Add a default location for feature type ontology

shashankbrgowda · Oct 20, 2024 · 7cc023b · 7cc023b
1 parent b8a4e94
commit 7cc023b
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diff --git a/packages/apollo-collaboration-server/.development.env b/packages/apollo-collaboration-server/.development.env
@@ -57,6 +57,7 @@ DESCRIPTION=A server for Apollo development purposes
 # URL (relative or absolute) of the Apollo JBrowse plugin.
 # Defaults to relative URL 'apollo.js'
 PLUGIN_LOCATION=http://localhost:9000/dist/jbrowse-plugin-apollo.umd.development.js
+FEATURE_TYPE_ONTOLOGY_LOCATION=test_data/so-v3.1.json
 
 # Application port, defaults to 3999
 # PORT=3999

diff --git a/packages/apollo-collaboration-server/src/app.module.ts b/packages/apollo-collaboration-server/src/app.module.ts
@@ -55,6 +55,7 @@ const validationSchema = Joi.object({
   SESSION_SECRET_FILE: Joi.string(),
   // Optional
   DESCRIPTION: Joi.string(),
+  FEATURE_TYPE_ONTOLOGY_LOCATION: Joi.string(),
   PLUGIN_LOCATION: Joi.string(),
   ALLOW_ROOT_USER: Joi.boolean().default(false),
   ROOT_USER_NAME: Joi.string(),

diff --git a/packages/apollo-collaboration-server/src/jbrowse/jbrowse.service.ts b/packages/apollo-collaboration-server/src/jbrowse/jbrowse.service.ts
@@ -25,6 +25,7 @@ export class JBrowseService {
         NAME: string
         DESCRIPTION?: string
         PLUGIN_LOCATION?: string
+        FEATURE_TYPE_ONTOLOGY_LOCATION?: string
       },
       true
     >,
@@ -38,6 +39,10 @@ export class JBrowseService {
   }
 
   getConfiguration() {
+    const feature_type_ontology_location =
+      this.configService.get('FEATURE_TYPE_ONTOLOGY_LOCATION', {
+        infer: true,
+      }) ?? 'sequence_ontology.json'
     return {
       theme: {
         palette: {
@@ -55,6 +60,17 @@ export class JBrowseService {
           },
         },
       },
+      ApolloPlugin: {
+        ontologies: [
+          {
+            name: 'Sequence Ontology',
+            source: {
+              uri: feature_type_ontology_location,
+              locationType: 'UriLocation',
+            },
+          },
+        ],
+      },
     }
   }