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;

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Document

Return a File handle for this resource.

Usage

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

@Test
@Transactional(propagation = Propagation.REQUIRES_NEW)
public void testNoIndexVcf() throws IOException, FeatureIndexException {
    Resource resource = context.getResource(CLASSPATH_TEMPLATES_FELIS_CATUS_VCF);

    FeatureIndexedFileRegistrationRequest request = new FeatureIndexedFileRegistrationRequest();
    request.setReferenceId(referenceId);
    request.setPath(resource.getFile().getAbsolutePath());
    request.setDoIndex(false);/*w  ww .  j ava 2  s.c  o m*/
    request.setName(UUID.randomUUID().toString());

    VcfFile vcfFile = vcfManager.registerVcfFile(request);

    Assert.assertNotNull(vcfFile);

    Project project = new Project();
    project.setName(TEST_PROJECT_NAME + UUID.randomUUID().toString());
    project.setItems(Arrays.asList(new ProjectItem(new BiologicalDataItem(vcfFile.getBioDataItemId())),
            new ProjectItem(new BiologicalDataItem(testReference.getBioDataItemId()))));

    projectManager.saveProject(project); // Index is created when vcf file is added

    TestUtils.assertFail(() -> featureIndexManager.filterVariations(new VcfFilterForm(), project.getId()),
            Collections.singletonList(IllegalArgumentException.class));
}

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

@Test
@Transactional(propagation = Propagation.REQUIRES_NEW)
public void testReindexVcf() throws FeatureIndexException, IOException {
    Resource resource = context.getResource(CLASSPATH_TEMPLATES_FELIS_CATUS_VCF);

    FeatureIndexedFileRegistrationRequest request = new FeatureIndexedFileRegistrationRequest();
    request.setReferenceId(referenceId);
    request.setPath(resource.getFile().getAbsolutePath());
    request.setName(UUID.randomUUID().toString());

    VcfFile vcfFile = vcfManager.registerVcfFile(request);

    VcfFilterForm vcfFilterForm = new VcfFilterForm();
    vcfFilterForm.setVcfFileIds(Collections.singletonList(vcfFile.getId()));
    vcfFilterForm/*from   w  w w . ja  v  a 2  s. c o  m*/
            .setGenes(new VcfFilterForm.FilterSection<>(Collections.singletonList(TEST_GENE_PREFIX), false));
    vcfFilterForm.setVariationTypes(
            new VcfFilterForm.FilterSection<>(Arrays.asList(VariationType.MNP, VariationType.SNV), false));
    IndexSearchResult<VcfIndexEntry> entryList = featureIndexManager.filterVariations(vcfFilterForm);
    Assert.assertFalse(entryList.getEntries().isEmpty());

    fileManager.deleteFileFeatureIndex(vcfFile);

    TestUtils.assertFail(() -> featureIndexManager.filterVariations(vcfFilterForm),
            Collections.singletonList(IllegalArgumentException.class));

    vcfManager.reindexVcfFile(vcfFile.getId());
    entryList = featureIndexManager.filterVariations(vcfFilterForm);
    Assert.assertFalse(entryList.getEntries().isEmpty());
}

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

@Before
public void setup() throws Exception {
    testChromosome = EntityHelper.createNewChromosome();
    testChromosome.setSize(TEST_CHROMOSOME_SIZE);
    testReference = EntityHelper.createNewReference(testChromosome, referenceGenomeManager.createReferenceId());

    referenceGenomeManager.register(testReference);
    referenceId = testReference.getId();

    Resource resource = context.getResource(CLASSPATH_TEMPLATES_GENES_SORTED);

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

    testGeneFile = gffManager.registerGeneFile(request);

    referenceGenomeManager.updateReferenceGeneFileId(testReference.getId(), testGeneFile.getId());

