@jbrowse/plugin-variants 2.0.0 → 2.1.2

package/src/VariantFeatureWidget/VariantSampleGrid.tsx

@@ -0,0 +1,105 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import React, { useState } from 'react'
+
+import {
+  FormControlLabel,
+  Checkbox,
+  TextField,
+  Typography,
+} from '@mui/material'
+
+import { DataGrid } from '@mui/x-data-grid'
+import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
+
+export default function VariantSamples(props: any) {
+  const [filter, setFilter] = useState<any>({})
+  const [showFilters, setShowFilters] = useState(false)
+  const { feature } = props
+
+  const { samples = {} } = feature
+  const preFilteredRows: any = Object.entries(samples)
+  if (!preFilteredRows.length) {
+    return null
+  }
+  const infoFields = ['sample', ...Object.keys(preFilteredRows[0][1])].map(
+    field => ({
+      field,
+    }),
+  )
+  let error
+  let rows = []
+  const filters = Object.keys(filter)
+
+  // catch some error thrown from regex
+  // note: maps all values into a string, if this is not done rows are not
+  // sortable by the data-grid
+  try {
+    rows = preFilteredRows
+      .map((row: any) => ({
+        ...Object.fromEntries(
+          Object.entries(row[1]).map(entry => [entry[0], String(entry[1])]),
+        ),
+        sample: row[0],
+        id: row[0],
+      }))
+      .filter((row: any) => {
+        return filters.length
+          ? filters.every(key => {
+              const val = row[key]
+              const currFilter = filter[key]
+              return currFilter ? val.match(new RegExp(currFilter, 'i')) : true
+            })
+          : true
+      })
+  } catch (e) {
+    error = e
+  }
+  // disableSelectionOnClick helps avoid
+  // https://github.com/mui-org/material-ui-x/issues/1197
+  return (
+    <BaseCard {...props} title="Samples">
+      {error ? <Typography color="error">{`${error}`}</Typography> : null}
+
+      <FormControlLabel
+        control={
+          <Checkbox
+            checked={showFilters}
+            onChange={() => setShowFilters(f => !f)}
+          />
+        }
+        label="Show sample filters"
+      />
+      {showFilters ? (
+        <>
+          <Typography>
+            These filters can use a plain text search or regex style query, e.g.
+            in the genotype field, entering 1 will query for all genotypes that
+            include the first alternate allele e.g. 0|1 or 1|1, entering
+            [1-9]\d* will find any non-zero allele e.g. 0|2 or 2/33
+          </Typography>
+          {infoFields.map(({ field }) => {
+            return (
+              <TextField
+                key={`filter-${field}`}
+                placeholder={`Filter ${field}`}
+                value={filter[field] || ''}
+                onChange={event =>
+                  setFilter({ ...filter, [field]: event.target.value })
+                }
+              />
+            )
+          })}
+        </>
+      ) : null}
+      <div style={{ height: 600, width: '100%', overflow: 'auto' }}>
+        <DataGrid
+          rows={rows}
+          columns={infoFields}
+          disableSelectionOnClick
+          rowHeight={25}
+          disableColumnMenu
+        />
+      </div>
+    </BaseCard>
+  )
+}

package/src/VariantFeatureWidget/__snapshots__/VariantFeatureWidget.test.js.snap

@@ -198,5 +198,11 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
   <hr
     class="MuiDivider-root MuiDivider-fullWidth css-9mgopn-MuiDivider-root"
   />
+  <hr
+    class="MuiDivider-root MuiDivider-fullWidth css-9mgopn-MuiDivider-root"
+  />
+  <hr
+    class="MuiDivider-root MuiDivider-fullWidth css-9mgopn-MuiDivider-root"
+  />
 </div>
 `;

package/src/VariantFeatureWidget/index.ts

@@ -1,4 +1,6 @@
+import { lazy } from 'react'
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { types } from 'mobx-state-tree'
 import { stateModelFactory as baseModelFactory } from '@jbrowse/core/BaseFeatureWidget'
@@ -15,3 +17,16 @@ export function stateModelFactory(pluginManager: PluginManager) {
     }),
   )
 }
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addWidgetType(
+    () =>
+      new WidgetType({
+        name: 'VariantFeatureWidget',
+        heading: 'Feature details',
+        configSchema,
+        stateModel: stateModelFactory(pluginManager),
+        ReactComponent: lazy(() => import('./VariantFeatureWidget')),
+      }),
+  )
+}

