@apollo-annotation/shared 0.1.20 → 0.1.21

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/shared",
-  "version": "0.1.20",
+  "version": "0.1.21",
   "main": "./dist/index.js",
   "scripts": {
     "build": "yarn clean && tsc --build",
@@ -10,9 +10,9 @@
     "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": "^0.1.21",
+    "@apollo-annotation/mst": "^0.1.21",
+    "@apollo-annotation/schemas": "^0.1.21",
     "@gmod/gff": "1.2.0",
     "@gmod/indexedfasta": "^2.0.4",
     "@jbrowse/core": "^2.13.1",

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

@@ -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
@@ -122,6 +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/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',
   )