Add authentication plugin to embedded components (#3298)

component_tests/cgv/package.json

@@ -27,6 +27,7 @@
   "resolutions": {
     "@jbrowse/core": "file:./packed/jbrowse-core.tgz",
     "@jbrowse/plugin-alignments": "file:./packed/jbrowse-plugin-alignments.tgz",
+    "@jbrowse/plugin-authentication": "file:./packed/jbrowse-plugin-authentication.tgz",
     "@jbrowse/plugin-bed": "file:./packed/jbrowse-plugin-bed.tgz",
     "@jbrowse/plugin-circular-view": "file:./packed/jbrowse-plugin-circular-view.tgz",
     "@jbrowse/plugin-config": "file:./packed/jbrowse-plugin-config.tgz",

component_tests/lgv/package.json

@@ -27,6 +27,7 @@
   "resolutions": {
     "@jbrowse/core": "file:./packed/jbrowse-core.tgz",
     "@jbrowse/plugin-alignments": "file:./packed/jbrowse-plugin-alignments.tgz",
+    "@jbrowse/plugin-authentication": "file:./packed/jbrowse-plugin-authentication.tgz",
     "@jbrowse/plugin-bed": "file:./packed/jbrowse-plugin-bed.tgz",
     "@jbrowse/plugin-circular-view": "file:./packed/jbrowse-plugin-circular-view.tgz",
     "@jbrowse/plugin-config": "file:./packed/jbrowse-plugin-config.tgz",

packages/core/util/io/index.ts

@@ -12,7 +12,7 @@ import {
   FileLocation,
   LocalPathLocation,
   BlobLocation,
-  isAppRootModel,
+  isRootModelWithInternetAccounts,
   isUriLocation,
   AuthNeededError,
   UriLocation,
@@ -109,7 +109,7 @@ function getInternetAccount(
 ): BaseInternetAccountModel | undefined {
   const { rootModel } = pluginManager
   // If there is an appRootModel, use it to find the internetAccount
-  if (rootModel && isAppRootModel(rootModel)) {
+  if (rootModel && isRootModelWithInternetAccounts(rootModel)) {
     return rootModel.findAppropriateInternetAccount(location)
   }
   // If there is no appRootModel, but there is pre-auth, create a temporary

packages/core/util/types/index.ts

@@ -324,6 +324,24 @@ export function isAppRootModel(thing: unknown): thing is AppRootModel {
   )
 }
 
+export interface RootModelWithInternetAccounts extends AbstractRootModel {
+  internetAccounts: BaseInternetAccountModel[]
+  findAppropriateInternetAccount(
+    location: UriLocation,
+  ): BaseInternetAccountModel | undefined
+}
+
+export function isRootModelWithInternetAccounts(
+  thing: unknown,
+): thing is RootModelWithInternetAccounts {
+  return (
+    typeof thing === 'object' &&
+    thing !== null &&
+    'internetAccounts' in thing &&
+    'findAppropriateInternetAccount' in thing
+  )
+}
+
 /** a root model that manages global menus */
 export interface AbstractMenuManager {
   appendMenu(menuName: string): void

products/jbrowse-desktop/src/rootModel.ts

@@ -1,12 +1,10 @@
 import {
   addDisposer,
   cast,
-  resolveIdentifier,
   getSnapshot,
   types,
   SnapshotIn,
   Instance,
-  IAnyModelType,
 } from 'mobx-state-tree'
 import { autorun } from 'mobx'
 import makeWorkerInstance from './makeWorkerInstance'
@@ -129,27 +127,25 @@ export default function rootModelFactory(pluginManager: PluginManager) {
           this.setSession(snapshot)
         }
       },
-      initializeInternetAccount(id: string, initialSnapshot = {}) {
-        const schema = pluginManager.pluggableConfigSchemaType(
-          'internet account',
-        ) as IAnyModelType
-        const configuration = resolveIdentifier(schema, self, id)
-
-        const accountType = pluginManager.getInternetAccountType(
-          configuration.type,
+      initializeInternetAccount(
+        internetAccountConfig: AnyConfigurationModel,
+        initialSnapshot = {},
+      ) {
+        const internetAccountType = pluginManager.getInternetAccountType(
+          internetAccountConfig.type,
         )
-        if (!accountType) {
-          throw new Error(`unknown internet account type ${configuration.type}`)
+        if (!internetAccountType) {
+          throw new Error(
+            `unknown internet account type ${internetAccountConfig.type}`,
+          )
         }
 
