resolve merge conflict

packages/apollo-cli/package.json

@@ -50,6 +50,7 @@
     "yaml": "^2.3.4"
   },
   "devDependencies": {
+    "@apollo-annotation/shared": "workspace:^",
     "@istanbuljs/esm-loader-hook": "^0.2.0",
     "@istanbuljs/nyc-config-typescript": "^1.0.2",
     "@oclif/test": "^3.1.3",

packages/apollo-cli/src/commands/feature/import.ts

@@ -1,5 +1,6 @@
 import * as fs from 'node:fs'
 
+import { type SerializedAddFeaturesFromFileChange } from '@apollo-annotation/shared'
 import { Flags } from '@oclif/core'
 import { Agent, RequestInit, fetch } from 'undici'
 
@@ -69,7 +70,7 @@ export default class Import extends BaseCommand<typeof Import> {
       'text/x-gff3',
     )
 
-    const body = {
+    const body: SerializedAddFeaturesFromFileChange = {
       typeName: 'AddFeaturesFromFileChange',
       assembly: assembly[0],
       fileId: uploadId,

packages/jbrowse-plugin-apollo/cypress/e2e/editFeature.cy.ts

@@ -1,5 +1,15 @@
 describe('Different ways of editing features', () => {
   before(() => {
+    cy.deleteAssemblies()
+    cy.wrap(
+      window.indexedDB.databases().then((dbs) => {
+        for (const db of dbs) {
+          if (db.name) {
+            window.indexedDB.deleteDatabase(db.name)
+          }
+        }
+      }),
+    )
     cy.addOntologies()
   })
 

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

@@ -1,3 +1,5 @@
+import { IDBPDatabase, openDB } from 'idb'
+
 Cypress.Commands.add('loginAsGuest', () => {
   cy.visit('/?config=http://localhost:3999/jbrowse/config.json')
   cy.contains('Linear Genome View', { timeout: 10_000 }).click()
@@ -16,6 +18,47 @@ Cypress.Commands.add('deleteAssemblies', () => {
   }
 })
 
+type OntologyKey = 'nodes' | 'edges' | 'meta'
+
+async function loadOntology(
+  ontologyGZip: Buffer,
+  name: string,
+  version: number,
+) {
+  const blob = new Blob([ontologyGZip])
+  const ds = new DecompressionStream('gzip')
+  const decompressedStream = blob.stream().pipeThrough(ds)
+  const ontologyBlob = await new Response(decompressedStream).blob()
+  const ontologyJSON = await ontologyBlob.text()
+  const ontologyData = JSON.parse(ontologyJSON) as Record<
+    OntologyKey,
+    unknown[]
+  >
+  await openDB(name, version, {
+    async upgrade(database: IDBPDatabase): Promise<void> {
+      const meta = database.createObjectStore('meta')
+      await meta.add(ontologyData.meta[0], 'meta')
+      const nodes = database.createObjectStore('nodes', { keyPath: 'id' })
+      nodes.createIndex('by-label', 'lbl')
+      nodes.createIndex('by-type', 'type')
+      nodes.createIndex('by-synonym', ['meta', 'synonyms', 'val'])
+      nodes.createIndex('full-text-words', 'fullTextWords', {
+        multiEntry: true,
+      })
+      for (const node of ontologyData.nodes) {
+        await nodes.add(node)
+      }
+      const edges = database.createObjectStore('edges', { autoIncrement: true })
+      edges.createIndex('by-subject', 'sub')
+      edges.createIndex('by-object', 'obj')
+      edges.createIndex('by-predicate', 'pred')
+      for (const edge of ontologyData.edges) {
+        await edges.add(edge)
+      }
+    },
+  })
+}
+
 Cypress.Commands.add('addOntologies', () => {
   cy.deleteMany({}, { collection: 'jbrowseconfigs' })
   cy.insertOne(
@@ -45,6 +88,12 @@ Cypress.Commands.add('addOntologies', () => {
     },
     { collection: 'jbrowseconfigs' },
   )
+  cy.readFile('cypress/data/go.json.gz', null).then((goGZip: Buffer) => {
+    cy.wrap<Promise<void>>(
+      loadOntology(goGZip, 'Apollo Ontology "Gene Ontology" "full"', 2),
+      { timeout: 120_000 },
+    )
+  })
 })
 
 Cypress.Commands.add('addAssemblyFromGff', (assemblyName, fin) => {

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

@@ -40,7 +40,7 @@ export const OntologyRecordType = types
       addDisposer(
         self,
         autorun(() => {
-          // this.initDataStore()
+          this.initDataStore()
         }),
       )
     },

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

@@ -142,7 +142,7 @@ export function clientDataStoreFactory(
       afterCreate() {
         addDisposer(
           self,
-          autorun((reaction) => {
+          autorun(() => {
             // Merge in the ontologies from our plugin configuration.
             // Ontologies of a given name that are already in the session
             // take precedence over the ontologies in the configuration.
@@ -171,7 +171,6 @@ export function clientDataStoreFactory(
             }
             // TODO: add in any configured ontology prefixes that we don't already
             // have in the session (or hardcoded in the model)
-            reaction.dispose()
           }),
         )
       },

yarn.lock

@@ -119,6 +119,7 @@ __metadata:
   version: 0.0.0-use.local
   resolution: "@apollo-annotation/cli@workspace:packages/apollo-cli"
   dependencies:
+    "@apollo-annotation/shared": "workspace:^"
     "@inquirer/input": "npm:^1.2.14"
     "@inquirer/password": "npm:^1.1.14"
     "@inquirer/select": "npm:^1.3.1"