Examples with DataUpdater ubic.gemma.core.loader.expression.geo.DataUpdater used on opensource projects

Example 1 with DataUpdater

use of ubic.gemma.core.loader.expression.geo.DataUpdater in project Gemma by PavlidisLab.

the class AffyDataFromCelCli method doWork.

@Override
protected Exception doWork(String[] args) {
    Exception e = super.processCommandLine(args);
    if (e != null)
        return e;
    DataUpdater serv = this.getBean(DataUpdater.class);
    // This can be done for multiple experiments under some conditions; we get this one just  to test for some multi-platform situations
    Collection<ArrayDesign> arrayDesignsUsed = this.eeService.getArrayDesignsUsed(this.expressionExperiments.iterator().next());
    if (StringUtils.isNotBlank(aptFile)) {
        if (this.expressionExperiments.size() > 1) {
            throw new IllegalArgumentException("Can't use " + AffyDataFromCelCli.APT_FILE_OPT + " unless you are doing just one experiment");
        }
        ExpressionExperiment thawedEe = (ExpressionExperiment) this.expressionExperiments.iterator().next();
        thawedEe = this.eeService.thawLite(thawedEe);
        if (arrayDesignsUsed.size() > 1) {
            throw new IllegalArgumentException("Cannot use " + AffyDataFromCelCli.APT_FILE_OPT + " for experiment that uses multiple platforms");
        }
        ArrayDesign ad = arrayDesignsUsed.iterator().next();
        try {
            AbstractCLI.log.info("Loading data from " + aptFile);
            if ((ad.getTechnologyType().equals(TechnologyType.ONECOLOR) && GeoPlatform.isAffymetrixExonArray(ad.getShortName())) || ad.getName().toLowerCase().contains("exon")) {
                serv.addAffyExonArrayData(thawedEe, aptFile);
            } else if (ad.getTechnologyType().equals(TechnologyType.ONECOLOR) && ad.getName().toLowerCase().contains("affy")) {
                serv.addAffyData(thawedEe, aptFile);
            } else {
                throw new IllegalArgumentException("Option " + AffyDataFromCelCli.APT_FILE_OPT + " only valid if you are using an exon array.");
            }
        } catch (Exception exception) {
            return exception;
        }
        return null;
    }
    if (StringUtils.isNotBlank(cdfFile)) {
        if (arrayDesignsUsed.size() > 1) {
            throw new IllegalArgumentException("Cannot use " + AffyDataFromCelCli.CDF_FILE_OPT + " for experiment that uses multiple platforms");
        }
    }
    for (BioAssaySet ee : this.expressionExperiments) {
        try {
            Collection<ArrayDesign> adsUsed = this.eeService.getArrayDesignsUsed(ee);
            /*
                 * if the audit trail already has a DataReplacedEvent, skip it, unless --force. Ignore this for
                 * multiplatform studies (at our peril)
                 */
            if (adsUsed.size() == 1 && !force && this.checkForAlreadyDone(ee)) {
                AbstractCLI.log.warn(ee + ": Already has been recomputed from raw data, skipping (use 'force' to override')");
                this.errorObjects.add(ee + ": Already has been computed from raw data");
                continue;
            }
            ExpressionExperiment thawedEe = (ExpressionExperiment) ee;
            thawedEe = this.eeService.thawLite(thawedEe);
            ArrayDesign ad = adsUsed.iterator().next();
            /*
                 * Even if there are multiple platforms, we assume they are all the same type. If not, that's your
                 * problem :) (seriously, we could check...)
                 */
            if ((ad.getTechnologyType().equals(TechnologyType.ONECOLOR) && GeoPlatform.isAffymetrixExonArray(ad.getShortName())) || ad.getName().toLowerCase().contains("exon")) {
                AbstractCLI.log.info(thawedEe + " looks like affy exon array");
                serv.addAffyExonArrayData(thawedEe);
                this.successObjects.add(thawedEe.toString());
                AbstractCLI.log.info("Successfully processed: " + thawedEe);
            } else if (ad.getTechnologyType().equals(TechnologyType.ONECOLOR) && ad.getName().toLowerCase().contains("affy")) {
                AbstractCLI.log.info(thawedEe + " looks like a affy 3-prime array");
                serv.reprocessAffyThreePrimeArrayData(thawedEe);
                this.successObjects.add(thawedEe.toString());
                AbstractCLI.log.info("Successfully processed: " + thawedEe);
            } else {
                AbstractCLI.log.warn(ee + ": This CLI can only deal with Affymetrix platforms (exon or 3' probe designs)");
                this.errorObjects.add(ee + ": This CLI can only deal with Affymetrix platforms (exon or 3' probe designs)");
            }
        } catch (Exception exception) {
            AbstractCLI.log.error(exception, exception);
            this.errorObjects.add(ee + " " + exception.getLocalizedMessage());
        }
    }
    super.summarizeProcessing();
    return null;
}

Example 2 with DataUpdater

use of ubic.gemma.core.loader.expression.geo.DataUpdater in project Gemma by PavlidisLab.

the class RNASeqDataAddCli method doWork.

