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

Example 21 with BibliographicReference

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

the class GeoServiceImpl method getPubMedInfo.

private void getPubMedInfo(Collection<ExpressionExperiment> result) {
    for (ExpressionExperiment experiment : result) {
        BibliographicReference pubmed = experiment.getPrimaryPublication();
        if (pubmed == null)
            continue;
        PubMedXMLFetcher fetcher = new PubMedXMLFetcher();
        try {
            pubmed = fetcher.retrieveByHTTP(Integer.parseInt(pubmed.getPubAccession().getAccession()));
        } catch (Exception e) {
            AbstractGeoService.log.warn("Filed to get data from pubmed, continuing without it.");
            AbstractGeoService.log.error(e, e);
        }
        if (pubmed == null)
            continue;
        experiment.setPrimaryPublication(pubmed);
    }
}

Example 22 with BibliographicReference

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

the class GeeqServiceImpl method scorePublication.

/*
     * Suitability scoring methods
     */
private void scorePublication(ExpressionExperiment ee, Geeq gq) {
    double score;
    boolean hasBib;
    BibliographicReference bib = null;
    if (ee.getPrimaryPublication() != null) {
        bib = ee.getPrimaryPublication();
    } else if (ee.getOtherRelevantPublications() != null && ee.getOtherRelevantPublications().size() > 0) {
        bib = ee.getOtherRelevantPublications().iterator().next();
    }
    hasBib = bib != null;
    score = !hasBib ? GeeqServiceImpl.N_10 : GeeqServiceImpl.P_10;
    gq.setsScorePublication(score);
}

Example 23 with BibliographicReference

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

the class BibliographicReferenceDaoImpl method getRelatedExperiments.

@Override
public Map<BibliographicReference, Collection<ExpressionExperiment>> getRelatedExperiments(Collection<BibliographicReference> records) {
    final String query = "select distinct e, b from ExpressionExperiment " + "e join e.primaryPublication b left join fetch b.pubAccession where b in (:recs)";
    Map<BibliographicReference, Collection<ExpressionExperiment>> result = new HashMap<>();
    for (Collection<BibliographicReference> batch : BatchIterator.batches(records, 200)) {
        // noinspection unchecked
        List<Object[]> os = this.getSessionFactory().getCurrentSession().createQuery(query).setParameterList("recs", batch).list();
        for (Object[] o : os) {
            ExpressionExperiment e = (ExpressionExperiment) o[0];
            BibliographicReference b = (BibliographicReference) o[1];
            if (!result.containsKey(b)) {
                result.put(b, new HashSet<ExpressionExperiment>());
            }
            result.get(b).add(e);
        }
    }
    return result;
}

Example 24 with BibliographicReference

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

the class PubMedSearcher method doWork.

@Override
protected Exception doWork(String[] args) {
    Exception err = this.processCommandLine(args);
    if (err != null)
        return err;
    try {
        @SuppressWarnings("unchecked") Collection<BibliographicReference> refs = PubMedSearcher.pms.searchAndRetrieveByHTTP((Collection<String>) this.getArgList());
        System.out.println(refs.size() + " references found");
        if (this.hasOption("d")) {
            this.getPersisterHelper().persist(refs);
        }
    } catch (IOException | ParserConfigurationException | SAXException e) {
        return e;
    }
    this.resetLogging();
    return null;
}

Example 25 with BibliographicReference

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

the class PubMedXMLFetcher method retrieveByHTTP.

public BibliographicReference retrieveByHTTP(int pubMedId) {
    Collection<BibliographicReference> results = null;
    try {
        for (int i = 0; i < MAX_TRIES; i++) {
            URL toBeGotten = new URL(uri + pubMedId);
            log.debug("Fetching " + toBeGotten);
            PubMedXMLParser pmxp = new PubMedXMLParser();
            results = pmxp.parse(toBeGotten.openStream());
            if (results != null && results.size() > 0)
                break;
            try {
                Thread.sleep(500);
            } catch (InterruptedException e) {
            // noop
            }
        }
        if (results == null || results.size() == 0) {
            return null;
        }
        assert results.size() == 1;
        return results.iterator().next();
    } catch (IOException e) {
        throw new RuntimeException(e);
    }
}