Create packages/product-core containing shared code between the various products

.eslintrc.json

@@ -154,7 +154,8 @@
         "test": true
       },
       "rules": {
-        "import/no-extraneous-dependencies": "off"
+        "import/no-extraneous-dependencies": "off",
+        "@typescript-eslint/no-non-null-assertion": "off"
       }
     },
     {

component_tests/cgv/package.json

@@ -41,6 +41,7 @@
     "@jbrowse/plugin-trix": "file:./packed/jbrowse-plugin-trix.tgz",
     "@jbrowse/plugin-variants": "file:./packed/jbrowse-plugin-variants.tgz",
     "@jbrowse/plugin-wiggle": "file:./packed/jbrowse-plugin-wiggle.tgz",
+    "@jbrowse/product-core": "file:./packed/jbrowse-product-core.tgz",
     "@jbrowse/react-linear-genome-view": "file:./packed/jbrowse-react-linear-genome-view.tgz",
     "@jbrowse/react-circular-genome-view": "file:./packed/jbrowse-react-circular-genome-view.tgz"
   },

component_tests/lgv/package.json

@@ -40,6 +40,7 @@
     "@jbrowse/plugin-trix": "file:./packed/jbrowse-plugin-trix.tgz",
     "@jbrowse/plugin-variants": "file:./packed/jbrowse-plugin-variants.tgz",
     "@jbrowse/plugin-wiggle": "file:./packed/jbrowse-plugin-wiggle.tgz",
+    "@jbrowse/product-core": "file:./packed/jbrowse-product-core.tgz",
     "@jbrowse/react-linear-genome-view": "file:./packed/jbrowse-react-linear-genome-view.tgz"
   },
   "scripts": {

packages/core/assemblyManager/assemblyConfigSchema.ts

@@ -104,3 +104,4 @@ function assemblyConfigSchema(pluginManager: PluginManager) {
 }
 
 export default assemblyConfigSchema
+export type BaseAssemblyConfigSchema = ReturnType<typeof assemblyConfigSchema>

packages/core/assemblyManager/index.ts

@@ -1,2 +1,3 @@
 export { default } from './assemblyManager'
 export { default as assemblyConfigSchemaFactory } from './assemblyConfigSchema'
+export type { BaseAssemblyConfigSchema } from './assemblyConfigSchema'

packages/core/configuration/index.ts

@@ -8,6 +8,7 @@ export type {
   AnyConfigurationModel,
   AnyConfigurationSlot,
   AnyConfigurationSlotType,
+  AnyConfiguration,
 } from './types'
 
 export * from './util'

packages/core/configuration/types.ts

@@ -1,5 +1,5 @@
 /* eslint-disable @typescript-eslint/no-explicit-any */
-import type { IStateTreeNode, Instance } from 'mobx-state-tree'
+import type { IStateTreeNode, Instance, SnapshotOut } from 'mobx-state-tree'
 import type {
   ConfigurationSchemaType,
   ConfigurationSchemaOptions,
@@ -61,5 +61,10 @@ export type AnyConfigurationModel = Instance<AnyConfigurationSchemaType>
 export type AnyConfigurationSlotType = ReturnType<typeof ConfigSlot>
 export type AnyConfigurationSlot = Instance<AnyConfigurationSlotType>
 
+/** any configuration model, or snapshot thereof */
+export type AnyConfiguration =
+  | AnyConfigurationModel
+  | SnapshotOut<AnyConfigurationModel>
+
 export type ConfigurationModel<SCHEMA extends AnyConfigurationSchemaType> =
   Instance<SCHEMA>

packages/core/pluggableElementTypes/models/BaseConnectionModelFactory.ts

@@ -1,7 +1,11 @@
 import { cast, types } from 'mobx-state-tree'
-import { AnyConfigurationModel } from '../../configuration'
+import {
+  AnyConfigurationModel,
+  ConfigurationReference,
+} from '../../configuration'
 import PluginManager from '../../PluginManager'
 
+import configSchema from './baseConnectionConfig'
 /**
  * #stateModel BaseConnectionModel
  */
@@ -16,6 +20,11 @@ function stateModelFactory(pluginManager: PluginManager) {
        * #property
        */
       tracks: types.array(pluginManager.pluggableConfigSchemaType('track')),
+
+      /**
+       * #property
+       */
+      configuration: ConfigurationReference(configSchema),
     })
     .actions(self => ({
       afterAttach() {
@@ -52,4 +61,5 @@ function stateModelFactory(pluginManager: PluginManager) {
     }))
 }
 
