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

Example 16 with RawExpressionDataVector

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

the class GeoConverterTest method testConvertGSE2982.

@SuppressWarnings("unchecked")
@Test
public void testConvertGSE2982() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/gse2982Short/GSE2982_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE2982");
    DatasetCombiner datasetCombiner = new DatasetCombiner();
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    Object result = this.gc.convert(series);
    assertNotNull(result);
    Collection<ExpressionExperiment> ees = (Collection<ExpressionExperiment>) result;
    assertEquals(1, ees.size());
    ExpressionExperiment ee = ees.iterator().next();
    boolean ok = false;
    for (RawExpressionDataVector dedv : ee.getRawExpressionDataVectors()) {
        QuantitationType qt = dedv.getQuantitationType();
        if (qt.getIsPreferred()) {
            ok = true;
            assertEquals("VALUE", qt.getName());
            assertEquals(StandardQuantitationType.AMOUNT, qt.getType());
            assertTrue(qt.getIsRatio());
        }
    }
    assertTrue(ok);
}

Example 17 with RawExpressionDataVector

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

the class TwoChannelMissingValueCLI method processExperiment.

private boolean processExperiment(ExpressionExperiment ee) {
    Collection<QuantitationType> types = eeService.getQuantitationTypes(ee);
    ee = this.eeService.thawLite(ee);
    if (!force && this.noNeedToRun(ee, MissingValueAnalysisEvent.class))
        return false;
    QuantitationType previousMissingValueQt = null;
    for (QuantitationType qType : types) {
        if (qType.getType() == StandardQuantitationType.PRESENTABSENT) {
            if (previousMissingValueQt != null) {
                AbstractCLI.log.warn("More than one present/absent quantitationtype!");
            }
            previousMissingValueQt = qType;
        }
    }
    if (previousMissingValueQt != null && !force) {
        AbstractCLI.log.warn(ee + " already has missing value vectors, skipping");
        return false;
    }
    if (force && previousMissingValueQt != null) {
        AbstractCLI.log.info("Removing old present/absent data");
        rawService.removeDataForQuantitationType(previousMissingValueQt);
        procService.removeDataForQuantitationType(previousMissingValueQt);
        quantitationTypeService.remove(previousMissingValueQt);
    }
    AbstractCLI.log.info("Got " + ee + ", thawing...");
    AbstractCLI.log.info("Computing missing value data..");
    Collection<RawExpressionDataVector> missingValueVectors = tcmv.computeMissingValues(ee, s2n, this.extraMissingValueIndicators);
    if (missingValueVectors.size() == 0) {
        AbstractCLI.log.warn("No missing value vectors computed");
        return false;
    }
    try {
        preprocessorService.process(ee, true);
    } catch (PreprocessingException e) {
        AbstractCLI.log.error("Error during postprocessing of " + ee + " , make sure additional steps are completed", e);
    }
    return true;
}

Example 18 with RawExpressionDataVector

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

the class ExpressionExperimentServiceTest method testGetRawExpressionDataVectors.

@Test
public final void testGetRawExpressionDataVectors() {
    ExpressionExperiment eel = this.getTestPersistentCompleteExpressionExperiment(false);
    Collection<CompositeSequence> designElements = new HashSet<>();
    QuantitationType quantitationType = eel.getRawExpressionDataVectors().iterator().next().getQuantitationType();
    Collection<RawExpressionDataVector> allv = eel.getRawExpressionDataVectors();
    assertNotNull(quantitationType);
    assertTrue(allv.size() > 1);
    for (RawExpressionDataVector anAllv : allv) {
        CompositeSequence designElement = anAllv.getDesignElement();
        assertNotNull(designElement);
        designElements.add(designElement);
        if (designElements.size() == 2)
            break;
    }
    assertEquals(2, designElements.size());
    Collection<? extends DesignElementDataVector> vectors = rawExpressionDataVectorService.find(designElements, quantitationType);
    assertEquals(2, vectors.size());
}

Example 19 with RawExpressionDataVector

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

the class ExpressionExperimentPlatformSwitchService method runOldAd.

