Add sequence adapter config in afterAttach for baseTrackConfig

packages/core/assemblyManager/assembly.ts

@@ -60,10 +60,19 @@ async function loadRefNameMap(
   signal?: AbortSignal,
 ) {
   const { sessionId } = options
-  await when(() => !!(assembly.regions && assembly.refNameAliases), {
-    signal,
-    name: 'when assembly ready',
-  })
+
+  await when(
+    () =>
+      !!(
+        assembly.regions &&
+        assembly.refNameAliases &&
+        adapterConfig.sequenceAdapter
+      ),
+    {
+      signal,
+      name: 'when assembly ready',
+    },
+  )
 
   const refNames = (await assembly.rpcManager.call(
     sessionId || 'assemblyRpc',
@@ -82,10 +91,9 @@ async function loadRefNameMap(
   }
 
   const refNameMap = Object.fromEntries(
-    refNames.map(name => {
-      checkRefName(name)
-      return [assembly.getCanonicalRefName(name), name]
-    }),
+    refNames
+      .map(name => checkRefName(name))
+      .map(name => [assembly.getCanonicalRefName(name), name]),
   )
 
   // make the reversed map too
@@ -107,6 +115,7 @@ function checkRefName(refName: string) {
   if (!refNameRegex.test(refName)) {
     throw new Error(`Encountered invalid refName: "${refName}"`)
   }
+  return refName
 }
 
 type RefNameAliases = Record<string, string | undefined>

packages/core/pluggableElementTypes/models/baseTrackConfig.ts

@@ -1,6 +1,14 @@
-import { types, Instance } from 'mobx-state-tree'
-import { ConfigurationSchema } from '../../configuration'
+import {
+  types,
+  Instance,
+  getSnapshot,
+  getRoot,
+  addDisposer,
+} from 'mobx-state-tree'
+import { ConfigurationSchema, readConfObject } from '../../configuration'
 import PluginManager from '../../PluginManager'
+import { AssemblyManager, notEmpty } from '../../util'
+import { autorun } from 'mobx'
 
 /**
  * #config BaseTrack
@@ -81,6 +89,14 @@ export function createBaseTrackConfig(pluginManager: PluginManager) {
         ),
       }),
 
+      /**
+       * #slot
+       */
+      sequenceAdapters: {
+        type: 'frozen',
+        defaultValue: {},
+      },
+
       /**
        * #slot
        */
@@ -180,20 +196,51 @@ export function createBaseTrackConfig(pluginManager: PluginManager) {
       explicitlyTyped: true,
       // eslint-disable-next-line @typescript-eslint/no-explicit-any
       actions: (self: any) => ({
-        addDisplayConf(conf: { type: string; displayId: string }) {
-          const { type } = conf
+        forceAddDisplay(c: { type: string; displayId: string }) {
+          self.displays.push(c)
+          return self.displays.at(-1)
+        },
+        addDisplayConf(c: { type: string; displayId: string }) {
+          const { type } = c
           if (!type) {
             throw new Error(`unknown display type ${type}`)
           }
-          const display = self.displays.find(
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            (d: any) => d?.displayId === conf.displayId,
+          return (
+            self.displays.find(
+              (d: { displayId: string }) => d?.displayId === c.displayId,
+            ) ?? self.forceAddDisplay(c)
+          )
+        },
+        setSequenceAdapters(a: Record<string, unknown>) {
+          self.sequenceAdapters = a
+        },
+        afterAttach() {
+          addDisposer(
+            self,
+            autorun(() => {
+              const { assemblyManager } = getRoot<{
+                assemblyManager: AssemblyManager
+              }>(self)
+              const assemblyNames = readConfObject(
+                self,
+                'assemblyNames',
+              ) as string[]
+              self.setSequenceAdapters(
+                assemblyNames
+                  .map(a => {
+                    const conf = assemblyManager.get(a)?.configuration
+                    return conf ? ([a, getSnapshot(conf)] as const) : undefined
+                  })
+                  .filter(notEmpty),
+              )
+              const c = assemblyManager.get(assemblyNames[0])?.configuration
+              if (c) {
+                self.adapter.setSequenceAdapter?.(
+                  readConfObject(c.sequence.adapter),
+                )
+              }
+            }),
           )
-          if (display) {
-            return display
-          }
-          const length = self.displays.push(conf)
-          return self.displays[length - 1]
         },
       }),
     },

packages/product-core/src/ui/AboutDialogContents.tsx

@@ -86,7 +86,13 @@ export default function AboutContents({
         ) : null}
         <Attributes
           attributes={confPostExt}
-          omit={['displays', 'baseUri', 'refNames', 'formatAbout']}
+          omit={[
+            'displays',
+            'baseUri',
+            'refNames',
+            'formatAbout',
+            'sequenceAdapters',
+          ]}
           hideUris={hideUris}
         />
       </BaseCard>

plugins/alignments/src/BamAdapter/configSchema.ts

@@ -5,61 +5,59 @@ import { types } from 'mobx-state-tree'
  * #config BamAdapter
  * used to configure BAM adapter
  */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const configSchema = ConfigurationSchema(
-  'BamAdapter',
-  {
-    /**
-     * #slot
-     */
-    bamLocation: {
-      type: 'fileLocation',
-      defaultValue: { uri: '/path/to/my.bam', locationType: 'UriLocation' },
-    },
+export default function configSchemaF() {
+  return ConfigurationSchema(
+    'BamAdapter',
+    {
+      /**
+       * #slot
+       */
+      bamLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.bam', locationType: 'UriLocation' },
+      },
 
