Examples with LocalFile ubic.gemma.model.common.description.LocalFile used on opensource projects

Example 26 with LocalFile

use of ubic.gemma.model.common.description.LocalFile in project Gemma by PavlidisLab.

the class GeoDomainObjectGenerator method processSeries.

/**
 * Download and parse a GEO series.
 *
 * @param seriesAccession series accession
 */
private GeoSeries processSeries(String seriesAccession) {
    Collection<LocalFile> fullSeries = seriesFetcher.fetch(seriesAccession);
    if (fullSeries == null) {
        GeoDomainObjectGenerator.log.warn("No series file found for " + seriesAccession);
        return null;
    }
    LocalFile seriesFile = (fullSeries.iterator()).next();
    String seriesPath = seriesFile.getLocalURL().getPath();
    parser.setProcessPlatformsOnly(this.processPlatformsOnly);
    try {
        parser.parse(seriesPath);
    } catch (IOException e1) {
        throw new RuntimeException(e1);
    }
    // Only allow one series...
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get(seriesAccession);
    if (series == null) {
        throw new RuntimeException("No series was parsed for " + seriesAccession);
    }
    Collection<String> datasetsToProcess = DatasetCombiner.findGDSforGSE(seriesAccession);
    if (datasetsToProcess != null) {
        for (String dataSetAccession : datasetsToProcess) {
            this.processDataSet(series, dataSetAccession);
        }
    }
    DatasetCombiner datasetCombiner = new DatasetCombiner(this.doSampleMatching);
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    assert correspondence != null;
    series.setSampleCorrespondence(correspondence);
    return series;
}

Example 27 with LocalFile

use of ubic.gemma.model.common.description.LocalFile in project Gemma by PavlidisLab.

the class AffyPowerToolsProbesetSummarize method getCelFiles.

/**
 * @param files                files
 * @param accessionsOfInterest Used for multiplatform studies; if null, ignored
 * @return strings
 */
private List<String> getCelFiles(Collection<LocalFile> files, Collection<String> accessionsOfInterest) {
    Set<String> celfiles = new HashSet<>();
    for (LocalFile f : files) {
        try {
            File fi = new File(f.getLocalURL().toURI());
            // If both unpacked and packed files are there, it looks at both of them. No major problem - the dups are resolved - just a little ugly.
            if (fi.canRead() && (fi.getName().toUpperCase().endsWith(".CEL") || fi.getName().toUpperCase().endsWith(".CEL.GZ"))) {
                if (accessionsOfInterest != null) {
                    String acc = fi.getName().replaceAll("(GSM[0-9]+).+", "$1");
                    if (!accessionsOfInterest.contains(acc)) {
                        continue;
                    }
                }
                if (FileTools.isGZipped(fi.getName())) {
                    AffyPowerToolsProbesetSummarize.log.info("Found CEL file " + fi + ", unzipping");
                    try {
                        String unGzipFile = FileTools.unGzipFile(fi.getAbsolutePath());
                        celfiles.add(unGzipFile);
                    } catch (IOException e) {
                        throw new RuntimeException(e);
                    }
                } else {
                    AffyPowerToolsProbesetSummarize.log.info("Found CEL file " + fi);
                    celfiles.add(fi.getAbsolutePath());
                }
            }
        } catch (URISyntaxException e) {
            throw new RuntimeException(e);
        }
    }
    if (celfiles.isEmpty()) {
        throw new IllegalArgumentException("No valid CEL files were found");
    }
    return new ArrayList<>(celfiles);
}

Example 28 with LocalFile

use of ubic.gemma.model.common.description.LocalFile in project Gemma by PavlidisLab.

the class AffyPowerToolsProbesetSummarize method tryRun.

private Collection<RawExpressionDataVector> tryRun(ExpressionExperiment ee, ArrayDesign targetPlatform, Collection<LocalFile> files, Collection<String> accessionsOfInterest, boolean threePrime, String cdfFileName) {
    List<String> celFiles = this.getCelFiles(files, accessionsOfInterest);
    AffyPowerToolsProbesetSummarize.log.info("Located " + celFiles.size() + " cel files");
    String outputPath = this.getOutputFilePath(ee);
    String cmd;
    if (threePrime) {
        cmd = this.getThreePrimeSummarizationCommand(targetPlatform, cdfFileName, celFiles, outputPath);
    } else {
        cmd = this.getCommand(targetPlatform, celFiles, outputPath);
    }
    AffyPowerToolsProbesetSummarize.log.info("Running: " + cmd);
    int exitVal = Integer.MIN_VALUE;
    StopWatch overallWatch = new StopWatch();
    overallWatch.start();
    try {
        final Process run = Runtime.getRuntime().exec(cmd);
        GenericStreamConsumer gscErr = new GenericStreamConsumer(run.getErrorStream());
        GenericStreamConsumer gscIn = new GenericStreamConsumer(run.getInputStream());
        gscErr.start();
        gscIn.start();
        while (exitVal == Integer.MIN_VALUE) {
            try {
                exitVal = run.exitValue();
            } catch (IllegalThreadStateException e) {
            // okay, still waiting.
            }
            Thread.sleep(AffyPowerToolsProbesetSummarize.AFFY_UPDATE_INTERVAL_MS);
            File outputFile = new File(outputPath + File.separator + "apt-probeset-summarize.log");
            Long size = outputFile.length();
            String minutes = TimeUtil.getMinutesElapsed(overallWatch);
            AffyPowerToolsProbesetSummarize.log.info(String.format("apt-probeset-summarize logging output so far: %.2f", size / 1024.0) + " kb (" + minutes + " minutes elapsed)");
        }
        overallWatch.stop();
        String minutes = TimeUtil.getMinutesElapsed(overallWatch);
        AffyPowerToolsProbesetSummarize.log.info("apt-probeset-summarize took a total of " + minutes + " minutes");
        return this.processData(ee, outputPath + File.separator + AffyPowerToolsProbesetSummarize.METHOD + ".summary.txt", targetPlatform);
    } catch (InterruptedException | IOException e) {
        throw new RuntimeException(e);
    }
}

Example 29 with LocalFile

use of ubic.gemma.model.common.description.LocalFile in project Gemma by PavlidisLab.

the class GeoFetcher method getFile.

Collection<LocalFile> getFile(String accession, String seekFileName) {
    LocalFile file = this.fetchedFile(seekFileName);
    AbstractFetcher.log.info("Found " + seekFileName + " for experiment(set) " + accession + ".");
    Collection<LocalFile> result = new HashSet<>();
    result.add(file);
    return result;
}

Example 30 with LocalFile

use of ubic.gemma.model.common.description.LocalFile in project Gemma by PavlidisLab.

the class LocalDatasetFetcher method fetch.

@Override
public Collection<LocalFile> fetch(String accession) {
    log.info("Seeking GSE file for " + accession);
    assert localPath != null;
    String seekFileName = localPath + "/" + accession + SOFT_GZ;
    File seekFile = new File(seekFileName);
    if (seekFile.canRead()) {
        return getFile(accession, seekFileName);
    }
    throw new RuntimeException("Failed to find " + seekFileName);
}