Example usage for org.apache.commons.io FilenameUtils getPath

List of usage examples for org.apache.commons.io FilenameUtils getPath

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Introduction

In this page you can find the example usage for org.apache.commons.io FilenameUtils getPath.

Prototype

public static String getPath(String filename)

Source Link

Document

Gets the path from a full filename, which excludes the prefix.

Usage

From source file:org.bdval.MakeSyntheticDataset.java

private void outputTasks(final String outputFilenamePrefix, final int numSamples,
        final IntSet positiveSampleIndices, final String outputFilename) throws IOException {
    final String tasksFilename = FilenameUtils.concat(outputDirectory,
            FilenameUtils.concat("tasks", outputFilename));
    FileUtils.forceMkdir(new File(FilenameUtils.getPath(tasksFilename)));

    PrintWriter tasksWriter = null;
    try {//  w  ww .j  av  a 2s.  c om
        tasksWriter = new PrintWriter(tasksFilename);

        tasksWriter.println(String.format("%s\tnegative\tpositive\t%d\t%d", outputFilenamePrefix,
                numSamples - positiveSampleIndices.size(), positiveSampleIndices.size()));
    } finally {
        IOUtils.closeQuietly(tasksWriter);
    }
}

From source file:org.bdval.MakeSyntheticDataset.java

private void outputCids(final IntSet positiveSampleIndices, final String outputFilenamePrefix,
        final IntList sampleIndices) throws IOException {
    final String cidsFilename = FilenameUtils.concat(outputDirectory,
            FilenameUtils.concat("cids", outputFilenamePrefix + ".cids"));
    FileUtils.forceMkdir(new File(FilenameUtils.getPath(cidsFilename)));
    PrintWriter cidsWriter = null;
    try {/*from  w  w  w  .  j  av a  2 s.  com*/
        cidsWriter = new PrintWriter(cidsFilename);

        for (final int sampleIndex : sampleIndices) {
            cidsWriter.print(positiveSampleIndices.contains(sampleIndex) ? "positive" : "negative");
            cidsWriter.print("\t");
            cidsWriter.print(sampleId(sampleIndex, positiveSampleIndices));
            cidsWriter.println();
        }
    } finally {
        IOUtils.closeQuietly(cidsWriter);
    }
}

From source file:org.codice.ddf.spatial.admin.module.service.Geocoding.java

@Override
public boolean updateGeoIndexWithUrl(String url, String createIndex) {
    progress = 0;/* w  w w  .  j av  a  2 s .com*/
    String countryCode = FilenameUtils.getBaseName(url);
    url = FilenameUtils.getPath(url);
    LOGGER.debug("Downloading : {}{}.zip", url, countryCode);
    LOGGER.debug("Create Index : {}", createIndex);

    geoEntryExtractor.setUrl(url);
    return updateIndex(countryCode, createIndex.equals("true"));

}

From source file:org.commonwl.view.researchobject.ROBundleFactory.java

/**
 * Creates a new Workflow Research Object Bundle from Git details
 * and saves it to a file/*  ww  w.jav  a 2 s.  com*/
 * @param workflow The workflow to generate a RO bundle for
 * @throws IOException Any API errors which may have occurred
 */
@Async
public void createWorkflowRO(Workflow workflow) throws IOException, InterruptedException {
    logger.info("Creating Research Object Bundle");

    // Get the whole containing folder, not just the workflow itself
    GitDetails githubInfo = workflow.getRetrievedFrom();
    GitDetails roDetails = new GitDetails(githubInfo.getRepoUrl(), githubInfo.getBranch(),
            FilenameUtils.getPath(githubInfo.getPath()));

    // Create a new Research Object Bundle
    Bundle bundle = roBundleService.createBundle(workflow, roDetails);

    // Save the bundle to the storage location in properties
    Path bundleLocation = roBundleService.saveToFile(bundle);

    // Add RO Bundle to associated workflow model
    workflow.setRoBundlePath(bundleLocation.toString());
    workflowRepository.save(workflow);
    logger.info("Finished saving Research Object Bundle");
}

