Create ApolloRefNameAliasAdapter (GMOD#417)

* ref name alias apollo configuration

* Fix error message

---------

Co-authored-by: Garrett Stevens <stevens.garrett.j@gmail.com>

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

@@ -0,0 +1,94 @@
+import { RefNameAliases } from './../BackendDrivers/BackendDriver'
+import {
+  BaseRefNameAliasAdapter,
+  BaseAdapter,
+} from '@jbrowse/core/data_adapters/BaseAdapter'
+import { readConfObject } from '@jbrowse/core/configuration'
+import { ApolloSessionModel } from '../session'
+import { BackendDriver } from '../BackendDrivers'
+import { nanoid } from 'nanoid'
+import RpcServer from 'librpc-web-mod/dist/server'
+
+declare global {
+  const rpcServer: RpcServer
+}
+
+interface ApolloRefNameAliasMessage {
+  apollo: true
+  messageId: string
+  refNameAliases: RefNameAliases[]
+}
+
+function isApolloRefNameAliasMessage(
+  data?: unknown,
+): data is ApolloRefNameAliasMessage {
+  return (
+    typeof data === 'object' &&
+    data !== null &&
+    'apollo' in data &&
+    data.apollo === true &&
+    'refNameAliases' in data
+  )
+}
+
+const isInWebWorker = typeof sessionStorage === 'undefined'
+
+export default class RefNameAliasAdapter
+  extends BaseAdapter
+  implements BaseRefNameAliasAdapter
+{
+  private refNameAliases: RefNameAliases[] | undefined
+
+  async getRefNameAliases() {
+    const assemblyId = readConfObject(this.config, 'assemblyId') as string
+    if (!isInWebWorker) {
+      const dataStore = (
+        this.pluginManager?.rootModel?.session as ApolloSessionModel | undefined
+      )?.apolloDataStore
+      if (!dataStore) {
+        throw new Error('No Apollo data store found')
+      }
+      const backendDriver = dataStore.getBackendDriver(
+        assemblyId,
+      ) as BackendDriver
+      const refNameAliases = await backendDriver.getRefNameAliases(assemblyId)
+      return refNameAliases
+    }
+    const refNameAliases = await new Promise(
+      (
+        resolve: (refNameAliases: RefNameAliases[]) => void,
+        reject: (reason: Error) => void,
+      ) => {
+        const timeoutId = setTimeout(() => {
+          reject(new Error('timeout'))
+        }, 20_000)
+        const messageId = nanoid()
+        const messageListener = (event: MessageEvent) => {
+          const data = event.data as ApolloRefNameAliasMessage
+          if (!isApolloRefNameAliasMessage(data)) {
+            return
+          }
+          if (data.messageId !== messageId) {
+            return
+          }
+          clearTimeout(timeoutId)
+          removeEventListener('message', messageListener)
+          resolve(data.refNameAliases)
+        }
+        addEventListener('message', messageListener)
+        rpcServer.emit('apollo', {
+          apollo: true,
+          method: 'getRefNameAliases',
+          assembly: assemblyId,
+          messageId,
+        })
+      },
+    )
+    this.refNameAliases = refNameAliases
+    return refNameAliases
+  }
+
+  async freeResources() {
+    // no resources to free
+  }
+}

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

@@ -0,0 +1,12 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+export default ConfigurationSchema(
+  'ApolloRefNameAliasAdapter',
+  {
+    assemblyId: {
+      type: 'string',
+      defaultValue: '',
+    },
+  },
+  { explicitlyTyped: true },
+)

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

@@ -0,0 +1,21 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
+import PluginManager from '@jbrowse/core/PluginManager'
+
+import configSchema from './configSchema'
+import ApolloRefNameAliasAdapter from './ApolloRefNameAliasAdapter'
+
+export function installApolloRefNameAliasAdapter(pluginManager: PluginManager) {
+  pluginManager.addAdapterType(
+    () =>
+      new AdapterType({
+        name: 'ApolloRefNameAliasAdapter',
+        configSchema,
+        adapterMetadata: {
+          category: undefined,
+          hiddenFromGUI: true,
+          description: undefined,
+        },
+        AdapterClass: ApolloRefNameAliasAdapter,
+      }),
+  )
+}