+export type BaseConnectionModel = ReturnType<typeof stateModelFactory>
 export default stateModelFactory

packages/core/pluggableElementTypes/models/BaseViewModel.ts

@@ -1,6 +1,7 @@
 import { types, Instance } from 'mobx-state-tree'
 import { ElementId } from '../../util/types/mst'
 import { MenuItem } from '../../ui'
+import { Region } from '../../util/types/mst'
 
 /**
  * #stateModel BaseViewModel
@@ -69,5 +70,12 @@ const BaseViewModel = types
   }))
 
 export default BaseViewModel
-// eslint-disable-next-line @typescript-eslint/no-empty-interface
-export interface IBaseViewModel extends Instance<typeof BaseViewModel> {}
+
+export type IBaseViewModel = Instance<typeof BaseViewModel>
+
+export const BaseViewModelWithDisplayedRegions = BaseViewModel.props({
+  displayedRegions: types.array(Region),
+})
+export type IBaseViewModelWithDisplayedRegions = Instance<
+  typeof BaseViewModelWithDisplayedRegions
+>

packages/core/pluggableElementTypes/models/baseConnectionConfig.ts

@@ -1,11 +1,12 @@
+import type { Instance } from 'mobx-state-tree'
 import { ConfigurationSchema } from '../../configuration'
 
 /**
  * #config BaseConnection
  */
 function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
 
-export default ConfigurationSchema(
+const BaseConnectionConfig = ConfigurationSchema(
   'BaseConnection',
   {
     /**
@@ -33,3 +34,7 @@ export default ConfigurationSchema(
     explicitIdentifier: 'connectionId',
   },
 )
+
+export default BaseConnectionConfig
+export type BaseConnectionConfigSchema = typeof BaseConnectionConfig
+export type BaseConnectionConfigModel = Instance<BaseConnectionConfigSchema>

packages/core/pluggableElementTypes/models/baseTrackConfig.ts

@@ -185,5 +185,5 @@ export function createBaseTrackConfig(pluginManager: PluginManager) {
   )
 }
 
-export type BaseTrackConfigModel = ReturnType<typeof createBaseTrackConfig>
-export type BaseTrackConfig = Instance<BaseTrackConfigModel>
+export type BaseTrackConfigSchema = ReturnType<typeof createBaseTrackConfig>
+export type BaseTrackConfig = Instance<BaseTrackConfigSchema>

packages/core/pluggableElementTypes/models/index.ts

@@ -16,4 +16,7 @@ export { BaseInternetAccountConfig } from './baseInternetAccountConfig'
 export { createBaseTrackModel } from './BaseTrackModel'
 export type { BaseTrackModel, BaseTrackStateModel } from './BaseTrackModel'
 export { createBaseTrackConfig } from './baseTrackConfig'
-export type { BaseTrackConfig, BaseTrackConfigModel } from './baseTrackConfig'
+export type {
+  BaseTrackConfig,
+  BaseTrackConfigSchema as BaseTrackConfigModel,
+} from './baseTrackConfig'

packages/core/util/types/index.ts

@@ -103,7 +103,6 @@ export interface AbstractSessionModel extends AbstractViewContainer {
   sessionConnections?: AnyConfigurationModel[]
   connectionInstances?: {
     name: string
-    connectionId: string
     tracks: AnyConfigurationModel[]
     configuration: AnyConfigurationModel
   }[]

packages/core/util/types/util.ts

@@ -1,6 +1,5 @@
 /* eslint-disable @typescript-eslint/no-explicit-any */
 import React from 'react'
-import { IAnyModelType, Instance } from 'mobx-state-tree'
 import PluginManager from '../../PluginManager'
 
 /**
@@ -21,8 +20,3 @@ export type AnyReactComponentType = React.ComponentType<any>
 /** get the type that a predicate asserts */
 export type TypeTestedByPredicate<PREDICATE extends (thing: any) => boolean> =
   PREDICATE extends (thing: any) => thing is infer TYPE ? TYPE : never
-
-/** get the type for an instance of an MST model in a PM factory function */
-export type InstanceOfModelReturnedBy<
-  FACTORY extends (pm: PluginManager) => IAnyModelType,
-> = Instance<ReturnType<FACTORY>>

