List of usage examples for org.apache.commons.io FilenameUtils getFullPath
public static String getFullPath(String filename)
From source file:MSUmpire.LCMSPeakStructure.LCMSPeakBase.java
public void ExportPeakClusterResultCSV() throws IOException { Logger.getRootLogger().info("Writing PeakCluster CSV:" + FilenameUtils.getFullPath(ScanCollectionName) + FilenameUtils.getBaseName(ScanCollectionName) + "_PeakCluster.csv..."); FileWriter writer = new FileWriter(FilenameUtils.getFullPath(ScanCollectionName) + FilenameUtils.getBaseName(ScanCollectionName) + "_PeakCluster.csv"); String mzstring = ""; String Idxstring = ""; String CorrString = ""; String SNRString = ""; String PeakheightString = ""; String PeakheightRTString = ""; String PeakAreaString = ""; String IdentifiedString = "0"; for (int i = 0; i < MaxNoPeakCluster; i++) { mzstring += ",mz" + (i + 1); Idxstring += ",PeakIdx" + (i + 1); if (i > 0) { CorrString += ",Corr" + (i + 1); }/*from w w w . j a v a 2 s .com*/ SNRString += ",SNR" + (i + 1); PeakheightString += ",PeakHeight" + (i + 1); PeakheightRTString += ",PeakHeightRT" + (i + 1); PeakAreaString += ",PeakArea" + (i + 1); } writer.write("Cluster_Index,StartRT,EndRT,StartScan,EndScan,Identified,Charge" + mzstring + Idxstring + CorrString + SNRString + PeakheightString + PeakheightRTString + PeakAreaString + ",IsoMapProb,ConflictCorr,LeftInt,RightInt,NoRidges,MS1Score,MS1Prob,MS1LProb\n"); for (PeakCluster cluster : PeakClusters) { IdentifiedString = "0"; if (cluster.Identified) { IdentifiedString = "1"; } String statementString = cluster.Index + "," + cluster.startRT + "," + cluster.endRT + "," + cluster.StartScan + "," + cluster.EndScan + "," + IdentifiedString + "," + cluster.Charge + ","; mzstring = ""; Idxstring = ""; CorrString = ""; SNRString = ""; PeakheightString = ""; PeakheightRTString = ""; PeakAreaString = ""; for (int i = 0; i < MaxNoPeakCluster; i++) { mzstring += cluster.mz[i] + ","; Idxstring += cluster.IsoPeakIndex[i] + ","; if (i > 0) { CorrString += cluster.Corrs[i - 1] + ","; } SNRString += cluster.GetSNR(i) + ","; PeakheightString += cluster.PeakHeight[i] + ","; PeakheightRTString += cluster.PeakHeightRT[i] + ","; PeakAreaString += cluster.PeakArea[i] + ","; } statementString += mzstring + Idxstring + CorrString + SNRString + PeakheightString + PeakheightRTString + PeakAreaString + cluster.IsoMapProb + "," + cluster.GetConflictCorr() + "," + cluster.LeftInt + "," + cluster.RightInt + "," + cluster.NoRidges + "," + cluster.MS1Score + "," + cluster.MS1ScoreProbability + "," + cluster.MS1ScoreLocalProb + "\n"; writer.write(statementString); } writer.close(); //System.out.print("Finished multithreading\n"); }
From source file:egovframework.rte.fdl.excel.impl.EgovExcelServiceImpl.java
public HSSFWorkbook createWorkbook(HSSFWorkbook wb, String filepath) throws BaseException, FileNotFoundException, IOException { String fullFileName = filepath; log.debug(//from w ww .ja va 2 s. c om "EgovExcelServiceImpl.createWorkbook : templatePath is " + FilenameUtils.getFullPath(fullFileName)); // ? if (!EgovFileUtil.isExistsFile(FilenameUtils.getFullPath(fullFileName))) { log.debug("make dir " + FilenameUtils.getFullPath(fullFileName)); try { FileUtils.forceMkdir(new File(FilenameUtils.getFullPath(fullFileName))); } catch (IOException e) { throw new IOException( "Cannot create directory for path: " + FilenameUtils.getFullPath(fullFileName)); } } FileOutputStream fileOut = new FileOutputStream(fullFileName); log.debug("EgovExcelServiceImpl.createWorkbook : templatePath is " + fullFileName); try { log.debug("ExcelServiceImpl loadExcelObject ..."); wb.write(fileOut); } catch (Exception e) { log.error(getMessageSource().getMessage("error.excel.runtime.error", new Object[] { "createWorkbook" }, Locale.getDefault()), e); } finally { log.debug("ExcelServiceImpl loadExcelObject end..."); fileOut.close(); } return wb; }
From source file:info.fetter.logstashforwarder.FileWatcher.java
private void addSingleFile(String fileToWatch, Event fields, int deadTime) throws Exception { logger.info("Watching file : " + new File(fileToWatch).getCanonicalPath()); String directory = FilenameUtils.getFullPath(fileToWatch); String fileName = FilenameUtils.getName(fileToWatch); IOFileFilter fileFilter = FileFilterUtils.and(FileFilterUtils.fileFileFilter(), FileFilterUtils.nameFileFilter(fileName), new LastModifiedFileFilter(deadTime)); initializeWatchMap(new File(directory), fileFilter, fields); }
From source file:it.grid.storm.info.SpaceInfoManager.java
/** * Populate with DU tasks/* w w w. j a v a 2 s . com*/ */ private void fakeSAtoAnalyze(List<String> absPaths) { // Create a list of SSD using the list of AbsPaths List<StorageSpaceData> toAnalyze = new ArrayList<StorageSpaceData>(); for (String path : absPaths) { path = path + File.separator; String pathNorm = FilenameUtils.normalize(FilenameUtils.getFullPath(path)); StorageSpaceData ssd = new StorageSpaceData(); try { PFN spaceFN = PFN.make(pathNorm); log.trace("PFN : ", spaceFN); ssd.setSpaceToken(TSpaceToken.make(new it.grid.storm.common.GUID().toString())); ssd.setSpaceFileName(spaceFN); toAnalyze.add(ssd); } catch (InvalidTSpaceTokenAttributesException e) { log.error("Unable to create Space Token. {}", e.getMessage(), e); } catch (InvalidPFNAttributeException e) { log.error("Unable to create PFN. {}", e.getMessage(), e); } } for (StorageSpaceData ssd : toAnalyze) { TSpaceToken sT = ssd.getSpaceToken(); String absPath = ssd.getSpaceFileNameString(); try { bDUTasks.addTask(sT, absPath); log.debug("Added {} to the DU-Task Queue. (Task queue size: {})", absPath, bDUTasks.howManyTask()); } catch (SAInfoException e) { log.error(e.getMessage(), e); } } log.info("Background DU tasks size: {}", bDUTasks.getTasks().size()); }
From source file:edu.scripps.fl.pubchem.xmltool.gui.PubChemXMLCreatorGUI.java
public void mouseClicked(MouseEvent e) { try {/*from w w w. jav a2 s . c o m*/ if (e.getClickCount() > 0) { setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); if (e.getSource() == jtpExample) { URL url = getClass().getClassLoader().getResource("ExampleExcel.xlsx"); File tmpFile = File.createTempFile("example", ".xlsx"); FileUtils.copyURLToFile(url, tmpFile); tmpFile.deleteOnExit(); Desktop.getDesktop().open(tmpFile); } else if (e.getSource() == jtpExcelTemplate) { File saveFile = gc.fileChooser(jtfFileExcel, ".xlsx", "save"); if (saveFile != null) { URL url = getClass().getClassLoader().getResource("ExcelTemplate_withBAO.xlsx"); OutputStream out = new FileOutputStream(saveFile, true); IOUtils.copy(url.openStream(), out); String output = FilenameUtils.concat(FilenameUtils.getFullPath(saveFile.toString()), FilenameUtils.getBaseName(saveFile.toString())); Desktop.getDesktop().open(new File(saveFile.toString())); } } else if (e.getSource() == jtfFileTemplate && jtfFileTemplate.getText().equals(template)) { jtfFileTemplate.setText(""); } else if (e.getSource() == this) { if (jtfFileTemplate.getText().equals("")) { jtfFileTemplate.setText(template); } } } setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } catch (Throwable throwable) { SwingGUI.handleError(this, throwable); } }