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

@@ -9,6 +9,12 @@ import { Region } from '@jbrowse/core/util'
 
 import { SubmitOpts } from '../ChangeManager'
 
+export interface RefNameAliases {
+  refName: string
+  aliases: string[]
+  uniqueId: string
+}
+
 export abstract class BackendDriver {
   constructor(protected clientStore: ClientDataStore) {}
 
@@ -22,6 +28,8 @@ export abstract class BackendDriver {
 
   abstract getAssemblies(internetAccountConfigId?: string): Assembly[]
 
+  abstract getRefNameAliases(assemblyName: string): Promise<RefNameAliases[]>
+
   abstract submitChange(
     change: Change,
     opts: SubmitOpts,

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

@@ -18,7 +18,8 @@ import { Socket } from 'socket.io-client'
 
 import { ChangeManager, SubmitOpts } from '../ChangeManager'
 import { createFetchErrorMessage } from '../util'
-import { BackendDriver } from './BackendDriver'
+import { BackendDriver, RefNameAliases } from './BackendDriver'
+import { ApolloRefSeqResponse } from '../session'
 
 export interface ApolloInternetAccount extends BaseInternetAccountModel {
   baseURL: string
@@ -235,6 +236,45 @@ export class CollaborationServerDriver extends BackendDriver {
     return seq
   }
 
+  async getRefNameAliases(assemblyName: string): Promise<RefNameAliases[]> {
+    const { assemblyManager } = getSession(this.clientStore)
+    const assembly = assemblyManager.get(assemblyName)
+    if (!assembly) {
+      throw new Error(`Could not find assembly with name "${assemblyName}"`)
+    }
+    const internetAccount = this.clientStore.getInternetAccount(
+      assemblyName,
+    ) as ApolloInternetAccount
+    const { baseURL } = internetAccount
+    const url = new URL('refSeqs', baseURL)
+    const searchParams = new URLSearchParams({ assembly: assemblyName })
+    url.search = searchParams.toString()
+    const uri = url.toString()
+
+    const response = await this.fetch(internetAccount, uri)
+    if (!response.ok) {
+      let errorMessage
+      try {
+        errorMessage = await response.text()
+      } catch {
+        errorMessage = ''
+      }
+      throw new Error(
+        `getRefNameAliases failed: ${response.status} (${response.statusText})${
+          errorMessage ? ` (${errorMessage})` : ''
+        }`,
+      )
+    }
+    const refSeqs = (await response.json()) as ApolloRefSeqResponse[]
+    return refSeqs.map((refSeq) => {
+      return {
+        refName: refSeq.name,
+        aliases: [refSeq._id],
+        uniqueId: `alias-${refSeq._id}`,
+      }
+    }) as RefNameAliases[]
+  }
+
   async getRegions(assemblyName: string): Promise<Region[]> {
     const { assemblyManager } = getSession(this.clientStore)
     const assembly = assemblyManager.get(assemblyName)

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

@@ -19,7 +19,7 @@ import { Region, getSession } from '@jbrowse/core/util'
 import { getSnapshot } from 'mobx-state-tree'
 
 import { checkFeatures, loadAssemblyIntoClient } from '../util'
-import { BackendDriver } from './BackendDriver'
+import { BackendDriver, RefNameAliases } from './BackendDriver'
 
 export class DesktopFileDriver extends BackendDriver {
   async loadAssembly(assemblyName: string) {
@@ -45,6 +45,19 @@ export class DesktopFileDriver extends BackendDriver {
     return assembly
   }
 
