Examples with Annotation gov.nih.nci.ctd2.dashboard.model.Annotation used on opensource projects

Example 1 with Annotation

use of gov.nih.nci.ctd2.dashboard.model.Annotation in project nci-ctd2-dashboard by CBIIT.

the class DashboardDaoImpl method findCellSampleByAnnotationField.

private List<CellSample> findCellSampleByAnnotationField(String field, String value) {
    List<CellSample> cellSamples = new ArrayList<CellSample>();
    List<Annotation> annoList = queryWithClass("from AnnotationImpl where " + field + " = :value", "value", value);
    for (Annotation anno : annoList) {
        List<CellSample> list = queryWithClass("from CellSampleImpl as cs where :anno member of cs.annotations", "anno", anno);
        for (CellSample cellSample : list) {
            if (!cellSamples.contains(cellSample)) {
                cellSamples.add(cellSample);
            }
        }
    }
    return cellSamples;
}

Example 2 with Annotation

use of gov.nih.nci.ctd2.dashboard.model.Annotation in project nci-ctd2-dashboard by CBIIT.

the class CellLineSampleFieldSetMapper method mapFieldSet.

public CellSample mapFieldSet(FieldSet fieldSet) throws BindException {
    String cellSampleId = fieldSet.readString(CELL_SAMPLE_ID);
    String taxonomyId = fieldSet.readString(TAXONOMY_ID);
    String gender = fieldSet.readString(GENDER);
    CellSample cellSample = dashboardFactory.create(CellSample.class);
    // display name will be set in next step
    Organism organism = getOrganism(taxonomyId);
    if (organism != null)
        cellSample.setOrganism(organism);
    if (gender != null && gender.length() > 0)
        cellSample.setGender(gender);
    if (cellLineAnnotationSampleMap.containsKey(cellSampleId)) {
        cellSample.setAnnotations(cellLineAnnotationSampleMap.get(cellSampleId));
    } else {
        cellSample.setAnnotations(new HashSet<Annotation>());
    }
    // optimization - avoid persisting CellSamples
    // - place in map and pass to cellLineNameStep
    cellSampleMap.put(cellSampleId, cellSample);
    return cellSample;
}

Example 3 with Annotation

use of gov.nih.nci.ctd2.dashboard.model.Annotation in project nci-ctd2-dashboard by CBIIT.

the class DashboardDaoImpl method summarizePerSubject.

private Summary summarizePerSubject(Class<? extends Subject> subjectClass, String label) {
    String tableName = "";
    Class<?> implClass = subjectClass.isInterface() ? dashboardFactory.getImplClass(subjectClass) : subjectClass;
    java.lang.annotation.Annotation[] annotation = implClass.getAnnotationsByType(javax.persistence.Table.class);
    if (annotation.length == 1) {
        javax.persistence.Table table = (javax.persistence.Table) annotation[0];
        tableName = table.name();
    } else {
        return new Summary("exception", 0, 0, 0, 0);
    }
    Session session = getSession();
    @SuppressWarnings("unchecked") org.hibernate.query.Query<BigInteger> query = session.createNativeQuery("SELECT count(DISTINCT submission_id) FROM " + tableName + " JOIN observed_subject ON observed_subject.subject_id=" + tableName + ".id" + " JOIN observation ON observation.id=observed_subject.observation_id");
    BigInteger submissions = query.getSingleResult();
    String tierQuery = "SELECT tier, COUNT(DISTINCT observation_id) FROM " + tableName + " JOIN observed_subject ON observed_subject.subject_id=" + tableName + ".id" + " JOIN observation ON observation.id=observed_subject.observation_id" + " JOIN submission ON submission.id=observation.submission_id" + " JOIN observation_template ON observation_template.id=submission.observationTemplate_id" + " GROUP BY tier";
    @SuppressWarnings("unchecked") org.hibernate.query.Query<Object[]> query2 = session.createNativeQuery(tierQuery);
    int[] tierCount = new int[3];
    List<Object[]> result = query2.list();
    for (Object[] obj : result) {
        Integer tier = (Integer) obj[0];
        BigInteger count = (BigInteger) obj[1];
        tierCount[tier - 1] = count.intValue();
    }
    session.close();
    return new Summary(label, submissions.intValue(), tierCount[0], tierCount[1], tierCount[2]);
}

Example 4 with Annotation

use of gov.nih.nci.ctd2.dashboard.model.Annotation in project nci-ctd2-dashboard by CBIIT.

the class AdminTest method importerTest.