From source file:org.commonwl.view.researchobject.ROBundleService.java

/**
 * Creates a new research object bundle for a workflow from a Git repository
 * @param workflow The workflow to create the research object for
 * @return The constructed bundle/*w w w . j  a v  a2  s  .c  om*/
 */
public Bundle createBundle(Workflow workflow, GitDetails gitInfo) throws IOException {

    // Create a new RO bundle
    Bundle bundle = Bundles.createBundle();
    Manifest manifest = bundle.getManifest();

    // Simplified attribution for RO bundle
    try {
        manifest.setId(new URI(workflow.getPermalink()));

        // Tool attribution in createdBy
        manifest.setCreatedBy(appAgent);

        // Retrieval Info
        // TODO: Make this importedBy/On/From
        manifest.setRetrievedBy(appAgent);
        manifest.setRetrievedOn(manifest.getCreatedOn());
        manifest.setRetrievedFrom(new URI(workflow.getPermalink(Format.ro)));

        // Make a directory in the RO bundle to store the files
        Path bundleRoot = bundle.getRoot();
        Path bundlePath = bundleRoot.resolve("workflow");
        Files.createDirectory(bundlePath);

        // Add the files from the repo to this workflow
        Set<HashableAgent> authors = new HashSet<>();

        boolean safeToAccess = gitSemaphore.acquire(gitInfo.getRepoUrl());
        try {
            Git gitRepo = gitService.getRepository(workflow.getRetrievedFrom(), safeToAccess);
            Path relativePath = Paths.get(FilenameUtils.getPath(gitInfo.getPath()));
            Path gitPath = gitRepo.getRepository().getWorkTree().toPath().resolve(relativePath);
            addFilesToBundle(gitInfo, bundle, bundlePath, gitRepo, gitPath, authors, workflow);
        } finally {
            gitSemaphore.release(gitInfo.getRepoUrl());
        }

        // Add combined authors
        manifest.setAuthoredBy(new ArrayList<>(authors));

        // Add visualisation images
        File png = graphVizService.getGraph(workflow.getID() + ".png", workflow.getVisualisationDot(), "png");
        Files.copy(png.toPath(), bundleRoot.resolve("visualisation.png"));
        PathMetadata pngAggr = bundle.getManifest().getAggregation(bundleRoot.resolve("visualisation.png"));
        pngAggr.setRetrievedFrom(new URI(workflow.getPermalink(Format.png)));

        File svg = graphVizService.getGraph(workflow.getID() + ".svg", workflow.getVisualisationDot(), "svg");
        Files.copy(svg.toPath(), bundleRoot.resolve("visualisation.svg"));
        PathMetadata svgAggr = bundle.getManifest().getAggregation(bundleRoot.resolve("visualisation.svg"));
        svgAggr.setRetrievedFrom(new URI(workflow.getPermalink(Format.svg)));

        // Add annotation files
        GitDetails wfDetails = workflow.getRetrievedFrom();

        // Get URL to run cwltool
        String rawUrl = wfDetails.getRawUrl();
        String packedWorkflowID = wfDetails.getPackedId();
        if (packedWorkflowID != null) {
            if (packedWorkflowID.charAt(0) != '#') {
                rawUrl += "#";
            }
            rawUrl += packedWorkflowID;
        }

        // Run cwltool for annotations
        List<PathAnnotation> manifestAnnotations = new ArrayList<>();
        try {
            addAggregation(bundle, manifestAnnotations, "merged.cwl", cwlTool.getPackedVersion(rawUrl));
        } catch (CWLValidationException ex) {
            logger.error("Could not pack workflow when creating Research Object", ex.getMessage());
        }
        String rdfUrl = workflow.getIdentifier();
        if (rdfService.graphExists(rdfUrl)) {
            addAggregation(bundle, manifestAnnotations, "workflow.ttl",
                    new String(rdfService.getModel(rdfUrl, "TURTLE")));
        }
        bundle.getManifest().setAnnotations(manifestAnnotations);

