use of ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow in project irida by phac-nml.
the class IridaWorkflowLoaderServiceIT method testLoadWorkflowFromDirectory.
/**
* Tests successfully loading up one version of a workflow from a directory.
*/
@Test
public void testLoadWorkflowFromDirectory() throws IOException, IridaWorkflowLoadException {
IridaWorkflow iridaWorkflowFromFile = workflowLoaderService.loadIridaWorkflowFromDirectory(workflowVersionDirectoryPath);
assertEquals("irida workflow is invalid", buildTestWorkflowSingle(), iridaWorkflowFromFile);
}
use of ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow in project irida by phac-nml.
the class IridaWorkflowLoaderServiceIT method testLoadAllWorkflowImplementationsSuccess.
/**
* Tests successfully loading up all implementations of a workflow from a
* directory.
*/
@Test
public void testLoadAllWorkflowImplementationsSuccess() throws IOException, IridaWorkflowLoadException {
Set<IridaWorkflow> iridaWorkflowsFromFile = workflowLoaderService.loadAllWorkflowImplementations(workflowDirectoryPath);
Set<String> workflowNamesSet = new HashSet<>();
Set<String> workflowVersionsSet = new HashSet<>();
assertEquals(11, iridaWorkflowsFromFile.size());
for (IridaWorkflow workflow : iridaWorkflowsFromFile) {
workflowNamesSet.add(workflow.getWorkflowDescription().getName());
workflowVersionsSet.add(workflow.getWorkflowDescription().getVersion());
}
assertEquals("irida workflow names are invalid", Sets.newHashSet("TestWorkflow"), workflowNamesSet);
Set<String> validVersionNumbers = Sets.newHashSet("1.0", "2.0", "1.0-invalid", "2.0-missing-output", "1.0-paired", "1.0-single-paired", "1.0-requires-single-sample", "1.0-requires-single-sample-unset", "1.0-not-requires-single-sample", "1.0-invalid-requires-single-sample", "1.0-paired-end-single-sample");
assertEquals("irida workflow versions are invalid", validVersionNumbers, workflowVersionsSet);
}
use of ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow in project irida by phac-nml.
the class IridaWorkflowsServiceIT method testRegisterWorkflowNullTypeFail.
/**
* Tests to make sure we fail to register a workflow with a null type.
*
* @throws IridaWorkflowException
*/
@Test(expected = NullPointerException.class)
public void testRegisterWorkflowNullTypeFail() throws IridaWorkflowException {
IridaWorkflow workflowNullAnalysisType = IridaWorkflowTestBuilder.buildTestWorkflowNullAnalysisType();
iridaWorkflowsService.registerWorkflow(workflowNullAnalysisType);
}
use of ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow 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));
}
use of ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow in project irida by phac-nml.
the class IridaWorkflowLoaderService method loadIridaWorkflow.
/**
* Loads up an {@link IridaWorkflow} from the given information files.
*
* @param descriptionFile
* The description file for the workflow.
* @param structureFile
* The file describing the structure of a workflow.
* @return An IridaWorkflow object for this workflow.
* @throws IOException
* If there was an issue reading the passed file.
* @throws IridaWorkflowLoadException
* If there was an issue loading up the workflow.
*/
public IridaWorkflow loadIridaWorkflow(Path descriptionFile, Path structureFile) throws IOException, IridaWorkflowLoadException {
checkNotNull(descriptionFile, "descriptionFile is null");
checkNotNull(structureFile, "structureFile is null");
IridaWorkflowDescription worklowDescription = loadWorkflowDescription(descriptionFile);
IridaWorkflowStructure workflowStructure = loadWorkflowStructure(structureFile);
return new IridaWorkflow(worklowDescription, workflowStructure);
}
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