Add ability to open refNameAliases+cytobands in "Open sequence" start screen on desktop

packages/core/CorePlugin.ts

@@ -3,12 +3,8 @@ import { configSchema, stateModelFactory } from './BaseFeatureWidget'
 import Plugin from './Plugin'
 import PluginManager from './PluginManager'
 import * as coreRpcMethods from './rpc/coreRpcMethods'
-import AdapterType from './pluggableElementTypes/AdapterType'
 import WidgetType from './pluggableElementTypes/WidgetType'
-import {
-  configSchema as cytobandConfigSchema,
-  DataAdapter,
-} from './data_adapters/CytobandAdapter'
+import CytobandAdapterF from './data_adapters/CytobandAdapter'
 
 // the core plugin, which registers types that ALL JBrowse applications are
 // expected to need.
@@ -21,14 +17,7 @@ export default class CorePlugin extends Plugin {
       pluginManager.addRpcMethod(() => new RpcMethod(pluginManager))
     })
 
-    pluginManager.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'CytobandAdapter',
-          configSchema: cytobandConfigSchema,
-          AdapterClass: DataAdapter,
-        }),
-    )
+    CytobandAdapterF(pluginManager)
 
     pluginManager.addWidgetType(() => {
       return new WidgetType({

packages/core/data_adapters/CytobandAdapter/CytobandAdapter.ts

@@ -0,0 +1,39 @@
+import { unzip } from '@gmod/bgzf-filehandle'
+
+// locals
+import { SimpleFeature } from '../../util'
+import { openLocation } from '../../util/io'
+import { BaseAdapter } from '../BaseAdapter'
+
+export function isGzip(buf: Buffer) {
+  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8
+}
+
+export default class CytobandAdapter extends BaseAdapter {
+  async getData() {
+    const pm = this.pluginManager
+    const loc = this.getConf('cytobandLocation')
+    if (loc.uri === '' || loc.uri === '/path/to/cytoband.txt.gz') {
+      return []
+    }
+    const buffer = (await openLocation(loc, pm).readFile()) as Buffer
+    const buf = isGzip(buffer) ? await unzip(buffer) : buffer
+    const text = new TextDecoder('utf8', { fatal: true }).decode(buf)
+    return text
+      .split(/\n|\r\n|\r/)
+      .filter(f => !!f.trim())
+      .map((line, i) => {
+        const [refName, start, end, name, type] = line.split('\t')
+        return new SimpleFeature({
+          uniqueId: `${i}`,
+          refName,
+          start: +start,
+          end: +end,
+          name,
+          type,
+        })
+      })
+  }
+
+  freeResources(/* { region } */): void {}
+}

packages/core/data_adapters/CytobandAdapter/configSchema.ts

@@ -0,0 +1,22 @@
+import { ConfigurationSchema } from '../../configuration'
+
+/**
+ * #config CytobandAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const configSchema = ConfigurationSchema(
+  'CytobandAdapter',
+  {
+    /**
+     * #slot
+     */
+    cytobandLocation: {
+      type: 'fileLocation',
+      defaultValue: { uri: '/path/to/cytoband.txt.gz' },
+    },
+  },
+  { explicitlyTyped: true },
+)
+
+export default configSchema

packages/core/data_adapters/CytobandAdapter/index.ts

@@ -0,0 +1,14 @@
+import { AdapterType } from '../../pluggableElementTypes'
+import PluginManager from '../../PluginManager'
+import configSchema from './configSchema'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addAdapterType(
+    () =>
+      new AdapterType({
+        name: 'CytobandAdapter',
+        configSchema,
+        getAdapterClass: () => import('./CytobandAdapter').then(f => f.default),
+      }),
+  )
+}

packages/core/package.json

@@ -29,6 +29,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.17.9",
+    "@gmod/bgzf-filehandle": "^1.4.3",
     "@mui/icons-material": "^5.0.1",
     "@types/clone": "^2.0.0",
     "abortable-promise-cache": "^1.5.0",

packages/core/ui/theme.ts

@@ -385,6 +385,11 @@ function createDefaultProps(theme?: ThemeOptions) {
           },
         },
       },
+      MuiToggleButtonGroup: {
+        defaultProps: {
+          size: 'small' as const,
+        },
+      },
     },
   }
 }

