Move more pluggable element initializations into factory functions (#…

…3349)

plugins/arc/src/ArcRenderer/index.ts

@@ -0,0 +1,17 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+
+import ReactComponent from './ArcRendering'
+import configSchema from './configSchema'
+import ArcRenderer from './ArcRenderer'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addRendererType(
+    () =>
+      new ArcRenderer({
+        name: 'ArcRenderer',
+        ReactComponent,
+        configSchema,
+        pluginManager,
+      }),
+  )
+}

plugins/arc/src/LinearArcDisplay/configSchema.tsx → plugins/arc/src/LinearArcDisplay/configSchema.ts

@@ -1,15 +1,12 @@
 import PluginManager from '@jbrowse/core/PluginManager'
 import { types } from 'mobx-state-tree'
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view'
 
 /**
  * #config LinearArcDisplay
  */
 export function configSchemaFactory(pluginManager: PluginManager) {
-  const LGVPlugin = pluginManager.getPlugin(
-    'LinearGenomeViewPlugin',
-  ) as import('@jbrowse/plugin-linear-genome-view').default
-  const { baseLinearDisplayConfigSchema } = LGVPlugin.exports
   return ConfigurationSchema(
     'LinearArcDisplay',
     {

plugins/arc/src/LinearArcDisplay/index.ts

@@ -0,0 +1,20 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import { DisplayType } from '@jbrowse/core/pluggableElementTypes'
+import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'
+
+import { configSchemaFactory } from './configSchema'
+import { stateModelFactory } from './model'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addDisplayType(() => {
+    const configSchema = configSchemaFactory(pluginManager)
+    return new DisplayType({
+      name: 'LinearArcDisplay',
+      configSchema,
+      stateModel: stateModelFactory(configSchema),
+      trackType: 'FeatureTrack',
+      viewType: 'LinearGenomeView',
+      ReactComponent: BaseLinearDisplayComponent,
+    })
+  })
+}

plugins/arc/src/LinearArcDisplay/model.tsx → plugins/arc/src/LinearArcDisplay/model.ts

@@ -2,18 +2,10 @@ import {
   AnyConfigurationSchemaType,
   ConfigurationReference,
 } from '@jbrowse/core/configuration/configurationSchema'
-import PluginManager from '@jbrowse/core/PluginManager'
 import { types } from 'mobx-state-tree'
+import { BaseLinearDisplay } from '@jbrowse/plugin-linear-genome-view'
 
-export function stateModelFactory(
-  configSchema: AnyConfigurationSchemaType,
-  pluginManager: PluginManager,
-) {
-  const LGVPlugin = pluginManager.getPlugin(
-    'LinearGenomeViewPlugin',
-  ) as import('@jbrowse/plugin-linear-genome-view').default
-  // @ts-ignore
-  const { BaseLinearDisplay } = LGVPlugin.exports
+export function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
   return types
     .compose(
       'LinearArcDisplay',

plugins/arc/src/index.ts

@@ -1,53 +1,18 @@
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
-import {
-  configSchemaFactory as linearArcDisplayConfigSchemaFactory,
-  stateModelFactory as LinearArcDisplayStateModelFactory,
-} from './LinearArcDisplay'
-import ArcRenderer, {
-  configSchema as ArcRendererConfigSchema,
-  ReactComponent as ArcRendererReactComponent,
-} from './ArcRenderer'
+import LinearArcDisplayF from './LinearArcDisplay'
+import ArcRendererF from './ArcRenderer'
+import { Feature } from '@jbrowse/core/util'
 
