Fix drawing inverted CIGAR segments on dotplot (#3170)

* Fix drawing inverted segments on dotplot renderer * Accomodate undefined MatePosition * Typescriptify test * More typescripting * Gzip + CIGAR gzip * More typescripting * More typescripting
GMOD · Sep 7, 2022 · 1b125fe · 1b125fe
1 parent 7ed81c2
commit 1b125fe
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Showing 43 changed files with 2,804 additions and 2,082 deletions.
diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView.ts b/plugins/breakpoint-split-view/src/BreakpointSplitView.ts
@@ -41,7 +41,7 @@ class BreakpointSplitViewType extends ViewType {
       const INFO = feature.get('INFO')
       endPos = INFO.END[0] - 1
       mateRefName = getCanonicalRefName(INFO.CHR2[0])
-    } else if (bnd) {
+    } else if (bnd?.MatePosition) {
       const matePosition = bnd.MatePosition.split(':')
       endPos = +matePosition[1] - 1
       mateRefName = getCanonicalRefName(matePosition[0])

diff --git a/plugins/breakpoint-split-view/src/components/Breakends.tsx b/plugins/breakpoint-split-view/src/components/Breakends.tsx
@@ -39,7 +39,7 @@ function getMatchedBreakendFeatures(features: Map<string, Feature>) {
           const bnd = parseBreakend(a)
           if (bnd) {
             if (!candidates[cur]) {
-              candidates[bnd.MatePosition] = [f]
+              candidates[bnd.MatePosition || 'none'] = [f]
             } else {
               candidates[cur].push(f)
             }

diff --git a/.../src/ConfigurationEditorWidget/components/__snapshots__/ConfigurationEditor.test.tsx.snap b/.../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"

diff --git a/...agement/src/AddConnectionWidget/components/__snapshots__/AddConnectionWidget.test.js.snap b/...agement/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"

diff --git a/plugins/dotplot-view/src/DotplotRenderer/DotplotRenderer.ts b/plugins/dotplot-view/src/DotplotRenderer/DotplotRenderer.ts
@@ -105,11 +105,17 @@ export default class DotplotRenderer extends ComparativeRenderer {
       max: number,
       feature: Feature,
     ) {
+      const strand = feature.get('strand') || 1
+      if (strand === -1) {
+        ;[max, min] = [min, max]
+      }
       if (num < min - fudgeFactor) {
-        const strand = feature.get('strand') || 1
-        const start = strand === 1 ? feature.get('start') : feature.get('end')
-        const end = strand === 1 ? feature.get('end') : feature.get('start')
+        let start = feature.get('start')
+        let end = feature.get('end')
         const refName = feature.get('refName')
+        if (strand === -1) {
+          ;[end, start] = [start, end]
+        }
 
         warnings.push({
           message: `feature at (X ${refName}:${start}-${end}) ${r} ${lt}`,

diff --git a/...r-genome-view/src/LinearGenomeView/components/__snapshots__/LinearGenomeView.test.js.snap b/...r-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;"
           >

diff --git a/...nome-view/src/JBrowseLinearGenomeView/__snapshots__/JBrowseLinearGenomeView.test.tsx.snap b/...nome-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;"
                   >

diff --git a/...rowse-web/src/tests/1.Spreadsheet.test.js → ...owse-web/src/tests/1.Spreadsheet.test.tsx b/...rowse-web/src/tests/1.Spreadsheet.test.js → ...owse-web/src/tests/1.Spreadsheet.test.tsx
@@ -1,25 +1,23 @@
-import React from 'react'
 import '@testing-library/jest-dom/extend-expect'
-import { fireEvent, render, waitFor } from '@testing-library/react'
-import { toMatchImageSnapshot } from 'jest-image-snapshot'
+import { fireEvent, waitFor } 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 { TextEncoder, TextDecoder } from 'web-encoding'
 
-import { JBrowse, setup, getPluginManager, generateReadBuffer } from './util'
+import { createView, setup, generateReadBuffer } from './util'
 
 window.TextEncoder = TextEncoder
 window.TextDecoder = TextDecoder
 
-expect.extend({ toMatchImageSnapshot })
-
 setup()
 
 beforeEach(() => {
   clearCache()
   clearAdapterCache()
+  // @ts-ignore
   fetch.resetMocks()
+  // @ts-ignore
   fetch.mockResponse(
     generateReadBuffer(
       url => new LocalFile(require.resolve(`../../test_data/volvox/${url}`)),
@@ -30,10 +28,7 @@ beforeEach(() => {
 const delay = { timeout: 10000 }
 
