Examples with DatabaseEntry ubic.gemma.model.common.description.DatabaseEntry used on opensource projects

Example 11 with DatabaseEntry

use of ubic.gemma.model.common.description.DatabaseEntry in project Gemma by PavlidisLab.

the class NcbiGeneConverter method convert.

public Collection<GeneProduct> convert(NCBIGene2Accession acc, Gene gene) {
    Collection<GeneProduct> geneProducts = new HashSet<>();
    // RNA section
    if (acc.getRnaNucleotideAccession() != null) {
        GeneProduct rna = GeneProduct.Factory.newInstance();
        // set available fields
        rna.setNcbiGi(acc.getRnaNucleotideGI());
        rna.setGene(gene);
        rna.setName(acc.getRnaNucleotideAccession());
        rna.setType(GeneProductType.RNA);
        String description = "Imported from NCBI Gene";
        if (acc.getStatus() != null) {
            description = description + " (Refseq status: " + acc.getStatus() + ").";
        }
        if (acc.getRnaNucleotideAccession() != null) {
            DatabaseEntry accession = DatabaseEntry.Factory.newInstance();
            accession.setAccession(acc.getRnaNucleotideAccession());
            accession.setAccessionVersion(acc.getRnaNucleotideAccessionVersion());
            accession.setExternalDatabase(NcbiGeneConverter.genBank);
            if (rna.getAccessions() == null) {
                rna.setAccessions(new HashSet<DatabaseEntry>());
            }
            rna.getAccessions().add(accession);
        }
        /*
             * Fill in physical location details.
             */
        if (acc.getGenomicNucleotideAccession() != null && gene.getPhysicalLocation() != null) {
            this.getChromosomeDetails(acc, gene);
            PhysicalLocation pl = this.getPhysicalLocation(acc, gene);
            rna.setPhysicalLocation(pl);
        }
        rna.setDescription(description);
        geneProducts.add(rna);
    }
    // Protein section
    if (NcbiGeneConverter.retainProteinInformation && acc.getProteinAccession() != null) {
        GeneProduct protein = GeneProduct.Factory.newInstance();
        // set available fields
        protein.setNcbiGi(acc.getProteinGI());
        protein.setGene(gene);
        protein.setName(acc.getProteinAccession());
        protein.setType(GeneProductType.PROTEIN);
        protein.setDescription("Imported from NCBI Gene" + (acc.getStatus() != null ? " (" + acc.getStatus() + ")" : ""));
        DatabaseEntry accession = DatabaseEntry.Factory.newInstance();
        accession.setAccession(acc.getProteinAccession());
        accession.setAccessionVersion(acc.getProteinAccessionVersion());
        accession.setExternalDatabase(NcbiGeneConverter.genBank);
        Collection<DatabaseEntry> accessions = new HashSet<>();
        accessions.add(accession);
        protein.setAccessions(accessions);
        geneProducts.add(protein);
    }
    return geneProducts;
}

Example 12 with DatabaseEntry

use of ubic.gemma.model.common.description.DatabaseEntry in project Gemma by PavlidisLab.

the class NcbiGeneConverter method convert.

public Gene convert(NCBIGeneInfo info) {
    Gene gene = Gene.Factory.newInstance();
    gene.setNcbiGeneId(Integer.parseInt(info.getGeneId()));
    gene.setName(info.getDefaultSymbol());
    gene.setOfficialSymbol(info.getDefaultSymbol());
    gene.setOfficialName(info.getDescription());
    gene.setEnsemblId(info.getEnsemblId());
    /*
         * NOTE we allow multiple discontinued or previous ids, separated by commas. This is a hack to account for cases
         * uncovered recently...can be minimized by running this regularly.
         */
    if (info.getHistory() != null) {
        assert info.getHistory().getCurrentId() == null || info.getGeneId().equals(info.getHistory().getCurrentId());
        assert info.getHistory().getPreviousIds() != null;
        if (!info.getHistory().getPreviousIds().isEmpty()) {
            String previousIds = StringUtils.join(info.getHistory().getPreviousIds(), ",");
            gene.setPreviousNcbiId(previousIds);
        }
    } else if (StringUtils.isNotBlank(info.getDiscontinuedId())) {
        if (NcbiGeneConverter.log.isDebugEnabled())
            NcbiGeneConverter.log.debug("Gene matches a gene that was discontinued: " + gene + " matches gene that had id " + info.getDiscontinuedId());
        gene.setPreviousNcbiId(info.getDiscontinuedId());
    }
    gene.setDescription("Imported from NCBI gene; Nomenclature status: " + info.getNomenclatureStatus());
    Taxon t = Taxon.Factory.newInstance();
    t.setNcbiId(info.getTaxId());
    t.setIsGenesUsable(false);
    t.setIsSpecies(true);
    gene.setTaxon(t);
    /*
         * We are going to stop maintaining this information
         */
    PhysicalLocation pl = PhysicalLocation.Factory.newInstance();
    Chromosome chrom = new Chromosome(info.getChromosome(), t);
    pl.setChromosome(chrom);
    gene.setPhysicalLocation(pl);
    Collection<GeneAlias> aliases = gene.getAliases();
    for (String alias : info.getSynonyms()) {
        GeneAlias newAlias = GeneAlias.Factory.newInstance();
        newAlias.setAlias(alias);
        aliases.add(newAlias);
    }
    for (String dbname : info.getDbXrefs().keySet()) {
        if (!dbname.equalsIgnoreCase("Ensembl"))
            continue;
        String identifier = info.getDbXrefs().get(dbname);
        DatabaseEntry crossref = DatabaseEntry.Factory.newInstance();
        crossref.setAccession(identifier);
        crossref.setExternalDatabase(NcbiGeneConverter.getEnsembl());
        gene.getAccessions().add(crossref);
    }
    return gene;
}

Example 13 with DatabaseEntry

use of ubic.gemma.model.common.description.DatabaseEntry in project Gemma by PavlidisLab.

the class CompositeSequenceDaoImpl method thaw.

