@jbrowse/web-core 2.6.1 → 2.6.3

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/web-core",
-  "version": "2.6.1",
+  "version": "2.6.3",
   "description": "JBrowse 2 code shared between web-app type products",
   "keywords": [
     "jbrowse",
@@ -26,13 +26,12 @@
   "module": "esm/index.js",
   "files": [
     "dist",
-    "esm",
-    "src"
+    "esm"
   ],
   "scripts": {
     "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:es5": "tsc --build tsconfig.build.es5.json",
-    "build": "npm run build:esm && npm run build:es5",
+    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
+    "build": "npm run build:esm && npm run build:commonjs",
     "test": "cd ../..; jest packages/web-core",
     "clean": "rimraf dist esm *.tsbuildinfo",
     "prebuild": "yarn clean",
@@ -43,8 +42,8 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
-    "@jbrowse/app-core": "^2.6.1",
-    "@jbrowse/product-core": "^2.6.1",
+    "@jbrowse/app-core": "^2.6.3",
+    "@jbrowse/product-core": "^2.6.3",
     "@mui/icons-material": "^5.0.0",
     "@mui/material": "^5.10.17",
     "clone": "^2.0.0",
@@ -64,5 +63,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+  "gitHead": "ed402c87efb0904858d602c363bd1757d5742129"
 }

package/src/BaseWebSession/AboutDialog.tsx

@@ -1 +0,0 @@
-export { AboutDialog as default } from '@jbrowse/product-core'

