@apollo-annotation/jbrowse-plugin-apollo 0.3.8 → 0.3.10

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/jbrowse-plugin-apollo",
-  "version": "0.3.8",
+  "version": "0.3.10",
   "description": "Apollo plugin for JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -27,7 +27,7 @@
     "start:watch": "JB_NPM=false NODE_ENV=development rollup --config --watch",
     "start:server": "serve --no-request-logging --cors --listen 9000 --no-port-switching .",
     "build": "yarn build:shared && yarn clean && rollup --config",
-    "browse": "serve --no-request-logging --listen 8999 --no-port-switching .jbrowse",
+    "browse": "serve --no-request-logging --listen 8999 --no-port-switching --symlinks .jbrowse",
     "test": "jest",
     "test:ci": "jest --coverage",
     "start:collab-cypress": "yarn workspace @apollo-annotation/collaboration-server run cypress:start",
@@ -48,12 +48,12 @@
     }
   },
   "dependencies": {
-    "@apollo-annotation/common": "^0.3.8",
-    "@apollo-annotation/mst": "^0.3.8",
-    "@apollo-annotation/shared": "^0.3.8",
+    "@apollo-annotation/common": "^0.3.10",
+    "@apollo-annotation/mst": "^0.3.10",
+    "@apollo-annotation/shared": "^0.3.10",
     "@emotion/react": "^11.10.6",
     "@emotion/styled": "^11.10.6",
-    "@gmod/gff": "1.2.0",
+    "@gmod/gff": "^2.0.0",
     "@jbrowse/plugin-authentication": "^3.6.5",
     "@jbrowse/plugin-linear-genome-view": "^3.6.5",
     "@mui/icons-material": "^6.5.0",
@@ -79,7 +79,7 @@
     "@mui/x-data-grid": "^8.0.0",
     "@types/autosuggest-highlight": "^3",
     "@types/file-saver": "^2",
-    "@types/node": "^18.14.2",
+    "@types/node": "^20.19.15",
     "@types/prop-types": "^15",
     "@types/react": "^18.3.4",
     "@types/react-dom": "^18",

package/src/ApolloInternetAccount/components/AuthTypeSelector.tsx

@@ -57,7 +57,7 @@ export const AuthTypeSelector = ({
       }
     })
     return () => {
-      controller.abort()
+      controller.abort('AuthTypeSelector')
     }
   }, [baseURL])
 

package/src/ApolloInternetAccount/model.ts

@@ -64,32 +64,20 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
       controller: new AbortController(),
     }))
 
