@jbrowse/plugin-config 2.5.0 → 2.6.2

package/src/RefNameAliasAdapter/configSchema.ts

@@ -1,36 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config RefNameAliasAdapter
- * can read "chromAliases" type files from UCSC or any tab separated file of
- * refName aliases
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const RefNameAliasAdapter = ConfigurationSchema(
-  'RefNameAliasAdapter',
-  {
-    /**
-     * #slot
-     */
-    location: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/my/aliases.txt',
-        locationType: 'UriLocation',
-      },
-    },
-    /**
-     * #slot
-     * by default, the "ref names that match the fasta" are assumed to be in the
-     * first column (0), change this variable if needed
-     */
-    refNameColumn: {
-      type: 'number',
-      defaultValue: 0,
-    },
-  },
-  { explicitlyTyped: true },
-)
-
-export default RefNameAliasAdapter

package/src/RefNameAliasAdapter/index.ts

@@ -1,19 +0,0 @@
-import { AdapterType } from '@jbrowse/core/pluggableElementTypes'
-import PluginManager from '@jbrowse/core/PluginManager'
-
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'RefNameAliasAdapter',
-        configSchema,
-        getAdapterClass: () =>
-          import('./RefNameAliasAdapter').then(r => r.default),
-        adapterMetadata: {
-          hiddenFromGUI: true,
-        },
-      }),
-  )
-}

package/src/RefNameAliasAdapter/test_data/simple_alias.txt

@@ -1,2 +0,0 @@
-chr1	1	NC_000001.10
-chr2	2	NC_000002.11

package/src/__snapshots__/index.test.ts.snap

@@ -1,10 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`Config editing adds config editor widget 1`] = `{}`;
-
-exports[`Config editing creates proper FromConfigAdapter 1`] = `
-{
-  "adapterId": "testFromConfigAdapterId",
-  "type": "FromConfigAdapter",
-}
-`;

package/src/index.test.ts

@@ -1,38 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { getSnapshot } from 'mobx-state-tree'
-import ThisPlugin from '.'
-
-describe('Config editing', () => {
-  let pluginManager: PluginManager
-
-  beforeAll(() => {
-    pluginManager = new PluginManager([new ThisPlugin()])
-    pluginManager.createPluggableElements()
-    pluginManager.configure()
-  })
-
-  it("won't add if already added", () => {
-    expect(() => pluginManager.addPlugin(new ThisPlugin())).toThrow(
-      /JBrowse already configured, cannot add plugins/,
-    )
-  })
-
-  it('adds config editor widget', () => {
-    const ConfigurationEditorWidget = pluginManager.getWidgetType(
-      'ConfigurationEditorWidget',
-    )
-    const config = ConfigurationEditorWidget.configSchema.create({
-      type: 'ConfigurationEditorWidget',
-    })
-    expect(getSnapshot(config)).toMatchSnapshot()
-  })
-
-  it('creates proper FromConfigAdapter', () => {
-    const adapter = pluginManager.getAdapterType('FromConfigAdapter')
-    const config = adapter.configSchema.create({
-      type: 'FromConfigAdapter',
-      adapterId: 'testFromConfigAdapterId',
-    })
-    expect(getSnapshot(config)).toMatchSnapshot()
-  })
-})

package/src/index.ts

@@ -1,42 +0,0 @@
-import { lazy } from 'react'
-import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType'
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
-import {
-  configSchema as ConfigurationEditorConfigSchema,
-  HeadingComponent as ConfigurationEditorHeadingComponent,
-  stateModelFactory as ConfigurationEditorStateModelFactory,
-} from './ConfigurationEditorWidget'
-import FromConfigAdapterF from './FromConfigAdapter'
-import FromConfigRegionsAdapterF from './FromConfigRegionsAdapter'
-import FromConfigSequenceAdapterF from './FromConfigSequenceAdapter'
-import RefNameAliasAdapterF from './RefNameAliasAdapter'
-
-const LazyConfigurationEditorComponent = lazy(
-  () => import('./ConfigurationEditorWidget/components/ConfigurationEditor'),
-)
-
-export default class extends Plugin {
-  name = 'ConfigurationPlugin'
-
-  install(pluginManager: PluginManager) {
-    FromConfigAdapterF(pluginManager)
-    FromConfigRegionsAdapterF(pluginManager)
-    FromConfigSequenceAdapterF(pluginManager)
-    RefNameAliasAdapterF(pluginManager)
-
-    pluginManager.addWidgetType(() => {
-      return new WidgetType({
-        name: 'ConfigurationEditorWidget',
-        HeadingComponent: ConfigurationEditorHeadingComponent,
-        configSchema: ConfigurationEditorConfigSchema,
-        stateModel: ConfigurationEditorStateModelFactory(pluginManager),
-        ReactComponent: LazyConfigurationEditorComponent,
-      })
-    })
-  }
-}
-
-export { default as JsonEditor } from './ConfigurationEditorWidget/components/JsonEditor'
-
-export { LazyConfigurationEditorComponent as ConfigurationEditor }