@apollo-annotation/shared 0.1.20 → 0.2.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/shared",
-  "version": "0.1.20",
+  "version": "0.2.0",
   "main": "./dist/index.js",
   "scripts": {
     "build": "yarn clean && tsc --build",
@@ -10,17 +10,15 @@
     "test:ci": "NODE_V8_COVERAGE=./coverage glob -c \"tsx --test --test-reporter spec --experimental-test-coverage \" \"**/*.test.ts\""
   },
   "dependencies": {
-    "@apollo-annotation/common": "^0.1.20",
-    "@apollo-annotation/mst": "^0.1.20",
-    "@apollo-annotation/schemas": "^0.1.20",
+    "@apollo-annotation/common": "^0.2.0",
+    "@apollo-annotation/mst": "^0.2.0",
+    "@apollo-annotation/schemas": "^0.2.0",
     "@gmod/gff": "1.2.0",
     "@gmod/indexedfasta": "^2.0.4",
     "@jbrowse/core": "^2.13.1",
     "bson-objectid": "^2.0.4",
     "generic-filehandle": "^3.0.0",
     "jwt-decode": "^3.1.2",
-    "regenerator-runtime": "^0.13.9",
-    "socket.io-client": "^4.5.4",
     "tslib": "^2.3.1"
   },
   "devDependencies": {
@@ -28,7 +26,6 @@
     "@nestjs/core": "^10.1.0",
     "@types/chai": "^4.3.19",
     "@types/node": "^18.14.2",
-    "@types/rimraf": "^3",
     "chai": "^5.1.1",
     "chai-exclude": "^3.0.0",
     "glob": "^11.0.0",

package/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()}"`,

package/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)
@@ -97,6 +97,8 @@ 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,
@@ -104,6 +106,7 @@ export class AddAssemblyFromExternalChange extends AssemblySpecificChange {
           user,
           status: -1,
           externalLocation,
+          checks,
         },
       ])
       logger.debug?.(

package/src/Changes/AddAssemblyFromFileChange.ts

@@ -87,34 +87,40 @@ export class AddAssemblyFromFileChange extends FromFileBaseChange {
       throw new Error('No FILE_UPLOAD_FOLDER found in .env file')
     }
 
-    const { fa, fai, gzi } = fileIds
-    const { assemblyModel, fileModel, filesService, refSeqModel, user } =
-      backend
-
-    const faDoc = await fileModel.findById(fa)
+    const { fa: faId, fai: faiId, gzi: gziId } = fileIds
+    const {
+      assemblyModel,
+      checkModel,
+      fileModel,
+      filesService,
+      refSeqModel,
+      user,
+    } = backend
+
+    const faDoc = await fileModel.findById(faId)
     const faChecksum = faDoc?.checksum
     if (!faChecksum) {
       throw new Error(`No checksum for file document ${faDoc}`)
     }
 
-    const faiDoc = await fileModel.findById(fai)
+    const faiDoc = await fileModel.findById(faiId)
     const faiChecksum = faiDoc?.checksum
     if (!faiChecksum) {
       throw new Error(`No checksum for file document ${faiDoc}`)
     }
 
-    const gziDoc = await fileModel.findById(gzi)
+    const gziDoc = await fileModel.findById(gziId)
     const gziChecksum = gziDoc?.checksum
     if (!gziChecksum) {
       throw new Error(`No checksum for file document ${gziDoc}`)
     }
 
-    const sequenceAdapter = new BgzipIndexedFasta({
-      fasta: filesService.getFileHandle(faDoc),
-      fai: filesService.getFileHandle(faiDoc),
-      gzi: filesService.getFileHandle(gziDoc),
-    })
+    const fasta = filesService.getFileHandle(faDoc)
+    const fai = filesService.getFileHandle(faiDoc)
+    const gzi = filesService.getFileHandle(gziDoc)
+    const sequenceAdapter = new BgzipIndexedFasta({ fasta, fai, gzi })
     const allSequenceSizes = await sequenceAdapter.getSequenceSizes()
+    await Promise.all([fasta.close(), fai.close(), gzi.close()])
 
     const assemblyDoc = await assemblyModel
       .findOne({ name: assemblyName })
@@ -122,6 +128,8 @@ export class AddAssemblyFromFileChange extends FromFileBaseChange {
     if (assemblyDoc) {
       throw new Error(`Assembly "${assemblyName}" already exists`)
     }
+    const checkDocs = await checkModel.find({ default: true }).exec()
+    const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString())
     const [newAssemblyDoc] = await assemblyModel.create([
       {
         _id: this.assembly,
@@ -129,6 +137,7 @@ export class AddAssemblyFromFileChange extends FromFileBaseChange {
         user,
         status: -1,
         fileIds,
+        checks,
       },
     ])
     this.logger.debug?.(
@@ -157,7 +166,7 @@ export class AddAssemblyFromFileChange extends FromFileBaseChange {
     assemblyName: string,
     fileId: string,
   ) {
-    const { assemblyModel, fileModel, user } = backend
+    const { assemblyModel, checkModel, fileModel, user } = backend
     // Get file checksum
     const fileDoc = await fileModel.findById(fileId).exec()
     if (!fileDoc) {
@@ -172,6 +181,8 @@ export class AddAssemblyFromFileChange extends FromFileBaseChange {
     if (assemblyDoc) {
       throw new Error(`Assembly "${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?.(

package/src/Changes/DeleteUserChange.ts

@@ -13,7 +13,7 @@ export interface SerializedDeleteUserChangeBase extends SerializedChange {
   userId: string
 }
 
-// eslint-disable-next-line @typescript-eslint/no-empty-interface
+// eslint-disable-next-line @typescript-eslint/no-empty-object-type
 export interface DeleteUserChangeDetails {}
 
 interface SerializedDeleteUserChangeSingle

package/src/Changes/ImportJBrowseConfigChange.ts

@@ -39,7 +39,8 @@ export interface SerializedImportJBrowseConfigChange {
 }
 
 export function filterJBrowseConfig(config: JBrowseConfig): JBrowseConfig {
-  const { assemblies, internetAccounts, plugins, tracks, ...rest } = config
+  const { __v, _id, assemblies, internetAccounts, plugins, tracks, ...rest } =
+    config
   const filteredAssemblies = assemblies?.filter(
     (a) => a.sequence.adapter.type !== 'ApolloSequenceAdapter',
   )

package/tsconfig.json

@@ -1,5 +1,5 @@
 {
-  "extends": "../../tsconfig.json",
+  "extends": "../../tsconfig-base.json",
   "compilerOptions": {
     "composite": true,
     "incremental": true,