package/src/BaseWebSession/index.ts

@@ -1,413 +0,0 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
-import { lazy } from 'react'
-import clone from 'clone'
-import { PluginDefinition } from '@jbrowse/core/PluginLoader'
-import {
-  getConf,
-  AnyConfigurationModel,
-  readConfObject,
-  AnyConfiguration,
-} from '@jbrowse/core/configuration'
-import { AssemblyManager, JBrowsePlugin } from '@jbrowse/core/util/types'
-import addSnackbarToModel from '@jbrowse/core/ui/SnackbarModel'
-import { localStorageGetItem, localStorageSetItem } from '@jbrowse/core/util'
-import { autorun } from 'mobx'
-import {
-  addDisposer,
-  cast,
-  getParent,
-  getSnapshot,
-  types,
-  SnapshotIn,
-  Instance,
-} from 'mobx-state-tree'
-import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager'
-import { BaseTrackConfig } from '@jbrowse/core/pluggableElementTypes'
-
-// icons
-import SettingsIcon from '@mui/icons-material/Settings'
-import CopyIcon from '@mui/icons-material/FileCopy'
-import DeleteIcon from '@mui/icons-material/Delete'
-import InfoIcon from '@mui/icons-material/Info'
-
-// locals
-import PluginManager from '@jbrowse/core/PluginManager'
-import {
-  DialogQueueSessionMixin,
-  DrawerWidgetSessionMixin,
-  MultipleViewsSessionMixin,
-  ReferenceManagementSessionMixin,
-  SessionTracksManagerSessionMixin,
-  ThemeManagerSessionMixin,
-} from '@jbrowse/product-core'
-import {
-  SessionAssembliesMixin,
-  TemporaryAssembliesMixin,
-} from '@jbrowse/app-core'
-import { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager'
-// locals
-import { WebSessionConnectionsMixin } from '../SessionConnections'
-import { BaseConnectionConfigModel } from '@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig'
-
-const AboutDialog = lazy(() => import('./AboutDialog'))
-
-export function BaseWebSession({
-  pluginManager,
-  assemblyConfigSchema,
-}: {
-  pluginManager: PluginManager
-  assemblyConfigSchema: BaseAssemblyConfigSchema
-}) {
-  const sessionModel = types
-    .compose(
-      'WebCoreSessionModel',
-      ReferenceManagementSessionMixin(pluginManager),
-      DrawerWidgetSessionMixin(pluginManager),
-      DialogQueueSessionMixin(pluginManager),
-      ThemeManagerSessionMixin(pluginManager),
-      MultipleViewsSessionMixin(pluginManager),
-      SessionTracksManagerSessionMixin(pluginManager),
-      SessionAssembliesMixin(pluginManager, assemblyConfigSchema),
-      TemporaryAssembliesMixin(pluginManager, assemblyConfigSchema),
-      WebSessionConnectionsMixin(pluginManager),
-    )
-    .props({
-      /**
-       * #property
-       */
-      margin: 0,
-      /**
-       * #property
-       */
-      sessionPlugins: types.array(types.frozen()),
-    })
-    .views(self => ({
-      /**
-       * #getter
-       */
-      get tracks(): AnyConfigurationModel[] {
-        return [...self.sessionTracks, ...self.jbrowse.tracks]
-      },
-      /**
-       * #getter
-       */
-      get root() {
-        return getParent<any>(self)
-      },
-      /**
-       * #getter
-       * list of sessionAssemblies and jbrowse config assemblies, does not
-       * include temporaryAssemblies. basically the list to be displayed in a
-       * AssemblySelector dropdown
-       */
-      get assemblies(): Instance<BaseAssemblyConfigSchema[]> {
-        return [...self.jbrowse.assemblies, ...self.sessionAssemblies]
-      },
-      /**
-       * #getter
-       * list of config connections and session connections
-       */
-      get connections(): BaseConnectionConfigModel[] {
-        return [...self.jbrowse.connections, ...self.sessionConnections]
-      },
-    }))
-    .actions(self => ({
-      /**
-       * #action
-       */
-      setName(str: string) {
-        self.name = str
-      },
-    }))
-    .volatile((/* self */) => ({
-      /**
-       * #volatile
-       */
-      sessionThemeName: localStorageGetItem('themeName') || 'default',
-      /**
-       * #volatile
-       * this is the current "task" that is being performed in the UI.
-       * this is usually an object of the form
-       * `{ taskName: "configure", target: thing_being_configured }`
-       */
-      task: undefined,
-    }))
-
-    .views(self => ({
-      /**
-       * #getter
-       * list of sessionAssemblies and jbrowse config assemblies, does not
-       * include temporaryAssemblies. basically the list to be displayed in a
-       * AssemblySelector dropdown
-       */
-      get assemblyNames() {
-        return self.assemblies.map(f => readConfObject(f, 'name') as string)
-      },
-      /**
-       * #getter
-       */
-      get version() {
-        return self.root.version
-      },
-      /**
-       * #getter
-       */
-      get shareURL() {
-        return getConf(self.jbrowse, 'shareURL')
-      },
-      /**
-       * #getter
-       */
-      get textSearchManager(): TextSearchManager {
-        return self.root.textSearchManager
-      },
-      /**
-       * #getter
-       */
-      get assemblyManager(): AssemblyManager {
-        return self.root.assemblyManager
-      },
-      /**
-       * #getter
-       */
-      get savedSessions() {
-        return self.root.savedSessions
-      },
-      /**
-       * #getter
-       */
-      get previousAutosaveId() {
-        return self.root.previousAutosaveId
-      },
-      /**
-       * #getter
-       */
-      get savedSessionNames() {
-        return self.root.savedSessionNames
-      },
-      /**
-       * #getter
-       */
-      get history() {
-        return self.root.history
-      },
-      /**
-       * #getter
-       */
-      get menus() {
-        return self.root.menus
-      },
-      /**
-       * #method
-       */
-      renderProps() {
-        return {
-          theme: self.theme,
-        }
-      },
-    }))
-    .actions(self => ({
-      /**
-       * #action
-       */
-      addAssemblyConf(conf: AnyConfiguration) {