package/src/VariantTrack/index.ts

@@ -0,0 +1,26 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'
+import {
+  createBaseTrackConfig,
+  createBaseTrackModel,
+} from '@jbrowse/core/pluggableElementTypes/models'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addTrackType(() => {
+    const configSchema = ConfigurationSchema(
+      'VariantTrack',
+      {},
+      { baseConfiguration: createBaseTrackConfig(pluginManager) },
+    )
+    return new TrackType({
+      name: 'VariantTrack',
+      configSchema,
+      stateModel: createBaseTrackModel(
+        pluginManager,
+        'VariantTrack',
+        configSchema,
+      ),
+    })
+  })
+}

package/src/VcfAdapter/VcfAdapter.ts

@@ -6,23 +6,24 @@ import { Region } from '@jbrowse/core/util/types'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import { Feature } from '@jbrowse/core/util/simpleFeature'
-import { readConfObject } from '@jbrowse/core/configuration'
 import IntervalTree from '@flatten-js/interval-tree'
 import { unzip } from '@gmod/bgzf-filehandle'
 import VCF from '@gmod/vcf'
 import VcfFeature from '../VcfTabixAdapter/VcfFeature'
 
 const readVcf = (f: string) => {
-  const lines = f.split('\n')
   const header: string[] = []
   const rest: string[] = []
-  lines.forEach(line => {
-    if (line.startsWith('#')) {
-      header.push(line)
-    } else if (line) {
-      rest.push(line)
-    }
-  })
+  f.split('\n')
+    .map(f => f.trim())
+    .filter(f => !!f)
+    .forEach(line => {
+      if (line.startsWith('#')) {
+        header.push(line)
+      } else if (line) {
+        rest.push(line)
+      }
+    })
   return { header: header.join('\n'), lines: rest }
 }
 
@@ -51,19 +52,17 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
 
   // converts lines into an interval tree
   public async setupP() {
-    const buffer = await openLocation(
-      readConfObject(this.config, 'vcfLocation'),
-      this.pluginManager,
-    ).readFile()
+    const pm = this.pluginManager
+    const buf = await openLocation(this.getConf('vcfLocation'), pm).readFile()
 
-    const buf = isGzip(buffer) ? await unzip(buffer) : buffer
+    const buffer = isGzip(buf) ? await unzip(buf) : buf
 
     // 512MB  max chrome string length is 512MB
-    if (buf.length > 536_870_888) {
+    if (buffer.length > 536_870_888) {
       throw new Error('Data exceeds maximum string length (512MB)')
     }
 
-    const str = new TextDecoder().decode(buf)
+    const str = new TextDecoder().decode(buffer)
     const { header, lines } = readVcf(str)
 
     const intervalTree = lines

package/src/VcfAdapter/index.ts

@@ -1 +1,14 @@
-export { default as configSchema } from './configSchema'
+import PluginManager from '@jbrowse/core/PluginManager'
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
+import configSchema from './configSchema'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addAdapterType(
+    () =>
+      new AdapterType({
+        name: 'VcfAdapter',
+        configSchema,
+        getAdapterClass: () => import('./VcfAdapter').then(r => r.default),
+      }),
+  )
+}

package/src/VcfTabixAdapter/VcfFeature.ts

@@ -106,7 +106,7 @@ export default class VCFFeature implements Feature {
     alt: string[],
   ): [string, string] | [undefined, undefined] {
     // it's just a remark if there are no alternate alleles
-    if (!alt || alt === []) {
+    if (!alt || alt.length === 0) {
       return ['remark', 'no alternative alleles']
     }
 

package/src/VcfTabixAdapter/VcfTabixAdapter.ts

@@ -118,9 +118,6 @@ export default class extends BaseFeatureDataAdapter {
     regions: Region[],
     opts: BaseOptions = {},
   ) {
-    // TODO: restore commented version below once TSDX supports Rollup v2
-    // xref: https://github.com/rollup/rollup/blob/master/CHANGELOG.md#bug-fixes-45
-    const superGetFeaturesInMultipleRegions = super.getFeaturesInMultipleRegions
     return ObservableCreate<Feature>(async (observer: Observer<Feature>) => {
       const { vcf } = await this.configure()
 
@@ -138,10 +135,7 @@ export default class extends BaseFeatureDataAdapter {
           `getFeaturesInMultipleRegions fetching ${pct}% of VCF file, but whole-file streaming not yet implemented`,
         )
       }
-      superGetFeaturesInMultipleRegions
-        .call(this, regions, opts)
-        .subscribe(observer)
-      // super.getFeaturesInMultipleRegions(regions, opts).subscribe(observer)
+      super.getFeaturesInMultipleRegions(regions, opts).subscribe(observer)
     })
   }
 

package/src/VcfTabixAdapter/index.ts

@@ -1 +1,16 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
+import configSchema from './configSchema'
+
 export { default as configSchema } from './configSchema'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addAdapterType(
+    () =>
+      new AdapterType({
+        name: 'VcfTabixAdapter',
+        configSchema,
+        getAdapterClass: () => import('./VcfTabixAdapter').then(r => r.default),
+      }),
+  )
+}

