Examples with Value org.springframework.beans.factory.annotation.Value used on opensource projects

Example 56 with Value

use of org.springframework.beans.factory.annotation.Value in project ArachneCentralAPI by OHDSI.

the class BaseAnalysisController method list.

@ApiOperation("List analyses.")
@RequestMapping(value = "/api/v1/analysis-management/analyses", method = GET)
public JsonResult<List<D>> list(Principal principal, @RequestParam("study-id") Long studyId) throws PermissionDeniedException, NotExistException {
    JsonResult<List<D>> result;
    IUser user = userService.getByUsername(principal.getName());
    if (user == null) {
        result = new JsonResult<>(PERMISSION_DENIED);
        return result;
    }
    Iterable<T> analyses = analysisService.list(user, studyId);
    result = new JsonResult<>(NO_ERROR);
    List<D> analysisDTOs = StreamSupport.stream(analyses.spliterator(), false).map(analysis -> conversionService.convert(analysis, getAnalysisDTOClass())).collect(Collectors.toList());
    result.setResult(analysisDTOs);
    return result;
}

Example 57 with Value

use of org.springframework.beans.factory.annotation.Value in project tephra by heisedebaise.

the class StatusImpl method setVersion.

private void setVersion(Map<String, Set<String>> map) {
    Set<String> set = new HashSet<>();
    map.forEach((key, value) -> {
        if (value.size() > 1)
            set.add(key);
    });
    set.forEach(map::remove);
    Map<String, String> versions = new HashMap<>();
    map.forEach((key, value) -> versions.put(key, value.iterator().next()));
    set.clear();
    versions.forEach((key, value) -> versions.forEach((k, v) -> {
        if (key.contains(k) && !key.equals(k) && value.equals(v))
            set.add(key);
    }));
    set.forEach(versions::remove);
    version = new JSONObject();
    versions.forEach((key, value) -> version.put(key.substring(1), value));
}

Example 58 with Value

use of org.springframework.beans.factory.annotation.Value in project irida by phac-nml.

the class ProjectsController method exportProjectsToFile.

/**
 * Export Projects table as either an excel file or CSV
 *
 * @param type
 * 		of file to export (csv or excel)
 * @param isAdmin
 * 		if the currently logged in user is an administrator
 * @param response
 * 		{@link HttpServletResponse}
 * @param principal
 * 		{@link Principal}
 * @param locale
 * 		{@link Locale}
 *
 * @throws IOException
 * 		thrown if cannot open the {@link HttpServletResponse} {@link OutputStream}
 */
@RequestMapping("/projects/ajax/export")
public void exportProjectsToFile(@RequestParam(value = "dtf") String type, @RequestParam(required = false, defaultValue = "false", value = "admin") Boolean isAdmin, HttpServletResponse response, Principal principal, Locale locale) throws IOException {
    // Let's make sure the export type is set properly
    if (!(type.equalsIgnoreCase("xlsx") || type.equalsIgnoreCase("csv"))) {
        throw new IllegalArgumentException("No file type sent for downloading all projects.  Expecting parameter 'dtf=' xlsx or csv");
    }
    List<Project> projects;
    // If viewing the admin projects page give the user all the projects.
    if (isAdmin) {
        projects = (List<Project>) projectService.findAll();
    } else // If on the users projects page, give the user their projects.
    {
        User user = userService.getUserByUsername(principal.getName());
        projects = projectService.getProjectsForUser(user).stream().map(Join::getSubject).collect(Collectors.toList());
    }
    List<DTProject> dtProjects = projects.stream().map(this::createDataTablesProject).collect(Collectors.toList());
    List<String> headers = ImmutableList.of("id", "name", "organism", "samples", "created", "modified").stream().map(h -> messageSource.getMessage("projects.table." + h, new Object[] {}, locale)).collect(Collectors.toList());
    // Create the filename
    Date date = new Date();
    DateFormat fileDateFormat = new SimpleDateFormat(messageSource.getMessage("date.iso-8601", null, locale));
    String filename = "IRIDA_projects_" + fileDateFormat.format(date);
    response.setHeader("Content-Disposition", "attachment; filename=\"" + filename + "." + type + "\"");
    if (type.equals("xlsx")) {
        writeProjectsToExcelFile(headers, dtProjects, locale, response);
    } else {
        writeProjectsToCsvFile(headers, dtProjects, locale, response);
    }
}

Example 59 with Value

use of org.springframework.beans.factory.annotation.Value in project irida by phac-nml.

the class ProjectExportController method getUploadNcbiPage.

