use of ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowParameterException in project irida by phac-nml.
the class AnalysisParameterServiceGalaxy method prepareAnalysisParameters.
/**
* {@inheritDoc}
*/
@Override
public WorkflowInputsGalaxy prepareAnalysisParameters(Map<String, String> parameters, IridaWorkflow iridaWorkflow) throws IridaWorkflowParameterException {
checkNotNull(parameters, "parameters is null");
checkNotNull(iridaWorkflow, "iridaWorkflow is null");
WorkflowInputs inputs = new WorkflowInputs();
Set<String> parameterNamesUsed = Sets.newHashSet();
if (!iridaWorkflow.getWorkflowDescription().acceptsParameters()) {
if (parameters.isEmpty()) {
logger.debug("workflow " + iridaWorkflow + " does not accept parameters and no parameters passed.");
} else {
throw new IridaWorkflowNoParameterException("The workflow " + iridaWorkflow + " does not accept parameters but parameters " + parameters + " were passed.");
}
} else {
List<IridaWorkflowParameter> iridaParameters = iridaWorkflow.getWorkflowDescription().getParameters();
ParameterBuilderGalaxy parameterBuilder = new ParameterBuilderGalaxy();
for (IridaWorkflowParameter iridaParameter : iridaParameters) {
String parameterName = iridaParameter.getName();
String value = parameters.get(parameterName);
parameterNamesUsed.add(parameterName);
if (ignoreDefaultValue(parameters, parameterName)) {
logger.debug("Parameter with name=" + parameterName + " will ignore the default value=" + iridaParameter.getDefaultValue());
} else {
if (useDefaultValue(parameters, parameterName)) {
value = iridaParameter.getDefaultValue();
logger.debug("Parameter with name=" + parameterName + ", for workflow=" + iridaWorkflow + ", has no value set, using defaultValue=" + value);
}
for (IridaToolParameter iridaToolParameter : iridaParameter.getToolParameters()) {
String toolId = iridaToolParameter.getToolId();
String galaxyParameterName = iridaToolParameter.getParameterName();
parameterBuilder.addParameter(toolId, galaxyParameterName, value);
logger.debug("Setting parameter iridaName=" + parameterName + ", galaxyToolId=" + toolId + ", galaxyParameterName=" + galaxyParameterName + ", value=" + value);
}
}
}
for (ParameterBuilderGalaxy.ParameterId parameterId : parameterBuilder.getParameterIds()) {
inputs.setToolParameter(parameterId.getToolId(), parameterId.getStartName(), parameterBuilder.getMappingForParameterId(parameterId));
}
}
Set<String> parameterNamesUnused = Sets.difference(parameters.keySet(), parameterNamesUsed);
if (!parameterNamesUnused.isEmpty()) {
throw new IridaWorkflowParameterException("The set of parameters " + parameterNamesUnused + " are not defined in " + iridaWorkflow);
} else {
return new WorkflowInputsGalaxy(inputs);
}
}
use of ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowParameterException in project irida by phac-nml.
the class IridaWorkflowLoaderService method loadWorkflowDescription.
/**
* Loads up the workflow description from the given file.
*
* @param descriptionFile
* The file to load up a workflow description.
* @return An IridaWorkflowDescription object.
* @throws IOException
* If there was an issue reading the passed file.
* @throws IridaWorkflowLoadException
* If there was an issue loading up the workflow description.
*/
public IridaWorkflowDescription loadWorkflowDescription(Path descriptionFile) throws IOException, IridaWorkflowLoadException {
checkNotNull(descriptionFile, "descriptionFile is null");
if (!Files.exists(descriptionFile)) {
throw new FileNotFoundException(descriptionFile.toAbsolutePath().toString());
}
Source source = new StreamSource(Files.newInputStream(descriptionFile));
IridaWorkflowDescription workflowDescription = (IridaWorkflowDescription) workflowDescriptionUnmarshaller.unmarshal(source);
if (workflowDescription.getId() == null) {
throw new IridaWorkflowLoadException("No id for workflow description from file " + descriptionFile);
} else if (workflowDescription.getAnalysisType() == null) {
throw new IridaWorkflowLoadException("Invalid analysisType for workflow description from file " + descriptionFile);
} else {
if (workflowDescription.acceptsParameters()) {
for (IridaWorkflowParameter workflowParameter : workflowDescription.getParameters()) {
if (workflowParameter.getDefaultValue() == null && !workflowParameter.isRequired()) {
throw new IridaWorkflowLoadException("Parameters with no default value must set the \"required\" attribute to \"true\"." + descriptionFile);
}
if (workflowParameter.hasDynamicSource() && !workflowParameter.isRequired()) {
throw new IridaWorkflowLoadException("Parameters loaded from Dynamic Sources must set the \"required\" attribute to \"true\"." + descriptionFile);
}
if (workflowParameter.isRequired() && workflowParameter.getDefaultValue() != null) {
throw new IridaWorkflowLoadException("Required parameters should not have a default value." + descriptionFile);
}
try {
workflowParameter.getDynamicSource();
} catch (IridaWorkflowParameterException e) {
throw new IridaWorkflowLoadException("Parameters may have no more than one Dynamic Source." + descriptionFile);
}
}
}
return workflowDescription;
}
}
use of ca.corefacility.bioinformatics.irida.exceptions.IridaWorkflowParameterException in project irida by phac-nml.
