(profile.getLastModified()); assertEquals(DEFAULT_TENANT, profile.getTenant()); assertEquals(AVASQUEZ_ROLES1, profile.getRoles()); assertNotNull(profile.getAttributes()); assertEquals(0, profile.getAttributes().size()); // Wait a few seconds so that the email can be sent Thread.sleep(3000); String email = GreenMailUtil.getBody(mailServer.getReceivedMessages()[0]); assertNotNull(email); Pattern emailPattern = Pattern.compile(VERIFICATION_EMAIL_REGEX, Pattern.DOTALL); Matcher emailMatcher = emailPattern.matcher(email); assertTrue(emailMatcher.matches()); String verificationTokenId = emailMatcher.group(1); Profile verifiedProfile = profileService.verifyProfile(verificationTokenId); assertNotNull(verifiedProfile); assertEquals(profile.getId(), verifiedProfile.getId()); assertTrue(verifiedProfile.isEnabled()); assertTrue(verifiedProfile.isVerified()); } finally { profileService.deleteProfile(profile.getId().toString()); tenantService.verifyNewProfiles(DEFAULT_TENANT, false); mailServer.stop(); } }
From source file:com.xebia.incubator.xebium.ExtendedSeleniumCommand.java
private Pattern globToRegExp(String glob) { return Pattern.compile("^\\Q" + glob.replace("*", "\\E.*\\Q").replace("?", "\\E.\\Q") + "\\E$", Pattern.DOTALL); }
From source file:org.ms123.common.libhelper.Utils.java
private static Object[] getLineNumberFromMsg(String msg) { try {/*from w w w .j a v a 2s. c o m*/ Pattern p = Pattern.compile(".*Script\\d{1,5}.groovy: (\\d{1,5}):(.*)", Pattern.DOTALL); Matcher m = p.matcher(msg); Object[] ret = new Object[2]; if (m.find()) { ret[0] = m.group(1); ret[1] = m.group(2); return ret; } } catch (Exception e) { e.printStackTrace(); } return null; }
From source file:fr.sanofi.fcl4transmart.controllers.listeners.geneExpression.LoadGeneExpressionDataListener.java
@Override public void handleEvent(Event event) { this.topNode = this.loadDataUI.getTopNode(); this.path = this.dataType.getPath().getAbsolutePath(); this.sortName = this.dataType.getStudy().getPath().getParentFile().getAbsolutePath() + File.separator + ".sort"; loadDataUI.openLoadingShell();//from ww w .ja va 2 s . c o m new Thread() { public void run() { try { String[] splited = topNode.split("\\\\", -1); if (splited[0].compareTo("") != 0) { loadDataUI.setMessage("A study node has to begin by the character '\\'"); loadDataUI.setIsLoading(false); return; } try { Class.forName("oracle.jdbc.driver.OracleDriver"); String connectionString = "jdbc:oracle:thin:@" + PreferencesHandler.getDbServer() + ":" + PreferencesHandler.getDbPort() + ":" + PreferencesHandler.getDbName(); Connection con = DriverManager.getConnection(connectionString, PreferencesHandler.getMetadataUser(), PreferencesHandler.getMetadataPwd()); Statement stmt = con.createStatement(); ResultSet rs = stmt .executeQuery("select * from table_access where c_name='" + splited[1] + "'"); if (!rs.next()) {//have to add a top node stmt.executeQuery("insert into table_access(" + "c_table_cd," + "c_table_name," + "c_protected_access," + "c_hlevel," + "c_fullname," + "c_name," + "c_synonym_cd," + "c_visualattributes," + "c_totalnum," + "c_facttablecolumn," + "c_dimtablename," + "c_columnname," + "c_columndatatype," + "c_operator," + "c_dimcode," + "c_tooltip," + "c_status_cd) values(" + "'" + splited[1] + "'," + "'i2b2'," + "'N'," + "0," + "'\\" + splited[1] + "\\'," + "'" + splited[1] + "'," + "'N'," + "'CA'," + "0," + "'concept_cd'," + "'concept_dimension'," + "'concept_path'," + "'T'," + "'LIKE'," + "'\\" + splited[1] + "\\'," + "'\\" + splited[1] + "\\'," + "'A')"); stmt.executeQuery("insert into i2b2 values(0, '\\" + splited[1] + "\\', '" + splited[1] + "','N','CA',0,null, null, 'CONCEPT_CD','CONCEPT_DIMENSION','CONCEPT_PATH', 'T', 'LIKE','\\" + splited[1] + "\\', null, '\\" + splited[1] + "\\', sysdate, null, null, null, null, null, '@', null, null, null)"); } con.close(); } catch (SQLException e) { e.printStackTrace(); loadDataUI.displayMessage("SQL error: " + e.getLocalizedMessage()); loadDataUI.setIsLoading(false); return; } catch (ClassNotFoundException e) { loadDataUI.displayMessage("Java error: Class not found exception"); // TODO Auto-generated catch block e.printStackTrace(); loadDataUI.setIsLoading(false); return; } //initiate kettle environment KettleEnvironment.init(false); //find the kettle job to initiate the loading URL jobUrl = new URL( "platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/load_gene_expression_data.kjb"); jobUrl = FileLocator.toFileURL(jobUrl); String jobPath = jobUrl.getPath(); //create a new job from the kettle file JobMeta jobMeta = new JobMeta(jobPath, null); Job job = new Job(null, jobMeta); //find the other files needed for this job and put them in the cache jobUrl = new URL( "platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/validate_gene_expression_params.ktr"); jobUrl = FileLocator.toFileURL(jobUrl); jobUrl = new URL( "platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/validate_gene_expression_columns.ktr"); jobUrl = FileLocator.toFileURL(jobUrl); jobUrl = new URL( "platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/check_gene_expression_filenames.ktr"); jobUrl = FileLocator.toFileURL(jobUrl); jobUrl = new URL( "platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/load_all_gene_expression_files_for_study.kjb"); jobUrl = FileLocator.toFileURL(jobUrl); jobUrl = new URL( "platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/run_i2b2_process_mrna_data.ktr"); jobUrl = FileLocator.toFileURL(jobUrl); jobUrl = new URL( "platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/load_subject_sample_map_to_lt.ktr"); jobUrl = FileLocator.toFileURL(jobUrl); jobUrl = new URL( "platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/get_list_of_gene_expression_filenames.ktr"); jobUrl = FileLocator.toFileURL(jobUrl); jobUrl = new URL( "platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/load_gene_expression_one_study.kjb"); jobUrl = FileLocator.toFileURL(jobUrl); jobUrl = new URL( "platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/set_gene_expression_filename.ktr"); jobUrl = FileLocator.toFileURL(jobUrl); jobUrl = new URL( "platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/validate_gene_expression_columns.ktr"); jobUrl = FileLocator.toFileURL(jobUrl); jobUrl = new URL( "platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/load_gene_expression_data_to_lz.ktr"); jobUrl = FileLocator.toFileURL(jobUrl); jobUrl = new URL("platform:/plugin/fr.sanofi.fcl4transmart/jobs_kettle/pivot_gene_file.ktr"); jobUrl = FileLocator.toFileURL(jobUrl); job.getJobMeta().setParameterValue("DATA_FILE_PREFIX", ((GeneExpressionData) dataType).getRawFile().getName()); job.getJobMeta().setParameterValue("DATA_LOCATION", path); job.getJobMeta().setParameterValue("MAP_FILENAME", ((GeneExpressionData) dataType).getStsmf().getName()); job.getJobMeta().setParameterValue("DATA_TYPE", "R"); job.getJobMeta().setParameterValue("FilePivot_LOCATION", ""); job.getJobMeta().setParameterValue("LOAD_TYPE", "I"); job.getJobMeta().setParameterValue("LOG_BASE", "2"); job.getJobMeta().setParameterValue("SAMPLE_REMAP_FILENAME", "NOSAMPLEREMAP"); job.getJobMeta().setParameterValue("SAMPLE_SUFFIX", ".rma-Signal"); job.getJobMeta().setParameterValue("SECURITY_REQUIRED", "N"); job.getJobMeta().setParameterValue("SOURCE_CD", "STD"); File sort = new File(sortName); if (!sort.exists()) { FileUtils.forceMkdir(sort); } path = sort.getAbsolutePath(); job.getJobMeta().setParameterValue("SORT_DIR", path); job.getJobMeta().setParameterValue("STUDY_ID", dataType.getStudy().toString()); job.getJobMeta().setParameterValue("TOP_NODE", topNode); //job.getJobMeta().setParameterValue("JAVA_HOME", "/usr/local/jdk1.6.0_31"); job.getJobMeta().setParameterValue("TM_CZ_DB_SERVER", PreferencesHandler.getDbServer()); job.getJobMeta().setParameterValue("TM_CZ_DB_NAME", PreferencesHandler.getDbName()); job.getJobMeta().setParameterValue("TM_CZ_DB_PORT", PreferencesHandler.getDbPort()); job.getJobMeta().setParameterValue("TM_CZ_DB_USER", PreferencesHandler.getTm_czUser()); job.getJobMeta().setParameterValue("TM_CZ_DB_PWD", PreferencesHandler.getTm_czPwd()); job.getJobMeta().setParameterValue("TM_LZ_DB_SERVER", PreferencesHandler.getDbServer()); job.getJobMeta().setParameterValue("TM_LZ_DB_NAME", PreferencesHandler.getDbName()); job.getJobMeta().setParameterValue("TM_LZ_DB_PORT", PreferencesHandler.getDbPort()); job.getJobMeta().setParameterValue("TM_LZ_DB_USER", PreferencesHandler.getTm_lzUser()); job.getJobMeta().setParameterValue("TM_LZ_DB_PWD", PreferencesHandler.getTm_lzPwd()); job.start(); job.waitUntilFinished(); @SuppressWarnings("unused") Result result = job.getResult(); loadDataUI.displayMessage("Loading process is over.\n Please check monitoring step."); Log4jBufferAppender appender = CentralLogStore.getAppender(); String logText = appender.getBuffer(job.getLogChannelId(), false).toString(); Pattern pattern = Pattern.compile(".*Finished job entry \\[run i2b2_process_mrna_data\\].*", Pattern.DOTALL); Matcher matcher = pattern.matcher(logText); if (matcher.matches()) { String connectionString = "jdbc:oracle:thin:@" + PreferencesHandler.getDbServer() + ":" + PreferencesHandler.getDbPort() + ":" + PreferencesHandler.getDbName(); Connection con = DriverManager.getConnection(connectionString, PreferencesHandler.getTm_czUser(), PreferencesHandler.getTm_czPwd()); Statement stmt = con.createStatement(); //remove rows for this study before adding new ones ResultSet rs = stmt.executeQuery( "select max(JOB_ID) from CZ_JOB_AUDIT where STEP_DESC='Starting i2b2_process_mrna_data'"); int jobId; if (rs.next()) { jobId = rs.getInt("max(JOB_ID)"); } else { con.close(); loadDataUI.setIsLoading(false); return; } logText += "\nOracle job id:\n" + String.valueOf(jobId); con.close(); } writeLog(logText); CentralLogStore.discardLines(job.getLogChannelId(), false); } catch (Exception e1) { //this.write(e1.getMessage()); loadDataUI.displayMessage("Error: " + e1.getLocalizedMessage()); loadDataUI.setIsLoading(false); e1.printStackTrace(); } loadDataUI.setIsLoading(false); } }.start(); this.loadDataUI.waitForThread(); WorkPart.updateSteps(); WorkPart.updateFiles(); }
From source file:gdsc.smlm.ij.plugins.PeakFit.java
public int setup(String arg, ImagePlus imp) { plugin_flags = FLAGS;//from w w w .j a va2 s . c o m extraOptions = Utils.isExtraOptions(); maximaIdentification = (arg != null && arg.contains("spot")); fitMaxima = (arg != null && arg.contains("maxima")); simpleFit = (arg != null && arg.contains("simple")); boolean runSeries = (arg != null && arg.contains("series")); ImageSource imageSource = null; if (fitMaxima) { imp = null; // The maxima will have been identified already. // The image source will be found from the peak results. if (!showMaximaDialog()) return DONE; MemoryPeakResults results = ResultsManager.loadInputResults(inputOption, false); if (results == null || results.size() == 0) { IJ.error(TITLE, "No results could be loaded"); return DONE; } imageSource = results.getSource(); plugin_flags |= NO_IMAGE_REQUIRED; } else if (runSeries) { imp = null; // Select input folder String inputDirectory; inputDirectory = IJ.getDirectory("Select image series ..."); //inputDirectory = getInputDirectory("Select image series ..."); if (inputDirectory == null) return DONE; // Load input series ... SeriesOpener series = new SeriesOpener(inputDirectory, true); if (series.getNumberOfImages() == 