Source:
public void setupClientEnvironment(List<String> args) { INIConfiguration config = getIniConfiguration(args); String token = config.getString("token", ""); String serverUrl = config.getString("server-url", "<LINK_0>"); if (serverUrl.contains(":8443")) { out("Dockstore webservice has deprecated port 8443 and may no longer expose it. Please change it to use the standard 443 port via the Dockstore config file (\"~/.dockstore/config\" by default)."); } ApiClient defaultApiClient; defaultApiClient = Configuration.getDefaultApiClient(); String cliVersion = getClientVersion(); defaultApiClient.setUserAgent("Dockstore-CLI/" + cliVersion + "/java"); ApiKeyAuth bearer = (ApiKeyAuth)defaultApiClient.getAuthentication("BEARER"); bearer.setApiKeyPrefix("BEARER"); bearer.setApiKey(token); defaultApiClient.setBasePath(serverUrl); this.containersApi = new ContainersApi(defaultApiClient); this.usersApi = new UsersApi(defaultApiClient); this.ga4ghApi = new Ga4GhApi(defaultApiClient); this.extendedGA4GHApi = new ExtendedGa4GhApi(defaultApiClient); this.metadataApi = new MetadataApi(defaultApiClient); try { if (this.usersApi.getApiClient() != null) { this.isAdmin = this.usersApi.getUser().isIsAdmin(); } } catch (ApiException | ProcessingException ex) { this.isAdmin = false; } this.toolClient = new ToolClient(containersApi, new ContainertagsApi(defaultApiClient), usersApi, this, isAdmin); this.workflowClient = new WorkflowClient(new WorkflowsApi(defaultApiClient), usersApi, this, isAdmin); this.checkerClient = new CheckerClient(new WorkflowsApi(defaultApiClient), usersApi, this, isAdmin); defaultApiClient.setDebugging(DEBUG.get()); CWLRunnerFactory.setConfig(config); }

Target:
public void setupClientEnvironment(List<String> args) { INIConfiguration config = getIniConfiguration(args); String token = config.getString("token", ""); String serverUrl = config.getString("server-url", "<LINK_0>"); if (serverUrl.contains(":8443")) { err(DEPRECATED_PORT_MESSAGE); } ApiClient defaultApiClient; defaultApiClient = Configuration.getDefaultApiClient(); String cliVersion = getClientVersion(); defaultApiClient.setUserAgent("Dockstore-CLI/" + cliVersion + "/java"); ApiKeyAuth bearer = (ApiKeyAuth)defaultApiClient.getAuthentication("BEARER"); bearer.setApiKeyPrefix("BEARER"); bearer.setApiKey(token); defaultApiClient.setBasePath(serverUrl); this.containersApi = new ContainersApi(defaultApiClient); this.usersApi = new UsersApi(defaultApiClient); this.ga4ghApi = new Ga4GhApi(defaultApiClient); this.extendedGA4GHApi = new ExtendedGa4GhApi(defaultApiClient); this.metadataApi = new MetadataApi(defaultApiClient); try { if (this.usersApi.getApiClient() != null) { this.isAdmin = this.usersApi.getUser().isIsAdmin(); } } catch (ApiException | ProcessingException ex) { this.isAdmin = false; } this.toolClient = new ToolClient(containersApi, new ContainertagsApi(defaultApiClient), usersApi, this, isAdmin); this.workflowClient = new WorkflowClient(new WorkflowsApi(defaultApiClient), usersApi, this, isAdmin); this.checkerClient = new CheckerClient(new WorkflowsApi(defaultApiClient), usersApi, this, isAdmin); defaultApiClient.setDebugging(DEBUG.get()); CWLRunnerFactory.setConfig(config); }