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

Example 96 with AnalysisSubmission

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

the class AnalysisSubmissionSampleProcessorImplIT method testUpdateFailPermissionNonSampleOwner.

@Test(expected = AccessDeniedException.class)
@WithMockUser(username = "fbristow", roles = "USER")
public void testUpdateFailPermissionNonSampleOwner() throws PostProcessingException {
    AnalysisSubmission a = analysisSubmissionRepository.findOne(2L);
    analysisSubmissionSampleProcessorImpl.updateSamples(a);
}

Example 97 with AnalysisSubmission

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

the class AnalysisSubmissionSampleProcessorImplIT method testUpdateSamplesSuccess.

@Test
@WithMockUser(username = "fbristow", roles = "USER")
public void testUpdateSamplesSuccess() throws PostProcessingException {
    AnalysisSubmission a = analysisSubmissionRepository.findOne(1L);
    assertEquals("Should be no join between sample and assembly", 0, sampleGenomeAssemblyJoinRepository.count());
    analysisSubmissionSampleProcessorImpl.updateSamples(a);
    assertEquals("Should exist a join between sample and assembly", 1, sampleGenomeAssemblyJoinRepository.count());
}

Example 98 with AnalysisSubmission

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

the class AnalysisSubmissionSampleProcessorImplIT method testUpdateFailPermissionNonProjectOwner.

@Test(expected = AccessDeniedException.class)
@WithMockUser(username = "dr-evil", roles = "USER")
public void testUpdateFailPermissionNonProjectOwner() throws PostProcessingException {
    AnalysisSubmission a = analysisSubmissionRepository.findOne(2L);
    analysisSubmissionSampleProcessorImpl.updateSamples(a);
}

Example 99 with AnalysisSubmission

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

the class AssemblySampleUpdaterIT method testUpdateFailMultipleSamples.

@Test(expected = IllegalArgumentException.class)
@WithMockUser(username = "fbristow", roles = "USER")
public void testUpdateFailMultipleSamples() {
    AnalysisSubmission a = analysisSubmissionRepository.findOne(1L);
    Sample s1 = sampleRepository.findOne(1L);
    Sample s2 = sampleRepository.findOne(2L);
    assemblySampleUpdater.update(Sets.newHashSet(s1, s2), a);
}

Example 100 with AnalysisSubmission

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

the class RESTAnalysisSubmissionController method getAnalysisOutputFileContents.

/**
 * Get the actual file contents for an analysis output file.
 *
 * @param submissionId
 *            The {@link AnalysisSubmission} id
 * @param fileType
 *            The {@link AnalysisOutputFile} type as defined in the
 *            {@link Analysis} subclass
 * @return a {@link FileSystemResource} containing the contents of the
 *         {@link AnalysisOutputFile}.
 */
@RequestMapping(value = "/{submissionId}/analysis/file/{fileType}", produces = MediaType.TEXT_PLAIN_VALUE)
@ResponseBody
public FileSystemResource getAnalysisOutputFileContents(@PathVariable Long submissionId, @PathVariable String fileType) {
    AnalysisSubmission read = analysisSubmissionService.read(submissionId);
    if (read.getAnalysisState() != AnalysisState.COMPLETED) {
        throw new EntityNotFoundException("Analysis is not completed");
    }
    AnalysisOutputFile analysisOutputFile = read.getAnalysis().getAnalysisOutputFile(fileType);
    return new FileSystemResource(analysisOutputFile.getFile().toFile());
}