Example usage for org.springframework.core.io Resource getFile

List of usage examples for org.springframework.core.io Resource getFile

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Introduction

In this page you can find the example usage for org.springframework.core.io Resource getFile.

Prototype

File getFile() throws IOException;

Source Link

Document

Return a File handle for this resource.

Usage

From source file:com.epam.catgenome.manager.GffManagerTest.java

private boolean testCollapsed(String path) throws IOException, FeatureIndexException, InterruptedException,
        NoSuchAlgorithmException, GeneReadingException {
    Resource resource = context.getResource(path);

    FeatureIndexedFileRegistrationRequest request = new FeatureIndexedFileRegistrationRequest();
    request.setReferenceId(referenceId);
    request.setPath(resource.getFile().getAbsolutePath());

    GeneFile geneFile = gffManager.registerGeneFile(request);
    Assert.assertNotNull(geneFile);//from  w w w. j  a  va  2s  . c o m
    Assert.assertNotNull(geneFile.getId());

    Track<Gene> track = new Track<>();
    track.setId(geneFile.getId());
    track.setStartIndex(1);
    track.setEndIndex(TEST_END_INDEX);
    track.setChromosome(testChromosome);
    track.setScaleFactor(FULL_QUERY_SCALE_FACTOR);

    Track<Gene> featureList = gffManager.loadGenes(track, false);
    Assert.assertTrue(featureList.getBlocks().stream().anyMatch(g -> g.getItems().size() > 1));

    track = new Track<>();
    track.setId(geneFile.getId());
    track.setStartIndex(1);
    track.setEndIndex(TEST_END_INDEX);
    track.setChromosome(testChromosome);
    track.setScaleFactor(FULL_QUERY_SCALE_FACTOR);

    double time1 = Utils.getSystemTimeMilliseconds();
    Track<Gene> featureListCollapsed = gffManager.loadGenes(track, true);
    double time2 = Utils.getSystemTimeMilliseconds();
    logger.info("genes loading : {} ms", time2 - time1);
    Assert.assertNotNull(featureListCollapsed);
    Assert.assertFalse(featureListCollapsed.getBlocks().isEmpty());
    Assert.assertTrue(featureListCollapsed.getBlocks().stream().filter(GeneUtils::isGene)
            .allMatch(g -> g.getItems().size() == 1));
    Assert.assertFalse(featureListCollapsed.getBlocks().stream().filter(GeneUtils::isGene)
            .allMatch(g -> g.getItems().get(0).getItems().isEmpty()));

    return true;
}

From source file:grails.core.DefaultGrailsApplication.java

/**
 * Loads a GrailsApplication using the given ResourceLocator instance which will search for appropriate class names
 *
 *//*w  ww . ja  va2  s .co  m*/
public DefaultGrailsApplication(Resource[] resources) {
    this();
    for (Resource resource : resources) {

        Class<?> aClass;
        try {
            aClass = classLoader
                    .loadClass(GrailsResourceUtils.getClassName(resource.getFile().getAbsolutePath()));
        } catch (ClassNotFoundException e) {
            throw new GrailsConfigurationException(
                    "Class not found loading Grails application: " + e.getMessage(), e);
        } catch (IOException e) {
            throw new GrailsConfigurationException(
                    "Class not found loading Grails application: " + e.getMessage(), e);
        }
        loadedClasses.add(aClass);
    }
}

From source file:com.epam.catgenome.manager.GffManagerTest.java

@Test
@Transactional(propagation = Propagation.REQUIRES_NEW)
public void testLoadExonsInTrack()
        throws IOException, FeatureIndexException, InterruptedException, NoSuchAlgorithmException {
    Resource resource = context.getResource(GENES_SORTED_GTF_PATH);

    FeatureIndexedFileRegistrationRequest request = new FeatureIndexedFileRegistrationRequest();
    request.setReferenceId(referenceId);
    request.setPath(resource.getFile().getAbsolutePath());

    GeneFile geneFile = gffManager.registerGeneFile(request);
    Assert.assertNotNull(geneFile);/* w  w w  . j a v a2  s.  c om*/
    Assert.assertNotNull(geneFile.getId());

    List<Block> exons = gffManager.loadExonsInViewPort(geneFile.getId(), testChromosome.getId(),
            TEST_CENTER_POSITION, TEST_VIEW_PORT_SIZE, TEST_INTRON_LENGTH);

    List<Block> exons2 = gffManager.loadExonsInTrack(geneFile.getId(), testChromosome.getId(),
            exons.get(0).getStartIndex(), exons.get(exons.size() - 1).getEndIndex(), TEST_INTRON_LENGTH);

