Merge branch 'dev' into tl_ID-1126_migrate_from_bond_to_ecm

integration-tests/package.json

@@ -4,7 +4,7 @@
   "private": true,
   "scripts": {
     "test": "jest",
-    "test-local": "TERRA_SA_KEY=$(vault read --format=json secret/dsde/firecloud/alpha/common/firecloud-account.json | jq .data) LYLE_SA_KEY=$(vault read --format=json secret/dsde/terra/envs/common/lyle-user-service-account-key | jq .data) TEST_URL=http://localhost:3000 yarn test",
+    "test-local": "TERRA_SA_KEY=$(vault read --format=json secret/dsde/firecloud/dev/common/firecloud-account.json | jq .data) LYLE_SA_KEY=$(vault read --format=json secret/dsde/terra/envs/common/lyle-user-service-account-key | jq .data) TEST_URL=http://localhost:3000 yarn test",
     "test-flakes": "FLAKES=true yarn test-local --runInBand"
   },
   "devDependencies": {

src/analysis/modals/GalaxyModal.js

@@ -476,7 +476,7 @@ export const GalaxyModalBase = withDisplayName('GalaxyModal')(
         div({ style: { ...computeStyles.whiteBoxContainer, marginTop: '1rem' } }, [
           div([
             div({ style: computeStyles.headerText }, ['Application configuration']),
-            div({ style: { marginTop: '0.5rem' } }, ['Galaxy version 23.1']),
+            div({ style: { marginTop: '0.5rem' } }, ['Galaxy version 24.0']),
             h(Link, { href: 'https://support.terra.bio/hc/en-us/articles/360050566271', ...Utils.newTabLinkProps }, [
               'Learn more about Galaxy interactive environments',
               icon('pop-out', { size: 12, style: { marginTop: '1rem', marginLeft: '0.25rem' } }),

src/dataset-builder/CohortEditor.ts

@@ -1,6 +1,6 @@
 import { Spinner } from '@terra-ui-packages/components';
 import _ from 'lodash/fp';
-import React, { Fragment, useEffect, useState } from 'react';
+import React, { Fragment, useEffect, useRef, useState } from 'react';
 import { div, h, h2, h3, strong } from 'react-hyperscript-helpers';
 import { ButtonOutline, ButtonPrimary, GroupedSelect, Link, Select } from 'src/components/common';
 import Slider from 'src/components/common/Slider';
@@ -56,17 +56,28 @@ export const CriteriaView = (props: CriteriaViewProps) => {
 
   const [criteriaCount, setCriteriaCount] = useLoadedData<DatasetParticipantCountResponse>();
 
-  useEffect(() => {
-    setCriteriaCount(async () =>
-      DataRepo()
-        .dataset(datasetId)
-        .getCounts({
-          // Create a "cohort" to get the count of participants for this criteria on its own.
-          cohorts: [{ criteriaGroups: [{ criteria: [criteria], name: '', meetAll: true, mustMeet: true }], name: '' }],
-        })
-    );
-  }, [criteria, datasetId, setCriteriaCount]);
+  const updateCriteriaCount = useRef(
+    _.debounce(250, (datasetId, criteria) => {
+      setCriteriaCount(
+        async () =>
+          await DataRepo()
+            .dataset(datasetId)
+            .getCounts({
+              cohorts: [
+                {
+                  // Create a "cohort" to get the count of participants for this criteria on its own.
+                  criteriaGroups: [{ criteria: [criteria], name: '', meetAll: true, mustMeet: true }],
+                  name: '',
+                },
+              ],
+            })
+      );
+    })
+  );
 
+  useEffect(() => {
+    updateCriteriaCount.current(datasetId, criteria);
+  }, [criteria, datasetId]);
   return div(
     {
       style: {
@@ -322,13 +333,19 @@ export const CriteriaGroupView: React.FC<CriteriaGroupViewProps> = (props) => {
 
   const [groupParticipantCount, setGroupParticipantCount] = useLoadedData<DatasetParticipantCountResponse>();
 
