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

Example 6 with ReferenceFile

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

the class ProjectServiceImplIT method testAddReferenceFileAmbiguouusBasesToProject.

@Test(expected = UnsupportedReferenceFileContentError.class)
@WithMockUser(username = "admin", roles = "ADMIN")
public void testAddReferenceFileAmbiguouusBasesToProject() throws IOException, URISyntaxException {
    ReferenceFile f = new ReferenceFile();
    Path referenceFilePath = Paths.get(getClass().getResource("/ca/corefacility/bioinformatics/irida/service/testReferenceAmbiguous.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);
    projectService.addReferenceFileToProject(p, f);
}

Example 7 with ReferenceFile

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

the class ReferenceFileServiceImplIT method testRead.

@Test
@WithMockUser(username = "fbristow", roles = "USER")
public void testRead() {
    ReferenceFile read = referenceFileService.read(1L);
    assertNotNull(read);
}

Example 8 with ReferenceFile

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

the class ReferenceFileServiceImplIT method testGetReferenceFilesForProject.

@Test
@WithMockUser(username = "fbristow", roles = "ADMIN")
public void testGetReferenceFilesForProject() {
    Project p = projectService.read(1L);
    List<Join<Project, ReferenceFile>> prs = referenceFileService.getReferenceFilesForProject(p);
    assertEquals("Wrong number of reference files for project.", 1, prs.size());
    ReferenceFile rf = prs.iterator().next().getObject();
    assertEquals("Wrong reference file attached to project.", Long.valueOf(1), rf.getId());
}

Example 9 with ReferenceFile

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

the class SampleServiceImplIT method testEstimateCoverageForSampleReferenceFile.

/**
 * Tests esimating coverage with a reference file.
 *
 * @throws SequenceFileAnalysisException
 */
@Test
@WithMockUser(username = "fbristow", roles = "USER")
public void testEstimateCoverageForSampleReferenceFile() throws SequenceFileAnalysisException {
    Long sampleID = 1L;
    Sample s = sampleService.read(sampleID);
    ReferenceFile referenceFile = new ReferenceFile();
    referenceFile.setFileLength(500L);
    double coverage = sampleService.estimateCoverageForSample(s, referenceFile);
    assertEquals(2.0, coverage, deltaFloatEquality);
}

Example 10 with ReferenceFile

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

the class ReferenceFileControllerTest method testDeleteReferenceFile.

@Test
public void testDeleteReferenceFile() {
    logger.debug("Testing delete reference file");
    MockHttpServletResponse response = new MockHttpServletResponse();
    Project project = TestDataFactory.constructProject();
    ReferenceFile file = TestDataFactory.constructReferenceFile();
    when(projectService.read(project.getId())).thenReturn(project);
    when(referenceFileService.read(file.getId())).thenReturn(file);
    Map<String, Object> result = controller.deleteReferenceFile(file.getId(), project.getId(), response, Locale.US);
    assertTrue(result.containsKey("result"));
    assertEquals("success", result.get("result"));
}