-    .actions((self) => {
-      let roleNotificationSent = false
-      return {
-        setRole() {
-          const token = self.retrieveToken()
-          if (!token) {
-            self.role = undefined
-            return
-          }
-          const dec = getDecodedToken(token)
-          const { role } = dec
-          if (!role && !roleNotificationSent) {
-            const { session } = getRoot<ApolloRootModel>(self)
-            ;(session as unknown as AbstractSessionModel).notify(
-              'You have registered as a user but have not been given access. Ask your administrator to enable access for your account.',
-              'warning',
-            )
-            // notify
-            roleNotificationSent = true
-          }
-          if (self.role !== role) {
-            self.role = role
-          }
-        },
-      }
-    })
+    .actions((self) => ({
+      setRole() {
+        const token = self.retrieveToken()
+        if (!token) {
+          self.role = undefined
+          return
+        }
+        const dec = getDecodedToken(token)
+        const { role } = dec
+        if (self.role !== role) {
+          self.role = role
+        }
+      },
+    }))
     .actions((self) => {
       let listener: (event: MessageEvent) => void
       return {
@@ -380,7 +368,7 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
     }))
     .actions((self) => {
       async function postUserLocation(userLoc: UserLocation[]) {
-        if (!isAlive(self)) {
+        if (!isAlive(self) || self.role === 'none') {
           return
         }
         const { baseURL, controller } = self
@@ -418,45 +406,73 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
       }
       return { postUserLocation: debouncePostUserLocation(postUserLocation) }
     })
-    .actions((self) => ({
-      initialize: flow(function* initialize(role: Role) {
-        if (role === 'admin') {
-          const rootModel = getRoot(self)
-          if (isAbstractMenuManager(rootModel)) {
-            addTopLevelAdminMenus(rootModel)
-          }
-        }
-        // Get and set server last change sequence into session storage
-        yield self.updateLastChangeSequenceNumber()
-        // Open socket listeners
-        self.addSocketListeners()
-        // request user locations
-        const { baseURL } = self
-        const uri = new URL('users/locations', baseURL).href
-        const apolloFetch = self.getFetcher({
-          locationType: 'UriLocation',
-          uri,
-        })
-        yield apolloFetch(uri, {
-          method: 'GET',
-          signal: self.controller.signal,
-        })
-        window.addEventListener('beforeunload', () => {
+    .volatile(() => ({ roleNotificationSent: false }))
+    .actions((self) => {
+      function beforeUnloadListener() {
+        self.postUserLocation([])
+      }
+      function visibilityChangeListener() {
+        // fires when user switches tabs, apps, goes to homescreen, etc.
+        if (document.visibilityState === 'hidden') {
           self.postUserLocation([])
-        })
-        document.addEventListener('visibilitychange', () => {
-          // fires when user switches tabs, apps, goes to homescreen, etc.
-          if (document.visibilityState === 'hidden') {
-            self.postUserLocation([])
+        }
+        // fires when app transitions from prerender, user returns to the app / tab.
+        if (document.visibilityState === 'visible') {
+          const { session } = getRoot<ApolloRootModel>(self)
+          session.broadcastLocations()
+        }
+      }
+      return {
+        initialize: flow(function* initialize(role: Role) {
+          if (role === 'none') {
+            if (!self.roleNotificationSent) {
+              const { session } = getRoot<ApolloRootModel>(self)
+              ;(session as unknown as AbstractSessionModel).notify(
+                'You have registered as an Apollo user but have not been given access. Ask your administrator to enable access for your account.',
+                'warning',
+              )
+              self.roleNotificationSent = true
+            }
+            return
           }
-          // fires when app transitions from prerender, user returns to the app / tab.
-          if (document.visibilityState === 'visible') {
-            const { session } = getRoot<ApolloRootModel>(self)
-            session.broadcastLocations()
+          if (role === 'admin') {
+            const rootModel = getRoot(self)
+            if (isAbstractMenuManager(rootModel)) {
+              addTopLevelAdminMenus(rootModel)
+            }
           }
-        })
-      }),
-    }))
+          // Get and set server last change sequence into session storage
+          yield self.updateLastChangeSequenceNumber()
+          // Open socket listeners
+          self.addSocketListeners()
+          // request user locations
+          const { baseURL } = self
+          const uri = new URL('users/locations', baseURL).href
+          const apolloFetch = self.getFetcher({
+            locationType: 'UriLocation',
+            uri,
+          })
+          yield apolloFetch(uri, {
+            method: 'GET',
+            signal: self.controller.signal,
+          })
+          window.addEventListener('beforeunload', beforeUnloadListener)
+          document.addEventListener(
+            'visibilitychange',
+            visibilityChangeListener,
+          )
+        }),
+        removeBeforeUnloadListener() {
+          window.removeEventListener('beforeunload', beforeUnloadListener)
+        },
+        removeVisibilityChangeListener() {
+          document.removeEventListener(
+            'visibilitychange',
+            visibilityChangeListener,
+          )
+        },
+      }
+    })
     .actions((self) => ({
       afterAttach() {
         self.setRole()
@@ -473,14 +489,20 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
               return
             }
             if (self.role) {
-              await self.initialize(self.role)
-              reaction.dispose()
+              try {
+                await self.initialize(self.role)
+                reaction.dispose()
+              } catch {
+                // if initialize fails, do nothing so the autorun runs again
+              }
             }
           },
           { name: 'ApolloInternetAccount' },
         )
       },
       beforeDestroy() {
+        self.removeBeforeUnloadListener()
+        self.removeVisibilityChangeListener()
         self.controller.abort('internet account beforeDestroy')
         self.socket.close()
       },

package/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
     }

package/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,
         )

package/src/BackendDrivers/CollaborationServerDriver.ts

@@ -18,6 +18,7 @@ import {
 import {
   type ChangeMessage,
   ValidationResultSet,
+  makeUserSessionId,
 } from '@apollo-annotation/shared'
 import { getConf } from '@jbrowse/core/configuration'
 import { type BaseInternetAccountModel } from '@jbrowse/core/pluggableElementTypes'
@@ -38,6 +39,14 @@ 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 +57,8 @@ 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 +108,12 @@ 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
@@ -145,6 +155,10 @@ export class CollaborationServerDriver extends BackendDriver {
   ) {
     const { socket } = internetAccount
     const token = internetAccount.retrieveToken()
+    if (!token) {
+      return
+    }
+    const localSessionId = makeUserSessionId(token)
     const channel = `${assembly}-${refSeq}`
     const changeManager = new ChangeManager(this.clientStore)
 
@@ -154,11 +168,12 @@ export class CollaborationServerDriver extends BackendDriver {
         internetAccount.setLastChangeSequenceNumber(
           Number(message.changeSequence),
         )
-        if (message.userSessionId !== token && message.channel === channel) {
-          const change = Change.fromJSON(message.changeInfo)
-          if (isFeatureChange(change) && this.haveDataForChange(change)) {
-            await changeManager.submit(change, { submitToBackend: false })
-          }
+        if (message.userSessionId === localSessionId) {
+          return // we did this change, no need to apply it again
+        }
+        const change = Change.fromJSON(message.changeInfo)
+        if (isFeatureChange(change) && this.haveDataForChange(change)) {
+          await changeManager.submit(change, { submitToBackend: false })
         }
       })
     }
@@ -192,13 +207,12 @@ 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 +283,11 @@ 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 +317,32 @@ export class CollaborationServerDriver extends BackendDriver {
       )
     }
     const refSeqs = (await response.json()) as ApolloRefSeqResponse[]
-    return refSeqs.map((refSeq) => {
-      return {
-        refName: refSeq.name,
-        aliases: [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[]> {

package/src/BackendDrivers/DesktopFileDriver.ts

@@ -13,7 +13,7 @@ import {
   annotationFeatureToGFF3,
   splitStringIntoChunks,
 } from '@apollo-annotation/shared'
-import gff, { type GFF3Item } from '@gmod/gff'
+import { type GFF3Item, formatSync } from '@gmod/gff'
 import { getConf } from '@jbrowse/core/configuration'
 import { type Region, getSession } from '@jbrowse/core/util'
 import { getSnapshot } from 'mobx-state-tree'
@@ -165,7 +165,7 @@ export class DesktopFileDriver extends BackendDriver {
       })
     }
 
