Fix for adding features to assembly or refSeq that's not loaded yet

packages/apollo-collaboration-server/src/jbrowse/jbrowse.service.ts

@@ -6,7 +6,7 @@ import { Injectable, Logger } from '@nestjs/common'
 import { ConfigService } from '@nestjs/config'
 import { InjectModel } from '@nestjs/mongoose'
 import merge from 'deepmerge'
-import { Model, Types } from 'mongoose'
+import { Model } from 'mongoose'
 
 import { AssembliesService } from '../assemblies/assemblies.service'
 import { RefSeqsService } from '../refSeqs/refSeqs.service'
@@ -138,58 +138,45 @@ export class JBrowseService {
   async getAssemblies() {
     const url = this.configService.get('URL', { infer: true })
     const assemblies = await this.assembliesService.findAll()
-    return Promise.all(
-      assemblies.map(async (assembly) => {
-        const assemblyId = assembly._id.toHexString()
-        const refSeqs = await this.refSeqsService.findAll({
-          assembly: assemblyId,
-        })
-        const ids: Record<string, string> = {}
-        refSeqs.map((refSeq) => {
-          ids[refSeq.name] = (refSeq._id as Types.ObjectId).toHexString()
-        })
-        this.logger.debug(`generating assembly ${assemblyId}`)
-        const trackId = `sequenceConfigId-${assembly.name}`
-        return {
-          name: assemblyId,
-          aliases:
-            assembly.aliases.length > 0
-              ? [...assembly.aliases]
-              : [assembly.name],
-          displayName: assembly.displayName || assembly.name,
-          sequence: {
-            trackId,
-            type: 'ReferenceSequenceTrack',
-            adapter: {
-              type: 'ApolloSequenceAdapter',
-              assemblyId,
-              baseURL: {
-                uri: url,
-                locationType: 'UriLocation',
-              },
-            },
-            displays: [
-              {
-                type: 'LinearApolloReferenceSequenceDisplay',
-                displayId: `${trackId}-LinearApolloReferenceSequenceDisplay`,
-              },
-            ],
-            metadata: {
-              apollo: true,
-              internetAccountConfigId: this.internetAccountId,
-              ids,
+    return assemblies.map((assembly) => {
+      const assemblyId = assembly._id.toHexString()
+      const trackId = `sequenceConfigId-${assembly.name}`
+      return {
+        name: assemblyId,
+        aliases:
+          assembly.aliases.length > 0 ? [...assembly.aliases] : [assembly.name],
+        displayName: assembly.displayName || assembly.name,
+        sequence: {
+          trackId,
+          type: 'ReferenceSequenceTrack',
+          adapter: {
+            type: 'ApolloSequenceAdapter',
+            assemblyId,
+            baseURL: {
+              uri: url,
+              locationType: 'UriLocation',
             },
           },
-          refNameAliases: {
-            adapter: {
-              type: 'ApolloRefNameAliasAdapter',
-              assemblyId,
-              baseURL: { uri: url, locationType: 'UriLocation' },
+          displays: [
+            {
+              type: 'LinearApolloReferenceSequenceDisplay',
+              displayId: `${trackId}-LinearApolloReferenceSequenceDisplay`,
             },
+          ],
+          metadata: {
+            apollo: true,
+            internetAccountConfigId: this.internetAccountId,
+          },
+        },
+        refNameAliases: {
+          adapter: {
+            type: 'ApolloRefNameAliasAdapter',
+            assemblyId,
+            baseURL: { uri: url, locationType: 'UriLocation' },
           },
-        }
-      }),
-    )
+        },
+      }
+    })
   }
 
   async getTracks() {

packages/apollo-common/src/Change.ts

@@ -27,7 +27,7 @@ export interface ClientDataStore {
     assemblyName?: string,
     internetAccountId?: string,
   ): AppRootModel['internetAccounts'][0]
-  loadFeatures(regions: Region[]): void
+  loadFeatures(regions: Region[]): Promise<void>
   loadRefSeq(regions: Region[]): void
   getFeature(featureId: string): AnnotationFeature | undefined
   addFeature(assemblyId: string, feature: AnnotationFeatureSnapshot): void

packages/apollo-shared/src/Changes/AddFeatureChange.ts

@@ -167,9 +167,23 @@ export class AddFeatureChange extends FeatureChange {
     for (const change of changes) {
       const { addedFeature, parentFeatureId } = change
       if (parentFeatureId) {
-        const parentFeature = dataStore.getFeature(parentFeatureId)
+        let parentFeature = dataStore.getFeature(parentFeatureId)
+        // maybe the parent feature hasn't been loaded yet
         if (!parentFeature) {
-          throw new Error(`Could not find parent feature "${parentFeatureId}"`)
+          await dataStore.loadFeatures([
+            {
+              assemblyName: assembly,
+              refName: addedFeature.refSeq,
+              start: addedFeature.min,
+              end: addedFeature.max,
+            },
+          ])
+          parentFeature = dataStore.getFeature(parentFeatureId)
+          if (!parentFeature) {
+            throw new Error(
+              `Could not find parent feature "${parentFeatureId}"`,
+            )
+          }
         }
         // create an ID for the parent feature if it does not have one
         if (!parentFeature.attributes.get('_id')) {

packages/jbrowse-plugin-apollo/src/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.ts