-        self.jbrowse.addAssemblyConf(conf)
-      },
-      /**
-       * #action
-       */
-      addSessionPlugin(plugin: JBrowsePlugin) {
-        if (self.sessionPlugins.some(p => p.name === plugin.name)) {
-          throw new Error('session plugin cannot be installed twice')
-        }
-        self.sessionPlugins.push(plugin)
-        self.root.setPluginsUpdated(true)
-      },
-
-      /**
-       * #action
-       */
-      removeSessionPlugin(pluginDefinition: PluginDefinition) {
-        self.sessionPlugins = cast(
-          self.sessionPlugins.filter(
-            plugin =>
-              plugin.url !== pluginDefinition.url ||
-              plugin.umdUrl !== pluginDefinition.umdUrl ||
-              plugin.cjsUrl !== pluginDefinition.cjsUrl ||
-              plugin.esmUrl !== pluginDefinition.esmUrl,
-          ),
-        )
-        getParent<any>(self).setPluginsUpdated(true)
-      },
-
-      /**
-       * #action
-       */
-      addSavedSession(sessionSnapshot: SnapshotIn<typeof self>) {
-        return self.root.addSavedSession(sessionSnapshot)
-      },
-
-      /**
-       * #action
-       */
-      removeSavedSession(sessionSnapshot: { name: string }) {
-        return self.root.removeSavedSession(sessionSnapshot)
-      },
-
-      /**
-       * #action
-       */
-      renameCurrentSession(sessionName: string) {
-        return self.root.renameCurrentSession(sessionName)
-      },
-
-      /**
-       * #action
-       */
-      duplicateCurrentSession() {
-        return self.root.duplicateCurrentSession()
-      },
-      /**
-       * #action
-       */
-      activateSession(sessionName: string) {
-        return self.root.activateSession(sessionName)
-      },
-
-      /**
-       * #action
-       */
-      setDefaultSession() {
-        return self.root.setDefaultSession()
-      },
-
-      /**
-       * #action
-       */
-      saveSessionToLocalStorage() {
-        return self.root.saveSessionToLocalStorage()
-      },
-
-      /**
-       * #action
-       */
-      loadAutosaveSession() {
-        return self.root.loadAutosaveSession()
-      },
-
-      /**
-       * #action
-       */
-      setSession(sessionSnapshot: SnapshotIn<typeof self>) {
-        return self.root.setSession(sessionSnapshot)
-      },
-    }))
-    .actions(self => ({
-      /**
-       * #action
-       */
-      editTrackConfiguration(configuration: AnyConfigurationModel) {
-        const { adminMode, sessionTracks } = self
-        if (!adminMode && !sessionTracks.includes(configuration)) {
-          throw new Error("Can't edit the configuration of a non-session track")
-        }
-        self.editConfiguration(configuration)
-      },
-    }))
-    .views(self => ({
-      /**
-       * #method
-       */
-      getTrackActionMenuItems(config: BaseTrackConfig) {
-        const { adminMode, sessionTracks } = self
-        const canEdit =
-          adminMode || sessionTracks.find(t => t.trackId === config.trackId)
-
-        // disable if it is a reference sequence track
-        const isRefSeq = config.type === 'ReferenceSequenceTrack'
-        return [
-          {
-            label: 'About track',
-            onClick: () => {
-              self.queueDialog(handleClose => [
-                AboutDialog,
-                { config, handleClose },
-              ])
-            },
-            icon: InfoIcon,
-          },
-          {
-            label: 'Settings',
-            disabled: !canEdit,
-            onClick: () => self.editTrackConfiguration(config),
-            icon: SettingsIcon,
-          },
-          {
-            label: 'Delete track',
-            disabled: !canEdit || isRefSeq,
-            onClick: () => self.deleteTrackConf(config),
-            icon: DeleteIcon,
-          },
-          {
-            label: 'Copy track',
-            disabled: isRefSeq,
-            onClick: () => {
-              type Display = { displayId: string }
-              const snap = clone(getSnapshot(config)) as {
-                [key: string]: unknown
-                displays: Display[]
-              }
-              const now = Date.now()
-              snap.trackId += `-${now}`
-              snap.displays.forEach(display => {
-                display.displayId += `-${now}`
-              })
-              // the -sessionTrack suffix to trackId is used as metadata for
-              // the track selector to store the track in a special category,
-              // and default category is also cleared
-              if (!self.adminMode) {
-                snap.trackId += '-sessionTrack'
-                snap.category = undefined
-              }
-              snap.name += ' (copy)'
-              self.addTrackConf(snap)
-            },
-            icon: CopyIcon,
-          },
-        ]
-      },
-    }))
-    .actions(self => ({
-      afterAttach() {
-        addDisposer(
-          self,
-          autorun(() => {
-            localStorageSetItem('drawerPosition', self.drawerPosition)
-            localStorageSetItem('themeName', self.themeName)
-          }),
-        )
-      },
-    }))
-
-  const extendedSessionModel = pluginManager.evaluateExtensionPoint(
-    'Core-extendSession',
-    sessionModel,
-  ) as typeof sessionModel
-
-  return types.snapshotProcessor(addSnackbarToModel(extendedSessionModel), {
-    // @ts-expect-error
-    preProcessor(snapshot) {
-      if (snapshot) {
-        // @ts-expect-error
-        const { connectionInstances, ...rest } = snapshot || {}
-        // connectionInstances schema changed from object to an array, so any
-        // old connectionInstances as object is in snapshot, filter it out
-        // https://github.com/GMOD/jbrowse-components/issues/1903
-        if (!Array.isArray(connectionInstances)) {
-          return rest
-        }
-      }
-      return snapshot
-    },
-  })
-}

