@jbrowse/app-core 2.6.1 → 2.6.3

package/src/JBrowseConfig/index.ts

@@ -1,173 +0,0 @@
-import {
-  AnyConfigurationSchemaType,
-  ConfigurationSchema,
-} from '@jbrowse/core/configuration'
-
-import { PluginDefinition } from '@jbrowse/core/PluginLoader'
-import PluginManager from '@jbrowse/core/PluginManager'
-import RpcManager from '@jbrowse/core/rpc/RpcManager'
-import { types } from 'mobx-state-tree'
-
-/**
- * #config JBrowseRootConfig
- * #category root
- * configuration in a config.json/file.jbrowse
- */
-export function JBrowseConfigF({
-  pluginManager,
-  assemblyConfigSchema,
-}: {
-  pluginManager: PluginManager
-  assemblyConfigSchema: AnyConfigurationSchemaType
-}) {
-  return types.model('JBrowseConfig', {
-    configuration: ConfigurationSchema('Root', {
-      /**
-       * #slot configuration.rpc
-       */
-      rpc: RpcManager.configSchema,
-
-      /**
-       * #slot configuration.highResolutionScaling
-       */
-      highResolutionScaling: {
-        type: 'number',
-        defaultValue: 2,
-      },
-
-      formatDetails: ConfigurationSchema('FormatDetails', {
-        /**
-         * #slot configuration.formatDetails.feature
-         */
-        feature: {
-          type: 'frozen',
-          description: 'adds extra fields to the feature details',
-          defaultValue: {},
-          contextVariable: ['feature'],
-        },
-        /**
-         * #slot configuration.formatDetails.subfeatures
-         */
-        subfeatures: {
-          type: 'frozen',
-          description: 'adds extra fields to the subfeatures of a feature',
-          defaultValue: {},
-          contextVariable: ['feature'],
-        },
-        /**
-         * #slot configuration.formatDetails.depth
-         */
-        depth: {
-          type: 'number',
-          defaultValue: 2,
-          description: 'depth to iterate on subfeatures',
-        },
-      }),
-      formatAbout: ConfigurationSchema('FormatAbout', {
-        /**
-         * #slot configuration.formatAbout.config
-         */
-        config: {
-          type: 'frozen',
-          description: 'formats configuration object in about dialog',
-          defaultValue: {},
-          contextVariable: ['config'],
-        },
-        /**
-         * #slot configuration.formatAbout.hideUris
-         */
-
-        hideUris: {
-          type: 'boolean',
-          defaultValue: false,
-        },
-      }),
-
-      /*
-       * #slot configuration.shareURL
-       */
-      shareURL: {
-        type: 'string',
-        defaultValue: 'https://share.jbrowse.org/api/v1/',
-      },
-      /**
-       * #slot configuration.disableAnalytics
-       */
-      disableAnalytics: {
-        type: 'boolean',
-        defaultValue: false,
-      },
-      /**
-       * #slot configuration.theme
-       */
-      theme: {
-        type: 'frozen',
-        defaultValue: {},
-      },
-      /**
-       * #slot configuration.extraThemes
-       */
-      extraThemes: { type: 'frozen', defaultValue: {} },
-      /**
-       * #slot configuration.logoPath
-       */
-      logoPath: {
-        type: 'fileLocation',
-        defaultValue: { uri: '', locationType: 'UriLocation' },
-      },
-      ...pluginManager.pluginConfigurationSchemas(),
-    }),
-    /**
-     * #slot
-     * defines plugins of the format
-     * ```typescript
-     * type PluginDefinition=
-     *    { umdUrl: string, name:string } |
-     *    { url: string, name: string } |
-     *    { esmUrl: string } |
-     *    { cjsUrl: string } |
-     *    { umdLoc: { uri: string } } |
-     *    { esmLoc: { uri: string } } |
-     * ```
-     */
-    plugins: types.array(types.frozen<PluginDefinition>()),
-    /**
-     * #slot
-     * configuration of the assemblies in the instance, see BaseAssembly
-     */
-    assemblies: types.array(assemblyConfigSchema),
-    /**
-     * #slot
-     * track configuration is an array of track config schemas. multiple
-     * instances of a track can exist that use the same configuration
-     */
-    tracks: types.array(pluginManager.pluggableConfigSchemaType('track')),
-    /**
-     * #slot
-     * configuration for internet accounts, see InternetAccounts
-     */
-    internetAccounts: types.array(
-      pluginManager.pluggableConfigSchemaType('internet account'),
-    ),
-    /**
-     * #slot
-     */
-    aggregateTextSearchAdapters: types.array(
-      pluginManager.pluggableConfigSchemaType('text search adapter'),
-    ),
-
-    /**
-     * #slot
-     */
-    connections: types.array(
-      pluginManager.pluggableConfigSchemaType('connection'),
-    ),
-
-    /**
-     * #slot
-     */
-    defaultSession: types.optional(types.frozen(), {
-      name: `New Session`,
-    }),
-  })
-}