        // Git2prov history
        List<Path> history = new ArrayList<>();
        // FIXME: Below is a a hack to pretend the URI is a Path
        String git2prov = "http://git2prov.org/git2prov?giturl=" + gitInfo.getRepoUrl()
                + "&serialization=PROV-JSON";
        Path git2ProvPath = bundle.getRoot().relativize(bundle.getRoot().resolve(git2prov));
        history.add(git2ProvPath);
        bundle.getManifest().setHistory(history);

    } catch (URISyntaxException ex) {
        logger.error("Error creating URI for RO Bundle", ex);
    } catch (GitAPIException ex) {
        logger.error("Error getting repository to create RO Bundle", ex);
    }

    // Return the completed bundle
    return bundle;

}

From source file:org.cryptomator.webdav.jackrabbit.AbstractEncryptedNode.java

@Override
public DavResource getCollection() {
    if (locator.isRootLocation()) {
        return null;
    }//  w ww . ja va2 s. c o m

    final String parentResource = FilenameUtils.getPath(locator.getResourcePath());
    final DavResourceLocator parentLocator = locator.getFactory().createResourceLocator(locator.getPrefix(),
            locator.getWorkspacePath(), parentResource);
    try {
        return getFactory().createResource(parentLocator, session);
    } catch (DavException e) {
        throw new IllegalStateException(
                "Unable to get parent resource with path " + parentLocator.getResourcePath(), e);
    }
}

From source file:org.csc.phynixx.common.TmpDirectory.java

public File assertExitsFile(String filename) throws IOException {
    File parentDir = this.assertExitsDirectory(FilenameUtils.getPath(filename));

    String name = FilenameUtils.getName(filename);
    String fullname = FilenameUtils.normalize(parentDir.getAbsolutePath() + File.separator + name);
    File file = new File(fullname);
    if (!file.createNewFile()) {
        file.delete();/*  w w w .  j a  v a2s .c  o m*/
        file.createNewFile();
    }

    return file;

}

From source file:org.dita.dost.module.BranchFilterModule.java

private void processAttributes(final Element elem, final Branch filter) {
    if (filter.resourcePrefix.isPresent() || filter.resourceSuffix.isPresent()) {
        final String href = elem.getAttribute(ATTRIBUTE_NAME_HREF);
        final String copyTo = elem.getAttribute(ATTRIBUTE_NAME_COPY_TO);
        final String scope = elem.getAttribute(ATTRIBUTE_NAME_SCOPE);
        if ((!href.isEmpty() || !copyTo.isEmpty()) && !scope.equals(ATTR_SCOPE_VALUE_EXTERNAL)) {
            final FileInfo hrefFileInfo = job.getFileInfo(currentFile.resolve(href));
            final FileInfo copyToFileInfo = !copyTo.isEmpty() ? job.getFileInfo(currentFile.resolve(copyTo))
                    : null;/*w w w .  j a  v a  2s.c o m*/
            final URI dstSource;
            dstSource = generateCopyTo((copyToFileInfo != null ? copyToFileInfo : hrefFileInfo).result, filter);
            final URI dstTemp = tempFileNameScheme.generateTempFileName(dstSource);
            final String dstPathFromMap = !copyTo.isEmpty() ? FilenameUtils.getPath(copyTo)
                    : FilenameUtils.getPath(href);
            final FileInfo.Builder dstBuilder = new FileInfo.Builder(hrefFileInfo).result(dstSource)
                    .uri(dstTemp);
            if (dstBuilder.build().format == null) {
                dstBuilder.format(ATTR_FORMAT_VALUE_DITA);
            }
            if (hrefFileInfo.src == null && href != null) {
                if (copyToFileInfo != null) {
                    dstBuilder.src(copyToFileInfo.src);
                }
            }
            final FileInfo dstFileInfo = dstBuilder.build();

            elem.setAttribute(BRANCH_COPY_TO, dstPathFromMap + FilenameUtils.getName(dstTemp.toString()));
            if (!copyTo.isEmpty()) {
                elem.removeAttribute(ATTRIBUTE_NAME_COPY_TO);
            }

