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

Example 41 with Project

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

the class CartController method removeProject.

/**
 * Delete an entire project from the cart
 *
 * @param projectId
 *            The ID of the {@link Project} to delete
 * @return a map stating success
 */
@RequestMapping(value = "/project/{projectId}", method = RequestMethod.DELETE)
@ResponseBody
public Map<String, Object> removeProject(@PathVariable Long projectId) {
    Project project = projectService.read(projectId);
    selected.remove(project);
    return ImmutableMap.of("success", true);
}

Example 42 with Project

use of ca.corefacility.bioinformatics.irida.model.project.Project 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 43 with Project

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

the class ReferenceFileController method deleteReferenceFile.

/**
 * Delete a reference file. This will remove it from the project.
 *
 * @param fileId
 *            The id of the file to remove.
 * @param projectId
 *            the project to delete the reference file for.
 * @param response
 *            {@link HttpServletResponse} required for returning an error
 *            state.
 * @param locale
 *            the locale specified by the browser.
 *
 * @return Success or error based on the result of deleting the file.
 */
@RequestMapping(value = "/delete", method = RequestMethod.POST)
@ResponseBody
public Map<String, Object> deleteReferenceFile(@RequestParam Long fileId, @RequestParam Long projectId, HttpServletResponse response, Locale locale) {
    Map<String, Object> result = new HashMap<>();
    Project project = projectService.read(projectId);
    ReferenceFile file = referenceFileService.read(fileId);
    try {
        logger.info("Removing file with id of : " + fileId);
        projectService.removeReferenceFileFromProject(project, file);
        result.put("result", "success");
        result.put("msg", messageSource.getMessage("projects.meta.reference-file.delete-success", new Object[] { file.getLabel(), project.getName() }, locale));
    } catch (EntityNotFoundException e) {
        // This is required else the client does not know that an error was thrown!
        response.setStatus(HttpServletResponse.SC_NOT_FOUND);
        logger.error("Failed to upload reference file, reason unknown.", e);
        result.put("result", "error");
        result.put("msg", messageSource.getMessage("projects.meta.reference-file.delete-error", new Object[] { file.getLabel(), project.getName() }, locale));
    }
    return result;
}

Example 44 with Project

use of ca.corefacility.bioinformatics.irida.model.project.Project 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 45 with Project

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

the class ProjectEventEmailScheduedTaskImplTest method testEmailUserPartialSubscriptoinTasks.

@SuppressWarnings("unchecked")
@Test
public void testEmailUserPartialSubscriptoinTasks() {
    User tom = new User("tom", null, null, null, null, null);
    Project p = new Project("testproject");
    Project p2 = new Project("testproject2");
    List<User> users = Lists.newArrayList(tom);
    ProjectUserJoin join = new ProjectUserJoin(p, tom, ProjectRole.PROJECT_OWNER);
    join.setEmailSubscription(true);
    ProjectUserJoin notSubscribed = new ProjectUserJoin(p2, tom, ProjectRole.PROJECT_OWNER);
    List<ProjectEvent> events = Lists.newArrayList(new UserRoleSetProjectEvent(join), new UserRoleSetProjectEvent(notSubscribed));
    when(userService.getUsersWithEmailSubscriptions()).thenReturn(users);
    when(eventService.getEventsForUserAfterDate(eq(tom), any(Date.class))).thenReturn(events);
    when(projectService.getProjectsForUser(tom)).thenReturn(Lists.newArrayList(join, notSubscribed));
    task.emailUserTasks();
    verify(userService).getUsersWithEmailSubscriptions();
    verify(eventService).getEventsForUserAfterDate(eq(tom), any(Date.class));
    @SuppressWarnings("rawtypes") ArgumentCaptor<List> eventCaptor = ArgumentCaptor.forClass(List.class);
    verify(emailController).sendSubscriptionUpdateEmail(eq(tom), eventCaptor.capture());
    List<ProjectEvent> sentEvents = eventCaptor.getValue();
    assertEquals("should send 1 event", 1, sentEvents.size());
    ProjectEvent sentEvent = sentEvents.iterator().next();
    assertEquals("should have sent from subscribed project", p, sentEvent.getProject());
}