Temp commit - not working yet

packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts

@@ -9,7 +9,7 @@ import { stopwords } from './fulltext-stopwords'
 import { OntologyDBNode } from './indexeddb-schema'
 import { applyPrefixes } from './prefixes'
 import OntologyStore, { Transaction } from '.'
-import { TextIndexFieldDefinition } from '..'
+import { TextIndexFieldDefinition } from '../../config'
 
 /** special value of jsonPath that gets the IRI (that is, ID) of the node with the configured prefixes applied */
 export const PREFIXED_ID_PATH = '$PREFIXED_ID'

packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/indexeddb-storage.ts

@@ -11,7 +11,7 @@ import {
 } from './indexeddb-schema'
 import { GraphDocument } from './obo-graph-json-schema'
 import OntologyStore from '.'
-import { defaultTextIndexFields } from '..'
+import { defaultTextIndexFields } from '../../config'
 
 /** schema version we are currently on, used for the IndexedDB schema open call */
 const schemaVersion = 2

packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts

@@ -1,4 +1,7 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import {
+  ConfigurationReference,
+  readConfObject,
+} from '@jbrowse/core/configuration'
 import {
   BlobLocation,
   LocalPathLocation,
@@ -11,6 +14,8 @@ import OntologyStore, { OntologyStoreOptions } from './OntologyStore'
 import { OntologyDBNode } from './OntologyStore/indexeddb-schema'
 import { applyPrefixes, expandPrefixes } from './OntologyStore/prefixes'
 
+import ApolloPluginConfigurationSchema from '../config'
+
 export { isDeprecated } from './OntologyStore/indexeddb-schema'
 
 export const OntologyRecordType = types
@@ -54,16 +59,25 @@ export const OntologyManagerType = types
       'GO:': 'http://purl.obolibrary.org/obo/GO_',
       'SO:': 'http://purl.obolibrary.org/obo/SO_',
     }),
+    pluginConfiguration: ConfigurationReference(
+      ApolloPluginConfigurationSchema,
+    ),
   })
+  .views((self) => ({
+    get featureTypeOntologyName(): string {
+      return readConfObject(
+        self.pluginConfiguration,
+        'featureTypeOntologyName',
+      ) as string
+    },
+  }))
   .views((self) => ({
     /**
      * gets the OntologyRecord for the ontology we should be
      * using for feature types (e.g. SO or maybe biotypes)
      **/
     get featureTypeOntology() {
-      // TODO: change this to read some configuration for which feature type ontology
-      // we should be using. currently hardcoded to use SO.
-      return this.findOntology('Sequence Ontology')
+      return this.findOntology(self.featureTypeOntologyName)
     },
 
     findOntology(name: string, version?: string) {
@@ -113,48 +127,6 @@ export const OntologyManagerType = types
 
 export default OntologyManagerType
 
-export interface TextIndexFieldDefinition {
-  /** name to display in the UI for text taken from this field or fields */
-  displayName: string
-  /** JSONPath of the field(s) */
-  jsonPath: string
-}
-export const defaultTextIndexFields: TextIndexFieldDefinition[] = [
-  { displayName: 'Label', jsonPath: '$.lbl' },
-  { displayName: 'Synonym', jsonPath: '$.meta.synonyms[*].val' },
-  { displayName: 'Definition', jsonPath: '$.meta.definition.val' },
-]
-
-export const OntologyRecordConfiguration = ConfigurationSchema(
-  'OntologyRecord',
-  {
-    name: {
-      type: 'string',
-      description: 'the full name of the ontology, e.g. "Gene Ontology"',
-      defaultValue: 'My Ontology',
-    },
-    version: {
-      type: 'string',
-      description: "the ontology's version string",
-      defaultValue: 'unversioned',
-    },
-    source: {
-      type: 'fileLocation',
-      description: "the download location for the ontology's source file",
-      defaultValue: {
-        locationType: 'UriLocation',
-        uri: 'http://example.com/myontology.json',
-      },
-    },
-    textIndexFields: {
-      type: 'frozen',
-      description:
-        'JSON paths for text fields that will be indexed for text searching',
-      defaultValue: defaultTextIndexFields,
-    },
-  },
-)
-
 // eslint disables because of
 // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time
 // eslint-disable-next-line @typescript-eslint/no-empty-interface

packages/jbrowse-plugin-apollo/src/config.ts

@@ -1,10 +1,60 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import { types } from 'mobx-state-tree'
 
-import { OntologyRecordConfiguration } from './OntologyManager'
+export interface TextIndexFieldDefinition {
+  /** name to display in the UI for text taken from this field or fields */
+  displayName: string
+  /** JSONPath of the field(s) */
+  jsonPath: string
+}
+export const defaultTextIndexFields: TextIndexFieldDefinition[] = [
+  { displayName: 'Label', jsonPath: '$.lbl' },
+  { displayName: 'Synonym', jsonPath: '$.meta.synonyms[*].val' },
+  { displayName: 'Definition', jsonPath: '$.meta.definition.val' },
+]
 
-const ApolloPluginConfigurationSchema = ConfigurationSchema('ApolloPlugin', {
-  ontologies: types.array(OntologyRecordConfiguration),
-})
+export const OntologyRecordConfiguration = ConfigurationSchema(
+  'OntologyRecord',
+  {
+    name: {
+      type: 'string',
+      description: 'the full name of the ontology, e.g. "Gene Ontology"',
+      defaultValue: 'My Ontology',
+    },
+    version: {
+      type: 'string',
+      description: "the ontology's version string",
+      defaultValue: 'unversioned',
+    },
+    source: {
+      type: 'fileLocation',
+      description: "the download location for the ontology's source file",
+      defaultValue: {
+        locationType: 'UriLocation',
+        uri: 'http://example.com/myontology.json',
+      },
+    },
+    textIndexFields: {
+      type: 'frozen',
+      description:
+        'JSON paths for text fields that will be indexed for text searching',
+      defaultValue: defaultTextIndexFields,
+    },
+  },
+  { explicitlyTyped: true },
+)
+
+const ApolloPluginConfigurationSchema = ConfigurationSchema(
+  'ApolloPlugin',
+  {
+    ontologies: types.array(OntologyRecordConfiguration),
+    featureTypeOntologyName: {
+      description: 'Name of the feature type ontology',
+      type: 'string',
+      defaultValue: 'Sequence Ontology',
+    },
+  },
+  { explicitlyTyped: true },
+)
 
 export default ApolloPluginConfigurationSchema

packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts

@@ -34,12 +34,11 @@ import {
   InMemoryFileDriver,
 } from '../BackendDrivers'
 import { ChangeManager } from '../ChangeManager'
-import ApolloPluginConfigurationSchema from '../config'
-import {
-  OntologyManagerType,
+import ApolloPluginConfigurationSchema, {
   OntologyRecordConfiguration,
   TextIndexFieldDefinition,
-} from '../OntologyManager'
+} from '../config'
+import { OntologyManagerType } from '../OntologyManager'
 import { ApolloRootModel } from '../types'
 import { autorun } from 'mobx'
 
@@ -136,7 +135,9 @@ export function clientDataStoreFactory(
       desktopFileDriver: isElectron
         ? new DesktopFileDriver(self as unknown as ClientDataStoreType)
         : undefined,
-      ontologyManager: OntologyManagerType.create(),
+      ontologyManager: OntologyManagerType.create({
+        pluginConfiguration: self.pluginConfiguration,
+      }),
     }))
     .actions((self) => ({
       afterCreate() {