Merge branch 'master' into 1928-fix-metadata-track-rename

codecov.yaml

@@ -11,8 +11,7 @@ coverage:
       default:                 
         target: auto
         # don't allow new commits to decrease coverage
-        # Temporary to merge pr https://github.com/hms-dbmi-cellenics/ui/pull/723
-        threshold: 1%
+        threshold: 0%
 
     patch:                    # measuring the coverage of new changes
       default:

src/__test__/components/ContentWrapper.test.jsx

@@ -15,14 +15,15 @@ import AppRouteProvider from 'utils/AppRouteProvider';
 import { makeStore } from 'redux/store';
 import { getBackendStatus } from 'redux/selectors';
 import { loadProjects, setActiveProject } from 'redux/actions/projects';
+import { loadExperiments } from 'redux/actions/experiments';
 import { updateExperimentInfo } from 'redux/actions/experimentSettings';
 import generateGem2sParamsHash from 'utils/data-management/generateGem2sParamsHash';
 
 import mockAPI, {
   generateDefaultMockAPIResponses,
 } from '__test__/test-utils/mockAPI';
 
-import { experiments } from '__test__/test-utils/mockData';
+import { projects } from '__test__/test-utils/mockData';
 
 jest.mock('redux/selectors');
 jest.mock('utils/socketConnection');
@@ -56,19 +57,18 @@ enableFetchMocks();
 
 generateGem2sParamsHash.mockImplementation(() => 'mockParamsHash');
 
-const experimentWithSamples = experiments.find((experiment) => experiment.samplesOrder.length > 0);
-
-const sampleIds = experimentWithSamples.samplesOrder;
-
-const experimentId = experimentWithSamples.id;
+const projectWithSamples = projects.find((project) => project.samples.length > 0);
+const experimentId = projectWithSamples.experiments[0];
+const projectUuid = projectWithSamples.uuid;
+const sampleIds = projectWithSamples.samples;
 
 const experimentName = 'test experiment';
 const experimentData = {
   experimentId,
   experimentName,
 };
 
-const mockAPIResponses = generateDefaultMockAPIResponses(experimentId);
+const mockAPIResponses = generateDefaultMockAPIResponses(experimentId, projectUuid);
 
 let store = null;
 
@@ -118,7 +118,8 @@ describe('ContentWrapper', () => {
     }));
 
     await store.dispatch(loadProjects());
-    await store.dispatch(setActiveProject(experimentId));
+    await store.dispatch(loadExperiments(projectUuid));
+    await store.dispatch(setActiveProject(projectUuid));
     await store.dispatch(updateExperimentInfo({ experimentId, experimentName, sampleIds }));
   });
 

src/__test__/components/PlotContainer.test.jsx

@@ -50,7 +50,7 @@ let store = null;
 fetchMock.mockIf(/.*/, (req) => {
   const path = req.url;
   // Saving config, return 200
-  if (path.match(`/v2/experiments/${experimentId}/plots/${plotUuid}`)) {
+  if (path.match(`/v1/experiments/${experimentId}/plots-tables/${plotUuid}`)) {
     return Promise.resolve({ body: JSON.stringify('Plot saved') });
   }
   return Promise.resolve({ status: 404, body: JSON.stringify('Plot config not found') });

src/__test__/components/data-exploration/differential-expression-tool/DiffExprCompute.test.jsx

@@ -26,6 +26,7 @@ const createMockStore = configureMockStore([thunk]);
 
 const mockOnCompute = jest.fn();
 const experimentId = fake.EXPERIMENT_ID;
+
 const defaultProps = {
   experimentId,
   onCompute: mockOnCompute,

src/__test__/components/data-management/ProjectMenu.test.jsx

@@ -18,7 +18,7 @@ import createTestComponentFactory from '__test__/test-utils/testComponentFactory
 import mockAPI, { generateDefaultMockAPIResponses } from '__test__/test-utils/mockAPI';
 
 import { loadProjects, setActiveProject } from 'redux/actions/projects';
-import { experiments } from '__test__/test-utils/mockData';
+import { projects } from '__test__/test-utils/mockData';
 import ProjectMenu from 'components/data-management/ProjectMenu';
 
 const mockNavigateTo = jest.fn();
@@ -37,20 +37,18 @@ jest.mock('utils/AppRouteProvider', () => ({
   })),
 }));
 
-const experimentWithSamples = experiments.find((experiment) => experiment.samplesOrder.length > 0);
-const experimentWithoutSamples = experiments.find(
-  (experiment) => experiment.samplesOrder.length === 0,
-);
+const projectWithSamples = projects.find((project) => project.samples.length > 0);
+const projectWithoutSamples = projects.find((project) => project.samples.length === 0);
 