private void runOldAd(ExpressionExperiment ee, ArrayDesign arrayDesign, Map<BioSequence, Collection<CompositeSequence>> designElementMap, BioAssayDimension maxBAD, Map<CompositeSequence, Collection<BioAssayDimension>> usedDesignElements, ArrayDesign oldAd) {
    if (oldAd.equals(arrayDesign))
        return;
    oldAd = arrayDesignService.thaw(oldAd);
    if (oldAd.getCompositeSequences().size() == 0 && !oldAd.getTechnologyType().equals(TechnologyType.NONE)) {
        /*
             * Bug 3451 - this is okay if it is a RNA-seq experiment etc. prior to data upload.
             */
        throw new IllegalStateException(oldAd + " has no elements");
    }
    Collection<QuantitationType> qts = expressionExperimentService.getQuantitationTypes(ee, oldAd);
    ExpressionExperimentPlatformSwitchService.log.info("Processing " + qts.size() + " quantitation types for vectors on " + oldAd);
    for (QuantitationType type : qts) {
        // use each design element only once per quantitation type + bioassaydimension per array design
        usedDesignElements.clear();
        Collection<RawExpressionDataVector> rawForQt = this.getRawVectorsForOneQuantitationType(oldAd, type);
        Collection<ProcessedExpressionDataVector> processedForQt = this.getProcessedVectorsForOneQuantitationType(oldAd, type);
        if (// 
        (rawForQt == null || rawForQt.size() == 0) && (processedForQt == null || processedForQt.size() == 0)) {
            /*
                 * This can happen when the quantitation types vary for the array designs.
                 */
            ExpressionExperimentPlatformSwitchService.log.debug("No vectors for " + type + " on " + oldAd);
            continue;
        }
        // This check assures we do not mix raw and processed vectors further down the line
        if ((rawForQt != null && rawForQt.size() > 0) && (processedForQt != null && processedForQt.size() > 0)) {
            throw new IllegalStateException("Two types of vector for quantitationType " + type);
        }
        Collection<DesignElementDataVector> vectors = new HashSet<>();
        if (rawForQt != null) {
            vectors.addAll(rawForQt);
        }
        if (processedForQt != null) {
            vectors.addAll(processedForQt);
        }
        ExpressionExperimentPlatformSwitchService.log.info("Switching " + vectors.size() + " vectors for " + type + " from " + oldAd.getShortName() + " to " + arrayDesign.getShortName());
        int count = 0;
        // noinspection MismatchedQueryAndUpdateOfCollection // Only used for logging
        Collection<DesignElementDataVector> unMatched = new HashSet<>();
        for (DesignElementDataVector vector : vectors) {
            assert RawExpressionDataVector.class.isAssignableFrom(vector.getClass()) : "Unexpected class: " + vector.getClass().getName();
            CompositeSequence oldDe = vector.getDesignElement();
            if (oldDe.getArrayDesign().equals(arrayDesign)) {
                continue;
            }
            this.processVector(designElementMap, usedDesignElements, vector, maxBAD);
            if (++count % 20000 == 0) {
                ExpressionExperimentPlatformSwitchService.log.info("Found matches for " + count + " vectors for " + type);
            }
        }
        /*
             * This is bad.
             */
        if (unMatched.size() > 0) {
            throw new IllegalStateException("There were " + unMatched.size() + " vectors that couldn't be matched to the new design for: " + type + ", example: " + unMatched.iterator().next());
        }
        // Force collection update
        if (rawForQt != null && rawForQt.size() > 0) {
            int s = ee.getRawExpressionDataVectors().size();
            ee.getRawExpressionDataVectors().removeAll(rawForQt);
            assert s > ee.getRawExpressionDataVectors().size();
            ee.getRawExpressionDataVectors().addAll(rawForQt);
            assert s == ee.getRawExpressionDataVectors().size();
        } else if (processedForQt != null && processedForQt.size() > 0) {
            int s = ee.getProcessedExpressionDataVectors().size();
            ee.getProcessedExpressionDataVectors().removeAll(processedForQt);
            assert s > ee.getProcessedExpressionDataVectors().size();
            ee.getProcessedExpressionDataVectors().addAll(processedForQt);
            assert s == ee.getProcessedExpressionDataVectors().size();
        }
    }
}

Example 20 with RawExpressionDataVector

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

the class ExpressionExperimentServiceImpl method removeRawVectors.

@Override
@Transactional
public int removeRawVectors(ExpressionExperiment ee, QuantitationType qt) {
    ExpressionExperiment eeToUpdate = this.load(ee.getId());
    Collection<RawExpressionDataVector> vectorsToRemove = new ArrayList<>();
    for (RawExpressionDataVector oldV : eeToUpdate.getRawExpressionDataVectors()) {
        if (oldV.getQuantitationType().equals(qt)) {
            vectorsToRemove.add(oldV);
        }
    }
    if (vectorsToRemove.isEmpty()) {
        throw new IllegalArgumentException("No vectors to remove for quantitation type=" + qt);
    }
    eeToUpdate.getRawExpressionDataVectors().removeAll(vectorsToRemove);
    AbstractService.log.info("Removing unused quantitation type: " + qt);
    eeToUpdate.getQuantitationTypes().remove(qt);
    return vectorsToRemove.size();
}