Examples with Join ca.corefacility.bioinformatics.irida.model.joins.Join used on opensource projects

Example 1 with Join

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

the class ProjectMembersController method getProjectUserMembers.

/**
 * Get a page of users on the project for display in a DataTable.
 *
 * @param params
 *            the datatables parameters for this DataTable
 * @param projectId
 *            the id of the project we're looking at
 * @return a {@link DataTablesResponseModel} of users on the project
 */
@RequestMapping(value = "/{projectId}/settings/ajax/members")
@ResponseBody
public DataTablesResponse getProjectUserMembers(@DataTablesRequest DataTablesParams params, @PathVariable final Long projectId) {
    final Project project = projectService.read(projectId);
    final Page<Join<Project, User>> usersForProject = userService.searchUsersForProject(project, params.getSearchValue(), params.getCurrentPage(), params.getLength(), params.getSort());
    List<DataTablesResponseModel> modelList = new ArrayList<>();
    for (Join<Project, User> join : usersForProject) {
        modelList.add(new DTProjectMember((ProjectUserJoin) join));
    }
    return new DataTablesResponse(params, usersForProject, modelList);
}

Example 2 with Join

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

the class ProjectSamplesController method getSampleNamesNotInProject.

/**
 * Get a listing of sample names not found in the current project based on a list.
 *
 * @param projectId   {@link Project} identifier for project
 * @param sampleNames {@link List} of sample names
 * @param projects    List of associated {@link Project} identifiers
 * @param locale      {@link Locale} local of current user
 * @return {@link Map} of Samples not in the current project
 */
@RequestMapping("/projects/{projectId}/ajax/samples/missing")
@ResponseBody
public Map<String, Object> getSampleNamesNotInProject(@PathVariable Long projectId, @RequestParam(value = "projects[]", defaultValue = "") List<Long> projects, @RequestParam(value = "sampleNames[]") List<String> sampleNames, Locale locale) {
    // Need to keep the count for comparison after.
    int originalCount = sampleNames.size();
    // Get a list of all samples for all projects
    projects.add(0, projectId);
    for (Long id : projects) {
        List<Join<Project, Sample>> psj = sampleService.getSamplesForProject(projectService.read(id));
        // See if the name is there
        for (Join<Project, Sample> join : psj) {
            Sample sample = join.getObject();
            if (sampleNames.contains(sample.getLabel())) {
                sampleNames.remove(sample.getLabel());
            }
            if (sampleNames.size() == 0) {
                break;
            }
        }
        if (sampleNames.size() == 0) {
            break;
        }
    }
    Map<String, Object> result = new HashMap<>();
    if (sampleNames.size() > 0) {
        result.put("missingNames", sampleNames);
        result.put("message", messageSource.getMessage("project.sample.filterByFile.error", new Object[] { originalCount - sampleNames.size(), originalCount }, locale));
    } else {
        result.put("success", messageSource.getMessage("project.sample.filterByFile.success", new Object[] {}, locale));
    }
    return result;
}

Example 3 with Join

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

the class CartController method addProject.

/**
 * Add an entire {@link Project} to the cart
 *
 * @param projectId
 *            The ID of the {@link Project}
 * @return a map stating success
 */
@RequestMapping(value = "/project/{projectId}", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE)
@ResponseBody
public Map<String, Object> addProject(@PathVariable Long projectId) {
    Project project = projectService.read(projectId);
    List<Join<Project, Sample>> samplesForProject = sampleService.getSamplesForProject(project);
    Set<Sample> samples = samplesForProject.stream().map((j) -> {
        return j.getObject();
    }).collect(Collectors.toSet());
    getSelectedSamplesForProject(project).addAll(samples);
    return ImmutableMap.of("success", true);
}

Example 4 with Join

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

the class ModifyProjectPermission method customPermissionAllowed.

/**
 * {@inheritDoc}
 */
public boolean customPermissionAllowed(Authentication authentication, Project p) {
    logger.trace("Testing permission for [" + authentication + "] can modify project [" + p + "]");
    // check if the user is a project owner for this project
    User u = userRepository.loadUserByUsername(authentication.getName());
    List<Join<Project, User>> projectUsers = pujRepository.getUsersForProjectByRole(p, ProjectRole.PROJECT_OWNER);
    for (Join<Project, User> projectUser : projectUsers) {
        if (projectUser.getObject().equals(u)) {
            logger.trace("Permission GRANTED for [" + authentication + "] on project [" + p + "]");
            // this user is an owner for the project.
            return true;
        }
    }
    // if we've made it this far, then that means that the user isn't
    // directly added to the project, so check if the user is in any groups
    // added to the project.
    final Collection<UserGroupProjectJoin> groups = ugpjRepository.findGroupsByProject(p);
    for (final UserGroupProjectJoin group : groups) {
        if (group.getProjectRole().equals(ProjectRole.PROJECT_OWNER)) {
            final Collection<UserGroupJoin> groupMembers = ugRepository.findUsersInGroup(group.getObject());
            final boolean inGroup = groupMembers.stream().anyMatch(j -> j.getSubject().equals(u));
            if (inGroup) {
                logger.trace("Permission GRANTED for [" + authentication + "] on project [" + p + "] by group membership in [" + group.getLabel() + "]");
                return true;
            }
        } else {
            logger.trace("Group is not PROJECT_OWNER, checking next project.");
        }
    }
    logger.trace("Permission DENIED for [" + authentication + "] on project [" + p + "]");
    return false;
}

Example 5 with Join

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

the class ProjectServiceImplTest method testUpdateProjectUserJoinIllegalChange.

@Test(expected = ProjectWithoutOwnerException.class)
public void testUpdateProjectUserJoinIllegalChange() throws ProjectWithoutOwnerException {
    Project project = new Project("Project 1");
    User user = new User();
    ProjectRole projectRole = ProjectRole.PROJECT_USER;
    ProjectUserJoin oldJoin = new ProjectUserJoin(project, user, ProjectRole.PROJECT_OWNER);
    @SuppressWarnings("unchecked") List<Join<Project, User>> owners = Lists.newArrayList(new ProjectUserJoin(project, user, ProjectRole.PROJECT_OWNER));
    when(pujRepository.getProjectJoinForUser(project, user)).thenReturn(oldJoin);
    when(pujRepository.getUsersForProjectByRole(project, ProjectRole.PROJECT_OWNER)).thenReturn(owners);
    projectService.updateUserProjectRole(project, user, projectRole);
}