-    const gff3Contents = gff.formatSync(gff3Items)
+    const gff3Contents = formatSync(gff3Items)
 
     // eslint-disable-next-line @typescript-eslint/no-require-imports, @typescript-eslint/consistent-type-imports
     const fs = require('node:fs') as typeof import('fs')

package/src/ChangeManager.ts

@@ -42,21 +42,31 @@ export class ChangeManager {
     const session = getSession(this.dataStore)
     const controller = new AbortController()
 
-    const { jobsManager, isLocked } = getSession(
-      this.dataStore,
-    ) as unknown as ApolloSessionModel
+    // eslint-disable-next-line @typescript-eslint/unbound-method
+    const { jobsManager, isLocked, changeInProgress, setChangeInProgress } =
+      getSession(this.dataStore) as unknown as ApolloSessionModel
 
     if (isLocked) {
       session.notify('Cannot submit changes in locked mode')
+      setChangeInProgress(false)
       return
     }
 
+    if (changeInProgress) {
+      session.notify(
+        'Could not submit change, there is another change still in progress',
+      )
+      return
+    }
+
+    setChangeInProgress(true)
+
     const job = {
       name: change.typeName,
       statusMessage: 'Pre-validating',
       progressPct: 0,
       cancelCallback: () => {
-        controller.abort()
+        controller.abort('ChangeManager')
       },
     }
 
@@ -71,6 +81,7 @@ export class ChangeManager {
         jobsManager.abortJob(job.name, msg)
       }
       session.notify(msg, 'error')
+      setChangeInProgress(false)
       return
     }
 
@@ -86,6 +97,7 @@ export class ChangeManager {
         `Error encountered in client: ${String(error)}. Data may be out of sync, please refresh the page`,
         'error',
       )
+      setChangeInProgress(false)
       return
     }
 
@@ -106,7 +118,9 @@ 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 {
@@ -118,6 +132,7 @@ export class ChangeManager {
         console.error(error)
         session.notify(String(error), 'error')
         await this.undo(change, false)
+        setChangeInProgress(false)
         return
       }
       if (!backendResult.ok) {
@@ -127,6 +142,7 @@ export class ChangeManager {
         }
         session.notify(msg, 'error')
         await this.undo(change, false)
+        setChangeInProgress(false)
         return
       }
       if (change.notification) {
@@ -141,6 +157,7 @@ export class ChangeManager {
     if (updateJobsManager) {
       jobsManager.done(job)
     }
+    setChangeInProgress(false)
   }
 
   async undo(change: Change, submitToBackend = true) {

package/src/FeatureDetailsWidget/BasicInformation.tsx

@@ -66,7 +66,7 @@ export const BasicInformation = observer(function BasicInformation({
     return changeManager.submit(change)
   }
 
-  function handleStartChange(newStart: number) {
+  function handleStartChange(newStart: number): boolean {
     newStart--
     const change = new LocationStartChange({
       typeName: 'LocationStartChange',
@@ -76,10 +76,11 @@ export const BasicInformation = observer(function BasicInformation({
       newStart,
       assembly,
     })
-    return changeManager.submit(change)
+    void changeManager.submit(change)
+    return true
   }
 
-  function handleEndChange(newEnd: number) {
+  function handleEndChange(newEnd: number): boolean {
     const change = new LocationEndChange({
       typeName: 'LocationEndChange',
       changedIds: [_id],
@@ -88,7 +89,8 @@ export const BasicInformation = observer(function BasicInformation({
       newEnd,
       assembly,
     })
-    return changeManager.submit(change)
+    void changeManager.submit(change)
+    return true
   }
 
   async function fetchValidTerms(

package/src/FeatureDetailsWidget/NumberTextField.tsx

@@ -15,7 +15,7 @@ interface NumberTextFieldProps
     | 'error'
     | 'helperText'
   > {
-  onChangeCommitted(newValue: number): void
+  onChangeCommitted(newValue: number): boolean
   value: unknown
 }
 
@@ -65,7 +65,10 @@ export const NumberTextField = observer(function NumberTextField({
           if (Number.isNaN(valueAsNumber)) {
             setValue(String(initialValue))
           } else {
-            onChangeCommitted(valueAsNumber)
+            const success = onChangeCommitted(valueAsNumber)
+            if (!success) {
+              setValue(String(initialValue))
+            }
           }
         }
       }}