    Resource bedResource = context.getResource(CLASSPATH_TEMPLATES_BED);
    FeatureIndexedFileRegistrationRequest bedFileRequest = new FeatureIndexedFileRegistrationRequest();
    bedFileRequest.setReferenceId(referenceId);
    bedFileRequest.setPath(bedResource.getFile().getAbsolutePath());

    testBedFile = bedManager.registerBed(bedFileRequest);
    // TODO Ask about indexing bed with registration
    bedManager.reindexBedFile(testBedFile.getId());

    resource = context.getResource(CLASSPATH_TEMPLATES_FELIS_CATUS_VCF);

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

    testVcf = vcfManager.registerVcfFile(request);

    testProject = new Project();
    testProject.setName(TEST_PROJECT_NAME);
    testProject.setItems(Arrays.asList(new ProjectItem(new BiologicalDataItem(testVcf.getBioDataItemId())),
            new ProjectItem(new BiologicalDataItem(testReference.getBioDataItemId()))));

    projectManager.saveProject(testProject); // Index is created when vcf file is added
}

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

@Test
@Transactional(propagation = Propagation.REQUIRES_NEW)
public void testCreateUnmappedGeneIndex()
        throws IOException, InterruptedException, FeatureIndexException, NoSuchAlgorithmException {
    Chromosome chr1 = EntityHelper.createNewChromosome("chr1");
    chr1.setSize(TEST_CHROMOSOME_SIZE);// w  ww .  j a  v  a  2  s  . co  m
    Reference testHumanReference = EntityHelper.createNewReference(chr1,
            referenceGenomeManager.createReferenceId());

    referenceGenomeManager.register(testHumanReference);
    Long humanReferenceId = testHumanReference.getId();

    Resource resource = context.getResource("classpath:templates/mrna.sorted.chunk.gtf");

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

    GeneFile geneFile = gffManager.registerGeneFile(request);
    Assert.assertNotNull(geneFile);
    Assert.assertNotNull(geneFile.getId());

    Project project = new Project();
    project.setName(TEST_PROJECT_NAME + 1);

    project.setItems(Arrays.asList(new ProjectItem(new BiologicalDataItem(geneFile.getBioDataItemId())),
            new ProjectItem(new BiologicalDataItem(testHumanReference.getBioDataItemId()))));
    projectManager.saveProject(project);

    List<FeatureIndexEntry> entryList = (List<FeatureIndexEntry>) featureIndexManager
            .searchFeaturesInProject("", project.getId()).getEntries();
    Assert.assertTrue(entryList.isEmpty());

    entryList = (List<FeatureIndexEntry>) featureIndexManager
            .searchFeaturesInProject("AM992871", project.getId()).getEntries();
    Assert.assertTrue(entryList.isEmpty()); // we don't search for exons
}

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

@Test
@Transactional(propagation = Propagation.REQUIRES_NEW)
public void testWickedVcfIndex() throws IOException, InterruptedException, FeatureIndexException,
        NoSuchAlgorithmException, ParseException, VcfReadingException {
    Chromosome chr1 = EntityHelper.createNewChromosome("chr21");
    chr1.setSize(TEST_WICKED_VCF_LENGTH);
    Chromosome chr2 = EntityHelper.createNewChromosome("chr22");
    chr2.setSize(TEST_WICKED_VCF_LENGTH);
    Reference testHumanReference = EntityHelper.createNewReference(Arrays.asList(chr1, chr2),
            referenceGenomeManager.createReferenceId());
    referenceGenomeManager.register(testHumanReference);
    Long humanReferenceId = testHumanReference.getId();

    Project project = new Project();
    project.setName(TEST_PROJECT_NAME + 1);
    project.setItems(Collections/* w  ww . j a v a 2 s . c  om*/
            .singletonList(new ProjectItem(new BiologicalDataItem(testHumanReference.getBioDataItemId()))));

    projectManager.saveProject(project);

    Resource resource = context.getResource("classpath:templates/Homo_sapiens.GRCh38.83.sorted.chr21-22.gtf");
    FeatureIndexedFileRegistrationRequest geneRequest = new FeatureIndexedFileRegistrationRequest();
    geneRequest.setPath(resource.getFile().getAbsolutePath());
    geneRequest.setReferenceId(humanReferenceId);

