Examples with Taxon ubic.gemma.model.genome.Taxon used on opensource projects

Example 56 with Taxon

use of ubic.gemma.model.genome.Taxon in project Gemma by PavlidisLab.

the class BiomartEnsemblNcbiObjectGenerator method generateRemote.

/**
 * @return Generates file from remote biomart location
 * @throws IOException if there is a problem while manipulating the file
 */
public Map<String, Ensembl2NcbiValueObject> generateRemote(Collection<Taxon> validTaxa) throws IOException {
    Map<String, Ensembl2NcbiValueObject> bioMartEnsemblNcbiIdsForValidAllGemmaTaxa = new HashMap<>();
    Map<Taxon, File> taxaBiomartFiles = this.biomartEnsemblNcbiFetcher.fetch(validTaxa);
    if (taxaBiomartFiles != null && !taxaBiomartFiles.isEmpty()) {
        for (Taxon taxon : taxaBiomartFiles.keySet()) {
            File fileForTaxon = taxaBiomartFiles.get(taxon);
            if (fileForTaxon != null) {
                log.info("Starting processing taxon " + taxon + " for file " + fileForTaxon);
                Map<String, Ensembl2NcbiValueObject> map = parseTaxonBiomartFile(taxon, fileForTaxon);
                bioMartEnsemblNcbiIdsForValidAllGemmaTaxa.putAll(map);
            } else {
                log.error("No biomart file retrieved for taxon " + taxon);
            }
        }
    } else {
        throw new RuntimeException("No files could be downloaded from Biomart for provided taxon");
    }
    return bioMartEnsemblNcbiIdsForValidAllGemmaTaxa;
}

Example 57 with Taxon

use of ubic.gemma.model.genome.Taxon in project Gemma by PavlidisLab.

the class ExternalFileGeneLoaderServiceImpl method load.

@Override
public int load(String geneFile, String taxonName) throws Exception {
    log.info("Starting loading gene file " + geneFile + " for taxon " + taxonName);
    Taxon taxon = validateTaxon(taxonName);
    log.info("Taxon and file validation passed for " + geneFile + " for taxon " + taxonName);
    try (BufferedReader bufferedReaderGene = readFile(geneFile)) {
        return load(bufferedReaderGene, taxon);
    }
}

Example 58 with Taxon

use of ubic.gemma.model.genome.Taxon in project Gemma by PavlidisLab.

the class ExternalFileGeneLoaderServiceImpl method updateTaxonWithGenesLoaded.

/**
 * Method to update taxon to indicate that genes have been loaded for that taxon. If the taxon has children taxa
 * then those child genes should not be used and the flag for those child taxon set to false.
 *
 * @param taxon The taxon to update
 */
private void updateTaxonWithGenesLoaded(Taxon taxon) {
    Collection<Taxon> childTaxa = taxonService.findChildTaxaByParent(taxon);
    // if this taxon has children flag not to use their genes
    if (childTaxa != null && !childTaxa.isEmpty()) {
        for (Taxon childTaxon : childTaxa) {
            if (childTaxon != null && childTaxon.getIsGenesUsable()) {
                childTaxon.setIsGenesUsable(false);
                taxonService.update(childTaxon);
                log.warn("Child taxa" + childTaxon + " genes have been loaded parent taxa should suppressed");
            }
        }
    }
    // set taxon flag indicating that use this taxon's genes
    if (!taxon.getIsGenesUsable()) {
        taxon.setIsGenesUsable(true);
        taxonService.update(taxon);
        log.info("Updating taxon genes loaded to true for taxon " + taxon);
    }
}

Example 59 with Taxon

use of ubic.gemma.model.genome.Taxon in project Gemma by PavlidisLab.

the class TaxonLoader method load.

public int load(final InputStream inputStream) throws IOException {
    TaxonParser parser = new TaxonParser();
    parser.parse(inputStream);
    Collection<Taxon> results = parser.getResults();
    int count = 0;
    for (Taxon taxon : results) {
        if (TaxonLoader.log.isDebugEnabled())
            TaxonLoader.log.debug("Loading " + taxon);
        persisterHelper.persist(taxon);
        count++;
    }
    TaxonLoader.log.info("Persisted " + count + " taxa");
    return count;
}

Example 60 with Taxon

use of ubic.gemma.model.genome.Taxon in project Gemma by PavlidisLab.

the class TaxonParser method parseOneLine.

@Override
public Taxon parseOneLine(String line) {
    String[] fields = StringUtils.splitPreserveAllTokens(line, '|');
    int ncbiid = Integer.parseInt(StringUtils.strip(fields[0]));
    if (!results.containsKey(ncbiid)) {
        Taxon t = Taxon.Factory.newInstance();
        t.setNcbiId(ncbiid);
        t.setIsGenesUsable(false);
        t.setIsSpecies(true);
        results.put(ncbiid, t);
    }
    String tag = StringUtils.strip(fields[3]);
    if (tag.equals("scientific name")) {
        results.get(ncbiid).setScientificName(StringUtils.strip(fields[1]));
    } else if (tag.equals("genbank common name")) {
        results.get(ncbiid).setCommonName(fields[1]);
    }
    return results.get(ncbiid);
}