use of ca.corefacility.bioinformatics.irida.model.upload.galaxy.GalaxyProjectName in project irida by phac-nml.
the class GalaxyLibrariesServiceTest method testBuildEmptyLibrary.
/**
* Tests create empty library.
* @throws CreateLibraryException
*/
@Test
public void testBuildEmptyLibrary() throws CreateLibraryException {
when(librariesClient.createLibrary(any(Library.class))).thenReturn(testLibrary);
Library library = new GalaxyLibrariesService(librariesClient, 1, 2, 1).buildEmptyLibrary(new GalaxyProjectName("test"));
assertNotNull(library);
assertEquals("test", library.getName());
assertEquals(LIBRARY_ID, library.getId());
}
use of ca.corefacility.bioinformatics.irida.model.upload.galaxy.GalaxyProjectName in project irida by phac-nml.
the class GalaxyLibrariesServiceTest method testBuildEmptyLibraryFail.
/**
* Tests create empty library.
*
* @throws CreateLibraryException
*/
@Test(expected = CreateLibraryException.class)
public void testBuildEmptyLibraryFail() throws CreateLibraryException {
when(librariesClient.createLibrary(any(Library.class))).thenReturn(null);
new GalaxyLibrariesService(librariesClient, 1, 2, 1).buildEmptyLibrary(new GalaxyProjectName("test"));
}
use of ca.corefacility.bioinformatics.irida.model.upload.galaxy.GalaxyProjectName in project irida by phac-nml.
the class AnalysisWorkspaceServiceGalaxy method prepareAnalysisFiles.
/**
* {@inheritDoc}
*/
@Override
public PreparedWorkflowGalaxy prepareAnalysisFiles(AnalysisSubmission analysisSubmission) throws ExecutionManagerException, IridaWorkflowException {
checkNotNull(analysisSubmission, "analysisSubmission is null");
checkNotNull(analysisSubmission.getRemoteAnalysisId(), "analysisId is null");
checkNotNull(analysisSubmission.getWorkflowId(), "workflowId is null");
checkNotNull(analysisSubmission.getRemoteWorkflowId(), "remoteWorkflowId is null");
IridaWorkflow iridaWorkflow = iridaWorkflowsService.getIridaWorkflow(analysisSubmission.getWorkflowId());
IridaWorkflowInput workflowInput = iridaWorkflow.getWorkflowDescription().getInputs();
Set<SingleEndSequenceFile> singleEndFiles = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SingleEndSequenceFile.class);
Set<SequenceFilePair> pairedEndFiles = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SequenceFilePair.class);
if (iridaWorkflow.getWorkflowDescription().requiresReference()) {
checkArgument(analysisSubmission.getReferenceFile().isPresent(), "workflow requires reference but none defined in submission");
} else {
checkArgument(!analysisSubmission.getReferenceFile().isPresent(), "workflow does not require a reference and a reference file is set in the submission");
}
if (!iridaWorkflow.getWorkflowDescription().acceptsSingleSequenceFiles()) {
checkArgument(singleEndFiles.isEmpty(), "workflow does not accept single sequence files, but single sequence files are passed as input to " + analysisSubmission);
}
if (!iridaWorkflow.getWorkflowDescription().acceptsPairedSequenceFiles()) {
checkArgument(pairedEndFiles.isEmpty(), "workflow does not accept paired sequence files, but paired sequence files are passed as input to " + analysisSubmission);
}
String temporaryLibraryName = AnalysisSubmission.class.getSimpleName() + "-" + UUID.randomUUID().toString();
History workflowHistory = galaxyHistoriesService.findById(analysisSubmission.getRemoteAnalysisId());
Library workflowLibrary = galaxyLibrariesService.buildEmptyLibrary(new GalaxyProjectName(temporaryLibraryName));
// get unique files for pairs and single files
Map<Sample, SingleEndSequenceFile> singleFiles = sequencingObjectService.getUniqueSamplesForSequencingObjects(singleEndFiles);
Map<Sample, SequenceFilePair> pairedFiles = sequencingObjectService.getUniqueSamplesForSequencingObjects(pairedEndFiles);
// check that there aren't common sample names between single and paired
if (samplesInCommon(singleFiles, pairedFiles)) {
throw new SampleAnalysisDuplicateException("Single and paired input files share a common sample for submission " + analysisSubmission);
}
String workflowId = analysisSubmission.getRemoteWorkflowId();
WorkflowDetails workflowDetails = galaxyWorkflowService.getWorkflowDetails(workflowId);
WorkflowInputsGalaxy workflowInputsGalaxy = analysisParameterServiceGalaxy.prepareAnalysisParameters(analysisSubmission.getInputParameters(), iridaWorkflow);
WorkflowInputs inputs = workflowInputsGalaxy.getInputsObject();
inputs.setDestination(new WorkflowInputs.ExistingHistory(workflowHistory.getId()));
inputs.setWorkflowId(workflowDetails.getId());
if (!singleFiles.isEmpty()) {
String sequenceFilesLabelSingle = workflowInput.getSequenceReadsSingle().get();
String workflowSequenceFileSingleInputId = galaxyWorkflowService.getWorkflowInputId(workflowDetails, sequenceFilesLabelSingle);
CollectionResponse collectionResponseSingle = analysisCollectionServiceGalaxy.uploadSequenceFilesSingleEnd(singleFiles, workflowHistory, workflowLibrary);
inputs.setInput(workflowSequenceFileSingleInputId, new WorkflowInputs.WorkflowInput(collectionResponseSingle.getId(), WorkflowInputs.InputSourceType.HDCA));
}
if (!pairedFiles.isEmpty()) {
String sequenceFilesLabelPaired = workflowInput.getSequenceReadsPaired().get();
String workflowSequenceFilePairedInputId = galaxyWorkflowService.getWorkflowInputId(workflowDetails, sequenceFilesLabelPaired);
CollectionResponse collectionResponsePaired = analysisCollectionServiceGalaxy.uploadSequenceFilesPaired(pairedFiles, workflowHistory, workflowLibrary);
inputs.setInput(workflowSequenceFilePairedInputId, new WorkflowInputs.WorkflowInput(collectionResponsePaired.getId(), WorkflowInputs.InputSourceType.HDCA));
}
String analysisId = workflowHistory.getId();
if (iridaWorkflow.getWorkflowDescription().requiresReference()) {
String referenceFileLabel = workflowInput.getReference().get();
prepareReferenceFile(analysisSubmission.getReferenceFile().get(), workflowHistory, referenceFileLabel, workflowDetails, inputs);
}
return new PreparedWorkflowGalaxy(analysisId, workflowLibrary.getId(), new WorkflowInputsGalaxy(inputs));
}
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