@apollo-annotation/shared 0.1.18 → 0.1.20

package/dist/util.d.ts

@@ -0,0 +1,4 @@
+import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+import { GFF3Feature } from '@gmod/gff';
+export declare function makeGFF3Feature(feature: AnnotationFeatureSnapshot, parentId?: string, refSeqNames?: Record<string, string | undefined>): GFF3Feature;
+export declare function splitStringIntoChunks(input: string, chunkSize: number): string[];

package/dist/util.js

@@ -0,0 +1,102 @@
+"use strict";
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.makeGFF3Feature = makeGFF3Feature;
+exports.splitStringIntoChunks = splitStringIntoChunks;
+function makeGFF3Feature(feature, parentId, refSeqNames) {
+    const locations = [{ start: feature.min, end: feature.max }];
+    // const locations = feature.discontinuousLocations?.length
+    //   ? feature.discontinuousLocations
+    //   : [{ start: feature.start, end: feature.end, phase: feature.phase }]
+    const attributes = JSON.parse(JSON.stringify(feature.attributes));
+    const ontologyTerms = [];
+    const source = feature.attributes?.source?.[0] ?? null;
+    delete attributes.source;
+    if (parentId) {
+        attributes.Parent = [parentId];
+    }
+    if (attributes._id) {
+        attributes.ID = attributes._id;
+        delete attributes._id;
+    }
+    if (attributes.gff_name) {
+        attributes.Name = attributes.gff_name;
+        delete attributes.gff_name;
+    }
+    if (attributes.gff_alias) {
+        attributes.Alias = attributes.gff_alias;
+        delete attributes.gff_alias;
+    }
+    if (attributes.gff_target) {
+        attributes.Target = attributes.gff_target;
+        delete attributes.gff_target;
+    }
+    if (attributes.gff_gap) {
+        attributes.Gap = attributes.gff_gap;
+        delete attributes.gff_gap;
+    }
+    if (attributes.gff_derives_from) {
+        attributes.Derives_from = attributes.gff_derives_from;
+        delete attributes.gff_derives_from;
+    }
+    if (attributes.gff_note) {
+        attributes.Note = attributes.gff_note;
+        delete attributes.gff_note;
+    }
+    if (attributes.gff_dbxref) {
+        attributes.Dbxref = attributes.gff_dbxref;
+        delete attributes.gff_dbxref;
+    }
+    if (attributes.gff_is_circular) {
+        attributes.Is_circular = attributes.gff_is_circular;
+        delete attributes.gff_is_circular;
+    }
+    if (attributes.gff_ontology_term) {
+        ontologyTerms.push(...attributes.gff_ontology_term);
+        delete attributes.gff_ontology_term;
+    }
+    if (attributes['Gene Ontology']) {
+        ontologyTerms.push(...attributes['Gene Ontology']);
+        delete attributes['Gene Ontology'];
+    }
+    if (attributes['Sequence Ontology']) {
+        ontologyTerms.push(...attributes['Sequence Ontology']);
+        delete attributes['Sequence Ontology'];
+    }
+    if (ontologyTerms.length > 0) {
+        attributes.Ontology_term = ontologyTerms;
+    }
+    return locations.map((location) => ({
+        start: location.start + 1,
+        end: location.end,
+        seq_id: refSeqNames ? refSeqNames[feature.refSeq] ?? null : feature.refSeq,
+        source,
+        type: feature.type,
+        score: null,
+        // score: feature.score ?? null,
+        strand: feature.strand ? (feature.strand === 1 ? '+' : '-') : null,
+        phase: null,
+        // phase:
+        //   location.phase === 0
+        //     ? '0'
+        //     : location.phase === 1
+        //       ? '1'
+        //       : location.phase === 2
+        //         ? '2'
+        //         : null,
+        attributes: Object.keys(attributes).length > 0 ? attributes : null,
+        derived_features: [],
+        child_features: feature.children
+            ? Object.values(feature.children).map((child) => makeGFF3Feature(child, attributes.ID?.[0], refSeqNames))
+            : [],
+    }));
+}
+function splitStringIntoChunks(input, chunkSize) {
+    const chunks = [];
+    for (let i = 0; i < input.length; i += chunkSize) {
+        const chunk = input.slice(i, i + chunkSize);
+        chunks.push(chunk);
+    }
+    return chunks;
+}
+//# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,19 +1,21 @@
 {
   "name": "@apollo-annotation/shared",
-  "version": "0.1.18",
+  "version": "0.1.20",
   "main": "./dist/index.js",
   "scripts": {
-    "start": "tsc --build --watch",
     "build": "yarn clean && tsc --build",
-    "clean": "rimraf dist"
+    "clean": "rimraf dist",
+    "start": "tsc --build --watch",
+    "test": "glob -c \"tsx --test --test-reporter spec \" \"**/*.test.ts\"",
+    "test:ci": "NODE_V8_COVERAGE=./coverage glob -c \"tsx --test --test-reporter spec --experimental-test-coverage \" \"**/*.test.ts\""
   },
   "dependencies": {
-    "@apollo-annotation/common": "^0.1.18",
-    "@apollo-annotation/mst": "^0.1.18",
-    "@apollo-annotation/schemas": "^0.1.18",
+    "@apollo-annotation/common": "^0.1.20",
+    "@apollo-annotation/mst": "^0.1.20",
+    "@apollo-annotation/schemas": "^0.1.20",
     "@gmod/gff": "1.2.0",
     "@gmod/indexedfasta": "^2.0.4",
-    "@jbrowse/core": "^2.7.0",
+    "@jbrowse/core": "^2.13.1",
     "bson-objectid": "^2.0.4",
     "generic-filehandle": "^3.0.0",
     "jwt-decode": "^3.1.2",
@@ -24,13 +26,20 @@
   "devDependencies": {
     "@nestjs/common": "^10.1.0",
     "@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",
     "mobx": "^6.6.1",
     "mobx-state-tree": "^5.1.7",
     "mongoose": "^6.12.0",
+    "react-dom": "^18.2.0",
     "rimraf": "^3.0.2",
-    "typescript": "^5.1.6"
+    "rxjs": "^7.4.0",
+    "tsx": "^4.6.2",
+    "typescript": "^5.5.3"
   },
   "peerDependencies": {
     "@mui/material": "^5.11.14",

