Allow opening "synteny tracks" from the default Add track workflow

packages/core/data_adapters/CytobandAdapter/index.ts

@@ -9,6 +9,9 @@ export default function CytobandAdapterF(pluginManager: PluginManager) {
       new AdapterType({
         name: 'CytobandAdapter',
         configSchema,
+        adapterMetadata: {
+          hiddenFromGUI: true,
+        },
         getAdapterClass: () => import('./CytobandAdapter').then(f => f.default),
       }),
   )

packages/core/pluggableElementTypes/AddTrackWorkflowType.ts

@@ -5,8 +5,6 @@ import PluggableElementBase from './PluggableElementBase'
 import type { IAnyModelType } from 'mobx-state-tree'
 
 type BasicComponent = React.ComponentType<{
-  // TODO: can we use AbstractViewModel here?
-
   model: any
 }>
 type AddTrackWorkflowComponentType =

packages/core/ui/AssemblySelector.tsx

@@ -4,7 +4,6 @@ import { MenuItem, TextField } from '@mui/material'
 import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
 
-import { getConf } from '../configuration'
 import { useLocalStorage } from '../util'
 
 import type { AbstractSessionModel } from '../util'
@@ -19,13 +18,15 @@ const useStyles = makeStyles()({
 const AssemblySelector = observer(function ({
   session,
   onChange,
+  label = 'Assembly',
   selected,
   InputProps,
   TextFieldProps,
   localStorageKey,
   helperText = 'Select assembly to view',
 }: {
   session: AbstractSessionModel
+  label?: string
   helperText?: string
   onChange: (arg: string) => void
   selected?: string
@@ -66,7 +67,7 @@ const AssemblySelector = observer(function ({
     <TextField
       select
       data-testid="assembly-selector-textfield"
-      label="Assembly"
+      label={label}
       variant="outlined"
       helperText={error || helperText}
       value={selection || ''}
@@ -84,15 +85,11 @@ const AssemblySelector = observer(function ({
         },
       }}
     >
-      {assemblyNames.map(name => {
-        const assembly = assemblyManager.get(name)
-        const displayName = assembly ? getConf(assembly, 'displayName') : ''
-        return (
-          <MenuItem key={name} value={name}>
-            {displayName || name}
-          </MenuItem>
-        )
-      })}
+      {assemblyNames.map(name => (
+        <MenuItem key={name} value={name}>
+          {assemblyManager.get(name)?.displayName || name}
+        </MenuItem>
+      ))}
     </TextField>
   )
 })

packages/core/util/index.ts

@@ -1424,6 +1424,14 @@ export function localStorageGetBoolean(key: string, defaultVal: boolean) {
   )
 }
 
+export function testAdapter(
+  fileName: string,
+  regex: RegExp,
+  adapterHint: string | undefined,
+  expected: string,
+) {
+  return (regex.test(fileName) && !adapterHint) || adapterHint === expected
+}
 export {
   type Feature,
   type SimpleFeatureSerialized,

plugins/alignments/src/GuessAlignmentsTypes/index.ts

@@ -1,3 +1,4 @@
+import { testAdapter } from '@jbrowse/core/util'
 import {
   getFileName,
   makeIndex,
@@ -20,53 +21,29 @@ export default function GuessAlignmentsTypesF(pluginManager: PluginManager) {
         index?: FileLocation,
         adapterHint?: string,
       ) => {
-        const regexGuess = /\.cram$/i
-        const adapterName = 'CramAdapter'
-        const fileName = getFileName(file)
-        const obj = {
-          type: adapterName,
-          cramLocation: file,
-          craiLocation: index || makeIndex(file, '.crai'),
-        }
-        if (regexGuess.test(fileName) && !adapterHint) {
-          return obj
-        }
-        if (adapterHint === adapterName) {
-          return obj
-        }
-        return adapterGuesser(file, index, adapterHint)
-      }
-    },
-  )
-
-  pluginManager.addToExtensionPoint(
-    'Core-guessAdapterForLocation',
-    (adapterGuesser: AdapterGuesser) => {
-      return (
-        file: FileLocation,
-        index?: FileLocation,
-        adapterHint?: string,
-      ) => {
-        const regexGuess = /\.bam$/i
-        const adapterName = 'BamAdapter'
         const fileName = getFileName(file)
         const indexName = index && getFileName(index)
 