-export default class MyProjectPlugin extends Plugin {
+export default class ArcPlugin extends Plugin {
   name = 'ArcRenderer'
   install(pluginManager: PluginManager) {
-    const LGVPlugin = pluginManager.getPlugin(
-      'LinearGenomeViewPlugin',
-    ) as import('@jbrowse/plugin-linear-genome-view').default
-    // @ts-ignore
-    const { BaseLinearDisplayComponent } = LGVPlugin.exports
-
-    pluginManager.addRendererType(
-      () =>
-        // @ts-ignore error "expected 0 arguments, but got 1"?
-        new ArcRenderer({
-          name: 'ArcRenderer',
-          ReactComponent: ArcRendererReactComponent,
-          configSchema: ArcRendererConfigSchema,
-          pluginManager,
-        }),
-    )
-    pluginManager.addDisplayType(() => {
-      const configSchema = linearArcDisplayConfigSchemaFactory(pluginManager)
-      return new DisplayType({
-        name: 'LinearArcDisplay',
-        configSchema,
-        stateModel: LinearArcDisplayStateModelFactory(
-          configSchema,
-          pluginManager,
-        ),
-        trackType: 'FeatureTrack',
-        viewType: 'LinearGenomeView',
-        ReactComponent: BaseLinearDisplayComponent,
-      })
-    })
+    ArcRendererF(pluginManager)
+    LinearArcDisplayF(pluginManager)
 
     pluginManager.jexl.addFunction(
       'logThickness',
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      (feature: any, attributeName: string) => {
+      (feature: Feature, attributeName: string) => {
         return Math.log(feature.get(attributeName) + 1)
       },
     )

plugins/gff3/src/Gff3Adapter/index.ts

@@ -1 +1,14 @@
-export { default as configSchema } from './configSchema'
+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: 'Gff3Adapter',
+        configSchema,
+        getAdapterClass: () => import('./Gff3Adapter').then(r => r.default),
+      }),
+  )
+}

plugins/gff3/src/Gff3TabixAdapter/index.ts

@@ -1 +1,15 @@
-export { default as configSchema } from './configSchema'
+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: 'Gff3TabixAdapter',
+        configSchema,
+        getAdapterClass: () =>
+          import('./Gff3TabixAdapter').then(r => r.default),
+      }),
+  )
+}

plugins/gff3/src/GuessGff3/index.ts

@@ -0,0 +1,63 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import { FileLocation } from '@jbrowse/core/util/types'
+import {
+  makeIndex,
+  makeIndexType,
+  getFileName,
+  AdapterGuesser,
+} from '@jbrowse/core/util/tracks'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addToExtensionPoint(
+    'Core-guessAdapterForLocation',
+    (adapterGuesser: AdapterGuesser) => {
+      return (
+        file: FileLocation,
+        index?: FileLocation,
+        adapterHint?: string,
+      ) => {
+        const regexGuess = /\.gff3?\.b?gz$/i
+        const adapterName = 'Gff3TabixAdapter'
+        const fileName = getFileName(file)
+        const indexName = index && getFileName(index)
+        if (regexGuess.test(fileName) || adapterHint === adapterName) {
+          return {
+            type: adapterName,
+            bamLocation: file,
+            gffGzLocation: file,
+            index: {
+              location: index || makeIndex(file, '.tbi'),
+              indexType: makeIndexType(indexName, 'CSI', 'TBI'),
+            },
+          }
+        }
+        return adapterGuesser(file, index, adapterHint)
+      }
+    },
+  )
+
+  pluginManager.addToExtensionPoint(
+    'Core-guessAdapterForLocation',
+    (adapterGuesser: AdapterGuesser) => {
+      return (
+        file: FileLocation,
+        index?: FileLocation,
+        adapterHint?: string,
+      ) => {
+        const regexGuess = /\.gff3?$/i
+        const adapterName = 'Gff3Adapter'
+        const fileName = getFileName(file)
+        const obj = {
+          type: adapterName,
+          gffLocation: file,
+        }
+        if (regexGuess.test(fileName) && !adapterHint) {
+          return obj
+        } else if (adapterHint === adapterName) {
+          return obj
+        }
+        return adapterGuesser(file, index, adapterHint)
+      }
+    },
+  )
+}

