Move change handlers into their own environments (#770)

* Get rid of operations

* Put change handlers in their execution environment

* Properly bind "this"

* Remove InjectModel that got missed

* Update actions/checkout and actions/setup-node

* Combine some files to avoid circular dependencies

Author: garrettjstevens

.github/workflows/cypress_debug.yml

@@ -7,10 +7,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Use Node.js 24.x
-        uses: actions/setup-node@v4
+        uses: actions/setup-node@v6
         with:
           node-version: 24
           cache: yarn

.github/workflows/deploy.yml

@@ -19,9 +19,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Use Node.js 24.x
-        uses: actions/setup-node@v4
+        uses: actions/setup-node@v6
         with:
           node-version: 24
           cache: yarn
@@ -58,7 +58,7 @@ jobs:
     needs: [build]
     steps:
       - name: Check out
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Download built plugin files
         uses: actions/download-artifact@v4
         with:

.github/workflows/pull_request.yml

@@ -11,9 +11,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Use Node.js 24.x
-        uses: actions/setup-node@v4
+        uses: actions/setup-node@v6
         with:
           node-version: 24
           cache: yarn

.github/workflows/push.yml

@@ -13,9 +13,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Use Node.js 24.x
-        uses: actions/setup-node@v4
+        uses: actions/setup-node@v6
         with:
           node-version: 24
           cache: yarn
@@ -32,9 +32,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Use Node.js 24.x
-        uses: actions/setup-node@v4
+        uses: actions/setup-node@v6
         with:
           node-version: 24
           cache: yarn

.github/workflows/reload_demo_data.yml

@@ -21,7 +21,7 @@ jobs:
     environment: ${{ inputs.environment }}
     steps:
       - name: Check out
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Configure AWS credentials
         uses: aws-actions/configure-aws-credentials@v4
         with:

.github/workflows/website.yml

@@ -10,9 +10,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Use Node.js 24.x
-        uses: actions/setup-node@v4
+        uses: actions/setup-node@v6
         with:
           node-version: 24
           cache: yarn

packages/apollo-collaboration-server/src/app.module.ts

@@ -21,7 +21,6 @@ import { FilesModule } from './files/files.module.js'
 import { HealthModule } from './health/health.module.js'
 import { JBrowseModule } from './jbrowse/jbrowse.module.js'
 import { MessagesModule } from './messages/messages.module.js'
-import { OperationsModule } from './operations/operations.module.js'
 import { PluginsModule } from './plugins/plugins.module.js'
 import { RefSeqChunksModule } from './refSeqChunks/refSeqChunks.module.js'
 import { RefSeqsModule } from './refSeqs/refSeqs.module.js'
@@ -165,7 +164,6 @@ async function mongoDBURIFactory(
       useFactory: mongoDBURIFactory,
       inject: [ConfigService],
     }),
-    OperationsModule,
     PluginsModule.registerAsync(),
     RefSeqChunksModule,
     RefSeqsModule,

packages/apollo-collaboration-server/src/assemblies/assemblies.module.ts

@@ -4,7 +4,6 @@ import { MongooseModule } from '@nestjs/mongoose'
 
 import { ChecksModule } from '../checks/checks.module.js'
 import { FeaturesModule } from '../features/features.module.js'
-import { OperationsModule } from '../operations/operations.module.js'
 import { RefSeqsModule } from '../refSeqs/refSeqs.module.js'
 
 import { AssembliesController } from './assemblies.controller.js'
@@ -19,7 +18,6 @@ import { AssembliesService } from './assemblies.service.js'
     ]),
     ChecksModule,
     FeaturesModule,
-    OperationsModule,
     RefSeqsModule,
   ],
   exports: [MongooseModule, AssembliesService],

packages/apollo-collaboration-server/src/assemblies/assemblies.service.ts

@@ -1,10 +1,4 @@
-import {
-  Assembly,
-  type AssemblyDocument,
-  Check,
-  type CheckDocument,
-} from '@apollo-annotation/schemas'
-import { GetAssembliesOperation } from '@apollo-annotation/shared'
+import { Assembly, type AssemblyDocument } from '@apollo-annotation/schemas'
 import {
   Injectable,
   Logger,
@@ -16,7 +10,6 @@ import { Model } from 'mongoose'
 
 import { ChecksService } from '../checks/checks.service.js'
 import { FeaturesService } from '../features/features.service.js'
-import { OperationsService } from '../operations/operations.service.js'
 import { RefSeqsService } from '../refSeqs/refSeqs.service.js'
 
 import { CreateAssemblyDto } from './dto/create-assembly.dto.js'
@@ -27,9 +20,6 @@ export class AssembliesService {
   constructor(
     @InjectModel(Assembly.name)
     private readonly assemblyModel: Model<AssemblyDocument>,
-    @InjectModel(Check.name)
-    private readonly checkModel: Model<CheckDocument>,
-    private readonly operationsService: OperationsService,
     private readonly checksService: ChecksService,
     private readonly featuresService: FeaturesService,
     private readonly refSeqsService: RefSeqsService,
@@ -65,7 +55,7 @@ export class AssembliesService {
     const refSeqs = await this.refSeqsService.findAll({ assembly: _id })
     for (const refSeq of refSeqs) {
       const features = await this.featuresService.findByRange({
-        refSeq: refSeq._id as string,
+        refSeq: refSeq._id.toString(),
         start: 0,
         end: refSeq.length,
       })
@@ -78,9 +68,7 @@ export class AssembliesService {
   }
 
   findAll() {
-    return this.operationsService.executeOperation<GetAssembliesOperation>({
-      typeName: 'GetAssembliesOperation',
-    })
+    return this.assemblyModel.find({ status: 0 }).exec()
   }
 
   async findOne(id: string) {