Source:
public void testNextFlowSecondaryFiles() throws Exception { CommonTestUtilities.cleanStatePrivate1(SUPPORT); final ApiClient webClient = getWebClient(); WorkflowsApi workflowApi = new WorkflowsApi(webClient); UsersApi usersApi = new UsersApi(webClient); User user = usersApi.getUser(); final List<Workflow> workflows = usersApi.refreshWorkflows(user.getId()); for (Workflow workflow: workflows) { assertNotSame("", workflow.getWorkflowName()); } Workflow workflowByPathGithub = workflowApi.getWorkflowByPath(DOCKSTORE_TEST_USER_NEXTFLOW_WORKFLOW); workflowByPathGithub.setWorkflowPath("/nextflow.config"); workflowByPathGithub.setDescriptorType(LanguageType.NEXTFLOW.toString()); workflowApi.updateWorkflow(workflowByPathGithub.getId(), workflowByPathGithub); workflowByPathGithub = workflowApi.getWorkflowByPath(DOCKSTORE_TEST_USER_NEXTFLOW_WORKFLOW); final Workflow refreshGithub = workflowApi.refresh(workflowByPathGithub.getId()); List<SourceFile> sourceFileList = new ArrayList<>( refreshGithub.getWorkflowVersions().stream().filter(version -> version.getName().equals("v2.0")).findFirst().get() .getSourceFiles()); Assert.assertEquals(4, sourceFileList.size()); Assert.assertTrue("files are what we expected", sourceFileList.stream().anyMatch(file -> file.getPath().equals("bin/AMPA-BIGTABLE.pl")) && sourceFileList.stream().anyMatch(file -> file.getPath().equals("bin/multi-AMPA-BIGTABLE.pl"))); Assert.assertEquals("test.user@test.com", refreshGithub.getAuthor()); Assert.assertEquals("Fast automated prediction of protein antimicrobial regions", refreshGithub.getDescription()); }

Target:
public void testNextFlowSecondaryFiles() throws Exception { CommonTestUtilities.cleanStatePrivate1(SUPPORT); final ApiClient webClient = getWebClient(); WorkflowsApi workflowApi = new WorkflowsApi(webClient); UsersApi usersApi = new UsersApi(webClient); User user = usersApi.getUser(); final List<Workflow> workflows = usersApi.refreshWorkflows(user.getId()); for (Workflow workflow: workflows) { assertNotSame("", workflow.getWorkflowName()); } Workflow workflowByPathGithub = workflowApi.getWorkflowByPath(DOCKSTORE_TEST_USER_NEXTFLOW_WORKFLOW); workflowByPathGithub.setWorkflowPath("/nextflow.config"); workflowByPathGithub.setDescriptorType(LanguageType.NEXTFLOW.toString()); workflowApi.updateWorkflow(workflowByPathGithub.getId(), workflowByPathGithub); workflowByPathGithub = workflowApi.getWorkflowByPath(DOCKSTORE_TEST_USER_NEXTFLOW_WORKFLOW); final Workflow refreshGithub = workflowApi.refresh(workflowByPathGithub.getId()); List<SourceFile> sourceFileList = new ArrayList<>( refreshGithub.getWorkflowVersions().stream().filter(version -> version.getName().equals("v2.0")).findFirst().get() .getSourceFiles()); Assert.assertEquals(4, sourceFileList.size()); Assert.assertTrue("files are not what we expected", sourceFileList.stream().anyMatch(file -> file.getPath().equals("bin/AMPA-BIGTABLE.pl")) && sourceFileList.stream().anyMatch(file -> file.getPath().equals("bin/multi-AMPA-BIGTABLE.pl"))); Assert.assertEquals("test.user@test.com", refreshGithub.getAuthor()); Assert.assertEquals("Fast automated prediction of protein antimicrobial regions", refreshGithub.getDescription()); }