Examples with ProjectAnalysisSubmissionJoin ca.corefacility.bioinformatics.irida.model.workflow.submission.ProjectAnalysisSubmissionJoin used on opensource projects

Example 6 with ProjectAnalysisSubmissionJoin

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.ProjectAnalysisSubmissionJoin in project irida by phac-nml.

the class ReadAnalysisSubmissionPermissionTest method testPermitProjectShare.

@Test
public void testPermitProjectShare() {
    String username = "aaron";
    User u = new User();
    u.setUsername(username);
    Authentication auth = new UsernamePasswordAuthenticationToken("aaron", "password1");
    Project p = new Project();
    AnalysisSubmission analysisSubmission = AnalysisSubmission.builder(workflowId).name("test").inputFiles(inputSingleFiles).referenceFile(referenceFile).build();
    analysisSubmission.setSubmitter(new User());
    when(pasRepository.getProjectsForSubmission(analysisSubmission)).thenReturn(ImmutableList.of(new ProjectAnalysisSubmissionJoin(p, analysisSubmission)));
    when(userRepository.loadUserByUsername(username)).thenReturn(u);
    when(analysisSubmissionRepository.findOne(1L)).thenReturn(analysisSubmission);
    when(readProjectPermission.customPermissionAllowed(auth, p)).thenReturn(true);
    assertTrue("permission should be granted.", readAnalysisSubmissionPermission.isAllowed(auth, 1L));
    verify(userRepository).loadUserByUsername(username);
    verify(analysisSubmissionRepository).findOne(1L);
}

Example 7 with ProjectAnalysisSubmissionJoin

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.ProjectAnalysisSubmissionJoin in project irida by phac-nml.

the class ReadAnalysisSubmissionPermissionTest method testPermitSISTR.

@Test
public void testPermitSISTR() {
    String username = "aaron";
    User u = new User();
    u.setUsername(username);
    Authentication auth = new UsernamePasswordAuthenticationToken("aaron", "password1");
    Project p = new Project();
    SequenceFilePair pair = new SequenceFilePair();
    AnalysisSubmission analysisSubmission = AnalysisSubmission.builder(workflowId).name("test").inputFiles(ImmutableSet.of(pair)).referenceFile(referenceFile).build();
    analysisSubmission.setSubmitter(new User());
    pair.setSistrTyping(analysisSubmission);
    /*
		 * testing that analysis is shared with a project that user isn't a part
		 * of
		 */
    when(pasRepository.getProjectsForSubmission(analysisSubmission)).thenReturn(ImmutableList.of(new ProjectAnalysisSubmissionJoin(p, analysisSubmission)));
    when(readProjectPermission.customPermissionAllowed(auth, p)).thenReturn(false);
    when(userRepository.loadUserByUsername(username)).thenReturn(u);
    when(analysisSubmissionRepository.findOne(1L)).thenReturn(analysisSubmission);
    when(seqObjectPermission.customPermissionAllowed(auth, pair)).thenReturn(true);
    when(sequencingObjectRepository.findSequencingObjectsForAnalysisSubmission(analysisSubmission)).thenReturn(ImmutableSet.of(pair));
    assertTrue("permission should be granted.", readAnalysisSubmissionPermission.isAllowed(auth, 1L));
    verify(userRepository).loadUserByUsername(username);
    verify(analysisSubmissionRepository).findOne(1L);
    verify(seqObjectPermission).customPermissionAllowed(auth, pair);
}

Example 8 with ProjectAnalysisSubmissionJoin

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.ProjectAnalysisSubmissionJoin in project irida by phac-nml.

the class ProjectServiceImplIT method testGetProjectForAnalysisSubmissionAsUser.

@Test
@WithMockUser(username = "analysisuser", password = "password1", roles = "USER")
public void testGetProjectForAnalysisSubmissionAsUser() {
    AnalysisSubmission analysis = analysisSubmissionService.read(1L);
    List<ProjectAnalysisSubmissionJoin> projects = projectService.getProjectsForAnalysisSubmission(analysis);
    assertEquals("should have found 1 project", 1, projects.size());
    ProjectAnalysisSubmissionJoin project = projects.iterator().next();
    assertEquals("should have found project 2", new Long(2L), project.getSubject().getId());
}

Example 9 with ProjectAnalysisSubmissionJoin

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.ProjectAnalysisSubmissionJoin in project irida by phac-nml.

the class ProjectServiceImplIT method testGetProjectForAnalysisSubmissionAsAdmin.

@Test
@WithMockUser(username = "admin", roles = "ADMIN")
public void testGetProjectForAnalysisSubmissionAsAdmin() {
    AnalysisSubmission analysis = analysisSubmissionService.read(1L);
    List<ProjectAnalysisSubmissionJoin> projects = projectService.getProjectsForAnalysisSubmission(analysis);
    assertEquals("should have found 2 projects", 2, projects.size());
}

Example 10 with ProjectAnalysisSubmissionJoin

use of ca.corefacility.bioinformatics.irida.model.workflow.submission.ProjectAnalysisSubmissionJoin in project irida by phac-nml.

the class AnalysisController method getSharedProjectsForAnalysis.

/**
 * Get the status of projects that can be shared with the given analysis
 *
 * @param submissionId
 *            the {@link AnalysisSubmission} id
 * @return a list of {@link AnalysisController.SharedProjectResponse}
 */
@RequestMapping(value = "/ajax/{submissionId}/share", method = RequestMethod.GET)
@ResponseBody
public List<SharedProjectResponse> getSharedProjectsForAnalysis(@PathVariable Long submissionId) {
    AnalysisSubmission submission = analysisSubmissionService.read(submissionId);
    // Input files
    // - Paired
    Set<SequenceFilePair> inputFilePairs = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(submission, SequenceFilePair.class);
    // get projects already shared with submission
    Set<Project> projectsShared = projectService.getProjectsForAnalysisSubmission(submission).stream().map(ProjectAnalysisSubmissionJoin::getSubject).collect(Collectors.toSet());
    // get available projects
    Set<Project> projectsInAnalysis = projectService.getProjectsForSequencingObjects(inputFilePairs);
    List<SharedProjectResponse> projectResponses = projectsShared.stream().map(p -> new SharedProjectResponse(p, true)).collect(Collectors.toList());
    // Create response for shared projects
    projectResponses.addAll(projectsInAnalysis.stream().filter(p -> !projectsShared.contains(p)).map(p -> new SharedProjectResponse(p, false)).collect(Collectors.toList()));
    projectResponses.sort(new Comparator<SharedProjectResponse>() {

        @Override
        public int compare(SharedProjectResponse p1, SharedProjectResponse p2) {
            return p1.getProject().getName().compareTo(p2.getProject().getName());
        }
    });
    return projectResponses;
}