List of usage examples for org.apache.commons.io FilenameUtils getBaseName
public static String getBaseName(String filename)
From source file:com.springsense.nutch.indexer.SpringSenseIndexingFilter.java
protected String preprocessUrlOrPath(String urlOrPath) { if (StringUtils.isBlank(urlOrPath)) { return null; }/*from www . jav a 2s .c o m*/ String path = null; URL url; try { url = new URL(urlOrPath); path = url.getPath(); } catch (MalformedURLException e) { // Assume we got a file path... We'll attempt to treat it so. path = urlOrPath; } String decodedUrlOrPath = null; try { decodedUrlOrPath = URLDecoder.decode(path, "UTF-8"); } catch (UnsupportedEncodingException e) { LOG.error(String.format("Couldn't decode URL or path: '%s' due to an error", urlOrPath), e); return null; } String fileBaseNameWithoutExtension = FilenameUtils .removeExtension(FilenameUtils.getBaseName(decodedUrlOrPath)); return splitCamelCase(fileBaseNameWithoutExtension); }
From source file:gov.nih.nci.caarray.plugins.illumina.SampleProbeProfileHandler.java
/** * {@inheritDoc}//w ww .j a v a 2s .c o m */ @Override public List<LSID> getReferencedArrayDesignCandidateIds() { final InfoHeadingParser p = new InfoHeadingParser(); processFile(getFile(), p); String fileName = p.getValues().get(InfoHeadingParser.KEY_ARRAY_CONTENT); if (fileName == null) { throw new IllegalStateException("Missing header field '" + InfoHeadingParser.KEY_ARRAY_CONTENT + "'"); } final List<LSID> lsids = new ArrayList<LSID>(); while (!StringUtils.isEmpty(FilenameUtils.getExtension(fileName))) { lsids.add(new LSID(IlluminaCsvDesignHandler.LSID_AUTHORITY, IlluminaCsvDesignHandler.LSID_NAMESPACE, fileName)); fileName = FilenameUtils.getBaseName(fileName); } lsids.add(new LSID(IlluminaCsvDesignHandler.LSID_AUTHORITY, IlluminaCsvDesignHandler.LSID_NAMESPACE, fileName)); return lsids; }
From source file:DIA_Umpire_Quant.DIA_Umpire_ProtQuant.java
/** * @param args the command line arguments *//*ww w . ja va 2s. c o m*/ public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println( "DIA-Umpire protein quantitation module (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_PortQuant.jar diaumpire_module.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_orotquant.log"); } catch (Exception e) { } Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version); Logger.getRootLogger().info("Parameter file:" + args[0]); BufferedReader reader = new BufferedReader(new FileReader(args[0])); String line = ""; String WorkFolder = ""; int NoCPUs = 2; String Combined_Prot = ""; boolean DefaultProtFiltering = true; float Freq = 0f; int TopNPep = 6; int TopNFrag = 6; String FilterWeight = "GW"; float MinWeight = 0.9f; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = new HashMap<>(); boolean ExportSaint = false; boolean SAINT_MS1 = false; boolean SAINT_MS2 = true; HashMap<String, String[]> BaitList = new HashMap<>(); HashMap<String, String> BaitName = new HashMap<>(); HashMap<String, String[]> ControlList = new HashMap<>(); HashMap<String, String> ControlName = new HashMap<>(); //<editor-fold defaultstate="collapsed" desc="Reading parameter file"> while ((line = reader.readLine()) != null) { line = line.trim(); Logger.getRootLogger().info(line); if (!"".equals(line) && !line.startsWith("#")) { //System.out.println(line); if (line.equals("==File list begin")) { do { line = reader.readLine(); line = line.trim(); if (line.equals("==File list end")) { continue; } else if (!"".equals(line)) { File newfile = new File(line); if (newfile.exists()) { AssignFiles.put(newfile.getAbsolutePath(), newfile); } else { Logger.getRootLogger().info("File: " + newfile + " does not exist."); } } } while (!line.equals("==File list end")); } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); String value = line.split("=")[1].trim(); switch (type) { case "Path": { WorkFolder = value; break; } case "path": { WorkFolder = value; break; } case "Thread": { NoCPUs = Integer.parseInt(value); break; } case "Fasta": { tandemPara.FastaPath = value; break; } case "Combined_Prot": { Combined_Prot = value; break; } case "DefaultProtFiltering": { DefaultProtFiltering = Boolean.parseBoolean(value); break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "ProteinFDR": { tandemPara.ProtFDR = Float.parseFloat(value); break; } case "FilterWeight": { FilterWeight = value; break; } case "MinWeight": { MinWeight = Float.parseFloat(value); break; } case "TopNFrag": { TopNFrag = Integer.parseInt(value); break; } case "TopNPep": { TopNPep = Integer.parseInt(value); break; } case "Freq": { Freq = Float.parseFloat(value); break; } //<editor-fold defaultstate="collapsed" desc="SaintOutput"> case "ExportSaintInput": { ExportSaint = Boolean.parseBoolean(value); break; } case "QuantitationType": { switch (value) { case "MS1": { SAINT_MS1 = true; SAINT_MS2 = false; break; } case "MS2": { SAINT_MS1 = false; SAINT_MS2 = true; break; } case "BOTH": { SAINT_MS1 = true; SAINT_MS2 = true; break; } } break; } // case "BaitInputFile": { // SaintBaitFile = value; // break; // } // case "PreyInputFile": { // SaintPreyFile = value; // break; // } // case "InterationInputFile": { // SaintInteractionFile = value; // break; // } default: { if (type.startsWith("BaitName_")) { BaitName.put(type.substring(9), value); } if (type.startsWith("BaitFile_")) { BaitList.put(type.substring(9), value.split("\t")); } if (type.startsWith("ControlName_")) { ControlName.put(type.substring(12), value); } if (type.startsWith("ControlFile_")) { ControlList.put(type.substring(12), value.split("\t")); } break; } //</editor-fold> } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); //Check if the fasta file can be found if (!new File(tandemPara.FastaPath).exists()) { Logger.getRootLogger().info("Fasta file :" + tandemPara.FastaPath + " cannot be found, the process will be terminated, please check."); System.exit(1); } //Check if the prot.xml file can be found if (!new File(Combined_Prot).exists()) { Logger.getRootLogger().info("ProtXML file: " + Combined_Prot + " cannot be found, the export protein summary table will be empty."); } LCMSID protID = null; //Parse prot.xml and generate protein master list given an FDR if (Combined_Prot != null && !Combined_Prot.equals("")) { protID = LCMSID.ReadLCMSIDSerialization(Combined_Prot); if (!"".equals(Combined_Prot) && protID == null) { protID = new LCMSID(Combined_Prot, tandemPara.DecoyPrefix, tandemPara.FastaPath); ProtXMLParser protxmlparser = new ProtXMLParser(protID, Combined_Prot, 0f); //Use DIA-Umpire default protein FDR calculation if (DefaultProtFiltering) { protID.RemoveLowLocalPWProtein(0.8f); protID.RemoveLowMaxIniProbProtein(0.9f); protID.FilterByProteinDecoyFDRUsingMaxIniProb(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } //Get protein FDR calculation without other filtering else { protID.FilterByProteinDecoyFDRUsingLocalPW(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } protID.LoadSequence(); protID.WriteLCMSIDSerialization(Combined_Prot); } Logger.getRootLogger().info("Protein No.:" + protID.ProteinList.size()); } HashMap<String, HashMap<String, FragmentPeak>> IDSummaryFragments = new HashMap<>(); //Generate DIA file list ArrayList<DIAPack> FileList = new ArrayList<>(); try { File folder = new File(WorkFolder); if (!folder.exists()) { Logger.getRootLogger().info("The path : " + WorkFolder + " cannot be found."); System.exit(1); } for (final File fileEntry : folder.listFiles()) { if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry.getAbsolutePath(), fileEntry); } if (fileEntry.isDirectory()) { for (final File fileEntry2 : fileEntry.listFiles()) { if (fileEntry2.isFile() && (fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry2.getAbsolutePath(), fileEntry2); } } } } Logger.getRootLogger().info("No. of files assigned :" + AssignFiles.size()); for (File fileEntry : AssignFiles.values()) { Logger.getRootLogger().info(fileEntry.getAbsolutePath()); } for (File fileEntry : AssignFiles.values()) { String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); Logger.getRootLogger().info( "================================================================================================="); Logger.getRootLogger().info("Processing " + mzXMLFile); if (!DiaFile.LoadDIASetting()) { Logger.getRootLogger().info("Loading DIA setting failed, job is incomplete"); System.exit(1); } if (!DiaFile.LoadParams()) { Logger.getRootLogger().info("Loading parameters failed, job is incomplete"); System.exit(1); } Logger.getRootLogger().info("Loading identification results " + mzXMLFile + "...."); //If the serialization file for ID file existed if (DiaFile.ReadSerializedLCMSID()) { DiaFile.IDsummary.ReduceMemoryUsage(); DiaFile.IDsummary.ClearAssignPeakCluster(); FileList.add(DiaFile); HashMap<String, FragmentPeak> FragMap = new HashMap<>(); IDSummaryFragments.put(FilenameUtils.getBaseName(mzXMLFile), FragMap); } } } //<editor-fold defaultstate="collapsed" desc="Peptide and fragment selection"> Logger.getRootLogger().info("Peptide and fragment selection across the whole dataset"); ArrayList<LCMSID> SummaryList = new ArrayList<>(); for (DIAPack diafile : FileList) { if (protID != null) { //Generate protein list according to mapping of peptide ions for each DIA file to the master protein list diafile.IDsummary.GenerateProteinByRefIDByPepSeq(protID, true); diafile.IDsummary.ReMapProPep(); } if ("GW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByGroupWeight(); } else if ("PepW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByWeight(); } SummaryList.add(diafile.IDsummary); } FragmentSelection fragselection = new FragmentSelection(SummaryList); fragselection.freqPercent = Freq; fragselection.GeneratePepFragScoreMap(); fragselection.GenerateTopFragMap(TopNFrag); fragselection.GenerateProtPepScoreMap(MinWeight); fragselection.GenerateTopPepMap(TopNPep); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Writing general reports"> ExportTable export = new ExportTable(WorkFolder, SummaryList, IDSummaryFragments, protID, fragselection); export.Export(TopNPep, TopNFrag, Freq); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="//<editor-fold defaultstate="collapsed" desc="Generate SAINT input files"> if (ExportSaint && protID != null) { HashMap<String, DIAPack> Filemap = new HashMap<>(); for (DIAPack DIAfile : FileList) { Filemap.put(DIAfile.GetBaseName(), DIAfile); } FileWriter baitfile = new FileWriter(WorkFolder + "SAINT_Bait_" + DateTimeTag.GetTag() + ".txt"); FileWriter preyfile = new FileWriter(WorkFolder + "SAINT_Prey_" + DateTimeTag.GetTag() + ".txt"); FileWriter interactionfileMS1 = null; FileWriter interactionfileMS2 = null; if (SAINT_MS1) { interactionfileMS1 = new FileWriter( WorkFolder + "SAINT_Interaction_MS1_" + DateTimeTag.GetTag() + ".txt"); } if (SAINT_MS2) { interactionfileMS2 = new FileWriter( WorkFolder + "SAINT_Interaction_MS2_" + DateTimeTag.GetTag() + ".txt"); } HashMap<String, String> PreyID = new HashMap<>(); for (String samplekey : ControlName.keySet()) { String name = ControlName.get(samplekey); for (String file : ControlList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "C\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } for (String samplekey : BaitName.keySet()) { String name = BaitName.get(samplekey); for (String file : BaitList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "T\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } baitfile.close(); if (SAINT_MS1) { interactionfileMS1.close(); } if (SAINT_MS2) { interactionfileMS2.close(); } for (String AccNo : PreyID.keySet()) { preyfile.write(AccNo + "\t" + PreyID.get(AccNo) + "\n"); } preyfile.close(); } //</editor-fold> Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:de.uzk.hki.da.grid.FakeGridFacade.java
/** * Scans AIP for marker file to mark this file as corrupted for sing in * acceptance testing on DEV machines/*from w w w . ja v a 2 s .c o m*/ * @author Jens Peters * @param custodyFile * @return */ private boolean checkForCorruptedMarker(File custodyFile) { try { FileUtils.copyFileToDirectory(custodyFile, new File(tmpFolder), false); String packname = custodyFile.getName(); String dirname = FilenameUtils.getBaseName(custodyFile.getName()); ArchiveBuilderFactory.getArchiveBuilderForFile(new File("/tmp/" + packname)) .unarchiveFolder(new File(tmpFolder + packname), new File("/tmp/")); logger.debug("Extracting " + packname + " to + " + tmpFolder + dirname); IOFileFilter filter = new WildcardFileFilter("DESTROYED*"); Collection<File> files = FileUtils.listFiles(new File(tmpFolder + dirname), filter, DirectoryFileFilter.DIRECTORY); if (files.size() > 0) { logger.debug("found destroy marker"); FolderUtils.deleteDirectorySafe(new File(tmpFolder + dirname)); return true; } else FolderUtils.deleteDirectorySafe(new File(tmpFolder + dirname)); } catch (Exception e) { logger.error("Error while checking validity on fakedGridfacade on " + custodyFile.getAbsolutePath() + ": " + e.getMessage()); } logger.debug("found no destroy marker!"); return false; }
From source file:com.haulmont.cuba.gui.theme.ThemeConstantsRepository.java
public String parseThemeName(String fileName) { String name = FilenameUtils.getBaseName(fileName); if (name.endsWith("-theme")) { int dashIndex = name.lastIndexOf("-theme"); return name.substring(0, dashIndex); } else {/*from ww w . ja v a 2 s .c o m*/ return name; } }
From source file:io.stallion.contentPublishing.UploadRequestProcessor.java
protected File downloadExternalToLocalFile(U uploaded) { URI uri = URI.create(urlToFetch); String fullFileName = FilenameUtils.getName(uri.getPath()); String extension = FilenameUtils.getExtension(fullFileName); String fileName = truncate(fullFileName, 85); String relativePath = GeneralUtils.slugify(truncate(FilenameUtils.getBaseName(fullFileName), 75)) + "-" + DateUtils.mils() + "." + extension; relativePath = "stallion-file-" + uploaded.getId() + "/" + GeneralUtils.secureRandomToken(8) + "/" + relativePath;/*from w w w . jav a 2 s . c o m*/ String destPath = uploadsFolder + relativePath; try { FileUtils.forceMkdir(new File(destPath).getParentFile()); } catch (IOException e) { throw new RuntimeException(e); } uploaded.setCloudKey(relativePath).setExtension(extension).setName(fileName) .setOwnerId(Context.getUser().getId()).setUploadedAt(DateUtils.utcNow()) .setType(fileController.getTypeForExtension(extension)); // Make raw URL String url = makeRawUrlForFile(uploaded, "org"); uploaded.setRawUrl(url); fileController.save(uploaded); File outFile = new File(destPath); try { IOUtils.copy(Unirest.get(urlToFetch).asBinary().getRawBody(), org.apache.commons.io.FileUtils.openOutputStream(outFile)); } catch (UnirestException e) { throw new ClientException("Error downloading file from " + url + ": " + e.getMessage(), 400, e); } catch (IOException e) { throw new RuntimeException(e); } return outFile; }
