@apollo-annotation/shared 0.3.10 → 0.3.12

package/dist/util.d.ts

@@ -1,6 +1,7 @@
-import { type Feature } from '@apollo-annotation/schemas';
-import { type IKeyValueMap } from 'mobx';
+import type { Feature } from '@apollo-annotation/schemas';
+import type { IKeyValueMap } from 'mobx';
 export declare function splitStringIntoChunks(input: string, chunkSize: number): string[];
 export declare function getPrintableId(feature: Feature): string;
 export declare function attributesToRecords(attributes: IKeyValueMap<readonly string[] | undefined> | undefined): Record<string, string[] | undefined>;
 export declare function stringifyAttributes(attributes: Record<string, string[] | undefined> | undefined): string;
+//# sourceMappingURL=util.d.ts.map

package/dist/util.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.d.ts","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,4BAA4B,CAAA;AACzD,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,MAAM,CAAA;AAExC,wBAAgB,qBAAqB,CACnC,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,MAAM,GAChB,MAAM,EAAE,CAOV;AAED,wBAAgB,cAAc,CAAC,OAAO,EAAE,OAAO,GAAG,MAAM,CAWvD;AAED,wBAAgB,mBAAmB,CACjC,UAAU,EAAE,YAAY,CAAC,SAAS,MAAM,EAAE,GAAG,SAAS,CAAC,GAAG,SAAS,GAClE,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC,CAStC;AAED,wBAAgB,mBAAmB,CACjC,UAAU,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC,GAAG,SAAS,GAC3D,MAAM,CAmBR"}

package/dist/util.js

@@ -1,10 +1,4 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.splitStringIntoChunks = splitStringIntoChunks;
-exports.getPrintableId = getPrintableId;
-exports.attributesToRecords = attributesToRecords;
-exports.stringifyAttributes = stringifyAttributes;
-function splitStringIntoChunks(input, chunkSize) {
+export function splitStringIntoChunks(input, chunkSize) {
     const chunks = [];
     for (let i = 0; i < input.length; i += chunkSize) {
         const chunk = input.slice(i, i + chunkSize);
@@ -12,7 +6,7 @@ function splitStringIntoChunks(input, chunkSize) {
     }
     return chunks;
 }
-function getPrintableId(feature) {
+export function getPrintableId(feature) {
     const ff = feature;
     const gff_id = ff.attributes.get('gff_id')?.join(',');
     if (gff_id) {
@@ -24,7 +18,7 @@ function getPrintableId(feature) {
     }
     return `_id: ${feature._id.toString()}`;
 }
-function attributesToRecords(attributes) {
+export function attributesToRecords(attributes) {
     const records = {};
     if (!attributes) {
         return records;
@@ -34,7 +28,7 @@ function attributesToRecords(attributes) {
     }
     return records;
 }
-function stringifyAttributes(attributes) {
+export function stringifyAttributes(attributes) {
     if (!attributes) {
         return '';
     }

