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

Example 11 with ReferenceFile

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

the class DatabaseSetupGalaxyITService method setupSubmissionInDatabase.

/**
 * Sets up an AnalysisSubmission and saves all dependencies in database.
 *
 * @param sampleId
 *            The id of the sample to associate with the given sequence
 *            file.
 * @param sequenceFileSet
 *            A set of sequence files to use for this submission.
 * @param referenceFilePath
 *            The path to an input reference file for this test.
 * @param iridaWorkflowId
 *            The id of an irida workflow.
 * @return An AnalysisSubmissionPhylogenomics which has been saved to the
 *         database.
 */
public AnalysisSubmission setupSubmissionInDatabase(long sampleId, Set<SequencingObject> sequenceFileSet, Path referenceFilePath, UUID iridaWorkflowId) {
    ReferenceFile referenceFile = referenceFileRepository.save(new ReferenceFile(referenceFilePath));
    AnalysisSubmission submission = AnalysisSubmission.builder(iridaWorkflowId).name("my analysis").inputFiles(sequenceFileSet).referenceFile(referenceFile).build();
    analysisSubmissionService.create(submission);
    return analysisSubmissionRepository.findOne(submission.getId());
}

Example 12 with ReferenceFile

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

the class DatabaseSetupGalaxyITService method setupPairSubmissionInDatabase.

/**
 * Sets up an {@link AnalysisSubmission} with a set of
 * {@link SequenceFilePair}s that have already been setup with samples.
 *
 * @param sequenceFilePairs
 *            The set of {@link SequenceFilePair}s to submit.
 * @param referenceFilePath
 *            The path to an input reference file for this test.
 * @param iridaWorkflowId
 *            The id of an irida workflow.
 * @param parameters
 *            The parameters to use.
 * @return An {@link AnalysisSubmission} which has been saved to the
 *         database.
 */
public AnalysisSubmission setupPairSubmissionInDatabase(Set<SequencingObject> sequenceFilePairs, Path referenceFilePath, Map<String, String> parameters, UUID iridaWorkflowId) {
    ReferenceFile referenceFile = referenceFileRepository.save(new ReferenceFile(referenceFilePath));
    AnalysisSubmission submission = AnalysisSubmission.builder(iridaWorkflowId).name("paired analysis").inputFiles(sequenceFilePairs).referenceFile(referenceFile).inputParameters(parameters).build();
    analysisSubmissionService.create(submission);
    return analysisSubmissionRepository.findOne(submission.getId());
}

Example 13 with ReferenceFile

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

the class TestDataFactory method constructAnalysisSubmission.

public static AnalysisSubmission constructAnalysisSubmission() {
    Set<SequencingObject> files = new HashSet<>();
    files.add(constructSingleEndSequenceFile());
    Long id = 5L;
    final ReferenceFile rf = new ReferenceFile(files.iterator().next().getFiles().iterator().next().getFile());
    rf.setId(id);
    AnalysisSubmission analysisSubmission = AnalysisSubmission.builder(UUID.randomUUID()).name("submission-" + id).inputFiles(files).referenceFile(rf).build();
    analysisSubmission.setId(id);
    analysisSubmission.setAnalysisState(AnalysisState.COMPLETED);
    try {
        analysisSubmission.setAnalysis(constructAnalysis());
    } catch (final AnalysisAlreadySetException e) {
        // this should *never* happen, we just constructed
        // AnalysisSubmission above.
        fail();
    }
    return analysisSubmission;
}

Example 14 with ReferenceFile

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

the class AnalysisSubmissionServiceImpl method createSingleSampleSubmission.