            job.add(dstFileInfo);
        }
    }

    if (filter.keyscopePrefix.isPresent() || filter.keyscopeSuffix.isPresent()) {
        final StringBuilder buf = new StringBuilder();
        final String keyscope = elem.getAttribute(ATTRIBUTE_NAME_KEYSCOPE);
        if (!keyscope.isEmpty()) {
            for (final String key : keyscope.trim().split("\\s+")) {
                filter.keyscopePrefix.ifPresent(buf::append);
                buf.append(key);
                filter.keyscopeSuffix.ifPresent(buf::append);
                buf.append(' ');
            }
        } else {
            filter.keyscopePrefix.ifPresent(buf::append);
            filter.keyscopeSuffix.ifPresent(buf::append);
        }
        elem.setAttribute(ATTRIBUTE_NAME_KEYSCOPE, buf.toString().trim());
    }
}

From source file:org.eclipse.smarthome.core.transform.AbstractFileTransformationService.java

/**
 * Returns the name of the localized transformation file
 * if it actually exists, keeps the original in the other case
 *
 * @param filename name of the requested transformation file
 * @return original or localized transformation file to use
 */// ww w  .j  ava  2s.  co  m
protected String getLocalizedProposedFilename(String filename) {
    String extension = FilenameUtils.getExtension(filename);
    String prefix = FilenameUtils.getPath(filename);
    String result = filename;

    if (!prefix.isEmpty()) {
        watchSubDirectory(prefix);
    }

    // the filename may already contain locale information
    if (!filename.matches(".*_[a-z]{2}." + extension + "$")) {
        String basename = FilenameUtils.getBaseName(filename);
        String alternateName = prefix + basename + "_" + getLocale().getLanguage() + "." + extension;
        String alternatePath = getSourcePath() + alternateName;

        File f = new File(alternatePath);
        if (f.exists()) {
            result = alternateName;
        }
    }

    result = getSourcePath() + result;
    return result;
}

From source file:org.entando.entando.plugins.jpcomponentinstaller.aps.system.services.installer.DefaultComponentUninstaller.java

@Override
public boolean uninstallComponent(Component component) throws ApsSystemException {
    ServletContext servletContext = ((ConfigurableWebApplicationContext) _applicationContext)
            .getServletContext();//from  ww  w. ja  v  a2s .  co  m
    ClassLoader cl = (ClassLoader) servletContext.getAttribute("componentInstallerClassLoader");
    List<ClassPathXmlApplicationContext> ctxList = (List<ClassPathXmlApplicationContext>) servletContext
            .getAttribute("pluginsContextsList");
    ClassPathXmlApplicationContext appCtx = null;
    if (ctxList != null) {
        for (ClassPathXmlApplicationContext ctx : ctxList) {
            if (component.getCode().equals(ctx.getDisplayName())) {
                appCtx = ctx;
            }
        }
    }
    String appRootPath = servletContext.getRealPath("/");
    String backupDirPath = appRootPath + "componentinstaller" + File.separator + component.getArtifactId()
            + "-backup";
    Map<File, File> resourcesMap = new HashMap<File, File>();
    try {
        ClassLoader currentClassLoader = Thread.currentThread().getContextClassLoader();
        try {
            if (cl != null) {
                Thread.currentThread().setContextClassLoader(cl);
            }
            if (null == component || null == component.getUninstallerInfo()) {
                return false;
            }
            this.getDatabaseManager().createBackup();//backup database
            SystemInstallationReport report = super.extractReport();
            ComponentUninstallerInfo ui = component.getUninstallerInfo();
            //remove records from db
            String[] dataSourceNames = this.extractBeanNames(DataSource.class);
            for (int j = 0; j < dataSourceNames.length; j++) {
                String dataSourceName = dataSourceNames[j];
                Resource resource = (null != ui) ? ui.getSqlResources(dataSourceName) : null;
                String script = (null != resource) ? this.readFile(resource) : null;
                if (null != script && script.trim().length() > 0) {
                    DataSource dataSource = (DataSource) this.getBeanFactory().getBean(dataSourceName);
                    String[] queries = QueryExtractor.extractDeleteQueries(script);
                    TableDataUtils.executeQueries(dataSource, queries, true);
                }
            }
            this.executePostProcesses(ui.getPostProcesses());