package/src/__snapshots__/index.test.js.snap

@@ -5,14 +5,14 @@ exports[`plugin in a stock JBrowse 1`] = `Object {}`;
 exports[`plugin in a stock JBrowse 2`] = `
 Object {
   "displays": Array [
-    Object {
-      "displayId": "trackId0-ChordVariantDisplay",
-      "type": "ChordVariantDisplay",
-    },
     Object {
       "displayId": "trackId0-LinearVariantDisplay",
       "type": "LinearVariantDisplay",
     },
+    Object {
+      "displayId": "trackId0-ChordVariantDisplay",
+      "type": "ChordVariantDisplay",
+    },
   ],
   "trackId": "trackId0",
   "type": "VariantTrack",

package/src/extensionPoints.ts

@@ -0,0 +1,74 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import { FileLocation } from '@jbrowse/core/util/types'
+import {
+  makeIndex,
+  makeIndexType,
+  getFileName,
+  AdapterGuesser,
+  TrackTypeGuesser,
+} from '@jbrowse/core/util/tracks'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addToExtensionPoint(
+    'Core-guessAdapterForLocation',
+    (adapterGuesser: AdapterGuesser) => {
+      return (
+        file: FileLocation,
+        index?: FileLocation,
+        adapterHint?: string,
+      ) => {
+        const regexGuess = /\.vcf\.b?gz$/i
+        const adapterName = 'VcfTabixAdapter'
+        const fileName = getFileName(file)
+        const indexName = index && getFileName(index)
+        const obj = {
+          type: adapterName,
+          vcfGzLocation: file,
+          index: {
+            location: index || makeIndex(file, '.tbi'),
+            indexType: makeIndexType(indexName, 'CSI', 'TBI'),
+          },
+        }
+        if (regexGuess.test(fileName) && !adapterHint) {
+          return obj
+        } else if (adapterHint === adapterName) {
+          return obj
+        }
+        return adapterGuesser(file, index, adapterHint)
+      }
+    },
+  )
+  pluginManager.addToExtensionPoint(
+    'Core-guessTrackTypeForLocation',
+    (trackTypeGuesser: TrackTypeGuesser) => {
+      return (adapterName: string) => {
+        if (adapterName === 'VcfTabixAdapter' || adapterName === 'VcfAdapter') {
+          return 'VariantTrack'
+        }
+        return trackTypeGuesser(adapterName)
+      }
+    },
+  )
+
+  pluginManager.addToExtensionPoint(
+    'Core-guessAdapterForLocation',
+    (adapterGuesser: AdapterGuesser) => {
+      return (
+        file: FileLocation,
+        index?: FileLocation,
+        adapterHint?: string,
+      ) => {
+        const regexGuess = /\.vcf$/i
+        const adapterName = 'VcfAdapter'
+        const fileName = getFileName(file)
+        if (regexGuess.test(fileName) || adapterHint === adapterName) {
+          return {
+            type: adapterName,
+            vcfLocation: file,
+          }
+        }
+        return adapterGuesser(file, index, adapterHint)
+      }
+    },
+  )
+}

package/src/index.ts

@@ -1,175 +1,32 @@
-import { lazy } from 'react'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
-import {
-  createBaseTrackConfig,
-  createBaseTrackModel,
-} from '@jbrowse/core/pluggableElementTypes/models'
-import { FileLocation } from '@jbrowse/core/util/types'
-import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'
-import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType'
+import VcfAdapterF from './VcfAdapter'
+import VcfTabixAdapterF from './VcfTabixAdapter'
+import ExtensionPointsF from './extensionPoints'
+import VariantTrackF from './VariantTrack'
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
-import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'
 import ChordVariantDisplay from './ChordVariantDisplay'
-import {
-  configSchemaFactory as linearVariantDisplayConfigSchemaFactory,
-  modelFactory as linearVariantDisplayModelFactory,
-} from './LinearVariantDisplay'
+import LinearVariantDisplayF from './LinearVariantDisplay'
 import StructuralVariantChordRendererFactory from './StructuralVariantChordRenderer'
-import {
-  configSchema as variantFeatureWidgetConfigSchema,
-  stateModelFactory as variantFeatureWidgetStateModelFactory,
-} from './VariantFeatureWidget'
-import { configSchema as vcfTabixAdapterConfigSchema } from './VcfTabixAdapter'
-import { configSchema as vcfAdapterConfigSchema } from './VcfAdapter'
-import {
-  makeIndex,
-  makeIndexType,
-  AdapterGuesser,
-  getFileName,
-  TrackTypeGuesser,
-} from '@jbrowse/core/util/tracks'
+import VariantFeatureWidgetF from './VariantFeatureWidget'
 