package/dist/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAIA,MAAM,UAAU,qBAAqB,CACnC,KAAa,EACb,SAAiB;IAEjB,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,IAAI,SAAS,EAAE,CAAC;QACjD,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,CAAA;QAC3C,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IACpB,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,OAAgB;IAC7C,MAAM,EAAE,GAAG,OAAuC,CAAA;IAClD,MAAM,MAAM,GAAG,EAAE,CAAC,UAAU,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAA;IACrD,IAAI,MAAM,EAAE,CAAC;QACX,OAAO,MAAM,MAAM,UAAU,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,GAAG,CAAA;IACxD,CAAC;IACD,MAAM,QAAQ,GAAG,EAAE,CAAC,UAAU,CAAC,GAAG,CAAC,UAAU,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAA;IACzD,IAAI,QAAQ,EAAE,CAAC;QACb,OAAO,QAAQ,QAAQ,UAAU,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,GAAG,CAAA;IAC5D,CAAC;IACD,OAAO,QAAQ,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,EAAE,CAAA;AACzC,CAAC;AAED,MAAM,UAAU,mBAAmB,CACjC,UAAmE;IAEnE,MAAM,OAAO,GAAyC,EAAE,CAAA;IACxD,IAAI,CAAC,UAAU,EAAE,CAAC;QAChB,OAAO,OAAO,CAAA;IAChB,CAAC;IACD,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE,CAAC;QACtD,OAAO,CAAC,GAAG,CAAC,GAAG,KAAK,EAAE,KAAK,EAAE,CAAA;IAC/B,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED,MAAM,UAAU,mBAAmB,CACjC,UAA4D;IAE5D,IAAI,CAAC,UAAU,EAAE,CAAC;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IACD,MAAM,GAAG,GAAG,EAAE,CAAA;IACd,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE,CAAC;QACtD,IAAI,aAAa,GAAG,GAAG,CAAA;QACvB,IAAI,aAAa,CAAC,UAAU,CAAC,MAAM,CAAC,EAAE,CAAC;YACrC,aAAa,GAAG,aAAa,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YACtC,aAAa;gBACX,aAAa,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,GAAG,aAAa,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAClE,CAAC;QACD,IAAI,KAAK,EAAE,CAAC;YACV,GAAG,CAAC,IAAI,CAAC,GAAG,aAAa,IAAI,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;QACjD,CAAC;aAAM,CAAC;YACN,GAAG,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;QACzB,CAAC;IACH,CAAC;IACD,OAAO,kBAAkB,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAA;AAC1C,CAAC"}

package/package.json

@@ -1,7 +1,9 @@
 {
   "name": "@apollo-annotation/shared",
-  "version": "0.3.10",
-  "main": "./dist/index.js",
+  "version": "0.3.12",
+  "sideEffects": false,
+  "type": "module",
+  "exports": "./dist/index.js",
   "scripts": {
     "build": "yarn clean && tsc --build",
     "clean": "rimraf dist",
@@ -10,27 +12,27 @@
     "test:ci": "NODE_V8_COVERAGE=./coverage glob -c \"tsx --test --test-reporter spec --experimental-test-coverage \" \"**/*.test.ts\""
   },
   "dependencies": {
-    "@apollo-annotation/common": "^0.3.10",
-    "@apollo-annotation/mst": "^0.3.10",
-    "@apollo-annotation/schemas": "^0.3.10",
-    "@gmod/gff": "^2.0.0",
-    "@gmod/indexedfasta": "^2.0.4",
-    "@jbrowse/core": "^3.6.5",
+    "@apollo-annotation/common": "^0.3.12",
+    "@apollo-annotation/mst": "^0.3.12",
+    "@apollo-annotation/schemas": "^0.3.12",
+    "@gmod/gff": "^2.1.0",
+    "@gmod/indexedfasta": "^5.0.2",
+    "@jbrowse/core": "^4.1.1",
     "bson-objectid": "^2.0.4",
-    "generic-filehandle": "^3.0.0",
+    "generic-filehandle2": "^2.0.18",
     "jwt-decode": "^3.1.2",
     "tslib": "^2.3.1"
   },
   "devDependencies": {
+    "@jbrowse/mobx-state-tree": "^5.5.0",
     "@nestjs/common": "^10.1.0",
     "@nestjs/core": "^10.1.0",
     "@types/chai": "^4.3.19",
-    "@types/node": "^20.19.15",
+    "@types/node": "^24.10.9",
     "chai": "^5.1.1",
     "chai-exclude": "^3.0.0",
     "glob": "^11.0.0",
     "mobx": "^6.6.1",
-    "mobx-state-tree": "^5.4.0",
     "mongoose": "^6.12.0",
     "react-dom": "^18.2.0",
     "rimraf": "^3.0.2",
@@ -39,14 +41,15 @@
     "typescript": "^5.5.3"
   },
   "peerDependencies": {
-    "@mui/material": "^7.0.0",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/material": "^7.3.7",
     "@mui/x-data-grid": "^8.0.0",
     "mobx": "^6.6.1",
     "mobx-react": "^7.2.1",
-    "mobx-state-tree": "^5.4.0",
     "prop-types": "^15.8.1",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
+    "reflect-metadata": "^0.1.13",
     "rxjs": "^7.4.0"
   },
   "publishConfig": {