@@ -6,7 +6,6 @@ import {
 import type RpcServer from 'librpc-web-mod/dist/server'
 import { nanoid } from 'nanoid'
 
-import { type BackendDriver } from '../BackendDrivers'
 import { type ApolloSessionModel } from '../session'
 
 import { type RefNameAliases } from './../BackendDrivers/BackendDriver'
@@ -50,9 +49,10 @@ export default class RefNameAliasAdapter
       if (!dataStore) {
         throw new Error('No Apollo data store found')
       }
-      const backendDriver = dataStore.getBackendDriver(
-        assemblyId,
-      ) as BackendDriver
+      const backendDriver = dataStore.getBackendDriver(assemblyId)
+      if (!backendDriver) {
+        throw new Error('No backend driver found')
+      }
       const refNameAliases = await backendDriver.getRefNameAliases(assemblyId)
       return refNameAliases
     }

packages/jbrowse-plugin-apollo/src/ApolloSequenceAdapter/ApolloSequenceAdapter.ts

@@ -10,7 +10,6 @@ import SimpleFeature, { type Feature } from '@jbrowse/core/util/simpleFeature'
 import { type NoAssemblyRegion, type Region } from '@jbrowse/core/util/types'
 import { nanoid } from 'nanoid'
 
-import { type BackendDriver } from '../BackendDrivers'
 import { type ApolloSessionModel } from '../session'
 
 // declare global {
@@ -62,9 +61,10 @@ export class ApolloSequenceAdapter extends BaseSequenceAdapter {
       if (!dataStore) {
         throw new Error('No Apollo data store found')
       }
-      const backendDriver = dataStore.getBackendDriver(
-        assemblyId,
-      ) as BackendDriver
+      const backendDriver = dataStore.getBackendDriver(assemblyId)
+      if (!backendDriver) {
+        throw new Error('No backend driver found')
+      }
       const regions = await backendDriver.getRegions(assemblyId)
       this.regions = regions
       return regions
@@ -124,9 +124,11 @@ export class ApolloSequenceAdapter extends BaseSequenceAdapter {
           observer.error('No Apollo data store found')
           return
         }
-        const backendDriver = dataStore.getBackendDriver(
-          assemblyId,
-        ) as BackendDriver
+        const backendDriver = dataStore.getBackendDriver(assemblyId)
+        if (!backendDriver) {
+          observer.error('No backend driver found')
+          return
+        }
         const regions = await backendDriver.getRegions(
           regionWithAssemblyName.assemblyName,
         )

packages/jbrowse-plugin-apollo/src/BackendDrivers/CollaborationServerDriver.ts

@@ -38,6 +38,14 @@ export interface ApolloRefSeqResponse {
   assembly: string
 }
 
+interface RefSeq {
+  refName: string
+  id: string
+  aliases: string[]
+}
+
+type RefSeqMap = Map<string, RefSeq>
+
 export interface ApolloInternetAccount extends BaseInternetAccountModel {
   baseURL: string
   socket: Socket
@@ -48,6 +56,8 @@ export interface ApolloInternetAccount extends BaseInternetAccountModel {
 export class CollaborationServerDriver extends BackendDriver {
   private inFlight = new Map<string, Promise<string>>()
 