 export default class VariantsPlugin extends Plugin {
   name = 'VariantsPlugin'
 
   install(pluginManager: PluginManager) {
-    pluginManager.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'VcfTabixAdapter',
-          configSchema: vcfTabixAdapterConfigSchema,
-          getAdapterClass: () =>
-            import('./VcfTabixAdapter/VcfTabixAdapter').then(r => r.default),
-        }),
-    )
-    pluginManager.addToExtensionPoint(
-      'Core-guessAdapterForLocation',
-      (adapterGuesser: AdapterGuesser) => {
-        return (
-          file: FileLocation,
-          index?: FileLocation,
-          adapterHint?: string,
-        ) => {
-          const regexGuess = /\.vcf\.b?gz$/i
-          const adapterName = 'VcfTabixAdapter'
-          const fileName = getFileName(file)
-          const indexName = index && getFileName(index)
-          const obj = {
-            type: adapterName,
-            vcfGzLocation: file,
-            index: {
-              location: index || makeIndex(file, '.tbi'),
-              indexType: makeIndexType(indexName, 'CSI', 'TBI'),
-            },
-          }
-          if (regexGuess.test(fileName) && !adapterHint) {
-            return obj
-          } else if (adapterHint === adapterName) {
-            return obj
-          }
-          return adapterGuesser(file, index, adapterHint)
-        }
-      },
-    )
-    pluginManager.addToExtensionPoint(
-      'Core-guessTrackTypeForLocation',
-      (trackTypeGuesser: TrackTypeGuesser) => {
-        return (adapterName: string) => {
-          if (
-            adapterName === 'VcfTabixAdapter' ||
-            adapterName === 'VcfAdapter'
-          ) {
-            return 'VariantTrack'
-          }
-          return trackTypeGuesser(adapterName)
-        }
-      },
-    )
-
-    pluginManager.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'VcfAdapter',
-          configSchema: vcfAdapterConfigSchema,
-          getAdapterClass: () =>
-            import('./VcfAdapter/VcfAdapter').then(r => r.default),
-        }),
-    )
-
-    pluginManager.addToExtensionPoint(
-      'Core-guessAdapterForLocation',
-      (adapterGuesser: AdapterGuesser) => {
-        return (
-          file: FileLocation,
-          index?: FileLocation,
-          adapterHint?: string,
-        ) => {
-          const regexGuess = /\.vcf$/i
-          const adapterName = 'VcfAdapter'
-          const fileName = getFileName(file)
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              vcfLocation: file,
-            }
-          }
-          return adapterGuesser(file, index, adapterHint)
-        }
-      },
-    )
+    VcfAdapterF(pluginManager)
+    VcfTabixAdapterF(pluginManager)
+    VariantFeatureWidgetF(pluginManager)
+    VariantTrackF(pluginManager)
+    ExtensionPointsF(pluginManager)
+    LinearVariantDisplayF(pluginManager)
 
     pluginManager.addRendererType(() =>
       pluginManager.jbrequire(StructuralVariantChordRendererFactory),
     )
-    pluginManager.addTrackType(() => {
-      const configSchema = ConfigurationSchema(
-        'VariantTrack',
-        {},
-        { baseConfiguration: createBaseTrackConfig(pluginManager) },
-      )
-      return new TrackType({
-        name: 'VariantTrack',
-        configSchema,
-        stateModel: createBaseTrackModel(
-          pluginManager,
-          'VariantTrack',
-          configSchema,
-        ),
-      })
-    })
 
     pluginManager.addDisplayType(() =>
       pluginManager.jbrequire(ChordVariantDisplay),
     )
-
-    pluginManager.addDisplayType(() => {
-      const configSchema =
-        linearVariantDisplayConfigSchemaFactory(pluginManager)
-      return new DisplayType({
-        name: 'LinearVariantDisplay',
-        configSchema,
-        stateModel: linearVariantDisplayModelFactory(configSchema),
-        trackType: 'VariantTrack',
-        viewType: 'LinearGenomeView',
-        ReactComponent: BaseLinearDisplayComponent,
-      })
-    })
-
-    pluginManager.addWidgetType(
-      () =>
-        new WidgetType({
-          name: 'VariantFeatureWidget',
-          heading: 'Feature details',
-          configSchema: variantFeatureWidgetConfigSchema,
-          stateModel: variantFeatureWidgetStateModelFactory(pluginManager),
-          ReactComponent: lazy(
-            () => import('./VariantFeatureWidget/VariantFeatureWidget'),
-          ),
-        }),
-    )
   }
 }