package/src/Changes/AddAssemblyAliasesChange.ts

@@ -1,3 +1,6 @@
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import {
   AssemblySpecificChange,
   type Change,
@@ -30,7 +33,6 @@ export class AddAssemblyAliasesChange extends AssemblySpecificChange {
     if (!assembly) {
       throw new Error(`assembly ${this.assembly} not found`)
     }
-    // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
     assembly.configuration.aliases.set(this.aliases)
     return Promise.resolve()
   }

package/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts

@@ -1,15 +1,18 @@
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/require-await */
 
-import {
-  type ChangeOptions,
-  type ClientDataStore,
-  type LocalGFF3DataStore,
-  type SerializedAssemblySpecificChange,
-  type ServerDataStore,
+import type {
+  ChangeOptions,
+  ClientDataStore,
+  LocalGFF3DataStore,
+  SerializedAssemblySpecificChange,
+  ServerDataStore,
 } from '@apollo-annotation/common'
-import { type GFF3Feature } from '@gmod/gff'
 
-import { FromFileBaseChange } from './FromFileBaseChange'
+import { FromFileBaseChange } from './FromFileBaseChange.js'
 
 export interface SerializedAddAssemblyAndFeaturesFromFileChangeBase
   extends SerializedAssemblySpecificChange {
@@ -19,7 +22,7 @@ export interface SerializedAddAssemblyAndFeaturesFromFileChangeBase
 export interface AddAssemblyAndFeaturesFromFileChangeDetails {
   assemblyName: string
   fileIds: { fa: string }
-  parseOptions?: { bufferSize: number }
+  parseOptions?: { bufferSize?: number; strict?: boolean }
 }
 
 export interface SerializedAddAssemblyAndFeaturesFromFileChangeSingle
@@ -111,18 +114,37 @@ export class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange {
         backend,
       )
 
-      const { bufferSize = 10_000 } = parseOptions ?? {}
+      const { bufferSize = 10_000, strict = true } = parseOptions ?? {}
       const featureStream = filesService.parseGFF3(
         filesService.getFileStream(fileDoc),
         { bufferSize },
       )
-      // @ts-expect-error type is wrong here
-      // eslint-disable-next-line @typescript-eslint/await-thenable
-      for await (const f of featureStream) {
-        const gff3Feature = f as GFF3Feature
-        logger.verbose?.(`ENTRY=${JSON.stringify(gff3Feature)}`)
+      let featureCount = 0
+      let errorCount = 0
+      for await (const gff3Feature of featureStream) {
         // Add new feature into database
-        await this.addFeatureIntoDb(gff3Feature, backend)
+        try {
+          await this.addFeatureIntoDb(gff3Feature, backend)
+        } catch (error) {
+          // if the first feature is an error, assume the file isn't valid and throw
+          if (strict || featureCount === 0) {
+            throw error
+          }
+          if (errorCount <= 99) {
+            logger.warn('Error parsing feature')
+            logger.warn(error)
+            if (errorCount === 99) {
+              logger.warn(
+                'Reached 100 parsing errors, omitting further warnings from log',
+              )
+            }
+          }
+          errorCount++
+        }
+        featureCount++
+        if (featureCount % 1000 === 0) {
+          logger.debug?.(`Processed ${featureCount} features`)
+        }
       }
     }
   }

package/src/Changes/AddAssemblyFromExternalChange.ts

@@ -1,4 +1,5 @@
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 
 /* eslint-disable @typescript-eslint/require-await */
@@ -11,7 +12,7 @@ import {
   type ServerDataStore,
 } from '@apollo-annotation/common'
 import { BgzipIndexedFasta, IndexedFasta } from '@gmod/indexedfasta'
-import { RemoteFile } from 'generic-filehandle'
+import { RemoteFile } from 'generic-filehandle2'
 
 export interface SerializedAddAssemblyFromExternalChangeBase
   extends SerializedAssemblySpecificChange {

package/src/Changes/AddAssemblyFromFileChange.ts

@@ -1,15 +1,18 @@
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/require-await */
-import {
-  type ChangeOptions,
-  type ClientDataStore,
-  type LocalGFF3DataStore,
-  type SerializedAssemblySpecificChange,
-  type ServerDataStore,
+import type {
+  ChangeOptions,
+  ClientDataStore,
+  LocalGFF3DataStore,
+  SerializedAssemblySpecificChange,
+  ServerDataStore,
 } from '@apollo-annotation/common'
 import { BgzipIndexedFasta } from '@gmod/indexedfasta'
 
