@jbrowse/plugin-sequence 1.4.4 → 1.5.3

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "1.4.4",
+  "version": "1.5.3",
   "description": "JBrowse 2 sequence adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -35,11 +35,11 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
-    "@gmod/indexedfasta": "^2.0.1",
-    "@gmod/twobit": "^1.1.10",
+    "@gmod/indexedfasta": "^2.0.2",
+    "@gmod/twobit": "^1.1.12",
     "abortable-promise-cache": "^1.3.0",
     "clsx": "^1.1.0",
-    "generic-filehandle": "^2.0.1"
+    "generic-filehandle": "^2.2.2"
   },
   "peerDependencies": {
     "@jbrowse/core": "^1.0.0",
@@ -55,5 +55,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "c12a2b1cef07dbc5ea40be5c76e03b655b7f3636"
+  "gitHead": "cea9023ebce8bbe5c08ae9e00c4e74fe3f02a7f1"
 }

package/src/BgzipFastaAdapter/BgzipFastaAdapter.test.ts

@@ -7,12 +7,15 @@ test('can use a indexed fasta with gzi', async () => {
     configSchema.create({
       fastaLocation: {
         localPath: require.resolve('../../test_data/volvox.fa.gz'),
+        locationType: 'LocalPathLocation',
       },
       faiLocation: {
         localPath: require.resolve('../../test_data/volvox.fa.gz.fai'),
+        locationType: 'LocalPathLocation',
       },
       gziLocation: {
         localPath: require.resolve('../../test_data/volvox.fa.gz.gzi'),
+        locationType: 'LocalPathLocation',
       },
     }),
   )

package/src/BgzipFastaAdapter/BgzipFastaAdapter.ts

@@ -4,10 +4,16 @@ import { openLocation } from '@jbrowse/core/util/io'
 import { readConfObject } from '@jbrowse/core/configuration'
 import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
 import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter'
+import PluginManager from '@jbrowse/core/PluginManager'
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 
 export default class extends IndexedFasta {
-  public constructor(config: AnyConfigurationModel) {
-    super(config)
+  public constructor(
+    config: AnyConfigurationModel,
+    getSubAdapter?: getSubAdapterType,
+    pluginManager?: PluginManager,
+  ) {
+    super(config, getSubAdapter, pluginManager)
     const fastaLocation = readConfObject(config, 'fastaLocation')
     const faiLocation = readConfObject(config, 'faiLocation')
     const gziLocation = readConfObject(config, 'gziLocation')
@@ -21,9 +27,9 @@ export default class extends IndexedFasta {
       throw new Error('must provide gziLocation')
     }
     const fastaOpts = {
-      fasta: openLocation(fastaLocation as FileLocation),
-      fai: openLocation(faiLocation as FileLocation),
-      gzi: openLocation(gziLocation as FileLocation),
+      fasta: openLocation(fastaLocation as FileLocation, this.pluginManager),
+      fai: openLocation(faiLocation as FileLocation, this.pluginManager),
+      gzi: openLocation(gziLocation as FileLocation, this.pluginManager),
     }
 
     this.fasta = new BgzipIndexedFasta(fastaOpts)

package/src/BgzipFastaAdapter/configSchema.ts

@@ -5,15 +5,21 @@ export default ConfigurationSchema(
   {
     fastaLocation: {
       type: 'fileLocation',
-      defaultValue: { uri: '/path/to/seq.fa.gz' },
+      defaultValue: { uri: '/path/to/seq.fa.gz', locationType: 'UriLocation' },
     },
     faiLocation: {
       type: 'fileLocation',
-      defaultValue: { uri: '/path/to/seq.fa.gz.fai' },
+      defaultValue: {
+        uri: '/path/to/seq.fa.gz.fai',
+        locationType: 'UriLocation',
+      },
     },
     gziLocation: {
       type: 'fileLocation',
-      defaultValue: { uri: '/path/to/seq.fa.gz.gzi' },
+      defaultValue: {
+        uri: '/path/to/seq.fa.gz.gzi',
+        locationType: 'UriLocation',
+      },
     },
   },
   { explicitlyTyped: true },

package/src/ChromSizesAdapter/ChromSizesAdapter.test.ts

@@ -6,6 +6,7 @@ test('adapter can fetch sequence from volvox.chrom.sizes', async () => {
     configSchema.create({
       chromSizesLocation: {
         localPath: require.resolve('./test_data/volvox.chrom.sizes'),
+        locationType: 'LocalPathLocation',
       },
     }),
   )

