Examples with IridaWorkflowNamedParameters ca.corefacility.bioinformatics.irida.model.workflow.submission.IridaWorkflowNamedParameters used on opensource projects

Example 1 with IridaWorkflowNamedParameters

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.IridaWorkflowNamedParameters in project irida by phac-nml.

the class WorkflowNamedParametersServiceImplIT method testGetAllNamedParameters.

@Test
@WithMockUser(username = "admin", roles = "ADMIN")
public void testGetAllNamedParameters() {
    final Iterable<IridaWorkflowNamedParameters> namedParameters = namedParametersService.findAll();
    final Set<UUID> uuids = new HashSet<>();
    for (final IridaWorkflowNamedParameters param : namedParameters) {
        uuids.add(param.getWorkflowId());
    }
    assertEquals("Should be 2 unique IDs.", 2, uuids.size());
}

Example 2 with IridaWorkflowNamedParameters

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.IridaWorkflowNamedParameters in project irida by phac-nml.

the class AnalysisSubmissionServiceImplIT method testCreateSubmissionWithUnsavedNamedParameters.

@Test(expected = UnsupportedOperationException.class)
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testCreateSubmissionWithUnsavedNamedParameters() {
    final SingleEndSequenceFile sequencingObject = (SingleEndSequenceFile) sequencingObjectRepository.findOne(1L);
    final IridaWorkflowNamedParameters params = new IridaWorkflowNamedParameters("named parameters.", workflowId, ImmutableMap.of("named", "parameter"));
    final AnalysisSubmission submission = AnalysisSubmission.builder(workflowId).inputFiles(Sets.newHashSet(sequencingObject)).withNamedParameters(params).build();
    analysisSubmissionService.create(submission);
}

Example 3 with IridaWorkflowNamedParameters

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.IridaWorkflowNamedParameters in project irida by phac-nml.

the class AnalysisSubmissionServiceImplIT method testCreateSubmissionWithNamedParameters.

@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testCreateSubmissionWithNamedParameters() {
    final SingleEndSequenceFile sequencingObject = (SingleEndSequenceFile) sequencingObjectRepository.findOne(1L);
    final IridaWorkflowNamedParameters params = parametersRepository.findOne(1L);
    final AnalysisSubmission submission = AnalysisSubmission.builder(workflowId).inputFiles(Sets.newHashSet(sequencingObject)).withNamedParameters(params).build();
    analysisSubmissionService.create(submission);
    assertNotNull("Should have saved and created an id for the submission", submission.getId());
    assertNotNull("Submission should have a map of parameters", submission.getInputParameters());
    assertEquals("Submission parameters should be the same as the named parameters", params.getInputParameters(), submission.getInputParameters());
}

Example 4 with IridaWorkflowNamedParameters

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.IridaWorkflowNamedParameters in project irida by phac-nml.

the class PipelineController method ajaxStartPipeline.