-const experimentWithSamplesId = experimentWithSamples.id;
-const experimentWithoutSamplesId = experimentWithoutSamples.id;
+const experimentWithSamplesId = projectWithSamples.experiments[0];
+const projectWithSamplesId = projectWithSamples.uuid;
 
 const defaultAPIResponse = generateDefaultMockAPIResponses(
   experimentWithSamplesId,
+  projectWithSamplesId,
 );
-
 const responses = _.merge(defaultAPIResponse, {
-  [`/v2/access/${fake.EXPERIMENT_ID}-1`]: () => (
+  [`/v1/access/${fake.EXPERIMENT_ID}-1`]: () => (
     Promise.resolve(
       new Response(JSON.stringify(
         [{
@@ -82,7 +80,7 @@ describe('ProjectMenu', () => {
     storeState = makeStore();
 
     await storeState.dispatch(loadProjects());
-    await storeState.dispatch(setActiveProject(experimentWithoutSamplesId));
+    await storeState.dispatch(setActiveProject(projectWithoutSamples.uuid));
   });
 
   it('Renders correctly when there is a project', async () => {

src/__test__/components/data-management/SamplesTable.test.jsx

@@ -4,15 +4,14 @@ import userEvent from '@testing-library/user-event';
 import { act } from 'react-dom/test-utils';
 import '@testing-library/jest-dom';
 import fetchMock, { enableFetchMocks } from 'jest-fetch-mock';
-import reactSortableHoc from 'react-sortable-hoc';
 
 import Storage from '@aws-amplify/storage';
 
 import _ from 'lodash';
 import { Provider } from 'react-redux';
 
 import mockAPI, { generateDefaultMockAPIResponses, statusResponse } from '__test__/test-utils/mockAPI';
-import { experiments, samples } from '__test__/test-utils/mockData';
+import { projects, samples } from '__test__/test-utils/mockData';
 
 import SamplesTable from 'components/data-management/SamplesTable';
 import { makeStore } from 'redux/store';
@@ -22,10 +21,14 @@ import createTestComponentFactory from '__test__/test-utils/testComponentFactory
 
 import { loadProjects, setActiveProject } from 'redux/actions/projects';
 import downloadFromUrl from 'utils/data-management/downloadFromUrl';
-
 import loadEnvironment from 'redux/actions/networkResources/loadEnvironment';
 import { loadExperiments } from 'redux/actions/experiments';
 
+import reactSortableHoc from 'react-sortable-hoc';
+
+import { api } from 'utils/constants';
+import config from 'config';
+
 jest.mock('config');
 
 jest.mock('@aws-amplify/auth', () => ({
@@ -73,23 +76,24 @@ const renderSamplesTable = async (store) => {
 
 enableFetchMocks();
 
-const experimentWithSamples = experiments.find((experiment) => experiment.samplesOrder.length > 0);
-const experimentWithoutSamples = experiments.find(
-  (experiment) => experiment.samplesOrder.length === 0,
-);
+const firstProjectWithSamples = projects.find((p) => p.samples.length > 0);
+const projectIdWithSamples = firstProjectWithSamples.uuid;
+const experimentIdWithSamples = firstProjectWithSamples.experiments[0];
 
-const experimentWithSamplesId = experimentWithSamples.id;
-const experimentWithoutSamplesId = experimentWithoutSamples.id;
+const firstProjectWithoutSamples = projects.find((p) => p.samples.length === 0);
+const projectIdWithoutSamples = firstProjectWithoutSamples.uuid;
+const experimentIdWithoutSamples = firstProjectWithoutSamples.experiments[0];
 
 // Mocking samples update / delete routes
 const customResponses = {
-  [`experiments/${experimentWithSamplesId}/samples/${experimentWithSamples.samplesOrder[0]}`]: () => statusResponse(200, 'OK'),
-  [`experiments/${experimentWithSamplesId}/samples/position`]: () => statusResponse(200, 'OK'),
+  [`/projects/${projectIdWithSamples}`]: () => statusResponse(200, JSON.stringify('OK')),
+  [`/projects/${projectIdWithSamples}/${experimentIdWithSamples}/samples`]: () => statusResponse(200, 'OK'),
+  [`/v2/experiments/${projectIdWithSamples}/samples/position`]: () => statusResponse(200, 'OK'),
 };
 
 const mockAPIResponse = _.merge(
-  generateDefaultMockAPIResponses(experimentWithSamplesId),
-  generateDefaultMockAPIResponses(experimentWithoutSamplesId),
+  generateDefaultMockAPIResponses(experimentIdWithSamples, projectIdWithSamples),
+  generateDefaultMockAPIResponses(experimentIdWithoutSamples, projectIdWithoutSamples),
   customResponses,
 );
 
