Examples with ExperimentCoexpressionLink ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink used on opensource projects

Example 1 with ExperimentCoexpressionLink

use of ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink in project Gemma by PavlidisLab.

the class CoexpressionDaoImpl method saveExperimentLevelLinks.

private void saveExperimentLevelLinks(Session sess, LinkCreator c, TreeMap<Long, NonPersistentNonOrderedCoexpLink> links, BioAssaySet bioAssaySet) {
    int progress = 0;
    int BATCH_SIZE = 1024;
    List<ExperimentCoexpressionLink> flippedLinks = new ArrayList<>();
    for (Long linkid : links.keySet()) {
        NonPersistentNonOrderedCoexpLink link = links.get(linkid);
        ExperimentCoexpressionLink ecl = c.createEELink(bioAssaySet, linkid, link.getFirstGene(), link.getSecondGene());
        /*
             * At same time, create flipped versions, but save them later for ordering. Notice that we use the SAME link
             * ID - not the one for the flipped version in the gene2gene table.
             *
             * Ideally we would ensure that the gene2gene link ID used is the same for all links that are between
             * the same pair of genes. That would let us be able to easily count the support directly from an
             * experiment-level query, without going to the supportDetails. I do not believe the current code guarantees
             * this.
             */
        flippedLinks.add(c.createEELink(bioAssaySet, linkid, link.getSecondGene(), link.getFirstGene()));
        sess.save(ecl);
        if (++progress % 50000 == 0) {
            CoexpressionDaoImpl.log.info("Created " + progress + "/" + links.size() + " experiment-level links...");
        }
        if (progress % BATCH_SIZE == 0) {
            sess.flush();
            sess.clear();
        }
    }
    sess.flush();
    sess.clear();
    /*
         * Sort the flipped links by the first gene
         */
    Collections.sort(flippedLinks, new Comparator<ExperimentCoexpressionLink>() {

        @Override
        public int compare(ExperimentCoexpressionLink o1, ExperimentCoexpressionLink o2) {
            return o1.getFirstGene().compareTo(o2.getFirstGene());
        }
    });
    /*
         * Save the flipped ones.
         */
    progress = 0;
    for (ExperimentCoexpressionLink fl : flippedLinks) {
        sess.save(fl);
        if (++progress % 50000 == 0) {
            CoexpressionDaoImpl.log.info("Created " + progress + "/" + links.size() + " flipped experiment-level links...");
        }
        if (progress % BATCH_SIZE == 0) {
            sess.flush();
            sess.clear();
        }
    }
    // one for the road.
    sess.flush();
    sess.clear();
}

Example 2 with ExperimentCoexpressionLink

use of ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink in project Gemma by PavlidisLab.

the class CoexpressionDaoImpl method getCoexpression.

@Override
@Transactional(readOnly = true)
public Collection<CoexpressionValueObject> getCoexpression(Taxon taxon, BioAssaySet experiment, boolean quick) {
    Session sess = this.getSessionFactory().getCurrentSession();
    // could just fetch linkId.
    Query q = sess.createQuery(" from " + CoexpressionQueryUtils.getExperimentLinkClassName(taxon) + " where experiment=:ee");
    q.setParameter("ee", experiment);
    List<ExperimentCoexpressionLink> links = q.list();
    Collection<CoexpressionValueObject> results = new HashSet<>();
    if (links.isEmpty()) {
        return results;
    }
    List<Long> linksToFetch = new ArrayList<>();
    for (ExperimentCoexpressionLink link : links) {
        linksToFetch.add(link.getLinkId());
    }
    String q2 = "from " + CoexpressionQueryUtils.getGeneLinkClassName(taxon) + " where id in (:ids)";
    BatchIterator<Long> it = BatchIterator.batches(linksToFetch, 1000);
    for (; it.hasNext(); ) {
        List<Gene2GeneCoexpression> rawResults = sess.createQuery(q2).setParameterList("ids", it.next()).list();
        for (Gene2GeneCoexpression g2g : rawResults) {
            CoexpressionValueObject g2gvo = new CoexpressionValueObject(g2g);
            results.add(g2gvo);
        }
    }
    if (!quick) {
        this.populateTestedInDetails(results);
    }
    return results;
}

Example 3 with ExperimentCoexpressionLink

use of ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink in project Gemma by PavlidisLab.

the class CoexpressionDaoImpl method getCoexpressionFromCacheOrDbViaExperiments.

/*
     * Get links from the cache or the database, querying in experiment-first mode, but constrained to involve the given
     * genes. Does not do the trimming step, nor are the results guaranteed to meet the stringency set.
     */
private Map<Long, List<CoexpressionValueObject>> getCoexpressionFromCacheOrDbViaExperiments(Taxon t, Collection<Long> genes, Collection<Long> bas, int stringency, boolean quick) {
    assert stringency <= bas.size();
    assert !genes.isEmpty();
    Map<Long, List<CoexpressionValueObject>> results = new HashMap<>();
    /*
         * First, check the cache -- if the stringency is >= limit
         */
    Collection<Long> genesNeeded = new HashSet<>(genes);
    if (stringency >= CoexpressionCache.CACHE_QUERY_STRINGENCY) {
        genesNeeded = this.checkCache(genes, results);
        if (genesNeeded.isEmpty()) {
            return results;
        }
    }
    /*
         * Get all the data for all the experiments queried, constrained to involve the genes in question.
         *
         * This uses the ECL1EFK index, which is of (experiment, gene1, gene2). Note that if there are a lot of genes
         * this can get slow ...
         */
    Query q = this.getSessionFactory().getCurrentSession().createQuery(" from " + CoexpressionQueryUtils.getExperimentLinkClassName(t) + " where experiment.id in (:ees) and firstGene in (:genes)");
    // May need to batch over genes...
    BatchIterator<Long> it = BatchIterator.batches(bas, CoexpressionDaoImpl.BATCH_SIZE_SMALL);
    StopWatch timer = new StopWatch();
    timer.start();
    List<ExperimentCoexpressionLink> links = new ArrayList<>();
    for (; it.hasNext(); ) {
        q.setParameterList("ees", it.next()).setParameterList("genes", genesNeeded);
        links.addAll(q.list());
    }
    if (timer.getTime() > 2000) {
        CoexpressionDaoImpl.log.info("Query for coexp for : " + genes.size() + " genes " + " in " + bas.size() + " experiments: " + timer.getTime() + "ms");
    }
    /*
         * Track the support for the links among the queried data sets as we go over this in experiment-major mode.
         */
    // noinspection MismatchedQueryAndUpdateOfCollection // We still need to compare it to stringency
    CountingMap<Long> supportCounts = new CountingMap<>();
    List<Long> keepers = new ArrayList<>();
    for (ExperimentCoexpressionLink link : links) {
        assert genes.contains(link.getFirstGene());
        if (supportCounts.increment(link.getLinkId()) >= stringency) {
            keepers.add(link.getLinkId());
        }
    }
    if (keepers.isEmpty()) {
        return new HashMap<>();
    }
    return this.loadAndConvertLinks(t, keepers, genes, quick);
}