@Test @Transactional(propagation = Propagation.REQUIRES_NEW) public void testGroupingForPlots() throws IOException { List<Group> counts = featureIndexManager.groupVariations(new VcfFilterForm(), testProject.getId(), IndexSortField.CHROMOSOME_NAME.name()); Assert.assertFalse(counts.isEmpty()); counts = featureIndexManager.groupVariations(new VcfFilterForm(), testProject.getId(), IndexSortField.VARIATION_TYPE.name()); Assert.assertFalse(counts.isEmpty()); counts = featureIndexManager.groupVariations(new VcfFilterForm(), testProject.getId(), IndexSortField.QUALITY.name()); Assert.assertFalse(counts.isEmpty()); }
public List<Group> groupVariations(VcfFilterForm filterForm, long projectId, String groupByField) 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 featureIndexDao.groupVariations(files, filterForm.computeQuery(FeatureType.VARIATION), groupByField); }
FeatureIndexManager { public List<Group> groupVariations(VcfFilterForm filterForm, long projectId, String groupByField) 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 featureIndexDao.groupVariations(files, filterForm.computeQuery(FeatureType.VARIATION), groupByField); } }
FeatureIndexManager { public List<Group> groupVariations(VcfFilterForm filterForm, long projectId, String groupByField) 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 featureIndexDao.groupVariations(files, filterForm.computeQuery(FeatureType.VARIATION), groupByField); }  }
FeatureIndexManager { public List<Group> groupVariations(VcfFilterForm filterForm, long projectId, String groupByField) 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 featureIndexDao.groupVariations(files, filterForm.computeQuery(FeatureType.VARIATION), groupByField); }  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 List<Group> groupVariations(VcfFilterForm filterForm, long projectId, String groupByField) 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 featureIndexDao.groupVariations(files, filterForm.computeQuery(FeatureType.VARIATION), groupByField); }  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);  }