From source file:info.fetter.logstashforwarder.FileWatcher.java
private void addWildCardFiles(String filesToWatch, Event fields, int deadTime) throws Exception { logger.info("Watching wildcard files : " + filesToWatch); String directory = FilenameUtils.getFullPath(filesToWatch); String wildcard = FilenameUtils.getName(filesToWatch); logger.trace("Directory : " + new File(directory).getCanonicalPath() + ", wildcard : " + wildcard); IOFileFilter fileFilter = FileFilterUtils.and(FileFilterUtils.fileFileFilter(), new WildcardFileFilter(wildcard), new LastModifiedFileFilter(deadTime)); initializeWatchMap(new File(directory), fileFilter, fields); }
From source file:it.drwolf.ridire.session.async.IndexMerger.java
private void transferFile(String www1localstore, String jobName, CrawledResource cr) throws JSchException, SftpException, IOException { int mode = ChannelSftp.OVERWRITE; String localDir = www1localstore + System.getProperty("file.separator") + jobName; FileUtils.forceMkdir(new File(localDir)); this.c.get(/* w ww.j a v a 2 s.com*/ FilenameUtils.getFullPath(cr.getArcFile()) + System.getProperty("file.separator") + "resources" + System.getProperty("file.separator") + cr.getDigest() + ".txt.pos", localDir + System.getProperty("file.separator") + cr.getDigest() + ".txt.pos", null, mode); }
From source file:com.jaspersoft.studio.server.editor.ReportRunControler.java
public void runReport() { final VSimpleErrorPreview errorView = pcontainer.getErrorView(); pcontainer.getRightContainer().switchView(null, errorView); errorView.setMessage(com.jaspersoft.studio.messages.Messages.ReportControler_generating); c = pcontainer.getConsole();/*from w ww . j a v a 2s .co m*/ c.showConsole(); c.clearConsole(); pcontainer.setJasperPrint(null, null); stats = new Statistics(); stats.startCount(ReportControler.ST_REPORTEXECUTIONTIME); c.addMessage(Messages.ReportRunControler_statsstart); pcontainer.setNotRunning(false); Job job = new Job(com.jaspersoft.studio.messages.Messages.PreviewEditor_preview_a + ": " + reportUnit //$NON-NLS-1$ + com.jaspersoft.studio.messages.Messages.PreviewEditor_preview_b) { @Override protected IStatus run(IProgressMonitor monitor) { monitor.beginTask(com.jaspersoft.studio.messages.Messages.ReportRunControler_3, IProgressMonitor.UNKNOWN); try { prmInput.setReportUnit(icm, icm.getReportUnit(), monitor, reportUnit); if (!prmInput.checkFieldsFilled()) return Status.CANCEL_STATUS; Map<String, Object> prmcopy = new HashMap<String, Object>(); for (ResourceDescriptor p : icm.getInputControls()) { if (p.isVisible() && !p.isReadOnly()) { if (p.isMandatory()) prmcopy.put(p.getName(), icm.getParameters().get(p.getName())); else if (icm.getParameters().get(p.getName()) != null) prmcopy.put(p.getName(), icm.getParameters().get(p.getName())); } } List<Argument> args = new ArrayList<Argument>(); String reptype = pcontainer.getCurrentViewer(); args.add(new Argument(Argument.RUN_OUTPUT_FORMAT, reptype)); args.add(new