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

Example 1 with Xref

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

the class DashboardDaoImpl method createObservedSubjectInfo.

private List<SubjectItem> createObservedSubjectInfo(Integer observationId) {
    Session session1 = getSession();
    @SuppressWarnings("unchecked") org.hibernate.query.Query<Object[]> query1 = session1.createNativeQuery("SELECT d2.displayName AS role, observed_subject_role.displayText AS description, d1.displayName AS name, subject.id, columnName, stableURL" + " FROM observed_subject join subject on observed_subject.subject_id=subject.id" + " JOIN dashboard_entity d1 ON subject.id=d1.id" + " JOIN observed_subject_role ON observed_subject.observedSubjectRole_id = observed_subject_role.id" + " JOIN subject_role ON observed_subject_role.subjectRole_id=subject_role.id" + " JOIN dashboard_entity AS d2 ON subject_role.id=d2.id" + " where observation_id=" + observationId);
    List<Object[]> subjects = query1.list();
    List<SubjectItem> list = new ArrayList<SubjectItem>();
    for (Object[] obj : subjects) {
        String role = (String) obj[0];
        String description = (String) obj[1];
        String name = (String) obj[2];
        Integer subjectId = (Integer) obj[3];
        String columnName = (String) obj[4];
        String stableURL = (String) obj[5];
        @SuppressWarnings("unchecked") org.hibernate.query.Query<String> query2 = session1.createNativeQuery("SELECT displayName FROM subject_synonym_map " + " JOIN synonym ON subject_synonym_map.synonyms_id=synonym.id " + " JOIN dashboard_entity ON synonym.id = dashboard_entity.id" + " WHERE SubjectImpl_id=" + subjectId);
        List<String> synonyms = query2.list();
        @SuppressWarnings("unchecked") org.hibernate.query.Query<Object[]> query3 = session1.createNativeQuery("SELECT databaseId, databaseName FROM subject_xref_map" + " JOIN xref ON subject_xref_map.xrefs_id=xref.id " + " WHERE SubjectImpl_id=" + subjectId);
        List<Object[]> xrefs = query3.list();
        List<XRefItem> xrefItems = new ArrayList<XRefItem>();
        for (Object[] x : xrefs) {
            xrefItems.add(new XRefItem((String) x[1], (String) x[0]));
        }
        SubjectItem subjectItem = new SubjectItem(stableURL, role, description, name, synonyms.toArray(new String[0]), xrefItems.toArray(new XRefItem[0]), columnName);
        list.add(subjectItem);
    }
    session1.close();
    return list;
}

Example 2 with Xref

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

the class GeneDataFieldSetMapper method mapFieldSet.

public Gene mapFieldSet(FieldSet fieldSet) throws BindException {
    Gene gene = dashboardFactory.create(Gene.class);
    String entrezGeneId = fieldSet.readString(1);
    gene.setEntrezGeneId(entrezGeneId);
    gene.setDisplayName(fieldSet.readString(2));
    // create synonym back to self
    Synonym synonym = dashboardFactory.create(Synonym.class);
    synonym.setDisplayName(fieldSet.readString(2));
    gene.getSynonyms().add(synonym);
    // create xref back to ncbi
    Xref xref = dashboardFactory.create(Xref.class);
    xref.setDatabaseId(entrezGeneId);
    xref.setDatabaseName(NCBI_GENE_DATABASE);
    gene.getXrefs().add(xref);
    for (String synonymName : fieldSet.readString(4).split("\\|")) {
        synonym = dashboardFactory.create(Synonym.class);
        synonym.setDisplayName(synonymName);
        gene.getSynonyms().add(synonym);
    }
    for (String synonymName : fieldSet.readString(13).split("\\|")) {
        synonym = dashboardFactory.create(Synonym.class);
        synonym.setDisplayName(synonymName);
        gene.getSynonyms().add(synonym);
    }
    // hgnc parsing
    for (String dbXrefs : fieldSet.readString(5).split("\\|")) {
        String[] parts = dbXrefs.split("\\:");
        if (parts[0].equals("HGNC")) {
            gene.setHGNCId(parts[1]);
            break;
        }
    }
    // set organism
    String taxonomyId = fieldSet.readString(0);
    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)
        gene.setOrganism(organism);
    String map_location = fieldSet.readString(7);
    gene.setMapLocation(map_location);
    String description = fieldSet.readString(8);
    gene.setFullName(description);
    String type_of_gene = fieldSet.readString(9);
    GeneType geneType = geneTypeMap.get(type_of_gene);
    if (geneType == null) {
        geneType = dashboardFactory.create(GeneType.class);
        geneType.setDisplayName(type_of_gene);
        geneTypeMap.put(type_of_gene, geneType);
        dashboardDao.save(geneType);
    }
    gene.setGeneType(geneType);
    return gene;
}

Example 3 with Xref

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

the class CompoundSynonymsFieldSetMapper method mapFieldSet.

public Compound mapFieldSet(FieldSet fieldSet) throws BindException {
    String compoundId = fieldSet.readString(CPD_ID);
    String compoundName = fieldSet.readString(CPD_NAME);
    // find compound by xref (broad)
    Compound compound = compoundMap.get(compoundId);
    if (compound != null) {
        Synonym synonym = dashboardFactory.create(Synonym.class);
        synonym.setDisplayName(compoundName);
        compound.getSynonyms().add(synonym);
    }
    return compound;
}

Example 4 with Xref

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

the class XrefDataWriter method write.

public void write(List<? extends XrefData> items) throws Exception {
    Map<Integer, Subject> all = new HashMap<Integer, Subject>();
    for (XrefData item : items) {
        List<? extends Subject> subjects = item.subjects;
        if (subjects == null || subjects.size() == 0) {
            continue;
        }
        Xref xref = item.xref;
        for (Subject subject : subjects) {
            Integer subjectId = subject.getId();
            Subject x = all.get(subjectId);
            if (x == null) {
                x = subject;
                all.put(subjectId, x);
            }
            x.getXrefs().add(xref);
        }
    }
    dashboardDao.batchMerge(all.values());
}

Example 5 with Xref

use of gov.nih.nci.ctd2.dashboard.model.Xref 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;
}