List of usage examples for java.io LineNumberReader LineNumberReader
public LineNumberReader(Reader in)
From source file:mitm.common.postfix.PostfixLogParser.java
public int getRawLogCount(Reader log) throws IOException { LineNumberReader lineReader = new LineNumberReader(log); int count = 0; String line;//from ww w .ja v a 2s. com while ((line = lineReader.readLine()) != null) { line = StringUtils.trimToNull(line); if (line == null) { continue; } if (searchPattern != null) { Matcher matcher = searchPattern.matcher(line); if (matcher.find()) { count++; } } else { count++; } } return count; }
From source file:massbank.BatchJobWorker.java
/** * Ytt@C???iHTML`?j//w w w . j a v a2 s. c om * @param time NGXg * @param resultFile t@C * @param htmlFile YtpHTMLt@C */ private void createHtmlFile(String time, File resultFile, File htmlFile) { NumberFormat nf = NumberFormat.getNumberInstance(); LineNumberReader in = null; PrintWriter out = null; try { in = new LineNumberReader(new FileReader(resultFile)); out = new PrintWriter(new BufferedWriter(new FileWriter(htmlFile))); // wb_?[?o String reqIonStr = "Both"; try { if (Integer.parseInt(this.ion) > 0) { reqIonStr = "Positive"; } else if (Integer.parseInt(this.ion) < 0) { reqIonStr = "Negative"; } } catch (NumberFormatException nfe) { nfe.printStackTrace(); } out.println("<html>"); out.println("<head><title>MassBank Batch Service Results</title></head>"); out.println("<body>"); out.println( "<h1><a href=\"http://www.massbank.jp/\" target=\"_blank\">MassBank</a> Batch Service Results</h1>"); out.println("<hr>"); out.println("<h2>Request Date : " + time + "<h2>"); out.println("Instrument Type : " + this.inst + "<br>"); out.println("Ion Mode : " + reqIonStr + "<br>"); out.println("<br><hr>"); // ?o String line; long queryCnt = 0; boolean readName = false; boolean readHit = false; boolean readNum = false; while ((line = in.readLine()) != null) { if (in.getLineNumber() < 4) { continue; } if (!readName) { queryCnt++; out.println("<h2>Query " + nf.format(queryCnt) + "</h2><br>"); out.println("Name: " + line.trim() + "<br>"); readName = true; } else if (!readHit) { out.println("Hit: " + nf.format(Integer.parseInt(line.trim())) + "<br>"); readHit = true; } else if (!readNum) { out.println("<table border=\"1\">"); out.println("<tr><td colspan=\"6\">Top " + line.trim() + " List</td></tr>"); out.println( "<tr><th>Accession</th><th>Title</th><th>Formula</th><th>Ion</th><th>Score</th><th>Hit</th></tr>"); readNum = true; } else { if (!line.trim().equals("")) { String[] data = formatLine(line); String acc = data[0]; String title = data[1]; String formula = data[2]; String ion = data[3]; String score = data[4]; String hit = data[5]; out.println("<tr>"); out.println("<td><a href=\"http://www.massbank.jp/jsp/FwdRecord.jsp?id=" + acc + "\" target=\"_blank\">" + acc + "</td>"); out.println("<td>" + title + "</td>"); out.println("<td>" + formula + "</td>"); out.println("<td>" + ion + "</td>"); out.println("<td>" + score + "</td>"); out.println("<td align=\"right\">" + hit + "</td>"); out.println("</tr>"); } else { out.println("</table>"); out.println("<hr>"); readName = false; readHit = false; readNum = false; } } } } catch (Exception e) { e.printStackTrace(); } finally { try { if (in != null) { in.close(); } } catch (IOException e) { } if (out != null) { out.flush(); out.close(); } } }
From source file:org.apache.lucene.search.SearchUtil.java
public void parse(File file) throws IOException, InterruptedException { FileInputStream fis = null;/*from w w w. j a va 2 s. c om*/ try { fis = new FileInputStream(file); HTMLParser parser = new HTMLParser(fis); // this.title=Entities.encode(parser.getTitle()); StringBuilder sb = new StringBuilder(); LineNumberReader reader = new LineNumberReader(parser.getReader()); for (String l = reader.readLine(); l != null; l = reader.readLine()) { // System.out.println(l); sb.append(l + " "); } this.contents = sb.toString(); // System.out.println("Parsed Contents: "+contents); } finally { if (fis != null) fis.close(); } }