 test('opens a vcf.gz file in the spreadsheet view', async () => {
-  const pluginManager = getPluginManager()
-  const { findByTestId, getByTestId, findByText } = render(
-    <JBrowse pluginManager={pluginManager} />,
-  )
+  const { session, findByTestId, getByTestId, findByText } = createView()
   fireEvent.click(await findByText('File'))
   fireEvent.click(await findByText('Add'))
   fireEvent.click(await findByText('Spreadsheet view'))
@@ -48,14 +43,11 @@ test('opens a vcf.gz file in the spreadsheet view', async () => {
     ).not.toBeDisabled(),
   )
   fireEvent.click(await findByTestId('open_spreadsheet'))
-  expect(pluginManager.rootModel.session.views.length).toBe(2)
+  expect(session.views.length).toBe(2)
 }, 15000)
 
 test('opens a bed.gz file in the spreadsheet view', async () => {
-  const pluginManager = getPluginManager()
-  const { findByTestId, getByTestId, findByText } = render(
-    <JBrowse pluginManager={pluginManager} />,
-  )
+  const { findByTestId, session, getByTestId, findByText } = createView()
   fireEvent.click(await findByText('File'))
   fireEvent.click(await findByText('Add'))
   fireEvent.click(await findByText('Spreadsheet view'))
@@ -70,5 +62,5 @@ test('opens a bed.gz file in the spreadsheet view', async () => {
     ).not.toBeDisabled(),
   )
   fireEvent.click(await findByTestId('open_spreadsheet'))
-  expect(pluginManager.rootModel.session.views.length).toBe(2)
+  expect(session.views.length).toBe(2)
 }, 15000)
diff --git a/...rowse-web/src/tests/2.SVInspector.test.js → ...owse-web/src/tests/2.SVInspector.test.tsx b/...rowse-web/src/tests/2.SVInspector.test.js → ...owse-web/src/tests/2.SVInspector.test.tsx
@@ -1,25 +1,23 @@
-import React from 'react'
 import '@testing-library/jest-dom/extend-expect'
-import { fireEvent, render, waitFor } from '@testing-library/react'
-import { toMatchImageSnapshot } from 'jest-image-snapshot'
+import { fireEvent, waitFor } 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 { TextEncoder, TextDecoder } from 'web-encoding'
 
-import { JBrowse, setup, getPluginManager, generateReadBuffer } from './util'
+import { setup, createView, generateReadBuffer } from './util'
 
 window.TextEncoder = TextEncoder
 window.TextDecoder = TextDecoder
 
-expect.extend({ toMatchImageSnapshot })
-
 setup()
 
 beforeEach(() => {
   clearCache()
   clearAdapterCache()
+  // @ts-ignore
   fetch.resetMocks()
+  // @ts-ignore
   fetch.mockResponse(
     generateReadBuffer(url => {
       return new LocalFile(require.resolve(`../../test_data/volvox/${url}`))
@@ -31,13 +29,8 @@ const delay = { timeout: 20000 }
 
 test('opens a vcf.gz file in the sv inspector view', async () => {
   console.warn = jest.fn()
-  const pluginManager = getPluginManager()
-  const { findByTestId, getByTestId, findByText } = render(
-    <JBrowse pluginManager={pluginManager} />,
-  )
-  const {
-    rootModel: { session },
-  } = pluginManager
+  const { session, findByTestId, getByTestId, findByText } = createView()
+
   fireEvent.click(await findByText('File'))
   fireEvent.click(await findByText('Add'))
   fireEvent.click(await findByText('SV inspector'))

diff --git a/products/jbrowse-web/src/tests/Alignments.test.tsx b/products/jbrowse-web/src/tests/Alignments.test.tsx
@@ -4,7 +4,6 @@ import { LocalFile } from 'generic-filehandle'
 // locals
 import { clearCache } from '@jbrowse/core/util/io/RemoteFileWithRangeCache'
 import { clearAdapterCache } from '@jbrowse/core/data_adapters/dataAdapterCache'
-import { toMatchImageSnapshot } from 'jest-image-snapshot'
 import {
   setup,
   expectCanvasMatch,
@@ -14,7 +13,6 @@ import {
   pc,
 } from './util'
 
-expect.extend({ toMatchImageSnapshot })
 setup()
 
 beforeEach(() => {

diff --git a/products/jbrowse-web/src/tests/AlignmentsFeatures.test.tsx b/products/jbrowse-web/src/tests/AlignmentsFeatures.test.tsx
@@ -4,7 +4,6 @@ import { LocalFile } from 'generic-filehandle'
 // locals
 import { clearCache } from '@jbrowse/core/util/io/RemoteFileWithRangeCache'
 import { clearAdapterCache } from '@jbrowse/core/data_adapters/dataAdapterCache'
-import { toMatchImageSnapshot } from 'jest-image-snapshot'
 import {
   setup,
   expectCanvasMatch,
@@ -14,7 +13,6 @@ import {
   hts,
 } from './util'
 
