Examples with EntityNotFoundException ca.corefacility.bioinformatics.irida.exceptions.EntityNotFoundException used on opensource projects

Example 1 with EntityNotFoundException

use of ca.corefacility.bioinformatics.irida.exceptions.EntityNotFoundException in project irida by phac-nml.

the class PasswordResetController method submitEmail.

/**
 * Create a password reset for the given email address
 *
 * @param email
 *            The email address to create a password reset for
 * @param model
 *            Model for the view
 *
 * @return Reset created page if the email exists in the system
 */
@RequestMapping(method = RequestMethod.POST)
public String submitEmail(@RequestParam String email, Model model) {
    setAuthentication();
    String page;
    model.addAttribute("email", email);
    try {
        User user = userService.loadUserByEmail(email);
        try {
            createNewPasswordReset(user);
            page = CREATED_REDIRECT + Base64.getEncoder().encodeToString(email.getBytes());
        } catch (final MailSendException e) {
            model.addAttribute("mailSendError", true);
            SecurityContextHolder.clearContext();
            page = noLoginResetPassword(model);
        }
    } catch (EntityNotFoundException ex) {
        model.addAttribute("emailError", true);
        SecurityContextHolder.clearContext();
        page = noLoginResetPassword(model);
    }
    return page;
}

Example 2 with EntityNotFoundException

use of ca.corefacility.bioinformatics.irida.exceptions.EntityNotFoundException in project irida by phac-nml.

the class AnalysisController method getAjaxDownloadAnalysisSubmissionIndividualFile.

/**
 * Download single output files from an {@link AnalysisSubmission}
 *
 * @param analysisSubmissionId Id for a {@link AnalysisSubmission}
 * @param fileId               the id of the file to download
 * @param response             {@link HttpServletResponse}
 */
@RequestMapping(value = "/ajax/download/{analysisSubmissionId}/file/{fileId}")
public void getAjaxDownloadAnalysisSubmissionIndividualFile(@PathVariable Long analysisSubmissionId, @PathVariable Long fileId, HttpServletResponse response) {
    AnalysisSubmission analysisSubmission = analysisSubmissionService.read(analysisSubmissionId);
    Analysis analysis = analysisSubmission.getAnalysis();
    Set<AnalysisOutputFile> files = analysis.getAnalysisOutputFiles();
    Optional<AnalysisOutputFile> optFile = files.stream().filter(f -> f.getId().equals(fileId)).findAny();
    if (!optFile.isPresent()) {
        throw new EntityNotFoundException("Could not find file with id " + fileId);
    }
    FileUtilities.createSingleFileResponse(response, optFile.get());
}

Example 3 with EntityNotFoundException

use of ca.corefacility.bioinformatics.irida.exceptions.EntityNotFoundException 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 4 with EntityNotFoundException

use of ca.corefacility.bioinformatics.irida.exceptions.EntityNotFoundException 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 5 with EntityNotFoundException

use of ca.corefacility.bioinformatics.irida.exceptions.EntityNotFoundException in project irida by phac-nml.

the class ProjectsController method syncProject.

/**
 * Get a {@link Project} from a remote api and mark it to be synchronized in
 * this IRIDA installation
 *
 * @param url           the URL of the remote project
 * @param syncFrequency How often to sync the project
 * @param model         Model for the view
 * @return Redirect to the new project. If an oauth exception occurs it will
 * be forwarded back to the creation page.
 */
@RequestMapping(value = "/projects/synchronize", method = RequestMethod.POST)
public String syncProject(@RequestParam String url, @RequestParam ProjectSyncFrequency syncFrequency, Model model) {
    try {
        Project read = projectRemoteService.read(url);
        read.setId(null);
        read.getRemoteStatus().setSyncStatus(SyncStatus.MARKED);
        read.setSyncFrequency(syncFrequency);
        read = projectService.create(read);
        return "redirect:/projects/" + read.getId() + "/metadata";
    } catch (IridaOAuthException ex) {
        Map<String, String> errors = new HashMap<>();
        errors.put("oauthError", ex.getMessage());
        model.addAttribute("errors", errors);
        return getSynchronizeProjectPage(model);
    } catch (EntityNotFoundException ex) {
        Map<String, String> errors = new HashMap<>();
        errors.put("urlError", ex.getMessage());
        model.addAttribute("errors", errors);
        return getSynchronizeProjectPage(model);
    }
}