-        const obj = {
-          type: adapterName,
-          bamLocation: file,
-          index: {
-            location: index || makeIndex(file, '.bai'),
-            indexType: makeIndexType(indexName, 'CSI', 'BAI'),
-          },
-        }
-        if (regexGuess.test(fileName) && !adapterHint) {
-          return obj
-        }
-        if (adapterHint === adapterName) {
-          return obj
+        if (testAdapter(fileName, /\.bam$/i, adapterHint, 'BamAdapter')) {
+          return {
+            type: 'BamAdapter',
+            bamLocation: file,
+            index: {
+              location: index || makeIndex(file, '.bai'),
+              indexType: makeIndexType(indexName, 'CSI', 'BAI'),
+            },
+          }
+        } else if (
+          testAdapter(fileName, /\.cram$/i, adapterHint, 'CramAdapter')
+        ) {
+          return {
+            type: 'CramAdapter',
+            cramLocation: file,
+            craiLocation: index || makeIndex(file, '.crai'),
+          }
+        } else {
+          return adapterGuesser(file, index, adapterHint)
         }
-        return adapterGuesser(file, index, adapterHint)
       }
     },
   )

plugins/bed/src/GuessAdapter/index.ts

@@ -0,0 +1,101 @@
+import { testAdapter } from '@jbrowse/core/util'
+import {
+  getFileName,
+  makeIndex,
+  makeIndexType,
+} from '@jbrowse/core/util/tracks'
+
+import type PluginManager from '@jbrowse/core/PluginManager'
+import type {
+  AdapterGuesser,
+  TrackTypeGuesser,
+} from '@jbrowse/core/util/tracks'
+import type { FileLocation } from '@jbrowse/core/util/types'
+
+export default function GuessAdapterF(pluginManager: PluginManager) {
+  pluginManager.addToExtensionPoint(
+    'Core-guessAdapterForLocation',
+    (adapterGuesser: AdapterGuesser) => {
+      return (
+        file: FileLocation,
+        index?: FileLocation,
+        adapterHint?: string,
+      ) => {
+        const fileName = getFileName(file)
+        const indexName = index && getFileName(index)
+        if (
+          testAdapter(fileName, /\.bedpe(\.gz)?$/i, adapterHint, 'BedpeAdapter')
+        ) {
+          return {
+            type: 'BedpeAdapter',
+            bedpeLocation: file,
+          }
+        } else if (
+          testAdapter(fileName, /\.bb$/i, adapterHint, 'BigBedAdapter') ||
+          testAdapter(fileName, /\.bigBed?$/i, adapterHint, 'BigBedAdapter')
+        ) {
+          return {
+            type: 'BigBedAdapter',
+            bigBedLocation: file,
+          }
+        } else if (
+          testAdapter(fileName, /\.bed$/i, adapterHint, 'BedAdapter')
+        ) {
+          return {
+            type: 'BedAdapter',
+            bedLocation: file,
+          }
+        } else if (
+          testAdapter(fileName, /\.bg$/i, adapterHint, 'BedGraphAdapter')
+        ) {
+          return {
+            type: 'BedGraphAdapter',
+            bedGraphLocation: file,
+          }
+        } else if (
+          testAdapter(
+            fileName,
+            /\.bg(\.gz)?$/i,
+            adapterHint,
+            'BedGraphTabixAdapter',
+          )
+        ) {
+          return {
+            type: 'BedGraphTabixAdapter',
+            bedGraphGzLocation: file,
+            index: {
+              location: index || makeIndex(file, '.tbi'),
+              indexType: makeIndexType(indexName, 'CSI', 'TBI'),
+            },
+          }
+        } else if (
+          testAdapter(fileName, /\.bed\.gz$/i, adapterHint, 'BedTabixAdapter')
+        ) {
+          return {
+            type: 'BedTabixAdapter',
+            bedGzLocation: file,
+            index: {
+              location: index || makeIndex(file, '.tbi'),
+              indexType: makeIndexType(indexName, 'CSI', 'TBI'),
+            },
+          }
+        } else {
+          return adapterGuesser(file, index, adapterHint)
+        }
+      }
+    },
+  )
+
+  pluginManager.addToExtensionPoint(
+    'Core-guessTrackTypeForLocation',
+    (trackTypeGuesser: TrackTypeGuesser) => (adapterName: string) => {
+      return (
+        {
+          BedpeAdapter: 'VariantTrack',
+          BedGraphAdapter: 'QuantitativeTrack',
+          BedGraphTabixAdapter: 'QuantitativeTrack',
+        }[adapterName] || trackTypeGuesser(adapterName)
+      )
+    },
+  )
+}