package/src/JBrowseModel/index.ts

@@ -1,150 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager'
-import { cast, getParent } from 'mobx-state-tree'
-import RpcManager from '@jbrowse/core/rpc/RpcManager'
-import {
-  AnyConfigurationModel,
-  readConfObject,
-} from '@jbrowse/core/configuration'
-import { PluginDefinition } from '@jbrowse/core/PluginLoader'
-
-// locals
-import { JBrowseConfigF } from '../JBrowseConfig'
-
-export function JBrowseModelF({
-  pluginManager,
-  assemblyConfigSchema,
-}: {
-  pluginManager: PluginManager
-  assemblyConfigSchema: BaseAssemblyConfigSchema
-}) {
-  return JBrowseConfigF({ pluginManager, assemblyConfigSchema })
-    .views(self => ({
-      /**
-       * #getter
-       */
-      get assemblyNames(): string[] {
-        return self.assemblies.map(assembly => readConfObject(assembly, 'name'))
-      },
-      /**
-       * #getter
-       */
-      get rpcManager(): RpcManager {
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        return getParent<any>(self).rpcManager
-      },
-    }))
-    .actions(self => ({
-      /**
-       * #action
-       */
-      addAssemblyConf(conf: AnyConfigurationModel) {
-        const { name } = conf
-        if (!name) {
-          throw new Error('Can\'t add assembly with no "name"')
-        }
-        if (self.assemblyNames.includes(name)) {
-          throw new Error(
-            `Can't add assembly with name "${name}", an assembly with that name already exists`,
-          )
-        }
-        const length = self.assemblies.push({
-          ...conf,
-          sequence: {
-            type: 'ReferenceSequenceTrack',
-            trackId: `${name}-${Date.now()}`,
-            ...conf.sequence,
-          },
-        })
-        return self.assemblies[length - 1]
-      },
-      /**
-       * #action
-       */
-      removeAssemblyConf(assemblyName: string) {
-        const toRemove = self.assemblies.find(a => a.name === assemblyName)
-        if (toRemove) {
-          self.assemblies.remove(toRemove)
-        }
-      },
-      /**
-       * #action
-       */
-      addTrackConf(trackConf: AnyConfigurationModel) {
-        const { type } = trackConf
-        if (!type) {
-          throw new Error(`unknown track type ${type}`)
-        }
-        const length = self.tracks.push(trackConf)
-        return self.tracks[length - 1]
-      },
-      /**
-       * #action
-       */
-      addConnectionConf(connectionConf: AnyConfigurationModel) {
-        const { type } = connectionConf
-        if (!type) {
-          throw new Error(`unknown connection type ${type}`)
-        }
-        const length = self.connections.push(connectionConf)
-        return self.connections[length - 1]
-      },
-      /**
-       * #action
-       */
-      deleteConnectionConf(configuration: AnyConfigurationModel) {
-        const elt = self.connections.find(conn => conn.id === configuration.id)
-        return self.connections.remove(elt)
-      },
-      /**
-       * #action
-       */
-      deleteTrackConf(trackConf: AnyConfigurationModel) {
-        const elt = self.tracks.find(t => t.trackId === trackConf.trackId)
-        return self.tracks.remove(elt)
-      },
-      /**
-       * #action
-       */
-      addPlugin(pluginDefinition: PluginDefinition) {
-        self.plugins.push(pluginDefinition)
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        const rootModel = getParent<any>(self)
-        rootModel.setPluginsUpdated(true)
-      },
-      /**
-       * #action
-       */
-      removePlugin(pluginDefinition: PluginDefinition) {
-        self.plugins = cast(
-          self.plugins.filter(
-            plugin =>
-              plugin.url !== pluginDefinition.url ||
-              plugin.umdUrl !== pluginDefinition.umdUrl ||
-              plugin.cjsUrl !== pluginDefinition.cjsUrl ||
-              plugin.esmUrl !== pluginDefinition.esmUrl,
-          ),
-        )
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        getParent<any>(self).setPluginsUpdated(true)
-      },
-      /**
-       * #action
-       */
-      addInternetAccountConf(internetAccountConf: AnyConfigurationModel) {
-        const { type } = internetAccountConf
-        if (!type) {
-          throw new Error(`unknown internetAccount type ${type}`)
-        }
-        const length = self.internetAccounts.push(internetAccountConf)
-        return self.internetAccounts[length - 1]
-      },
-      /**
-       * #action
-       */
-      deleteInternetAccountConf(configuration: AnyConfigurationModel) {
-        const elt = self.internetAccounts.find(a => a.id === configuration.id)
-        return self.internetAccounts.remove(elt)
-      },
-    }))
-}