@Override
public void thaw(final Collection<CompositeSequence> compositeSequences) {
    HibernateTemplate templ = this.getHibernateTemplate();
    templ.executeWithNativeSession(new org.springframework.orm.hibernate3.HibernateCallback<Object>() {

        @Override
        public Object doInHibernate(org.hibernate.Session session) throws org.hibernate.HibernateException {
            int i = 0;
            int numToDo = compositeSequences.size();
            for (CompositeSequence cs : compositeSequences) {
                session.buildLockRequest(LockOptions.NONE).lock(cs);
                Hibernate.initialize(cs.getArrayDesign());
                BioSequence bs = cs.getBiologicalCharacteristic();
                if (bs == null) {
                    continue;
                }
                session.buildLockRequest(LockOptions.NONE).lock(bs);
                Hibernate.initialize(bs);
                Hibernate.initialize(bs.getTaxon());
                DatabaseEntry dbEntry = bs.getSequenceDatabaseEntry();
                if (dbEntry != null) {
                    Hibernate.initialize(dbEntry);
                    Hibernate.initialize(dbEntry.getExternalDatabase());
                    session.evict(dbEntry);
                    session.evict(dbEntry.getExternalDatabase());
                }
                if (bs.getBioSequence2GeneProduct() == null) {
                    continue;
                }
                for (BioSequence2GeneProduct bs2gp : bs.getBioSequence2GeneProduct()) {
                    if (bs2gp == null) {
                        continue;
                    }
                    GeneProduct geneProduct = bs2gp.getGeneProduct();
                    if (geneProduct != null && geneProduct.getGene() != null) {
                        Gene g = geneProduct.getGene();
                        g.getAliases().size();
                        session.evict(g);
                        session.evict(geneProduct);
                    }
                }
                if (++i % 2000 == 0) {
                    AbstractDao.log.info("Progress: " + i + "/" + numToDo + "...");
                    try {
                        Thread.sleep(10);
                    } catch (InterruptedException e) {
                    // 
                    }
                }
                session.evict(bs);
            }
            session.clear();
            return null;
        }
    });
}

Example 14 with DatabaseEntry

use of ubic.gemma.model.common.description.DatabaseEntry in project Gemma by PavlidisLab.

the class GeneProductServiceImpl method remove.

@Override
@Transactional
public void remove(Collection<GeneProduct> toRemove) {
    Collection<BlatAssociation> associations = this.blatAssociationDao.find(toRemove);
    if (!associations.isEmpty()) {
        AbstractService.log.info("Removing " + associations.size() + " blat associations involving up to " + toRemove.size() + " products.");
        this.blatAssociationDao.remove(associations);
    }
    Collection<AnnotationAssociation> annotationAssociations = this.annotationAssociationDao.find(toRemove);
    if (!annotationAssociations.isEmpty()) {
        AbstractService.log.info("Removing " + annotationAssociations.size() + " annotationAssociations involving up to " + toRemove.size() + " products.");
        this.annotationAssociationDao.remove(annotationAssociations);
    }
    // remove associations to database entries that are still associated with sequences.
    for (GeneProduct gp : toRemove) {
        gp = this.thaw(gp);
        Collection<DatabaseEntry> accessions = gp.getAccessions();
        Collection<DatabaseEntry> toRelease = new HashSet<>();
        for (DatabaseEntry de : accessions) {
            if (this.bioSequenceDao.findByAccession(de) != null) {
                toRelease.add(de);
            }
        }
        gp.getAccessions().removeAll(toRelease);
        this.geneProductDao.remove(gp);
    }
}

Example 15 with DatabaseEntry

use of ubic.gemma.model.common.description.DatabaseEntry in project Gemma by PavlidisLab.

the class CompositeSequenceParser method parseOneLine.

@Override
public CompositeSequence parseOneLine(String line) {
    String[] tokens = StringUtils.splitPreserveAllTokens(line, '\t');
    if (tokens.length != 3) {
        return null;
    }
    String probeid = tokens[0];
    String genbankAcc = tokens[1];
    String description = tokens[2];
    CompositeSequence result = CompositeSequence.Factory.newInstance();
    result.setName(probeid);
    result.setDescription(description);
    DatabaseEntry dbEntry = ExternalDatabaseUtils.getGenbankAccession(genbankAcc);
    BioSequence biologicalCharacteristic = BioSequence.Factory.newInstance();
    // this will be changed later, typically.
    biologicalCharacteristic.setName(genbankAcc);
    // this will be changed later, typically.
    biologicalCharacteristic.setDescription(description + " (From platform source)");
    biologicalCharacteristic.setSequenceDatabaseEntry(dbEntry);
    result.setBiologicalCharacteristic(biologicalCharacteristic);
    return result;
}