@@ -100,24 +104,27 @@ describe('Samples table', () => {
     fetchMock.mockClear();
     fetchMock.mockIf(/.*/, mockAPI(mockAPIResponse));
 
+    config.currentApiVersion = api.V1;
+
     storeState = makeStore();
 
     await storeState.dispatch(loadProjects());
 
     // Loading experiment is usually called in Data Management, so we have to load them manually
-    await storeState.dispatch(loadExperiments(experimentWithSamplesId));
-    await storeState.dispatch(loadExperiments(experimentWithoutSamplesId));
+    await storeState.dispatch(loadExperiments(projectIdWithSamples));
+    await storeState.dispatch(loadExperiments(projectIdWithoutSamples));
 
     // Defaults to project with samples
-    await storeState.dispatch(setActiveProject(experimentWithSamplesId));
+    await storeState.dispatch(setActiveProject(projectIdWithSamples));
+
     await storeState.dispatch(loadEnvironment('test'));
   });
 
   it('Shows option to download datasets if there are no samples', async () => {
     await renderSamplesTable(storeState);
 
     // Load project without samples
-    storeState.dispatch(setActiveProject(experimentWithoutSamplesId));
+    storeState.dispatch(setActiveProject(projectIdWithoutSamples));
 
     expect(screen.getByText(/Start uploading your samples by clicking on Add samples./i)).toBeInTheDocument();
     expect(screen.getByText(/Don't have data\? Get started using one of our example datasets:/i)).toBeInTheDocument();
@@ -151,7 +158,7 @@ describe('Samples table', () => {
     await renderSamplesTable(storeState);
 
     // Load project without samples
-    storeState.dispatch(setActiveProject(experimentWithoutSamplesId));
+    storeState.dispatch(setActiveProject(projectIdWithoutSamples));
 
     // This prompt to upload samples is still visible
     expect(screen.getByText(/Start uploading your samples by clicking on Add samples./i)).toBeInTheDocument();
@@ -172,7 +179,7 @@ describe('Samples table', () => {
     await renderSamplesTable(storeState);
 
     // Load project without samples
-    storeState.dispatch(setActiveProject(experimentWithoutSamplesId));
+    storeState.dispatch(setActiveProject(projectIdWithoutSamples));
 
     const linksContainer = screen.getByText(expectedSampleNames[0]).closest('ul');
     const links = Array.from(linksContainer.children).map((el) => el.textContent);
@@ -275,6 +282,8 @@ describe('Samples table', () => {
   });
 
   it('Reorder samples send correct request in api v2', async () => {
+    config.currentApiVersion = api.V2;
+
     let onSortEndProp;
     reactSortableHoc.sortableContainer.mockImplementationOnce(() => (...params) => {
       onSortEndProp = params[0].onSortEnd;
@@ -288,7 +297,7 @@ describe('Samples table', () => {
     });
 
     expect(fetchMock).toHaveBeenCalledWith(
-      `http://localhost:3000/v2/experiments/${experimentWithSamplesId}/samples/position`,
+      `http://localhost:3000/v2/experiments/${projectIdWithSamples}/samples/position`,
       {
         method: 'PUT',
         headers: expect.anything(),

src/__test__/components/data-management/__snapshots__/ShareExperimentModal.test.jsx.snap

@@ -2,7 +2,7 @@
 
 exports[`Share expeirment modal Inviting users works 1`] = `
 Array [
-  "http://localhost:3000/v2/access/testae48e318dab9a1bd0bexperiment",
+  "http://localhost:3000/v1/access/testae48e318dab9a1bd0bexperiment",
   Object {
     "body": "{\\"projectUuid\\":\\"test24b6-8600-test-mock-63822d2fmock\\",\\"role\\":\\"explorer\\",\\"userEmail\\":\\"asd@asd.com\\"}",
     "headers": Object {

src/__test__/components/plots/DotPlot.test.jsx

@@ -40,7 +40,7 @@ const experimentId = fake.EXPERIMENT_ID;
 const plotUuid = 'dotPlotMain';
 
 const customAPIResponses = {
-  [`/plots/${plotUuid}`]: () => statusResponse(404, 'Not found'),
+  [`/plots-tables/${plotUuid}`]: () => statusResponse(404, 'Not found'),
 };
 
 const mockAPIResponses = _.merge(