+  private refSeqMaps = new Map<string, RefSeqMap>()
+
   private async fetch(
     internetAccount: ApolloInternetAccount,
     info: RequestInfo,
@@ -97,13 +107,12 @@ export class CollaborationServerDriver extends BackendDriver {
     if (!assembly) {
       throw new Error(`Could not find assembly with name "${assemblyName}"`)
     }
-    const { ids } = getConf(assembly, ['sequence', 'metadata']) as {
-      ids: Record<string, string>
-    }
-    const refSeq = ids[refName]
-    if (!refSeq) {
+    const refSeqMap = await this.getRefSeqMapping(assemblyName)
+    const refSeqEntry = refSeqMap.get(refName)
+    if (!refSeqEntry) {
       throw new Error(`Could not find refSeq "${refName}"`)
     }
+    const refSeq = refSeqEntry.id
     const internetAccount = this.clientStore.getInternetAccount(
       assemblyName,
     ) as ApolloInternetAccount
@@ -192,13 +201,12 @@ export class CollaborationServerDriver extends BackendDriver {
     if (!assembly) {
       throw new Error(`Could not find assembly with name "${assemblyName}"`)
     }
-    const { ids } = getConf(assembly, ['sequence', 'metadata']) as {
-      ids: Record<string, string>
-    }
-    const refSeq = ids[refName]
-    if (!refSeq) {
+    const refSeqMap = await this.getRefSeqMapping(assemblyName)
+    const refSeqEntry = refSeqMap.get(refName)
+    if (!refSeqEntry) {
       throw new Error(`Could not find refSeq "${refName}"`)
     }
+    const refSeq = refSeqEntry.id
     if (inFlightPromise) {
       const seq = await inFlightPromise
       return { seq, refSeq }
@@ -269,7 +277,11 @@ export class CollaborationServerDriver extends BackendDriver {
     return seq
   }
 
-  async getRefNameAliases(assemblyName: string): Promise<RefNameAliases[]> {
+  async getRefSeqMapping(assemblyName: string): Promise<RefSeqMap> {
+    const cachedRefSeqMap = this.refSeqMaps.get(assemblyName)
+    if (cachedRefSeqMap) {
+      return cachedRefSeqMap
+    }
     const { assemblyManager } = getSession(this.clientStore)
     const assembly = assemblyManager.get(assemblyName)
     if (!assembly) {
@@ -299,13 +311,32 @@ export class CollaborationServerDriver extends BackendDriver {
       )
     }
     const refSeqs = (await response.json()) as ApolloRefSeqResponse[]
-    return refSeqs.map((refSeq) => {
-      return {
-        refName: refSeq.name,
-        aliases: [...new Set([refSeq._id, ...refSeq.aliases])],
-        uniqueId: `alias-${refSeq._id}`,
-      }
-    }) as RefNameAliases[]
+    const refSeqMap = new Map<string, RefSeq>(
+      refSeqs.map((refSeq) => [
+        refSeq.name,
+        { refName: refSeq.name, id: refSeq._id, aliases: refSeq.aliases },
+      ]),
+    )
+    this.refSeqMaps.set(assemblyName, refSeqMap)
+    return refSeqMap
+  }
+
+  async getRefNameAliases(assemblyName: string): Promise<RefNameAliases[]> {
+    const refSeqMap = await this.getRefSeqMapping(assemblyName)
+    return [...refSeqMap.values()].map((refSeq) => ({
+      refName: refSeq.refName,
+      aliases: [...new Set([refSeq.id, ...refSeq.aliases])],
+      uniqueId: `alias-${refSeq.id}`,
+    }))
+  }
+
+  async getRefSeqId(assemblyName: string, refName: string) {
+    const refSeqMap = await this.getRefSeqMapping(assemblyName)
+    if (!refSeqMap) {
+      return
+    }
+    const refSeq = refSeqMap.get(refName)
+    return refSeq?.id
   }
 
   async getRegions(assemblyName: string): Promise<Region[]> {

packages/jbrowse-plugin-apollo/src/ChangeManager.ts

@@ -106,7 +106,9 @@ export class ChangeManager {
       // submit to driver
       const { collaborationServerDriver, getBackendDriver } = this.dataStore
       const backendDriver = isAssemblySpecificChange(change)
-        ? getBackendDriver(change.assembly)
+        ? // for assembly-specific change, fall back in case it's an
+          // add-assembly change, since that won't exist in the driver yet
+          getBackendDriver(change.assembly) ?? collaborationServerDriver
         : collaborationServerDriver
       let backendResult: ValidationResultSet
       try {

packages/jbrowse-plugin-apollo/src/components/AddAssembly.tsx

@@ -178,13 +178,12 @@ export function AddAssembly({
     const formData = new FormData()
     let filename = file.name
     const isGzip =
+      fileType === FileType.BGZIP_FASTA ||
       (fileType === FileType.FASTA &&
         (!sequenceIsEditable || fastaGzipChecked)) ||
       (fileType === FileType.GFF3 && gff3GzipChecked)
 
-    if (fileType === FileType.FAI || fileType === FileType.GZI) {
-      filename = `${filename}.txt`
-    } else if (isGzip && !file.name.toLocaleLowerCase().endsWith('.gz')) {
+    if (isGzip && !file.name.toLocaleLowerCase().endsWith('.gz')) {
       filename = `${filename}.gz`
     } else if (!isGzip && file.name.toLocaleLowerCase().endsWith('.gz')) {
       filename = `${filename}.txt`