Add default checks to assembly when it is created

GMOD · Oct 21, 2024 · 144fef9 · 144fef9
1 parent 83c1409
commit 144fef9
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Showing 9 changed files with 42 additions and 7 deletions.
diff --git a/packages/apollo-collaboration-server/src/changes/changes.module.ts b/packages/apollo-collaboration-server/src/changes/changes.module.ts
@@ -6,6 +6,7 @@ import idValidator from 'mongoose-id-validator'
 
 import { AssembliesModule } from '../assemblies/assemblies.module'
 import { CountersModule } from '../counters/counters.module'
+import { ChecksModule } from '../checks/checks.module'
 import { FeaturesModule } from '../features/features.module'
 import { FilesModule } from '../files/files.module'
 import { JBrowseModule } from '../jbrowse/jbrowse.module'
@@ -37,6 +38,7 @@ import { ChangesService } from './changes.service'
     FilesModule,
     UsersModule,
     CountersModule,
+    ChecksModule,
     MessagesModule,
     JBrowseModule,
   ],

diff --git a/packages/apollo-collaboration-server/src/changes/changes.service.ts b/packages/apollo-collaboration-server/src/changes/changes.service.ts
@@ -9,6 +9,8 @@ import {
   AssemblyDocument,
   Change,
   ChangeDocument,
+  Check,
+  CheckDocument,
   Feature,
   FeatureDocument,
   File,
@@ -68,6 +70,8 @@ export class ChangesService {
     private readonly jbrowseConfigModel: Model<JBrowseConfigDocument>,
     @InjectModel(Change.name)
     private readonly changeModel: Model<ChangeDocument>,
+    @InjectModel(Check.name)
+    private readonly checkModel: Model<CheckDocument>,
     private readonly filesService: FilesService,
     private readonly countersService: CountersService,
     private readonly pluginsService: PluginsService,
@@ -123,6 +127,7 @@ export class ChangesService {
           fileModel: this.fileModel,
           userModel: this.userModel,
           jbrowseConfigModel: this.jbrowseConfigModel,
+          checkModel: this.checkModel,
           session,
           filesService: this.filesService,
           counterService: this.countersService,

diff --git a/packages/apollo-collaboration-server/src/checks/checks.module.ts b/packages/apollo-collaboration-server/src/checks/checks.module.ts
@@ -97,7 +97,7 @@ import { SequenceModule } from '../sequence/sequence.module'
     ]),
   ],
 
-  exports: [ChecksService],
+  exports: [ChecksService, MongooseModule],
   controllers: [ChecksController],
 })
 export class ChecksModule {}
diff --git a/packages/apollo-collaboration-server/src/operations/operations.module.ts b/packages/apollo-collaboration-server/src/operations/operations.module.ts
@@ -1,6 +1,7 @@
 import { Module, forwardRef } from '@nestjs/common'
 
 import { AssembliesModule } from '../assemblies/assemblies.module'
+import { ChecksModule } from '../checks/checks.module'
 import { CountersModule } from '../counters/counters.module'
 import { FeaturesModule } from '../features/features.module'
 import { FilesModule } from '../files/files.module'
@@ -22,6 +23,7 @@ import { OperationsService } from './operations.service'
     CountersModule,
     MessagesModule,
     JBrowseModule,
+    ChecksModule,
   ],
   providers: [OperationsService],
   exports: [OperationsService],

diff --git a/packages/apollo-collaboration-server/src/operations/operations.service.ts b/packages/apollo-collaboration-server/src/operations/operations.service.ts
@@ -2,6 +2,8 @@ import { Operation, operationRegistry } from '@apollo-annotation/common'
 import {
   Assembly,
   AssemblyDocument,
+  Check,
+  CheckDocument,
   Feature,
   FeatureDocument,
   File,
@@ -40,6 +42,8 @@ export class OperationsService {
     private readonly refSeqModel: Model<RefSeqDocument>,
     @InjectModel(RefSeqChunk.name)
     private readonly refSeqChunkModel: Model<RefSeqChunkDocument>,
+    @InjectModel(Check.name)
+    private readonly checkModel: Model<CheckDocument>,
     private readonly filesService: FilesService,
     private readonly countersService: CountersService,
     private readonly pluginsService: PluginsService,
@@ -53,6 +57,7 @@ export class OperationsService {
   ): Promise<ReturnType<T['executeOnServer']>> {
     const {
       assemblyModel,
+      checkModel,
       connection,
       countersService,
       featureModel,
@@ -79,6 +84,7 @@ export class OperationsService {
       fileModel,
       userModel,
       jbrowseConfigModel,
+      checkModel,
       session,
       filesService,
       counterService: countersService,