package/src/RootMenu/index.ts

@@ -1,157 +0,0 @@
-import { MenuItem } from '@jbrowse/core/ui/Menu'
-import { types } from 'mobx-state-tree'
-
-export interface Menu {
-  label: string
-  menuItems: MenuItem[]
-}
-export function RootAppMenuMixin() {
-  return types.model({}).actions(s => {
-    const self = s as { menus: Menu[] }
-    return {
-      /**
-       * #action
-       */
-      setMenus(newMenus: Menu[]) {
-        self.menus = newMenus
-      },
-      /**
-       * #action
-       * Add a top-level menu
-       * @param menuName - Name of the menu to insert.
-       * @returns The new length of the top-level menus array
-       */
-      appendMenu(menuName: string) {
-        return self.menus.push({ label: menuName, menuItems: [] })
-      },
-      /**
-       * #action
-       * Insert a top-level menu
-       * @param menuName - Name of the menu to insert.
-       * @param position - Position to insert menu. If negative, counts from th
-       * end, e.g. `insertMenu('My Menu', -1)` will insert the menu as the
-       * second-to-last one.
-       * @returns The new length of the top-level menus array
-       */
-      insertMenu(menuName: string, position: number) {
-        self.menus.splice(
-          (position < 0 ? self.menus.length : 0) + position,
-          0,
-          {
-            label: menuName,
-            menuItems: [],
-          },
-        )
-        return self.menus.length
-      },
-      /**
-       * #action
-       * Add a menu item to a top-level menu
-       * @param menuName - Name of the top-level menu to append to.
-       * @param menuItem - Menu item to append.
-       * @returns The new length of the menu
-       */
-      appendToMenu(menuName: string, menuItem: MenuItem) {
-        const menu = self.menus.find(m => m.label === menuName)
-        if (!menu) {
-          self.menus.push({ label: menuName, menuItems: [menuItem] })
-          return 1
-        }
-        return menu.menuItems.push(menuItem)
-      },
-      /**
-       * #action
-       * Insert a menu item into a top-level menu
-       * @param menuName - Name of the top-level menu to insert into
-       * @param menuItem - Menu item to insert
-       * @param position - Position to insert menu item. If negative, counts
-       * from the end, e.g. `insertMenu('My Menu', -1)` will insert the menu as
-       * the second-to-last one.
-       * @returns The new length of the menu
-       */
-      insertInMenu(menuName: string, menuItem: MenuItem, position: number) {
-        const menu = self.menus.find(m => m.label === menuName)
-        if (!menu) {
-          self.menus.push({ label: menuName, menuItems: [menuItem] })
-          return 1
-        }
-        const insertPosition =
-          position < 0 ? menu.menuItems.length + position : position
-        menu.menuItems.splice(insertPosition, 0, menuItem)
-        return menu.menuItems.length
-      },
-      /**
-       * #action
