Examples with ExpressionExperimentSubSet ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet used on opensource projects

Example 1 with ExpressionExperimentSubSet

use of ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet in project Gemma by PavlidisLab.

the class ExpressionExperimentPlatformSwitchService method switchExperimentToArrayDesign.

/**
 * If you know the arraydesigns are already in a merged state, you should use switchExperimentToMergedPlatform
 *
 * @param ee          ee
 * @param arrayDesign The array design to switch to. If some samples already use that array design, nothing will be
 *                    changed for them.
 */
public ExpressionExperiment switchExperimentToArrayDesign(ExpressionExperiment ee, ArrayDesign arrayDesign) {
    assert arrayDesign != null;
    // remove stuff that will be in the way.
    processedExpressionDataVectorService.removeProcessedDataVectors(ee);
    sampleCoexpressionMatrixService.delete(ee);
    for (ExpressionExperimentSubSet subset : expressionExperimentService.getSubSets(ee)) {
        subsetService.remove(subset);
    }
    // get relation between sequence and designelements.
    Map<BioSequence, Collection<CompositeSequence>> designElementMap = new HashMap<>();
    Collection<CompositeSequence> elsWithNoSeq = new HashSet<>();
    this.populateCSeq(arrayDesign, designElementMap, elsWithNoSeq);
    ee = expressionExperimentService.thaw(ee);
    ExpressionExperimentPlatformSwitchService.log.info(elsWithNoSeq.size() + " elements on the new platform have no associated sequence.");
    designElementMap.put(ExpressionExperimentPlatformSwitchService.NULL_BIOSEQUENCE, elsWithNoSeq);
    boolean multiPlatformPerSample = this.checkMultiPerSample(ee, arrayDesign);
    /*
         * For a multiplatform-per-sample case: (note that some samples might just be on one platform...)
         * 1. Pick a BAD that can be used for all DataVectors (it has all BioAssays in it).
         * 2. Switch vectors to use it - may require adding NaNs and reordering the vectors
         * 3. Delete the Bioassays that are using other BADs
         */
    /*
         * Now we have to get the BADs. Problem to watch out for: they might not be the same length, we need one that
         * includes all BioMaterials.
         */
    Collection<BioAssayDimension> unusedBADs = new HashSet<>();
    BioAssayDimension maxBAD = null;
    int maxSize = 0;
    if (multiPlatformPerSample) {
        maxBAD = this.doMultiSample(ee, unusedBADs, maxSize);
    }
    Collection<ArrayDesign> oldArrayDesigns = expressionExperimentService.getArrayDesignsUsed(ee);
    Map<CompositeSequence, Collection<BioAssayDimension>> usedDesignElements = new HashMap<>();
    for (ArrayDesign oldAd : oldArrayDesigns) {
        this.runOldAd(ee, arrayDesign, designElementMap, maxBAD, usedDesignElements, oldAd);
    }
    ee.setDescription(ee.getDescription() + " [Switched to use " + arrayDesign.getShortName() + " by Gemma]");
    helperService.persist(ee, arrayDesign);
    /*
         * This might need to be done inside the transaction we're using to make the switch.
         */
    if (maxBAD != null && !unusedBADs.isEmpty()) {
        this.checkUnused(unusedBADs, maxBAD);
    }
    return ee;
}

Example 2 with ExpressionExperimentSubSet

use of ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet in project Gemma by PavlidisLab.

the class ExpressionExperimentSubSetDaoImpl method find.

@Override
public ExpressionExperimentSubSet find(ExpressionExperimentSubSet entity) {
    Criteria queryObject = this.getSessionFactory().getCurrentSession().createCriteria(ExpressionExperimentSubSet.class);
    BusinessKey.checkKey(entity);
    BusinessKey.createQueryObject(queryObject, entity);
    return (ExpressionExperimentSubSet) queryObject.uniqueResult();
}

Example 3 with ExpressionExperimentSubSet

use of ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet in project Gemma by PavlidisLab.

the class ProcessedExpressionDataVectorDaoImpl method checkCache.