    GeneFile geneFile = gffManager.registerGeneFile(geneRequest);
    referenceGenomeManager.updateReferenceGeneFileId(humanReferenceId, geneFile.getId());

    resource = context.getResource("classpath:templates/Dream.set3.VarDict.SV.vcf");

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

    VcfFile vcfFile = vcfManager.registerVcfFile(request);
    Assert.assertNotNull(vcfFile);
    Assert.assertNotNull(vcfFile.getId());

    project.setItems(Arrays.asList(new ProjectItem(geneFile), new ProjectItem(vcfFile)));

    projectManager.saveProject(project);

    IndexSearchResult<VcfIndexEntry> entries = featureIndexManager.filterVariations(new VcfFilterForm(),
            project.getId());
    Assert.assertFalse(entries.getEntries().isEmpty());

    long varGenesCount = entries.getEntries().stream().filter(e -> StringUtils.isNotBlank(e.getGene())).count();
    Assert.assertTrue(varGenesCount > 0);
    /*entries.stream().filter(e -> StringUtils.isNotBlank(e.getGene())).forEach(e -> logger.info("{} - {}, {}", e
        .getStartIndex(), e.getEndIndex(), e.getGeneIds()));*/

    // check chromosome filter
    VcfFilterForm chr21Form = new VcfFilterForm();
    chr21Form.setChromosomeIds(Collections.singletonList(chr1.getId()));
    IndexSearchResult<VcfIndexEntry> chr21Entries = featureIndexManager.filterVariations(chr21Form,
            project.getId());
    Assert.assertFalse(chr21Entries.getEntries().isEmpty());
    Assert.assertTrue(
            chr21Entries.getEntries().stream().allMatch(e -> e.getChromosome().getId().equals(chr1.getId())));

    VcfFilterForm chr22Form = new VcfFilterForm();
    chr22Form.setChromosomeIds(Collections.singletonList(chr2.getId()));
    IndexSearchResult<VcfIndexEntry> chr22Entries = featureIndexManager.filterVariations(chr22Form,
            project.getId());
    Assert.assertFalse(chr22Entries.getEntries().isEmpty());
    Assert.assertTrue(
            chr22Entries.getEntries().stream().allMatch(e -> e.getChromosome().getId().equals(chr2.getId())));

    VcfFilterForm chr2122Form = new VcfFilterForm();
    chr2122Form.setChromosomeIds(Arrays.asList(chr1.getId(), chr2.getId()));
    IndexSearchResult<VcfIndexEntry> chr2122Entries = featureIndexManager.filterVariations(chr2122Form,
            project.getId());
    Assert.assertFalse(chr2122Entries.getEntries().isEmpty());
    Assert.assertTrue(
            chr2122Entries.getEntries().stream().anyMatch(e -> e.getChromosome().getId().equals(chr1.getId())));
    Assert.assertTrue(
            chr2122Entries.getEntries().stream().anyMatch(e -> e.getChromosome().getId().equals(chr2.getId())));
    Assert.assertEquals(chr21Entries.getEntries().size() + chr22Entries.getEntries().size(),
            chr2122Entries.getEntries().size());
}

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

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

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

    GeneFile geneFile = gffManager.registerGeneFile(request);
    Assert.assertNotNull(geneFile);//from  w  w  w . j  a  v a2s  . c o  m
    Assert.assertNotNull(geneFile.getId());

    referenceGenomeManager.updateReferenceGeneFileId(testReference.getId(), geneFile.getId());

    Project project = new Project();
    project.setName(TEST_PROJECT_NAME + "_INT");

    project.setItems(Arrays.asList(new ProjectItem(new BiologicalDataItem(testReference.getBioDataItemId())),
            new ProjectItem(new BiologicalDataItem(geneFile.getBioDataItemId()))));
    projectManager.saveProject(project);

    IndexSearchResult result1 = featureIndexDao.searchFeaturesInInterval(Collections.singletonList(geneFile),
            INTERVAL1_START, INTERVAL1_END, testChromosome);

    Assert.assertEquals(3, result1.getEntries().size());