-        const internetAccount = accountType.stateModel.create({
+        const length = self.internetAccounts.push({
           ...initialSnapshot,
-          type: configuration.type,
-          configuration,
+          type: internetAccountConfig.type,
+          configuration: internetAccountConfig,
         })
-
-        self.internetAccounts.push(internetAccount)
-        return internetAccount
+        return self.internetAccounts[length - 1]
       },
       createEphemeralInternetAccount(
         internetAccountId: string,
@@ -580,7 +576,7 @@ export default function rootModelFactory(pluginManager: PluginManager) {
           self,
           autorun(() => {
             self.jbrowse.internetAccounts.forEach(account => {
-              self.initializeInternetAccount(account.internetAccountId)
+              self.initializeInternetAccount(account)
             })
           }),
         )

products/jbrowse-react-circular-genome-view/package.json

@@ -44,6 +44,7 @@
     "@emotion/react": "^11.9.0",
     "@emotion/styled": "^11.8.1",
     "@jbrowse/core": "^2.2.0",
+    "@jbrowse/plugin-authentication": "^2.1.7",
     "@jbrowse/plugin-circular-view": "^2.2.0",
     "@jbrowse/plugin-config": "^2.2.0",
     "@jbrowse/plugin-data-management": "^2.2.0",

products/jbrowse-react-circular-genome-view/src/corePlugins.ts

@@ -1,3 +1,4 @@
+import Authentication from '@jbrowse/plugin-authentication'
 import Config from '@jbrowse/plugin-config'
 import DataManagement from '@jbrowse/plugin-data-management'
 import CircularGenomeView from '@jbrowse/plugin-circular-view'
@@ -6,6 +7,7 @@ import Variants from '@jbrowse/plugin-variants'
 import Wiggle from '@jbrowse/plugin-wiggle'
 
 const corePlugins = [
+  Authentication,
   Config,
   DataManagement,
   CircularGenomeView,

products/jbrowse-react-circular-genome-view/src/createModel/createConfigModel.ts

@@ -53,6 +53,9 @@ export default function createConfigModel(
       }),
       assembly: assemblyConfigSchemasType,
       tracks: types.array(pluginManager.pluggableConfigSchemaType('track')),
+      internetAccounts: types.array(
+        pluginManager.pluggableConfigSchemaType('internet account'),
+      ),
       connections: types.array(
         pluginManager.pluggableConfigSchemaType('connection'),
       ),

products/jbrowse-react-circular-genome-view/src/createModel/createModel.ts

@@ -5,6 +5,7 @@ import { PluginConstructor } from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
 import RpcManager from '@jbrowse/core/rpc/RpcManager'
 import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager'
+import { UriLocation } from '@jbrowse/core/util'
 import { cast, getSnapshot, Instance, SnapshotIn, types } from 'mobx-state-tree'
 import corePlugins from '../corePlugins'
 import createConfigModel from './createConfigModel'
@@ -26,6 +27,9 @@ export default function createModel(runtimePlugins: PluginConstructor[]) {
       config: createConfigModel(pluginManager, assemblyConfigSchema),
       session: Session,
       assemblyManager: assemblyManagerType,
+      internetAccounts: types.array(
+        pluginManager.pluggableMstType('internet account', 'stateModel'),
+      ),
     })
     .volatile(() => ({
       error: undefined as Error | undefined,
@@ -44,6 +48,34 @@ export default function createModel(runtimePlugins: PluginConstructor[]) {
       setError(errorMessage: Error | undefined) {
         self.error = errorMessage
       },
+      addInternetAccount(
+        internetAccount: SnapshotIn<typeof self.internetAccounts[0]>,
+      ) {
+        self.internetAccounts.push(internetAccount)
+      },
+      findAppropriateInternetAccount(location: UriLocation) {
+        // find the existing account selected from menu
+        const selectedId = location.internetAccountId
+        if (selectedId) {
+          const selectedAccount = self.internetAccounts.find(account => {
+            return account.internetAccountId === selectedId
+          })
+          if (selectedAccount) {
+            return selectedAccount
+          }
+        }
+
+        // if no existing account or not found, try to find working account
+        for (const account of self.internetAccounts) {
+          const handleResult = account.handlesLocation(location)
+          if (handleResult) {
+            return account
+          }
+        }
+
+        // no available internet accounts
+        return null
+      },
     }))
     .views(self => ({
       get jbrowse() {