-       * Add a menu item to a sub-menu
-       * @param menuPath - Path to the sub-menu to add to, starting with the
-       * top-level menu (e.g. `['File', 'Insert']`).
-       * @param menuItem - Menu item to append.
-       * @returns The new length of the sub-menu
-       */
-      appendToSubMenu(menuPath: string[], menuItem: MenuItem) {
-        let topMenu = self.menus.find(m => m.label === menuPath[0])
-        if (!topMenu) {
-          const idx = this.appendMenu(menuPath[0])
-          topMenu = self.menus[idx - 1]
-        }
-        let { menuItems: subMenu } = topMenu
-        const pathSoFar = [menuPath[0]]
-        menuPath.slice(1).forEach(menuName => {
-          pathSoFar.push(menuName)
-          let sm = subMenu.find(mi => 'label' in mi && mi.label === menuName)
-          if (!sm) {
-            const idx = subMenu.push({ label: menuName, subMenu: [] })
-            sm = subMenu[idx - 1]
-          }
-          if (!('subMenu' in sm)) {
-            throw new Error(
-              `"${menuName}" in path "${pathSoFar}" is not a subMenu`,
-            )
-          }
-          subMenu = sm.subMenu
-        })
-        return subMenu.push(menuItem)
-      },
-      /**
-       * #action
-       * Insert a menu item into a sub-menu
-       * @param menuPath - Path to the sub-menu to add to, starting with the
-       * top-level menu (e.g. `['File', 'Insert']`).
-       * @param menuItem - Menu item to insert.
-       * @param position - Position to insert menu item. If negative, counts
-       * from the end, e.g. `insertMenu('My Menu', -1)` will insert the menu as
-       * the second-to-last one.
-       * @returns The new length of the sub-menu
-       */
-      insertInSubMenu(
-        menuPath: string[],
-        menuItem: MenuItem,
-        position: number,
-      ) {
-        let topMenu = self.menus.find(m => m.label === menuPath[0])
-        if (!topMenu) {
-          const idx = this.appendMenu(menuPath[0])
-          topMenu = self.menus[idx - 1]
-        }
-        let { menuItems: subMenu } = topMenu
-        const pathSoFar = [menuPath[0]]
-        menuPath.slice(1).forEach(menuName => {
-          pathSoFar.push(menuName)
-          let sm = subMenu.find(mi => 'label' in mi && mi.label === menuName)
-          if (!sm) {
-            const idx = subMenu.push({ label: menuName, subMenu: [] })
-            sm = subMenu[idx - 1]
-          }
-          if (!('subMenu' in sm)) {
-            throw new Error(
-              `"${menuName}" in path "${pathSoFar}" is not a subMenu`,
-            )
-          }
-          subMenu = sm.subMenu
-        })
-        subMenu.splice(position, 0, menuItem)
-        return subMenu.length
-      },
-    }
-  })
-}

package/src/index.ts

@@ -1,6 +0,0 @@
-export * from './ui'
-export * from './HistoryManagement'
-export * from './JBrowseConfig'
-export * from './JBrowseModel'
-export * from './Assemblies'
-export * from './RootMenu'

