Merge branch 'dev' into sps_edit_method

src/libs/ajax/ExternalCredentials.ts

@@ -75,3 +75,5 @@ export const ExternalCredentials = (signal?: AbortSignal) => (oAuth2Provider: OA
     },
   };
 };
+
+export type ExternalCredentialsContract = ReturnType<ReturnType<typeof ExternalCredentials>>;

src/libs/ajax/User.ts

@@ -346,3 +346,4 @@ export const User = (signal?: AbortSignal) => {
 };
 
 export type UserContract = ReturnType<typeof User>;
+export type UserProfileContract = UserContract['profile'];

src/libs/ajax/workspaces/Workspaces.ts

@@ -478,6 +478,12 @@ export const Workspaces = (signal?: AbortSignal) => ({
           _.mergeAll([authOpts(), { signal }])
         ).then((r) => r.blob()),
 
+      autoGenerateTsv: (entityType: string, prefix: string): Promise<Blob> =>
+        fetchOrchestration(
+          `api/workspaces/${namespace}/${name}/entities/${entityType}/paired-tsv`,
+          _.mergeAll([authOpts(), jsonBody({ prefix }), { signal, method: 'POST' }])
+        ).then((r: { blob: () => any }) => r.blob()),
+
       copyEntities: async (
         destNamespace: string,
         destName: string,

src/libs/events.ts

@@ -94,6 +94,7 @@ const eventsList = {
   uploaderUploadMetadata: 'uploader:metadata:upload',
   uploaderCreateTable: 'uploader:table:create',
   uploaderUpdateTable: 'uploader:table:update',
+  uploaderAutoGenerateTable: 'uploader:table:autoGenerate',
   user: {
     authToken: {
       load: {

src/libs/feature-previews-config.ts

@@ -7,6 +7,7 @@ export const FIRECLOUD_UI_MIGRATION = 'firecloudUiMigration';
 export const COHORT_BUILDER_CARD = 'cohortBuilderCard';
 export const GCP_BUCKET_LIFECYCLE_RULES = 'gcpBucketLifecycleRules';
 export const SPEND_REPORTING = 'spendReporting';
+export const AUTO_GENERATE_DATA_TABLES = 'autoGenerateDataTables';
 
 // If the groups option is defined for a FeaturePreview, it must contain at least one group.
 type GroupsList = readonly [string, ...string[]];
@@ -126,6 +127,16 @@ const featurePreviewsConfig: readonly FeaturePreview[] = [
     )}`,
     lastUpdated: '11/19/2024',
   },
+  {
+    id: AUTO_GENERATE_DATA_TABLES,
+    title: 'Autogenerate data table for single and paired end sequencing',
+    description:
+      'Enabling this feature will show a new option in the data uploader to autogenerate a data table instead of uploading your own TSV. This feature will attempt to automatch known file patterns for single and paired end sequencing and autogenerate a data table linking to those files.',
+    feedbackUrl: `mailto:[email protected]?subject=${encodeURIComponent(
+      'Feedback on Autogenerate data table for single and paired end sequencing'
+    )}`,
+    lastUpdated: '11/26/2024',
+  },
 ];
 
 export default featurePreviewsConfig;

src/profile/external-identities/LinkOAuth2Account.tsx

@@ -2,7 +2,7 @@ import { ClickableProps } from '@terra-ui-packages/components';
 import React, { ReactNode } from 'react';
 import { ButtonPrimary, Link } from 'src/components/common';
 import { icon } from 'src/components/icons';
-import { Ajax } from 'src/libs/ajax';
+import { ExternalCredentials } from 'src/libs/ajax/ExternalCredentials';
 import { withErrorReporting } from 'src/libs/error';
 import { useCancellation } from 'src/libs/react-utils';
 import * as Utils from 'src/libs/utils';
@@ -22,7 +22,7 @@ export const LinkOAuth2Account = (props: LinkOAuth2AccountProps): ReactNode => {
 
   const getAuthUrlAndRedirect = withErrorReporting(`Error getting Authorization URL for ${provider.short}`)(
     async () => {
-      const url = await Ajax(signal).ExternalCredentials(provider).getAuthorizationUrl();
+      const url = await ExternalCredentials(signal)(provider).getAuthorizationUrl();
       window.open(url, Utils.newTabLinkProps.target, 'noopener,noreferrer');
     }
   );