+  const updateGroupParticipantCount = useRef(
+    _.debounce(250, (dataset, criteriaGroup) =>
+      setGroupParticipantCount(async () =>
+        DataRepo()
+          .dataset(dataset.id)
+          .getCounts({ cohorts: [{ criteriaGroups: [criteriaGroup], name: '' }] })
+      )
+    )
+  );
+
   useEffect(() => {
-    setGroupParticipantCount(async () =>
-      DataRepo()
-        .dataset(dataset.id)
-        .getCounts({ cohorts: [{ criteriaGroups: [criteriaGroup], name: '' }] })
-    );
-  }, [criteriaGroup, dataset.id, setGroupParticipantCount]);
+    updateGroupParticipantCount.current(dataset, criteriaGroup);
+  }, [criteriaGroup, dataset]);
 
   return div(
     {

src/workflows-app/SubmissionDetails.test.js

@@ -6,7 +6,7 @@ import { Ajax } from 'src/libs/ajax';
 import { renderWithAppContexts as render, SelectHelper } from 'src/testing/test-utils';
 import { metadata as runDetailsMetadata } from 'src/workflows-app/fixtures/test-workflow';
 import { BaseSubmissionDetails } from 'src/workflows-app/SubmissionDetails';
-import { methodData, mockRunsData, runSetData, simpleRunsData } from 'src/workflows-app/utils/mock-data';
+import { methodData, mockRunsData, runSetData, runSetDataWithLiteral, simpleRunsData } from 'src/workflows-app/utils/mock-data';
 import { mockAzureApps, mockAzureWorkspace, runSetOutputDef, runSetResponse } from 'src/workflows-app/utils/mock-responses';
 
 const submissionId = 'e8347247-4738-4ad1-a591-56c119f93f58';
@@ -704,6 +704,69 @@ describe('Submission Details page', () => {
     expect(row1cells[4]).toHaveTextContent('foo_name');
   });
 
+  it('Inputs tab handles literal values', async () => {
+    // Arrange
+    const user = userEvent.setup();
+    const getRuns = jest.fn(() => Promise.resolve(mockRunsData));
+    const getRunsSets = jest.fn(() => Promise.resolve(runSetDataWithLiteral));
+    const getMethods = jest.fn(() => Promise.resolve(methodData));
+    const mockLeoResponse = jest.fn(() => Promise.resolve(mockAzureApps));
+    Ajax.mockImplementation(() => {
+      return {
+        Cbas: {
+          runs: {
+            get: getRuns,
+          },
+          runSets: {
+            get: getRunsSets,
+          },
+          methods: {
+            getById: getMethods,
+          },
+        },
+        Apps: {
+          listAppsV2: mockLeoResponse,
+        },
+        Metrics: {
+          captureEvent,
+        },
+        AzureStorage: {
+          details: jest.fn().mockResolvedValue({ sas: { token: '1234-this-is-a-mock-sas-token-5678' } }),
+        },
+      };
+    });
+
+    // Act
+    await act(async () => {
+      render(
+        h(BaseSubmissionDetails, {
+          name: 'test-azure-ws-name',
+          namespace: 'test-azure-ws-namespace',
+          workspace: mockAzureWorkspace,
+          submissionId,
+        })
+      );
+    });
+
+    const workflowsTabButton = screen.getByRole('tab', { name: 'Workflows' });
+    expect(workflowsTabButton !== undefined);
+
+    const inputsTabButton = screen.getByRole('tab', { name: 'Inputs' });
+    expect(inputsTabButton !== undefined);
+
+    // ** ACT **
+    // user clicks on inputs tab button
+    await user.click(inputsTabButton);
+
+    // Assert
+    const inputTable = screen.getByRole('table');
+    const rows = within(inputTable).getAllByRole('row');
+
+    const row1cells = within(rows[1]).getAllByRole('cell');
+    expect(row1cells[3]).toHaveTextContent('literal');
+    expect(row1cells[4]).toHaveTextContent('foo bar');
+  });
+
   it('should display outputs on the Outputs tab', async () => {
     // Add output definition to temporary runset data variable
     const tempRunSetData = runSetData;

src/workflows-app/components/SubmissionDetailsInputsTable.ts

@@ -5,7 +5,7 @@ import { FlexTable, Sortable, TextCell } from 'src/components/table';
 import { WorkflowTableColumnNames } from 'src/libs/workflow-utils';
 import { getInputTableData, InputTableData } from 'src/workflows-app/utils/submission-utils';
 