Argument(Argument.RUN_OUTPUT_IMAGES_URI, "")); //$NON-NLS-1$ repExec.setArgs(args); repExec.setStatus("refresh"); //$NON-NLS-1$ while (repExec.getStatus().equals("refresh") || repExec.getStatus().equals("queued") //$NON-NLS-1$//$NON-NLS-2$ || repExec.getStatus().equals("execution")) { //$NON-NLS-1$ monitor.setTaskName(repExec.getStatus()); repExec = WSClientHelper.runReportUnit(monitor, repExec, prmcopy); if (repExec.getStatus().equals("ready")) { //$NON-NLS-1$ stats.endCount(ReportControler.ST_REPORTEXECUTIONTIME); if (repExec.getTotalPages() != null) stats.setValue(ReportControler.ST_PAGECOUNT, repExec.getTotalPages()); if (repExec.getReportOutputURL() != null) { showURL(repExec); } else { Map<String, FileContent> files = repExec.getFiles(); if (files.isEmpty()) showReport(null); for (String key : files.keySet()) { FileContent fc = (FileContent) files.get(key); stats.setValue(ReportControler.ST_REPORTSIZE, fc.getData().length); if (reptype.equals(Argument.RUN_OUTPUT_FORMAT_JRPRINT)) { //$NON-NLS-1$ Object obj = JRLoader.loadObject(new ByteArrayInputStream(fc.getData())); if (obj instanceof JasperPrint) showReport((JasperPrint) obj); break; } else { // System.out.println(new // String(fc.getMimeType())); File f = null; if (fc.getName().contains("/")) //$NON-NLS-1$ f = new File(FilenameUtils.getFullPath(fc.getName()), FilenameUtils.getBaseName(fc.getName())); else f = new File(tempDir, fc.getName()); if (f == null || !f.exists()) { f.deleteOnExit(); f.createNewFile(); } if (!key.equals("report")) { //$NON-NLS-1$ if (!f.getName().equals(key)) { File dest = new File(tempDir, key); f.renameTo(dest); f = dest; } } else if (f.getName().endsWith(".att")) { //$NON-NLS-1$ int ind = fc.getMimeType().indexOf("/"); //$NON-NLS-1$ if (ind >= 0) { String str = fc.getMimeType().substring(ind + 1); File dest = new File( f.getAbsolutePath().replaceAll(".att$", "." + str)); //$NON-NLS-1$ //$NON-NLS-2$ f.renameTo(dest); f = dest; } } FileOutputStream htmlFile = new FileOutputStream(f); htmlFile.write(fc.getData()); htmlFile.close(); if (key.equals("report")) //$NON-NLS-1$ showURL(f.toURI().toASCIIString()); // UIUtils.getDisplay().asyncExec(new // Runnable() { // // @Override // public void run() { // errorView.setMessage("This file will be opened in an external editor"); // SelectionHelper.openEditor(f); // } // }); } } } } else if (repExec.getStatus().equals("queued") //$NON-NLS-1$ || repExec.getStatus().equals("execution")) { //$NON-NLS-1$ showURL(repExec); Thread.sleep(100); } else if (repExec.getStatus().equals("failed") //$NON-NLS-1$ || repExec.getStatus().equals("cancelled")) { //$NON-NLS-1$ RESTv2ExceptionHandler reh = new RESTv2ExceptionHandler( (ARestV2Connection) WSClientHelper.getClient(monitor, repExec.getReportURIFull())); throw new Exception(reh.buildMessage(monitor, "", repExec.getErrorDescriptor())); //$NON-NLS-1$ } if (monitor.isCanceled()) { WSClientHelper.cancelReportUnit(monitor, repExec); break; } } } catch (Throwable e) { ReportControler.showRunReport(c, pcontainer, e); } finally { monitor.done(); finishReport(); } return Status.OK_STATUS; } private void showReport(final JasperPrint obj) { UIUtils.getDisplay().asyncExec(new Runnable() { @Override public void run() { stats.setValue(ReportControler.ST_PAGECOUNT, obj == null ? 