0) { IJ.error(TITLE, "No images in the selected directory:\n" + inputDirectory); return DONE; } imageSource = new SeriesImageSource(getName(series.getImageList()), series); ((SeriesImageSource) imageSource).setLogProgress(true); plugin_flags |= NO_IMAGE_REQUIRED; } else { if (imp == null) { IJ.noImage(); return DONE; } // Check it is not a previous result if (imp.getTitle().endsWith(IJImagePeakResults.IMAGE_SUFFIX)) { IJImageSource tmpImageSource = null; // Check the image to see if it has an image source XML structure in the info property Object o = imp.getProperty("Info"); Pattern pattern = Pattern.compile("Source: (<.*IJImageSource>.*<.*IJImageSource>)", Pattern.DOTALL); Matcher match = pattern.matcher((o == null) ? "" : o.toString()); if (match.find()) { ImageSource source = ImageSource.fromXML(match.group(1)); if (source instanceof IJImageSource) { tmpImageSource = (IJImageSource) source; if (!tmpImageSource.open()) { tmpImageSource = null; } else { imp = WindowManager.getImage(tmpImageSource.getName()); } } } if (tmpImageSource == null) { // Look for a parent using the title String parentTitle = imp.getTitle().substring(0, imp.getTitle().length() - IJImagePeakResults.IMAGE_SUFFIX.length() - 1); ImagePlus parentImp = WindowManager.getImage(parentTitle); if (parentImp != null) { tmpImageSource = new IJImageSource(parentImp); imp = parentImp; } } String message = "The selected image may be a previous fit result"; if (tmpImageSource != null) message += " of: \n \n" + tmpImageSource.getName() + " \n \nFit the parent?"; else message += " \n \nDo you want to continue?"; YesNoCancelDialog d = new YesNoCancelDialog(null, TITLE, message); if (tmpImageSource == null) { if (!d.yesPressed()) return DONE; } else { if (d.yesPressed()) imageSource = tmpImageSource; if (d.cancelPressed()) return DONE; } } if (imageSource == null) imageSource = new IJImageSource(imp); } time = -1; if (!initialiseImage(imageSource, getBounds(imp), false)) { IJ.error(TITLE, "Failed to initialise the source image: " + imageSource.getName()); return DONE; } int flags = showDialog(imp); if ((flags & DONE) == 0) { // Repeat so that we pass in the selected option for ignoring the bounds. // This should not be necessary since it is set within the readDialog method. //if (ignoreBoundsForNoise) // initialiseImage(imageSource, bounds, ignoreBoundsForNoise); initialiseFitting(); } return flags; }
From source file:br.org.acessobrasil.ases.ferramentas_de_reparo.vista.css.FerramentaCSSPanel.java
/** * Retorna o caminho do CSS/*from www . ja v a 2 s . c o m*/ * * @param codHtml * @return String com o path ou null */ private String getCssUrl(String codHtml) { Pattern pat = Pattern.compile("<link\\s.*?>", Pattern.DOTALL); Matcher mat = pat.matcher(codHtml); RegrasHardCodedEmag regra = new RegrasHardCodedEmag(); while (mat.find()) { String tag = mat.group(); String tipo = regra.getAtributo(tag, "type"); String href = regra.getAtributo(tag, "href"); if (tipo.equals("text/css") || href.toLowerCase().endsWith(".css")) { return href; } } return null; }
From source file:org.apache.nifi.processors.standard.EvaluateRegularExpression.java
int getCompileFlags(ProcessContext context) { int flags = (context.getProperty(UNIX_LINES).asBoolean() ? Pattern.UNIX_LINES : 0) | (context.getProperty(CASE_INSENSITIVE).asBoolean() ? Pattern.CASE_INSENSITIVE : 0) | (context.getProperty(COMMENTS).asBoolean() ? Pattern.COMMENTS : 0) | (context.getProperty(MULTILINE).asBoolean() ? Pattern.MULTILINE : 0) | (context.getProperty(LITERAL).asBoolean() ? Pattern.LITERAL : 0) | (context.getProperty(DOTALL).asBoolean() ? Pattern.DOTALL : 0) | (context.getProperty(UNICODE_CASE).asBoolean() ? Pattern.UNICODE_CASE : 0) | (context.getProperty(CANON_EQ).asBoolean() ? Pattern.CANON_EQ : 0) | (context.getProperty(UNICODE_CHARACTER_CLASS).asBoolean() ? Pattern.UNICODE_CHARACTER_CLASS : 0); return flags; }