the class PipelineController method getSpecifiedPipelinePage.
/**
* Get a generic pipeline page.
*
* @param model
* the the model for the current request
* @param principal
* the user in the current request
* @param locale
* the locale that the user is using
* @param pipelineId
* the pipeline to load
* @return a page reference or redirect to load.
*/
@RequestMapping(value = "/{pipelineId}")
public String getSpecifiedPipelinePage(final Model model, Principal principal, Locale locale, @PathVariable UUID pipelineId) {
String response = URL_EMPTY_CART_REDIRECT;
boolean canUpdateAllSamples;
Map<Project, Set<Sample>> cartMap = cartController.getSelected();
// Cannot run a pipeline on an empty cart!
if (!cartMap.isEmpty()) {
Authentication authentication = SecurityContextHolder.getContext().getAuthentication();
IridaWorkflow flow = null;
try {
flow = workflowsService.getIridaWorkflow(pipelineId);
} catch (IridaWorkflowNotFoundException e) {
logger.error("Workflow not found - See stack:", e);
return "redirect:errors/not_found";
}
// Check if there even is functionality to update samples from results for this pipeline
canUpdateAllSamples = analysisSubmissionSampleProcessor.hasRegisteredAnalysisSampleUpdater(flow.getWorkflowDescription().getAnalysisType());
User user = userService.getUserByUsername(principal.getName());
// Get all the reference files that could be used for this pipeline.
List<Map<String, Object>> referenceFileList = new ArrayList<>();
List<Map<String, Object>> projectList = new ArrayList<>();
List<Map<String, Object>> addRefList = new ArrayList<>();
IridaWorkflowDescription description = flow.getWorkflowDescription();
final String workflowName = description.getName().toLowerCase();
for (Project project : cartMap.keySet()) {
// Check to see if it requires a reference file.
if (description.requiresReference()) {
List<Join<Project, ReferenceFile>> joinList = referenceFileService.getReferenceFilesForProject(project);
for (Join<Project, ReferenceFile> join : joinList) {
referenceFileList.add(ImmutableMap.of("project", project, "file", join.getObject()));
}
if (referenceFileList.size() == 0) {
if (user.getSystemRole().equals(Role.ROLE_ADMIN) || projectService.userHasProjectRole(user, project, ProjectRole.PROJECT_OWNER)) {
addRefList.add(ImmutableMap.of("name", project.getLabel(), "id", project.getId()));
}
}
}
Set<Sample> samples = cartMap.get(project);
Map<String, Object> projectMap = new HashMap<>();
List<Map<String, Object>> sampleList = new ArrayList<>();
for (Sample sample : samples) {
Map<String, Object> sampleMap = new HashMap<>();
sampleMap.put("name", sample.getLabel());
sampleMap.put("id", sample.getId().toString());
Map<String, List<? extends Object>> files = new HashMap<>();
// Paired end reads
if (description.acceptsPairedSequenceFiles()) {
Collection<SampleSequencingObjectJoin> pairs = sequencingObjectService.getSequencesForSampleOfType(sample, SequenceFilePair.class);
files.put("paired_end", pairs.stream().map(SampleSequencingObjectJoin::getObject).collect(Collectors.toList()));
}
// Singe end reads
if (description.acceptsSingleSequenceFiles()) {
Collection<SampleSequencingObjectJoin> singles = sequencingObjectService.getSequencesForSampleOfType(sample, SingleEndSequenceFile.class);
files.put("single_end", singles.stream().map(SampleSequencingObjectJoin::getObject).collect(Collectors.toList()));
}
sampleMap.put("files", files);
sampleList.add(sampleMap);
}
projectMap.put("id", project.getId().toString());
projectMap.put("name", project.getLabel());
projectMap.put("samples", sampleList);
projectList.add(projectMap);
canUpdateAllSamples &= updateSamplePermission.isAllowed(authentication, samples);
}
// Need to add the pipeline parameters
final List<IridaWorkflowParameter> defaultWorkflowParameters = flow.getWorkflowDescription().getParameters();
final List<Map<String, Object>> parameters = new ArrayList<>();
if (defaultWorkflowParameters != null) {
final List<Map<String, String>> defaultParameters = new ArrayList<>();
for (IridaWorkflowParameter p : defaultWorkflowParameters) {
if (p.isRequired()) {
continue;
}
