@jbrowse/plugin-linear-genome-view 2.2.2 → 2.3.0

package/src/LinearGenomeView/components/LinearGenomeView.test.tsx

@@ -30,143 +30,141 @@ const assemblyConf = {
   },
 }
 
-describe('<LinearGenomeView />', () => {
-  it('renders setup wizard', async () => {
-    const session = createTestSession()
-    session.addAssemblyConf(assemblyConf)
-    session.addView('LinearGenomeView', { id: 'lgv' })
-    const model = session.views[0]
-    model.setWidth(800)
-    const { findByText } = render(<LinearGenomeView model={model} />)
-    expect(model.displayedRegions.length).toEqual(0)
-    const elt = await findByText('Open')
-    await waitFor(() => expect(elt.getAttribute('disabled')).toBe(null))
-    fireEvent.click(elt)
-    await waitFor(() => expect(model.displayedRegions.length).toEqual(1), {
-      timeout: 15000,
-    })
-  }, 15000)
-
-  it('renders one track, one region', async () => {
-    const session = createTestSession()
-    session.addAssemblyConf(assemblyConf)
-    session.addTrackConf({
-      trackId: 'testConfig',
-      assemblyNames: ['volMyt1'],
-      name: 'Foo Track',
-      type: 'BasicTrack',
-      adapter: { type: 'FromConfigAdapter', features: [] },
-    })
-    session.addView('LinearGenomeView', {
-      type: 'LinearGenomeView',
-      id: 'lgv',
-      offsetPx: 0,
-      bpPerPx: 1,
-      tracks: [
-        {
-          id: 'foo',
-          type: 'BasicTrack',
-          height: 20,
-          configuration: 'testConfig',
-          displays: [
-            {
-              type: 'LinearBareDisplay',
-              configuration: 'testConfig-LinearBareDisplay',
-            },
-          ],
-        },
-      ],
-      displayedRegions: [
-        { assemblyName: 'volMyt1', refName: 'ctgA', start: 0, end: 100 },
-      ],
-    })
-    const model = session.views[0]
-    model.setWidth(800)
-    const { container, queryByText, getByPlaceholderText, findByText } = render(
-      <LinearGenomeView model={model} />,
-    )
-    await findByText('Foo Track')
-    // test needs to wait until it's updated to display 100 bp in the header to
-    // make snapshot pass
-    await findByText('100bp')
+test('renders setup wizard', async () => {
+  const session = createTestSession()
+  session.addAssemblyConf(assemblyConf)
+  session.addView('LinearGenomeView', { id: 'lgv' })
+  const model = session.views[0]
+  model.setWidth(800)
+  const { findByText } = render(<LinearGenomeView model={model} />)
+  expect(model.displayedRegions.length).toEqual(0)
+  const elt = await findByText('Open')
+  await waitFor(() => expect(elt.getAttribute('disabled')).toBe(null))
+  fireEvent.click(elt)
+  await waitFor(() => expect(model.displayedRegions.length).toEqual(1), {
+    timeout: 15000,
+  })
+}, 15000)
 
-    await waitFor(() => {
-      expect(
-        (getByPlaceholderText('Search for location') as HTMLInputElement).value,
-      ).toEqual('ctgA:1..100')
-    })
-    await waitFor(() => expect(queryByText('Loading')).not.toBeInTheDocument())
-    expect(container.firstChild).toMatchSnapshot()
+test('renders one track, one region', async () => {
+  const session = createTestSession()
+  session.addAssemblyConf(assemblyConf)
+  session.addTrackConf({
+    trackId: 'testConfig',
+    assemblyNames: ['volMyt1'],
+    name: 'Foo Track',
+    type: 'BasicTrack',
+    adapter: { type: 'FromConfigAdapter', features: [] },
   })
+  session.addView('LinearGenomeView', {
+    type: 'LinearGenomeView',
+    id: 'lgv',
+    offsetPx: 0,
+    bpPerPx: 1,
+    tracks: [
+      {
+        id: 'foo',
+        type: 'BasicTrack',
+        height: 20,
+        configuration: 'testConfig',
+        displays: [
+          {
+            type: 'LinearBareDisplay',
+            configuration: 'testConfig-LinearBareDisplay',
+          },
+        ],
+      },
+    ],
+    displayedRegions: [
+      { assemblyName: 'volMyt1', refName: 'ctgA', start: 0, end: 100 },
+    ],
+  })
+  const model = session.views[0]
+  model.setWidth(800)
+  const { container, queryByText, getByPlaceholderText, findByText } = render(
+    <LinearGenomeView model={model} />,
+  )
+  await findByText('Foo Track')
+  // test needs to wait until it's updated to display 100 bp in the header to
+  // make snapshot pass
+  await findByText('100bp')
 