src/profile/external-identities/NihAccount.test.ts

@@ -1,10 +1,11 @@
 import { act, screen } from '@testing-library/react';
 import userEvent from '@testing-library/user-event';
 import { h } from 'react-hyperscript-helpers';
-import { Ajax } from 'src/libs/ajax';
+import { Metrics, MetricsContract } from 'src/libs/ajax/Metrics';
+import { User, UserContract } from 'src/libs/ajax/User';
 import { authStore } from 'src/libs/state';
 import { NihAccount } from 'src/profile/external-identities/NihAccount';
-import { asMockedFn, renderWithAppContexts } from 'src/testing/test-utils';
+import { asMockedFn, MockedFn, partial, renderWithAppContexts } from 'src/testing/test-utils';
 
 jest.mock('src/libs/nav', () => ({
   ...jest.requireActual('src/libs/nav'),
@@ -25,7 +26,8 @@ jest.mock('react-notifications-component', () => {
   };
 });
 
-jest.mock('src/libs/ajax');
+jest.mock('src/libs/ajax/Metrics');
+jest.mock('src/libs/ajax/User');
 
 const nihStatus = {
   linkedNihUsername: 'TEST_USERNAME',
@@ -42,14 +44,10 @@ describe('NihAccount', () => {
   describe('when given a token', () => {
     it('links the NIH Account and renders a linked NIH Account', async () => {
       // Arrange
-      const linkNihAccountFunction = jest.fn().mockReturnValue(Promise.resolve(nihStatus));
-      asMockedFn(Ajax).mockImplementation(
-        () =>
-          ({
-            Metrics: { captureEvent: jest.fn() } as Partial<ReturnType<typeof Ajax>['Metrics']>,
-            User: { linkNihAccount: linkNihAccountFunction } as Partial<ReturnType<typeof Ajax>['User']>,
-          } as ReturnType<typeof Ajax>)
-      );
+      const linkNihAccountFunction: MockedFn<UserContract['linkNihAccount']> = jest.fn();
+      linkNihAccountFunction.mockResolvedValue(nihStatus);
+      asMockedFn(Metrics).mockReturnValue(partial<MetricsContract>({ captureEvent: jest.fn() }));
+      asMockedFn(User).mockReturnValue(partial<UserContract>({ linkNihAccount: linkNihAccountFunction }));
 
       // Act
       await act(async () => {
@@ -115,14 +113,11 @@ describe('NihAccount', () => {
       // Arrange
       const user = userEvent.setup();
 
-      const unlinkNihAccountFunction = jest.fn().mockReturnValue(Promise.resolve());
-      asMockedFn(Ajax).mockImplementation(
-        () =>
-          ({
-            Metrics: { captureEvent: jest.fn() } as Partial<ReturnType<typeof Ajax>['Metrics']>,
-            User: { unlinkNihAccount: unlinkNihAccountFunction } as Partial<ReturnType<typeof Ajax>['User']>,
-          } as ReturnType<typeof Ajax>)
-      );
+      const unlinkNihAccountFunction: MockedFn<UserContract['unlinkNihAccount']> = jest.fn();
+      unlinkNihAccountFunction.mockResolvedValue(undefined);
+      asMockedFn(Metrics).mockReturnValue(partial<MetricsContract>({ captureEvent: jest.fn() }));
+      asMockedFn(User).mockReturnValue(partial<UserContract>({ unlinkNihAccount: unlinkNihAccountFunction }));
+
       // Act
       await act(async () => {
         authStore.update((state) => ({ ...state, nihStatus, nihStatusLoaded: true }));