-import { FromFileBaseChange } from './FromFileBaseChange'
+import { FromFileBaseChange } from './FromFileBaseChange.js'
 
 export interface SerializedAddAssemblyFromFileChangeBase
   extends SerializedAssemblySpecificChange {

package/src/Changes/AddFeatureChange.ts

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/restrict-template-expressions */
 /* eslint-disable @typescript-eslint/require-await */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
@@ -9,9 +10,9 @@ import {
   type SerializedFeatureChange,
   type ServerDataStore,
 } from '@apollo-annotation/common'
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 
-import { DeleteFeatureChange } from './DeleteFeatureChange'
+import { DeleteFeatureChange } from './DeleteFeatureChange.js'
 
 interface SerializedAddFeatureChangeBase extends SerializedFeatureChange {
   typeName: 'AddFeatureChange'
@@ -123,6 +124,7 @@ export class AddFeatureChange extends FeatureChange {
         )
         featureCnt++
       } else {
+        const indexedIds = this.getIndexedIds(addedFeature, idsToIndex)
         // Adding new child feature
         if (parentFeatureId) {
           const topLevelFeature = await featureModel
@@ -146,11 +148,14 @@ export class AddFeatureChange extends FeatureChange {
           this.addChild(parentFeature, addedFeature)
           const childIds = this.getChildFeatureIds(addedFeature)
           topLevelFeature.allIds.push(_id, ...childIds)
+          if (indexedIds.length > 0 && !topLevelFeature.indexedIds) {
+            topLevelFeature.indexedIds = []
+          }
+          topLevelFeature.indexedIds?.push(...indexedIds)
           await topLevelFeature.save()
         } else {
           const childIds = this.getChildFeatureIds(addedFeature)
           const allIdsV2 = [_id, ...childIds]
-          const indexedIds = this.getIndexedIds(addedFeature, idsToIndex)
           const [newFeatureDoc] = await featureModel.create(
             [{ allIds: allIdsV2, indexedIds, status: 0, ...addedFeature }],
             { session },

package/src/Changes/AddFeaturesFromFileChange.ts

@@ -1,14 +1,13 @@
 /* eslint-disable @typescript-eslint/require-await */
-import {
-  type ChangeOptions,
-  type ClientDataStore,
-  type LocalGFF3DataStore,
-  type SerializedAssemblySpecificChange,
-  type ServerDataStore,
+import type {
+  ChangeOptions,
+  ClientDataStore,
+  LocalGFF3DataStore,
+  SerializedAssemblySpecificChange,
+  ServerDataStore,
 } from '@apollo-annotation/common'
-import { type GFF3Feature } from '@gmod/gff'
 
-import { FromFileBaseChange } from './FromFileBaseChange'
+import { FromFileBaseChange } from './FromFileBaseChange.js'
 
 export interface SerializedAddFeaturesFromFileChangeBase
   extends SerializedAssemblySpecificChange {
@@ -18,7 +17,7 @@ export interface SerializedAddFeaturesFromFileChangeBase
 
 export interface AddFeaturesFromFileChangeDetails {
   fileId: string
-  parseOptions?: { bufferSize: number }
+  parseOptions?: { bufferSize?: number; strict?: boolean }
 }
 
 export interface SerializedAddFeaturesFromFileChangeSingle
@@ -89,21 +88,39 @@ export class AddFeaturesFromFileChange extends FromFileBaseChange {
       }
       logger.debug?.(`FileId "${fileId}", checksum "${fileDoc.checksum}"`)
 