products/jbrowse-react-circular-genome-view/src/createViewState.ts

@@ -10,11 +10,13 @@ type SessionSnapshot = SnapshotIn<ReturnType<typeof createSessionModel>>
 type ConfigSnapshot = SnapshotIn<ReturnType<typeof createConfigModel>>
 type Assembly = ConfigSnapshot['assembly']
 type Tracks = ConfigSnapshot['tracks']
+type InternetAccounts = ConfigSnapshot['internetAccounts']
 type AggregateTextSearchAdapters = ConfigSnapshot['aggregateTextSearchAdapters']
 
 interface ViewStateOptions {
   assembly: Assembly
   tracks: Tracks
+  internetAccounts?: InternetAccounts
   aggregateTextSearchAdapters?: AggregateTextSearchAdapters
   configuration?: Record<string, unknown>
   plugins?: PluginConstructor[]
@@ -26,6 +28,7 @@ export default function createViewState(opts: ViewStateOptions) {
   const {
     assembly,
     tracks,
+    internetAccounts,
     configuration,
     aggregateTextSearchAdapters,
     plugins,
@@ -47,13 +50,26 @@ export default function createViewState(opts: ViewStateOptions) {
       configuration,
       assembly,
       tracks,
+      internetAccounts,
       aggregateTextSearchAdapters,
       defaultSession,
     },
     assemblyManager: {},
     session: defaultSession,
   }
   const stateTree = model.create(stateSnapshot, { pluginManager })
+  stateTree.config.internetAccounts.forEach(account => {
+    const internetAccountType = pluginManager.getInternetAccountType(
+      account.type,
+    )
+    if (!internetAccountType) {
+      throw new Error(`unknown internet account type ${account.type}`)
+    }
+    stateTree.addInternetAccount({
+      type: account.type,
+      configuration: account,
+    })
+  })
   pluginManager.setRootModel(stateTree)
   pluginManager.configure()
   autorun(reaction => {

products/jbrowse-react-linear-genome-view/package.json

@@ -45,6 +45,7 @@
     "@emotion/styled": "^11.8.1",
     "@jbrowse/core": "^2.2.0",
     "@jbrowse/plugin-alignments": "^2.2.0",
+    "@jbrowse/plugin-authentication": "^2.1.7",
     "@jbrowse/plugin-bed": "^2.2.0",
     "@jbrowse/plugin-circular-view": "^2.2.0",
     "@jbrowse/plugin-config": "^2.2.0",

products/jbrowse-react-linear-genome-view/src/corePlugins.ts

@@ -1,4 +1,5 @@
 import Alignments from '@jbrowse/plugin-alignments'
+import Authentication from '@jbrowse/plugin-authentication'
 import BED from '@jbrowse/plugin-bed'
 import Config from '@jbrowse/plugin-config'
 import DataManagement from '@jbrowse/plugin-data-management'
@@ -15,6 +16,7 @@ import Trix from '@jbrowse/plugin-trix'
 const corePlugins = [
   SVG,
   Alignments,
+  Authentication,
   BED,
   Config,
   DataManagement,