@Test
public void importerTest() throws Exception {
    // import taxonomy data
    jobExecution = executeJob("taxonomyDataImporterJob");
    assertEquals("COMPLETED", jobExecution.getExitStatus().getExitCode());
    assertEquals("Organism count", 2, dashboardDao.countEntities(Organism.class).intValue());
    List<Organism> organisms = dashboardDao.findOrganismByTaxonomyId("9606");
    assertEquals(1, organisms.size());
    assertEquals("Homo sapiens", organisms.iterator().next().getDisplayName());
    // animal model
    jobExecution = executeJob("animalModelImporterJob");
    assertEquals("COMPLETED", jobExecution.getExitStatus().getExitCode());
    assertEquals("AnimalModel count", 1, dashboardDao.countEntities(AnimalModel.class).intValue());
    List<AnimalModel> models = dashboardDao.findAnimalModelByName("[FVB/N x SPRET/Ei] x FVB/N");
    assertEquals("AnimalModel found by name", 1, models.size());
    assertEquals("10090", models.iterator().next().getOrganism().getTaxonomyId());
    // import some cell line data
    jobExecution = executeJob("cellLineDataImporterJob");
    assertEquals("COMPLETED", jobExecution.getExitStatus().getExitCode());
    assertEquals("CellSample count", 3, dashboardDao.countEntities(CellSample.class).intValue());
    List<CellSample> cellSamples = dashboardDao.findCellSampleByAnnoSource("COSMIC (Sanger)");
    assertEquals("CellSample found by source", 3, cellSamples.size());
    cellSamples = dashboardDao.findCellSampleByAnnoType("primary_site");
    assertEquals(3, cellSamples.size());
    cellSamples = dashboardDao.findCellSampleByAnnoName("acute_lymphoblastic_B_cell_leukaemia");
    assertEquals("CellSample size", 1, cellSamples.size());
    CellSample cellSample = (CellSample) cellSamples.iterator().next();
    assertEquals(8, cellSample.getAnnotations().size());
    assertEquals("CellSamples synonyms size", 2, cellSample.getSynonyms().size());
    Annotation annotation = cellSample.getAnnotations().iterator().next();
    cellSamples = dashboardDao.findCellSampleByAnnotation(annotation);
    assertEquals(1, cellSamples.size());
    assertEquals(cellSample, cellSamples.iterator().next());
    List<Subject> cellSampleSubjects = dashboardDao.findSubjectsBySynonym("5637", true);
    assertEquals(1, cellSampleSubjects.size());
    cellSample = (CellSample) cellSampleSubjects.iterator().next();
    assertEquals("M", cellSample.getGender());
    // import some compound data
    jobExecution = executeJob("compoundDataImporterJob");
    assertEquals("COMPLETED", jobExecution.getExitStatus().getExitCode());
    assertEquals("Compound count", 10, dashboardDao.countEntities(Compound.class).intValue());
    List<Subject> compoundSubjects = dashboardDao.findSubjectsByXref(CompoundsFieldSetMapper.BROAD_COMPOUND_DATABASE, "411739");
    assertEquals(1, compoundSubjects.size());
    List<Compound> compounds = dashboardDao.findCompoundsBySmilesNotation("CCCCCCCCC1OC(=O)C(=C)C1C(O)=O");
    assertEquals(1, compounds.size());
    assertEquals(3, compounds.iterator().next().getSynonyms().size());
    List<Subject> compoundSubjectsWithImage = dashboardDao.findSubjectsByXref(CompoundsFieldSetMapper.COMPOUND_IMAGE_DATABASE, "BRD-A01145011.png");
    assertEquals(1, compoundSubjectsWithImage.size());
    assertEquals("zebularine", compoundSubjectsWithImage.iterator().next().getDisplayName());
    // import some gene data
    jobExecution = executeJob("geneDataImporterJob");
    assertEquals("COMPLETED", jobExecution.getExitStatus().getExitCode());
    assertEquals("Gene count", 19, dashboardDao.countEntities(Gene.class).intValue());
    List<Gene> genes = dashboardDao.findGenesByEntrezId("7529");
    assertEquals(1, genes.size());
    assertEquals("synonym number for 7529", 12, genes.iterator().next().getSynonyms().size());
    List<Subject> geneSubjects = dashboardDao.findSubjectsBySynonym("RB1", true);
    assertEquals(1, geneSubjects.size());
    // import some protein data
    jobExecution = executeJob("proteinDataImporterJob");
    assertEquals("COMPLETED", jobExecution.getExitStatus().getExitCode());
    assertEquals("Protein count", 15, dashboardDao.countEntities(Protein.class).intValue());
    List<Protein> proteins = dashboardDao.findProteinsByUniprotId("P31946");
    assertEquals(1, proteins.size());
    // some transcripts get created along with proteins