+      let errorCount = 0
+      // eslint-disable-next-line unicorn/consistent-function-scoping
+      const errorLogger = (error: unknown) => {
+        if (errorCount <= 99) {
+          logger.warn('Error parsing or adding feature')
+          logger.warn(error)
+          if (errorCount === 99) {
+            logger.warn(
+              'Reached 100 feature errors, omitting further warnings from log',
+            )
+          }
+        }
+        errorCount++
+      }
+
       // Read data from compressed file and parse the content
-      const { bufferSize = 10_000 } = parseOptions ?? {}
+      const { bufferSize = 10_000, strict = true } = parseOptions ?? {}
       const featureStream = filesService.parseGFF3(
         filesService.getFileStream(fileDoc),
-        { bufferSize },
+        { bufferSize, errorCallback: strict ? undefined : errorLogger },
       )
       let featureCount = 0
-      // @ts-expect-error type is wrong here
-      // eslint-disable-next-line @typescript-eslint/await-thenable
-      for await (const f of featureStream) {
-        const gff3Feature = f as GFF3Feature
-
+      for await (const gff3Feature of featureStream) {
         // Add new feature into database
-        // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
-        await this.addFeatureIntoDb(gff3Feature, backend)
+        try {
+          await this.addFeatureIntoDb(gff3Feature, backend)
+        } catch (error) {
+          // if the first feature is an error, assume the file isn't valid and throw
+          if (strict || featureCount === 0) {
+            throw error
+          }
+          errorLogger(error)
+        }
         featureCount++
         if (featureCount % 1000 === 0) {
           logger.debug?.(`Processed ${featureCount} features`)

package/src/Changes/AddRefSeqAliasesChange.ts

@@ -1,3 +1,6 @@
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import {
   AssemblySpecificChange,
   type Change,

package/src/Changes/DeleteAssemblyChange.ts

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
 /* eslint-disable @typescript-eslint/require-await */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */

package/src/Changes/DeleteFeatureChange.ts

@@ -9,10 +9,10 @@ import {
   type SerializedFeatureChange,
   type ServerDataStore,
 } from '@apollo-annotation/common'
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
-import { type Feature } from '@apollo-annotation/schemas'
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import type { Feature } from '@apollo-annotation/schemas'
 
-import { AddFeatureChange } from './AddFeatureChange'
+import { AddFeatureChange } from './AddFeatureChange.js'
 
 interface SerializedDeleteFeatureChangeBase extends SerializedFeatureChange {
   typeName: 'DeleteFeatureChange'
@@ -67,6 +67,12 @@ export class DeleteFeatureChange extends FeatureChange {
     const { featureModel, session } = backend
     const { changes, logger } = this
 
+    const { INDEXED_IDS } = process.env
+    let idsToIndex: string[] | undefined
+    if (INDEXED_IDS) {
+      idsToIndex = INDEXED_IDS.split(',')
+    }
+
     // Loop the changes
     for (const change of changes) {
       const { deletedFeature, parentFeatureId } = change
@@ -105,6 +111,18 @@ export class DeleteFeatureChange extends FeatureChange {
       featureDoc.allIds = featureDoc.allIds.filter(
         (id) => !deletedIds.includes(id),
       )
+      const indexedIds = this.getIndexedIds(featureDoc, idsToIndex)
+      if (featureDoc.indexedIds) {
+        if (indexedIds.length > 0) {
+          featureDoc.indexedIds = indexedIds
+        } else {
+          delete featureDoc.indexedIds
+        }
+      } else {
+        if (indexedIds.length > 0) {
+          featureDoc.indexedIds = indexedIds
+        }
+      }
       // Save updated document in Mongo
       featureDoc.markModified('children') // Mark as modified. Without this save() -method is not updating data in database
       try {

package/src/Changes/FeatureAttributeChange.ts

@@ -9,7 +9,7 @@ import {
   type SerializedFeatureChange,
   type ServerDataStore,
 } from '@apollo-annotation/common'
-import { type Feature, type FeatureDocument } from '@apollo-annotation/schemas'
+import type { Feature, FeatureDocument } from '@apollo-annotation/schemas'
 
 interface SerializedFeatureAttributeChangeBase extends SerializedFeatureChange {
   typeName: 'FeatureAttributeChange'
@@ -100,11 +100,24 @@ export class FeatureAttributeChange extends FeatureChange {
       featuresForChanges.push({ feature: foundFeature, topLevelFeature })
     }
 