    IndexSearchResult result2 = featureIndexDao.searchFeaturesInInterval(Collections.singletonList(geneFile),
            INTERVAL2_START, INTERVAL2_END, testChromosome);
    Assert.assertEquals(0, result2.getEntries().size());

    IndexSearchResult result3 = featureIndexDao.searchFeaturesInInterval(Collections.singletonList(geneFile),
            INTERVAL3_START, INTERVAL3_END, testChromosome);
    Assert.assertEquals(3, result3.getEntries().size());
}

From source file:architecture.ee.component.core.lifecycle.RepositoryImpl.java

public void setServletContext(ServletContext servletContext) {

    // 1.  ?? ? ? ?  : ARCHITECTURE_INSTALL_ROOT
    String value = servletContext.getInitParameter(ApplicationConstants.ARCHITECTURE_PROFILE_ROOT_ENV_KEY);
    if (!StringUtils.isEmpty(value)) {
        try {/*from w  ww .j  av  a  2  s.  c  o m*/
            ServletContextResourceLoader servletResoruceLoader = new ServletContextResourceLoader(
                    servletContext);
            Resource resource = servletResoruceLoader.getResource(value);
            if (resource.exists()) {
                log.debug(L10NUtils.format("003003", ApplicationConstants.ARCHITECTURE_PROFILE_ROOT_ENV_KEY,
                        resource.getURI()));
                this.rootResource = resource;
                setState(State.INITIALIZED);
                initailized = true;
            }
        } catch (Throwable e) {
            this.rootResource = null;
        }
    }

    if (!initailized && !StringUtils.isEmpty(value)) {
        Resource obj;
        try {
            obj = resoruceLoader.getResource(value);
            if (obj.exists()) {
                log.debug(L10NUtils.format("003003", ApplicationConstants.ARCHITECTURE_PROFILE_ROOT_ENV_KEY,
                        obj.getURI()));
                this.rootResource = obj;
                setState(State.INITIALIZED);
                initailized = true;

            }
        } catch (Throwable e) {
            log.error(e);
        }
    }

    if (!initailized) {
        try {
            ServletContextResource resource = new ServletContextResource(servletContext, "/WEB-INF");
            File file = resource.getFile();
            if (file.exists()) {
                this.rootResource = new FileSystemResource(file);
                setState(State.INITIALIZED);
                initailized = true;
            }
        } catch (Throwable e) {
            log.error(e);
        }
    }
}

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

/**
 * Testes indexing a vcf file with populated gene information. Therefore this information should be read from
 * VCF, not from gff files/*w ww.ja  v  a  2  s  .  c  o m*/
 * @throws Exception
 */
@Ignore
@Test
@Transactional(propagation = Propagation.REQUIRES_NEW)
public void testCreateFeatureIndex2() throws Exception {
    Chromosome chr14 = EntityHelper.createNewChromosome("chr14");
    chr14.setSize(TEST_CHROMOSOME_SIZE);
    Reference testHumanReference = EntityHelper.createNewReference(chr14,
            referenceGenomeManager.createReferenceId());

    referenceGenomeManager.register(testHumanReference);
    Long humanReferenceId = testHumanReference.getId();

    Resource resource = context.getResource("classpath:templates/sample_2-lumpy.vcf");
    FeatureIndexedFileRegistrationRequest request = new FeatureIndexedFileRegistrationRequest();
    request.setReferenceId(humanReferenceId);
    request.setPath(resource.getFile().getAbsolutePath());

    VcfFile vcfFile = vcfManager.registerVcfFile(request);

    Project project = new Project();
    project.setName(TEST_PROJECT_NAME);
    project.setItems(
            Collections.singletonList(new ProjectItem(new BiologicalDataItem(vcfFile.getBioDataItemId()))));

    projectManager.saveProject(project); // Index is created when vcf file is added
    VcfFilterInfo info = featureIndexManager.loadVcfFilterInfoForProject(project.getId());