    Assert.assertFalse(exons2.isEmpty());
    Assert.assertEquals(exons.size(), exons2.size());
    for (int i = 0; i < exons2.size(); i++) {
        Assert.assertEquals(exons.get(i).getStartIndex(), exons2.get(i).getStartIndex());
        Assert.assertEquals(exons.get(i).getEndIndex(), exons2.get(i).getEndIndex());
    }

    testOverlapping(exons2);
}

From source file:com.helpinput.spring.SourceScaner.java

private void initBeanInfosAndFileReaders() {
    for (Map<String, BeanInfo> beanInfosInPath : scanedBeanInfos.values()) {
        for (BeanInfo beanInfo : beanInfosInPath.values()) {
            beanInfo.scaned = false;/*from www .j av  a2s  .c o  m*/
            beanInfo.needParse = true;
            beanInfo.isNew = false;
        }
    }

    if (!Utils.hasLength(this.dirs))
        return;

    String rootPath = new File(Thread.currentThread().getContextClassLoader().getResource("").toString())
            .getParentFile().getParent().substring(5);

    rootPath = rootPath.replace('\\', '/');

    for (String path : dirs) {
        path = path.replace('\\', '/');

        if (path.startsWith("/"))
            path = rootPath + path;
        path = "file:" + path;

        Map<String, BeanInfo> beanInfosInPath = scanedBeanInfos.get(path);
        if (beanInfosInPath == null) {
            beanInfosInPath = new ConcurrentHashMap<>();
            scanedBeanInfos.put(path, beanInfosInPath);
        }

        Resource[] resources;
        try {
            resources = resourcePatternResolver.getResources(path);
        } catch (Exception e) {
            //??????
            if (hasLength(beanInfosInPath)) {
                for (BeanInfo beanInfo : beanInfosInPath.values()) {
                    parserBeanInfoError(beanInfo);
                }
            }
            logger.info("read \"" + path + "\" error?", e);
            continue;
        }

        for (Resource resource : resources) {
            String fileName = null;
            BeanInfo beanInfo = null;
            String relativePath = null;

            try {
                File resourceFile = resource.getFile();
                fileName = resourceFile.toURI().getPath();
                relativePath = PathUtil.getRelativePath(rootPath, fileName);
                long newModified = resourceFile.lastModified();

                beanInfo = beanInfosInPath.get(relativePath);

                if (beanInfo != null) {
                    beanInfo.needParse = (newModified != beanInfo.lastModified);
                    beanInfo.isUpdate = true;
                } else {
                    beanInfo = new BeanInfo(fileName, relativePath, newModified);
                    beanInfosInPath.put(relativePath, beanInfo);
                    beanInfo.needParse = true;
                }

                beanInfo.scaned = true;
                beanInfo.lastModified = newModified;

                if (beanInfo.needParse) {
                    BufferedReader reader = null;
                    try {
                        reader = FileUtils.getFileBufferedReader(fileName);
                        CompilationUnit cu = JavaParser.parse(reader, true);
                        beanInfo.cu = cu;
                        beanInfo.packageName = ParserUtils.getPackageName(cu);
                        ClassOrInterfaceDeclaration real = ParserUtils.getClassName(cu);
                        if (real != null) {
                            beanInfo.isInterface = real.isInterface();
                            beanInfo.scanName = real.getName();
                            beanInfo.needParse = beanInfo.needParse && (!beanInfo.isInterface);
                        }
                        beanInfo.importName = beanInfo.packageName + "." + beanInfo.scanName;
                        beanInfo.referencWrapPt = Pattern.compile("^.*\\W+" + beanInfo.scanName + "\\W+.*$");
                    } finally {
                        closeWithWarning(reader);
                    }
                }
            } catch (IOException | ParseException e) {
                e.printStackTrace();
                if (beanInfo != null) {
                    parserBeanInfoError(beanInfo);
                    continue;
                }
            }
        }
    }
}

From source file:de.ingrid.admin.Config.java

public void initialize() throws IOException {
    Resource confOverride = getOverrideConfigResource();
    File configFile = confOverride.getFile();
    // create override file if it does not exist
    if (!configFile.exists()) {
        // if override file does not exist then try to look for previous
        // communication and plug description to get the configuration
        try {//from ww w  .  ja v a  2s . com
            log.warn("No config.override.properties found in conf-directory. Trying to recover "
                    + "configuration from previously generated files.");
            configFile.getParentFile().mkdir();
            configFile.createNewFile();
            // read communicaton and write properties
            this.ibusses = readFromCommunicationXml();
            if (this.ibusses != null)
                writeCommunicationToProperties();
            // read plug description and write properties
            PlugdescriptionCommandObject pd = new PlugdescriptionCommandObject(
                    new File("conf/plugdescription.xml"));
            writePlugdescriptionToProperties(pd);
        } catch (IOException e1) {
            log.error("Error creating override configuration", e1);
            e1.printStackTrace();
        }
    }