/**
 * {@inheritDoc}
 */
@Override
@Transactional
@PreAuthorize("hasRole('ROLE_USER')")
public Collection<AnalysisSubmission> createSingleSampleSubmission(IridaWorkflow workflow, Long ref, List<SingleEndSequenceFile> sequenceFiles, List<SequenceFilePair> sequenceFilePairs, Map<String, String> params, IridaWorkflowNamedParameters namedParameters, String name, String analysisDescription, List<Project> projectsToShare, boolean writeResultsToSamples) {
    final Collection<AnalysisSubmission> createdSubmissions = new HashSet<AnalysisSubmission>();
    // Single end reads
    IridaWorkflowDescription description = workflow.getWorkflowDescription();
    if (description.acceptsSingleSequenceFiles()) {
        final Map<Sample, SingleEndSequenceFile> samplesMap = sequencingObjectService.getUniqueSamplesForSequencingObjects(Sets.newHashSet(sequenceFiles));
        for (final Map.Entry<Sample, SingleEndSequenceFile> entry : samplesMap.entrySet()) {
            Sample s = entry.getKey();
            SingleEndSequenceFile file = entry.getValue();
            // Build the analysis submission
            AnalysisSubmission.Builder builder = AnalysisSubmission.builder(workflow.getWorkflowIdentifier());
            builder.name(name + "_" + s.getSampleName());
            builder.inputFiles(ImmutableSet.of(file));
            builder.updateSamples(writeResultsToSamples);
            builder.priority(AnalysisSubmission.Priority.MEDIUM);
            // Add reference file
            if (ref != null && description.requiresReference()) {
                // Note: This cannot be empty if through the UI if the
                // pipeline required a reference file.
                ReferenceFile referenceFile = referenceFileRepository.findOne(ref);
                builder.referenceFile(referenceFile);
            }
            if (description.acceptsParameters()) {
                if (namedParameters != null) {
                    builder.withNamedParameters(namedParameters);
                } else {
                    if (!params.isEmpty()) {
                        // Note: This cannot be empty if through the UI if
                        // the pipeline required params.
                        builder.inputParameters(params);
                    }
                }
            }
            // Create the submission
            createdSubmissions.add(create(builder.build()));
        }
    }
    // Paired end reads
    if (description.acceptsPairedSequenceFiles()) {
        final Map<Sample, SequenceFilePair> samplesMap = sequencingObjectService.getUniqueSamplesForSequencingObjects(Sets.newHashSet(sequenceFilePairs));
        for (final Map.Entry<Sample, SequenceFilePair> entry : samplesMap.entrySet()) {
            Sample s = entry.getKey();
            SequenceFilePair filePair = entry.getValue();
            // Build the analysis submission
            AnalysisSubmission.Builder builder = AnalysisSubmission.builder(workflow.getWorkflowIdentifier());
            builder.name(name + "_" + s.getSampleName());
            builder.inputFiles(ImmutableSet.of(filePair));
            builder.updateSamples(writeResultsToSamples);
            // Add reference file
            if (ref != null && description.requiresReference()) {
                ReferenceFile referenceFile = referenceFileRepository.findOne(ref);
                builder.referenceFile(referenceFile);
            }
            if (description.acceptsParameters()) {
                if (namedParameters != null) {
                    builder.withNamedParameters(namedParameters);
                } else {
                    if (!params.isEmpty()) {
                        // Note: This cannot be empty if through the UI if
                        // the pipeline required params.
                        builder.inputParameters(params);
                    }
                }
            }
            // Add description to submission, can be null
            builder.analysisDescription(analysisDescription);
            // Create the submission
            createdSubmissions.add(create(builder.build()));
        }
    }
    // Share with the required projects
    for (AnalysisSubmission submission : createdSubmissions) {
        for (Project project : projectsToShare) {
            pasRepository.save(new ProjectAnalysisSubmissionJoin(project, submission));
        }
    }
    return createdSubmissions;
}

Example 15 with ReferenceFile

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

the class AnalysisSubmissionServiceImpl method createMultipleSampleSubmission.

/**
 * {@inheritDoc}
 */
@Transactional
@PreAuthorize("hasRole('ROLE_USER')")
public AnalysisSubmission createMultipleSampleSubmission(IridaWorkflow workflow, Long ref, List<SingleEndSequenceFile> sequenceFiles, List<SequenceFilePair> sequenceFilePairs, Map<String, String> params, IridaWorkflowNamedParameters namedParameters, String name, String newAnalysisDescription, List<Project> projectsToShare, boolean writeResultsToSamples) {
    AnalysisSubmission.Builder builder = AnalysisSubmission.builder(workflow.getWorkflowIdentifier());
    builder.name(name);
    builder.priority(AnalysisSubmission.Priority.MEDIUM);
    builder.updateSamples(writeResultsToSamples);
    IridaWorkflowDescription description = workflow.getWorkflowDescription();
    // Add reference file
    if (ref != null && description.requiresReference()) {
        ReferenceFile referenceFile = referenceFileRepository.findOne(ref);
        builder.referenceFile(referenceFile);
    }
    // Add any single end sequencing files.
    if (description.acceptsSingleSequenceFiles()) {
        if (!sequenceFiles.isEmpty()) {
            builder.inputFiles(Sets.newHashSet(sequenceFiles));
        }
    }
    // Add any paired end sequencing files.
    if (description.acceptsPairedSequenceFiles()) {
        if (!sequenceFilePairs.isEmpty()) {
            builder.inputFiles(Sets.newHashSet(sequenceFilePairs));
        }
    }
    if (description.acceptsParameters()) {
        if (namedParameters != null) {
            builder.withNamedParameters(namedParameters);
        } else {
            if (!params.isEmpty()) {
                // Note: This cannot be empty if through the UI if
                // the pipeline required params.
                builder.inputParameters(params);
            }
        }
    }
    // Add description to submission, can be null
    builder.analysisDescription(newAnalysisDescription);
    // Create the submission
    AnalysisSubmission submission = create(builder.build());
    // Share with the required projects
    for (Project project : projectsToShare) {
        pasRepository.save(new ProjectAnalysisSubmissionJoin(project, submission));
    }
    return submission;
}