    VcfFilterForm vcfFilterForm = new VcfFilterForm();
    vcfFilterForm.setVcfFileIds(Collections.singletonList(vcfFile.getId()));
    vcfFilterForm
            .setGenes(new VcfFilterForm.FilterSection<>(Collections.singletonList("ENSG00000185070"), false));
    vcfFilterForm.setVariationTypes(
            new VcfFilterForm.FilterSection<>(Arrays.asList(VariationType.DEL, VariationType.SNV), false));

    String cipos95 = "CIPOS95";
    vcfFilterForm
            .setInfoFields(info.getInfoItems().stream().map(InfoItem::getName).collect(Collectors.toList()));
    vcfFilterForm.setAdditionalFilters(Collections.singletonMap(cipos95, Arrays.asList(CONST_42, CONST_42)));

    IndexSearchResult<VcfIndexEntry> entryList2 = featureIndexManager.filterVariations(vcfFilterForm,
            project.getId());
    Assert.assertFalse(entryList2.getEntries().isEmpty());
    Assert.assertTrue(entryList2.getEntries().stream().anyMatch(e -> e.getInfo().containsKey(cipos95)));
    Assert.assertTrue(
            entryList2.getEntries().stream().filter(e -> e.getInfo().containsKey(cipos95)).allMatch(e -> {
                String cipos = (String) e.getInfo().get(cipos95);
                return cipos.startsWith("[") && cipos.endsWith("]");
            }));

    // check info properly loaded
    for (VcfIndexEntry e : entryList2.getEntries()) {
        VariationQuery query = new VariationQuery();
        query.setId(e.getFeatureFileId());
        query.setProjectId(project.getId());
        query.setChromosomeId(e.getChromosome().getId());
        query.setPosition(e.getStartIndex());
        Variation variation = vcfManager.loadVariation(query);
        Assert.assertNotNull(variation);

        for (Map.Entry<String, Variation.InfoField> i : variation.getInfo().entrySet()) {
            if (i.getValue().getValue() != null) {
                Assert.assertTrue(
                        String.format("%s expected, %s found", i.getValue().getValue(),
                                e.getInfo().get(i.getKey())),
                        i.getValue().getValue().toString()
                                .equalsIgnoreCase(e.getInfo().get(i.getKey()).toString()));
            } else {
                Assert.assertEquals(i.getValue().getValue(), e.getInfo().get(i.getKey()));
            }
        }
    }

    // flrt2

    vcfFilterForm.setGenes(new VcfFilterForm.FilterSection<>(Collections.singletonList("FLRT2"), false));
    IndexSearchResult<VcfIndexEntry> entryList21 = featureIndexManager.filterVariations(vcfFilterForm,
            project.getId());
    Assert.assertFalse(entryList21.getEntries().isEmpty());
    Assert.assertEquals(entryList21.getEntries().size(), entryList2.getEntries().size());
    Assert.assertEquals(entryList21.getEntries().get(0).getGene(), entryList2.getEntries().get(0).getGene());

    // empty filter test
    entryList2 = featureIndexManager.filterVariations(new VcfFilterForm(), project.getId());
    Assert.assertFalse(entryList2.getEntries().isEmpty());
    checkDuplicates(entryList2.getEntries());
}

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

@Test
@Transactional(propagation = Propagation.REQUIRES_NEW)
public void testIndexUpdateOnProjectOperations() throws Exception {
    Resource gffResource = context.getResource(CLASSPATH_TEMPLATES_GENES_SORTED);

    FeatureIndexedFileRegistrationRequest request = new FeatureIndexedFileRegistrationRequest();
    request.setReferenceId(referenceId);
    request.setPath(gffResource.getFile().getAbsolutePath());
    request.setName("testGeneFile");

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

    referenceGenomeManager.updateReferenceGeneFileId(testReference.getId(), geneFile.getId());

    Resource vcfResource = context.getResource(CLASSPATH_TEMPLATES_FELIS_CATUS_VCF);

    request = new FeatureIndexedFileRegistrationRequest();
    request.setReferenceId(referenceId);
    request.setPath(vcfResource.getFile().getAbsolutePath());
    request.setName("testVcf");

    VcfFile vcfFile = vcfManager.registerVcfFile(request);

