More typescripting

plugins/config/src/ConfigurationEditorWidget/components/__snapshots__/ConfigurationEditor.test.tsx.snap

@@ -1192,7 +1192,6 @@ exports[`ConfigurationEditor widget renders with defaults of the PileupTrack sch
                               </label>
                               <div
                                 class="MuiInputBase-root MuiOutlinedInput-root MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl css-md26zr-MuiInputBase-root-MuiOutlinedInput-root"
-                                variant="outlined"
                               >
                                 <div
                                   aria-describedby="mui-16-helper-text"
@@ -1358,7 +1357,6 @@ exports[`ConfigurationEditor widget renders with defaults of the PileupTrack sch
                                 </label>
                                 <div
                                   class="MuiInputBase-root MuiOutlinedInput-root MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl css-md26zr-MuiInputBase-root-MuiOutlinedInput-root"
-                                  variant="outlined"
                                 >
                                   <div
                                     aria-describedby="mui-18-helper-text"
@@ -1435,7 +1433,6 @@ exports[`ConfigurationEditor widget renders with defaults of the PileupTrack sch
                                 </label>
                                 <div
                                   class="MuiInputBase-root MuiOutlinedInput-root MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl css-md26zr-MuiInputBase-root-MuiOutlinedInput-root"
-                                  variant="outlined"
                                 >
                                   <div
                                     aria-describedby="mui-19-helper-text"

plugins/data-management/src/AddConnectionWidget/components/__snapshots__/AddConnectionWidget.test.js.snap

@@ -77,7 +77,6 @@ exports[`<AddConnectionWidget /> renders 1`] = `
                   </label>
                   <div
                     class="MuiInputBase-root MuiOutlinedInput-root MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl css-md26zr-MuiInputBase-root-MuiOutlinedInput-root"
-                    variant="outlined"
                   >
                     <div
                       aria-describedby="mui-1-helper-text"

plugins/linear-genome-view/src/LinearGenomeView/components/__snapshots__/LinearGenomeView.test.js.snap

@@ -157,7 +157,7 @@ exports[`<LinearGenomeView /> renders one track, one region 1`] = `
             />
           </button>
           <div
-            class="MuiAutocomplete-root css-16awh2u-MuiAutocomplete-root"
+            class="MuiAutocomplete-root css-1qqsdnr-MuiAutocomplete-root"
             data-testid="autocomplete"
             style="width: 200px;"
           >
@@ -722,7 +722,7 @@ exports[`<LinearGenomeView /> renders two tracks, two regions 1`] = `
             />
           </button>
           <div
-            class="MuiAutocomplete-root css-16awh2u-MuiAutocomplete-root"
+            class="MuiAutocomplete-root css-1qqsdnr-MuiAutocomplete-root"
             data-testid="autocomplete"
             style="width: 255.27500000000003px;"
           >

products/jbrowse-react-linear-genome-view/src/JBrowseLinearGenomeView/__snapshots__/JBrowseLinearGenomeView.test.tsx.snap

@@ -247,7 +247,7 @@ exports[`<JBrowseLinearGenomeView /> renders successfully 1`] = `
                     />
                   </button>
                   <div
-                    class="MuiAutocomplete-root mui-1auycx3-MuiAutocomplete-root"
+                    class="MuiAutocomplete-root mui-1kxbtff-MuiAutocomplete-root"
                     data-testid="autocomplete"
                     style="width: 200px;"
                   >

products/jbrowse-web/src/tests/BookmarkWidget.test.js → products/jbrowse-web/src/tests/BookmarkWidget.test.tsx

@@ -1,17 +1,22 @@
+/* eslint-disable @typescript-eslint/no-non-null-assertion */
 import React from 'react'
 import { fireEvent, render } from '@testing-library/react'
 import { LocalFile } from 'generic-filehandle'
 import { clearCache } from '@jbrowse/core/util/io/RemoteFileWithRangeCache'
 import { clearAdapterCache } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 import { JBrowse, setup, generateReadBuffer, getPluginManager } from './util'
 