package/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts

@@ -1,8 +1,6 @@
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
 /* eslint-disable @typescript-eslint/require-await */
 
 import {
-  AssemblySpecificChange,
   ChangeOptions,
   ClientDataStore,
   LocalGFF3DataStore,
@@ -11,6 +9,8 @@ import {
 } from '@apollo-annotation/common'
 import { GFF3Feature } from '@gmod/gff'
 
+import { FromFileBaseChange } from './FromFileBaseChange'
+
 export interface SerializedAddAssemblyAndFeaturesFromFileChangeBase
   extends SerializedAssemblySpecificChange {
   typeName: 'AddAssemblyAndFeaturesFromFileChange'
@@ -18,7 +18,7 @@ export interface SerializedAddAssemblyAndFeaturesFromFileChangeBase
 
 export interface AddAssemblyAndFeaturesFromFileChangeDetails {
   assemblyName: string
-  fileId: string
+  fileIds: { fa: string }
 }
 
 export interface SerializedAddAssemblyAndFeaturesFromFileChangeSingle
@@ -34,7 +34,7 @@ export type SerializedAddAssemblyAndFeaturesFromFileChange =
   | SerializedAddAssemblyAndFeaturesFromFileChangeSingle
   | SerializedAddAssemblyAndFeaturesFromFileChangeMultiple
 
-export class AddAssemblyAndFeaturesFromFileChange extends AssemblySpecificChange {
+export class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange {
   typeName = 'AddAssemblyAndFeaturesFromFileChange' as const
   changes: AddAssemblyAndFeaturesFromFileChangeDetails[]
 
@@ -53,8 +53,8 @@ export class AddAssemblyAndFeaturesFromFileChange extends AssemblySpecificChange
   toJSON(): SerializedAddAssemblyAndFeaturesFromFileChange {
     const { assembly, changes, typeName } = this
     if (changes.length === 1) {
-      const [{ assemblyName, fileId }] = changes
-      return { typeName, assembly, assemblyName, fileId }
+      const [{ assemblyName, fileIds }] = changes
+      return { typeName, assembly, assemblyName, fileIds }
     }
     return { typeName, assembly, changes }
   }
@@ -68,7 +68,8 @@ export class AddAssemblyAndFeaturesFromFileChange extends AssemblySpecificChange
     const { assemblyModel, fileModel, filesService, user } = backend
     const { assembly, changes, logger } = this
     for (const change of changes) {
-      const { assemblyName, fileId } = change
+      const { assemblyName, fileIds } = change
+      const fileId = fileIds.fa
 