defaultParameters.add(ImmutableMap.of("label", messageSource.getMessage("pipeline.parameters." + workflowName + "." + p.getName(), null, locale), "value", p.getDefaultValue(), "name", p.getName()));
}
parameters.add(ImmutableMap.of("id", DEFAULT_WORKFLOW_PARAMETERS_ID, "label", messageSource.getMessage("workflow.parameters.named.default", null, locale), "parameters", defaultParameters));
final List<IridaWorkflowNamedParameters> namedParameters = namedParameterService.findNamedParametersForWorkflow(pipelineId);
for (final IridaWorkflowNamedParameters p : namedParameters) {
final List<Map<String, String>> namedParametersList = new ArrayList<>();
for (final Map.Entry<String, String> parameter : p.getInputParameters().entrySet()) {
namedParametersList.add(ImmutableMap.of("label", messageSource.getMessage("pipeline.parameters." + workflowName + "." + parameter.getKey(), null, locale), "value", parameter.getValue(), "name", parameter.getKey()));
}
parameters.add(ImmutableMap.of("id", p.getId(), "label", p.getLabel(), "parameters", namedParametersList));
}
model.addAttribute("parameterModalTitle", messageSource.getMessage("pipeline.parameters.modal-title." + workflowName, null, locale));
} else {
model.addAttribute("noParameters", messageSource.getMessage("pipeline.no-parameters", null, locale));
}
// Parameters should be added not matter what, even if they are empty.
model.addAttribute("parameters", parameters);
model.addAttribute("title", messageSource.getMessage("pipeline.title." + description.getName(), null, locale));
model.addAttribute("mainTitle", messageSource.getMessage("pipeline.h1." + description.getName(), null, locale));
model.addAttribute("name", description.getName());
model.addAttribute("pipelineId", pipelineId.toString());
model.addAttribute("referenceFiles", referenceFileList);
model.addAttribute("referenceRequired", description.requiresReference());
model.addAttribute("addRefProjects", addRefList);
model.addAttribute("projects", projectList);
model.addAttribute("canUpdateSamples", canUpdateAllSamples);
model.addAttribute("workflowName", workflowName);
model.addAttribute("dynamicSourceRequired", description.requiresDynamicSource());
final List<Map<String, Object>> dynamicSources = new ArrayList<>();
if (description.requiresDynamicSource()) {
TabularToolDataTable galaxyToolDataTable = new TabularToolDataTable();
IridaWorkflowDynamicSourceGalaxy dynamicSource = new IridaWorkflowDynamicSourceGalaxy();
for (IridaWorkflowParameter parameter : description.getParameters()) {
if (parameter.isRequired() && parameter.hasDynamicSource()) {
try {
dynamicSource = parameter.getDynamicSource();
} catch (IridaWorkflowParameterException e) {
logger.debug("Dynamic Source error: ", e);
}
List<Object> parametersList = new ArrayList<>();
String dynamicSourceName;
Map<String, Object> toolDataTable = new HashMap<>();
try {
dynamicSourceName = dynamicSource.getName();
toolDataTable.put("id", dynamicSourceName);
toolDataTable.put("label", messageSource.getMessage("dynamicsource.label." + dynamicSourceName, null, locale));
toolDataTable.put("parameters", parametersList);
galaxyToolDataTable = galaxyToolDataService.getToolDataTable(dynamicSourceName);
List<String> labels = galaxyToolDataTable.getFieldsForColumn(dynamicSource.getDisplayColumn());
Iterator<String> labelsIterator = labels.iterator();
List<String> values = galaxyToolDataTable.getFieldsForColumn(dynamicSource.getParameterColumn());
Iterator<String> valuesIterator = values.iterator();
while (labelsIterator.hasNext() && valuesIterator.hasNext()) {
String label = labelsIterator.next();
String value = valuesIterator.next();
HashMap<String, String> toolDataTableFieldsMap = new HashMap<>();
toolDataTableFieldsMap.put("label", label);
toolDataTableFieldsMap.put("value", value);
toolDataTableFieldsMap.put("name", parameter.getName());
parametersList.add(toolDataTableFieldsMap);
}
dynamicSources.add(toolDataTable);
} catch (Exception e) {
logger.debug("Tool Data Table not found: ", e);
}
}
}
model.addAttribute("dynamicSources", dynamicSources);
}
response = URL_GENERIC_PIPELINE;
}
return response;
}
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