package/src/ChromSizesAdapter/ChromSizesAdapter.ts

@@ -8,6 +8,8 @@ import { GenericFilehandle } from 'generic-filehandle'
 import { readConfObject } from '@jbrowse/core/configuration'
 import { Instance } from 'mobx-state-tree'
 import MyConfigSchema from './configSchema'
+import PluginManager from '@jbrowse/core/PluginManager'
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 
 export default class extends BaseAdapter implements RegionsAdapter {
   // the map of refSeq to length
@@ -15,13 +17,20 @@ export default class extends BaseAdapter implements RegionsAdapter {
 
   protected source: string
 
-  public constructor(config: Instance<typeof MyConfigSchema>) {
-    super(config)
+  public constructor(
+    config: Instance<typeof MyConfigSchema>,
+    getSubAdapter?: getSubAdapterType,
+    pluginManager?: PluginManager,
+  ) {
+    super(config, getSubAdapter, pluginManager)
     const chromSizesLocation = readConfObject(config, 'chromSizesLocation')
     if (!chromSizesLocation) {
       throw new Error('must provide chromSizesLocation')
     }
-    const file = openLocation(chromSizesLocation as FileLocation)
+    const file = openLocation(
+      chromSizesLocation as FileLocation,
+      this.pluginManager,
+    )
     this.source = file.toString()
     this.refSeqs = this.init(file)
   }

package/src/ChromSizesAdapter/configSchema.ts

@@ -5,7 +5,10 @@ export default ConfigurationSchema(
   {
     chromSizesLocation: {
       type: 'fileLocation',
-      defaultValue: { uri: '/path/to/species.chrom.sizes' },
+      defaultValue: {
+        uri: '/path/to/species.chrom.sizes',
+        locationType: 'UriLocation',
+      },
     },
   },
   { explicitlyTyped: true },

package/src/IndexedFastaAdapter/IndexedFastaAdapter.test.ts

@@ -7,9 +7,11 @@ test('adapter can fetch sequence from volvox.fa', async () => {
     configSchema.create({
       fastaLocation: {
         localPath: require.resolve('../../test_data/volvox.fa'),
+        locationType: 'LocalPathLocation',
       },
       faiLocation: {
         localPath: require.resolve('../../test_data/volvox.fa.fai'),
+        locationType: 'LocalPathLocation',
       },
     }),
   )

package/src/IndexedFastaAdapter/IndexedFastaAdapter.ts

@@ -12,6 +12,8 @@ import { readConfObject } from '@jbrowse/core/configuration'
 import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
 import AbortablePromiseCache from 'abortable-promise-cache'
 import LRU from '@jbrowse/core/util/QuickLRU'
+import PluginManager from '@jbrowse/core/PluginManager'
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 
 export default class extends BaseFeatureDataAdapter implements SequenceAdapter {
   protected fasta: typeof IndexedFasta
@@ -27,13 +29,17 @@ export default class extends BaseFeatureDataAdapter implements SequenceAdapter {
     },
   })
 
-  public constructor(config: AnyConfigurationModel) {
-    super(config)
+  public constructor(
+    config: AnyConfigurationModel,
+    getSubAdapter?: getSubAdapterType,
+    pluginManager?: PluginManager,
+  ) {
+    super(config, getSubAdapter, pluginManager)
     const fastaLocation = readConfObject(config, 'fastaLocation')
     const faiLocation = readConfObject(config, 'faiLocation')
     const fastaOpts = {
-      fasta: openLocation(fastaLocation as FileLocation),
-      fai: openLocation(faiLocation as FileLocation),
+      fasta: openLocation(fastaLocation as FileLocation, this.pluginManager),
+      fai: openLocation(faiLocation as FileLocation, this.pluginManager),
     }
 
     this.fasta = new IndexedFasta(fastaOpts)

package/src/IndexedFastaAdapter/configSchema.ts

@@ -5,11 +5,11 @@ export default ConfigurationSchema(
   {
     fastaLocation: {
       type: 'fileLocation',
-      defaultValue: { uri: '/path/to/seq.fa' },
+      defaultValue: { uri: '/path/to/seq.fa', locationType: 'UriLocation' },
     },
     faiLocation: {
       type: 'fileLocation',
-      defaultValue: { uri: '/path/to/seq.fa.fai' },
+      defaultValue: { uri: '/path/to/seq.fa.fai', locationType: 'UriLocation' },
     },
   },
   { explicitlyTyped: true },