    assertEquals(35, dashboardDao.countEntities(Transcript.class).intValue());
    List<Transcript> transcripts = dashboardDao.findTranscriptsByRefseqId("NM_003404");
    assertEquals(1, transcripts.size());
    // import some shrna
    jobExecution = executeJob("TRCshRNADataImporterJob");
    assertEquals("COMPLETED", jobExecution.getExitStatus().getExitCode());
    assertEquals("ShRna count", 1, dashboardDao.countEntities(ShRna.class).intValue());
    List<Subject> shRNASubjects = dashboardDao.findSubjectsByXref("BROAD_SHRNA", "TRCN0000000001");
    assertEquals(1, shRNASubjects.size());
    ShRna shRNA = (ShRna) shRNASubjects.get(0);
    assertEquals("CCCTGCCAAACAAGCTAATAT", shRNA.getDisplayName());
    assertEquals("CCCTGCCAAACAAGCTAATAT", shRNA.getTargetSequence());
    // import some tissue sample data
    jobExecution = executeJob("tissueSampleDataImporterJob");
    assertEquals("COMPLETED", jobExecution.getExitStatus().getExitCode());
    assertEquals("TissueSample count", 2, dashboardDao.countEntities(TissueSample.class).intValue());
    List<TissueSample> tissueSamples = dashboardDao.findTissueSampleByName("neoplasm by morphology");
    assertEquals(1, tissueSamples.size());
    TissueSample tissueSample = tissueSamples.get(0);
    assertEquals(1, tissueSample.getSynonyms().size());
    assertEquals("Xrefs size", 2, tissueSample.getXrefs().size());
    // check tissue xref import
    tissueSamples = dashboardDao.findTissueSampleByName("neoplasm");
    assertEquals(1, tissueSamples.size());
    String doid = "not found";
    for (Xref xref : tissueSamples.get(0).getXrefs()) {
        if ("DISEASE ONTOLOGY".equals(xref.getDatabaseName())) {
            doid = xref.getDatabaseId();
        }
    }
    assertEquals("DOID:14566", doid);
    tissueSamples = dashboardDao.findTissueSampleByName("neoplasm by morphology");
    assertEquals(1, tissueSamples.size());
    doid = "not found";
    for (Xref xref : tissueSamples.get(0).getXrefs()) {
        if ("DISEASE ONTOLOGY".equals(xref.getDatabaseName())) {
            doid = xref.getDatabaseId();
        }
    }
    assertEquals("not found", doid);
    // import controlled vocabulary
    jobExecution = executeJob("controlledVocabularyImporterJob");
    assertEquals("COMPLETED", jobExecution.getExitStatus().getExitCode());
    // we get some subject/observed subject roles
    assertEquals("SubjectRole count", 18, dashboardDao.countEntities(SubjectRole.class).intValue());
    assertEquals("ObservedSubjectRole count", 75, dashboardDao.countEntities(ObservedSubjectRole.class).intValue());
    assertTrue("findObservedSubjectRole", dashboardDao.findObservedSubjectRole("broad_cpd_sens_lineage_enrich", "compound_name") != null);
    // we get some evidence/observed evidence roles
    assertEquals("countEntities EvidenceRole", 9, dashboardDao.countEntities(EvidenceRole.class).intValue());
    assertEquals("countEntities ObservedEvidenceRole", 186, dashboardDao.countEntities(ObservedEvidenceRole.class).intValue());
    assertTrue(dashboardDao.findObservedEvidenceRole("broad_cpd_sens_lineage_enrich", "cell_line_subset") != null);
    // we get observation template data
    assertEquals("countEntities ObservationTemplate", 25, dashboardDao.countEntities(ObservationTemplate.class).intValue());
    ObservationTemplate observationTemplate = dashboardDao.findObservationTemplateByName("broad_cpd_sens_lineage_enrich");
    assertNotNull(observationTemplate);
    assertFalse(observationTemplate.getIsSubmissionStory());
    assertEquals(0, observationTemplate.getSubmissionStoryRank().intValue());
    observationTemplate = dashboardDao.findObservationTemplateByName("broad_beta-catenin_navitoclax");
    assertNotNull(observationTemplate);
    assertFalse(observationTemplate.getIsSubmissionStory());
    assertEquals(0, observationTemplate.getSubmissionStoryRank().intValue());
    // check compound xref import
    compounds = dashboardDao.findCompoundsByName("navitoclax");
    assertEquals(1, compounds.size());
    String drugBankId = "not found";
    for (Xref xref : compounds.get(0).getXrefs()) {
        if ("DRUG BANK".equals(xref.getDatabaseName())) {
            drugBankId = xref.getDatabaseId();
        }
    }
    assertEquals("DB12340", drugBankId);
    compoundSubjects = dashboardDao.findSubjectsByXref("DRUG BANK", "DB12025");
    assertEquals(1, compoundSubjects.size());
}

