@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.setVcfFileIdsByProject(singletonMap(testProject.getId(), singletonList(vcfFile.getId()))); vcfFilterForm.setGenes(new VcfFilterForm.FilterSection<>(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), singletonList(IllegalArgumentException.class)); vcfManager.reindexVcfFile(vcfFile.getId(), false); entryList = featureIndexManager.filterVariations(vcfFilterForm); Assert.assertFalse(entryList.getEntries().isEmpty()); }
public IndexSearchResult<VcfIndexEntry> filterVariations(VcfFilterForm filterForm, long projectId) throws IOException { Project project = projectManager.load(projectId); List<VcfFile> files = project.getItems().stream() .filter(i -> i.getBioDataItem().getFormat() == BiologicalDataItemFormat.VCF) .map(i -> (VcfFile) i.getBioDataItem()) .collect(Collectors.toList()); return getVcfSearchResult(filterForm, files); }
FeatureIndexManager { public IndexSearchResult<VcfIndexEntry> filterVariations(VcfFilterForm filterForm, long projectId) throws IOException { Project project = projectManager.load(projectId); List<VcfFile> files = project.getItems().stream() .filter(i -> i.getBioDataItem().getFormat() == BiologicalDataItemFormat.VCF) .map(i -> (VcfFile) i.getBioDataItem()) .collect(Collectors.toList()); return getVcfSearchResult(filterForm, files); } }
FeatureIndexManager { public IndexSearchResult<VcfIndexEntry> filterVariations(VcfFilterForm filterForm, long projectId) throws IOException { Project project = projectManager.load(projectId); List<VcfFile> files = project.getItems().stream() .filter(i -> i.getBioDataItem().getFormat() == BiologicalDataItemFormat.VCF) .map(i -> (VcfFile) i.getBioDataItem()) .collect(Collectors.toList()); return getVcfSearchResult(filterForm, files); }  }
FeatureIndexManager { public IndexSearchResult<VcfIndexEntry> filterVariations(VcfFilterForm filterForm, long projectId) throws IOException { Project project = projectManager.load(projectId); List<VcfFile> files = project.getItems().stream() .filter(i -> i.getBioDataItem().getFormat() == BiologicalDataItemFormat.VCF) .map(i -> (VcfFile) i.getBioDataItem()) .collect(Collectors.toList()); return getVcfSearchResult(filterForm, files); }  void deleteFromIndexByFileId(final long projectId, List<Pair<FeatureType, Long>> fileIds); Set<String> searchGenesInVcfFilesInProject(long projectId, String gene, List<Long> vcfFileIds); Set<String> searchGenesInVcfFiles(String gene, List<Long> vcfFileIds); List<Chromosome> filterChromosomes(VcfFilterForm filterForm, long projectId); List<Chromosome> filterChromosomes(VcfFilterForm filterForm); IndexSearchResult<VcfIndexEntry> filterVariations(VcfFilterForm filterForm, long projectId); int getTotalPagesCount(VcfFilterForm filterForm); int getTotalPagesCount(VcfFilterForm filterForm, long projectId); List<Group> groupVariations(VcfFilterForm filterForm, long projectId, String groupByField); List<Group> groupVariations(VcfFilterForm filterForm, String groupByField); IndexSearchResult<VcfIndexEntry> filterVariations(VcfFilterForm filterForm); IndexSearchResult searchFeaturesInProject(String featureId, long projectId); IndexSearchResult searchFeaturesByReference(String featureId, long referenceId); VcfFilterInfo loadVcfFilterInfoForProject(long projectId); void buildIndexForFile(FeatureFile featureFile); Set<String> fetchGeneIds(int start, int end, List<GeneFile> geneFiles, Chromosome chromosome); void writeLuceneIndexForFile(final FeatureFile featureFile,
            final List<? extends FeatureIndexEntry> entries,
            VcfFilterInfo vcfFilterInfo); void makeIndexForBedReader(BedFile bedFile, AbstractFeatureReader<NggbBedFeature, LineIterator> reader,
                                      Map<String, Chromosome> chromosomeMap); void makeIndexForVcfReader(VcfFile vcfFile, FeatureReader<VariantContext> reader, List<GeneFile> geneFiles,
                                       Map<String, Chromosome> chromosomeMap, VcfFilterInfo info); void processGeneFile(GeneFile geneFile, final Map<String, Chromosome> chromosomeMap,
            boolean full); void addGeneFeatureToIndex(List<FeatureIndexEntry> allEntries, GeneFeature feature,
                                     Map<String, Chromosome> chromosomeMap); }
FeatureIndexManager { public IndexSearchResult<VcfIndexEntry> filterVariations(VcfFilterForm filterForm, long projectId) throws IOException { Project project = projectManager.load(projectId); List<VcfFile> files = project.getItems().stream() .filter(i -> i.getBioDataItem().getFormat() == BiologicalDataItemFormat.VCF) .map(i -> (VcfFile) i.getBioDataItem()) .collect(Collectors.toList()); return getVcfSearchResult(filterForm, files); }  void deleteFromIndexByFileId(final long projectId, List<Pair<FeatureType, Long>> fileIds); Set<String> searchGenesInVcfFilesInProject(long projectId, String gene, List<Long> vcfFileIds); Set<String> searchGenesInVcfFiles(String gene, List<Long> vcfFileIds); List<Chromosome> filterChromosomes(VcfFilterForm filterForm, long projectId); List<Chromosome> filterChromosomes(VcfFilterForm filterForm); IndexSearchResult<VcfIndexEntry> filterVariations(VcfFilterForm filterForm, long projectId); int getTotalPagesCount(VcfFilterForm filterForm); int getTotalPagesCount(VcfFilterForm filterForm, long projectId); List<Group> groupVariations(VcfFilterForm filterForm, long projectId, String groupByField); List<Group> groupVariations(VcfFilterForm filterForm, String groupByField); IndexSearchResult<VcfIndexEntry> filterVariations(VcfFilterForm filterForm); IndexSearchResult searchFeaturesInProject(String featureId, long projectId); IndexSearchResult searchFeaturesByReference(String featureId, long referenceId); VcfFilterInfo loadVcfFilterInfoForProject(long projectId); void buildIndexForFile(FeatureFile featureFile); Set<String> fetchGeneIds(int start, int end, List<GeneFile> geneFiles, Chromosome chromosome); void writeLuceneIndexForFile(final FeatureFile featureFile,
            final List<? extends FeatureIndexEntry> entries,
            VcfFilterInfo vcfFilterInfo); void makeIndexForBedReader(BedFile bedFile, AbstractFeatureReader<NggbBedFeature, LineIterator> reader,
                                      Map<String, Chromosome> chromosomeMap); void makeIndexForVcfReader(VcfFile vcfFile, FeatureReader<VariantContext> reader, List<GeneFile> geneFiles,
                                       Map<String, Chromosome> chromosomeMap, VcfFilterInfo info); void processGeneFile(GeneFile geneFile, final Map<String, Chromosome> chromosomeMap,
            boolean full); void addGeneFeatureToIndex(List<FeatureIndexEntry> allEntries, GeneFeature feature,
                                     Map<String, Chromosome> chromosomeMap);  }