+type LGV = LinearGenomeViewModel
 setup()
 
 beforeEach(() => {
   clearCache()
   clearAdapterCache()
+  // @ts-ignore
   fetch.resetMocks()
+  // @ts-ignore
   fetch.mockResponse(
     generateReadBuffer(url => {
       return new LocalFile(require.resolve(`../../test_data/volvox/${url}`))
@@ -23,43 +28,46 @@ const delay = { timeout: 15000 }
 
 test('click and drag rubberBand, bookmarks region', async () => {
   const pm = getPluginManager()
-  const state = pm.rootModel
   const { findByTestId, findByText } = render(<JBrowse pluginManager={pm} />)
-  const rubberBandComponent = await findByTestId(
-    'rubberBand_controls',
-    {},
-    delay,
-  )
+  const state = pm.rootModel!
+  const session = state.session!
+  const view = session.views[0] as LGV
 
-  expect(state.session.views[0].bpPerPx).toEqual(0.05)
-  fireEvent.mouseDown(rubberBandComponent, { clientX: 100, clientY: 0 })
-  fireEvent.mouseMove(rubberBandComponent, { clientX: 250, clientY: 0 })
-  fireEvent.mouseUp(rubberBandComponent, { clientX: 250, clientY: 0 })
+  const rubberband = await findByTestId('rubberBand_controls', {}, delay)
+  expect(view.bpPerPx).toEqual(0.05)
+  fireEvent.mouseDown(rubberband, { clientX: 100, clientY: 0 })
+  fireEvent.mouseMove(rubberband, { clientX: 250, clientY: 0 })
+  fireEvent.mouseUp(rubberband, { clientX: 250, clientY: 0 })
   const bookmarkMenuItem = await findByText('Bookmark region')
   fireEvent.click(bookmarkMenuItem)
-  const { widgets } = state.session
+  // @ts-ignore
+  const { widgets } = session
   const bookmarkWidget = widgets.get('GridBookmark')
   expect(bookmarkWidget.bookmarkedRegions[0].assemblyName).toEqual('volvox')
 }, 20000)
 
 test('bookmarks current region', async () => {
   const pm = getPluginManager()
-  const state = pm.rootModel
+  const state = pm.rootModel!
+  const session = state.session!
   const { findByTestId, findByText } = render(<JBrowse pluginManager={pm} />)
 
   fireEvent.click(await findByTestId('view_menu_icon'))
   fireEvent.click(await findByText('Bookmark current region'))
-  const { widgets } = state.session
+  // @ts-ignore
+  const { widgets } = session
   const { bookmarkedRegions } = widgets.get('GridBookmark')
   expect(bookmarkedRegions[0].start).toEqual(100)
   expect(bookmarkedRegions[0].end).toEqual(140)
 }, 20000)
 
 test('navigates to bookmarked region from widget', async () => {
   const pm = getPluginManager()
-  const state = pm.rootModel
 
   const { findByTestId, findByText } = render(<JBrowse pluginManager={pm} />)
+  const state = pm.rootModel!
+  const session = state.session!
+  const view = session.views[0] as LGV
 
   // need this to complete before we can try to navigate
   fireEvent.click(
@@ -75,17 +83,17 @@ test('navigates to bookmarked region from widget', async () => {
   fireEvent.click(viewMenu)
   fireEvent.click(await findByText('Open bookmark widget'))
 
-  const { widgets } = state.session
+  // @ts-ignore
+  const { widgets } = session
   const bookmarkWidget = widgets.get('GridBookmark')
   bookmarkWidget.addBookmark({
     start: 200,
     end: 240,
     refName: 'ctgA',
     assemblyName: 'volvox',
   })
-  const view = state.session.views[0]
 
-  fireEvent.click(await findByText('ctgA:201..240'), {}, delay)
+  fireEvent.click(await findByText('ctgA:201..240', {}, delay))
   const newRegion = view.getSelectedRegions(
     view.leftOffset,
     view.rightOffset,

products/jbrowse-web/src/tests/BreakpointSplitView.test.js → products/jbrowse-web/src/tests/BreakpointSplitView.test.tsx