    // set system property for use in JSP file!
    if (indexing) {
        System.setProperty(IKeys.INDEXING, "true");
    }

    // plug description
    String plugDescription = System.getProperty(IKeys.PLUG_DESCRIPTION);
    if (plugDescription == null) {
        System.setProperty(IKeys.PLUG_DESCRIPTION, plugdescriptionLocation);
    }

    // ignore the following properties from the plug description, which do not need to be written
    // to the configuration file
    IGNORE_LIST.add("QUERY_EXTENSION_CONTAINER");
    IGNORE_LIST.add("connection");

    //
    writeCommunication(this.communicationLocation, this.ibusses);
}

From source file:com.epam.catgenome.manager.ProjectManagerTest.java

@Test
@Transactional(propagation = Propagation.REQUIRES_NEW, rollbackFor = Exception.class)
public void testAllFileTypesLoading() throws IOException, InterruptedException, FeatureIndexException,
        NoSuchAlgorithmException, VcfReadingException {
    Project project = new Project();
    project.setName(TEST_PROJECT_NAME);/*from  w ww  . j  av  a2s. co m*/
    project.setItems(Collections
            .singletonList(new ProjectItem(new BiologicalDataItem(testReference.getBioDataItemId()))));
    projectManager.saveProject(project);

    Project loadedProject = projectManager.loadProject(project.getId());
    Assert.assertNotNull(loadedProject);
    Assert.assertEquals(1, loadedProject.getItems().size());

    // Add Vcf
    addVcfFileToProject(project.getId(), TEST_VCF_FILE_NAME1, TEST_VCF_FILE_PATH);

    // Add genes
    Resource resource = context.getResource("classpath:templates/genes_sorted.gtf");

    FeatureIndexedFileRegistrationRequest geneRequest = new FeatureIndexedFileRegistrationRequest();
    geneRequest.setReferenceId(referenceId);
    geneRequest.setName("genes");
    geneRequest.setPath(resource.getFile().getAbsolutePath());

    GeneFile geneFile = gffManager.registerGeneFile(geneRequest);
    projectManager.addProjectItem(project.getId(), geneFile.getBioDataItemId());

    // Add BED file
    resource = context.getResource("classpath:templates/genes_sorted.bed");

    IndexedFileRegistrationRequest request = new IndexedFileRegistrationRequest();
    request.setReferenceId(referenceId);
    request.setName("bed");
    request.setPath(resource.getFile().getAbsolutePath());

    BedFile bedFile = bedManager.registerBed(request);
    projectManager.addProjectItem(project.getId(), bedFile.getBioDataItemId());

    // Add SEG file
    resource = context.getResource("classpath:templates/test_seg.seg");

    request = new IndexedFileRegistrationRequest();
    request.setReferenceId(referenceId);
    request.setName("seg");
    request.setPath(resource.getFile().getAbsolutePath());

    SegFile segFile = segManager.registerSegFile(request);
    projectManager.addProjectItem(project.getId(), segFile.getBioDataItemId());

    // Add MAF file
    resource = context.getResource("classpath:templates/maf/"
            + "TCGA.ACC.mutect.abbe72a5-cb39-48e4-8df5-5fd2349f2bb2.somatic.sorted.maf.gz");

    request = new IndexedFileRegistrationRequest();
    request.setPath(resource.getFile().getAbsolutePath());
    request.setReferenceId(referenceId);

    MafFile mafFile = mafManager.registerMafFile(request);
    Assert.assertNotNull(mafFile);
    projectManager.addProjectItem(project.getId(), mafFile.getBioDataItemId());

    loadedProject = projectManager.loadProject(project.getId());

    // Test VCF item
    ProjectItem vcfItem = loadedProject.getItems().stream()
            .filter(i -> i.getBioDataItem().getFormat() == BiologicalDataItemFormat.VCF).findFirst().get();
    Assert.assertNotNull(vcfItem);
    Assert.assertNotNull(vcfItem.getBioDataItem());
    VcfFile loadedVcf = (VcfFile) vcfItem.getBioDataItem();
    Assert.assertNotNull(loadedVcf.getId());
    Assert.assertNotNull(loadedVcf.getIndex());
    Assert.assertFalse(loadedVcf.getIndex().getPath().isEmpty());
    Assert.assertFalse(loadedVcf.getPath().isEmpty());
    Assert.assertFalse(loadedVcf.getSamples().isEmpty());

