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

Example 11 with Project

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

the class ProjectSamplesController method downloadSamples.

/**
 * Download a set of sequence files from selected samples within a project
 *
 * @param projectId Id for a {@link Project}
 * @param ids       List of ids ofr {@link Sample} within the project
 * @param response  {@link HttpServletResponse}
 * @throws IOException if we fail to read a file from the filesystem.
 */
@RequestMapping(value = "/projects/{projectId}/download/files")
public void downloadSamples(@PathVariable Long projectId, @RequestParam(value = "ids[]") List<Long> ids, HttpServletResponse response) throws IOException {
    Project project = projectService.read(projectId);
    List<Sample> samples = (List<Sample>) sampleService.readMultiple(ids);
    // Add the appropriate headers
    response.setContentType("application/zip");
    response.setHeader("Content-Disposition", "attachment; filename=\"" + project.getName() + ".zip\"");
    response.setHeader("Transfer-Encoding", "chunked");
    // storing used file names to ensure we don't have a conflict
    Set<String> usedFileNames = new HashSet<>();
    try (ZipOutputStream outputStream = new ZipOutputStream(response.getOutputStream())) {
        for (Sample sample : samples) {
            Collection<SampleSequencingObjectJoin> sequencingObjectsForSample = sequencingObjectService.getSequencingObjectsForSample(sample);
            for (SampleSequencingObjectJoin join : sequencingObjectsForSample) {
                for (SequenceFile file : join.getObject().getFiles()) {
                    Path path = file.getFile();
                    String fileName = project.getName() + "/" + sample.getSampleName() + "/" + path.getFileName().toString();
                    if (usedFileNames.contains(fileName)) {
                        fileName = handleDuplicate(fileName, usedFileNames);
                    }
                    final ZipEntry entry = new ZipEntry(fileName);
                    // set the file creation time on the zip entry to be
                    // whatever the creation time is on the filesystem
                    final BasicFileAttributes attr = Files.readAttributes(path, BasicFileAttributes.class);
                    entry.setCreationTime(attr.creationTime());
                    entry.setLastModifiedTime(attr.creationTime());
                    outputStream.putNextEntry(entry);
                    usedFileNames.add(fileName);
                    Files.copy(path, outputStream);
                    outputStream.closeEntry();
                }
            }
        }
        outputStream.finish();
    } catch (IOException e) {
        // this generally means that the user has cancelled the download
        // from their web browser; we can safely ignore this
        logger.debug("This *probably* means that the user cancelled the download, " + "but it might be something else, see the stack trace below for more information.", e);
    } catch (Exception e) {
        logger.error("Download failed...", e);
    } finally {
        // close the response outputStream so that we're not leaking
        // streams.
        response.getOutputStream().close();
    }
}

Example 12 with Project

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

the class ProjectSamplesController method getProjectsAvailableToCopySamples.

/**
 * Search for projects available for a user to copy samples to. If the user is an admin it will show all projects.
 *
 * @param projectId identifier for the current {@link Project}
 * @param term      A search term
 * @param pageSize  The size of the page requests
 * @param page      The page number (0 based)
 * @return a {@code Map<String,Object>} containing: total: total number of elements results: A {@code
 * Map<Long,String>} of project IDs and project names.
 */
@RequestMapping(value = "/projects/{projectId}/ajax/samples/available_projects")
@ResponseBody
public Map<String, Object> getProjectsAvailableToCopySamples(@PathVariable final Long projectId, @RequestParam String term, @RequestParam(required = false, defaultValue = "10") int pageSize, @RequestParam int page) {
    final Project projectToExclude = projectService.read(projectId);
    List<Map<String, String>> projectMap = new ArrayList<>();
    Map<String, Object> response = new HashMap<>();
    final Page<Project> projects = projectService.getUnassociatedProjects(projectToExclude, term, page, pageSize, Direction.ASC, PROJECT_NAME_PROPERTY);
    for (Project p : projects) {
        Map<String, String> map = new HashMap<>();
        map.put("id", p.getId().toString());
        map.put("text", p.getName());
        projectMap.add(map);
    }
    response.put("total", projects.getTotalElements());
    response.put("projects", projectMap);
    return response;
}

Example 13 with Project

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

the class ProjectSamplesController method ajaxSamplesMerge.