plugins/gff3/src/index.ts

@@ -1,88 +1,16 @@
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
 import PluginManager from '@jbrowse/core/PluginManager'
 import Plugin from '@jbrowse/core/Plugin'
-import { configSchema as gff3TabixAdapterConfigSchema } from './Gff3TabixAdapter'
-import { FileLocation } from '@jbrowse/core/util/types'
-import {
-  makeIndex,
-  makeIndexType,
-  AdapterGuesser,
-  getFileName,
-} from '@jbrowse/core/util/tracks'
-import { configSchema as gff3AdapterConfigSchema } from './Gff3Adapter'
+
+import Gff3TabixAdapterF from './Gff3TabixAdapter'
+import Gff3AdapterF from './Gff3Adapter'
+import GuessGff3F from './GuessGff3'
 
 export default class extends Plugin {
   name = 'GFF3Plugin'
 
   install(pluginManager: PluginManager) {
-    pluginManager.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'Gff3TabixAdapter',
-          configSchema: gff3TabixAdapterConfigSchema,
-          getAdapterClass: () =>
-            import('./Gff3TabixAdapter/Gff3TabixAdapter').then(r => r.default),
-        }),
-    )
-    pluginManager.addToExtensionPoint(
-      'Core-guessAdapterForLocation',
-      (adapterGuesser: AdapterGuesser) => {
-        return (
-          file: FileLocation,
-          index?: FileLocation,
-          adapterHint?: string,
-        ) => {
-          const regexGuess = /\.gff3?\.b?gz$/i
-          const adapterName = 'Gff3TabixAdapter'
-          const fileName = getFileName(file)
-          const indexName = index && getFileName(index)
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              bamLocation: file,
-              gffGzLocation: file,
-              index: {
-                location: index || makeIndex(file, '.tbi'),
-                indexType: makeIndexType(indexName, 'CSI', 'TBI'),
-              },
-            }
-          }
-          return adapterGuesser(file, index, adapterHint)
-        }
-      },
-    )
-    pluginManager.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'Gff3Adapter',
-          configSchema: gff3AdapterConfigSchema,
-          getAdapterClass: () =>
-            import('./Gff3Adapter/Gff3Adapter').then(r => r.default),
-        }),
-    )
-    pluginManager.addToExtensionPoint(
-      'Core-guessAdapterForLocation',
-      (adapterGuesser: AdapterGuesser) => {
-        return (
-          file: FileLocation,
-          index?: FileLocation,
-          adapterHint?: string,
-        ) => {
-          const regexGuess = /\.gff3?$/i
-          const adapterName = 'Gff3Adapter'
-          const fileName = getFileName(file)
-          const obj = {
-            type: adapterName,
-            gffLocation: file,
-          }
-          if (regexGuess.test(fileName) && !adapterHint) {
-            return obj
-          } else if (adapterHint === adapterName) {
-            return obj
-          }
-          return adapterGuesser(file, index, adapterHint)
-        }
-      },
-    )
+    Gff3TabixAdapterF(pluginManager)
+    Gff3AdapterF(pluginManager)
+    GuessGff3F(pluginManager)
   }
 }

plugins/hic/src/HicAdapter/index.ts

@@ -0,0 +1,14 @@
+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: 'HicAdapter',
+        configSchema,
+        getAdapterClass: () => import('./HicAdapter').then(r => r.default),
+      }),
+  )
+}

plugins/hic/src/HicRenderer/index.ts

@@ -1,3 +1,17 @@
-export { default as ReactComponent } from './components/HicRendering'
-export { default as configSchema } from './configSchema'
-export { default } from './HicRenderer'
+import PluginManager from '@jbrowse/core/PluginManager'
+
+import ReactComponent from './components/HicRendering'
+import configSchema from './configSchema'
+import HicRenderer from './HicRenderer'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addRendererType(
+    () =>
+      new HicRenderer({
+        name: 'HicRenderer',
+        ReactComponent,
+        configSchema,
+        pluginManager,
+      }),
+  )
+}

plugins/hic/src/HicTrack/index.ts

@@ -0,0 +1,15 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'
+import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models'
+import configSchemaF from './configSchema'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addTrackType(() => {
+    const configSchema = configSchemaF(pluginManager)
+    return new TrackType({
+      name: 'HicTrack',
+      configSchema,
+      stateModel: createBaseTrackModel(pluginManager, 'HicTrack', configSchema),
+    })
+  })
+}