+    const { INDEXED_IDS } = process.env
+    let idsToIndex: string[] | undefined
+    if (INDEXED_IDS) {
+      idsToIndex = INDEXED_IDS.split(',')
+    }
     // Let's update objects
     for (const [idx, change] of changes.entries()) {
       const { newAttributes } = change
       const { feature, topLevelFeature } = featuresForChanges[idx]
+      const indexedIdsChanged = idsToIndex?.some(
+        (id) => id in newAttributes || id in (feature?.attributes ?? {}),
+      )
       feature.attributes = newAttributes
+      if (indexedIdsChanged) {
+        const indexedIds = this.getIndexedIds(topLevelFeature, idsToIndex)
+        topLevelFeature.indexedIds = indexedIds
+        topLevelFeature.markModified('indexedIds')
+      }
       if (topLevelFeature._id.equals(feature._id)) {
         topLevelFeature.markModified('attributes') // Mark as modified. Without this save() -method is not updating data in database
       } else {

package/src/Changes/FromFileBaseChange.ts

@@ -4,14 +4,11 @@ import {
   AssemblySpecificChange,
   type ServerDataStore,
 } from '@apollo-annotation/common'
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
-import {
-  type FileDocument,
-  type RefSeqDocument,
-} from '@apollo-annotation/schemas'
-import { type GFF3Feature } from '@gmod/gff'
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import type { FileDocument, RefSeqDocument } from '@apollo-annotation/schemas'
+import type { GFF3Feature } from '@gmod/gff'
 
-import { gff3ToAnnotationFeature } from '../GFF3'
+import { gff3ToAnnotationFeature } from '../GFF3/index.js'
 
 export abstract class FromFileBaseChange extends AssemblySpecificChange {
   async addRefSeqIntoDb(
@@ -37,8 +34,6 @@ export abstract class FromFileBaseChange extends AssemblySpecificChange {
     logger.debug?.('starting sequence stream')
     let lineCount = 0
     const decoder = new TextDecoder()
-    // @ts-expect-error type is wrong here
-    // eslint-disable-next-line @typescript-eslint/await-thenable
     for await (const data of sequenceStream) {
       const chunk = decoder.decode(data)
       lastLineIsIncomplete = !chunk.endsWith('\n')

package/src/Changes/LocationEndChange.ts

@@ -9,7 +9,7 @@ import {
   type SerializedFeatureChange,
   type ServerDataStore,
 } from '@apollo-annotation/common'
-import { type Feature, type FeatureDocument } from '@apollo-annotation/schemas'
+import type { Feature, FeatureDocument } from '@apollo-annotation/schemas'
 
 interface SerializedLocationEndChangeBase extends SerializedFeatureChange {
   typeName: 'LocationEndChange'

package/src/Changes/LocationStartChange.ts

@@ -9,7 +9,7 @@ import {
   type SerializedFeatureChange,
   type ServerDataStore,
 } from '@apollo-annotation/common'
-import { type Feature, type FeatureDocument } from '@apollo-annotation/schemas'
+import type { Feature, FeatureDocument } from '@apollo-annotation/schemas'
 
 interface SerializedLocationStartChangeBase extends SerializedFeatureChange {
   typeName: 'LocationStartChange'

package/src/Changes/MergeExonsChange.ts

@@ -10,12 +10,12 @@ import {
   type SerializedFeatureChange,
   type ServerDataStore,
 } from '@apollo-annotation/common'
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 
-import { attributesToRecords, stringifyAttributes } from '../util'
+import { attributesToRecords, stringifyAttributes } from '../util.js'
 