/**
 * Get the page for exporting a given {@link Project} and selected
 * {@link Sample}s
 *
 * @param projectId
 *            The ID of the project to export
 * @param sampleIds
 *            A List of sample ids to export
 * @param model
 *            model for the view to render
 * @return Name of the NCBI export page
 */
@RequestMapping(value = "/projects/{projectId}/export/ncbi", method = RequestMethod.GET)
public String getUploadNcbiPage(@PathVariable Long projectId, @RequestParam("ids[]") List<Long> sampleIds, Model model) {
    Project project = projectService.read(projectId);
    logger.trace("Reading " + sampleIds.size() + " samples");
    Iterable<Sample> samples = sampleService.readMultiple(sampleIds);
    logger.trace("Got samples");
    Set<Long> checkedSingles = new HashSet<>();
    Set<Long> checkedPairs = new HashSet<>();
    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());
        logger.trace("Doing sample " + sample.getId());
        Map<String, List<? extends Object>> files = new HashMap<>();
        Collection<SampleSequencingObjectJoin> singleEndFiles = sequencingObjectService.getSequencesForSampleOfType(sample, SingleEndSequenceFile.class);
        Collection<SampleSequencingObjectJoin> pairedEndFiles = sequencingObjectService.getSequencesForSampleOfType(sample, SequenceFilePair.class);
        List<SingleEndSequenceFile> singleEndFilesForSample = singleEndFiles.stream().map(j -> (SingleEndSequenceFile) j.getObject()).collect(Collectors.toList());
        List<SequenceFilePair> sequenceFilePairsForSample = pairedEndFiles.stream().map(j -> (SequenceFilePair) j.getObject()).collect(Collectors.toList());
        Optional<SequenceFilePair> newestPair = sequenceFilePairsForSample.stream().sorted((f1, f2) -> f2.getCreatedDate().compareTo(f1.getCreatedDate())).findFirst();
        Optional<SingleEndSequenceFile> newestSingle = singleEndFilesForSample.stream().sorted((f1, f2) -> f2.getCreatedDate().compareTo(f1.getCreatedDate())).findFirst();
        if (newestPair.isPresent() && newestSingle.isPresent()) {
            SequenceFilePair sequenceFilePair = newestPair.get();
            SingleEndSequenceFile join = newestSingle.get();
            if (sequenceFilePair.getCreatedDate().after(join.getCreatedDate())) {
                checkedPairs.add(newestPair.get().getId());
            } else {
                checkedSingles.add(newestSingle.get().getId());
            }
        } else {
            if (newestPair.isPresent()) {
                checkedPairs.add(newestPair.get().getId());
            } else if (newestSingle.isPresent()) {
                checkedSingles.add(newestSingle.get().getId());
            }
        }
        files.put("paired_end", sequenceFilePairsForSample);
        files.put("single_end", singleEndFilesForSample);
        sampleMap.put("files", files);
        sampleList.add(sampleMap);
    }
    sampleList.sort(new Comparator<Map<String, Object>>() {

        @Override
        public int compare(Map<String, Object> o1, Map<String, Object> o2) {
            String s1Name = (String) o1.get("name");
            String s2Name = (String) o2.get("name");
            return s1Name.compareTo(s2Name);
        }
    });
    model.addAttribute("project", project);
    model.addAttribute("samples", sampleList);
    model.addAttribute("newestSingles", checkedSingles);
    model.addAttribute("newestPairs", checkedPairs);
    model.addAttribute("instrument_model", NcbiInstrumentModel.values());
    model.addAttribute("library_selection", NcbiLibrarySelection.values());
    model.addAttribute("library_source", NcbiLibrarySource.values());
    model.addAttribute("library_strategy", NcbiLibraryStrategy.values());
    model.addAttribute("defaultNamespace", namespace);
    model.addAttribute("activeNav", "export");
    return NCBI_EXPORT_VIEW;
}

Example 60 with Value

use of org.springframework.beans.factory.annotation.Value in project spring-security by spring-projects.

the class OAuth2ResourceServerSpecTests method getWhenUsingCustomAuthenticationManagerResolverThenUsesItAccordingly.

@Test
public void getWhenUsingCustomAuthenticationManagerResolverThenUsesItAccordingly() {
    this.spring.register(CustomAuthenticationManagerResolverConfig.class).autowire();
    ReactiveAuthenticationManagerResolver<ServerWebExchange> authenticationManagerResolver = this.spring.getContext().getBean(ReactiveAuthenticationManagerResolver.class);
    ReactiveAuthenticationManager authenticationManager = this.spring.getContext().getBean(ReactiveAuthenticationManager.class);
    given(authenticationManagerResolver.resolve(any(ServerWebExchange.class))).willReturn(Mono.just(authenticationManager));
    given(authenticationManager.authenticate(any(Authentication.class))).willReturn(Mono.error(new OAuth2AuthenticationException(new OAuth2Error("mock-failure"))));
    // @formatter:off
    this.client.get().headers((headers) -> headers.setBearerAuth(this.messageReadToken)).exchange().expectStatus().isUnauthorized().expectHeader().value(HttpHeaders.WWW_AUTHENTICATE, startsWith("Bearer error=\"mock-failure\""));
// @formatter:on
}