From source file:ee.ria.DigiDoc.activity.OpenExternalFileActivity.java
public ContainerFacade createContainer(Uri uri) { String fileName = FileUtils.resolveFileName(uri, getContentResolver()); if (OpenExternalFileActivity.containerExt.contains(FilenameUtils.getExtension(fileName))) { try {//w ww . j av a 2s . c o m return ContainerBuilder.aContainer(this).fromExternalContainer(uri).build(); } catch (ContainerBuilder.ExternalContainerSaveException e) { Timber.e(e, "Failed to create container"); return null; } } else { return ContainerBuilder.aContainer(this).withDataFile(uri) .withContainerName(FilenameUtils.getBaseName(fileName) + "." + getContainerFormat()).build(); } }
From source file:de.xirp.profile.ProfileGenerator.java
/** * Generates a BOT file with the given path from the given * {@link de.xirp.profile.CommunicationSpecification comm-spec} * bean./*from w w w . j av a2s.c o m*/ * * @param commSpec * The comm-spec to generate the XML for. * @param cmsFile * The file to write the result to. Must be the full path. * * @throws JAXBException if the given comm-spec was null, or something * went wrong generating the xml. * @throws FileNotFoundException if something went wrong generating the xml. */ public static void generateCMS(CommunicationSpecification commSpec, File cmsFile) throws JAXBException, FileNotFoundException { if (commSpec == null) { throw new JAXBException(I18n.getString("ProfileGenerator.exception.comSpecNull")); //$NON-NLS-1$ } String fileName = FilenameUtils.getBaseName(cmsFile.getName()); JAXBContext jc = JAXBContext.newInstance(CommunicationSpecification.class); Marshaller m = jc.createMarshaller(); m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE); m.marshal(commSpec, new FileOutputStream( Constants.CONF_COMMSPECS_DIR + File.separator + fileName + Constants.COMM_SPEC_POSTFIX)); }
From source file:net.mitnet.tools.pdf.book.pdf.builder.ui.cli.PdfBookBuilderCLI.java
public PdfBookBuilderConfig parseConfig(String[] args) throws Exception { PdfBookBuilderConfig config = new PdfBookBuilderConfig(); CommandLineParser commandLineParser = new PosixParser(); CommandLine commandLine = commandLineParser.parse(CLI_OPTIONS, args); CommandLineHelper commandLineHelper = new CommandLineHelper(commandLine); if (!commandLineHelper.hasOption(CliOptions.OPTION_INPUT_DIR)) { System.err.println("Must specify " + CliOptions.OPTION_INPUT_DIR.getDescription()); showHelp();//w ww .j a v a 2 s.c om } File inputDir = commandLineHelper.getOptionValueAsFile(CliOptions.OPTION_INPUT_DIR); config.setInputDir(inputDir); if (!commandLineHelper.hasOption(CliOptions.OPTION_OUTPUT_BOOK_FILE)) { System.err.println("Must specify " + CliOptions.OPTION_OUTPUT_BOOK_FILE.getDescription()); showHelp(); } File outputBookFile = commandLineHelper.getOptionValueAsFile(CliOptions.OPTION_OUTPUT_BOOK_FILE); config.setOutputBookFile(outputBookFile); Rectangle pageSize = ConfigHelper.parsePageSize(commandLineHelper); config.setPageSize(pageSize); boolean debug = false; if (commandLineHelper.hasOption(CliOptions.OPTION_DEBUG)) { debug = true; } config.setDebugEnabled(debug); boolean verbose = false; if (commandLineHelper.hasOption(CliOptions.OPTION_VERBOSE)) { verbose = true; } config.setVerboseEnabled(verbose); String metaTitle = FilenameUtils.getBaseName(outputBookFile.getName()); if (metaTitle != null) { metaTitle = metaTitle.toUpperCase(); } if (commandLineHelper.hasOption(CliOptions.OPTION_META_TITLE)) { metaTitle = commandLineHelper.getOptionValue(CliOptions.OPTION_META_TITLE); } config.setMetaTitle(metaTitle); String metaAuthor = System.getProperty("user.name"); if (commandLineHelper.hasOption(CliOptions.OPTION_META_AUTHOR)) { metaAuthor = commandLineHelper.getOptionValue(CliOptions.OPTION_META_AUTHOR); } config.setMetaAuthor(metaAuthor); int nup = CliDefaultValues.DEFAULT_NUP; if (commandLineHelper.hasOption(CliOptions.OPTION_NUP)) { nup = commandLineHelper.getOptionValueAsInt(CliOptions.OPTION_NUP); } config.setNup(nup); PdfPageEvent pdfPageEventListener = new PdfPageEventLogger(); config.setPdfPageEventListener(pdfPageEventListener); config.setBuildTocEnabled(true); TocBuilder tocBuilder = new TocBuilder(); // config.setTocBuilder(tocBuilder); config.setTocRowChangeListener(tocBuilder); return config; }
From source file:eu.udig.catalog.jgrass.workspacecreation.NewJGrassLocationFromFileWizard.java
@Override public boolean performFinish() { try {/*from ww w .j a va 2 s .c o m*/ String importFilePath = props.importFilePath; File mapFile = new File(importFilePath); CoordinateReferenceSystem fileCrs = null; GridCoverage2D geodata = null; if (mapFile.getName().endsWith(".asc")) { ArcGridReader arcGridReader = new ArcGridReader(mapFile); geodata = arcGridReader.read(null); geodata = geodata.view(ViewType.GEOPHYSICS); geodata = JGrassCatalogUtilities.removeNovalues(geodata); fileCrs = arcGridReader.getCrs(); } else if (mapFile.getName().endsWith(".tif") || mapFile.getName().endsWith(".tiff")) { GeoTiffReader geotiffGridReader = new GeoTiffReader(mapFile); geodata = geotiffGridReader.read(null); geodata = geodata.view(ViewType.GEOPHYSICS); geodata = JGrassCatalogUtilities.removeNovalues(geodata); fileCrs = geotiffGridReader.getCrs(); } HashMap<String, Double> regionParams = JGrassCatalogUtilities.getRegionParamsFromGridCoverage(geodata); double n = regionParams.get(JGrassCatalogUtilities.NORTH); double s = regionParams.get(JGrassCatalogUtilities.SOUTH); double e = regionParams.get(JGrassCatalogUtilities.EAST); double w = regionParams.get(JGrassCatalogUtilities.WEST); double xres = regionParams.get(JGrassCatalogUtilities.XRES); double yres = regionParams.get(JGrassCatalogUtilities.YRES); // create the location and mapset JGrassRegion window = new JGrassRegion(w, e, s, n, xres, yres); File baseFolderFile = new File(props.basePath); File locationFile = new File(baseFolderFile, props.locationName); File mapsetFile = new File(locationFile, props.mapsetName); String locationPath = locationFile.getAbsolutePath(); JGrassCatalogUtilities.createLocation(locationPath, fileCrs, window); JGrassCatalogUtilities.createMapset(locationPath, mapsetFile.getName(), null, null); JGrassRegion.writeWINDToMapset(mapsetFile.getAbsolutePath(), window); // write the map into it String mapName = mapFile.getName(); mapName = FilenameUtils.getBaseName(mapName); JGrassMapEnvironment mapEnvironment = new JGrassMapEnvironment(mapsetFile, mapName); GrassCoverageFormat format = new GrassCoverageFormatFactory().createFormat(); GrassCoverageWriter writer = format.getWriter(mapEnvironment.getCELL(), null); GeneralParameterValue[] readParams = null; writer.write(geodata, readParams); JGrassCatalogUtilities.addServiceToCatalog( locationPath + File.separator + JGrassCatalogUtilities.JGRASS_WORKSPACE_FILENAME, new NullProgressMonitor()); } catch (IOException e) { JGrassPlugin.log( "JGrassPlugin problem: eu.hydrologis.udig.catalog.workspacecreation.wizard#NewJGrassLocationWizard#performFinish", //$NON-NLS-1$ e); e.printStackTrace(); } return true; }