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

Example 1 with IridaWorkflow

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

the class AnalysisController method getDetailsPage.

/**
 * View details about an individual analysis submission
 *
 * @param submissionId the ID of the submission
 * @param model        Model for the view
 * @param locale       User's locale
 * @return name of the details page view
 */
@RequestMapping(value = "/{submissionId}", produces = MediaType.TEXT_HTML_VALUE)
public String getDetailsPage(@PathVariable Long submissionId, Model model, Locale locale) {
    logger.trace("reading analysis submission " + submissionId);
    AnalysisSubmission submission = analysisSubmissionService.read(submissionId);
    model.addAttribute("analysisSubmission", submission);
    UUID workflowUUID = submission.getWorkflowId();
    logger.trace("Workflow ID is " + workflowUUID);
    IridaWorkflow iridaWorkflow;
    try {
        iridaWorkflow = workflowsService.getIridaWorkflow(workflowUUID);
    } catch (IridaWorkflowNotFoundException e) {
        logger.error("Error finding workflow, ", e);
        throw new EntityNotFoundException("Couldn't find workflow for submission " + submission.getId(), e);
    }
    // Get the name of the workflow
    AnalysisType analysisType = iridaWorkflow.getWorkflowDescription().getAnalysisType();
    model.addAttribute("analysisType", analysisType);
    String viewName = getViewForAnalysisType(analysisType);
    String workflowName = messageSource.getMessage("workflow." + analysisType.toString() + ".title", null, locale);
    model.addAttribute("workflowName", workflowName);
    model.addAttribute("version", iridaWorkflow.getWorkflowDescription().getVersion());
    // Input files
    // - Paired
    Set<SequenceFilePair> inputFilePairs = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(submission, SequenceFilePair.class);
    model.addAttribute("paired_end", inputFilePairs);
    // Check if user can update analysis
    Authentication authentication = SecurityContextHolder.getContext().getAuthentication();
    model.addAttribute("updatePermission", updateAnalysisPermission.isAllowed(authentication, submission));
    if (iridaWorkflow.getWorkflowDescription().requiresReference() && submission.getReferenceFile().isPresent()) {
        logger.debug("Adding reference file to page for submission with id [" + submission.getId() + "].");
        model.addAttribute("referenceFile", submission.getReferenceFile().get());
    } else {
        logger.debug("No reference file required for workflow.");
    }
    /*
		 * Preview information
		 */
    try {
        if (submission.getAnalysisState().equals(AnalysisState.COMPLETED)) {
            if (analysisType.equals(AnalysisType.PHYLOGENOMICS)) {
                tree(submission, model);
            } else if (analysisType.equals(AnalysisType.SISTR_TYPING)) {
                model.addAttribute("sistr", true);
            }
        }
    } catch (IOException e) {
        logger.error("Couldn't get preview for analysis", e);
    }
    return viewName;
}

Example 2 with IridaWorkflow

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

the class AnalysisController method getSistrAnalysis.