diff --git a/packages/apollo-common/src/Operation.ts b/packages/apollo-common/src/Operation.ts
@@ -12,6 +12,7 @@ import {
   RefSeqDocument,
   JBrowseConfigDocument,
   UserDocument,
+  CheckDocument,
 } from '@apollo-annotation/schemas'
 import type { LoggerService } from '@nestjs/common'
 import type { ClientSession, Model } from 'mongoose'
@@ -36,6 +37,7 @@ export interface ServerDataStore {
   assemblyModel: Model<AssemblyDocument>
   refSeqModel: Model<RefSeqDocument>
   refSeqChunkModel: Model<RefSeqChunkDocument>
+  checkModel: Model<CheckDocument>
   fileModel: Model<FileDocument>
   userModel: Model<UserDocument>
   jbrowseConfigModel: Model<JBrowseConfigDocument>

diff --git a/packages/apollo-shared/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts b/packages/apollo-shared/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts
@@ -65,7 +65,7 @@ export class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange {
    * @returns
    */
   async executeOnServer(backend: ServerDataStore) {
-    const { assemblyModel, fileModel, filesService, user } = backend
+    const { assemblyModel, checkModel, fileModel, filesService, user } = backend
     const { assembly, changes, logger } = this
     for (const change of changes) {
       const { assemblyName, fileIds } = change
@@ -89,9 +89,12 @@ export class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange {
       if (assemblyDoc) {
         throw new Error(`Assembly "${assemblyName}" already exists`)
       }
+      // get checks
+      const checkDocs = await checkModel.find({ default: true }).exec()
+      const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString())
       // Add assembly
       const [newAssemblyDoc] = await assemblyModel.create([
-        { _id: assembly, name: assemblyName, user, status: -1, fileId },
+        { _id: assembly, name: assemblyName, user, status: -1, fileId, checks },
       ])
       logger.debug?.(
         `Added new assembly "${assemblyName}", docId "${newAssemblyDoc._id.toHexString()}"`,

diff --git a/packages/apollo-shared/src/Changes/AddAssemblyFromExternalChange.ts b/packages/apollo-shared/src/Changes/AddAssemblyFromExternalChange.ts
@@ -67,7 +67,7 @@ export class AddAssemblyFromExternalChange extends AssemblySpecificChange {
    * @returns
    */
   async executeOnServer(backend: ServerDataStore) {
-    const { assemblyModel, refSeqModel, user } = backend
+    const { assemblyModel, checkModel, refSeqModel, user } = backend
     const { assembly, changes, logger } = this
     const { CHUNK_SIZE } = process.env
     const customChunkSize = CHUNK_SIZE && Number(CHUNK_SIZE)
@@ -97,13 +97,16 @@ export class AddAssemblyFromExternalChange extends AssemblySpecificChange {
       if (assemblyDoc) {
         throw new Error(`Assembly "${assemblyName}" already exists`)
       }
+      const checkDocs = await checkModel.find({ default: true }).exec()
+      const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString())
       const [newAssemblyDoc] = await assemblyModel.create([
         {
           _id: assembly,
           name: assemblyName,
           user,
           status: -1,
           externalLocation,
+          checks,
         },
       ])
       logger.debug?.(

diff --git a/packages/apollo-shared/src/Changes/AddAssemblyFromFileChange.ts b/packages/apollo-shared/src/Changes/AddAssemblyFromFileChange.ts
@@ -88,8 +88,14 @@ export class AddAssemblyFromFileChange extends FromFileBaseChange {
     }
 
     const { fa, fai, gzi } = fileIds
-    const { assemblyModel, fileModel, filesService, refSeqModel, user } =
-      backend
+    const {
+      assemblyModel,
+      checkModel,
+      fileModel,
+      filesService,
+      refSeqModel,
+      user,
+    } = backend
 
     const faDoc = await fileModel.findById(fa)
     const faChecksum = faDoc?.checksum
@@ -122,13 +128,16 @@ export class AddAssemblyFromFileChange extends FromFileBaseChange {
     if (assemblyDoc) {
       throw new Error(`Assembly "${assemblyName}" already exists`)
     }
+    const checkDocs = await checkModel.find({ default: true }).exec()
+    const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString())
     const [newAssemblyDoc] = await assemblyModel.create([
       {
         _id: this.assembly,
         name: assemblyName,
         user,
         status: -1,
         fileIds,
+        checks,
       },
     ])
     this.logger.debug?.(
@@ -157,7 +166,7 @@ export class AddAssemblyFromFileChange extends FromFileBaseChange {
     assemblyName: string,
     fileId: string,
   ) {
-    const { assemblyModel, fileModel, user } = backend
+    const { assemblyModel, checkModel, fileModel, user } = backend
     // Get file checksum
     const fileDoc = await fileModel.findById(fileId).exec()
     if (!fileDoc) {
@@ -172,6 +181,8 @@ export class AddAssemblyFromFileChange extends FromFileBaseChange {
     if (assemblyDoc) {
       throw new Error(`Assembly "${assemblyName}" already exists`)
     }
+    const checkDocs = await checkModel.find({ default: true }).exec()
+    const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString())
     // Add assembly
     const [newAssemblyDoc] = await assemblyModel.create([
       {
@@ -180,6 +191,7 @@ export class AddAssemblyFromFileChange extends FromFileBaseChange {
         user,
         status: -1,
         fileIds: { fa: fileId },
+        checks,
       },
     ])
     this.logger.debug?.(