    Project project = new Project();
    project.setName(TEST_PROJECT_NAME + 1);
    project.setItems(Arrays.asList(new ProjectItem(new BiologicalDataItem(vcfFile.getBioDataItemId())),
            new ProjectItem(new BiologicalDataItem(geneFile.getBioDataItemId())),
            new ProjectItem(new BiologicalDataItem(testReference.getBioDataItemId()))));

    projectManager.saveProject(project); // Index is created when vcf file is added

    VcfFilterForm vcfFilterForm = new VcfFilterForm();
    vcfFilterForm.setVcfFileIds(Collections.singletonList(vcfFile.getId()));
    vcfFilterForm.setChromosomeIds(Collections.singletonList(testChromosome.getId()));
    vcfFilterForm
            .setGenes(new VcfFilterForm.FilterSection<>(Collections.singletonList(TEST_GENE_PREFIX), false));
    vcfFilterForm.setVariationTypes(
            new VcfFilterForm.FilterSection<>(Arrays.asList(VariationType.MNP, VariationType.SNV), false));
    IndexSearchResult<VcfIndexEntry> entryList = featureIndexManager.filterVariations(vcfFilterForm,
            project.getId());
    Assert.assertFalse(entryList.getEntries().isEmpty());

    // try to add an vcf item
    request = new FeatureIndexedFileRegistrationRequest();
    request.setReferenceId(referenceId);
    request.setPath(vcfResource.getFile().getAbsolutePath());
    request.setName(vcfResource.getFilename() + "2");
    VcfFile vcfFile2 = vcfManager.registerVcfFile(request);

    project = projectManager.addProjectItem(project.getId(), vcfFile2.getBioDataItemId());

    entryList = featureIndexManager.filterVariations(vcfFilterForm, project.getId());
    Assert.assertFalse(entryList.getEntries().isEmpty());
    Assert.assertTrue(
            entryList.getEntries().stream().allMatch(e -> e.getFeatureFileId().equals(vcfFile.getId())));

    VcfFilterForm vcfFilterForm2 = new VcfFilterForm();
    vcfFilterForm2.setVcfFileIds(Collections.singletonList(vcfFile2.getId()));
    vcfFilterForm.setChromosomeIds(Collections.singletonList(testChromosome.getId()));
    vcfFilterForm2
            .setGenes(new VcfFilterForm.FilterSection<>(Collections.singletonList(TEST_GENE_PREFIX), false));
    vcfFilterForm2.setVariationTypes(
            new VcfFilterForm.FilterSection<>(Arrays.asList(VariationType.MNP, VariationType.SNV), false));
    IndexSearchResult<VcfIndexEntry> entryList2 = featureIndexManager.filterVariations(vcfFilterForm2,
            project.getId());
    Assert.assertFalse(entryList2.getEntries().isEmpty());
    Assert.assertEquals(entryList.getEntries().size(), entryList2.getEntries().size());

    Assert.assertTrue(
            entryList2.getEntries().stream().allMatch(e -> e.getFeatureFileId().equals(vcfFile2.getId())));

    // test no vcfFileIds
    vcfFilterForm2.setVcfFileIds(null);
    entryList2 = featureIndexManager.filterVariations(vcfFilterForm2, project.getId());
    Assert.assertFalse(entryList2.getEntries().isEmpty());
    Assert.assertEquals(entryList2.getEntries().size(), entryList.getEntries().size() * 2);

    // test with multiple vcfFileIds
    vcfFilterForm2.setVcfFileIds(Arrays.asList(vcfFile.getId(), vcfFile2.getId()));
    entryList2 = featureIndexManager.filterVariations(vcfFilterForm2, project.getId());
    Assert.assertFalse(entryList2.getEntries().isEmpty());
    Assert.assertEquals(entryList2.getEntries().size(), entryList.getEntries().size() * 2);