products/jbrowse-react-linear-genome-view/src/createModel/createConfigModel.ts

@@ -59,6 +59,9 @@ export default function createConfigModel(
       }),
       assembly: assemblyConfigSchemasType,
       tracks: types.array(pluginManager.pluggableConfigSchemaType('track')),
+      internetAccounts: types.array(
+        pluginManager.pluggableConfigSchemaType('internet account'),
+      ),
       connections: types.array(
         pluginManager.pluggableConfigSchemaType('connection'),
       ),

products/jbrowse-react-linear-genome-view/src/createModel/createModel.ts

@@ -5,6 +5,7 @@ import { PluginConstructor } from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
 import RpcManager from '@jbrowse/core/rpc/RpcManager'
 import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager'
+import { UriLocation } from '@jbrowse/core/util'
 import { cast, getSnapshot, Instance, SnapshotIn, types } from 'mobx-state-tree'
 import corePlugins from '../corePlugins'
 import createConfigModel from './createConfigModel'
@@ -29,6 +30,9 @@ export default function createModel(
       session: Session,
       assemblyManager: types.optional(AssemblyManager, {}),
       disableAddTracks: types.optional(types.boolean, false),
+      internetAccounts: types.array(
+        pluginManager.pluggableMstType('internet account', 'stateModel'),
+      ),
     })
     .volatile(self => ({
       error: undefined as Error | undefined,
@@ -55,6 +59,34 @@ export default function createModel(
       setError(errorMessage: Error | undefined) {
         self.error = errorMessage
       },
+      addInternetAccount(
+        internetAccount: SnapshotIn<typeof self.internetAccounts[0]>,
+      ) {
+        self.internetAccounts.push(internetAccount)
+      },
+      findAppropriateInternetAccount(location: UriLocation) {
+        // find the existing account selected from menu
+        const selectedId = location.internetAccountId
+        if (selectedId) {
+          const selectedAccount = self.internetAccounts.find(account => {
+            return account.internetAccountId === selectedId
+          })
+          if (selectedAccount) {
+            return selectedAccount
+          }
+        }
+
+        // if no existing account or not found, try to find working account
+        for (const account of self.internetAccounts) {
+          const handleResult = account.handlesLocation(location)
+          if (handleResult) {
+            return account
+          }
+        }
+
+        // no available internet accounts
+        return null
+      },
     }))
 
     .views(self => ({

products/jbrowse-react-linear-genome-view/src/createViewState.ts

@@ -10,6 +10,7 @@ type SessionSnapshot = SnapshotIn<ReturnType<typeof createSessionModel>>
 type ConfigSnapshot = SnapshotIn<ReturnType<typeof createConfigModel>>
 type Assembly = ConfigSnapshot['assembly']
 type Tracks = ConfigSnapshot['tracks']
+type InternetAccounts = ConfigSnapshot['internetAccounts']
 type AggregateTextSearchAdapters = ConfigSnapshot['aggregateTextSearchAdapters']
 
 interface Location {
@@ -22,6 +23,7 @@ interface Location {
 interface ViewStateOptions {
   assembly: Assembly
   tracks: Tracks
+  internetAccounts?: InternetAccounts
   aggregateTextSearchAdapters?: AggregateTextSearchAdapters
   configuration?: Record<string, unknown>
   plugins?: PluginConstructor[]
@@ -36,6 +38,7 @@ export default function createViewState(opts: ViewStateOptions) {
   const {
     assembly,
     tracks,
+    internetAccounts,
     configuration,
     aggregateTextSearchAdapters,
     plugins,
@@ -64,13 +67,26 @@ export default function createViewState(opts: ViewStateOptions) {
         configuration,
         assembly,
         tracks,
+        internetAccounts,
         aggregateTextSearchAdapters,
       },
       disableAddTracks,
       session: defaultSession,
     },
     { pluginManager },
   )
+  stateTree.config.internetAccounts.forEach(account => {
+    const internetAccountType = pluginManager.getInternetAccountType(
+      account.type,
+    )
+    if (!internetAccountType) {
+      throw new Error(`unknown internet account type ${account.type}`)
+    }
+    stateTree.addInternetAccount({
+      type: account.type,
+      configuration: account,
+    })
+  })
   pluginManager.setRootModel(stateTree)
   pluginManager.configure()
   if (location) {