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

Example 76 with Taxon

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

the class ExpressionExperimentSearchServiceImpl method initialSearch.

private Map<Class<?>, List<SearchResult>> initialSearch(String query, Long taxonId) {
    SearchSettings settings = SearchSettingsImpl.expressionExperimentSearch(query);
    // add searching for experimentSets
    settings.setSearchExperimentSets(true);
    Taxon taxonParam;
    if (taxonId != null) {
        taxonParam = taxonService.load(taxonId);
        settings.setTaxon(taxonParam);
    }
    return searchService.search(settings);
}

Example 77 with Taxon

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

the class GeneSetValueObjectHelperImpl method fillSessionBoundValueObject.

private void fillSessionBoundValueObject(SessionBoundGeneSetValueObject sbgsvo, GeneSet gs) {
    sbgsvo.setName(gs.getName());
    sbgsvo.setDescription(gs.getDescription());
    // GO group gene sets don't have ids
    if (gs.getId() == null) {
        sbgsvo.setSize(gs.getMembers() != null ? gs.getMembers().size() : 0);
    } else {
        // this case may never happen as this is only called from convertToGoValueObject() leaving here in case
        // this method is ever called from somewhere else
        sbgsvo.setSize(this.geneSetService.getSize(new GeneSetValueObject(gs.getId())));
    }
    Collection<Long> gids = new HashSet<>();
    for (GeneSetMember gm : gs.getMembers()) {
        gids.add(gm.getGene().getId());
    }
    sbgsvo.setGeneIds(gids);
    Taxon tax = this.geneSetService.getTaxon(gs);
    if (tax != null) {
        while (tax.getParentTaxon() != null) {
            tax = tax.getParentTaxon();
        }
        sbgsvo.setTaxonId(tax.getId());
        sbgsvo.setTaxonName(tax.getCommonName());
    }
    sbgsvo.setId(new Long(-1));
    sbgsvo.setModified(false);
}

Example 78 with Taxon

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

the class GeneCoreServiceImpl method searchGenes.

/**
 * Search for genes (by name or symbol)
 *
 * @param taxonId, can be null to not constrain by taxon
 * @return Collection of Gene entity objects
 */
@Override
public Collection<GeneValueObject> searchGenes(String query, Long taxonId) {
    Taxon taxon = null;
    if (taxonId != null) {
        taxon = this.taxonService.load(taxonId);
    }
    SearchSettings settings = SearchSettingsImpl.geneSearch(query, taxon);
    List<SearchResult> geneSearchResults = this.searchService.search(settings).get(Gene.class);
    Collection<Gene> genes = new HashSet<>();
    if (geneSearchResults == null || geneSearchResults.isEmpty()) {
        GeneCoreServiceImpl.log.info("No Genes for search: " + query + " taxon=" + taxonId);
        return new HashSet<>();
    }
    GeneCoreServiceImpl.log.info("Gene search: " + query + " taxon=" + taxonId + ", " + geneSearchResults.size() + " found");
    for (SearchResult sr : geneSearchResults) {
        Gene g = (Gene) sr.getResultObject();
        g = geneService.thaw(g);
        genes.add(g);
        GeneCoreServiceImpl.log.debug("Gene search result: " + g.getOfficialSymbol());
    }
    Collection<GeneValueObject> geneValueObjects = geneService.loadValueObjects(genes);
    GeneCoreServiceImpl.log.debug("Gene search: " + geneValueObjects.size() + " value objects returned.");
    return geneValueObjects;
}

Example 79 with Taxon

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

the class ArrayDesignSequenceAssociationCli method doWork.

@Override
protected Exception doWork(String[] args) {
    try {
        Exception err = this.processCommandLine(args);
        if (err != null)
            return err;
        // this is kind of an oddball function of this tool.
        if (this.hasOption('s')) {
            BioSequence updated = arrayDesignSequenceProcessingService.processSingleAccession(this.sequenceId, new String[] { "nt", "est_others", "est_human", "est_mouse" }, null, force);
            if (updated != null) {
                AbstractCLI.log.info("Updated or created " + updated);
            }
            return null;
        }
        for (ArrayDesign arrayDesign : this.arrayDesignsToProcess) {
            arrayDesign = this.thaw(arrayDesign);
            SequenceType sequenceTypeEn = SequenceType.fromString(sequenceType);
            if (sequenceTypeEn == null) {
                AbstractCLI.log.error("No sequenceType " + sequenceType + " found");
                this.bail(ErrorCode.INVALID_OPTION);
            }
            if (this.hasOption('f')) {
                try (InputStream sequenceFileIs = FileTools.getInputStreamFromPlainOrCompressedFile(sequenceFile)) {
                    if (sequenceFileIs == null) {
                        AbstractCLI.log.error("No file " + sequenceFile + " was readable");
                        this.bail(ErrorCode.INVALID_OPTION);
                        return null;
                    }
                    Taxon taxon = null;
                    if (this.hasOption('t')) {
                        taxon = taxonService.findByCommonName(this.taxonName);
                        if (taxon == null) {
                            throw new IllegalArgumentException("No taxon named " + taxonName);
                        }
                    }
                    AbstractCLI.log.info("Processing ArrayDesign...");
                    arrayDesignSequenceProcessingService.processArrayDesign(arrayDesign, sequenceFileIs, sequenceTypeEn, taxon);
                    this.audit(arrayDesign, "Sequences read from file: " + sequenceFile);
                }
            } else if (this.hasOption('i')) {
                try (InputStream idFileIs = FileTools.getInputStreamFromPlainOrCompressedFile(idFile)) {
                    if (idFileIs == null) {
                        AbstractCLI.log.error("No file " + idFile + " was readable");
                        this.bail(ErrorCode.INVALID_OPTION);
                    }
                    Taxon taxon = null;
                    if (this.hasOption('t')) {
                        taxon = taxonService.findByCommonName(this.taxonName);
                        if (taxon == null) {
                            throw new IllegalArgumentException("No taxon named " + taxonName);
                        }
                    }
                    AbstractCLI.log.info("Processing ArrayDesign...");
                    arrayDesignSequenceProcessingService.processArrayDesign(arrayDesign, idFileIs, new String[] { "nt", "est_others", "est_human", "est_mouse" }, null, taxon, force);
                    this.audit(arrayDesign, "Sequences identifiers from file: " + idFile);
                }
            } else {
                AbstractCLI.log.info("Retrieving sequences from BLAST databases");
                arrayDesignSequenceProcessingService.processArrayDesign(arrayDesign, new String[] { "nt", "est_others", "est_human", "est_mouse" }, null, force);
                this.audit(arrayDesign, "Sequence looked up from BLAST databases");
            }
        }
    } catch (Exception e) {
        AbstractCLI.log.error(e, e);
        return e;
    }
    return null;
}

Example 80 with Taxon

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

the class GeneMultifunctionalityPopulationServiceImpl method updateMultifunctionality.

@Override
public void updateMultifunctionality() {
    for (Taxon t : taxonService.loadAll()) {
        GeneMultifunctionalityPopulationServiceImpl.log.info("Processing multifunctionality for " + t);
        this.updateMultifunctionality(t);
    }
}