Examples with JobError ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError used on opensource projects

Example 6 with JobError

use of ca.corefacility.bioinformatics.irida.model.workflow.analysis.JobError in project irida by phac-nml.

the class GalaxyJobErrorsServiceIT method testFailingAnalysisReturnsJobError.

/**
 * Test that a failure producing Galaxy workflow analysis returns a {@link JobError}
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testFailingAnalysisReturnsJobError() throws Exception {
    databaseSetupGalaxyITService.setupSubmissionInDatabase(1L, sequenceFilePath, referenceFilePath, iridaWorkflowIdWithError, false);
    AnalysisSubmission submission = runAnalysis();
    assertEquals(AnalysisState.ERROR, submission.getAnalysisState());
    List<JobError> errors = galaxyJobErrorsService.createNewJobErrors(submission);
    assertTrue("There should only be one JobError", errors.size() == 1);
    JobError jobError = errors.get(0);
    assertTrue("JobError should have some stderr message", jobError.getStandardError() != null && !jobError.getStandardError().equals(""));
    assertTrue("JobError should be triggered by 'IndexError: list index out of range'", jobError.getStandardError().contains("IndexError: list index out of range"));
    assertTrue("JobError tool ID should be 'Filter1'", jobError.getToolId().equals("Filter1"));
    assertTrue("JobError exit code should be '1'", jobError.getExitCode() == 1);
}