src/profile/external-identities/NihAccount.ts

@@ -5,7 +5,7 @@ import { div, h, h3, span } from 'react-hyperscript-helpers';
 import Collapse from 'src/components/Collapse';
 import { ButtonPrimary, Link, spinnerOverlay } from 'src/components/common';
 import { InfoBox } from 'src/components/InfoBox';
-import { Ajax } from 'src/libs/ajax';
+import { User } from 'src/libs/ajax/User';
 import { NihDatasetPermission } from 'src/libs/ajax/User';
 import { withErrorReporting } from 'src/libs/error';
 import * as Nav from 'src/libs/nav';
@@ -30,7 +30,7 @@ export const NihAccount = ({ nihToken }) => {
       withErrorReporting('Error linking NIH account'),
       Utils.withBusyState(setIsLinking)
     )(async () => {
-      const nihStatus = await Ajax().User.linkNihAccount(nihToken);
+      const nihStatus = await User().linkNihAccount(nihToken);
       authStore.update((oldState: AuthState) => ({
         ...oldState,
         nihStatus,
@@ -157,7 +157,7 @@ export const NihAccount = ({ nihToken }) => {
                 Utils.withBusyState(setIsUnlinking)
               )(async () => {
                 authStore.update(_.set('nihStatusLoaded', false));
-                await Ajax().User.unlinkNihAccount();
+                await User().unlinkNihAccount();
                 authStore.update((oldState: AuthState) => ({
                   ...oldState,
                   nihStatus: undefined,

src/profile/external-identities/OAuth2Account.test.tsx

@@ -1,19 +1,20 @@
-import { DeepPartial } from '@terra-ui-packages/core-utils';
 import { act, screen } from '@testing-library/react';
 import userEvent from '@testing-library/user-event';
 import { axe } from 'jest-axe';
 import React from 'react';
-import { Ajax } from 'src/libs/ajax';
+import { ExternalCredentials, ExternalCredentialsContract } from 'src/libs/ajax/ExternalCredentials';
+import { Metrics, MetricsContract } from 'src/libs/ajax/Metrics';
 import Events from 'src/libs/events';
 import { getCurrentRoute } from 'src/libs/nav';
 import { authStore } from 'src/libs/state';
 import * as Utils from 'src/libs/utils';
 import { OAuth2Provider } from 'src/profile/external-identities/OAuth2Providers';
-import { asMockedFn, renderWithAppContexts as render } from 'src/testing/test-utils';
+import { asMockedFn, MockedFn, partial, renderWithAppContexts as render } from 'src/testing/test-utils';
 
 import { OAuth2Account } from './OAuth2Account';
 
-jest.mock('src/libs/ajax');
+jest.mock('src/libs/ajax/ExternalCredentials');
+jest.mock('src/libs/ajax/Metrics');
 
 jest.mock('src/auth/auth', () => ({
   ...jest.requireActual('src/auth/auth'),
@@ -45,9 +46,6 @@ jest.mock(
   })
 );
 