Example 5 with Annotation

use of gov.nih.nci.ctd2.dashboard.model.Annotation in project nci-ctd2-dashboard by CBIIT.

the class CellLineAnnotationSampleFieldSetMapper method mapFieldSet.

public Annotation mapFieldSet(FieldSet fieldSet) throws BindException {
    String cellSampleId = fieldSet.readString(CELL_SAMPLE_ID);
    if (!cellLineAnnotationSampleMap.containsKey(cellSampleId)) {
        cellLineAnnotationSampleMap.put(cellSampleId, new HashSet<Annotation>());
    }
    Annotation annotation = dashboardFactory.create(Annotation.class);
    if (cellLineAnnotationNameMap.containsKey(fieldSet.readString(CELL_ANNO_NAME_ID))) {
        annotation.setDisplayName(cellLineAnnotationNameMap.get(fieldSet.readString(CELL_ANNO_NAME_ID)));
    }
    if (cellLineAnnotationTypeMap.containsKey(fieldSet.readString(CELL_ANNO_TYPE_ID))) {
        annotation.setType(cellLineAnnotationTypeMap.get(fieldSet.readString(CELL_ANNO_TYPE_ID)));
    }
    if (cellLineAnnotationSourceMap.containsKey(fieldSet.readString(CELL_ANNO_SOURCE_ID))) {
        annotation.setSource(cellLineAnnotationSourceMap.get(fieldSet.readString(CELL_ANNO_SOURCE_ID)));
    }
    cellLineAnnotationSampleMap.get(cellSampleId).add(annotation);
    // if we don't return something, spring batch will think EOF has been reached
    return annotation;
}