Examples with ApiClient io.swagger.client.ApiClient used on opensource projects

Example 1 with ApiClient

use of io.swagger.client.ApiClient in project CommandHelper by EngineHub.

the class AppsApiUtil method getClient.

public ApiClient getClient() {
    ApiClient client = new ApiClient();
    client.setBasePath(baseApiUrl);
    client.setConnectTimeout(TIMEOUT);
    client.setDebugging(debug);
    return client;
}

Example 2 with ApiClient

use of io.swagger.client.ApiClient in project dockstore by dockstore.

the class CRUDClientIT method testUpdatingDefaultVersionHostedTool.

/**
 * Ensures that hosted tools can have their default path updated
 */
@Test
public void testUpdatingDefaultVersionHostedTool() throws IOException {
    ApiClient webClient = getWebClient(ADMIN_USERNAME, testingPostgres);
    ContainersApi containersApi = new ContainersApi(webClient);
    HostedApi hostedApi = new HostedApi(webClient);
    // Add a tool with a version
    DockstoreTool hostedTool = hostedApi.createHostedTool("awesomeTool", Registry.QUAY_IO.getDockerPath().toLowerCase(), CWL.getShortName(), "coolNamespace", null);
    SourceFile descriptorFile = new SourceFile();
    descriptorFile.setContent(FileUtils.readFileToString(new File(ResourceHelpers.resourceFilePath("tar-param.cwl")), StandardCharsets.UTF_8));
    descriptorFile.setType(SourceFile.TypeEnum.DOCKSTORE_CWL);
    descriptorFile.setPath("/Dockstore.cwl");
    descriptorFile.setAbsolutePath("/Dockstore.cwl");
    SourceFile dockerfile = new SourceFile();
    dockerfile.setContent("FROM ubuntu:latest");
    dockerfile.setType(SourceFile.TypeEnum.DOCKERFILE);
    dockerfile.setPath("/Dockerfile");
    dockerfile.setAbsolutePath("/Dockerfile");
    DockstoreTool dockstoreTool = hostedApi.editHostedTool(hostedTool.getId(), Lists.newArrayList(descriptorFile, dockerfile));
    Optional<Tag> first = dockstoreTool.getWorkflowVersions().stream().max(Comparator.comparingInt((Tag t) -> Integer.parseInt(t.getName())));
    assertTrue(first.isPresent());
    assertEquals("correct number of source files", 2, fileDAO.findSourceFilesByVersion(first.get().getId()).size());
    // Update the default version of the tool
    containersApi.updateToolDefaultVersion(hostedTool.getId(), first.get().getName());
    // test deletion of hosted tool for #3171
    containersApi.deleteContainer(hostedTool.getId());
}

Example 3 with ApiClient

use of io.swagger.client.ApiClient in project dockstore by dockstore.

the class CheckerWorkflowIT method testCWLWorkflowAddCheckerRefreshPublishUnpublish.