// ************************************************************************************************
// AJAX
// ************************************************************************************************
/**
 * Launch a pipeline
 *
 * @param locale     the locale that the browser is using for the current request.
 * @param parameters DTO of pipeline start parameters
 * @return a JSON response with the status and any messages.
 */
@RequestMapping(value = "/ajax/start", method = RequestMethod.POST)
@ResponseBody
public Map<String, Object> ajaxStartPipeline(Locale locale, @RequestBody final PipelineStartParameters parameters) {
    try {
        IridaWorkflow flow = workflowsService.getIridaWorkflow(parameters.getWorkflowId());
        IridaWorkflowDescription description = flow.getWorkflowDescription();
        // The pipeline needs to have a name.
        String name = parameters.getName();
        if (Strings.isNullOrEmpty(name)) {
            return ImmutableMap.of("error", messageSource.getMessage("workflow.no-name-provided", null, locale));
        }
        // Check to see if a reference file is required.
        Long ref = parameters.getRef();
        if (description.requiresReference() && ref == null) {
            return ImmutableMap.of("error", messageSource.getMessage("pipeline.error.no-reference.pipeline-start", null, locale));
        }
        // Get a list of the files to submit
        List<SingleEndSequenceFile> singleEndFiles = new ArrayList<>();
        List<SequenceFilePair> sequenceFilePairs = new ArrayList<>();
        List<Long> single = parameters.getSingle();
        if (single != null) {
            Iterable<SequencingObject> readMultiple = sequencingObjectService.readMultiple(single);
            readMultiple.forEach(f -> {
                if (!(f instanceof SingleEndSequenceFile)) {
                    throw new IllegalArgumentException("file " + f.getId() + " not a SingleEndSequenceFile");
                }
                singleEndFiles.add((SingleEndSequenceFile) f);
            });
            // Check the single files for duplicates in a sample, throws SampleAnalysisDuplicateException
            sequencingObjectService.getUniqueSamplesForSequencingObjects(Sets.newHashSet(singleEndFiles));
        }
        List<Long> paired = parameters.getPaired();
        if (paired != null) {
            Iterable<SequencingObject> readMultiple = sequencingObjectService.readMultiple(paired);
            readMultiple.forEach(f -> {
                if (!(f instanceof SequenceFilePair)) {
                    throw new IllegalArgumentException("file " + f.getId() + " not a SequenceFilePair");
                }
                sequenceFilePairs.add((SequenceFilePair) f);
            });
            // Check the pair files for duplicates in a sample, throws SampleAnalysisDuplicateException
            sequencingObjectService.getUniqueSamplesForSequencingObjects(Sets.newHashSet(sequenceFilePairs));
        }
        // Get the pipeline parameters
        Map<String, String> params = new HashMap<>();
        IridaWorkflowNamedParameters namedParameters = null;
        Map<String, Object> selectedParameters = parameters.getSelectedParameters();
        if (selectedParameters != null) {
            try {
                final String selectedParametersId = selectedParameters.get("id").toString();
                if (!DEFAULT_WORKFLOW_PARAMETERS_ID.equals(selectedParametersId) && !CUSTOM_UNSAVED_WORKFLOW_PARAMETERS_ID.equals(selectedParametersId)) {
                    // this means that a named parameter set was selected
                    // and unmodified, so load up that named parameter set
                    // to pass along.
                    namedParameters = namedParameterService.read(Long.valueOf(selectedParametersId));
                } else {
                    @SuppressWarnings("unchecked") final List<Map<String, String>> unnamedParameters = (List<Map<String, String>>) selectedParameters.get("parameters");
                    for (final Map<String, String> parameter : unnamedParameters) {
                        params.put(parameter.get("name"), parameter.get("value"));
                    }
                }
            } catch (Exception e) {
                return ImmutableMap.of("parameterError", messageSource.getMessage("pipeline.parameters.error", null, locale));
            }
        }
        List<Project> projectsToShare = new ArrayList<>();
        List<Long> sharedProjects = parameters.getSharedProjects();
        if (sharedProjects != null && !sharedProjects.isEmpty()) {
            projectsToShare = Lists.newArrayList(projectService.readMultiple(sharedProjects));
        }
        String analysisDescription = parameters.getDescription();
        Boolean writeResultsToSamples = parameters.getWriteResultsToSamples();
        if (description.getInputs().requiresSingleSample()) {
            analysisSubmissionService.createSingleSampleSubmission(flow, ref, singleEndFiles, sequenceFilePairs, params, namedParameters, name, analysisDescription, projectsToShare, writeResultsToSamples);
        } else {
            analysisSubmissionService.createMultipleSampleSubmission(flow, ref, singleEndFiles, sequenceFilePairs, params, namedParameters, name, analysisDescription, projectsToShare, writeResultsToSamples);
        }
    } catch (IridaWorkflowNotFoundException e) {
        logger.error("Cannot find IridaWorkflow [" + parameters.getWorkflowId() + "]", e);
        return ImmutableMap.of("pipelineError", messageSource.getMessage("pipeline.error.invalid-pipeline", null, locale));
    } catch (DuplicateSampleException e) {
        logger.error("Multiple files for Sample found", e);
        return ImmutableMap.of("pipelineError", messageSource.getMessage("pipeline.error.duplicate-samples", null, locale));
    }
    return ImmutableMap.of("success", true);
}

Example 5 with IridaWorkflowNamedParameters

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.IridaWorkflowNamedParameters 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;
}