-import { findAndDeleteChildFeature } from './DeleteFeatureChange'
-import { UndoMergeExonsChange } from './UndoMergeExonsChange'
+import { findAndDeleteChildFeature } from './DeleteFeatureChange.js'
+import { UndoMergeExonsChange } from './UndoMergeExonsChange.js'
 
 interface SerializedMergeExonsChangeBase extends SerializedFeatureChange {
   typeName: 'MergeExonsChange'

package/src/Changes/MergeTranscriptsChange.ts

@@ -10,18 +10,18 @@ import {
   type SerializedFeatureChange,
   type ServerDataStore,
 } from '@apollo-annotation/common'
-import {
-  type AnnotationFeature,
-  type AnnotationFeatureSnapshot,
+import type {
+  AnnotationFeature,
+  AnnotationFeatureSnapshot,
 } from '@apollo-annotation/mst'
-import { type Feature } from '@apollo-annotation/schemas'
+import type { Feature } from '@apollo-annotation/schemas'
 import { doesIntersect2 } from '@jbrowse/core/util'
-import { getSnapshot } from 'mobx-state-tree'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 
-import { attributesToRecords, stringifyAttributes } from '../util'
+import { attributesToRecords, stringifyAttributes } from '../util.js'
 
-import { findAndDeleteChildFeature } from './DeleteFeatureChange'
-import { UndoMergeTranscriptsChange } from './UndoMergeTranscriptsChange'
+import { findAndDeleteChildFeature } from './DeleteFeatureChange.js'
+import { UndoMergeTranscriptsChange } from './UndoMergeTranscriptsChange.js'
 
 interface SerializedMergeTranscriptsChangeBase extends SerializedFeatureChange {
   typeName: 'MergeTranscriptsChange'

package/src/Changes/SplitExonChange.ts

@@ -9,10 +9,10 @@ import {
   type SerializedFeatureChange,
   type ServerDataStore,
 } from '@apollo-annotation/common'
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 
-import { findAndDeleteChildFeature } from './DeleteFeatureChange'
-import { UndoSplitExonChange } from './UndoSplitExonChange'
+import { findAndDeleteChildFeature } from './DeleteFeatureChange.js'
+import { UndoSplitExonChange } from './UndoSplitExonChange.js'
 
 interface SerializedSplitExonChangeBase extends SerializedFeatureChange {
   typeName: 'SplitExonChange'

package/src/Changes/StrandChange.ts

@@ -9,7 +9,7 @@ import {
   type SerializedFeatureChange,
   type ServerDataStore,
 } from '@apollo-annotation/common'
-import { type Feature, type FeatureDocument } from '@apollo-annotation/schemas'
+import type { Feature, FeatureDocument } from '@apollo-annotation/schemas'
 
 interface SerializedStrandChangeBase extends SerializedFeatureChange {
   typeName: 'StrandChange'

package/src/Changes/TypeChange.ts

@@ -9,7 +9,7 @@ import {
   type SerializedFeatureChange,
   type ServerDataStore,
 } from '@apollo-annotation/common'
-import { type Feature, type FeatureDocument } from '@apollo-annotation/schemas'
+import type { Feature, FeatureDocument } from '@apollo-annotation/schemas'
 
 interface SerializedTypeChangeBase extends SerializedFeatureChange {
   typeName: 'TypeChange'

package/src/Changes/UndoMergeExonsChange.ts

@@ -8,9 +8,9 @@ import {
   type SerializedFeatureChange,
   type ServerDataStore,
 } from '@apollo-annotation/common'
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 
-import { MergeExonsChange } from './MergeExonsChange'
+import { MergeExonsChange } from './MergeExonsChange.js'
 
 interface SerializedUndoMergeExonsChangeBase extends SerializedFeatureChange {
   typeName: 'UndoMergeExonsChange'

package/src/Changes/UndoMergeTranscriptsChange.ts

@@ -8,9 +8,9 @@ import {
   type SerializedFeatureChange,
   type ServerDataStore,
 } from '@apollo-annotation/common'
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 
-import { MergeTranscriptsChange } from './MergeTranscriptsChange'
+import { MergeTranscriptsChange } from './MergeTranscriptsChange.js'
 
 interface SerializedUndoMergeTranscriptsChangeBase
   extends SerializedFeatureChange {