Misc

packages/core/assemblyManager/assembly.ts

@@ -61,7 +61,6 @@ async function loadRefNameMap(
 ) {
   const { sessionId } = options
 
-  console.log('wpw', adapterConfig)
   await when(
     () =>
       !!(

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

@@ -6,60 +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,
-    },
-  },
-  {
-    explicitlyTyped: true,
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    actions: (self: any) => ({
-      setSequenceAdapter(s: Record<string, unknown>) {
-        self.sequenceAdapter = s
+      /**
+       * #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,
       },
-    }),
-  },
-)
-export default configSchema
+    },
+    {
+      explicitlyTyped: true,
+      // eslint-disable-next-line @typescript-eslint/no-explicit-any
+      actions: (self: any) => ({
+        setSequenceAdapter(s: Record<string, unknown>) {
+          self.sequenceAdapter = s
+        },
+      }),
+    },
+  )
+}

plugins/alignments/src/CramAdapter/index.ts

@@ -2,14 +2,14 @@ import PluginManager from '@jbrowse/core/PluginManager'
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
 
 // locals
-import configSchema from './configSchema'
+import configSchemaF from './configSchema'
 
 export default function CramAdapterF(pluginManager: PluginManager) {
   pluginManager.addAdapterType(() => {
     return new AdapterType({
       name: 'CramAdapter',
       displayName: 'CRAM adapter',
-      configSchema,
+      configSchema: configSchemaF(),
       getAdapterClass: () => import('./CramAdapter').then(r => r.default),
     })
   })

plugins/alignments/src/LinearPileupDisplay/model.ts

@@ -188,9 +188,10 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
           trackMaxHeight,
           mismatchAlpha,
           rendererTypeName,
+          rendererType,
         } = self
         const configBlob = getConf(self, ['renderers', rendererTypeName]) || {}
-        return self.rendererType.configSchema.create(
+        return rendererType.configSchema.create(
           {
             ...configBlob,
             ...(featureHeight !== undefined ? { height: featureHeight } : {}),
@@ -218,9 +219,7 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
          */
         renderReady() {
           const view = getContainingView(self) as LGV
-          console.log(self.adapterConfig.sequenceAdapter)
           return (
-            self.adapterConfig.sequenceAdapter &&
             self.modificationsReady &&
             self.currSortBpPerPx === view.bpPerPx &&
             superRenderReady()
@@ -372,7 +371,6 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
               (!sortReady || self.currSortBpPerPx === view.bpPerPx)
             ) {
               const { pos, refName, assemblyName } = sortedBy
-              console.log(adapterConfig)
               // render just the sorted region first
               // @ts-expect-error
               await self.rendererType.renderInClient(rpcManager, {

plugins/linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts

@@ -291,10 +291,6 @@ async function renderBlockEffect(
     return undefined
   }
 
-  console.log(renderArgs?.adapterConfig.sequenceAdapter)
-  if (!renderArgs?.adapterConfig.sequenceAdapter) {
-    return undefined
-  }
   if (displayError) {
     self.setError(displayError)
     return undefined