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Add authentication plugin to embedded components #3298

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merged 5 commits into from
Nov 17, 2022
Merged

Add authentication plugin to embedded components #3298

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c8cdf7b
Avoid a resolveIdentifier call
garrettjstevens Oct 28, 2022
0bed7bc
Add internetAccounts to embedded LGV and CGV
garrettjstevens Oct 28, 2022
e5a3214
Merge origin/main
cmdcolin Nov 8, 2022
6d6531b
Use built version of authentication plugin in component_tests
cmdcolin Nov 14, 2022
783e603
Add example and docs to Storybook
garrettjstevens Nov 14, 2022
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4 changes: 2 additions & 2 deletions packages/core/util/io/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ import {
FileLocation,
LocalPathLocation,
BlobLocation,
isAppRootModel,
isRootModelWithInternetAccounts,
isUriLocation,
AuthNeededError,
UriLocation,
Expand Down Expand Up @@ -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
Expand Down
18 changes: 18 additions & 0 deletions packages/core/util/types/index.ts
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Expand Up @@ -322,6 +322,24 @@ 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
Expand Down
34 changes: 15 additions & 19 deletions products/jbrowse-desktop/src/rootModel.ts
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Original file line number Diff line number Diff line change
@@ -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'
Expand Down Expand Up @@ -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 = {},
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any reason for changing it to take a config instead of id?

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In the only place this is called, the calling code already has a handle the config. By passing it directly, we avoid having to call resolveIdentifier with the ID.

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I will note that things like onAction listeners cannot handle full configuration objects, and this is one reason why e.g. showTrack take a trackId even if they have a full conf object to supply generally. Internet account would probably rarely be attached to a onAction listener but it's just a data point for the use of ids in the api

) {
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,
Expand Down Expand Up @@ -579,7 +575,7 @@ export default function rootModelFactory(pluginManager: PluginManager) {
self,
autorun(() => {
self.jbrowse.internetAccounts.forEach(account => {
self.initializeInternetAccount(account.internetAccountId)
self.initializeInternetAccount(account)
})
}),
)
Expand Down
1 change: 1 addition & 0 deletions products/jbrowse-react-circular-genome-view/package.json
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Expand Up @@ -44,6 +44,7 @@
"@emotion/react": "^11.9.0",
"@emotion/styled": "^11.8.1",
"@jbrowse/core": "^2.1.7",
"@jbrowse/plugin-authentication": "^2.1.7",
"@jbrowse/plugin-circular-view": "^2.1.7",
"@jbrowse/plugin-config": "^2.1.7",
"@jbrowse/plugin-data-management": "^2.1.7",
Expand Down
2 changes: 2 additions & 0 deletions products/jbrowse-react-circular-genome-view/src/corePlugins.ts
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Original file line number Diff line number Diff line change
@@ -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'
Expand All @@ -6,6 +7,7 @@ import Variants from '@jbrowse/plugin-variants'
import Wiggle from '@jbrowse/plugin-wiggle'

const corePlugins = [
Authentication,
Config,
DataManagement,
CircularGenomeView,
Expand Down
3 changes: 3 additions & 0 deletions products/jbrowse-react-circular-genome-view/src/createModel/createConfigModel.ts
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Expand Up @@ -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'),
),
Expand Down
32 changes: 32 additions & 0 deletions products/jbrowse-react-circular-genome-view/src/createModel/createModel.ts
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Expand Up @@ -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'
Expand All @@ -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,
Expand All @@ -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() {
Expand Down
16 changes: 16 additions & 0 deletions products/jbrowse-react-circular-genome-view/src/createViewState.ts
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Expand Up @@ -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[]
Expand All @@ -26,6 +28,7 @@ export default function createViewState(opts: ViewStateOptions) {
const {
assembly,
tracks,
internetAccounts,
configuration,
aggregateTextSearchAdapters,
plugins,
Expand All @@ -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 => {
Expand Down
1 change: 1 addition & 0 deletions products/jbrowse-react-linear-genome-view/package.json
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Expand Up @@ -45,6 +45,7 @@
"@emotion/styled": "^11.8.1",
"@jbrowse/core": "^2.1.7",
"@jbrowse/plugin-alignments": "^2.1.7",
"@jbrowse/plugin-authentication": "^2.1.7",
"@jbrowse/plugin-bed": "^2.1.7",
"@jbrowse/plugin-circular-view": "^2.1.7",
"@jbrowse/plugin-config": "^2.1.7",
Expand Down
2 changes: 2 additions & 0 deletions products/jbrowse-react-linear-genome-view/src/corePlugins.ts
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@@ -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'
Expand All @@ -14,6 +15,7 @@ import Trix from '@jbrowse/plugin-trix'
const corePlugins = [
SVG,
Alignments,
Authentication,
BED,
Config,
DataManagement,
Expand Down
3 changes: 3 additions & 0 deletions products/jbrowse-react-linear-genome-view/src/createModel/createConfigModel.ts
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Expand Up @@ -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'),
),
Expand Down
32 changes: 32 additions & 0 deletions products/jbrowse-react-linear-genome-view/src/createModel/createModel.ts
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Expand Up @@ -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'
Expand All @@ -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,
Expand All @@ -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 => ({
Expand Down
16 changes: 16 additions & 0 deletions products/jbrowse-react-linear-genome-view/src/createViewState.ts
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Expand Up @@ -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 {
Expand All @@ -22,6 +23,7 @@ interface Location {
interface ViewStateOptions {
assembly: Assembly
tracks: Tracks
internetAccounts?: InternetAccounts
aggregateTextSearchAdapters?: AggregateTextSearchAdapters
configuration?: Record<string, unknown>
plugins?: PluginConstructor[]
Expand All @@ -36,6 +38,7 @@ export default function createViewState(opts: ViewStateOptions) {
const {
assembly,
tracks,
internetAccounts,
configuration,
aggregateTextSearchAdapters,
plugins,
Expand Down Expand Up @@ -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) {
Expand Down
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