/**
 * Get the sistr analysis information to display
 *
 * @param id ID of the analysis submission
 * @return Json results for the SISTR analysis
 */
@SuppressWarnings("resource")
@RequestMapping("/ajax/sistr/{id}")
@ResponseBody
public Map<String, Object> getSistrAnalysis(@PathVariable Long id) {
    AnalysisSubmission submission = analysisSubmissionService.read(id);
    Collection<Sample> samples = sampleService.getSamplesForAnalysisSubmission(submission);
    Map<String, Object> result = ImmutableMap.of("parse_results_error", true);
    final String sistrFileKey = "sistr-predictions";
    // Get details about the workflow
    UUID workflowUUID = submission.getWorkflowId();
    IridaWorkflow iridaWorkflow;
    try {
        iridaWorkflow = workflowsService.getIridaWorkflow(workflowUUID);
    } catch (IridaWorkflowNotFoundException e) {
        logger.error("Error finding workflow, ", e);
        throw new EntityNotFoundException("Couldn't find workflow for submission " + submission.getId(), e);
    }
    AnalysisType analysisType = iridaWorkflow.getWorkflowDescription().getAnalysisType();
    if (analysisType.equals(AnalysisType.SISTR_TYPING)) {
        Analysis analysis = submission.getAnalysis();
        Path path = analysis.getAnalysisOutputFile(sistrFileKey).getFile();
        try {
            String json = new Scanner(new BufferedReader(new FileReader(path.toFile()))).useDelimiter("\\Z").next();
            // verify file is proper json file
            ObjectMapper mapper = new ObjectMapper();
            List<Map<String, Object>> sistrResults = mapper.readValue(json, new TypeReference<List<Map<String, Object>>>() {
            });
            if (sistrResults.size() > 0) {
                // should only ever be one sample for these results
                if (samples.size() == 1) {
                    Sample sample = samples.iterator().next();
                    result = sistrResults.get(0);
                    result.put("parse_results_error", false);
                    result.put("sample_name", sample.getSampleName());
                } else {
                    logger.error("Invalid number of associated samles for submission " + submission);
                }
            } else {
                logger.error("SISTR results for file [" + path + "] are not correctly formatted");
            }
        } catch (FileNotFoundException e) {
            logger.error("File [" + path + "] not found", e);
        } catch (JsonParseException | JsonMappingException e) {
            logger.error("Error attempting to parse file [" + path + "] as JSON", e);
        } catch (IOException e) {
            logger.error("Error reading file [" + path + "]", e);
        }
    }
    return result;
}

Example 3 with IridaWorkflow

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

the class IridaWorkflowLoaderServiceIT method testLoadWorkflowWithParameters.

/**
 * Test to make sure we can load a workflow with parameters.
 *
 * @throws IridaWorkflowLoadException
 * @throws IOException
 */
@Test
public void testLoadWorkflowWithParameters() throws IridaWorkflowLoadException, IOException {
    IridaWorkflow iridaWorkflowFromFile = workflowLoaderService.loadIridaWorkflowFromDirectory(workflowDirectoryPathWithParameters);
    assertTrue("workflow loaded with no parameters", iridaWorkflowFromFile.getWorkflowDescription().acceptsParameters());
    List<IridaWorkflowParameter> parameters = iridaWorkflowFromFile.getWorkflowDescription().getParameters();
    assertNotNull("parameters should not be null", parameters);
    assertEquals("parameters does not have the correct size", 1, parameters.size());
    IridaWorkflowParameter parameter = parameters.get(0);
    assertEquals("parameter does not have the correct name", "test-parameter", parameter.getName());
    assertEquals("default value is not correct", "1", parameter.getDefaultValue());
    assertEquals("parameter does not have correct number of tool parameters", 1, parameter.getToolParameters().size());
}

Example 4 with IridaWorkflow

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

the class IridaWorkflowLoaderServiceIT method testLoadWorkflow.

/**
 * Tests loading up a workflow from a file.
 *
 * @throws IOException
 * @throws IridaWorkflowLoadException
 */
@Test
public void testLoadWorkflow() throws IOException, IridaWorkflowLoadException {
    IridaWorkflow iridaWorkflow = buildTestWorkflowSingle();
    IridaWorkflow iridaWorkflowFromFile = workflowLoaderService.loadIridaWorkflow(workflowSingleXmlPath, workflowStructurePath);
    assertEquals("irida workflow is invalid", iridaWorkflowFromFile, iridaWorkflow);
}

Example 5 with IridaWorkflow

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

the class IridaWorkflowLoaderServiceIT method testLoadWorkflowWithParametersNoDefaultValueIsRequiredSuccess.

/**
 * Test to make sure we fail to load a workflow with no default value and without a required="true" attribute.
 *
 * @throws IridaWorkflowLoadException
 * @throws IOException
 */
@Test
public void testLoadWorkflowWithParametersNoDefaultValueIsRequiredSuccess() throws IridaWorkflowLoadException, IOException {
    IridaWorkflow iridaWorkflow = workflowLoaderService.loadIridaWorkflowFromDirectory(workflowDirectoryPathWithParametersNoDefaultIsRequired);
    IridaWorkflowParameter parameter = iridaWorkflow.getWorkflowDescription().getParameters().get(0);
    assertNull("defaultValue should be null if none provided", parameter.getDefaultValue());
    assertTrue("parameter should be required", parameter.isRequired());
}