       const { FILE_UPLOAD_FOLDER } = process.env
       if (!FILE_UPLOAD_FOLDER) {
@@ -90,10 +91,10 @@ export class AddAssemblyAndFeaturesFromFileChange extends AssemblySpecificChange
       }
       // Add assembly
       const [newAssemblyDoc] = await assemblyModel.create([
-        { _id: assembly, name: assemblyName, user, status: -1 },
+        { _id: assembly, name: assemblyName, user, status: -1, fileId },
       ])
       logger.debug?.(
-        `Added new assembly "${assemblyName}", docId "${newAssemblyDoc._id}"`,
+        `Added new assembly "${assemblyName}", docId "${newAssemblyDoc._id.toHexString()}"`,
       )
       logger.debug?.(`File type: "${fileDoc.type}"`)
 
@@ -106,6 +107,9 @@ export class AddAssemblyAndFeaturesFromFileChange extends AssemblySpecificChange
       )
 
       // Loop all features
+      logger.debug?.(
+        `**************** LOOPATAAN KAIKKI FEATURET SEURAAVAKSI File type: "${fileDoc.type}"`,
+      )
       const featureStream = filesService.parseGFF3(
         filesService.getFileStream(fileDoc),
       )

package/src/Changes/AddAssemblyFromFileChange.ts

@@ -1,13 +1,15 @@
 /* eslint-disable @typescript-eslint/restrict-template-expressions */
 /* eslint-disable @typescript-eslint/require-await */
 import {
-  AssemblySpecificChange,
   ChangeOptions,
   ClientDataStore,
   LocalGFF3DataStore,
   SerializedAssemblySpecificChange,
   ServerDataStore,
 } from '@apollo-annotation/common'
+import { BgzipIndexedFasta } from '@gmod/indexedfasta'
+
+import { FromFileBaseChange } from './FromFileBaseChange'
 
 export interface SerializedAddAssemblyFromFileChangeBase
   extends SerializedAssemblySpecificChange {
@@ -16,7 +18,7 @@ export interface SerializedAddAssemblyFromFileChangeBase
 
 export interface AddAssemblyFromFileChangeDetails {
   assemblyName: string
-  fileId: string
+  fileIds: { fa: string } | { fa: string; fai: string; gzi: string }
 }
 
 export interface SerializedAddAssemblyFromFileChangeSingle
@@ -32,7 +34,7 @@ export type SerializedAddAssemblyFromFileChange =
   | SerializedAddAssemblyFromFileChangeSingle
   | SerializedAddAssemblyFromFileChangeMultiple
 
-export class AddAssemblyFromFileChange extends AssemblySpecificChange {
+export class AddAssemblyFromFileChange extends FromFileBaseChange {
   typeName = 'AddAssemblyFromFileChange' as const
   changes: AddAssemblyFromFileChangeDetails[]
 