-import { InputDefinition, RecordLookupInputSource } from '../models/submission-models';
+import { InputDefinition, LiteralInputSource, RecordLookupInputSource } from '../models/submission-models';
 import { tableContainerStyle, tableStyle } from './submission-tables-styles';
 
 const rowWidth = 100;
@@ -96,6 +96,10 @@ const SubmissionDetailsInputsTable = ({ configuredInputDefinition }: SubmissionD
                         .source as RecordLookupInputSource;
                       return h(TextCell, [source.record_attribute]);
                     }
+                    if (inputTableData[rowIndex].source.type === 'literal') {
+                      const source: LiteralInputSource = inputTableData[rowIndex].source as LiteralInputSource;
+                      return h(TextCell, [source.parameter_value]);
+                    }
                     return h(TextCell, []);
                   },
                 },

src/workflows-app/utils/mock-data.ts

@@ -1,6 +1,6 @@
 import { WorkflowMethod } from 'src/workflows-app/components/WorkflowCard';
 
-export const workflowParams = [
+export const workflowParamsRecordLookup = [
   {
     input_name: 'wf_hello.hello.addressee',
     input_type: {
@@ -14,6 +14,20 @@ export const workflowParams = [
   },
 ];
 
+export const workflowParamsLiteral = [
+  {
+    input_name: 'wf_hello.hello.addressee',
+    input_type: {
+      type: 'primitive',
+      primitive_type: 'String',
+    },
+    source: {
+      type: 'literal',
+      parameter_value: 'foo bar',
+    },
+  },
+];
+
 export const mockRunsData = {
   runs: [
     {
@@ -23,7 +37,7 @@ export const mockRunsData = {
       record_id: 'FOO2',
       workflow_url: 'https://xyz.wdl',
       state: 'SYSTEM_ERROR',
-      workflow_params: JSON.stringify(workflowParams),
+      workflow_params: JSON.stringify(workflowParamsRecordLookup),
       workflow_outputs: '[]',
       submission_date: '2022-07-14T22:22:15.591Z',
       last_modified_timestamp: '2022-07-14T23:14:25.791Z',
@@ -37,7 +51,7 @@ export const mockRunsData = {
       workflow_url:
         'https://raw.githubusercontent.com/broadinstitute/cromwell/a40de672c565c4bbd40f57ff96d4ee520dc2b4fc/centaur/src/main/resources/standardTestCases/hello/hello.wdl',
       state: 'COMPLETE',
-      workflow_params: JSON.stringify(workflowParams),
+      workflow_params: JSON.stringify(workflowParamsRecordLookup),
       workflow_outputs: '[]',
       submission_date: '2022-12-08T23:29:18.675+00:00',
       last_modified_timestamp: '2022-12-08T23:29:55.695+00:00',
@@ -60,7 +74,28 @@ export const runSetData = {
       last_modified_timestamp: '2022-12-09T16:30:50.280+00:00',
       run_count: 1,
       error_count: 0,
-      input_definition: JSON.stringify(workflowParams),
+      input_definition: JSON.stringify(workflowParamsRecordLookup),
+      output_definition: '[]',
+    },
+  ],
+};
+
+export const runSetDataWithLiteral = {
+  run_sets: [
+    {
+      run_set_id: 'e8347247-4738-4ad1-a591-56c119f93f58',
+      method_id: '00000000-0000-0000-0000-000000000004',
+      method_version_id: '20000000-0000-0000-0000-000000000004',
+      is_template: false,
+      run_set_name: 'hello world',
+      run_set_description: 'test',
+      state: 'COMPLETE',
+      record_type: 'FOO',
+      submission_timestamp: '2022-12-08T23:28:50.280+00:00',
+      last_modified_timestamp: '2022-12-09T16:30:50.280+00:00',
+      run_count: 1,
+      error_count: 0,
+      input_definition: JSON.stringify(workflowParamsLiteral),
       output_definition: '[]',
     },
   ],
@@ -159,7 +194,7 @@ export const simpleRunsData = {
       record_id: 'FOO2',
       workflow_url: 'https://xyz.wdl',
       state: 'RUNNING',
-      workflow_params: JSON.stringify(workflowParams),
+      workflow_params: JSON.stringify(workflowParamsRecordLookup),
       workflow_outputs: '[]',
       submission_date: new Date().toISOString(),
       last_modified_timestamp: new Date().toISOString(),

