Get rid of operations

Author: garrettjstevens

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

@@ -2,9 +2,7 @@ import {
   Assembly,
   type AssemblyDocument,
   Check,
-  type CheckDocument,
 } from '@apollo-annotation/schemas'
-import { GetAssembliesOperation } from '@apollo-annotation/shared'
 import {
   Injectable,
   Logger,
@@ -16,7 +14,6 @@ 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'
@@ -28,8 +25,6 @@ export class AssembliesService {
     @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,
@@ -78,9 +73,7 @@ export class AssembliesService {
   }
 
   findAll() {
-    return this.operationsService.executeOperation<GetAssembliesOperation>({
-      typeName: 'GetAssembliesOperation',
-    })
+    return this.assemblyModel.find({ status: 0 }).exec()
   }
 
   async findOne(id: string) {

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

@@ -3,14 +3,13 @@ import {
   type FeatureDocument,
   FeatureSchema,
 } from '@apollo-annotation/schemas'
-import { Module, forwardRef } from '@nestjs/common'
+import { Module } from '@nestjs/common'
 import { MongooseModule, getConnectionToken } from '@nestjs/mongoose'
 import type { Connection } from 'mongoose'
 import idValidator from 'mongoose-id-validator'
 
 import { ChecksModule } from '../checks/checks.module.js'
 import { ChecksService } from '../checks/checks.service.js'
-import { OperationsModule } from '../operations/operations.module.js'
 import { RefSeqsModule } from '../refSeqs/refSeqs.module.js'
 import { SequenceModule } from '../sequence/sequence.module.js'
 
@@ -22,7 +21,6 @@ import { FeaturesService } from './features.service.js'
   providers: [FeaturesService],
   imports: [
     ChecksModule,
-    forwardRef(() => OperationsModule),
     RefSeqsModule,
     SequenceModule,
     MongooseModule.forFeatureAsync([

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

@@ -6,14 +6,12 @@ import {
   RefSeq,
   type RefSeqDocument,
 } from '@apollo-annotation/schemas'
-import { GetFeaturesOperation } from '@apollo-annotation/shared'
 import { Injectable, Logger, NotFoundException } from '@nestjs/common'
 import { InjectModel } from '@nestjs/mongoose'
 import { Model } from 'mongoose'
 
 import { ChecksService } from '../checks/checks.service.js'
 import type { FeatureRangeSearchDto } from '../entity/gff3Object.dto.js'
-import { OperationsService } from '../operations/operations.service.js'
 
 import type {
   FeatureCountRequest,
@@ -23,7 +21,6 @@ import type {
 @Injectable()
 export class FeaturesService {
   constructor(
-    private readonly operationsService: OperationsService,
     private readonly checksService: ChecksService,
     @InjectModel(Feature.name)
     private readonly featureModel: Model<FeatureDocument>,
@@ -226,13 +223,14 @@ export class FeaturesService {
   }
 
   async findByRange(searchDto: FeatureRangeSearchDto) {
-    const featureDocs =
-      await this.operationsService.executeOperation<GetFeaturesOperation>({
-        typeName: 'GetFeaturesOperation',
+    const featureDocs = await this.featureModel
+      .find({
         refSeq: searchDto.refSeq,
-        start: searchDto.start,
-        end: searchDto.end,
+        min: { $lte: searchDto.end },
+        max: { $gte: searchDto.start },
+        status: 0,
       })
+      .exec()
     for (const featureDoc of featureDocs) {
       await this.checksService.checkFeature(featureDoc)
     }

packages/apollo-collaboration-server/src/main.ts

@@ -7,7 +7,6 @@ import {
   type Check,
   changeRegistry,
   checkRegistry,
-  operationRegistry,
 } from '@apollo-annotation/common'
 import { CheckSchema } from '@apollo-annotation/schemas'
 import {
@@ -16,7 +15,6 @@ import {
   ParentChildValidation,
   TranscriptCheck,
   changes,
-  operations,
   validationRegistry,
 } from '@apollo-annotation/shared'
 import type { LogLevel } from '@nestjs/common'
@@ -75,10 +73,6 @@ async function bootstrap() {
     changeRegistry.registerChange(changeName, change)
   }
 
-  for (const [operationName, operation] of Object.entries(operations)) {
-    operationRegistry.registerOperation(operationName, operation)
-  }
-
   const cdsCheck = new CDSCheck()
   checkRegistry.registerCheck(cdsCheck.name, cdsCheck)