Update SO definitions

Author: garrettjstevens

packages/apollo-collaboration-server/.development.env

@@ -11,7 +11,7 @@ MICROSOFT_CLIENT_ID=fabdd045-163c-4712-9d40-dbbb043b3090
 MICROSOFT_CLIENT_SECRET=~Gr8Q~h6RTU7SMC-fjNxXy_~nabTD-ME_rFyLa.M
 DESCRIPTION=A server for Apollo development purposes
 PLUGIN_LOCATION=http://localhost:9000/dist/jbrowse-plugin-apollo.umd.development.js
-FEATURE_TYPE_ONTOLOGY_LOCATION=http://localhost:9000/test_data/so-v3.1.json
+FEATURE_TYPE_ONTOLOGY_LOCATION=http://localhost:9000/test_data/so-2024-11-18.json
 LOG_LEVELS=error,warn,log,debug
 ALLOW_ROOT_USER=true
 ROOT_USER_PASSWORD=password

packages/jbrowse-plugin-apollo/cypress/data/so.json.gz

@@ -76,7 +76,7 @@ Cypress.Commands.add('addOntologies', () => {
               name: 'Sequence Ontology',
               version: 'unversioned',
               source: {
-                uri: 'http://localhost:9000/test_data/so-v3.1.json',
+                uri: 'http://localhost:9000/test_data/so-2024-11-18.json',
                 locationType: 'UriLocation',
               },
             },
@@ -86,6 +86,8 @@ Cypress.Commands.add('addOntologies', () => {
     },
     { collection: 'jbrowseconfigs' },
   )
+  // so.json.gz was generated from an IndexedDB dump using the script found at
+  // https://gist.github.com/loilo/ed43739361ec718129a15ae5d531095b
   cy.readFile('cypress/data/so.json.gz', null).then((soGZip: Buffer) => {
     cy.wrap<Promise<void>>(
       loadOntology(

packages/jbrowse-plugin-apollo/cypress/support/commands.ts

@@ -30,7 +30,7 @@
           "name": "Sequence Ontology",
           "version": "3.1",
           "source": {
-            "uri": "test_data/so-v3.1.json",
+            "uri": "test_data/so-2024-11-18.json",
             "locationType": "UriLocation"
           }
         }