/**
 * This tests the process of adding a checker workflow to a CWL workflow entry and that some calls to the workflow will also trigger the calls to the checker
 * - Refresh workflow should refresh checker
 * - Publish workflow should publish checker
 * - Unpublish workflow should unpublish checker
 *
 * @throws ApiException
 */
@Test
public void testCWLWorkflowAddCheckerRefreshPublishUnpublish() throws ApiException {
    // Setup for test
    final ApiClient webClient = getWebClient(USER_2_USERNAME, testingPostgres);
    WorkflowsApi workflowApi = new WorkflowsApi(webClient);
    final PublishRequest publishRequest = CommonTestUtilities.createPublishRequest(true);
    final PublishRequest unpublishRequest = CommonTestUtilities.createPublishRequest(false);
    // Manually register a workflow
    Workflow githubWorkflow = workflowApi.manualRegister("github", "DockstoreTestUser2/md5sum-checker", "/md5sum/md5sum-workflow.cwl", "altname", "cwl", "/testcwl.json");
    final long count = testingPostgres.runSelectStatement("select count(*) from workflow where mode = '" + Workflow.ModeEnum.FULL + "'", long.class);
    assertEquals("No workflows are in full mode, there are " + count, 0, count);
    // Refresh the workflow
    workflowApi.refresh(githubWorkflow.getId(), false);
    final long count2 = testingPostgres.runSelectStatement("select count(*) from workflow where mode = '" + Workflow.ModeEnum.FULL + "'", long.class);
    assertEquals("One workflow should be full, there are " + count2, 1, count2);
    // Add checker workflow
    workflowApi.registerCheckerWorkflow("/checker-workflow-wrapping-workflow.cwl", githubWorkflow.getId(), "cwl", null);
    // Refresh workflow
    Workflow refreshedEntry = workflowApi.refresh(githubWorkflow.getId(), false);
    // Should be able to download zip for first version
    Workflow checkerWorkflow = workflowApi.getWorkflow(refreshedEntry.getCheckerId(), null);
    workflowApi.getWorkflowZip(checkerWorkflow.getId(), checkerWorkflow.getWorkflowVersions().get(0).getId());
    // Refreshing the entry also calls the update user metadata function which populates the user profile
    refreshedEntry.getUsers().forEach(entryUser -> {
        Assert.assertNotEquals("refresh() endpoint should have user profiles", null, entryUser.getUserProfiles());
    });
    // Checker workflow should refresh
    final long count3 = testingPostgres.runSelectStatement("select count(*) from workflow where mode = '" + Workflow.ModeEnum.FULL + "'", long.class);
    assertEquals("Two workflows should be full (one being the checker), there are " + count3, 2, count3);
    // Checker workflow should have the same test path as entry
    final long count4 = testingPostgres.runSelectStatement("select count(*) from workflow w, entry_defaultpaths ed where ed.path = '/testcwl.json' and w.id = ed.entry_id", long.class);
    assertEquals("There should be two workflows with default test parameter file path of /testcwl.json, there are " + count4, 2, count4);
    // Checker workflow should have the correct workflow path
    final long count5 = testingPostgres.runSelectStatement("select count(*) from workflow where sourcecontrol = 'github.com' and organization = 'DockstoreTestUser2' and repository = 'md5sum-checker' and workflowname = 'altname_cwl_checker' and giturl = 'git@github.com:DockstoreTestUser2/md5sum-checker.git'", long.class);
    assertEquals("The workflow should have the correct path, there are " + count5, 1, count5);
    // Publish workflow
    final long count6 = testingPostgres.runSelectStatement("select count(*) from workflow where ispublished = true", long.class);
    assertEquals("No workflows should be published, there are " + count6, 0, count6);
    workflowApi.publish(githubWorkflow.getId(), publishRequest);
    // Checker workflow should publish
    final long count7 = testingPostgres.runSelectStatement("select count(*) from workflow where ispublished = true", long.class);
    assertEquals("Two workflows should be published (one being the checker), there are " + count7, 2, count7);
    // Should still be able to download zip for first version
    workflowApi.getWorkflowZip(checkerWorkflow.getId(), checkerWorkflow.getWorkflowVersions().get(0).getId());
    // Unpublish workflow
    workflowApi.publish(githubWorkflow.getId(), unpublishRequest);
    // Checker workflow should unpublish
    final long count8 = testingPostgres.runSelectStatement("select count(*) from workflow where ispublished = true", long.class);
    assertEquals("No workflows should be published, there are " + count8, 0, count8);
    // Should not be able to directly publish the checker
    try {
        workflowApi.publish(refreshedEntry.getCheckerId(), publishRequest);
        fail("Should not reach this statement.");
    } catch (ApiException ex) {
        assertEquals(ex.getCode(), HttpStatus.SC_BAD_REQUEST);
    }
}

Example 4 with ApiClient

use of io.swagger.client.ApiClient in project dockstore by dockstore.

the class CheckerWorkflowIT method testAddCheckerToStub.

/**
 * Should not be able to add a checker workflow to a stub workflow (Should fail)
 *
 * @throws ApiException
 */
@Test
public void testAddCheckerToStub() throws ApiException {
    // Setup for test
    final ApiClient webClient = getWebClient(USER_2_USERNAME, testingPostgres);
    WorkflowsApi workflowApi = new WorkflowsApi(webClient);
    // Manually register a workflow
    Workflow githubWorkflow = workflowApi.manualRegister("github", "DockstoreTestUser2/md5sum-checker", "/md5sum/md5sum-workflow.cwl", "altname", "cwl", "/testcwl.json");
    final long count = testingPostgres.runSelectStatement("select count(*) from workflow where mode = '" + Workflow.ModeEnum.FULL + "'", long.class);
    assertEquals("No workflows are in full mode, there are " + count, 0, count);
    thrown.expect(ApiException.class);
    // Add checker workflow
    workflowApi.registerCheckerWorkflow("checker-workflow-wrapping-workflow.cwl", githubWorkflow.getId(), "cwl", null);
}

