Make ontology for feature types configurable

[garrettjstevens]

This should be configurable in the JBrowse config.json in the ApolloPlugin section:

{
  "configuration": {
    "ApolloPlugin": {
      "featureTypeOntology": "Some Ontology Name",
      "ontologies": [
        {
          "name": "Some Ontology Name",
          "version": "full",
          "source": {
            "uri": "path/to/some_ontology.json",
            "locationType": "UriLocation"
          }
        },
      ]
    }
  }
}

You can add a slot to the ApolloPlugin schema like this:

--- a/packages/jbrowse-plugin-apollo/src/config.ts
+++ b/packages/jbrowse-plugin-apollo/src/config.ts
@@ -5,6 +5,11 @@ import { OntologyRecordConfiguration } from './OntologyManager'
 
 const ApolloPluginConfigurationSchema = ConfigurationSchema('ApolloPlugin', {
   ontologies: types.array(OntologyRecordConfiguration),
+  featureTypeOntologyName: {
+    description: 'Name of the feature type ontology',
+    type: 'string',
+    defaultValue: 'Sequence Ontology',
+  },
 })
 
 export default ApolloPluginConfigurationSchema

And then read it with something like this:

--- a/packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts
+++ b/packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts
@@ -1,15 +1,26 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import {
+  ConfigurationSchema,
+  readConfObject,
+} from '@jbrowse/core/configuration'
 import {
   BlobLocation,
   LocalPathLocation,
   UriLocation,
 } from '@jbrowse/core/util/types/mst'
 import { autorun } from 'mobx'
-import { Instance, addDisposer, getSnapshot, types } from 'mobx-state-tree'
+import {
+  Instance,
+  addDisposer,
+  getRoot,
+  getSnapshot,
+  types,
+} from 'mobx-state-tree'
 
 import OntologyStore, { OntologyStoreOptions } from './OntologyStore'
 import { OntologyDBNode } from './OntologyStore/indexeddb-schema'
 import { applyPrefixes, expandPrefixes } from './OntologyStore/prefixes'
+import { ApolloRootModel } from '../types'
+import ApolloPluginConfigurationSchema from '../config'
 
 export { isDeprecated } from './OntologyStore/indexeddb-schema'
 
@@ -61,9 +72,15 @@ export const OntologyManagerType = types
      * 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')
+      const pluginConfiguration = getRoot<ApolloRootModel>(self).jbrowse
+        .configuration.ApolloPlugin as Instance<
+        typeof ApolloPluginConfigurationSchema
+      >
+      const featureTypeOntologyName = readConfObject(
+        pluginConfiguration,
+        'featureTypeOntologyName',
+      )
+      return this.findOntology(featureTypeOntologyName)
     },
 
     findOntology(name: string, version?: string) {

[garrettjstevens]

It turns out getRoot doesn't work the way I thought it would here, so instead let's try passing the configuration into the ontologyManager like this:

--- a/packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts
+++ b/packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts
@@ -1,4 +1,4 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import { ConfigurationSchema, readConfObject } from '@jbrowse/core/configuration'
 import {
   BlobLocation,
   LocalPathLocation,
@@ -7,6 +7,8 @@ import {
 import { autorun } from 'mobx'
 import { Instance, addDisposer, getSnapshot, types } from 'mobx-state-tree'
 
+import ApolloPluginConfigurationSchema from '../config'
+
 import OntologyStore, { OntologyStoreOptions } from './OntologyStore'
 import { OntologyDBNode } from './OntologyStore/indexeddb-schema'
 import { applyPrefixes, expandPrefixes } from './OntologyStore/prefixes'
@@ -54,16 +56,23 @@ export const OntologyManagerType = types
       'GO:': 'http://purl.obolibrary.org/obo/GO_',
       'SO:': 'http://purl.obolibrary.org/obo/SO_',
     }),
+    pluginConfiguration: 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) {
--- a/packages/jbrowse-plugin-apollo/src/config.ts
+++ b/packages/jbrowse-plugin-apollo/src/config.ts
@@ -5,6 +5,11 @@ import { OntologyRecordConfiguration } from './OntologyManager'
 
 const ApolloPluginConfigurationSchema = ConfigurationSchema('ApolloPlugin', {
   ontologies: types.array(OntologyRecordConfiguration),
+  featureTypeOntologyName: {
+    description: 'Name of the feature type ontology',
+    type: 'string',
+    defaultValue: 'Sequence Ontology',
+  },
 })
 
 export default ApolloPluginConfigurationSchema
--- a/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts
+++ b/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts
@@ -136,7 +136,9 @@ 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() {

[garrettjstevens]

@dariober, after the issues we saw earlier today with the most recent approach, I tried a different approach. See my branch here: configurable-ontology-issue458-gs.

Could you try this branch out and see if it works on your end?