@jbrowse/plugin-config 1.5.0 → 1.5.4

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-config",
-  "version": "1.5.0",
+  "version": "1.5.4",
   "description": "JBrowse 2 config utilities",
   "keywords": [
     "jbrowse",
@@ -36,7 +36,7 @@
   },
   "dependencies": {
     "@material-ui/icons": "^4.9.1",
-    "generic-filehandle": "^2.2.0",
+    "generic-filehandle": "^2.2.2",
     "pluralize": "^8.0.0",
     "react-color": "^2.19.3",
     "react-simple-code-editor": "0.9.3",
@@ -55,5 +55,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "542025578a39bd170c8a166f2568ee7edbd54072"
+  "gitHead": "0c398214590969168694b4ed8e20b595178b9efd"
 }

package/src/ConfigurationEditorWidget/components/CallbackEditor.js

@@ -1,12 +1,14 @@
 import React, { useEffect, useState } from 'react'
 import { useDebounce } from '@jbrowse/core/util'
 import { stringToJexlExpression } from '@jbrowse/core/util/jexlStrings'
-import FormControl from '@material-ui/core/FormControl'
-import FormHelperText from '@material-ui/core/FormHelperText'
-import InputLabel from '@material-ui/core/InputLabel'
-import { makeStyles } from '@material-ui/core/styles'
-import Tooltip from '@material-ui/core/Tooltip'
-import IconButton from '@material-ui/core/IconButton'
+import {
+  FormControl,
+  FormHelperText,
+  InputLabel,
+  Tooltip,
+  IconButton,
+  makeStyles,
+} from '@material-ui/core'
 import HelpIcon from '@material-ui/icons/Help'
 import { getEnv } from 'mobx-state-tree'
 import { observer, PropTypes } from 'mobx-react'

package/src/ConfigurationEditorWidget/components/ColorEditor.tsx

@@ -11,7 +11,7 @@ const ColorPicker = lazy(() => import('./ColorPicker'))
 function serializeColor(color: Color) {
   if (color instanceof Object) {
     const { r, g, b, a } = color as RGBColor
-    return `rgb(${r},${g},${b},${a})`
+    return a === undefined ? `rgb(${r},${g},${b})` : `rgba(${r},${g},${b},${a})`
   }
   return color
 }

package/src/ConfigurationEditorWidget/components/__snapshots__/ConfigurationEditor.test.js.snap

@@ -992,13 +992,13 @@ exports[`ConfigurationEditor widget renders with defaults of the PileupTrack sch
             </label>
             <div
               class="MuiInputBase-root MuiInput-root MuiInput-underline MuiInputBase-fullWidth MuiInput-fullWidth MuiInputBase-formControl MuiInput-formControl"
-              style="color: rgb(200, 200, 200); border-right-width: 25px; border-right-style: solid; border-right-color: #c8c8c8;"
+              style="color: rgb(255, 0, 255); border-right-width: 25px; border-right-style: solid; border-right-color: #f0f;"
             >
               <input
                 aria-invalid="false"
                 class="MuiInputBase-input MuiInput-input"
                 type="text"
-                value="#c8c8c8"
+                value="#f0f"
               />
             </div>
             <p

package/src/RefNameAliasAdapter/RefNameAliasAdapter.ts

@@ -1,40 +1,20 @@
 import {
   BaseRefNameAliasAdapter,
-  Alias,
   BaseAdapter,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { openLocation } from '@jbrowse/core/util/io'
-import { GenericFilehandle } from 'generic-filehandle'
 import { readConfObject } from '@jbrowse/core/configuration'
 
-import { ConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
-import MyConfigAdapterSchema from './configSchema'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
-
 export default class RefNameAliasAdapter
   extends BaseAdapter
   implements BaseRefNameAliasAdapter
 {
-  private location: GenericFilehandle
-
-  private promise: Promise<Alias[]>
-
-  constructor(
-    config: ConfigurationModel<typeof MyConfigAdapterSchema>,
-    getSubAdapter?: getSubAdapterType,
-    pluginManager?: PluginManager,
-  ) {
-    super(config, getSubAdapter, pluginManager)
-    this.location = openLocation(
-      readConfObject(config, 'location'),
-      this.pluginManager,
-    )
-    this.promise = this.downloadResults()
-  }
-
-  private async downloadResults() {
-    const results = (await this.location.readFile('utf8')) as string
+  async getRefNameAliases() {
+    const loc = readConfObject(this.config, 'location')
+    if (loc.uri === '' || loc.uri === '/path/to/my/aliases.txt') {
+      return []
+    }
+    const results = await openLocation(loc).readFile('utf8')
     return results
       .trim()
       .split('\n')
@@ -44,9 +24,5 @@ export default class RefNameAliasAdapter
       })
   }
 
-  getRefNameAliases() {
-    return this.promise
-  }
-
   async freeResources() {}
 }

package/src/index.ts

@@ -35,6 +35,12 @@ export default class extends Plugin {
           name: 'FromConfigAdapter',
           configSchema: fromConfigAdapterConfigSchema,
           AdapterClass: FromConfigAdapterClass,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+          },
         }),
     )
     pluginManager.addAdapterType(
@@ -43,6 +49,12 @@ export default class extends Plugin {
           name: 'FromConfigRegionsAdapter',
           configSchema: fromConfigRegionsAdapterConfigSchema,
           AdapterClass: FromConfigRegionsAdapterClass,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+          },
         }),
     )
     pluginManager.addAdapterType(
@@ -51,6 +63,12 @@ export default class extends Plugin {
           name: 'FromConfigSequenceAdapter',
           configSchema: fromConfigSequenceAdapterConfigSchema,
           AdapterClass: FromConfigSequenceAdapterClass,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+          },
         }),
     )
     pluginManager.addAdapterType(
@@ -59,6 +77,12 @@ export default class extends Plugin {
           name: 'RefNameAliasAdapter',
           configSchema: refNameAliasAdapterConfigSchema,
           AdapterClass: RefNameAliasAdapterClass,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+          },
         }),
     )