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

Example 51 with AnalysisSubmission

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

the class AnalysisSubmissionServiceImplIT method testRemoveAnalysisSubmissionFromProject.

@Test
@WithMockUser(username = "aaron", roles = "USER")
public void testRemoveAnalysisSubmissionFromProject() {
    AnalysisSubmission read = analysisSubmissionService.read(3L);
    Project project2 = projectService.read(1L);
    analysisSubmissionService.removeAnalysisProjectShare(read, project2);
}

Example 52 with AnalysisSubmission

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

the class AnalysisSubmissionServiceImplIT method testCreateSubmissionWithUnsavedNamedParameters.

@Test(expected = UnsupportedOperationException.class)
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testCreateSubmissionWithUnsavedNamedParameters() {
    final SingleEndSequenceFile sequencingObject = (SingleEndSequenceFile) sequencingObjectRepository.findOne(1L);
    final IridaWorkflowNamedParameters params = new IridaWorkflowNamedParameters("named parameters.", workflowId, ImmutableMap.of("named", "parameter"));
    final AnalysisSubmission submission = AnalysisSubmission.builder(workflowId).inputFiles(Sets.newHashSet(sequencingObject)).withNamedParameters(params).build();
    analysisSubmissionService.create(submission);
}

Example 53 with AnalysisSubmission

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

the class AnalysisSubmissionServiceImplIT method searchAnalyses.

@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void searchAnalyses() {
    Page<AnalysisSubmission> paged = analysisSubmissionService.listAllSubmissions(null, null, null, null, new PageRequest(0, 10, new Sort(Direction.ASC, "createdDate")));
    assertEquals(10, paged.getContent().size());
    // Try filtering a by names
    String name = "My";
    paged = analysisSubmissionService.listAllSubmissions(null, name, null, null, new PageRequest(0, 10, new Sort(Direction.ASC, "createdDate")));
    assertEquals(8, paged.getContent().size());
    // Add a state filter
    AnalysisState state = AnalysisState.COMPLETED;
    paged = analysisSubmissionService.listAllSubmissions(null, name, state, null, new PageRequest(0, 10, new Sort(Direction.ASC, "createdDate")));
    assertEquals(2, paged.getContent().size());
}

Example 54 with AnalysisSubmission

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

the class AnalysisSubmissionServiceImplIT method testGetAnalysisSubmissionsForUserAsAdminUser.

/**
 * Tests getting a set of submissions as an admin user for a different user.
 */
@Test
@WithMockUser(username = "otheraaron", roles = "ADMIN")
public void testGetAnalysisSubmissionsForUserAsAdminUser() {
    User user = userRepository.findOne(1L);
    Set<AnalysisSubmission> submissions = analysisSubmissionService.getAnalysisSubmissionsForUser(user);
    assertNotNull("should get submissions for the user", submissions);
    assertEquals("submissions should have correct number", 9, submissions.size());
}

Example 55 with AnalysisSubmission

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

the class AnalysisSubmissionServiceImplIT method testCreateSubmissionWithNamedParameters.

@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testCreateSubmissionWithNamedParameters() {
    final SingleEndSequenceFile sequencingObject = (SingleEndSequenceFile) sequencingObjectRepository.findOne(1L);
    final IridaWorkflowNamedParameters params = parametersRepository.findOne(1L);
    final AnalysisSubmission submission = AnalysisSubmission.builder(workflowId).inputFiles(Sets.newHashSet(sequencingObject)).withNamedParameters(params).build();
    analysisSubmissionService.create(submission);
    assertNotNull("Should have saved and created an id for the submission", submission.getId());
    assertNotNull("Submission should have a map of parameters", submission.getInputParameters());
    assertEquals("Submission parameters should be the same as the named parameters", params.getInputParameters(), submission.getInputParameters());
}