    // Test BED item
    ProjectItem bedItem = loadedProject.getItems().stream()
            .filter(i -> i.getBioDataItem().getFormat() == BiologicalDataItemFormat.BED).findFirst().get();
    Assert.assertNotNull(bedItem);
    Assert.assertNotNull(bedItem.getBioDataItem());
    BedFile loadedBed = (BedFile) bedItem.getBioDataItem();
    Assert.assertNotNull(loadedBed.getId());
    Assert.assertNotNull(loadedBed.getIndex());
    Assert.assertFalse(loadedBed.getIndex().getPath().isEmpty());
    Assert.assertFalse(loadedBed.getPath().isEmpty());

    // Test SEG Files
    ProjectItem segItem = loadedProject.getItems().stream()
            .filter(i -> i.getBioDataItem().getFormat() == BiologicalDataItemFormat.SEG).findFirst().get();
    Assert.assertNotNull(segItem);
    Assert.assertNotNull(segItem.getBioDataItem());
    SegFile loadedSeg = (SegFile) segItem.getBioDataItem();
    Assert.assertNotNull(loadedSeg.getId());
    Assert.assertNotNull(loadedSeg.getIndex());
    Assert.assertFalse(loadedSeg.getPath().isEmpty());
    Assert.assertFalse(loadedSeg.getSamples().isEmpty());

    // Test MAF Files
    ProjectItem mafItem = loadedProject.getItems().stream()
            .filter(i -> i.getBioDataItem().getFormat() == BiologicalDataItemFormat.MAF).findFirst().get();
    Assert.assertNotNull(mafItem);
    Assert.assertNotNull(mafItem.getBioDataItem());
    SegFile loadedMaf = (SegFile) segItem.getBioDataItem();
    Assert.assertNotNull(loadedMaf.getId());
    Assert.assertNotNull(loadedMaf.getIndex());
    Assert.assertFalse(loadedMaf.getPath().isEmpty());
    Assert.assertFalse(loadedMaf.getSamples().isEmpty());

    // Test load my projects
    List<Project> myProjects = projectManager.loadTopLevelProjectsForCurrentUser();
    Assert.assertFalse(myProjects.isEmpty());
}

From source file:com.epam.catgenome.manager.GffManagerTest.java

@Test
@Transactional(propagation = Propagation.REQUIRES_NEW)
public void testLoadExonsInViewPort()
        throws InterruptedException, NoSuchAlgorithmException, FeatureIndexException, IOException {
    Resource resource = context.getResource(GENES_SORTED_GTF_PATH);

    FeatureIndexedFileRegistrationRequest request = new FeatureIndexedFileRegistrationRequest();
    request.setReferenceId(referenceId);
    request.setPath(resource.getFile().getAbsolutePath());

    GeneFile geneFile = gffManager.registerGeneFile(request);
    Assert.assertNotNull(geneFile);/*  w ww .j a v  a  2  s.c  o  m*/
    Assert.assertNotNull(geneFile.getId());

    double time1 = Utils.getSystemTimeMilliseconds();
    List<Block> exons = gffManager.loadExonsInViewPort(geneFile.getId(), testChromosome.getId(),
            TEST_CENTER_POSITION, TEST_VIEW_PORT_SIZE, TEST_INTRON_LENGTH);
    double time2 = Utils.getSystemTimeMilliseconds();
    Assert.assertFalse(exons.isEmpty());
    logger.info("Loading exons took {} ms", time2 - time1);
    List<Block> exonsBelow = exons.stream().filter(e -> e.getEndIndex() < TEST_CENTER_POSITION)
            .collect(Collectors.toList());
    List<Block> exonsAbove = exons.stream().filter(e -> e.getStartIndex() > TEST_CENTER_POSITION)
            .collect(Collectors.toList());
    Assert.assertFalse(exonsBelow.isEmpty());
    Assert.assertFalse(exonsAbove.isEmpty());

    testOverlapping(exons);

    final Map<String, Pair<Integer, Integer>> metaMap = fileManager.loadIndexMetadata(geneFile);
    Pair<Integer, Integer> bounds = metaMap.get(testChromosome.getName());
    if (bounds == null) {
        bounds = metaMap.get(Utils.changeChromosomeName(testChromosome.getName()));
    }

    testFillRange(exonsBelow, TEST_VIEW_PORT_SIZE / 2, TEST_CENTER_POSITION, false, bounds.getLeft());
    testFillRange(exonsAbove, TEST_VIEW_PORT_SIZE / 2, TEST_CENTER_POSITION, true, bounds.getRight());
}

