Merge pull request #1711 from GMOD/1535_tp_lvl_plugin_config

Add plugin top-level configuration

packages/core/Plugin.ts

@@ -1,4 +1,5 @@
 import PluginManager from './PluginManager'
+import { AnyConfigurationSchemaType } from './configuration/configurationSchema'
 
 /**
  * base class for a JBrowse plugin
@@ -9,6 +10,8 @@ export default abstract class Plugin {
   install(_pluginManager: PluginManager): void {}
 
   configure(_pluginManager: PluginManager): void {}
+
+  configurationSchema: AnyConfigurationSchemaType | undefined = undefined
 }
 
 export type PluginConstructor = new (...args: unknown[]) => Plugin

packages/core/PluginManager.ts

@@ -161,6 +161,16 @@ export default class PluginManager {
     })
   }
 
+  pluginConfigurationSchemas() {
+    const configurationSchemas: { [key: string]: unknown } = {}
+    this.plugins.forEach(plugin => {
+      if (plugin.configurationSchema) {
+        configurationSchemas[plugin.name] = plugin.configurationSchema
+      }
+    })
+    return configurationSchemas
+  }
+
   addPlugin(plugin: Plugin) {
     if (this.configured) {
       throw new Error('JBrowse already configured, cannot add plugins')

products/jbrowse-web/src/jbrowseModel.js

@@ -39,6 +39,7 @@ export default function JBrowseWeb(
           defaultValue: false,
         },
         theme: { type: 'frozen', defaultValue: {} },
+        ...pluginManager.pluginConfigurationSchemas(),
       }),
       plugins: types.frozen(),
       assemblies: types.array(assemblyConfigSchemasType),

products/jbrowse-web/src/tests/JBrowse.test.js

@@ -11,11 +11,16 @@ import { TextEncoder } from 'fastestsmallesttextencoderdecoder'
 // locals
 import { clearCache } from '@jbrowse/core/util/io/rangeFetcher'
 import { clearAdapterCache } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import { readConfObject, getConf } from '@jbrowse/core/configuration'
+import PluginManager from '@jbrowse/core/PluginManager'
+import JBrowseRootModelFactory from '../rootModel'
+import corePlugins from '../corePlugins'
 import * as sessionSharing from '../sessionSharing'
 import volvoxConfigSnapshot from '../../test_data/volvox/config.json'
 import chromeSizesConfig from '../../test_data/config_chrom_sizes_test.json'
 import JBrowse from '../JBrowse'
 import { setup, getPluginManager, generateReadBuffer } from './util'
+import TestPlugin from './TestPlugin'
 
 window.TextEncoder = TextEncoder
 
@@ -65,6 +70,29 @@ test('lollipop track test', async () => {
   await expect(findByTestId('three')).resolves.toBeTruthy()
 })
 
+test('toplevel configuration', () => {
+  const pluginManager = new PluginManager(
+    corePlugins.concat([TestPlugin]).map(P => new P()),
+  )
+  pluginManager.createPluggableElements()
+  const JBrowseRootModel = JBrowseRootModelFactory(pluginManager, true)
+  const rootModel = JBrowseRootModel.create({
+    jbrowse: volvoxConfigSnapshot,
+    assemblyManager: {},
+  })
+  rootModel.setDefaultSession()
+  pluginManager.setRootModel(rootModel)
+  pluginManager.configure()
+  const state = pluginManager.rootModel
+  const { jbrowse } = state
+  const { configuration } = jbrowse
+  // test reading top level configurations added by Test Plugin
+  const test = getConf(jbrowse, ['TestPlugin', 'topLevelTest'])
+  const test2 = readConfObject(configuration, ['TestPlugin', 'topLevelTest'])
+  expect(test).toEqual('test works')
+  expect(test2).toEqual('test works')
+})
+
 test('variant track test - opens feature detail view', async () => {
   const pluginManager = getPluginManager()
   const state = pluginManager.rootModel

products/jbrowse-web/src/tests/TestPlugin.ts

@@ -0,0 +1,16 @@
+import Plugin from '@jbrowse/core/Plugin'
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+export default class TestPlugin extends Plugin {
+  name = 'TestPlugin'
+
+  configurationSchema = ConfigurationSchema('TestPlugin', {
+    topLevelTest: {
+      description: 'Test for top level configuration',
+      type: 'string',
+      defaultValue: 'test works',
+    },
+  })
+
+  configure() {}
+}