package/src/ui/App/App.tsx

@@ -1,117 +0,0 @@
-import React, { Suspense, lazy } from 'react'
-import { AppBar } from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
-import { observer } from 'mobx-react'
-import { SessionWithDrawerWidgets } from '@jbrowse/core/util'
-import Snackbar from '@jbrowse/core/ui/Snackbar'
-import { SnackbarMessage } from '@jbrowse/core/ui/SnackbarModel'
-import { MenuItem as JBMenuItem } from '@jbrowse/core/ui/Menu'
-
-// locals
-import AppToolbar from './AppToolbar'
-import ViewLauncher from './ViewLauncher'
-import ViewPanel from './ViewPanel'
-import DialogQueue from './DialogQueue'
-import AppFab from './AppFab'
-
-const DrawerWidget = lazy(() => import('./DrawerWidget'))
-
-const useStyles = makeStyles()(theme => ({
-  root: {
-    display: 'grid',
-    height: '100vh',
-    width: '100%',
-    colorScheme: theme.palette.mode,
-  },
-  appContainer: {
-    gridColumn: 'main',
-    display: 'grid',
-    gridTemplateRows: '[menubar] min-content [components] auto',
-    height: '100vh',
-  },
-  viewContainer: {
-    overflowY: 'auto',
-    gridRow: 'components',
-  },
-  appBar: {
-    flexGrow: 1,
-    gridRow: 'menubar',
-  },
-}))
-
-type Props = {
-  HeaderButtons?: React.ReactElement
-  session: SessionWithDrawerWidgets & {
-    savedSessionNames: string[]
-    menus: { label: string; menuItems: JBMenuItem[] }[]
-    renameCurrentSession: (arg: string) => void
-    snackbarMessages: SnackbarMessage[]
-    popSnackbarMessage: () => unknown
-  }
-}
-
-const LazyDrawerWidget = observer(function (props: Props) {
-  const { session } = props
-  return (
-    <Suspense fallback={<React.Fragment />}>
-      <DrawerWidget session={session} />
-    </Suspense>
-  )
-})
-
-const ViewContainer = observer(function (props: Props) {
-  const { session } = props
-  const { views } = session
-  const { classes } = useStyles()
-  return (
-    <div className={classes.viewContainer}>
-      {views.length > 0 ? (
-        views.map(view => (
-          <ViewPanel key={`view-${view.id}`} view={view} session={session} />
-        ))
-      ) : (
-        <ViewLauncher {...props} />
-      )}
-
-      {/* blank space at the bottom of screen allows scroll */}
-      <div style={{ height: 300 }} />
-    </div>
-  )
-})
-
-const App = observer(function (props: Props) {
-  const { session } = props
-  const { classes } = useStyles()
-  const { minimized, visibleWidget, drawerWidth, drawerPosition } = session
-  const drawerVisible = visibleWidget && !minimized
-  const d = drawerVisible ? `[drawer] ${drawerWidth}px` : undefined
-  const grid =
-    drawerPosition === 'right' ? ['[main] 1fr', d] : [d, '[main] 1fr']
-
-  return (
-    <div
-      className={classes.root}
-      style={{ gridTemplateColumns: grid?.filter(f => !!f).join(' ') }}
-    >
-      {drawerVisible && drawerPosition === 'left' ? (
-        <LazyDrawerWidget session={session} />
-      ) : null}
-      <DialogQueue session={session} />
-      <div className={classes.appContainer}>
-        <AppBar className={classes.appBar} position="static">
-          <AppToolbar {...props} />
-        </AppBar>
-        <ViewContainer {...props} />
-      </div>
-      <AppFab session={session} />
-
-      {drawerVisible && drawerPosition === 'right' ? (
-        <LazyDrawerWidget session={session} />
-      ) : null}
-
-      <Snackbar session={session} />
-    </div>
-  )
-})
-
-export { App }

package/src/ui/App/AppFab.tsx

@@ -1,45 +0,0 @@
-import React from 'react'
-import { Fab, Tooltip } from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
-import { observer } from 'mobx-react'
-import { SessionWithDrawerWidgets } from '@jbrowse/core/util'
-
-// icons
-import LaunchIcon from '@mui/icons-material/Launch'
-
-const useStyles = makeStyles()(theme => ({
-  left: {
-    zIndex: 10000,
-    position: 'fixed',
-    bottom: theme.spacing(2),
-    left: theme.spacing(2),
-  },
-  right: {
-    zIndex: 10000,
-    position: 'fixed',
-    bottom: theme.spacing(2),
-    right: theme.spacing(2),
-  },
-}))
-
-export default observer(function AppFab({
-  session,
-}: {
-  session: SessionWithDrawerWidgets
-}) {
-  const { minimized, activeWidgets, drawerPosition } = session
-  const { classes } = useStyles()
-
-  return activeWidgets.size > 0 && minimized ? (
-    <Tooltip title="Open drawer widget">
-      <Fab
-        className={drawerPosition === 'right' ? classes.right : classes.left}
-        color="primary"
-        data-testid="drawer-maximize"
-        onClick={() => session.showWidgetDrawer()}
-      >
-        <LaunchIcon />
-      </Fab>
-    </Tooltip>
-  ) : null
-})