+  async getRefNameAliases(assemblyName: string): Promise<RefNameAliases[]> {
+    const assembly = await this.getAssembly(assemblyName)
+    const refNameAliases: RefNameAliases[] = []
+    for (const [, refSeq] of assembly.refSeqs) {
+      refNameAliases.push({
+        refName: refSeq.name,
+        aliases: [refSeq._id],
+        uniqueId: `alias-${refSeq._id}`,
+      })
+    }
+    return refNameAliases
+  }
+
   async getFeatures(
     region: Region,
   ): Promise<[AnnotationFeatureSnapshot[], CheckResultSnapshot[]]> {

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

@@ -9,7 +9,7 @@ import { getConf } from '@jbrowse/core/configuration'
 import { Region, getSession } from '@jbrowse/core/util'
 
 import { SubmitOpts } from '../ChangeManager'
-import { BackendDriver } from './BackendDriver'
+import { BackendDriver, RefNameAliases } from './BackendDriver'
 
 export class InMemoryFileDriver extends BackendDriver {
   async getFeatures(): Promise<
@@ -32,6 +32,22 @@ export class InMemoryFileDriver extends BackendDriver {
     return { seq, refSeq: refName }
   }
 
+  async getRefNameAliases(assemblyName: string): Promise<RefNameAliases[]> {
+    const assembly = this.clientStore.assemblies.get(assemblyName)
+    const refNameAliases: RefNameAliases[] = []
+    if (!assembly) {
+      return refNameAliases
+    }
+    for (const [, refSeq] of assembly.refSeqs) {
+      refNameAliases.push({
+        refName: refSeq.name,
+        aliases: [refSeq._id],
+        uniqueId: `alias-${refSeq._id}`,
+      })
+    }
+    return refNameAliases
+  }
+
   async getRegions(assemblyName: string): Promise<Region[]> {
     const assembly = this.clientStore.assemblies.get(assemblyName)
     if (!assembly) {

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

@@ -72,6 +72,7 @@ import {
   stateModelFactory as SixFrameFeatureDisplayStateModelFactory,
   configSchemaFactory as sixFrameFeatureDisplayConfigSchemaFactory,
 } from './SixFrameFeatureDisplay'
+import { installApolloRefNameAliasAdapter } from './ApolloRefNameAliasAdapter'
 
 interface RpcHandle {
   on(event: string, listener: (event: MessageEvent) => void): this
@@ -114,6 +115,7 @@ export default class ApolloPlugin extends Plugin {
 
   install(pluginManager: PluginManager) {
     installApolloSequenceAdapter(pluginManager)
+    installApolloRefNameAliasAdapter(pluginManager)
     installApolloTextSearchAdapter(pluginManager)
 
     pluginManager.addWidgetType(() => {
@@ -317,6 +319,28 @@ export default class ApolloPlugin extends Plugin {
                 })
                 break
               }
+              case 'getRefNameAliases': {
+                const { assembly } = event
+                const dataStore = (
+                  pluginManager.rootModel?.session as
+                    | ApolloSessionModel
+                    | undefined
+                )?.apolloDataStore
+                if (!dataStore) {
+                  break
+                }
+                const backendDriver = dataStore.getBackendDriver(
+                  assembly,
+                ) as BackendDriver
+                const refNameAliases =
+                  await backendDriver.getRefNameAliases(assembly)
+                handle.workers[0].postMessage({
+                  apollo,
+                  messageId,
+                  refNameAliases,
+                })
+                break
+              }
               default: {
                 break
               }

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

@@ -318,11 +318,6 @@ export function extendSession(
             const ids: Record<string, string> = {}
             const refNameAliasesFeatures = f.map((contig) => {
               ids[contig.name] = contig._id
-              return {
-                refName: contig.name,
-                aliases: [contig._id],
-                uniqueId: `alias-${contig._id}`,
-              }
             })
             const assemblyConfig = {
               name: assembly._id,
@@ -344,8 +339,9 @@ export function extendSession(
               },
               refNameAliases: {
                 adapter: {
-                  type: 'FromConfigAdapter',
-                  features: refNameAliasesFeatures,
+                  type: 'ApolloRefNameAliasAdapter',
+                  assemblyId: assembly._id,
+                  baseURL: { uri: baseURL, locationType: 'UriLocation' },
                 },
               },
             }