@@ -51,8 +53,8 @@ export class AddAssemblyFromFileChange extends AssemblySpecificChange {
   toJSON(): SerializedAddAssemblyFromFileChange {
     const { assembly, changes, typeName } = this
     if (changes.length === 1) {
-      const [{ assemblyName, fileId }] = changes
-      return { typeName, assembly, assemblyName, fileId }
+      const [{ assemblyName, fileIds }] = changes
+      return { typeName, assembly, assemblyName, fileIds }
     }
     return { typeName, assembly, changes }
   }
@@ -63,49 +65,133 @@ export class AddAssemblyFromFileChange extends AssemblySpecificChange {
    * @returns
    */
   async executeOnServer(backend: ServerDataStore) {
-    const { assemblyModel, fileModel, user } = backend
-    const { assembly, changes, logger } = this
-
+    const { changes } = this
     for (const change of changes) {
-      const { assemblyName, fileId } = change
-
-      const { FILE_UPLOAD_FOLDER } = process.env
-      if (!FILE_UPLOAD_FOLDER) {
-        throw new Error('No FILE_UPLOAD_FOLDER found in .env file')
-      }
-      // Get file checksum
-      const fileDoc = await fileModel.findById(fileId).exec()
-      if (!fileDoc) {
-        throw new Error(`File "${fileId}" not found in Mongo`)
-      }
-      logger.debug?.(`FileId "${fileId}", checksum "${fileDoc.checksum}"`)
-
-      // Check and add new assembly
-      const assemblyDoc = await assemblyModel
-        .findOne({ name: assemblyName })
-        .exec()
-      if (assemblyDoc) {
-        throw new Error(`Assembly "${assemblyName}" already exists`)
-      }
-      // Add assembly
-      const [newAssemblyDoc] = await assemblyModel.create([
-        { _id: assembly, name: assemblyName, user, status: -1 },
+      const { assemblyName, fileIds } = change
+      await ('gzi' in fileIds
+        ? this.executeOnServerIndexed(backend, assemblyName, fileIds)
+        : this.executeOnServerFasta(backend, assemblyName, fileIds.fa))
+    }
+  }
+
+  async executeOnServerIndexed(
+    backend: ServerDataStore,
+    assemblyName: string,
+    fileIds: { fa: string; fai: string; gzi: string },
+  ) {
+    const { CHUNK_SIZE } = process.env
+    const customChunkSize = CHUNK_SIZE && Number(CHUNK_SIZE)
+
+    const { FILE_UPLOAD_FOLDER } = process.env
+    if (!FILE_UPLOAD_FOLDER) {
+      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 faChecksum = faDoc?.checksum
+    if (!faChecksum) {
+      throw new Error(`No checksum for file document ${faDoc}`)
+    }
+
+    const faiDoc = await fileModel.findById(fai)
+    const faiChecksum = faiDoc?.checksum
+    if (!faiChecksum) {
+      throw new Error(`No checksum for file document ${faiDoc}`)
+    }
+
+    const gziDoc = await fileModel.findById(gzi)
+    const gziChecksum = gziDoc?.checksum
+    if (!gziChecksum) {
+      throw new Error(`No checksum for file document ${gziDoc}`)
+    }
+
+    const sequenceAdapter = new BgzipIndexedFasta({
+      fasta: filesService.getFileHandle(faDoc),
+      fai: filesService.getFileHandle(faiDoc),
+      gzi: filesService.getFileHandle(gziDoc),
+    })
+    const allSequenceSizes = await sequenceAdapter.getSequenceSizes()
+
+    const assemblyDoc = await assemblyModel
+      .findOne({ name: assemblyName })
+      .exec()
+    if (assemblyDoc) {
+      throw new Error(`Assembly "${assemblyName}" already exists`)
+    }
+    const [newAssemblyDoc] = await assemblyModel.create([
+      {
+        _id: this.assembly,
+        name: assemblyName,
+        user,
+        status: -1,
+        fileIds,
+      },
+    ])
+    this.logger.debug?.(
+      `Added new assembly "${assemblyName}", docId "${newAssemblyDoc._id}"`,
+    )
+
+    for (const sequenceName in allSequenceSizes) {
+      const [newRefSeqDoc] = await refSeqModel.create([
+        {
+          name: sequenceName,
+          assembly: newAssemblyDoc._id,
+          length: allSequenceSizes[sequenceName],
+          ...(customChunkSize ? { chunkSize: customChunkSize } : null),
+          user,
+          status: -1,
+        },
       ])
-      logger.debug?.(
-        `Added new assembly "${assemblyName}", docId "${newAssemblyDoc._id}"`,
-      )
-      logger.debug?.(
-        `File type: "${fileDoc.type}", assemblyId: "${newAssemblyDoc._id}"`,
+      this.logger.debug?.(
+        `Added new refSeq "${sequenceName}", docId "${newRefSeqDoc._id}"`,
       )
+    }
+  }
 
