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

Example 1 with ShRna

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

the class DashboardDaoImpl method summarize.

@Override
public void summarize() {
    findEntities(Summary.class).forEach(s -> delete(s));
    Map<Class<?>, String> summaryClasses = new HashMap<Class<?>, String>();
    summaryClasses.put(AnimalModel.class, "Animal Models");
    summaryClasses.put(CellSample.class, "Cell Lines");
    summaryClasses.put(Compound.class, "Compounds");
    summaryClasses.put(Gene.class, "Genes");
    summaryClasses.put(ShRna.class, "shRNA");
    summaryClasses.put(TissueSample.class, "Disease Contexts (Tissues)");
    summaryClasses.forEach((clazz, label) -> {
        @SuppressWarnings("unchecked") Summary s = summarizePerSubject((Class<? extends Subject>) clazz, label);
        save(s);
    });
    Summary s = summarizeStories();
    save(s);
    Summary eco = summarizeECO();
    save(eco);
    Summary total = summarizeTotal();
    save(total);
}

Example 2 with ShRna

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

the class TRCshRNADataProcessor method process.

@Override
public ShRna process(ShRna shRNA) throws Exception {
    if (shRNA == null)
        return null;
    if (shRNA.getOrganism() == null)
        return null;
    // allow null transcript relationship
    // if (shRNA.getTranscript() == null) return null;
    String stableURL = new StableURL().createURLWithPrefix("rna", shRNA.getTargetSequence());
    shRNA.setStableURL(stableURL);
    return shRNA;
}

Example 3 with ShRna

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

the class siRNADataFieldSetMapper method mapFieldSet.

public ShRna mapFieldSet(FieldSet fieldSet) throws BindException {
    ShRna shRNA = dashboardFactory.create(ShRna.class);
    shRNA.setType("sirna");
    shRNA.setDisplayName(fieldSet.readString(REAGENT_NAME_COL_INDEX));
    shRNA.setReagentName(shRNA.getDisplayName());
    // create synonym back to self
    Synonym synonym = dashboardFactory.create(Synonym.class);
    synonym.setDisplayName(fieldSet.readString(REAGENT_NAME_COL_INDEX));
    shRNA.getSynonyms().add(synonym);
    // set target seq
    shRNA.setTargetSequence(fieldSet.readString(TARGET_SEQ_COL_INDEX));
    // set organism
    if (fieldSet.readString(ORGANISM_COL_INDEX).equals("Homo sapiens")) {
        Organism organism = organismMap.get("9606");
        if (organism == null) {
            List<Organism> organisms = dashboardDao.findOrganismByTaxonomyId("9606");
            if (organisms.size() == 1)
                organism = organisms.get(0);
            organismMap.put("9606", organism);
        }
        if (organism != null)
            shRNA.setOrganism(organism);
    }
    // set transcript
    Transcript transcript = getTranscript(fieldSet.readString(TARGET_GENE_COL_INDEX), fieldSet.readString(TRANSCRIPT_ID_COL_INDEX));
    if (transcript != null)
        shRNA.setTranscript(transcript);
    return shRNA;
}

Example 4 with ShRna

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

the class TRCshRNADataFieldSetMapper method mapFieldSet.

public ShRna mapFieldSet(FieldSet fieldSet) throws BindException {
    ShRna shRNA = dashboardFactory.create(ShRna.class);
    shRNA.setType("shrna");
    // sanity check
    String cloneId = fieldSet.readString(CLONE_ID_COL_INDEX);
    if (cloneId.equalsIgnoreCase(MISSING_ENTRY))
        return shRNA;
    // only process records that exist in our map
    if (!tRCshRNAFilterMap.isEmpty() && !tRCshRNAFilterMap.containsKey(cloneId))
        return shRNA;
    shRNA.setDisplayName(fieldSet.readString(TARGET_SEQ_COL_INDEX));
    shRNA.setReagentName(cloneId);
    // create synonym back to self
    Synonym synonym = dashboardFactory.create(Synonym.class);
    synonym.setDisplayName(fieldSet.readString(CLONE_NAME_COL_INDEX));
    shRNA.getSynonyms().add(synonym);
    // create xref back to broad
    Xref xref = dashboardFactory.create(Xref.class);
    xref.setDatabaseId(cloneId);
    xref.setDatabaseName(BROAD_SHRNA_DATABASE);
    shRNA.getXrefs().add(xref);
    // set target seq
    shRNA.setTargetSequence(fieldSet.readString(TARGET_SEQ_COL_INDEX));
    // set organism
    String taxonomyId = fieldSet.readString(TAX_ID_COL_INDEX);
    Organism organism = organismMap.get(taxonomyId);
    if (organism == null) {
        List<Organism> organisms = dashboardDao.findOrganismByTaxonomyId(taxonomyId);
        if (organisms.size() == 1)
            organism = organisms.get(0);
        organismMap.put(taxonomyId, organism);
    }
    if (organism != null)
        shRNA.setOrganism(organism);
    // set transcript
    Transcript transcript = getTranscript(fieldSet.readString(TRANSCRIPT_ID_COL_INDEX));
    if (transcript != null) {
        shRNA.setTranscript(transcript);
    } else {
        transcript = getTranscript(fieldSet.readString(ALT_TRANSCRIPT_ID_COL_INDEX));
        if (transcript != null)
            shRNA.setTranscript(transcript);
        else {
            missingTranscriptCount++;
            log.debug("null transcript " + missingTranscriptCount + ": " + fieldSet.readString(TARGET_SEQ_COL_INDEX) + " [" + fieldSet.readString(TRANSCRIPT_ID_COL_INDEX) + "][" + fieldSet.readString(ALT_TRANSCRIPT_ID_COL_INDEX) + "]");
        }
    }
    return shRNA;
}

Example 5 with ShRna

use of gov.nih.nci.ctd2.dashboard.model.ShRna 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());
}