From source file:org.haplo.javascript.Runtime.java
/** * Initialize the shared JavaScript environment. Loads libraries and removes * methods of escaping the sandbox.//from ww w . j a v a 2 s .co m */ public static void initializeSharedEnvironment(String frameworkRoot, boolean pluginDebuggingEnabled) throws java.io.IOException { // Don't allow this to be called twice if (sharedScope != null) { return; } long startTime = System.currentTimeMillis(); final Context cx = Runtime.enterContext(); try { final ScriptableObject scope = cx.initStandardObjects(null, false /* don't seal the standard objects yet */); if (!scope.has("JSON", scope)) { throw new RuntimeException( "Expecting built-in JSON support in Rhino, check version is at least 1.7R3"); } if (standardTemplateLoader == null) { throw new RuntimeException("StandardTemplateLoader for Runtime hasn't been set."); } String standardTemplateJSON = standardTemplateLoader.standardTemplateJSON(); scope.put("$STANDARDTEMPLATES", scope, standardTemplateJSON); // Define the HaploTemplate host object now, so the JS code can use it to parse templates // TODO: Convert all standard templates from Handlebars, move HaploTemplate host object declaraction back with the others, remove $HaploTemplate from whitelist defineSealedHostClass(scope, HaploTemplate.class); // Load the library code FileReader bootScriptsFile = new FileReader(frameworkRoot + "/lib/javascript/bootscripts.txt"); LineNumberReader bootScripts = new LineNumberReader(bootScriptsFile); String scriptFilename = null; while ((scriptFilename = bootScripts.readLine()) != null) { FileReader script = new FileReader(frameworkRoot + "/" + scriptFilename); cx.evaluateReader(scope, script, scriptFilename, 1, null /* no security domain */); script.close(); } bootScriptsFile.close(); // Insert plugin debugging flag if (pluginDebuggingEnabled) { Scriptable o = (Scriptable) scope.get("O", scope); o.put("PLUGIN_DEBUGGING_ENABLED", o, true); } // Load the list of allowed globals FileReader globalsWhitelistFile = new FileReader( frameworkRoot + "/lib/javascript/globalswhitelist.txt"); HashSet<String> globalsWhitelist = new HashSet<String>(); LineNumberReader whitelist = new LineNumberReader(globalsWhitelistFile); String globalName = null; while ((globalName = whitelist.readLine()) != null) { String g = globalName.trim(); if (g.length() > 0) { globalsWhitelist.add(g); } } globalsWhitelistFile.close(); // Remove all the globals which aren't allowed, using a whitelist for (Object propertyName : scope.getAllIds()) // the form which includes the DONTENUM hidden properties { if (propertyName instanceof String) // ConsString is checked { // Delete any property which isn't in the whitelist if (!(globalsWhitelist.contains(propertyName))) { scope.delete((String) propertyName); // ConsString is checked } } else { // Not expecting any other type of property name in the global namespace throw new RuntimeException( "Not expecting global JavaScript scope to contain a property which isn't a String"); } } // Run through the globals again, just to check nothing escaped for (Object propertyName : scope.getAllIds()) { if (!