-type AjaxExports = typeof import('src/libs/ajax');
-type AjaxContract = ReturnType<AjaxExports['Ajax']>;
-
 const testAccessTokenProvider: OAuth2Provider = {
   key: 'github',
   name: 'Test Provider',
@@ -64,19 +62,17 @@ describe('OAuth2Account', () => {
   describe('When no account is linked', () => {
     it('shows the button to link an account', async () => {
       // Arrange
-      const getLinkStatusFn = jest.fn().mockResolvedValue(undefined);
-      const getAuthorizationUrlFn = jest.fn().mockResolvedValue('https://foo.bar.com/oauth2/authorize');
-      asMockedFn(Ajax).mockImplementation(
-        () =>
-          ({
-            ExternalCredentials: () => {
-              return {
-                getAccountLinkStatus: getLinkStatusFn,
-                getAuthorizationUrl: getAuthorizationUrlFn,
-              };
-            },
-          } as DeepPartial<AjaxContract> as AjaxContract)
+      const getLinkStatusFn: MockedFn<ExternalCredentialsContract['getAccountLinkStatus']> = jest.fn();
+      getLinkStatusFn.mockResolvedValue(undefined);
+      const getAuthorizationUrlFn: MockedFn<ExternalCredentialsContract['getAuthorizationUrl']> = jest.fn();
+      getAuthorizationUrlFn.mockResolvedValue('https://foo.bar.com/oauth2/authorize');
+      asMockedFn(ExternalCredentials).mockReturnValue(() =>
+        partial<ExternalCredentialsContract>({
+          getAccountLinkStatus: getLinkStatusFn,
+          getAuthorizationUrl: getAuthorizationUrlFn,
+        })
       );
+
       // Act
       const { container } = await act(() =>
         render(<OAuth2Account queryParams={{}} provider={testAccessTokenProvider} />)
@@ -93,19 +89,19 @@ describe('OAuth2Account', () => {
       // Arrange
       const user = userEvent.setup();
       jest.spyOn(window, 'open').mockImplementation(() => null);
-      const getLinkStatusFn = jest.fn().mockResolvedValue(undefined);
-      const getAuthorizationUrlFn = jest.fn().mockResolvedValue('https://foo.bar.com/oauth2/authorize');
-      asMockedFn(Ajax).mockImplementation(
-        () =>
-          ({
-            ExternalCredentials: () => {
-              return {
-                getAccountLinkStatus: getLinkStatusFn,
-                getAuthorizationUrl: getAuthorizationUrlFn,
-              };
-            },
-          } as DeepPartial<AjaxContract> as AjaxContract)
+
+      const getLinkStatusFn: MockedFn<ExternalCredentialsContract['getAccountLinkStatus']> = jest.fn();
+      getLinkStatusFn.mockResolvedValue(undefined);
+      const getAuthorizationUrlFn: MockedFn<ExternalCredentialsContract['getAuthorizationUrl']> = jest.fn();
+      getAuthorizationUrlFn.mockResolvedValue('https://foo.bar.com/oauth2/authorize');
+
+      asMockedFn(ExternalCredentials).mockReturnValue(() =>
+        partial<ExternalCredentialsContract>({
+          getAccountLinkStatus: getLinkStatusFn,
+          getAuthorizationUrl: getAuthorizationUrlFn,
+        })
       );
+
       // Act
       await act(() => render(<OAuth2Account queryParams={{}} provider={testAccessTokenProvider} />));
 
@@ -122,28 +118,28 @@ describe('OAuth2Account', () => {
         oauthcode: 'abcde12345',
         state: btoa(JSON.stringify({ provider: testAccessTokenProvider.key, nonce: 'abcxyz' })),
       };
-      const getLinkStatusFn = jest.fn().mockResolvedValue(undefined);
-      const getAuthorizationUrlFn = jest.fn().mockResolvedValue('https://foo.bar.com/oauth2/authorize');
-      const linkAccountFn = jest
-        .fn()
-        .mockResolvedValue({ externalUserId: 'testUser', expirationTimestamp: new Date(), authenticated: true });
-      const captureEventFn = jest.fn();
-
-      asMockedFn(Ajax).mockImplementation(
-        () =>
-          ({
-            ExternalCredentials: () => {
-              return {
-                getAccountLinkStatus: getLinkStatusFn,
-                getAuthorizationUrl: getAuthorizationUrlFn,
-                linkAccountWithAuthorizationCode: linkAccountFn,
-              };
-            },
-            Metrics: {
-              captureEvent: captureEventFn,
-            },
-          } as DeepPartial<AjaxContract> as AjaxContract)
+
+      const getLinkStatusFn: MockedFn<ExternalCredentialsContract['getAccountLinkStatus']> = jest.fn();
+      getLinkStatusFn.mockResolvedValue(undefined);
+      const getAuthorizationUrlFn: MockedFn<ExternalCredentialsContract['getAuthorizationUrl']> = jest.fn();
+      getAuthorizationUrlFn.mockResolvedValue('https://foo.bar.com/oauth2/authorize');
+      const linkAccountFn: MockedFn<ExternalCredentialsContract['linkAccountWithAuthorizationCode']> = jest.fn();
+      linkAccountFn.mockResolvedValue({
+        externalUserId: 'testUser',
+        expirationTimestamp: new Date(),
+        authenticated: true,
+      });
+      const captureEventFn: MockedFn<MetricsContract['captureEvent']> = jest.fn();
+
+      asMockedFn(ExternalCredentials).mockReturnValue(() =>
+        partial<ExternalCredentialsContract>({
+          getAccountLinkStatus: getLinkStatusFn,
+          getAuthorizationUrl: getAuthorizationUrlFn,
+          linkAccountWithAuthorizationCode: linkAccountFn,
+        })
       );
+      asMockedFn(Metrics).mockReturnValue(partial<MetricsContract>({ captureEvent: captureEventFn }));
+
       // Act
       await act(() => render(<OAuth2Account queryParams={queryParams} provider={testAccessTokenProvider} />));
 