@Override
protected Exception doWork(String[] args) {
    Exception exception = super.processCommandLine(args);
    if (exception != null)
        return exception;
    DataUpdater serv = this.getBean(DataUpdater.class);
    if (this.justbackfillLog2cpm) {
        for (BioAssaySet bas : this.expressionExperiments) {
            try {
                ExpressionExperiment ee = (ExpressionExperiment) bas;
                Collection<QuantitationType> pqts = this.eeService.getPreferredQuantitationType(ee);
                if (pqts.size() > 1)
                    throw new IllegalArgumentException("Cannot process when there is more than one preferred QT");
                if (pqts.isEmpty())
                    throw new IllegalArgumentException("No preferred quantitation type for " + ee.getShortName());
                QuantitationType qt = pqts.iterator().next();
                if (!qt.getType().equals(StandardQuantitationType.COUNT)) {
                    AbstractCLI.log.warn("Preferred data is not counts for " + ee);
                    this.errorObjects.add(ee.getShortName() + ": Preferred data is not counts");
                    continue;
                }
                serv.log2cpmFromCounts(ee, qt);
                this.successObjects.add(ee);
            } catch (Exception e) {
                AbstractCLI.log.error(e, e);
                this.errorObjects.add(((ExpressionExperiment) bas).getShortName() + ": " + e.getMessage());
            }
        }
        this.summarizeProcessing();
        return null;
    }
    /*
         * Usual cases.
         */
    if (this.expressionExperiments.size() > 1) {
        throw new IllegalArgumentException("Sorry, can only process one experiment with this tool.");
    }
    ArrayDesign targetArrayDesign = this.locateArrayDesign(this.platformName);
    ExpressionExperiment ee = (ExpressionExperiment) this.expressionExperiments.iterator().next();
    if (this.expressionExperiments.size() > 1) {
        AbstractCLI.log.warn("This CLI can only deal with one experiment at a time; only the first one will be processed");
    }
    DoubleMatrixReader reader = new DoubleMatrixReader();
    try {
        DoubleMatrix<String, String> countMatrix = null;
        DoubleMatrix<String, String> rpkmMatrix = null;
        if (this.countFile != null) {
            countMatrix = reader.read(countFile);
        }
        if (this.rpkmFile != null) {
            rpkmMatrix = reader.read(rpkmFile);
        }
        serv.addCountData(ee, targetArrayDesign, countMatrix, rpkmMatrix, readLength, isPairedReads, allowMissingSamples);
    } catch (IOException e) {
        AbstractCLI.log.error("Failed while processing " + ee, e);
        return e;
    }
    return null;
}

Example 3 with DataUpdater

use of ubic.gemma.core.loader.expression.geo.DataUpdater in project Gemma by PavlidisLab.

the class ReplaceDataCli method doWork.

@Override
protected Exception doWork(String[] args) {
    Exception exception = super.processCommandLine(args);
    if (exception != null) {
        return exception;
    }
    DataUpdater dataUpdater = this.getBean(DataUpdater.class);
    if (this.expressionExperiments.size() > 1) {
        throw new IllegalArgumentException("Sorry, This CLI can only deal with one experiment at a time.");
    }
    ExpressionExperiment ee = (ExpressionExperiment) this.expressionExperiments.iterator().next();
    Collection<ArrayDesign> arrayDesignsUsed = this.eeService.getArrayDesignsUsed(ee);
    if (arrayDesignsUsed.size() > 1) {
        throw new IllegalArgumentException("Sorry, can only process single-platform data sets with this tool.");
    }
    ArrayDesign targetArrayDesign = arrayDesignsUsed.iterator().next();
    Collection<QuantitationType> qts = eeService.getPreferredQuantitationType(ee);
    if (qts.size() > 1) {
        throw new IllegalArgumentException("Experiment must have just one preferred quantitation type to replace data for");
    }
    QuantitationType qt = qts.iterator().next();
    if (qt == null) {
        throw new IllegalArgumentException("Experiment must have a preferred quantitation type to replace data for");
    }
    try {
        DoubleMatrixReader reader = new DoubleMatrixReader();
        DoubleMatrix<String, String> data = reader.read(file);
        dataUpdater.replaceData(ee, targetArrayDesign, qt, data);
    } catch (IOException e) {
        AbstractCLI.log.error("Failed while processing " + ee, e);
        return e;
    }
    return null;
}