src/workspaces/list/NoContentMessage.ts

@@ -9,13 +9,12 @@ import { WorkspaceUserActionsContext } from 'src/workspaces/list/WorkspaceUserAc
 
 interface NoContentMessageProps {
   loadingWorkspaces: boolean;
-  loadingSubmissionStats: boolean;
   workspaces: CategorizedWorkspaces;
   filters: WorkspaceFilterValues;
 }
 
 export const NoContentMessage = (props: NoContentMessageProps): ReactNode => {
-  const { loadingWorkspaces, loadingSubmissionStats, workspaces, filters } = props;
+  const { loadingWorkspaces, workspaces, filters } = props;
   const { setUserActions } = useContext(WorkspaceUserActionsContext);
 
   return cond(
@@ -27,7 +26,6 @@ export const NoContentMessage = (props: NoContentMessageProps): ReactNode => {
           onClick: () => setUserActions({ creatingNewWorkspace: true }),
         }),
     ],
-    [!_.isEmpty(filters.submissions) && loadingSubmissionStats, () => h(Fragment, ['Loading submission statuses...'])],
     () => div({ style: { fontStyle: 'italic' } }, ['No matching workspaces'])
   );
 };

src/workspaces/list/RecentlyViewedWorkspaceCard.js

@@ -7,10 +7,9 @@ import Events, { extractWorkspaceDetails } from 'src/libs/events';
 import * as Nav from 'src/libs/nav';
 import * as Style from 'src/libs/style';
 import * as Utils from 'src/libs/utils';
-import { WorkspaceSubmissionStatusIcon } from 'src/workspaces/list/WorkspaceSubmissionStatusIcon';
 import { getCloudProviderFromWorkspace } from 'src/workspaces/utils';
 
-export const RecentlyViewedWorkspaceCard = ({ workspace, submissionStatus, loadingSubmissionStats, timestamp }) => {
+export const RecentlyViewedWorkspaceCard = ({ workspace, timestamp }) => {
   const {
     workspace: { namespace, name },
   } = workspace;
@@ -36,12 +35,8 @@ export const RecentlyViewedWorkspaceCard = ({ workspace, submissionStatus, loadi
       div({ style: { flex: 'none' } }, [
         div({ style: { color: colors.accent(), ...Style.noWrapEllipsis, fontSize: 16, marginBottom: 7 } }, name),
         div({ style: { display: 'flex', justifyContent: 'space-between' } }, [
-          div({ style: { ...Style.noWrapEllipsis, whiteSpace: 'pre-wrap', fontStyle: 'italic' } }, `Viewed ${dateViewed}`),
+          div({ style: { ...Style.noWrapEllipsis, whiteSpace: 'pre-wrap', fontStyle: 'italic' } }, [`Viewed ${dateViewed}`]),
           div({ style: { display: 'flex', alignItems: 'center' } }, [
-            h(WorkspaceSubmissionStatusIcon, {
-              status: submissionStatus,
-              loadingSubmissionStats,
-            }),
             h(CloudProviderIcon, { cloudProvider: getCloudProviderFromWorkspace(workspace), style: { marginLeft: 5 } }),
           ]),
         ]),

src/workspaces/list/RecentlyViewedWorkspaces.test.ts

@@ -45,7 +45,7 @@ describe('The recently viewed workspaces component', () => {
     asMockedFn(getLocalPref).mockImplementation(mockgetLocalPref);
 
