Examples with RawExpressionDataVector ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector used on opensource projects

Example 21 with RawExpressionDataVector

use of ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector in project Gemma by PavlidisLab.

the class ExpressionExperimentServiceImpl method addRawVectors.

@Override
@Transactional
public ExpressionExperiment addRawVectors(ExpressionExperiment ee, Collection<RawExpressionDataVector> newVectors) {
    Collection<BioAssayDimension> BADs = new HashSet<>();
    Collection<QuantitationType> qts = new HashSet<>();
    for (RawExpressionDataVector vec : newVectors) {
        BADs.add(vec.getBioAssayDimension());
        qts.add(vec.getQuantitationType());
    }
    if (BADs.size() > 1) {
        throw new IllegalArgumentException("Vectors must share a common bioassay dimension");
    }
    if (qts.size() > 1) {
        throw new UnsupportedOperationException("Can only replace with one type of vector (only one quantitation type)");
    }
    BioAssayDimension bad = BADs.iterator().next();
    bad = this.bioAssayDimensionService.findOrCreate(bad);
    assert bad.getBioAssays().size() > 0;
    QuantitationType newQt = qts.iterator().next();
    if (newQt.getId() == null) {
        newQt = this.quantitationTypeDao.create(newQt);
    } else {
        AbstractService.log.warn("Quantitation type already had an ID...:" + newQt);
    }
    /*
         * This is probably a more or less redundant setting, but doesn't hurt to make sure.
         */
    ArrayDesign vectorAd = newVectors.iterator().next().getDesignElement().getArrayDesign();
    for (BioAssay ba : bad.getBioAssays()) {
        ba.setArrayDesignUsed(vectorAd);
    }
    for (RawExpressionDataVector vec : newVectors) {
        vec.setBioAssayDimension(bad);
        vec.setQuantitationType(newQt);
    }
    ee = rawExpressionDataVectorDao.addVectors(ee.getId(), newVectors);
    // this is a denormalization; easy to forget to update this.
    ee.getQuantitationTypes().add(newQt);
    AbstractService.log.info(ee.getRawExpressionDataVectors().size() + " vectors for experiment");
    return ee;
}

Example 22 with RawExpressionDataVector

use of ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector in project Gemma by PavlidisLab.

the class ExpressionExperimentServiceImpl method replaceRawVectors.

@Override
@Transactional
public ExpressionExperiment replaceRawVectors(ExpressionExperiment ee, Collection<RawExpressionDataVector> newVectors) {
    if (newVectors == null || newVectors.isEmpty()) {
        throw new UnsupportedOperationException("Only use this method for replacing vectors, not erasing them");
    }
    // to attach to session correctly.
    ExpressionExperiment eeToUpdate = this.load(ee.getId());
    Collection<QuantitationType> qtsToRemove = new HashSet<>();
    for (RawExpressionDataVector oldV : eeToUpdate.getRawExpressionDataVectors()) {
        qtsToRemove.add(oldV.getQuantitationType());
    }
    rawExpressionDataVectorDao.remove(eeToUpdate.getRawExpressionDataVectors());
    processedVectorService.remove(eeToUpdate.getProcessedExpressionDataVectors());
    eeToUpdate.getProcessedExpressionDataVectors().clear();
    eeToUpdate.getRawExpressionDataVectors().clear();
    // These QTs might still be getting used by the replaced vectors.
    for (RawExpressionDataVector newVec : newVectors) {
        qtsToRemove.remove(newVec.getQuantitationType());
    }
    for (QuantitationType oldQt : qtsToRemove) {
        quantitationTypeDao.remove(oldQt);
    }
    // Split the vectors up by bioassay dimension, if need be. This could be modified to handle multiple quantitation types if need be.
    Map<BioAssayDimension, Collection<RawExpressionDataVector>> BADs = new HashMap<>();
    for (RawExpressionDataVector vec : newVectors) {
        BioAssayDimension b = vec.getBioAssayDimension();
        if (!BADs.containsKey(b)) {
            BADs.put(b, new HashSet<RawExpressionDataVector>());
        }
        BADs.get(b).add(vec);
    }
    for (Collection<RawExpressionDataVector> vectors : BADs.values()) {
        ee = this.addRawVectors(eeToUpdate, vectors);
    }
    return ee;
}

Example 23 with RawExpressionDataVector

use of ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector in project Gemma by PavlidisLab.

the class ExpressionExperimentDaoImpl method removeDataVectors.