From source file:de.ingrid.admin.Config.java

public void writeCommunicationToProperties() {
    Resource override = getOverrideConfigResource();
    try (InputStream is = new FileInputStream(override.getFile().getAbsolutePath())) {

        Properties props = new Properties() {
            private static final long serialVersionUID = 6956076060462348684L;

            @Override//  ww  w  .  j  a  v a2  s.c  o  m
            public synchronized Enumeration<Object> keys() {
                return Collections.enumeration(new TreeSet<Object>(super.keySet()));
            }
        };
        props.load(is);
        // ---------------------------
        props.setProperty("communication.clientName", communicationProxyUrl);

        String communications = "";
        for (int i = 0; i < ibusses.size(); i++) {
            CommunicationCommandObject ibus = ibusses.get(i);
            communications += ibus.getBusProxyServiceUrl() + "," + ibus.getIp() + "," + ibus.getPort();
            if (i != (ibusses.size() - 1))
                communications += "##";
        }
        props.setProperty("communications.ibus", communications);

        // ---------------------------
        try (OutputStream os = new FileOutputStream(override.getFile().getAbsolutePath())) {
            props.store(os, "Override configuration written by the application");
        }
    } catch (Exception e) {
        log.error("Error writing properties: ", e);
    }
}

From source file:grails.core.DefaultGrailsApplication.java

/**
 * Loads a GrailsApplication using the given ResourceLocator instance which will search for appropriate class names
 *
 *//* ww  w  .  ja va2s  .c om*/
public DefaultGrailsApplication(org.grails.io.support.Resource[] resources) {
    this();
    for (org.grails.io.support.Resource resource : resources) {

        Class<?> aClass;
        try {
            aClass = classLoader
                    .loadClass(GrailsResourceUtils.getClassName(resource.getFile().getAbsolutePath()));
        } catch (ClassNotFoundException e) {
            throw new GrailsConfigurationException(
                    "Class not found loading Grails application: " + e.getMessage(), e);
        } catch (IOException e) {
            throw new GrailsConfigurationException(
                    "Class not found loading Grails application: " + e.getMessage(), e);
        }
        loadedClasses.add(aClass);
    }
}

From source file:it.infn.mw.iam.config.saml.SamlConfig.java

private List<MetadataProvider> metadataProviders()
        throws MetadataProviderException, IOException, ResourceException {

    List<MetadataProvider> providers = new ArrayList<>();

    for (IamSamlIdpMetadataProperties p : samlProperties.getIdpMetadata()) {
        String trimmedMedataUrl = p.getMetadataUrl().trim();

        if (trimmedMedataUrl.startsWith("classpath:")) {
            LOG.info("Adding classpath based metadata provider for URL: {}", trimmedMedataUrl);

            ClasspathResource cpMetadataResources = new ClasspathResource(
                    trimmedMedataUrl.replaceFirst("classpath:", ""));

            ResourceBackedMetadataProvider metadataProvider = new ResourceBackedMetadataProvider(
                    metadataFetchTimer, cpMetadataResources);

            metadataProvider.setParserPool(basicParserPool);
            providers.add(metadataDelegate(metadataProvider, p));

        } else if (trimmedMedataUrl.startsWith("file:")) {

            LOG.info("Adding File based metadata provider for URL: {}", trimmedMedataUrl);
            Resource metadataResource = resourceLoader.getResource(trimmedMedataUrl);

            FilesystemMetadataProvider metadataProvider = new FilesystemMetadataProvider(
                    metadataResource.getFile());

            metadataProvider.setParserPool(basicParserPool);
            providers.add(metadataDelegate(metadataProvider, p));

        } else if (trimmedMedataUrl.startsWith("http")) {

            LOG.info("Adding HTTP metadata provider for URL: {}", trimmedMedataUrl);

            File metadataBackupFile = Files.createTempFile("metadata", "xml").toFile();
            metadataBackupFile.deleteOnExit();

            FileBackedHTTPMetadataProvider metadataProvider = new FileBackedHTTPMetadataProvider(
                    metadataFetchTimer, httpClient(), trimmedMedataUrl, metadataBackupFile.getAbsolutePath());

            metadataProvider.setParserPool(basicParserPool);
            providers.add(metadataDelegate(metadataProvider, p));
        } else {//from   ww w  .j  a v  a 2 s .  co  m
            LOG.error("Skipping invalid saml.idp-metatadata value: {}", trimmedMedataUrl);
        }
    }

    if (providers.isEmpty()) {
        String message = "Empty SAML metadata providers after initialization";
        LOG.error(message);
        throw new IllegalStateException(message);
    }

    return providers;
}