     // Act
-    render(h(RecentlyViewedWorkspaces, { workspaces: [defaultAzureWorkspace], loadingSubmissionStats: false }));
+    render(h(RecentlyViewedWorkspaces, { workspaces: [defaultAzureWorkspace] }));
     expect(mockgetLocalPref).toBeCalled();
     const renderedAzureWS = screen.getAllByText(defaultAzureWorkspace.workspace.name);
     expect(renderedAzureWS).toHaveLength(1);
@@ -62,7 +62,7 @@ describe('The recently viewed workspaces component', () => {
 
     // Act
     const workspaces = [defaultAzureWorkspace];
-    render(h(RecentlyViewedWorkspaces, { workspaces, loadingSubmissionStats: false }));
+    render(h(RecentlyViewedWorkspaces, { workspaces }));
 
     // Assert
     expect(getLocalPref).toBeCalled();
@@ -81,7 +81,7 @@ describe('The recently viewed workspaces component', () => {
 
     // Act
     const workspaces = [defaultAzureWorkspace];
-    render(h(RecentlyViewedWorkspaces, { workspaces, loadingSubmissionStats: false }));
+    render(h(RecentlyViewedWorkspaces, { workspaces }));
 
     // Assert
     expect(getLocalPref).toBeCalled();
@@ -100,7 +100,7 @@ describe('The recently viewed workspaces component', () => {
 
     // Act
     const workspaces = [defaultAzureWorkspace, defaultGoogleWorkspace];
-    render(h(RecentlyViewedWorkspaces, { workspaces, loadingSubmissionStats: false }));
+    render(h(RecentlyViewedWorkspaces, { workspaces }));
 
     // Assert
     const renderedAzureWS = screen.getAllByText(defaultAzureWorkspace.workspace.name);
@@ -133,7 +133,7 @@ describe('The recently viewed workspaces component', () => {
       },
       defaultGoogleWorkspace,
     ];
-    render(h(RecentlyViewedWorkspaces, { workspaces, loadingSubmissionStats: false }));
+    render(h(RecentlyViewedWorkspaces, { workspaces }));
 
     // Assert
     const renderedAzureWS = screen.queryAllByText(defaultAzureWorkspace.workspace.name);

src/workspaces/list/RecentlyViewedWorkspaces.ts

@@ -6,16 +6,14 @@ import { getLocalPref, setLocalPref } from 'src/libs/prefs';
 import { recentlyViewedPersistenceId } from 'src/workspaces/common/state/recentlyViewedWorkspaces';
 import { RecentlyViewedWorkspaceCard } from 'src/workspaces/list/RecentlyViewedWorkspaceCard';
 import { getWorkspace, persistenceId } from 'src/workspaces/list/WorkspacesList';
-import { workspaceSubmissionStatus } from 'src/workspaces/list/WorkspaceSubmissionStatusIcon';
 import { WorkspaceWrapper as Workspace } from 'src/workspaces/utils';
 
 interface RecentlyViewedWorkspacesProps {
   workspaces: Workspace[];
-  loadingSubmissionStats: boolean;
 }
 
 export const RecentlyViewedWorkspaces = (props: RecentlyViewedWorkspacesProps): ReactNode => {
-  const { workspaces, loadingSubmissionStats } = props;
+  const { workspaces } = props;
   const [recentlyViewedOpen, setRecentlyViewedOpen] = useState<boolean>(() =>
     _.defaultTo(true, getLocalPref(persistenceId)?.recentlyViewedOpen)
   );
@@ -51,9 +49,7 @@ export const RecentlyViewedWorkspaces = (props: RecentlyViewedWorkspacesProps):
                 const workspace = getWorkspace(workspaceId, workspaces);
                 return h(RecentlyViewedWorkspaceCard, {
                   workspace,
-                  loadingSubmissionStats,
                   timestamp,
-                  submissionStatus: workspaceSubmissionStatus(workspace),
                 });
               }, recentlyViewed)
             ),