package/src/TwoBitAdapter/TwoBitAdapter.test.ts

@@ -7,6 +7,7 @@ test('adapter can fetch features from volvox.2bit', async () => {
     configSchema.create({
       twoBitLocation: {
         localPath: require.resolve('../../test_data/volvox.2bit'),
+        locationType: 'LocalPathLocation',
       },
     }),
   )
@@ -44,6 +45,7 @@ test('adapter can fetch regions from with chrom.sizes', async () => {
     configSchema.create({
       chromSizesLocation: {
         localPath: require.resolve('../../test_data/volvox.chrom.sizes'),
+        locationType: 'LocalPathLocation',
       },
     }),
   )

package/src/TwoBitAdapter/TwoBitAdapter.ts

@@ -9,10 +9,13 @@ import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
 import { TwoBitFile } from '@gmod/twobit'
 import { readConfObject } from '@jbrowse/core/configuration'
 import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
+import PluginManager from '@jbrowse/core/PluginManager'
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 
 export default class TwoBitAdapter
   extends BaseFeatureDataAdapter
-  implements SequenceAdapter {
+  implements SequenceAdapter
+{
   private twobit: typeof TwoBitFile
 
   // the chromSizesData can be used to speed up loading since TwoBit has to do
@@ -25,7 +28,7 @@ export default class TwoBitAdapter
     // config editor, may want better way to check "optional config slots" in
     // future
     if (conf.uri !== '/path/to/default.chrom.sizes' && conf.uri !== '') {
-      const file = openLocation(conf)
+      const file = openLocation(conf, this.pluginManager)
       const data = (await file.readFile('utf8')) as string
       return Object.fromEntries(
         data
@@ -40,11 +43,18 @@ export default class TwoBitAdapter
     return undefined
   }
 
-  constructor(config: AnyConfigurationModel) {
-    super(config)
+  constructor(
+    config: AnyConfigurationModel,
+    getSubAdapter?: getSubAdapterType,
+    pluginManager?: PluginManager,
+  ) {
+    super(config, getSubAdapter, pluginManager)
     this.chromSizesData = this.initChromSizes()
     this.twobit = new TwoBitFile({
-      filehandle: openLocation(readConfObject(config, 'twoBitLocation')),
+      filehandle: openLocation(
+        readConfObject(config, 'twoBitLocation'),
+        this.pluginManager,
+      ),
     })
   }
 

package/src/TwoBitAdapter/configSchema.ts

@@ -5,11 +5,14 @@ export default ConfigurationSchema(
   {
     twoBitLocation: {
       type: 'fileLocation',
-      defaultValue: { uri: '/path/to/my.2bit' },
+      defaultValue: { uri: '/path/to/my.2bit', locationType: 'UriLocation' },
     },
     chromSizesLocation: {
       type: 'fileLocation',
-      defaultValue: { uri: '/path/to/default.chrom.sizes' },
+      defaultValue: {
+        uri: '/path/to/default.chrom.sizes',
+        locationType: 'UriLocation',
+      },
       description:
         'An optional chrom.sizes file can be supplied to speed up loading since parsing the twobit file can take time',
     },

package/src/index.ts

@@ -6,6 +6,8 @@ import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'
+import { FileLocation } from '@jbrowse/core/util/types'
+import { makeIndex } from '@jbrowse/core/util/tracks'
 import { configSchema as bgzipFastaAdapterConfigSchema } from './BgzipFastaAdapter'
 import { configSchema as chromSizesAdapterConfigSchema } from './ChromSizesAdapter'
 import {
@@ -20,6 +22,11 @@ import {
 import { configSchema as twoBitAdapterConfigSchema } from './TwoBitAdapter'
 import GCContentAdapterF from './GCContentAdapter'
 import { createReferenceSeqTrackConfig } from './referenceSeqTrackConfig'
+import {
+  AdapterGuesser,
+  getFileName,
+  TrackTypeGuesser,
+} from '@jbrowse/core/util/tracks'
 