private int removeDataVectors(Session session, Set<BioAssayDimension> dims, Set<QuantitationType> qts, Collection<RawExpressionDataVector> designElementDataVectors, int count) {
    AbstractDao.log.info("Removing Design Element Data Vectors ...");
    for (RawExpressionDataVector dv : designElementDataVectors) {
        BioAssayDimension bad = dv.getBioAssayDimension();
        dims.add(bad);
        QuantitationType qt = dv.getQuantitationType();
        qts.add(qt);
        dv.setBioAssayDimension(null);
        dv.setQuantitationType(null);
        session.delete(dv);
        if (++count % 1000 == 0) {
            session.flush();
        }
        // put back...
        dv.setBioAssayDimension(bad);
        dv.setQuantitationType(qt);
        if (count % 20000 == 0) {
            AbstractDao.log.info(count + " design Element data vectors deleted");
        }
    }
    count = 0;
    return count;
}

Example 24 with RawExpressionDataVector

use of ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector in project Gemma by PavlidisLab.

the class RawExpressionDataVectorDaoImpl method find.

@Override
public RawExpressionDataVector find(RawExpressionDataVector designElementDataVector) {
    BusinessKey.checkKey(designElementDataVector);
    DetachedCriteria crit = DetachedCriteria.forClass(RawExpressionDataVector.class);
    crit.createCriteria("designElement").add(Restrictions.eq("name", designElementDataVector.getDesignElement().getName())).createCriteria("arrayDesign").add(Restrictions.eq("name", designElementDataVector.getDesignElement().getArrayDesign().getName()));
    crit.createCriteria("quantitationType").add(Restrictions.eq("name", designElementDataVector.getQuantitationType().getName()));
    crit.createCriteria("expressionExperiment").add(Restrictions.eq("name", designElementDataVector.getExpressionExperiment().getName()));
    List<?> results = this.getHibernateTemplate().findByCriteria(crit);
    Object result = null;
    if (results != null) {
        if (results.size() > 1) {
            throw new org.springframework.dao.InvalidDataAccessResourceUsageException("More than one instance of '" + DesignElementDataVector.class.getName() + "' was found when executing query");
        } else if (results.size() == 1) {
            result = results.iterator().next();
        }
    }
    return (RawExpressionDataVector) result;
}

Example 25 with RawExpressionDataVector

use of ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector in project Gemma by PavlidisLab.

the class PersistentDummyObjectHelper method getTestPersistentExpressionExperiment.

/**
 * Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test
 * objects. This implementation does NOT fill in associations of the created object except for the creation of
 * persistent BioMaterials and BioAssays so that database taxon lookups for this experiment will work.
 *
 * @param taxon the experiment will have this taxon
 * @return EE
 */
public ExpressionExperiment getTestPersistentExpressionExperiment(Taxon taxon) {
    BioAssay ba;
    BioMaterial bm;
    ArrayDesign ad;
    bm = this.getTestPersistentBioMaterial(taxon);
    ad = this.getTestPersistentArrayDesign(4, true, true);
    ba = this.getTestPersistentBioAssay(ad, bm);
    Set<BioAssay> bas1 = new HashSet<>();
    bas1.add(ba);
    ExpressionExperiment ee = ExpressionExperiment.Factory.newInstance();
    ee.setName(RandomStringUtils.randomNumeric(PersistentDummyObjectHelper.RANDOM_STRING_LENGTH) + "_testee");
    ee.setShortName(RandomStringUtils.randomNumeric(PersistentDummyObjectHelper.RANDOM_STRING_LENGTH) + "_testee");
    ee.setBioAssays(bas1);
    Collection<FactorValue> allFactorValues = new HashSet<>();
    ExperimentalDesign ed = this.getExperimentalDesign(allFactorValues);
    ee.setExperimentalDesign(ed);
    ee.setOwner(this.getTestPersistentContact());
    log.debug("expression experiment => design element data vectors");
    Collection<RawExpressionDataVector> vectors = new HashSet<>();
    Collection<QuantitationType> quantitationTypes = this.addQuantitationTypes(new HashSet<QuantitationType>());
    assert quantitationTypes.size() > 0;
    ee.setQuantitationTypes(quantitationTypes);
    ee.setRawExpressionDataVectors(vectors);
    ArrayDesignsForExperimentCache c = persisterHelper.prepare(ee);
    return persisterHelper.persist(ee, c);
}