plugins/config/src/RefNameAliasAdapter/RefNameAliasAdapter.ts

@@ -3,19 +3,18 @@ import {
   BaseAdapter,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { openLocation } from '@jbrowse/core/util/io'
-import { readConfObject } from '@jbrowse/core/configuration'
 
 export default class RefNameAliasAdapter
   extends BaseAdapter
   implements BaseRefNameAliasAdapter
 {
   async getRefNameAliases() {
-    const loc = readConfObject(this.config, 'location')
+    const loc = this.getConf('location')
     if (loc.uri === '' || loc.uri === '/path/to/my/aliases.txt') {
       return []
     }
-    const results = await openLocation(loc).readFile('utf8')
-    const refColumn = readConfObject(this.config, 'refNameColumn')
+    const results = await openLocation(loc, this.pluginManager).readFile('utf8')
+    const refColumn = this.getConf('refNameColumn')
     return results
       .trim()
       .split(/\n|\r\n|\r/)

products/jbrowse-desktop/src/AdapterInput.tsx

@@ -0,0 +1,115 @@
+import React from 'react'
+import { Grid } from '@mui/material'
+import { FileSelector } from '@jbrowse/core/ui'
+import { FileLocation } from '@jbrowse/core/util/types'
+
+export default function AdapterInput({
+  adapterSelection,
+  fastaLocation,
+  setFastaLocation,
+  faiLocation,
+  setFaiLocation,
+  chromSizesLocation,
+  gziLocation,
+  setGziLocation,
+  twoBitLocation,
+  setTwoBitLocation,
+  setChromSizesLocation,
+}: {
+  adapterSelection: string
+  fastaLocation: FileLocation
+  setFastaLocation: Function
+  faiLocation: FileLocation
+  setFaiLocation: Function
+  gziLocation: FileLocation
+  chromSizesLocation: FileLocation
+  setGziLocation: Function
+  twoBitLocation: FileLocation
+  setTwoBitLocation: Function
+  setChromSizesLocation: Function
+}) {
+  if (adapterSelection === 'IndexedFastaAdapter') {
+    return (
+      <Grid container spacing={2}>
+        <Grid item>
+          <FileSelector
+            name="fastaLocation"
+            location={fastaLocation}
+            setLocation={loc => setFastaLocation(loc)}
+          />
+        </Grid>
+        <Grid item>
+          <FileSelector
+            name="faiLocation"
+            location={faiLocation}
+            setLocation={loc => setFaiLocation(loc)}
+          />
+        </Grid>
+      </Grid>
+    )
+  }
+  if (adapterSelection === 'BgzipFastaAdapter') {
+    return (
+      <Grid container spacing={2}>
+        <Grid item>
+          <FileSelector
+            name="fastaLocation"
+            location={fastaLocation}
+            setLocation={loc => setFastaLocation(loc)}
+          />
+        </Grid>
+        <Grid item>
+          <FileSelector
+            name="faiLocation"
+            location={faiLocation}
+            setLocation={loc => setFaiLocation(loc)}
+          />
+        </Grid>
+        <Grid item>
+          <FileSelector
+            name="gziLocation"
+            location={gziLocation}
+            setLocation={loc => setGziLocation(loc)}
+          />
+        </Grid>
+      </Grid>
+    )
+  }
+
+  if (adapterSelection === 'TwoBitAdapter') {
+    return (
+      <Grid container spacing={2}>
+        <Grid item>
+          <FileSelector
+            name="twoBitLocation"
+            location={twoBitLocation}
+            setLocation={loc => setTwoBitLocation(loc)}
+          />
+        </Grid>
+        <Grid item>
+          <FileSelector
+            name="chromSizesLocation (optional, can be added to speed up loading 2bit files with many contigs)"
+            location={chromSizesLocation}
+            setLocation={loc => setChromSizesLocation(loc)}
+          />
+        </Grid>
+      </Grid>
+    )
+  }
+
+  if (adapterSelection === 'FastaAdapter') {
+    return (
+      <Grid container spacing={2}>
+        <Grid item>
+          <FileSelector
+            name="fastaLocation"
+            location={fastaLocation}
+            setLocation={loc => setFastaLocation(loc)}
+          />
+        </Grid>
+      </Grid>
+    )
+  }
+
+  return null
+}