Example 5 with ApiClient

use of io.swagger.client.ApiClient in project dockstore by dockstore.

the class CheckerWorkflowIT method testCheckerWorkflowAndRefresh.

private void testCheckerWorkflowAndRefresh(boolean workflow, boolean all) {
    // Setup for test
    final ApiClient webClient = getWebClient(USER_2_USERNAME, testingPostgres);
    WorkflowsApi workflowApi = new WorkflowsApi(webClient);
    ContainersApi containersApi = new ContainersApi(webClient);
    long baseEntryId;
    if (workflow) {
        // Manually register a workflow
        Workflow githubWorkflow = workflowApi.manualRegister("github", "DockstoreTestUser2/md5sum-checker", "/md5sum/md5sum-workflow.cwl", "", "cwl", "/testcwl.json");
        Assert.assertEquals("Should be able to get license after manual register", "Apache License 2.0", githubWorkflow.getLicenseInformation().getLicenseName());
        // Clear license name to mimic old workflow that does not have a license associated with it
        testingPostgres.runUpdateStatement("update workflow set licensename=null");
        Workflow refreshedWorkflow = workflowApi.refresh(githubWorkflow.getId(), false);
        Assert.assertEquals("Should be able to get license after refresh", "Apache License 2.0", refreshedWorkflow.getLicenseInformation().getLicenseName());
        // Refresh the workflow
        baseEntryId = refreshedWorkflow.getId();
    } else {
        // Manually register a tool
        DockstoreTool newTool = new DockstoreTool();
        newTool.setMode(DockstoreTool.ModeEnum.MANUAL_IMAGE_PATH);
        newTool.setName("my-md5sum");
        newTool.setGitUrl("git@github.com:DockstoreTestUser2/md5sum-checker.git");
        newTool.setDefaultDockerfilePath("/md5sum/Dockerfile");
        newTool.setDefaultCwlPath("/md5sum/md5sum-tool.cwl");
        newTool.setRegistryString(Registry.QUAY_IO.getDockerPath());
        newTool.setNamespace("dockstoretestuser2");
        newTool.setToolname("altname");
        newTool.setPrivateAccess(false);
        newTool.setDefaultCWLTestParameterFile("/testcwl.json");
        DockstoreTool githubTool = containersApi.registerManual(newTool);
        // Refresh the workflow
        DockstoreTool refresh = containersApi.refresh(githubTool.getId());
        baseEntryId = refresh.getId();
    }
    // Add checker workflow
    final Entry checkerWorkflowBase = workflowApi.registerCheckerWorkflow("/checker-workflow-wrapping-workflow.cwl", baseEntryId, "cwl", null);
    final Workflow stubCheckerWorkflow = workflowApi.getWorkflow(checkerWorkflowBase.getCheckerId(), null);
    assertSame(stubCheckerWorkflow.getMode(), Workflow.ModeEnum.STUB);
    // should be able to refresh all or the organization when a checker stub is present without a failure (constraints issue from #1405)
    List<Workflow> workflows = new ArrayList<>();
    workflows.add(workflowApi.manualRegister(SourceControl.GITHUB.name(), "DockstoreTestUser/dockstore-whalesay-wdl", "/dockstore.wdl", "", DescriptorLanguage.WDL.getShortName(), ""));
    workflows.add(workflowApi.manualRegister(SourceControl.GITHUB.name(), "DockstoreTestUser/dockstore-whalesay-2", "/dockstore.wdl", "", DescriptorLanguage.WDL.getShortName(), ""));
    workflows.add(workflowApi.manualRegister(SourceControl.GITHUB.name(), "DockstoreTestUser/ampa-nf", "/nextflow.config", "", DescriptorLanguage.NEXTFLOW.getShortName(), ""));
    workflows.add(workflowApi.manualRegister("github", "DockstoreTestUser2/dockstore_workflow_cnv", "/workflow/cnv.cwl", "", "cwl", "/test.json"));
    if (all) {
        for (Workflow workflowItem : workflows) {
            workflowApi.refresh(workflowItem.getId(), false);
        }
    } else {
        for (Workflow workflowItem : workflows) {
            if (workflowItem.getOrganization().equalsIgnoreCase(stubCheckerWorkflow.getOrganization())) {
                workflowApi.refresh(workflowItem.getId(), false);
            }
        }
    }
}