Examples with IridaSequenceFile ca.corefacility.bioinformatics.irida.model.irida.IridaSequenceFile used on opensource projects

Example 1 with IridaSequenceFile

use of ca.corefacility.bioinformatics.irida.model.irida.IridaSequenceFile in project irida by phac-nml.

the class AnalysisCollectionServiceGalaxy method uploadSequenceFilesPaired.

/**
 * Uploads a list of paired sequence files belonging to the given samples to
 * Galaxy.
 *
 * @param sampleSequenceFilesPaired
 *            A map between {@link Sample} and {@link SequenceFilePair}.
 * @param workflowHistory
 *            The history to upload the sequence files into.
 * @param workflowLibrary
 *            A temporary library to upload files into.
 * @return A CollectionResponse for the dataset collection constructed from
 *         the given files.
 * @throws ExecutionManagerException
 *             If there was an error uploading the files.
 */
public CollectionResponse uploadSequenceFilesPaired(Map<Sample, ? extends IridaSequenceFilePair> sampleSequenceFilesPaired, History workflowHistory, Library workflowLibrary) throws ExecutionManagerException {
    CollectionDescription description = new CollectionDescription();
    description.setCollectionType(DatasetCollectionType.LIST_PAIRED.toString());
    description.setName(COLLECTION_NAME_PAIRED);
    Map<Sample, Path> samplesMapPairForward = new HashMap<>();
    Map<Sample, Path> samplesMapPairReverse = new HashMap<>();
    Set<Path> pathsToUpload = new HashSet<>();
    for (Sample sample : sampleSequenceFilesPaired.keySet()) {
        IridaSequenceFilePair sequenceFilePair = sampleSequenceFilesPaired.get(sample);
        IridaSequenceFile fileForward = sequenceFilePair.getForwardSequenceFile();
        IridaSequenceFile fileReverse = sequenceFilePair.getReverseSequenceFile();
        samplesMapPairForward.put(sample, fileForward.getFile());
        samplesMapPairReverse.put(sample, fileReverse.getFile());
        pathsToUpload.add(fileForward.getFile());
        pathsToUpload.add(fileReverse.getFile());
    }
    // upload files to library and then to a history
    Map<Path, String> pathHistoryDatasetId = galaxyHistoriesService.filesToLibraryToHistory(pathsToUpload, InputFileType.FASTQ_SANGER, workflowHistory, workflowLibrary, DataStorage.LOCAL);
    for (Sample sample : sampleSequenceFilesPaired.keySet()) {
        Path fileForward = samplesMapPairForward.get(sample);
        Path fileReverse = samplesMapPairReverse.get(sample);
        if (!pathHistoryDatasetId.containsKey(fileForward)) {
            throw new UploadException("Error, no corresponding history item found for " + fileForward);
        } else if (!pathHistoryDatasetId.containsKey(fileReverse)) {
            throw new UploadException("Error, no corresponding history item found for " + fileReverse);
        } else {
            String datasetHistoryIdForward = pathHistoryDatasetId.get(fileForward);
            String datasetHistoryIdReverse = pathHistoryDatasetId.get(fileReverse);
            CollectionElement pairedElement = new CollectionElement();
            pairedElement.setName(sample.getSampleName());
            pairedElement.setCollectionType(DatasetCollectionType.PAIRED.toString());
            HistoryDatasetElement datasetElementForward = new HistoryDatasetElement();
            datasetElementForward.setId(datasetHistoryIdForward);
            datasetElementForward.setName(FORWARD_NAME);
            pairedElement.addCollectionElement(datasetElementForward);
            HistoryDatasetElement datasetElementReverse = new HistoryDatasetElement();
            datasetElementReverse.setId(datasetHistoryIdReverse);
            datasetElementReverse.setName(REVERSE_NAME);
            pairedElement.addCollectionElement(datasetElementReverse);
            description.addDatasetElement(pairedElement);
        }
    }
    return galaxyHistoriesService.constructCollection(description, workflowHistory);
}

Example 2 with IridaSequenceFile

use of ca.corefacility.bioinformatics.irida.model.irida.IridaSequenceFile in project irida by phac-nml.

the class SequenceFilePair method getForwardSequenceFile.

/**
 * Gets the forward {@link SequenceFile} from the pair.
 *
 * @return The forward {@link SequenceFile} from the pair.
 */
public SequenceFile getForwardSequenceFile() {
    IridaSequenceFile[] pair = getFiles().toArray(new IridaSequenceFile[getFiles().size()]);
    String[] filenames = { pair[0].getFile().getFileName().toString(), pair[1].getFile().getFileName().toString() };
    int index = StringUtils.indexOfDifference(filenames[0], filenames[1]);
    if (Stream.of(forwardMatches).anyMatch(x -> String.valueOf(filenames[0].charAt(index)).equals(x))) {
        return (SequenceFile) pair[0];
    } else if (Stream.of(forwardMatches).anyMatch(x -> String.valueOf(filenames[1].charAt(index)).equals(x))) {
        return (SequenceFile) pair[1];
    } else {
        throw new NoSuchElementException();
    }
}

Example 3 with IridaSequenceFile

use of ca.corefacility.bioinformatics.irida.model.irida.IridaSequenceFile in project irida by phac-nml.

the class SequenceFilePair method getReverseSequenceFile.

/**
 * Gets the reverse {@link SequenceFile} from the pair.
 *
 * @return The reverse {@link SequenceFile} from the pair.
 */
public SequenceFile getReverseSequenceFile() {
    IridaSequenceFile[] pair = getFiles().toArray(new IridaSequenceFile[getFiles().size()]);
    String[] filenames = { pair[0].getFile().getFileName().toString(), pair[1].getFile().getFileName().toString() };
    int index = StringUtils.indexOfDifference(filenames[0], filenames[1]);
    if (Stream.of(reverseMatches).anyMatch(x -> String.valueOf(filenames[0].charAt(index)).equals(x))) {
        return (SequenceFile) pair[0];
    } else if (Stream.of(reverseMatches).anyMatch(x -> String.valueOf(filenames[1].charAt(index)).equals(x))) {
        return (SequenceFile) pair[1];
    } else {
        throw new NoSuchElementException();
    }
}