Examples with GalaxyWorkflowState ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState used on opensource projects

Example 1 with GalaxyWorkflowState

use of ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState in project irida by phac-nml.

the class AnalysisExecutionScheduledTaskImplTest method testMonitorRunningAnalysesSuccessError.

/**
 * Tests successfully switching an analysis to {@link AnalysisState.ERROR}
 * if there was an error Galaxy state.
 *
 * @throws ExecutionManagerException
 * @throws IridaWorkflowNotFoundException
 */
@Test
public void testMonitorRunningAnalysesSuccessError() throws ExecutionManagerException, IridaWorkflowNotFoundException {
    analysisSubmission.setAnalysisState(AnalysisState.RUNNING);
    Map<GalaxyWorkflowState, Set<String>> stateIds = Util.buildStateIdsWithStateFilled(GalaxyWorkflowState.ERROR, Sets.newHashSet("1"));
    GalaxyWorkflowStatus galaxyWorkflowStatus = new GalaxyWorkflowStatus(GalaxyWorkflowState.ERROR, stateIds);
    when(analysisSubmissionRepository.findByAnalysisState(AnalysisState.RUNNING)).thenReturn(Arrays.asList(analysisSubmission));
    when(analysisExecutionService.getWorkflowStatus(analysisSubmission)).thenReturn(galaxyWorkflowStatus);
    analysisExecutionScheduledTask.monitorRunningAnalyses();
    assertEquals(AnalysisState.ERROR, analysisSubmission.getAnalysisState());
    verify(analysisSubmissionRepository).save(analysisSubmission);
}

Example 2 with GalaxyWorkflowState

use of ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState in project irida by phac-nml.

the class AnalysisExecutionScheduledTaskImplTest method testMonitorRunningAnalysesSuccessFinished.

/**
 * Tests successfully switching analysis state to
 * {@link AnalysisState.FINISHED_RUNNING} on success in Galaxy.
 *
 * @throws ExecutionManagerException
 * @throws IridaWorkflowNotFoundException
 */
@Test
public void testMonitorRunningAnalysesSuccessFinished() throws ExecutionManagerException, IridaWorkflowNotFoundException {
    analysisSubmission.setAnalysisState(AnalysisState.RUNNING);
    Map<GalaxyWorkflowState, Set<String>> stateIds = Util.buildStateIdsWithStateFilled(GalaxyWorkflowState.OK, Sets.newHashSet("1"));
    GalaxyWorkflowStatus galaxyWorkflowStatus = new GalaxyWorkflowStatus(GalaxyWorkflowState.OK, stateIds);
    when(analysisSubmissionRepository.findByAnalysisState(AnalysisState.RUNNING)).thenReturn(Arrays.asList(analysisSubmission));
    when(analysisExecutionService.getWorkflowStatus(analysisSubmission)).thenReturn(galaxyWorkflowStatus);
    analysisExecutionScheduledTask.monitorRunningAnalyses();
    assertEquals(AnalysisState.FINISHED_RUNNING, analysisSubmission.getAnalysisState());
    verify(analysisSubmissionRepository).save(analysisSubmission);
}

Example 3 with GalaxyWorkflowState

use of ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState in project irida by phac-nml.

the class AnalysisExecutionScheduledTaskImplTest method testMonitorRunningAnalysesSuccessErrorStillRunning.

/**
 * Tests successfully switching an analysis to {@link AnalysisState.ERROR}
 * if there was an Galaxy job with an error, but still running.
 *
 * @throws ExecutionManagerException
 * @throws IridaWorkflowNotFoundException
 */
@Test
public void testMonitorRunningAnalysesSuccessErrorStillRunning() throws ExecutionManagerException, IridaWorkflowNotFoundException {
    analysisSubmission.setAnalysisState(AnalysisState.RUNNING);
    Map<GalaxyWorkflowState, Set<String>> stateIds = Util.buildStateIdsWithStateFilled(GalaxyWorkflowState.ERROR, Sets.newHashSet("1"));
    GalaxyWorkflowStatus galaxyWorkflowStatus = new GalaxyWorkflowStatus(GalaxyWorkflowState.RUNNING, stateIds);
    when(analysisSubmissionRepository.findByAnalysisState(AnalysisState.RUNNING)).thenReturn(Arrays.asList(analysisSubmission));
    when(analysisExecutionService.getWorkflowStatus(analysisSubmission)).thenReturn(galaxyWorkflowStatus);
    analysisExecutionScheduledTask.monitorRunningAnalyses();
    assertEquals(AnalysisState.ERROR, analysisSubmission.getAnalysisState());
    verify(analysisSubmissionRepository).save(analysisSubmission);
}

Example 4 with GalaxyWorkflowState

use of ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState in project irida by phac-nml.

the class AnalysisExecutionScheduledTaskImplTest method testMonitorRunningAnalysesSuccessQueued.

/**
 * Tests successfully skipping over switching analysis state for a queued
 * analysis in Galaxy.
 *
 * @throws ExecutionManagerException
 * @throws IridaWorkflowNotFoundException
 */
@Test
public void testMonitorRunningAnalysesSuccessQueued() throws ExecutionManagerException, IridaWorkflowNotFoundException {
    analysisSubmission.setAnalysisState(AnalysisState.RUNNING);
    Map<GalaxyWorkflowState, Set<String>> stateIds = Util.buildStateIdsWithStateFilled(GalaxyWorkflowState.QUEUED, Sets.newHashSet("1"));
    when(analysisSubmissionRepository.findByAnalysisState(AnalysisState.RUNNING)).thenReturn(Arrays.asList(analysisSubmission));
    when(analysisExecutionService.getWorkflowStatus(analysisSubmission)).thenReturn(new GalaxyWorkflowStatus(GalaxyWorkflowState.QUEUED, stateIds));
    analysisExecutionScheduledTask.monitorRunningAnalyses();
    assertEquals(AnalysisState.RUNNING, analysisSubmission.getAnalysisState());
    verify(analysisSubmissionRepository, never()).save(analysisSubmission);
}

Example 5 with GalaxyWorkflowState

use of ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.GalaxyWorkflowState in project irida by phac-nml.

the class AnalysisExecutionScheduledTaskImplTest method testMonitorRunningAnalysesSuccessRunning.

/**
 * Tests successfully skipping over switching analysis state for a running
 * analysis in Galaxy.
 *
 * @throws ExecutionManagerException
 * @throws IridaWorkflowNotFoundException
 */
@Test
public void testMonitorRunningAnalysesSuccessRunning() throws ExecutionManagerException, IridaWorkflowNotFoundException {
    analysisSubmission.setAnalysisState(AnalysisState.RUNNING);
    Map<GalaxyWorkflowState, Set<String>> stateIds = Util.buildStateIdsWithStateFilled(GalaxyWorkflowState.RUNNING, Sets.newHashSet("1"));
    when(analysisSubmissionRepository.findByAnalysisState(AnalysisState.RUNNING)).thenReturn(Arrays.asList(analysisSubmission));
    when(analysisExecutionService.getWorkflowStatus(analysisSubmission)).thenReturn(new GalaxyWorkflowStatus(GalaxyWorkflowState.RUNNING, stateIds));
    analysisExecutionScheduledTask.monitorRunningAnalyses();
    assertEquals(AnalysisState.RUNNING, analysisSubmission.getAnalysisState());
    verify(analysisSubmissionRepository, never()).save(analysisSubmission);
}