(globalsWhitelist.contains(propertyName))) { throw new RuntimeException("JavaScript global was not destroyed: " + propertyName.toString()); } } // Run through the whilelist, and make sure that everything in it exists for (String propertyName : globalsWhitelist) { if (!scope.has(propertyName, scope)) { // The whitelist should only contain non-host objects created by the JavaScript source files. throw new RuntimeException( "JavaScript global specified in whitelist does not exist: " + propertyName); } } // And make sure java has gone, to check yet again that everything expected has been removed if (scope.get("java", scope) != Scriptable.NOT_FOUND) { throw new RuntimeException("JavaScript global 'java' escaped destruction"); } // Seal the scope and everything within in, so nothing else can be added and nothing can be changed // Asking initStandardObjects() to seal the standard library doesn't actually work, as it will leave some bits // unsealed so that decodeURI.prototype.pants = 43; works, and can pass information between runtimes. // This recursive object sealer does actually work. It can't seal the main host object class, so that's // added to the scope next, with the (working) seal option set to true. HashSet<Object> sealedObjects = new HashSet<Object>(); recursiveSealObjects(scope, scope, sealedObjects, false /* don't seal the root object yet */); if (sealedObjects.size() == 0) { throw new RuntimeException("Didn't seal any JavaScript globals"); } // Add the host object classes. The sealed option works perfectly, so no need to use a special seal function. defineSealedHostClass(scope, KHost.class); defineSealedHostClass(scope, KPlatformGenericInterface.class); defineSealedHostClass(scope, KObjRef.class); defineSealedHostClass(scope, KScriptable.class); defineSealedHostClass(scope, KLabelList.class); defineSealedHostClass(scope, KLabelChanges.class); defineSealedHostClass(scope, KLabelStatements.class); defineSealedHostClass(scope, KDateTime.class); defineSealedHostClass(scope, KObject.class); defineSealedHostClass(scope, KText.class); defineSealedHostClass(scope, KQueryClause.class); defineSealedHostClass(scope, KQueryResults.class); defineSealedHostClass(scope, KPluginAppGlobalStore.class); defineSealedHostClass(scope, KPluginResponse.class); defineSealedHostClass(scope, KTemplatePartialAutoLoader.class); defineSealedHostClass(scope, KAuditEntry.class); defineSealedHostClass(scope, KAuditEntryQuery.class); defineSealedHostClass(scope, KUser.class); defineSealedHostClass(scope, KUserData.class); defineSealedHostClass(scope, KWorkUnit.class); defineSealedHostClass(scope, KWorkUnitQuery.class); defineSealedHostClass(scope, KEmailTemplate.class); defineSealedHostClass(scope, KBinaryData.class); defineSealedHostClass(scope, KBinaryDataInMemory.class, true /* map inheritance */); defineSealedHostClass(scope, KBinaryDataStaticFile.class, true /* map inheritance */); defineSealedHostClass(scope, KBinaryDataTempFile.class, true /* map inheritance */); defineSealedHostClass(scope, KUploadedFile.class, true /* map inheritance */); defineSealedHostClass(scope, KStoredFile.class); defineSealedHostClass(scope, KJob.class); defineSealedHostClass(scope, KFilePipelineResult.class); defineSealedHostClass(scope, KSessionStore.class); defineSealedHostClass(scope, KKeychainCredential.class); // HaploTemplate created earlier as required by some of the setup defineSealedHostClass(scope, HaploTemplateDeferredRender.class); defineSealedHostClass(scope, JSFunctionThis.class); defineSealedHostClass(scope, GenericDeferredRender.class); defineSealedHostClass(scope, KSecurityRandom.class); defineSealedHostClass(scope, KSecurityBCrypt.class); defineSealedHostClass(scope, KSecurityDigest.class); defineSealedHostClass(scope, KSecurityHMAC.class); defineSealedHostClass(scope, JdNamespace.class); defineSealedHostClass(scope, JdTable.class); defineSealedHostClass(scope, JdDynamicTable.class, true /* map inheritance */); defineSealedHostClass(scope, JdSelectClause.class); defineSealedHostClass(scope, JdSelect.class, true /* map inheritance */); defineSealedHostClass(scope, KGenerateTable.class, true /* map inheritance */); defineSealedHostClass(scope, KGenerateXLS.class, true /* map inheritance */); defineSealedHostClass(scope, KRefKeyDictionary.class); defineSealedHostClass(scope, KRefKeyDictionaryHierarchical.class, true /* map inheritance */); defineSealedHostClass(scope, KRefSet.class); defineSealedHostClass(scope, KCheckingLookupObject.class); defineSealedHostClass(scope, WorkUnitTags.class); defineSealedHostClass(scope, GetterDictionaryBase.class); defineSealedHostClass(scope, InterRuntimeSignal.class); defineSealedHostClass(scope, KRequestContinuation.class); defineSealedHostClass(scope, JsBigDecimal.class); defineSealedHostClass(scope, JsDecimalFormat.class); defineSealedHostClass(scope, XmlDocument.class); defineSealedHostClass(scope, XmlCursor.class); defineSealedHostClass(scope, KCollaborationService.class); defineSealedHostClass(scope, KCollaborationFolder.class); defineSealedHostClass(scope, KCollaborationItemList.class); defineSealedHostClass(scope, KCollaborationItem.class); defineSealedHostClass(scope, KAuthenticationService.class); defineSealedHostClass(scope, KMessageBusPlatformSupport.class); defineSealedHostClass(scope, KUUIDPlatformSupport.class); defineSealedHostClass(scope, StdReporting.class); defineSealedHostClass(scope, StdWebPublisher.class); defineSealedHostClass(scope, StdWebPublisher.RenderedAttributeListView.class); defineSealedHostClass(scope, StdWebPublisher.ValueView.class); // Seal the root now everything has been added scope.sealObject(); // Check JavaScript TimeZone checkJavaScriptTimeZoneIsGMT(); // Templating integration JSPlatformIntegration.parserConfiguration = new TemplateParserConfiguration(); JSPlatformIntegration.includedTemplateRenderer = new TemplateIncludedRenderer(); JSPlatformIntegration.platformFunctionRenderer = new TemplateFunctionRenderer(); sharedScope = scope; } finally { cx.exit(); } initializeSharedEnvironmentTimeTaken = System.currentTimeMillis() - startTime; }
From source file:com.jkoolcloud.tnt4j.streams.utils.Utils.java
/** * Counts text lines available in input. * * @param reader//w w w . ja v a 2s .com * a {@link java.io.Reader} object to provide the underlying input stream * @return number of lines currently available in input * @throws java.io.IOException * If an I/O error occurs * @deprecated use {@link #countLines(java.io.InputStream)} instead */ @Deprecated public static int countLines(Reader reader) throws IOException { int lCount = 0; LineNumberReader lineReader = null; try { lineReader = new LineNumberReader(reader); lineReader.skip(Long.MAX_VALUE); // NOTE: Add 1 because line index starts at 0 lCount = lineReader.getLineNumber() + 1; } finally { close(lineReader); } return lCount; }
From source file:org.openadaptor.auxil.connector.socket.SocketWriteConnector.java
protected LineNumberReader getInputStream() throws IOException { return new LineNumberReader(new InputStreamReader(socket.getInputStream())); }
From source file:org.agnitas.web.ImportProfileColumnsAction.java
/** * Adds column mappings from uploaded csv-file using import profile settings * for parsing csv file//from w w w. j av a 2 s . c o m * * @param aForm a form * @param request request */ private void addColumnsFromFile(ImportProfileColumnsForm aForm, HttpServletRequest request) { RecipientDao recipientDao = (RecipientDao) getWebApplicationContext().getBean("RecipientDao"); if (aForm.getProfile() == null) { loadImportProfile(aForm, request); } ImportProfile profile = aForm.getProfile(); List<ColumnMapping> columnMappings = profile.getColumnMapping(); File file = getCurrentFile(request); if (file == null) { return; } try { Map dbColumns = recipientDao.readDBColumns(AgnUtils.getCompanyID(request)); String profileCharset = Charset.getValue(profile.getCharset()); String fileString = FileUtils.readFileToString(file, profileCharset); LineNumberReader aReader = new LineNumberReader(new StringReader(fileString)); String firstLine = aReader.readLine(); firstLine = firstLine.trim(); CsvTokenizer tokenizer = new CsvTokenizer(firstLine, Separator.getValue(profile.getSeparator()), TextRecognitionChar.getValue(profile.getTextRecognitionChar())); String[] newCsvColumns = tokenizer.toArray(); List<ColumnMapping> newMappings = new ArrayList<ColumnMapping>(); for (String newCsvColumn : newCsvColumns) { if (!aForm.columnExists(newCsvColumn, columnMappings) && !StringUtils.isEmpty(newCsvColumn)) { ColumnMapping newMapping = new ColumnMappingImpl(); newMapping.setProfileId(profile.getId()); newMapping.setMandatory(false); newMapping.setFileColumn(newCsvColumn); if (dbColumns.get(newCsvColumn) != null) { String dbColumn = getInsensetiveMapKey(dbColumns, newCsvColumn); if (dbColumn == null) { // if dbColumn is NULL mapping is invalid continue; } newMapping.setDatabaseColumn(dbColumn); String defaultValue = aForm.getDbColumnsDefaults().get(dbColumn); if (defaultValue != null) { newMapping.setDefaultValue(defaultValue); } } newMappings.add(newMapping); } } profile.getColumnMapping().addAll(newMappings); } catch (IOException e) { AgnUtils.logger().error("Error reading csv-file: " + e + "\n" + AgnUtils.getStackTrace(e)); } catch (Exception e) { AgnUtils.logger().error("Error reading csv-file: " + e + "\n" + AgnUtils.getStackTrace(e)); } }
From source file:com.haulmont.cuba.uberjar.ServerRunner.java
protected void stop(int port, String key) { try {/*from www.j a v a 2s . co m*/ try (Socket s = new Socket(InetAddress.getByName("127.0.0.1"), port)) { s.setSoTimeout(STOP_TIMEOUT * 1000); try (OutputStream out = s.getOutputStream()) { out.write((key + "\r\nstop\r\n").getBytes(StandardCharsets.UTF_8)); out.flush(); System.out.println(String.format("Waiting %,d seconds for server to stop", STOP_TIMEOUT)); LineNumberReader lin = new LineNumberReader( new InputStreamReader(s.getInputStream(), StandardCharsets.UTF_8)); String response; while ((response = lin.readLine()) != null) { System.out.println(String.format("Received \"%s\"", response)); if ("Stopped".equals(response)) { System.out.println("Server reports itself as Stopped"); } } } } } catch (SocketTimeoutException e) { System.out.println("Timed out waiting for stop confirmation"); } catch (Exception e) { e.printStackTrace(); } }
From source file:edu.stanford.muse.index.Indexer.java
public static Set<String> readStreamAndInternStrings(Reader r) { Set<String> result = new LinkedHashSet<String>(); try {// ww w . j a v a2 s . c o m LineNumberReader lnr = new LineNumberReader(r); while (true) { String word = lnr.readLine(); if (word == null) { lnr.close(); break; } word = word.trim(); if (word.startsWith("#") || word.length() == 0) continue; word = IndexUtils.canonicalizeMultiWordTerm(word, false); // TOFIX: not really sure if stemming shd be off word = InternTable.intern(word); result.add(word); } } catch (IOException e) { log.warn("Exception reading reader " + r + ": " + e + Util.stackTrace(e)); } return result; }
From source file:org.apache.pig.scripting.Pig.java
private static String getScriptFromFile(String filename) throws IOException { LineNumberReader rd = new LineNumberReader(new FileReader(filename)); StringBuilder sb = new StringBuilder(); try {//from w w w. j a v a 2 s. c o m String line = rd.readLine(); while (line != null) { sb.append(line); sb.append("\n"); line = rd.readLine(); } } finally { rd.close(); } return sb.toString(); }