/**
 * Merges a list of samples into either the first sample in the list with a new name if provided, or into the
 * selected sample based on the id.
 *
 * @param projectId
 * 		The id for the current {@link Project}
 * @param mergeSampleId
 * 		An id for a {@link Sample} to merge the other samples into.
 * @param sampleIds
 * 		A list of ids for {@link Sample} to merge together.
 * @param sampleName
 * 		An optional new name for the {@link Sample}.
 * @param locale
 * 		The {@link Locale} of the current user.
 *
 * @return a map of {@link Sample} properties representing the merged sample.
 */
@RequestMapping(value = "/projects/{projectId}/ajax/samples/merge", method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE)
@ResponseBody
public Map<String, Object> ajaxSamplesMerge(@PathVariable Long projectId, @RequestParam Long mergeSampleId, @RequestParam(value = "sampleIds[]") List<Long> sampleIds, @RequestParam String sampleName, Locale locale) {
    Map<String, Object> result = new HashMap<>();
    int samplesMergeCount = sampleIds.size();
    Project project = projectService.read(projectId);
    // Determine which sample to merge into
    Sample mergeIntoSample = sampleService.read(mergeSampleId);
    sampleIds.remove(mergeSampleId);
    if (!Strings.isNullOrEmpty(sampleName)) {
        try {
            mergeIntoSample.setSampleName(sampleName);
            mergeIntoSample = sampleService.update(mergeIntoSample);
        } catch (ConstraintViolationException e) {
            logger.error(e.getLocalizedMessage());
            result.put("result", "error");
            result.put("warnings", getErrorsFromViolationException(e));
            return result;
        }
    }
    // Create an update map
    List<Sample> mergeSamples = sampleIds.stream().map(sampleService::read).collect(Collectors.toList());
    // Merge the samples
    sampleService.mergeSamples(project, mergeIntoSample, mergeSamples);
    result.put("result", "success");
    result.put("message", messageSource.getMessage("project.samples.combine-success", new Object[] { samplesMergeCount, mergeIntoSample.getSampleName() }, locale));
    return result;
}

Example 14 with Project

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

the class ProjectSamplesController method getLinkerCommandModal.

/**
 * Generate a modal for displaying the ngs-linker command
 *
 * @param ids       List of {@link Sample} identifiers
 * @param projectId identtifier for the current {@link Project}
 * @param model     UI Model
 * @return Path to template
 */
@RequestMapping(value = "/projects/{projectId}/templates/linker-modal", produces = MediaType.TEXT_HTML_VALUE)
public String getLinkerCommandModal(@RequestParam(name = "sampleIds[]", defaultValue = "") List<Long> ids, @PathVariable Long projectId, Model model) {
    Project project = projectService.read(projectId);
    int totalSamples = sampleService.getSamplesForProject(project).size();
    String cmd = LINKER_SCRIPT + " -p " + projectId;
    if (ids.size() != 0 && ids.size() != totalSamples) {
        cmd += " -s " + StringUtils.join(ids, " -s ");
    }
    model.addAttribute("command", cmd);
    return PROJECT_TEMPLATE_DIR + "linker-modal.tmpl";
}

Example 15 with Project

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

the class ProjectSamplesController method getShareSamplesModal.

/**
 * Create a modal dialogue for moving or sharing {@link Sample} to another {@link Project}
 *
 * @param ids       {@link List} of identifiers for {@link Sample}s to copy or move.
 * @param projectId Identifier for the current {@link Project}
 * @param model     UI Model
 * @param move      Whether or not to display share or move wording.
 * @return Path to share or move modal template.
 */
@RequestMapping(value = "/projects/{projectId}/templates/copy-move-modal", produces = MediaType.TEXT_HTML_VALUE)
public String getShareSamplesModal(@RequestParam(name = "sampleIds[]") List<Long> ids, @PathVariable Long projectId, Model model, @RequestParam(required = false) boolean move) {
    Project project = projectService.read(projectId);
    model.addAllAttributes(generateShareMoveSamplesContent(project, ids));
    model.addAttribute("projectId", projectId);
    model.addAttribute("type", move ? "move" : "copy");
    model.addAttribute("isRemoteProject", project.isRemote());
    return PROJECT_TEMPLATE_DIR + "copy-move-modal.tmpl";
}