-  it('renders two tracks, two regions', async () => {
-    const session = createTestSession()
-    session.addAssemblyConf(assemblyConf)
-    session.addTrackConf({
-      trackId: 'testConfig',
-      name: 'Foo Track',
-      assemblyNames: ['volMyt1'],
-      type: 'BasicTrack',
-      adapter: { type: 'FromConfigAdapter', features: [] },
-    })
+  await waitFor(() => {
+    expect(
+      (getByPlaceholderText('Search for location') as HTMLInputElement).value,
+    ).toEqual('ctgA:1..100')
+  })
+  await waitFor(() => expect(queryByText('Loading')).not.toBeInTheDocument())
+  expect(container.firstChild).toMatchSnapshot()
+})
 
-    session.addTrackConf({
-      trackId: 'testConfig2',
-      name: 'Bar Track',
-      assemblyNames: ['volMyt1'],
-      type: 'BasicTrack',
-      adapter: { type: 'FromConfigAdapter', features: [] },
-    })
-    session.addView('LinearGenomeView', {
-      id: 'lgv',
-      offsetPx: 0,
-      bpPerPx: 1,
-      displayedRegions: [
-        { assemblyName: 'volMyt1', refName: 'ctgA', start: 0, end: 100 },
-        {
-          assemblyName: 'volMyt1',
-          refName: 'ctgB',
-          start: 1000,
-          end: 2000,
-        },
-      ],
-      tracks: [
-        {
-          id: 'foo',
-          type: 'BasicTrack',
-          height: 20,
-          configuration: 'testConfig',
-          displays: [
-            {
-              type: 'LinearBareDisplay',
-              configuration: 'testConfig-LinearBareDisplay',
-            },
-          ],
-        },
-        {
-          id: 'bar',
-          type: 'BasicTrack',
-          height: 20,
-          configuration: 'testConfig2',
-          displays: [
-            {
-              type: 'LinearBareDisplay',
-              configuration: 'testConfig2-LinearBareDisplay',
-            },
-          ],
-        },
-      ],
-    })
-    const model = session.views[0]
-    model.setWidth(800)
-    const { container, findByText, queryByText, findAllByTestId } = render(
-      <LinearGenomeView model={model} />,
-    )
-    await findByText('Foo Track')
-    await findByText('798bp')
-    await findAllByTestId('svgfeatures')
-    await waitFor(() => expect(queryByText('Loading')).not.toBeInTheDocument())
+test('renders two tracks, two regions', async () => {
+  const session = createTestSession()
+  session.addAssemblyConf(assemblyConf)
+  session.addTrackConf({
+    trackId: 'testConfig',
+    name: 'Foo Track',
+    assemblyNames: ['volMyt1'],
+    type: 'BasicTrack',
+    adapter: { type: 'FromConfigAdapter', features: [] },
+  })
 
