Examples with ReferenceFile ca.corefacility.bioinformatics.irida.model.project.ReferenceFile used on opensource projects

Example 26 with ReferenceFile

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

the class ReferenceFileServiceImplIT method testAddReferenceFileWithAmbiguousBases.

@Test(expected = UnsupportedReferenceFileContentError.class)
@WithMockUser(username = "user", roles = "USER")
public void testAddReferenceFileWithAmbiguousBases() throws URISyntaxException {
    final ReferenceFile rf = new ReferenceFile();
    final Path ambiguousBasesRefFile = Paths.get(getClass().getResource("/ca/corefacility/bioinformatics/irida/service/testReferenceAmbiguous.fasta").toURI());
    rf.setFile(ambiguousBasesRefFile);
    referenceFileService.create(rf);
}

Example 27 with ReferenceFile

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

the class ProjectReferenceFileController method getReferenceFilesForProject.

/**
 * Get the reference files fro a project
 *
 * @param projectId the ID of the project
 * @param locale    locale of the logged in user
 * @return information about the reference files in the project
 */
@RequestMapping("/{projectId}/settings/ajax/reference/all")
@ResponseBody
public Map<String, Object> getReferenceFilesForProject(@PathVariable Long projectId, Locale locale) {
    Project project = projectService.read(projectId);
    // Let's add the reference files
    List<Join<Project, ReferenceFile>> joinList = referenceFileService.getReferenceFilesForProject(project);
    List<Map<String, Object>> files = new ArrayList<>();
    for (Join<Project, ReferenceFile> join : joinList) {
        ReferenceFile file = join.getObject();
        Map<String, Object> map = new HashMap<>();
        map.put("id", file.getId().toString());
        map.put("label", file.getLabel());
        map.put("createdDate", file.getCreatedDate());
        Path path = file.getFile();
        try {
            map.put("size", Files.size(path));
        } catch (IOException e) {
            logger.error("Cannot find the size of file " + file.getLabel());
            map.put("size", messageSource.getMessage("projects.reference-file.not-found", new Object[] {}, locale));
        }
        files.add(map);
    }
    return ImmutableMap.of("files", files);
}

Example 28 with ReferenceFile

use of ca.corefacility.bioinformatics.irida.model.project.ReferenceFile 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;
}

Example 29 with ReferenceFile

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

the class ReferenceFileController method addReferenceFileToProject.

/**
 * Add a new reference file to a project.
 *
 * @param projectId The id of the project to add the file to.
 * @param files     {@link List} of {@link MultipartFile} file being uploaded.
 * @param response  {@link HttpServletResponse}
 * @param locale    locale of the logged in user
 * @return Success message if file was successfully uploaded
 */
@RequestMapping("/project/{projectId}/new")
@ResponseBody
public Map<String, String> addReferenceFileToProject(@PathVariable Long projectId, @RequestParam(value = "file") List<MultipartFile> files, HttpServletResponse response, final Locale locale) {
    Project project = projectService.read(projectId);
    logger.debug("Adding reference file to project " + projectId);
    try {
        for (MultipartFile file : files) {
            // Prepare a new reference file using the multipart file supplied by the caller
            Path temp = Files.createTempDirectory(null);
            Path target = temp.resolve(file.getOriginalFilename());
            file.transferTo(target.toFile());
            ReferenceFile referenceFile = new ReferenceFile(target);
            projectService.addReferenceFileToProject(project, referenceFile);
            // Clean up temporary files
            Files.deleteIfExists(target);
            Files.deleteIfExists(temp);
        }
    } catch (final UnsupportedReferenceFileContentError e) {
        logger.error("User uploaded a reference file that biojava couldn't parse as DNA.", e);
        response.setStatus(HttpServletResponse.SC_UNSUPPORTED_MEDIA_TYPE);
        return ImmutableMap.of("error_message", messageSource.getMessage("projects.meta.reference-file.invalid-content", new Object[] {}, locale));
    } catch (IOException e) {
        logger.error("Error writing sequence file", e);
        response.setStatus(HttpServletResponse.SC_UNSUPPORTED_MEDIA_TYPE);
        return ImmutableMap.of("error_message", messageSource.getMessage("projects.meta.reference-file.unknown-error", new Object[] {}, locale));
    }
    // method so doesn't need to be i18n.
    return ImmutableMap.of("success", "upload complete.");
}

Example 30 with ReferenceFile

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

the class ReferenceFileController method downloadReferenceFile.

/**
 * Download a reference file based on the id passed.
 *
 * @param fileId
 *            The id of the file to download
 * @param response
 *            {@link HttpServletResponse} to write to file to
 *
 * @throws IOException
 *             if we fail to read the file from disk.
 */
@RequestMapping(value = "/download/{fileId}")
public void downloadReferenceFile(@PathVariable Long fileId, HttpServletResponse response) throws IOException {
    ReferenceFile file = referenceFileService.read(fileId);
    Path path = file.getFile();
    response.setHeader("Content-Disposition", "attachment; filename=\"" + file.getLabel() + "\"");
    Files.copy(path, response.getOutputStream());
    response.flushBuffer();
}