            //drop tables
            Map<String, List<String>> tableMapping = component.getTableMapping();
            if (tableMapping != null) {
                for (int j = 0; j < dataSourceNames.length; j++) {
                    String dataSourceName = dataSourceNames[j];
                    List<String> tableClasses = tableMapping.get(dataSourceName);
                    if (null != tableClasses && tableClasses.size() > 0) {
                        List<String> newList = new ArrayList<String>();
                        newList.addAll(tableClasses);
                        Collections.reverse(newList);
                        DataSource dataSource = (DataSource) this.getBeanFactory().getBean(dataSourceName);
                        IDatabaseManager.DatabaseType type = this.getDatabaseManager()
                                .getDatabaseType(dataSource);
                        TableFactory tableFactory = new TableFactory(dataSourceName, dataSource, type);
                        tableFactory.dropTables(newList);
                    }
                }
            }

            //move resources (jar, files and folders) on temp folder  
            List<String> resourcesPaths = ui.getResourcesPaths();
            if (resourcesPaths != null) {
                for (String resourcePath : resourcesPaths) {
                    try {
                        String fullResourcePath = servletContext.getRealPath(resourcePath);
                        File resFile = new File(fullResourcePath);
                        String relResPath = FilenameUtils.getPath(resFile.getAbsolutePath());
                        File newResFile = new File(
                                backupDirPath + File.separator + relResPath + resFile.getName());
                        if (resFile.isDirectory()) {
                            FileUtils.copyDirectory(resFile, newResFile);
                            resourcesMap.put(resFile, newResFile);
                            FileUtils.deleteDirectory(resFile);
                        } else {
                            FileUtils.copyFile(resFile, newResFile);
                            resourcesMap.put(resFile, newResFile);
                            FileUtils.forceDelete(resFile);
                        }
                    } catch (Exception e) {
                    }
                }
            }

            //upgrade report
            ComponentInstallationReport cir = report.getComponentReport(component.getCode(), true);
            cir.getDataSourceReport().upgradeDatabaseStatus(SystemInstallationReport.Status.UNINSTALLED);
            cir.getDataReport().upgradeDatabaseStatus(SystemInstallationReport.Status.UNINSTALLED);
            this.saveReport(report);

            //remove plugin's xmlapplicationcontext if present
            if (appCtx != null) {
                appCtx.close();
                ctxList.remove(appCtx);
            }
            InitializerManager initializerManager = (InitializerManager) _applicationContext
                    .getBean("InitializerManager");
            initializerManager.reloadCurrentReport();
            ComponentManager componentManager = (ComponentManager) _applicationContext
                    .getBean("ComponentManager");
            componentManager.refresh();
        } catch (Exception e) {
            _logger.error("Unexpected error in component uninstallation process", e);
            throw new ApsSystemException("Unexpected error in component uninstallation process.", e);
        } finally {
            Thread.currentThread().setContextClassLoader(currentClassLoader);
            ApsWebApplicationUtils.executeSystemRefresh(servletContext);
        }
    } catch (Throwable t) {
        //restore files on temp folder
        try {
            for (Object object : resourcesMap.entrySet()) {
                File resFile = ((Map.Entry<File, File>) object).getKey();
                File newResFile = ((Map.Entry<File, File>) object).getValue();
                if (newResFile.isDirectory()) {
                    FileUtils.copyDirectoryToDirectory(newResFile, resFile.getParentFile());
                } else {
                    FileUtils.copyFile(newResFile, resFile.getParentFile());
                }
            }
        } catch (Exception e) {
        }
        _logger.error("Unexpected error in component uninstallation process", t);
        throw new ApsSystemException("Unexpected error in component uninstallation process.", t);
    } finally {
        //clean temp folder
    }
    return true;
}