package/src/SessionConnections.ts

@@ -1,73 +0,0 @@
-import { types } from 'mobx-state-tree'
-
-import {
-  ConnectionManagementSessionMixin,
-  SessionWithSessionTracks,
-} from '@jbrowse/product-core'
-import type { BaseSession } from '@jbrowse/product-core'
-
-import PluginManager from '@jbrowse/core/PluginManager'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration'
-import { BaseConnectionConfigModel } from '@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig'
-
-/**
- * #stateModel WebSessionConnectionsMixin
- * #category session
- */
-export function WebSessionConnectionsMixin(pluginManager: PluginManager) {
-  return types
-    .compose(
-      'SessionConnectionsManagement',
-      ConnectionManagementSessionMixin(pluginManager),
-      types.model({
-        /**
-         * #property
-         */
-        sessionConnections: types.array(
-          pluginManager.pluggableConfigSchemaType('connection'),
-        ),
-      }),
-    )
-    .actions(s => {
-      const self = s as typeof s & BaseSession & SessionWithSessionTracks
-      const superDeleteConnection = self.deleteConnection
-      const superAddConnectionConf = self.addConnectionConf
-      return {
-        addConnectionConf(connectionConf: BaseConnectionConfigModel) {
-          if (self.adminMode) {
-            return superAddConnectionConf(connectionConf)
-          }
-          const { connectionId, type } = connectionConf
-          if (!type) {
-            throw new Error(`unknown connection type ${type}`)
-          }
-          const connection = self.sessionTracks.find(
-            c => c.connectionId === connectionId,
-          )
-          if (connection) {
-            return connection
-          }
-          const length = self.sessionConnections.push(connectionConf)
-          return self.sessionConnections[length - 1]
-        },
-
-        deleteConnection(configuration: AnyConfigurationModel) {
-          let deletedConn
-          if (self.adminMode) {
-            deletedConn = superDeleteConnection(configuration)
-          }
-          if (!deletedConn) {
-            const { connectionId } = configuration
-            const idx = self.sessionConnections.findIndex(
-              c => c.connectionId === connectionId,
-            )
-            if (idx === -1) {
-              return undefined
-            }
-            return self.sessionConnections.splice(idx, 1)
-          }
-          return deletedConn
-        },
-      }
-    })
-}

package/src/index.ts

@@ -1,2 +0,0 @@
-export * from './SessionConnections'
-export * from './BaseWebSession'