@jbrowse/app-core 2.6.1 → 2.6.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/app-core",
-  "version": "2.6.1",
+  "version": "2.6.2",
   "description": "JBrowse 2 code shared between the 'full featured' apps e.g. jbrowse-web and jbrowse-desktop",
   "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/app-core",
     "clean": "rimraf dist esm *.tsbuildinfo",
     "prebuild": "yarn clean",
@@ -43,7 +42,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
-    "@jbrowse/product-core": "^2.6.1",
+    "@jbrowse/product-core": "^2.6.2",
     "@mui/icons-material": "^5.0.0",
     "@mui/material": "^5.10.17",
     "copy-to-clipboard": "^3.3.1",
@@ -62,5 +61,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+  "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
 }

package/src/Assemblies/SessionAssembliesMixin.ts

@@ -1,50 +0,0 @@
-import { types } from 'mobx-state-tree'
-
-import PluginManager from '@jbrowse/core/PluginManager'
-import { AnyConfiguration } from '@jbrowse/core/configuration'
-import { BaseSession } from '@jbrowse/product-core'
-import { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager'
-
-/**
- * #stateModel SessionAssembliesMixin
- * #category root
- */
-export function SessionAssembliesMixin(
-  pluginManager: PluginManager,
-  assemblyConfigSchemasType: BaseAssemblyConfigSchema,
-) {
-  return types
-    .model({
-      /**
-       * #property
-       */
-      sessionAssemblies: types.array(assemblyConfigSchemasType),
-    })
-    .actions(s => {
-      const self = s as typeof s & BaseSession
-      return {
-        /**
-         * #action
-         */
-        addSessionAssembly(conf: AnyConfiguration) {
-          const asm = self.sessionAssemblies.find(f => f.name === conf.name)
-          if (asm) {
-            console.warn(`Assembly ${conf.name} already exists`)
-            return asm
-          }
-          const length = self.sessionAssemblies.push(conf)
-          return self.sessionAssemblies[length - 1]
-        },
-
-        /**
-         * #action
-         */
-        removeSessionAssembly(assemblyName: string) {
-          const elt = self.sessionAssemblies.find(a => a.name === assemblyName)
-          if (elt) {
-            self.sessionAssemblies.remove(elt)
-          }
-        },
-      }
-    })
-}

package/src/Assemblies/TemporaryAssembliesMixin.ts

@@ -1,51 +0,0 @@
-import { types } from 'mobx-state-tree'
-
-import PluginManager from '@jbrowse/core/PluginManager'
-import { AnyConfiguration } from '@jbrowse/core/configuration'
-import { BaseSession } from '@jbrowse/product-core'
-
-/**
- * #stateModel TemporaryAssembliesMixin
- * #category root
- */
-export function TemporaryAssembliesMixin(
-  pluginManager: PluginManager,
-  assemblyConfigSchemasType = types.frozen(),
-) {
-  return types
-    .model({
-      /**
-       * #property
-       */
-      temporaryAssemblies: types.array(assemblyConfigSchemasType),
-    })
-
-    .actions(s => {
-      const self = s as typeof s & BaseSession
-      return {
-        /**
-         * #action
-         * used for read vs ref type assemblies.
-         */
-        addTemporaryAssembly(conf: AnyConfiguration) {
-          const asm = self.temporaryAssemblies.find(f => f.name === conf.name)
-          if (asm) {
-            console.warn(`Assembly ${conf.name} was already existing`)
-            return asm
-          }
-          const length = self.temporaryAssemblies.push(conf)
-          return self.temporaryAssemblies[length - 1]
-        },
-
-        /**
-         * #action
-         */
-        removeTemporaryAssembly(name: string) {
-          const elt = self.temporaryAssemblies.find(a => a.name === name)
-          if (elt) {
-            self.temporaryAssemblies.remove(elt)
-          }
-        },
-      }
-    })
-}

package/src/Assemblies/index.ts

@@ -1,2 +0,0 @@
-export * from './SessionAssembliesMixin'
-export * from './TemporaryAssembliesMixin'

package/src/HistoryManagement/index.ts

@@ -1,56 +0,0 @@
-import TimeTraveller from '@jbrowse/core/util/TimeTraveller'
-import type { BaseRootModel } from '@jbrowse/product-core'
-import { autorun } from 'mobx'
-import { addDisposer, types } from 'mobx-state-tree'
-
-/**
- * #stateModel HistoryManagementMixin
- * #category root
- */
-export function HistoryManagementMixin() {
-  return types
-    .model({
-      /**
-       * #property
-       * used for undo/redo
-       */
-      history: types.optional(TimeTraveller, { targetPath: '../session' }),
-    })
-    .actions(self => ({
-      afterCreate() {
-        document.addEventListener('keydown', e => {
-          if (
-            self.history.canRedo &&
-            // ctrl+shift+z or cmd+shift+z
-            (((e.ctrlKey || e.metaKey) && e.shiftKey && e.code === 'KeyZ') ||
-              // ctrl+y
-              (e.ctrlKey && !e.shiftKey && e.code === 'KeyY'))
-          ) {
-            self.history.redo()
-          }
-          if (
-            self.history.canUndo &&
-            // ctrl+z or cmd+z
-            (e.ctrlKey || e.metaKey) &&
-            !e.shiftKey &&
-            e.code === 'KeyZ'
-          ) {
-            self.history.undo()
-          }
-        })
-        addDisposer(
-          self,
-          autorun(() => {
-            const { session } = self as typeof self & BaseRootModel
-            if (session) {
-              // we use a specific initialization routine after session is
-              // created to get it to start tracking itself sort of related
-              // issue here
-              // https://github.com/mobxjs/mobx-state-tree/issues/1089#issuecomment-441207911
-              self.history.initialize()
-            }
-          }),
-        )
-      },
-    }))
-}

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'