packages/product-core/package.json

@@ -0,0 +1,58 @@
+{
+  "name": "@jbrowse/product-core",
+  "version": "2.5.0",
+  "description": "JBrowse 2 code shared between products but not used by plugins",
+  "keywords": [
+    "jbrowse",
+    "jbrowse2",
+    "bionode",
+    "biojs",
+    "genomics"
+  ],
+  "license": "Apache-2.0",
+  "homepage": "https://jbrowse.org",
+  "bugs": "https://github.com/GMOD/jbrowse-components/issues",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/GMOD/jbrowse-components.git",
+    "directory": "packages/text-indexing"
+  },
+  "author": "JBrowse Team",
+  "distMain": "dist/index.js",
+  "distModule": "esm/index.js",
+  "srcMain": "src/index.ts",
+  "srcModule": "src/index.ts",
+  "main": "src/index.ts",
+  "module": "",
+  "files": [
+    "dist",
+    "esm",
+    "src"
+  ],
+  "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",
+    "test": "cd ../..; jest packages/text-indexing",
+    "clean": "rimraf dist esm *.tsbuildinfo",
+    "prebuild": "yarn clean",
+    "prepack": "yarn build && yarn useDist",
+    "postpack": "yarn useSrc",
+    "useDist": "node ../../scripts/useDist.js",
+    "useSrc": "node ../../scripts/useSrc.js"
+  },
+  "dependencies": {
+    "@babel/runtime": "^7.16.3",
+    "@mui/material": "^5.10.17",
+    "shortid": "^2.2.15"
+  },
+  "peerDependencies": {
+    "mobx": "^6.0.0",
+    "mobx-react": "^7.0.0",
+    "mobx-state-tree": "^5.0.0",
+    "react": "^17.0.0",
+    "react-dom": "^17.0.0",
+    "rxjs": "^7.0.0"
+  },
+  "private": true
+}

packages/product-core/src/RootModel/Base.ts

@@ -0,0 +1,131 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import assemblyManagerFactory, {
+  BaseAssemblyConfigSchema,
+} from '@jbrowse/core/assemblyManager'
+import RpcManager from '@jbrowse/core/rpc/RpcManager'
+import {
+  IAnyType,
+  Instance,
+  SnapshotIn,
+  cast,
+  getSnapshot,
+  isStateTreeNode,
+  types,
+} from 'mobx-state-tree'
+import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager'
+
+/**
+ * factory function for the Base-level root model shared by all products
+ */
+export default function BaseRootModelTypeF(
+  pluginManager: PluginManager,
+  jbrowseModelType: IAnyType,
+  sessionModelType: IAnyType,
+  assemblyConfigSchema: BaseAssemblyConfigSchema,
+) {
+  return types
+    .model('BaseRootModel', {
+      /**
+       * #property
+       * `jbrowse` is a mapping of the config.json into the in-memory state tree
+       */
+      jbrowse: jbrowseModelType,
+      /**
+       * #property
+       */
+      version: 'development',
+
+      /**
+       * #property
+       * `session` encompasses the currently active state of the app, including
+       * views open, tracks open in those views, etc.
+       */
+      session: types.maybe(sessionModelType),
+      /**
+       * #property
+       */
+      sessionPath: types.optional(types.string, ''),
+
+      /**
+       * #property
+       */
+      assemblyManager: types.optional(
+        assemblyManagerFactory(assemblyConfigSchema, pluginManager),
+        {},
+      ),
+    })
+    .volatile(self => ({
+      rpcManager: new RpcManager(
+        pluginManager,
+        self.jbrowse.configuration.rpc,
+        {
+          MainThreadRpcDriver: {},
+        },
+      ),
+
+      /**
+       * #volatile
+       * Boolean indicating whether the session is in admin mode or not
+       */
+      adminMode: true,
+      isAssemblyEditing: false,
+      error: undefined as unknown,
+      textSearchManager: new TextSearchManager(pluginManager),
+      pluginManager,
+    }))
+    .actions(self => ({
+      /**
+       * #action
+       */
+      setError(error: unknown) {
+        self.error = error
+      },
+      /**
+       * #action
+       */
+      setSession(sessionSnapshot?: SnapshotIn<IAnyType>) {
+        self.session = cast(sessionSnapshot)
+      },
+      /**
+       * #action
+       */
+      setDefaultSession() {
+        this.setSession(self.jbrowse.defaultSession)
+      },
+      /**
+       * #action
+       */
+      setSessionPath(path: string) {
+        self.sessionPath = path
+      },
+      /**
+       * #action
+       */
+      async renameCurrentSession(newName: string) {
+        if (self.session) {
+          const snapshot = JSON.parse(JSON.stringify(getSnapshot(self.session)))
+          snapshot.name = newName
+          this.setSession(snapshot)
+        }
+      },
+      /**
+       * #action
+       */
+      setAssemblyEditing(flag: boolean) {
+        self.isAssemblyEditing = flag
+      },
+    }))
+}
+
+export type BaseRootModelType = ReturnType<typeof BaseRootModelTypeF>
+export type BaseRootModel = Instance<BaseRootModelType>
+
+/** Type guard for checking if something is a JB root model */
+export function isRootModel(thing: unknown): thing is BaseRootModelType {
+  return (
+    isStateTreeNode(thing) &&
+    'session' in thing &&
+    'jbrowse' in thing &&
+    'assemblyManager' in thing
+  )
+}