@@ -13,7 +13,9 @@ setup()
 beforeEach(() => {
   clearCache()
   clearAdapterCache()
+  // @ts-ignore
   fetch.resetMocks()
+  // @ts-ignore
   fetch.mockResponse(
     generateReadBuffer(url => {
       return new LocalFile(require.resolve(`../../test_data/breakpoint/${url}`))

products/jbrowse-web/src/tests/ConfigurationEditor.test.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-non-null-assertion */
 import React from 'react'
 import '@testing-library/jest-dom/extend-expect'
 import { fireEvent, render, waitFor } from '@testing-library/react'

products/jbrowse-web/src/tests/CopyAndDelete.test.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-non-null-assertion */
 import React from 'react'
 import '@testing-library/jest-dom/extend-expect'
 import { fireEvent, render, waitFor } from '@testing-library/react'

products/jbrowse-web/src/tests/ReadVsRef.test.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-non-null-assertion */
 import React from 'react'
 import { fireEvent, render, waitFor } from '@testing-library/react'
 import { LocalFile } from 'generic-filehandle'

products/jbrowse-web/src/tests/StartScreen.test.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-non-null-assertion */
 import React from 'react'
 import '@testing-library/jest-dom/extend-expect'
 import { fireEvent, render } from '@testing-library/react'
@@ -25,37 +26,32 @@ describe('<StartScreen />', () => {
 test('Add New Session', async () => {
   const pluginManager = getPluginManager()
   const root = pluginManager.rootModel!
-  const session = root.session!
   const { findByText } = render(
     <StartScreen rootModel={root} onFactoryReset={factoryReset} />,
   )
   await findByText('Start a new session')
   fireEvent.click(await findByText('Empty'))
-  expect(session).toBeTruthy()
+  expect(root.session).toBeTruthy()
 })
 
 test('Add New LGV Session', async () => {
   const pluginManager = getPluginManager()
   const root = pluginManager.rootModel!
-  const session = root.session!
   const { findByText } = render(
     <StartScreen rootModel={root} onFactoryReset={factoryReset} />,
   )
   await findByText('Start a new session')
   fireEvent.click(await findByText('Linear Genome View'))
-  expect(session).toBeTruthy()
-  expect(session.views.length).toBeGreaterThan(0)
+  expect(root.session!.views.length).toBeGreaterThan(0)
 })
 
 test('Add New SV Inspector Session', async () => {
   const pluginManager = getPluginManager()
   const root = pluginManager.rootModel!
-  const session = root.session!
   const { findByText } = render(
     <StartScreen rootModel={root} onFactoryReset={factoryReset} />,
   )
   await findByText('Start a new session')
   fireEvent.click(await findByText('Structural Variant Inspector'))
-  expect(session).toBeTruthy()
-  expect(session.views.length).toBeGreaterThan(0)
+  expect(root.session!.views.length).toBeGreaterThan(0)
 })

products/jbrowse-web/src/tests/TextSearching.test.tsx

@@ -40,7 +40,7 @@ async function doSetup(val?: unknown) {
   const view = state.session.views[0] as LGV
   fireEvent.click(await findByText('Help'))
 
-  const autocomplete = await findByTestId('autocomplete')
+  const autocomplete = await findByTestId('autocomplete', {}, delay)
   const input = await findByPlaceholderText('Search for location')
 
   autocomplete.focus()
@@ -123,7 +123,7 @@ test(
     fireEvent.change(input, { target: { value: 'ctgb' } })
     fireEvent.keyDown(input, { key: 'Enter', code: 'Enter' })
     fireEvent.keyDown(autocomplete, { key: 'Enter', code: 'Enter' })
-    fireEvent.click((await findAllByText('Go'))[0])
+    fireEvent.click((await findAllByText('Go', {}, delay))[0])
     await waitFor(() => expect(view.displayedRegions[0].refName).toBe('ctgB'))
   },
   total,