-      // Add refSeqs
-      // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
-      await this.addRefSeqIntoDb(
-        fileDoc,
-        newAssemblyDoc._id.toString(),
-        backend,
-      )
+  async executeOnServerFasta(
+    backend: ServerDataStore,
+    assemblyName: string,
+    fileId: string,
+  ) {
+    const { assemblyModel, fileModel, user } = backend
+    // Get file checksum
+    const fileDoc = await fileModel.findById(fileId).exec()
+    if (!fileDoc) {
+      throw new Error(`File "${fileId}" not found in Mongo`)
+    }
+    this.logger.debug?.(`FileId "${fileId}", checksum "${fileDoc.checksum}"`)
+
+    // Check and add new assembly
+    const assemblyDoc = await assemblyModel
+      .findOne({ name: assemblyName })
+      .exec()
+    if (assemblyDoc) {
+      throw new Error(`Assembly "${assemblyName}" already exists`)
     }
+    // Add assembly
+    const [newAssemblyDoc] = await assemblyModel.create([
+      {
+        _id: this.assembly,
+        name: assemblyName,
+        user,
+        status: -1,
+        fileIds: { fa: fileId },
+      },
+    ])
+    this.logger.debug?.(
+      `Added new assembly "${assemblyName}", docId "${newAssemblyDoc._id}"`,
+    )
+    this.logger.debug?.(
+      `File type: "${fileDoc.type}", assemblyId: "${newAssemblyDoc._id}"`,
+    )
+
+    // Add refSeqs
+    // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
+    await this.addRefSeqIntoDb(fileDoc, newAssemblyDoc._id.toString(), backend)
   }
 
   async executeOnLocalGFF3(_backend: LocalGFF3DataStore) {

package/src/Changes/AddFeatureChange.ts

@@ -34,7 +34,7 @@ interface SerializedAddFeatureChangeMultiple
   changes: AddFeatureChangeDetails[]
 }
 
-type SerializedAddFeatureChange =
+export type SerializedAddFeatureChange =
   | SerializedAddFeatureChangeSingle
   | SerializedAddFeatureChangeMultiple
 
@@ -113,7 +113,6 @@ export class AddFeatureChange extends FeatureChange {
         )
         featureCnt++
       } else {
-        addedFeature.gffId = _id // User added manually new feature so then gffId = _id
         // Adding new child feature
         if (parentFeatureId) {
           const topLevelFeature = await featureModel
@@ -158,7 +157,7 @@ export class AddFeatureChange extends FeatureChange {
           // Child features should be sorted for click and drag of gene glyphs to work properly
           parentFeature.children = new Map(
             [...parentFeature.children.entries()].sort(
-              (a, b) => a[1].start - b[1].start,
+              (a, b) => a[1].min - b[1].min,
             ),
           )
           const childIds = this.getChildFeatureIds(addedFeature)

package/src/Changes/AddFeaturesFromFileChange.ts

@@ -1,6 +1,5 @@
 /* eslint-disable @typescript-eslint/require-await */
 import {
-  AssemblySpecificChange,
   ChangeOptions,
   ClientDataStore,
   LocalGFF3DataStore,
@@ -9,6 +8,8 @@ import {
 } from '@apollo-annotation/common'
 import { GFF3Feature } from '@gmod/gff'
 
+import { FromFileBaseChange } from './FromFileBaseChange'
+
 export interface SerializedAddFeaturesFromFileChangeBase
   extends SerializedAssemblySpecificChange {
   typeName: 'AddFeaturesFromFileChange'
@@ -32,7 +33,7 @@ export type SerializedAddFeaturesFromFileChange =
   | SerializedAddFeaturesFromFileChangeSingle
   | SerializedAddFeaturesFromFileChangeMultiple
 
-export class AddFeaturesFromFileChange extends AssemblySpecificChange {
+export class AddFeaturesFromFileChange extends FromFileBaseChange {
   typeName = 'AddFeaturesFromFileChange' as const
   changes: AddFeaturesFromFileChangeDetails[]
   deleteExistingFeatures = false
@@ -91,13 +92,17 @@ export class AddFeaturesFromFileChange extends AssemblySpecificChange {
       const featureStream = filesService.parseGFF3(
         filesService.getFileStream(fileDoc),
       )
+      let featureCount = 0
       for await (const f of featureStream) {
         const gff3Feature = f as GFF3Feature
-        logger.verbose?.(`ENTRY=${JSON.stringify(gff3Feature)}`)
 
         // 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)
+        featureCount++
+        if (featureCount % 1000 === 0) {
+          logger.debug?.(`Processed ${featureCount} features`)
+        }
       }
     }
     logger.debug?.('New features added into database!')