-    expect(container.firstChild).toMatchSnapshot()
+  session.addTrackConf({
+    trackId: 'testConfig2',
+    name: 'Bar Track',
+    assemblyNames: ['volMyt1'],
+    type: 'BasicTrack',
+    adapter: { type: 'FromConfigAdapter', features: [] },
   })
-})
+  session.addView('LinearGenomeView', {
+    id: 'lgv',
+    offsetPx: 0,
+    bpPerPx: 1,
+    displayedRegions: [
+      { assemblyName: 'volMyt1', refName: 'ctgA', start: 0, end: 100 },
+      {
+        assemblyName: 'volMyt1',
+        refName: 'ctgB',
+        start: 1000,
+        end: 2000,
+      },
+    ],
+    tracks: [
+      {
+        id: 'foo',
+        type: 'BasicTrack',
+        height: 20,
+        configuration: 'testConfig',
+        displays: [
+          {
+            type: 'LinearBareDisplay',
+            configuration: 'testConfig-LinearBareDisplay',
+          },
+        ],
+      },
+      {
+        id: 'bar',
+        type: 'BasicTrack',
+        height: 20,
+        configuration: 'testConfig2',
+        displays: [
+          {
+            type: 'LinearBareDisplay',
+            configuration: 'testConfig2-LinearBareDisplay',
+          },
+        ],
+      },
+    ],
+  })
+  const model = session.views[0]
+  model.setWidth(800)
+  const { container, findByText, queryByText, findAllByTestId } = render(
+    <LinearGenomeView model={model} />,
+  )
+  await findByText('Foo Track')
+  await findByText('798bp')
+  await findAllByTestId('svgfeatures', {}, { timeout: 10000 })
+  await waitFor(() => expect(queryByText('Loading')).not.toBeInTheDocument())
+
+  expect(container.firstChild).toMatchSnapshot()
+}, 15000)

package/src/LinearGenomeView/components/LinearGenomeViewSvg.tsx

@@ -276,8 +276,7 @@ export async function renderToSvg(model: LGV, opts: ExportSvgOptions) {
     tracks.map(async track => {
       const display = track.displays[0]
       await when(() => (display.ready !== undefined ? display.ready : true))
-      const result = await display.renderSvg(opts)
-      return { track, result }
+      return { track, result: await display.renderSvg(opts) }
     }),
   )
 

package/src/LinearGenomeView/components/Ruler.tsx

@@ -1,39 +1,37 @@
+import React from 'react'
 import { makeStyles } from 'tss-react/mui'
 import { observer } from 'mobx-react'
-import ReactPropTypes from 'prop-types'
-import React from 'react'
-import { makeTicks } from '../util'
 import { getTickDisplayStr } from '@jbrowse/core/util'
 
-const useStyles = makeStyles()((/* theme */) => ({
+// locals
+import { makeTicks } from '../util'
+
+const useStyles = makeStyles()({
   majorTickLabel: {
     fontSize: '11px',
-    // fill: theme.palette.text.primary,
   },
   majorTick: {
     stroke: '#555',
-    // stroke: theme.palette.text.secondary,
   },
   minorTick: {
     stroke: '#999',
-    // stroke: theme.palette.text.hint,
   },
-}))
+})
 
 function Ruler({
   start,
   end,
   bpPerPx,
-  reversed,
-  major,
-  minor,
+  reversed = false,
+  major = true,
+  minor = true,
 }: {
   start: number
   end: number
   bpPerPx: number
   reversed?: boolean
-  major: boolean
-  minor: boolean
+  major?: boolean
+  minor?: boolean
 }) {
   const { classes } = useStyles()
   const ticks = makeTicks(start, end, bpPerPx, major, minor)
@@ -77,19 +75,4 @@ function Ruler({
   )
 }
 