0 : obj.getPages().size()); APreview pv = pcontainer.getDefaultViewer(); if (pv instanceof IJRPrintable) try { ((IJRPrintable) pv).setJRPRint(stats, obj, true); VBookmarks vs = (VBookmarks) viewmap.get(ReportControler.FORM_BOOKMARKS); vs.setJasperPrint(obj); } catch (Exception e) { e.printStackTrace(); } pcontainer.setJasperPrint(stats, obj); pcontainer.setCurrentViewer(pcontainer.getDefaultViewerKey(), true); if (obj == null) errorView.setMessage(com.jaspersoft.studio.messages.Messages.ReportRunControler_22); } }); } private void showURL(final String url) { UIUtils.getDisplay().asyncExec(new Runnable() { @Override public void run() { APreview pv = pcontainer.getDefaultViewer(); if (pv instanceof IURLViewable) try { ((IURLViewable) pv).setURL(url); pcontainer.setCurrentViewer(pcontainer.getDefaultViewerKey(), true); } catch (Exception e) { e.printStackTrace(); } } }); } private void showURL(final ReportExecution re) { if (re.getReportOutputURL() != null) { UIUtils.getDisplay().asyncExec(new Runnable() { @Override public void run() { APreview pv = pcontainer.getDefaultViewer(); if (pv instanceof ABrowserViewer) try { String urlcookie = re.getBaseUrl(); String scookie = null; for (Cookie c : re.getReportOutputCookie()) { if (c.getName().equals("JSESSIONID")) { //$NON-NLS-1$ scookie = c.getName() + "=" + c.getValue(); //$NON-NLS-1$ break; } } ((ABrowserViewer) pv).setURL(re.getReportOutputURL(), urlcookie, scookie); pcontainer.setCurrentViewer(pcontainer.getDefaultViewerKey(), true); } catch (Exception e) { e.printStackTrace(); } } }); } } }; job.setPriority(Job.LONG); job.schedule(); }
From source file:MSUmpire.SearchResultParser.TPPResult.java
public void ReadSearchResultByRefIDUseRefProtID(LCMSID lcmsid, ArrayList<String> pepxmls, LCMSID RefID, boolean UseMappIon) throws ParserConfigurationException, IOException, SAXException, XmlPullParserException, ClassNotFoundException, InterruptedException { for (String pepxml : pepxmls) { LCMSID pepxmlid = new LCMSID(FilenameUtils.getFullPath(lcmsid.mzXMLFileName) + FilenameUtils.getBaseName(lcmsid.mzXMLFileName), DecoyTag, lcmsid.FastaPath); PepXMLParser pepxmlparser = new PepXMLParser(pepxmlid, pepxml, 0f); pepxmlid.FilterByPepDecoyFDR(DecoyTag, FDR); Logger.getRootLogger().info("peptide No.:" + pepxmlid.GetPepIonList().size() + "; Peptide level threshold: " + pepxmlid.PepProbThreshold); for (PepIonID pepID : pepxmlid.GetPepIonList().values()) { lcmsid.AddPeptideID(pepID);//from w w w . j ava 2s .co m } } lcmsid.GenerateProteinByRefIDByPepSeq(RefID, UseMappIon); lcmsid.LoadSequence(); lcmsid.ReMapProPep(); lcmsid.CreateInstanceForAllPepIon(); Logger.getRootLogger() .info("Protein No.:" + lcmsid.ProteinList.size() + "; Assigned Peptide No.:" + lcmsid.AssignedPepIonList.size() + "; All peptide No.:" + lcmsid.GetPepIonList().size() + "; Spectrum level threshold: " + lcmsid.SpecProbThreshold + "; Peptide level threshold: " + lcmsid.PepProbThreshold + "; Protein level threshold: " + lcmsid.ProteinProbThreshold); }
From source file:it.drwolf.ridire.session.async.Mapper.java