 /* adjust in both directions */
 class DivSequenceRenderer extends FeatureRendererType {
@@ -43,16 +50,60 @@ export default class SequencePlugin extends Plugin {
         new AdapterType({
           name: 'TwoBitAdapter',
           configSchema: twoBitAdapterConfigSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+          },
           getAdapterClass: () =>
             import('./TwoBitAdapter/TwoBitAdapter').then(r => r.default),
         }),
     )
+    pluginManager.addToExtensionPoint(
+      'Core-guessAdapterForLocation',
+      (adapterGuesser: AdapterGuesser) => {
+        return (
+          file: FileLocation,
+          index?: FileLocation,
+          adapterHint?: string,
+        ) => {
+          const regexGuess = /\.2bit$/i
+          const adapterName = 'TwoBitAdapter'
+          const fileName = getFileName(file)
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              twoBitLocation: file,
+            }
+          }
+          return adapterGuesser(file, index, adapterHint)
+        }
+      },
+    )
+    pluginManager.addToExtensionPoint(
+      'Core-guessTrackTypeForLocation',
+      (trackTypeGuesser: TrackTypeGuesser) => {
+        return (adapterName: string) => {
+          if (adapterName === 'TwoBitAdapter') {
+            return 'ReferenceSequenceTrack'
+          }
+          return trackTypeGuesser(adapterName)
+        }
+      },
+    )
 
     pluginManager.addAdapterType(
       () =>
         new AdapterType({
           name: 'ChromSizesAdapter',
           configSchema: chromSizesAdapterConfigSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+          },
           getAdapterClass: () =>
             import('./ChromSizesAdapter/ChromSizesAdapter').then(
               r => r.default,
@@ -65,18 +116,63 @@ export default class SequencePlugin extends Plugin {
         new AdapterType({
           name: 'IndexedFastaAdapter',
           configSchema: indexedFastaAdapterConfigSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+          },
           getAdapterClass: () =>
             import('./IndexedFastaAdapter/IndexedFastaAdapter').then(
               r => r.default,
             ),
         }),
     )
+    pluginManager.addToExtensionPoint(
+      'Core-guessAdapterForLocation',
+      (adapterGuesser: AdapterGuesser) => {
+        return (
+          file: FileLocation,
+          index?: FileLocation,
+          adapterHint?: string,
+        ) => {
+          const regexGuess = /\.(fa|fasta|fas|fna|mfa)$/i
+          const adapterName = 'IndexedFastaAdapter'
+          const fileName = getFileName(file)
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              fastaLocation: file,
+              faiLocation: index || makeIndex(file, '.fai'),
+            }
+          }
+          return adapterGuesser(file, index, adapterHint)
+        }
+      },
+    )
+    pluginManager.addToExtensionPoint(
+      'Core-guessTrackTypeForLocation',
+      (trackTypeGuesser: TrackTypeGuesser) => {
+        return (adapterName: string) => {
+          if (adapterName === 'IndexedFastaAdapter') {
+            return 'ReferenceSequenceTrack'
+          }
+          return trackTypeGuesser(adapterName)
+        }
+      },
+    )
 
     pluginManager.addAdapterType(
       () =>
         new AdapterType({
           name: 'BgzipFastaAdapter',
           configSchema: bgzipFastaAdapterConfigSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+          },
           getAdapterClass: () =>
             import('./BgzipFastaAdapter/BgzipFastaAdapter').then(
               r => r.default,
@@ -84,10 +180,50 @@ export default class SequencePlugin extends Plugin {
         }),
     )
 
+    pluginManager.addToExtensionPoint(
+      'Core-guessAdapterForLocation',
+      (adapterGuesser: AdapterGuesser) => {
+        return (
+          file: FileLocation,
+          index?: FileLocation,
+          adapterHint?: string,
+        ) => {
+          const regexGuess = /\.(fa|fasta|fas|fna|mfa)\.b?gz$/i
+          const adapterName = 'BgzipFastaAdapter'
+          const fileName = getFileName(file)
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              faiLocation: makeIndex(file, '.fai'),
+              gziLocation: makeIndex(file, '.gzi'),
+            }
+          }
+          return adapterGuesser(file, index, adapterHint)
+        }
+      },
+    )
+    pluginManager.addToExtensionPoint(
+      'Core-guessTrackTypeForLocation',
+      (trackTypeGuesser: TrackTypeGuesser) => {
+        return (adapterName: string) => {
+          if (adapterName === 'BgzipFastaAdapter') {
+            return 'ReferenceSequenceTrack'
+          }
+          return trackTypeGuesser(adapterName)
+        }
+      },
+    )
+
     pluginManager.addAdapterType(
       () =>
         new AdapterType({
           name: 'GCContentAdapter',
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+          },
           ...pluginManager.load(GCContentAdapterF),
         }),
     )