-Ruler.propTypes = {
-  start: ReactPropTypes.number.isRequired,
-  end: ReactPropTypes.number.isRequired,
-  bpPerPx: ReactPropTypes.number.isRequired,
-  reversed: ReactPropTypes.bool,
-  major: ReactPropTypes.bool,
-  minor: ReactPropTypes.bool,
-}
-
-Ruler.defaultProps = {
-  reversed: false,
-  major: true,
-  minor: true,
-}
-
 export default observer(Ruler)

package/src/LinearGenomeView/components/SearchBox.tsx

@@ -53,6 +53,8 @@ function SearchBox({
     try {
       if (option.hasLocation()) {
         await navToOption(option)
+      } else if (option.results?.length) {
+        model.setSearchResults(option.results, option.getLabel())
       } else {
         const input = option.getLabel()
         const [ref, rest] = splitLast(input, ':')

package/src/LinearGenomeView/components/__snapshots__/LinearGenomeView.test.tsx.snap

@@ -1,6 +1,6 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
-exports[`<LinearGenomeView /> renders one track, one region 1`] = `
+exports[`renders one track, one region 1`] = `
 <div
   style="position: relative;"
 >
@@ -511,7 +511,6 @@ exports[`<LinearGenomeView /> renders one track, one region 1`] = `
           >
             <div
               class="css-d6gpow-linearBlocks"
-              data-testid="Blockset"
               style="left: -800px;"
             >
               <div
@@ -544,7 +543,7 @@ exports[`<LinearGenomeView /> renders one track, one region 1`] = `
 </div>
 `;
 
-exports[`<LinearGenomeView /> renders two tracks, two regions 1`] = `
+exports[`renders two tracks, two regions 1`] = `
 <div
   style="position: relative;"
 >
@@ -1308,7 +1307,6 @@ exports[`<LinearGenomeView /> renders two tracks, two regions 1`] = `
           >
             <div
               class="css-d6gpow-linearBlocks"
-              data-testid="Blockset"
               style="left: -800px;"
             >
               <div
@@ -1440,7 +1438,6 @@ exports[`<LinearGenomeView /> renders two tracks, two regions 1`] = `
           >
             <div
               class="css-d6gpow-linearBlocks"
-              data-testid="Blockset"
               style="left: -800px;"
             >
               <div

package/src/LinearGenomeView/index.ts

@@ -8,6 +8,7 @@ export default (pluginManager: PluginManager) => {
     () =>
       new ViewType({
         name: 'LinearGenomeView',
+        displayName: 'Linear genome view',
         stateModel: stateModelFactory(pluginManager),
         ReactComponent: lazy(() => import('./components/LinearGenomeView')),
       }),

package/src/index.ts

@@ -5,10 +5,12 @@ import { AbstractSessionModel, isAbstractMenuManager } from '@jbrowse/core/util'
 // icons
 import LineStyleIcon from '@mui/icons-material/LineStyle'
 
+// locals
 import {
   BaseLinearDisplay,
   BaseLinearDisplayComponent,
   BlockModel,
+  BlockMsg,
   baseLinearDisplayConfigSchema,
 } from './BaseLinearDisplay'
 import LinearBareDisplayF, {
@@ -76,6 +78,7 @@ export {
   BaseLinearDisplay,
   RefNameAutocomplete,
   SearchBox,
+  BlockMsg,
 }
 
 export type { LinearGenomeViewModel, LinearGenomeViewStateModel, BlockModel }

package/dist/BaseLinearDisplay/models/TooLargeMessage.js.map

@@ -1 +0,0 @@
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package/dist/BaseLinearDisplay/models/baseLinearDisplayConfigSchema.d.ts

@@ -1 +0,0 @@
-export declare const baseLinearDisplayConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/dist/BaseLinearDisplay/models/baseLinearDisplayConfigSchema.js.map

@@ -1 +0,0 @@
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package/esm/BaseLinearDisplay/models/TooLargeMessage.js.map

@@ -1 +0,0 @@
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package/esm/BaseLinearDisplay/models/baseLinearDisplayConfigSchema.d.ts

@@ -1 +0,0 @@
-export declare const baseLinearDisplayConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/esm/BaseLinearDisplay/models/baseLinearDisplayConfigSchema.js.map

@@ -1 +0,0 @@
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