/**
 * We cache vectors at the experiment level. If we need subsets, we have to slice them out.
 *
 * @param bioAssaySets  that we exactly need the data for.
 * @param genes         that might have cached results
 * @param results       from the cache will be put here
 * @param needToSearch  experiments that need to be searched (not fully cached); this will be populated
 * @param genesToSearch that still need to be searched (not in cache)
 */
private void checkCache(Collection<? extends BioAssaySet> bioAssaySets, Collection<Long> genes, Collection<DoubleVectorValueObject> results, Collection<ExpressionExperiment> needToSearch, Collection<Long> genesToSearch) {
    for (BioAssaySet ee : bioAssaySets) {
        ExpressionExperiment experiment = null;
        boolean needSubSet = false;
        if (ee instanceof ExpressionExperiment) {
            experiment = (ExpressionExperiment) ee;
        } else if (ee instanceof ExpressionExperimentSubSet) {
            experiment = ((ExpressionExperimentSubSet) ee).getSourceExperiment();
            needSubSet = true;
        }
        assert experiment != null;
        for (Long g : genes) {
            Collection<DoubleVectorValueObject> obs = processedDataVectorCache.get(ee, g);
            if (obs != null) {
                if (needSubSet) {
                    obs = this.sliceSubSet((ExpressionExperimentSubSet) ee, obs);
                }
                results.addAll(obs);
            } else {
                genesToSearch.add(g);
            }
        }
        /*
             * This experiment is not fully cached for the genes in question.
             */
        if (genesToSearch.size() > 0) {
            needToSearch.add(experiment);
        }
    }
}

Example 4 with ExpressionExperimentSubSet

use of ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet in project Gemma by PavlidisLab.

the class ProcessedExpressionDataVectorDaoImpl method sliceSubsets.

/**
 * @param ees  Experiments and/or subsets required
 * @param vecs vectors to select from and if necessary slice, obviously from the given ees.
 * @return vectors that are for the requested subset. If an ee is not a subset, vectors will be unchanged. Otherwise
 * the data in a vector will be for the subset of samples in the ee subset.
 */
private Collection<DoubleVectorValueObject> sliceSubsets(Collection<? extends BioAssaySet> ees, Collection<DoubleVectorValueObject> vecs) {
    Collection<DoubleVectorValueObject> results = new HashSet<>();
    if (vecs == null || vecs.isEmpty())
        return results;
    for (BioAssaySet bas : ees) {
        if (bas instanceof ExpressionExperimentSubSet) {
            for (DoubleVectorValueObject d : vecs) {
                if (d.getExpressionExperiment().getId().equals(((ExpressionExperimentSubSet) bas).getSourceExperiment().getId())) {
                    Collection<DoubleVectorValueObject> ddvos = new HashSet<>();
                    ddvos.add(d);
                    // coll
                    results.addAll(this.sliceSubSet((ExpressionExperimentSubSet) bas, ddvos));
                }
            }
        } else {
            for (DoubleVectorValueObject d : vecs) {
                if (d.getExpressionExperiment().getId().equals(bas.getId())) {
                    results.add(d);
                }
            }
        }
    }
    return results;
}

Example 5 with ExpressionExperimentSubSet

use of ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet in project Gemma by PavlidisLab.

the class ExpressionExperimentSubSetServiceTest method testFind.

@Test
public final void testFind() {
    ExpressionExperiment ee = super.testHelper.getTestPersistentBasicExpressionExperiment();
    aclTestUtils.checkEEAcls(ee);
    ExpressionExperimentSubSet subset = ExpressionExperimentSubSet.Factory.newInstance();
    subset.setSourceExperiment(ee);
    subset.getBioAssays().addAll(ee.getBioAssays());
    subset.setName("foo");
    ExpressionExperimentSubSet persisted = expressionExperimentSubSetService.create(subset);
    assertNotNull(persisted);
    aclTestUtils.checkEESubSetAcls(persisted);
    ExpressionExperimentSubSet hit = expressionExperimentSubSetService.find(persisted);
    assertEquals(persisted, hit);
}