Examples with AssemblyFileProcessor ca.corefacility.bioinformatics.irida.processing.impl.AssemblyFileProcessor used on opensource projects

Example 1 with AssemblyFileProcessor

use of ca.corefacility.bioinformatics.irida.processing.impl.AssemblyFileProcessor in project irida by phac-nml.

the class AssemblyFileProcessorTest method setUp.

@Before
public void setUp() throws IridaWorkflowNotFoundException {
    MockitoAnnotations.initMocks(this);
    processor = new AssemblyFileProcessor(objectRepository, submissionRepository, workflowsService, userRepository, ssoRepository, psjRepository);
    UUID workflowUUID = UUID.randomUUID();
    IridaWorkflowDescription workflowDescription = new IridaWorkflowDescription(workflowUUID, null, null, null, null, ImmutableList.of(), ImmutableList.of(), ImmutableList.of());
    IridaWorkflow workflow = new IridaWorkflow(workflowDescription, null);
    when(workflowsService.getDefaultWorkflowByType(AnalysisType.ASSEMBLY_ANNOTATION)).thenReturn(workflow);
    when(userRepository.loadUserByUsername("admin")).thenReturn(new User());
}