private StringWithEncoding createPlainTextResource(File f, CrawledResource cr, EntityManager entityManager) throws SAXException, TikaException, IOException, TransformerConfigurationException, InterruptedException {/*from www . ja v a 2s.c om*/ File resourceDir = new File(FilenameUtils.getFullPath(f.getCanonicalPath().replaceAll("__\\d+", "")) + JobMapperMonitor.RESOURCESDIR); String alchemyKey = entityManager.find(Parameter.class, Parameter.ALCHEMY_KEY.getKey()).getValue(); String readabilityKey = entityManager.find(Parameter.class, Parameter.READABILITY_KEY.getKey()).getValue(); String resourceFileName = cr.getDigest() + ".gz"; File resourceFile = new File(resourceDir, resourceFileName); StringWithEncoding rawContentAndEncoding = null; String contentType = cr.getContentType(); // long t1 = System.currentTimeMillis(); if (contentType != null && contentType.contains("application/msword")) { rawContentAndEncoding = this.transformDOC2HTML(resourceFile, entityManager); } if (contentType != null && contentType.contains("application/rtf")) { rawContentAndEncoding = this.transformRTF2HTML(resourceFile, entityManager); } if (contentType != null && contentType.contains("text/plain")) { // txt -> html -> txt is for txt cleaning rawContentAndEncoding = this.transformTXT2HTML(resourceFile, entityManager); } if (contentType != null && contentType.contains("pdf")) { rawContentAndEncoding = this.transformPDF2HTML(resourceFile, entityManager); } if (contentType != null && contentType.contains("html")) { rawContentAndEncoding = this.getGuessedEncodingAndSetRawContentFromGZFile(resourceFile); } // long t2 = System.currentTimeMillis(); // System.out.println("Transformation: " + (t2 - t1)); if (rawContentAndEncoding != null) { if (rawContentAndEncoding.getEncoding() == null) { rawContentAndEncoding = new StringWithEncoding(rawContentAndEncoding.getString(), "UTF8"); } // t1 = System.currentTimeMillis(); String cleanText = this.replaceUnsupportedChars(rawContentAndEncoding.getString()); rawContentAndEncoding = new StringWithEncoding(cleanText, rawContentAndEncoding.getEncoding()); File tmpFile = File.createTempFile("ridire", null); FileUtils.writeStringToFile(tmpFile, rawContentAndEncoding.getString(), "UTF-8"); String ridireCleanerJar = entityManager .find(CommandParameter.class, CommandParameter.RIDIRE_CLEANER_EXECUTABLE_KEY).getCommandValue(); String host = entityManager.find(Parameter.class, Parameter.READABILITY_HOSTAPP.getKey()).getValue(); CommandLine commandLine = CommandLine .parse("java -Xmx128m -Djava.io.tmpdir=" + this.tempDir + " -jar " + ridireCleanerJar); commandLine.addArgument("-f"); commandLine.addArgument(tmpFile.getPath()); commandLine.addArgument("-e"); commandLine.addArgument("UTF-8"); commandLine.addArgument("-h"); commandLine.addArgument(host); commandLine.addArgument("-k"); commandLine.addArgument(alchemyKey); commandLine.addArgument("-r"); commandLine.addArgument(readabilityKey); DefaultExecutor executor = new DefaultExecutor(); executor.setExitValue(0); ExecuteWatchdog watchdog = new ExecuteWatchdog(Mapper.READABILITY_TIMEOUT); executor.setWatchdog(watchdog); ByteArrayOutputStream baosStdOut = new ByteArrayOutputStream(1024); ByteArrayOutputStream baosStdErr = new ByteArrayOutputStream(1024); ExecuteStreamHandler executeStreamHandler = new PumpStreamHandler(baosStdOut, baosStdErr, null); executor.setStreamHandler(executeStreamHandler); int exitValue = executor.execute(commandLine); if (exitValue == 0) { rawContentAndEncoding = new StringWithEncoding(baosStdOut.toString(), "UTF-8"); // TODO filter real errors rawContentAndEncoding.setCleaner(baosStdErr.toString().trim()); } FileUtils.deleteQuietly(tmpFile); } return rawContentAndEncoding; }