    // try to remove a vcf item by save - should be not indexed
    project.setItems(project.getItems().stream()
            .filter(i -> !(i.getBioDataItem() instanceof VcfFile)
                    || !((VcfFile) i.getBioDataItem()).getId().equals(vcfFile2.getId()))
            .collect(Collectors.toList()));

    project = projectManager.saveProject(project);

    vcfFilterForm2.setVcfFileIds(Collections.singletonList(vcfFile2.getId()));
    entryList2 = featureIndexManager.filterVariations(vcfFilterForm2, project.getId());
    Assert.assertTrue(entryList2.getEntries().isEmpty());

    // try to remove gene file
    project.setItems(project.getItems().stream().filter(i -> !(i.getBioDataItem() instanceof GeneFile))
            .collect(Collectors.toList()));
    project = projectManager.saveProject(project);

    vcfFilterForm.setGenes(null);
    entryList = featureIndexManager.filterVariations(vcfFilterForm, project.getId());
    Assert.assertFalse(entryList.getEntries().isEmpty());

    // add multiple files
    project.getItems().clear();
    projectManager.saveProject(project);
    Project loadedProject = projectManager.loadProject(project.getId());
    Assert.assertTrue(loadedProject.getItems().isEmpty());
    entryList2 = featureIndexManager.filterVariations(new VcfFilterForm(), project.getId());
    Assert.assertTrue(entryList2.getEntries().isEmpty());

    project.setItems(Arrays.asList(new ProjectItem(new BiologicalDataItem(vcfFile.getBioDataItemId())),
            new ProjectItem(new BiologicalDataItem(vcfFile2.getBioDataItemId())),
            new ProjectItem(new BiologicalDataItem(testReference.getBioDataItemId()))));
    projectManager.saveProject(project);
    entryList2 = featureIndexManager.filterVariations(new VcfFilterForm(), project.getId());
    Assert.assertTrue(
            entryList2.getEntries().stream().anyMatch(e -> e.getFeatureFileId().equals(vcfFile.getId())));
    Assert.assertTrue(
            entryList2.getEntries().stream().anyMatch(e -> e.getFeatureFileId().equals(vcfFile2.getId())));
}

From source file:org.cloudifysource.usm.UniversalServiceManagerBean.java

@Override
public void setApplicationContext(final ApplicationContext arg0) throws BeansException {
    // CHECKSTYLE:ON
    this.applicationContext = arg0;

    if (arg0.getClassLoader() instanceof ServiceClassLoader) {
        // running in GSC
        this.runningInGSC = true;
        final ServiceClassLoader scl = (ServiceClassLoader) arg0.getClassLoader();

        final URL url = scl.getSlashPath();
        logger.fine("The slashpath URL is: " + url);
        URI uri;/*from   w w  w .  java2 s .c o  m*/
        try {
            uri = url.toURI();
        } catch (final URISyntaxException e) {
            throw new IllegalArgumentException(e);
        }
        logger.fine("The slashpath URI is: " + uri);
        this.puWorkDir = new File(uri);
        this.puExtDir = new File(this.puWorkDir, "ext");
        return;

    }

    final ResourceApplicationContext rac = (ResourceApplicationContext) arg0;

    try {
        this.runningInGSC = false;
        final Field resourcesField = rac.getClass().getDeclaredField("resources");
        final boolean accessibleBefore = resourcesField.isAccessible();

        resourcesField.setAccessible(true);
        final Resource[] resources = (Resource[]) resourcesField.get(rac);
        for (final Resource resource : resources) {
            // find META-INF/spring/pu.xml
            final File file = resource.getFile();
            if (file.getName().equals("pu.xml") && file.getParentFile().getName().equals("spring")
                    && file.getParentFile().getParentFile().getName().equals("META-INF")) {
                puWorkDir = resource.getFile().getParentFile().getParentFile().getParentFile();
                puExtDir = new File(puWorkDir, "ext");
                break;
            }

        }

        resourcesField.setAccessible(accessibleBefore);
    } catch (final Exception e) {
        throw new IllegalArgumentException("Could not find pu.xml in the ResourceApplicationContext", e);
    }
    if (puWorkDir == null) {
        throw new IllegalArgumentException("Could not find pu.xml in the ResourceApplicationContext");
    }

}