@@ -170,26 +166,24 @@ describe('OAuth2Account', () => {
       screen.getByText('Link Expiration:');
       screen.getByText(Utils.makeCompleteDate(linkStatus.expirationTimestamp));
     });
+
     it("unlinks the account when 'Unlink' is clicked", async () => {
       // Arrange
       const user = userEvent.setup();
       const linkStatus = { externalUserId: 'testUser', expirationTimestamp: new Date(), authenticated: true };
       authStore.update((state) => ({ ...state, oAuth2AccountStatus: { [testAccessTokenProvider.key]: linkStatus } }));
-      const unlinkAccountFn = jest.fn().mockResolvedValue(undefined);
-      const captureEventFn = jest.fn();
-      asMockedFn(Ajax).mockImplementation(
-        () =>
-          ({
-            ExternalCredentials: () => {
-              return {
-                unlinkAccount: unlinkAccountFn,
-              };
-            },
-            Metrics: {
-              captureEvent: captureEventFn,
-            },
-          } as DeepPartial<AjaxContract> as AjaxContract)
+
+      const unlinkAccountFn: MockedFn<ExternalCredentialsContract['unlinkAccount']> = jest.fn();
+      unlinkAccountFn.mockResolvedValue(undefined);
+      const captureEventFn: MockedFn<MetricsContract['captureEvent']> = jest.fn();
+
+      asMockedFn(ExternalCredentials).mockReturnValue(() =>
+        partial<ExternalCredentialsContract>({
+          unlinkAccount: unlinkAccountFn,
+        })
       );
+      asMockedFn(Metrics).mockReturnValue(partial<MetricsContract>({ captureEvent: captureEventFn }));
+
       // Act
       const { container } = await act(() =>
         render(<OAuth2Account queryParams={{}} provider={testAccessTokenProvider} />)

src/profile/external-identities/OAuth2Account.tsx

@@ -1,7 +1,8 @@
 import _ from 'lodash/fp';
 import React, { useState } from 'react';
 import { ClipboardButton } from 'src/components/ClipboardButton';
-import { Ajax } from 'src/libs/ajax';
+import { ExternalCredentials } from 'src/libs/ajax/ExternalCredentials';
+import { Metrics } from 'src/libs/ajax/Metrics';
 import colors from 'src/libs/colors';
 import { withErrorReporting } from 'src/libs/error';
 import Events from 'src/libs/events';
@@ -76,11 +77,9 @@ export const OAuth2Account = (props: OAuth2AccountProps) => {
 
   useOnMount(() => {
     const linkAccount = withErrorReporting(`Error linking ${provider.short} account`)(async (code, state) => {
-      const accountInfo = await Ajax(signal)
-        .ExternalCredentials(provider)
-        .linkAccountWithAuthorizationCode(code, state);
+      const accountInfo = await ExternalCredentials(signal)(provider).linkAccountWithAuthorizationCode(code, state);
       authStore.update(_.set(['oAuth2AccountStatus', provider.key], accountInfo));
-      Ajax().Metrics.captureEvent(Events.user.externalCredential.link, { provider: provider.key });
+      void Metrics().captureEvent(Events.user.externalCredential.link, { provider: provider.key });
       setIsLinking(false);
     });
 
@@ -117,7 +116,7 @@ export const OAuth2Account = (props: OAuth2AccountProps) => {
               <UnlinkOAuth2Account linkText='Unlink' provider={provider} />
             </div>
             {provider.supportsIdToken && (
-              <ClipboardButton text={Ajax(signal).ExternalCredentials(provider).getIdentityToken}>
+              <ClipboardButton text={ExternalCredentials(signal)(provider).getIdentityToken}>
                 Copy identity token to clipboard
               </ClipboardButton>
             )}