@jbrowse/plugin-legacy-jbrowse 1.5.0 → 1.5.4

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "1.5.0",
+  "version": "1.5.4",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
     "jbrowse",
@@ -37,7 +37,7 @@
   "dependencies": {
     "@gmod/nclist": "^0.1.1",
     "buffer-crc32": "^0.2.13",
-    "generic-filehandle": "^2.2.0",
+    "generic-filehandle": "^2.2.2",
     "get-value": "^3.0.1",
     "set-value": "^4.0.1"
   },
@@ -49,5 +49,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "542025578a39bd170c8a166f2568ee7edbd54072"
+  "gitHead": "0c398214590969168694b4ed8e20b595178b9efd"
 }

package/src/JBrowse1Connection/jb1ConfigLoad.ts

@@ -101,9 +101,6 @@ export async function createFinalConfig(
 
 export async function fetchConfigFile(location: JBLocation): Promise<Config> {
   const result = await openLocation(location).readFile('utf8')
-  if (typeof result !== 'string') {
-    throw new Error(`Error opening location: ${location}`)
-  }
   if (isUriLocation(location)) {
     return parseJb1(result, location.uri)
   }

package/src/JBrowse1Connection/jb1ToJb2.ts

@@ -404,7 +404,7 @@ export function convertTrackConfig(
   jb2TrackConfig.adapter = guessAdapter(
     { uri: urlTemplate, locationType: 'UriLocation' },
     undefined,
-    () => urlTemplate,
+    urlTemplate,
   )
   if (!jb2TrackConfig.adapter) {
     throw new Error('Could not determine adapter')
@@ -500,7 +500,7 @@ export async function createRefSeqsAdapter(
       uri: refSeqs.url,
       locationType: 'UriLocation',
     }).readFile('utf8')
-    const refSeqsData: RefSeq[] = JSON.parse(refSeqsJson as string)
+    const refSeqsData: RefSeq[] = JSON.parse(refSeqsJson)
     return refSeqAdapterFromConfig(refSeqsData)
   }
   if ('data' in refSeqs) {

package/src/NCListAdapter/NCListFeature.ts

@@ -11,16 +11,12 @@ const jb1ToJb2 = { seq_id: 'refName' }
  * wrapper to adapt nclist features to act like jbrowse 2 features
  */
 export default class NCListFeature implements Feature {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  private ncFeature: any
-
   private parentHandle?: Feature
 
   private uniqueId: string
 
   // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  constructor(ncFeature: any, parent?: Feature, id?: string) {
-    this.ncFeature = ncFeature
+  constructor(private ncFeature: any, parent?: Feature, id?: string) {
     this.uniqueId = id || ncFeature.id()
     this.parentHandle = parent
   }

package/src/index.ts

@@ -3,11 +3,13 @@ import TextSearchAdapterType from '@jbrowse/core/pluggableElementTypes/TextSearc
 import ConnectionType from '@jbrowse/core/pluggableElementTypes/ConnectionType'
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
+import { FileLocation } from '@jbrowse/core/util/types'
 import { configSchema as ncListAdapterConfigSchema } from './NCListAdapter'
 import {
   AdapterClass as JBrowse1TextSearchAdapterClass,
   configSchema as jbrowse1AdapterConfigSchema,
 } from './JBrowse1TextSeachAdapter'
+import { AdapterGuesser, getFileName } from '@jbrowse/core/util/tracks'
 
 import {
   configSchema as jbrowse1ConfigSchema,
@@ -27,6 +29,27 @@ export default class LegacyJBrowsePlugin extends Plugin {
             import('./NCListAdapter/NCListAdapter').then(r => r.default),
         }),
     )
+    pluginManager.addToExtensionPoint(
+      'Core-guessAdapterForLocation',
+      (adapterGuesser: AdapterGuesser) => {
+        return (
+          file: FileLocation,
+          index?: FileLocation,
+          adapterHint?: string,
+        ) => {
+          const regexGuess = /trackData.jsonz?$/i
+          const adapterName = 'NCListAdapter'
+          const fileName = getFileName(file)
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              rootUrlTemplate: file,
+            }
+          }
+          return adapterGuesser(file, index, adapterHint)
+        }
+      },
+    )
 
     pluginManager.addTextSearchAdapterType(
       () =>