-expect.extend({ toMatchImageSnapshot })
 setup()
 
 beforeEach(() => {

diff --git a/...owse-web/src/tests/Authentication.test.js → ...wse-web/src/tests/Authentication.test.tsx b/...owse-web/src/tests/Authentication.test.js → ...wse-web/src/tests/Authentication.test.tsx
@@ -1,29 +1,27 @@
-import React from 'react'
-import { fireEvent, render, waitFor, within } from '@testing-library/react'
+import { fireEvent, waitFor, within } from '@testing-library/react'
 import { LocalFile, RemoteFile } from 'generic-filehandle'
 import { clearCache } from '@jbrowse/core/util/io/RemoteFileWithRangeCache'
 import { clearAdapterCache } from '@jbrowse/core/data_adapters/dataAdapterCache'
 import crypto from 'crypto'
-import { toMatchImageSnapshot } from 'jest-image-snapshot'
 import config from '../../test_data/volvox/config.json'
 import {
-  JBrowse,
   setup,
+  createView,
   expectCanvasMatch,
   generateReadBuffer,
-  getPluginManager,
 } from './util'
 
-expect.extend({ toMatchImageSnapshot })
 setup()
-
+// @ts-ignore
 global.crypto = { getRandomValues: crypto.randomFillSync }
 
 beforeEach(() => {
   clearCache()
   clearAdapterCache()
   sessionStorage.clear()
+  // @ts-ignore
   fetch.resetMocks()
+  // @ts-ignore
   fetch.mockResponse(
     generateReadBuffer(
       url => new LocalFile(require.resolve(`../../test_data/volvox/${url}`)),
@@ -34,7 +32,7 @@ beforeEach(() => {
 const delay = { timeout: 20000 }
 
 test('open a bigwig track that needs oauth authentication and has existing token', async () => {
-  const pm = getPluginManager({
+  const { state, view, findByTestId, findByText } = createView({
     ...config,
     tracks: [
       {
@@ -54,17 +52,18 @@ test('open a bigwig track that needs oauth authentication and has existing token
       },
     ],
   })
-  const state = pm.rootModel
-  const { findByTestId, findByText } = render(<JBrowse pluginManager={pm} />)
   const token = '1234'
   sessionStorage.setItem('dropboxOAuth-token', token)
+  // @ts-ignore
   await waitFor(() => expect(state.internetAccounts.length).toBe(2))
+  // @ts-ignore
   state.internetAccounts[0].validateToken = jest.fn().mockReturnValue(token)
+  // @ts-ignore
   state.internetAccounts[0].openLocation = jest
     .fn()
     .mockReturnValue(new RemoteFile('volvox_microarray_dropbox.bw'))
   await findByText('Help')
-  state.session.views[0].setNewView(5, 0)
+  view.setNewView(5, 0)
   fireEvent.click(
     await findByTestId('htsTrackEntry-volvox_microarray_dropbox', {}, delay),
   )
@@ -78,7 +77,7 @@ test('open a bigwig track that needs oauth authentication and has existing token
 }, 25000)
 
 test('opens a bigwig track that needs external token authentication', async () => {
-  const pm = getPluginManager({
+  const { view, findByTestId } = createView({
     ...config,
     internetAccounts: [
       {
@@ -107,9 +106,7 @@ test('opens a bigwig track that needs external token authentication', async () =
       },
     ],
   })
-  const state = pm.rootModel
-  const { findByTestId } = render(<JBrowse pluginManager={pm} />)
-  state.session.views[0].setNewView(5, 0)
+  view.setNewView(5, 0)
   fireEvent.click(
     await findByTestId(
       'htsTrackEntry-volvox_microarray_externaltoken',
@@ -138,7 +135,7 @@ test('opens a bigwig track that needs external token authentication', async () =
 }, 25000)
 
 test('opens a bigwig track that needs httpbasic authentication', async () => {
-  const pm = getPluginManager({
+  const { view, findByTestId, findByText } = createView({
     ...config,
     tracks: [
       {
@@ -158,9 +155,7 @@ test('opens a bigwig track that needs httpbasic authentication', async () => {
       },
     ],
   })
-  const state = pm.rootModel
-  const { findByTestId, findByText } = render(<JBrowse pluginManager={pm} />)
-  state.session.views[0].setNewView(5, 0)
+  view.setNewView(5, 0)
   fireEvent.click(
     await findByTestId('htsTrackEntry-volvox_microarray_httpbasic', {}, delay),
   )

diff --git a/products/jbrowse-web/src/tests/BigWig.test.tsx b/products/jbrowse-web/src/tests/BigWig.test.tsx
@@ -2,7 +2,6 @@ import { fireEvent } 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 { toMatchImageSnapshot } from 'jest-image-snapshot'
 
 import {
   setup,
@@ -13,7 +12,6 @@ import {
   hts,
 } from './util'
 
-expect.extend({ toMatchImageSnapshot })
 setup()
 
 beforeEach(() => {