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

Example 96 with Project

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

the class ProjectServiceImplIT method testAddReferenceFileToProject.

@Test
@WithMockUser(username = "admin", roles = "ADMIN")
public void testAddReferenceFileToProject() throws IOException, URISyntaxException {
    ReferenceFile f = new ReferenceFile();
    Path referenceFilePath = Paths.get(getClass().getResource("/ca/corefacility/bioinformatics/irida/service/testReference.fasta").toURI());
    Path createTempFile = Files.createTempFile("testReference", ".fasta");
    Files.delete(createTempFile);
    referenceFilePath = Files.copy(referenceFilePath, createTempFile);
    referenceFilePath.toFile().deleteOnExit();
    f.setFile(referenceFilePath);
    Project p = projectService.read(1L);
    Join<Project, ReferenceFile> pr = projectService.addReferenceFileToProject(p, f);
    assertEquals("Project was set in the join.", p, pr.getSubject());
    // verify that the reference file was persisted beneath the reference
    // file directory
    ReferenceFile rf = pr.getObject();
    assertTrue("reference file should be beneath the base directory for reference files.", rf.getFile().startsWith(referenceFileBaseDirectory));
}

Example 97 with Project

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

the class ProjectServiceImplIT method testMoveSamplesWithoutOwner.

@Test
@WithMockUser(username = "user1", roles = "USER")
public void testMoveSamplesWithoutOwner() {
    Project source = projectService.read(2L);
    Project destination = projectService.read(10L);
    List<Join<Project, Sample>> samplesForProject = sampleService.getSamplesForProject(source);
    Set<Sample> samples = samplesForProject.stream().map(j -> j.getObject()).collect(Collectors.toSet());
    List<ProjectSampleJoin> movedSamples = projectService.moveSamples(source, destination, samples, false);
    assertEquals(samples.size(), movedSamples.size());
    movedSamples.forEach(j -> {
        assertFalse("Project shouldn't be owner for sample", j.isOwner());
    });
    assertEquals("Samples should not exist in source project", Long.valueOf(0L), projectSampleJoinRepository.countSamplesForProject(source));
    assertEquals("Samples should exist in destination project", Sets.newHashSet(1L, 2L), projectSampleJoinRepository.getSamplesForProject(destination).stream().map(j -> j.getObject().getId()).collect(Collectors.toSet()));
}

Example 98 with Project

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

the class ProjectServiceImplIT method testAddUserToProject.

@Test
@WithMockUser(username = "admin", roles = "ADMIN")
public void testAddUserToProject() {
    Project p = projectService.read(1L);
    User u = userService.read(1L);
    Join<Project, User> join = projectService.addUserToProject(p, u, ProjectRole.PROJECT_OWNER);
    assertNotNull("Join was not populated.", join);
    assertEquals("Join has wrong project.", p, join.getSubject());
    assertEquals("Join has wrong user.", u, join.getObject());
    List<Join<Project, User>> projects = projectService.getProjectsForUser(u);
    assertEquals("User is not part of project.", p, projects.iterator().next().getSubject());
}

Example 99 with Project

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

the class ProjectServiceImplIT method testGetProjectForSequencingObjectsAsUser.

@Test
@WithMockUser(username = "analysisuser", password = "password1", roles = "USER")
public void testGetProjectForSequencingObjectsAsUser() {
    SequencingObject read = sequencingObjectService.read(1L);
    Set<Project> projectsForSequencingObjects = projectService.getProjectsForSequencingObjects(ImmutableList.of(read));
    assertEquals("should have found 1 project", 1, projectsForSequencingObjects.size());
    Project project = projectsForSequencingObjects.iterator().next();
    assertEquals("should have found project 2", new Long(2), project.getId());
}

Example 100 with Project

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

the class ProjectServiceImplIT method p.

private Project p() {
    Project p = new Project();
    p.setName("Project name");
    p.setProjectDescription("Description");
    p.setRemoteURL("http://google.com");
    return p;
}