use of com.github.jmchilton.blend4j.galaxy.beans.TabularToolDataTable in project irida by phac-nml.
the class GalaxyToolDataService method getToolDataTable.
/**
* Gets details about a given tool data table.
*
* @param dataTableId
* The id of the tool data table.
* @return The Tool Data Table Object.
* @throws GalaxyToolDataTableException
* If there was an issue getting the details of the tool data table.
*/
public TabularToolDataTable getToolDataTable(String dataTableId) throws GalaxyToolDataTableException {
checkNotNull(dataTableId, "dataTableId is null");
checkNotNull(toolDataClient, "toolDataClient is null");
TabularToolDataTable toolDataTable = toolDataClient.showDataTable(dataTableId);
if (toolDataTable != null) {
return toolDataTable;
} else {
throw new GalaxyToolDataTableException("Could not find Tool Data Table named: " + dataTableId);
}
}
use of com.github.jmchilton.blend4j.galaxy.beans.TabularToolDataTable in project irida by phac-nml.
the class GalaxyToolDataServiceIT method testGetToolDataTableValid.
/**
* Tests getting a Galaxy Tool Data Table from the GalaxyToolDataService.
* @throws Exception
*/
@Test
public void testGetToolDataTableValid() throws Exception {
TabularToolDataTable toolDataTable;
toolDataTable = galaxyToolDataService.getToolDataTable(VALID_TOOL_DATA_TABLE_ID);
assertNotNull(toolDataTable);
assertEquals(VALID_TOOL_DATA_TABLE_ID, toolDataTable.getName());
}
use of com.github.jmchilton.blend4j.galaxy.beans.TabularToolDataTable 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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