package/src/Changes/AddRefSeqAliasesChange.ts

@@ -0,0 +1,88 @@
+import {
+  AssemblySpecificChange,
+  Change,
+  ChangeOptions,
+  ClientDataStore,
+  LocalGFF3DataStore,
+  SerializedAssemblySpecificChange,
+  ServerDataStore,
+} from '@apollo-annotation/common'
+import { getSession } from '@jbrowse/core/util'
+
+export interface SerializedRefSeqAliases {
+  refName: string
+  aliases: string[]
+}
+
+export interface SerializedRefSeqAliasesChange
+  extends SerializedAssemblySpecificChange {
+  typeName: 'AddRefSeqAliasesChange'
+  refSeqAliases: SerializedRefSeqAliases[]
+}
+
+export class AddRefSeqAliasesChange extends AssemblySpecificChange {
+  typeName = 'AddRefSeqAliasesChange' as const
+  refSeqAliases: SerializedRefSeqAliases[]
+
+  constructor(json: SerializedRefSeqAliasesChange, options?: ChangeOptions) {
+    super(json, options)
+    this.refSeqAliases = json.refSeqAliases
+  }
+
+  executeOnClient(clientDataStore: ClientDataStore) {
+    const { assemblyManager } = getSession(clientDataStore)
+    const assembly = assemblyManager.get(this.assembly)
+    if (!assembly) {
+      throw new Error(`assembly ${this.assembly} not found`)
+    }
+    const sessionAliases = assembly.refNameAliases
+    const sessionLCAliases = assembly.lowerCaseRefNameAliases
+
+    if (!sessionAliases || !sessionLCAliases) {
+      throw new Error('Session refNameAliases not found in assembly')
+    }
+
+    for (const refSeqAlias of this.refSeqAliases) {
+      const { aliases, refName } = refSeqAlias
+      for (const alias of aliases) {
+        sessionAliases[alias] = refName
+        sessionLCAliases[alias.toLowerCase()] = refName
+      }
+    }
+    assembly.setRefNameAliases(sessionAliases, sessionLCAliases)
+    return Promise.resolve()
+  }
+
+  getInverse(): Change {
+    throw new Error('Method not implemented.')
+  }
+
+  toJSON(): SerializedRefSeqAliasesChange {
+    const { assembly, refSeqAliases, typeName } = this
+    return { assembly, typeName, refSeqAliases }
+  }
+
+  async executeOnServer(backend: ServerDataStore) {
+    const { refSeqModel, session } = backend
+    const { assembly, logger, refSeqAliases } = this
+
+    for (const refSeqAlias of refSeqAliases) {
+      logger.debug?.(
+        `Updating Refname alias for assembly: ${assembly}, refSeqAlias: ${JSON.stringify(refSeqAlias)}`,
+      )
+      const { aliases, refName } = refSeqAlias
+      await refSeqModel
+        .updateOne({ assembly, name: refName }, { $set: { aliases } })
+        .session(session)
+    }
+  }
+
+  executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<unknown> {
+    throw new Error('Method not implemented.')
+  }
+
+  // eslint-disable-next-line @typescript-eslint/class-literal-property-style
+  get notification(): string {
+    return 'RefSeq aliases have been added.'
+  }
+}

package/src/Changes/DeleteAssemblyChange.ts

@@ -11,7 +11,7 @@ import {
 } from '@apollo-annotation/common'
 import { getSession } from '@jbrowse/core/util'
 
-interface SerializedDeleteAssemblyChange
+export interface SerializedDeleteAssemblyChange
   extends SerializedAssemblySpecificChange {
   typeName: 'DeleteAssemblyChange'
 }

package/src/Changes/DeleteFeatureChange.ts

@@ -32,7 +32,7 @@ interface SerializedDeleteFeatureChangeMultiple
   changes: DeleteFeatureChangeDetails[]
 }
 
-type SerializedDeleteFeatureChange =
+export type SerializedDeleteFeatureChange =
   | SerializedDeleteFeatureChangeSingle
   | SerializedDeleteFeatureChangeMultiple
 

package/src/Changes/FeatureAttributeChange.ts

@@ -29,7 +29,7 @@ interface SerializedFeatureAttributeChangeMultiple
   changes: FeatureAttributeChangeDetails[]
 }
 
-type SerializedFeatureAttributeChange =
+export type SerializedFeatureAttributeChange =
   | SerializedFeatureAttributeChangeSingle
   | SerializedFeatureAttributeChangeMultiple