Examples with DatabaseBackedGeneSetValueObject ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject used on opensource projects

Example 1 with DatabaseBackedGeneSetValueObject

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

the class GeneSetController method removeUserAndSessionGroups.

/**
 * AJAX Given valid gene groups will remove them from the session or the database appropriately.
 *
 * @param vos vos
 * @return gene set vos
 */
public Collection<GeneSetValueObject> removeUserAndSessionGroups(Collection<GeneSetValueObject> vos) {
    Collection<GeneSetValueObject> removedSets = new HashSet<>();
    Collection<DatabaseBackedGeneSetValueObject> databaseCollection = new HashSet<>();
    Collection<SessionBoundGeneSetValueObject> sessionCollection = new HashSet<>();
    for (GeneSetValueObject geneSetValueObject : vos) {
        if (geneSetValueObject instanceof SessionBoundGeneSetValueObject) {
            sessionCollection.add((SessionBoundGeneSetValueObject) geneSetValueObject);
        } else if (geneSetValueObject instanceof DatabaseBackedGeneSetValueObject) {
            databaseCollection.add((DatabaseBackedGeneSetValueObject) geneSetValueObject);
        }
    }
    sessionCollection = this.removeSessionGroups(sessionCollection);
    databaseCollection = this.remove(databaseCollection);
    removedSets.addAll(sessionCollection);
    removedSets.addAll(databaseCollection);
    return removedSets;
}

Example 2 with DatabaseBackedGeneSetValueObject

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

the class GeneSetController method updateUserAndSessionGroups.

/**
 * AJAX Updates the session group and user database groups.
 *
 * @param vos vos
 * @return gene set vos
 */
public Collection<GeneSetValueObject> updateUserAndSessionGroups(Collection<GeneSetValueObject> vos) {
    Collection<GeneSetValueObject> updatedSets = new HashSet<>();
    Collection<DatabaseBackedGeneSetValueObject> databaseCollection = new HashSet<>();
    Collection<SessionBoundGeneSetValueObject> sessionCollection = new HashSet<>();
    for (GeneSetValueObject geneSetValueObject : vos) {
        if (geneSetValueObject instanceof SessionBoundGeneSetValueObject) {
            sessionCollection.add((SessionBoundGeneSetValueObject) geneSetValueObject);
        } else if (geneSetValueObject instanceof DatabaseBackedGeneSetValueObject) {
            databaseCollection.add((DatabaseBackedGeneSetValueObject) geneSetValueObject);
        }
    }
    sessionCollection = this.updateSessionGroups(sessionCollection);
    databaseCollection = this.update(databaseCollection);
    updatedSets.addAll(sessionCollection);
    updatedSets.addAll(databaseCollection);
    return updatedSets;
}

Example 3 with DatabaseBackedGeneSetValueObject

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

the class GeneSetDaoImpl method loadValueObjects.

@Override
public Collection<DatabaseBackedGeneSetValueObject> loadValueObjects(Collection<Long> ids) {
    Collection<DatabaseBackedGeneSetValueObject> result = this.loadValueObjectsLite(ids);
    for (GeneSetValueObject res : result) {
        res.setGeneIds(new HashSet<Long>());
        // noinspection unchecked
        res.getGeneIds().addAll(this.getSessionFactory().getCurrentSession().createQuery("select genes.id from GeneSet g join g.members m join m.gene genes where g.id = :id").setParameter("id", res.getId()).list());
    }
    return result;
}

Example 4 with DatabaseBackedGeneSetValueObject

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

the class GeneSetDaoImpl method loadValueObjectsLite.

@Override
public Collection<DatabaseBackedGeneSetValueObject> loadValueObjectsLite(Collection<Long> ids) {
    Collection<DatabaseBackedGeneSetValueObject> result = new HashSet<>();
    if (ids.isEmpty())
        return result;
    // Left join: includes one that have no members. Caller has to filter them out if they need to.
    // noinspection unchecked
    List<Object[]> list = this.getSessionFactory().getCurrentSession().createQuery("select g.id, g.description, count(m), g.name from GeneSet g" + " left join g.members m where g.id in (:ids) group by g.id").setParameterList("ids", ids).list();
    Map<Long, Taxon> taxa = this.getTaxa(ids);
    for (Object[] oa : list) {
        DatabaseBackedGeneSetValueObject dvo = new DatabaseBackedGeneSetValueObject();
        dvo.setDescription((String) oa[1]);
        dvo.setId((Long) oa[0]);
        dvo.setSize(((Long) oa[2]).intValue());
        dvo.setName((String) oa[3]);
        Taxon t = taxa.get(dvo.getId());
        dvo.setTaxonId(t.getId());
        dvo.setTaxonName(t.getCommonName());
        result.add(dvo);
    }
    return result;
}

Example 5 with DatabaseBackedGeneSetValueObject

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

the class GeneSetValueObjectHelperImpl method convertToValueObject.

@Override
public DatabaseBackedGeneSetValueObject convertToValueObject(GeneSet gs) {
    if (gs == null)
        return null;
    DatabaseBackedGeneSetValueObject dbgsvo = convertToLightValueObject(gs);
    Collection<Long> ids = EntityUtils.getIds(this.geneSetService.getGenesInGroup(new GeneSetValueObject(gs.getId())));
    dbgsvo.getGeneIds().addAll(ids);
    dbgsvo.setSize(ids.size());
    return dbgsvo;
}