-    index: ConfigurationSchema('BamIndex', {
+      index: ConfigurationSchema('BamIndex', {
+        /**
+         * #slot index.indexType
+         */
+        indexType: {
+          model: types.enumeration('IndexType', ['BAI', 'CSI']),
+          type: 'stringEnum',
+          defaultValue: 'BAI',
+        },
+        /**
+         * #slot index.location
+         */
+        location: {
+          type: 'fileLocation',
+          defaultValue: {
+            uri: '/path/to/my.bam.bai',
+            locationType: 'UriLocation',
+          },
+        },
+      }),
       /**
-       * #slot index.indexType
+       * #slot
        */
-      indexType: {
-        model: types.enumeration('IndexType', ['BAI', 'CSI']),
-        type: 'stringEnum',
-        defaultValue: 'BAI',
+      fetchSizeLimit: {
+        type: 'number',
+        description:
+          'size to fetch in bytes over which to display a warning to the user that too much data will be fetched',
+        defaultValue: 5_000_000,
       },
       /**
-       * #slot index.location
+       * #slot
+       * generally refers to the reference genome assembly's sequence adapter
+       * currently needs to be manually added
        */
-      location: {
-        type: 'fileLocation',
-        defaultValue: {
-          uri: '/path/to/my.bam.bai',
-          locationType: 'UriLocation',
-        },
+      sequenceAdapter: {
+        type: 'frozen',
+        description:
+          'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
+        defaultValue: null,
       },
-    }),
-    /**
-     * #slot
-     */
-    fetchSizeLimit: {
-      type: 'number',
-      description:
-        'size to fetch in bytes over which to display a warning to the user that too much data will be fetched',
-      defaultValue: 5_000_000,
-    },
-    /**
-     * #slot
-     * generally refers to the reference genome assembly's sequence adapter
-     * currently needs to be manually added
-     */
-    sequenceAdapter: {
-      type: 'frozen',
-      description:
-        'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
-      defaultValue: null,
     },
-  },
-  { explicitlyTyped: true },
-)
-
-export default configSchema
+    { explicitlyTyped: true },
+  )
+}

plugins/alignments/src/BamAdapter/index.ts

@@ -1,13 +1,13 @@
 import PluginManager from '@jbrowse/core/PluginManager'
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import configSchema from './configSchema'
+import configSchemaF from './configSchema'
 
 export default function BamAdapterF(pluginManager: PluginManager) {
   pluginManager.addAdapterType(() => {
     return new AdapterType({
       name: 'BamAdapter',
       displayName: 'BAM adapter',
-      configSchema,
+      configSchema: configSchemaF(),
       getAdapterClass: () => import('./BamAdapter').then(r => r.default),
     })
   })

plugins/alignments/src/CramAdapter/configSchema.ts

@@ -6,52 +6,62 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration'
  */
 function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
 
-const configSchema = ConfigurationSchema(
-  'CramAdapter',
-  {
-    /**
-     * #slot fetchSizeLimit
-     */
-    fetchSizeLimit: {
-      type: 'number',
-      description:
-        'size in bytes over which to display a warning to the user that too much data will be fetched',
-      defaultValue: 3_000_000,
-    },
+export default function configSchemaF() {
+  return ConfigurationSchema(
+    'CramAdapter',
+    {
+      /**
+       * #slot fetchSizeLimit
+       */
+      fetchSizeLimit: {
+        type: 'number',
+        description:
+          'size in bytes over which to display a warning to the user that too much data will be fetched',
+        defaultValue: 3_000_000,
+      },
 
-    /**
-     * #slot cramLocation
-     */
-    cramLocation: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/my.cram',
-        locationType: 'UriLocation',
+      /**
+       * #slot cramLocation
+       */
+      cramLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+          uri: '/path/to/my.cram',
+          locationType: 'UriLocation',
+        },
       },
-    },
 
-    /**
-     * #slot craiLocation
-     */
-    craiLocation: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/my.cram.crai',
-        locationType: 'UriLocation',
+      /**
+       * #slot craiLocation
+       */
+      craiLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+          uri: '/path/to/my.cram.crai',
+          locationType: 'UriLocation',
+        },
       },
-    },
 
-    /**
-     * #slot sequenceAdapter
-     * generally refers to the reference genome assembly's sequence adapter
-     * currently needs to be manually added
-     */
-    sequenceAdapter: {
-      type: 'frozen',
-      description: 'sequence data adapter',
-      defaultValue: null,
+      /**
+       * #slot sequenceAdapter
+       * generally refers to the reference genome assembly's sequence adapter
+       * this can be manually added via the baseTrackConfig autorun, or manually
+       * specified
+       */
+      sequenceAdapter: {
+        type: 'frozen',
+        description: 'sequence data adapter',
+        defaultValue: null,
+      },
+    },
+    {
+      explicitlyTyped: true,
+      // eslint-disable-next-line @typescript-eslint/no-explicit-any
+      actions: (self: any) => ({
+        setSequenceAdapter(s: Record<string, unknown>) {
+          self.sequenceAdapter = s
+        },
+      }),
     },
-  },
-  { explicitlyTyped: true },
-)
-export default configSchema
+  )
+}