From source file:org.eclipse.mylyn.internal.web.tasks.WebRepositoryConnector.java
public static IStatus performQuery(String resource, String regexp, String taskPrefix, IProgressMonitor monitor, TaskDataCollector resultCollector, TaskRepository repository) { NamedPattern p = new NamedPattern(regexp, Pattern.CASE_INSENSITIVE | Pattern.MULTILINE | Pattern.DOTALL | Pattern.UNICODE_CASE | Pattern.CANON_EQ); Matcher matcher = p.matcher(resource); if (!matcher.find()) { return Status.OK_STATUS; } else {/*w ww . j a v a2 s . c o m*/ boolean isCorrect = true; do { if (p.getGroups().isEmpty()) { // "classic" mode, no named patterns if (matcher.groupCount() < 2) { isCorrect = false; } if (matcher.groupCount() >= 1) { String id = matcher.group(1); String description = matcher.groupCount() > 1 ? cleanup(matcher.group(2), repository) : null; description = unescapeHtml(description); TaskData data = createTaskData(repository, id); TaskMapper mapper = new TaskMapper(data, true); mapper.setCreationDate(DEFAULT_DATE); mapper.setTaskUrl(taskPrefix + id); mapper.setSummary(description); mapper.setValue(KEY_TASK_PREFIX, taskPrefix); resultCollector.accept(data); } } else { String id = p.group("Id", matcher); //$NON-NLS-1$ String description = p.group("Description", matcher); //$NON-NLS-1$ if (id == null || description == null) { isCorrect = false; } if (id != null) { description = unescapeHtml(description); String owner = unescapeHtml(cleanup(p.group("Owner", matcher), repository)); //$NON-NLS-1$ String type = unescapeHtml(cleanup(p.group("Type", matcher), repository)); //$NON-NLS-1$ TaskData data = createTaskData(repository, id); TaskMapper mapper = new TaskMapper(data, true); mapper.setCreationDate(DEFAULT_DATE); mapper.setTaskUrl(taskPrefix + id); mapper.setSummary(description); mapper.setValue(KEY_TASK_PREFIX, taskPrefix); mapper.setOwner(owner); mapper.setTaskKind(type); String status = p.group("Status", matcher); //$NON-NLS-1$ if (status != null) { if (COMPLETED_STATUSES.contains(status.toLowerCase())) { // TODO set actual completion date here mapper.setCompletionDate(DEFAULT_DATE); } } resultCollector.accept(data); } } } while (matcher.find() && !monitor.isCanceled()); if (isCorrect) { return Status.OK_STATUS; } else { return new Status(IStatus.ERROR, TasksWebPlugin.ID_PLUGIN, IStatus.ERROR, Messages.WebRepositoryConnector_Require_two_matching_groups, null); } } }
From source file:org.kepler.kar.karxml.KarXmlGenerator.java
/** * Strip out the "<?xml" tag from the xml. Also removes a header DOCTYPE, if present. * //from w ww. j av a2s .co m * @param xml * @return */ public String processXmlEntryContents(String xml) { xml = xml.replaceAll("<\\?xml.*?>", ""); xml = Pattern.compile("<!DOCTYPE.*?>", Pattern.DOTALL).matcher(xml).replaceAll(""); return xml; }
From source file:com.parse.OfflineQueryLogic.java
/** * Matches $regex constraints./* w w w . ja v a2s . c o m*/ */ private static boolean matchesRegexConstraint(Object constraint, Object value, String options) throws ParseException { if (value == null || value == JSONObject.NULL) { return false; } if (options == null) { options = ""; } if (!options.matches("^[imxs]*$")) { throw new ParseException(ParseException.INVALID_QUERY, String.format("Invalid regex options: %s", options)); } int flags = 0; if (options.contains("i")) { flags = flags | Pattern.CASE_INSENSITIVE; } if (options.contains("m")) { flags = flags | Pattern.MULTILINE; } if (options.contains("x")) { flags = flags | Pattern.COMMENTS; } if (options.contains("s")) { flags = flags | Pattern.DOTALL; } String regex = (String) constraint; Pattern pattern = Pattern.compile(regex, flags); Matcher matcher = pattern.matcher((String) value); return matcher.find(); }