Avoid using origName, origId, origType

GMOD · Jun 7, 2022 · 68c0974 · 68c0974
1 parent dfb87e8
commit 68c0974
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Showing 4 changed files with 26 additions and 50 deletions.
diff --git a/packages/core/BaseFeatureWidget/BaseFeatureDetail.tsx b/packages/core/BaseFeatureWidget/BaseFeatureDetail.tsx
@@ -1,5 +1,6 @@
 /* eslint-disable @typescript-eslint/no-explicit-any */
 import React, { useState } from 'react'
+import dompurify from 'dompurify'
 import { ErrorBoundary } from 'react-error-boundary'
 import {
   Accordion,
@@ -30,9 +31,6 @@ const MAX_FIELD_NAME_WIDTH = 170
 
 // these are always omitted as too detailed
 const globalOmit = [
-  'origId',
-  'origName',
-  'origType',
   'length',
   'position',
   'subfeatures',
@@ -524,30 +522,32 @@ function isEmpty(obj: Record<string, unknown>) {
   return Object.keys(obj).length === 0
 }
 
+function clean(value: string) {
+  const node = document.createElement('div')
+  node.innerHTML = dompurify.sanitize(value)
+  return node.innerText
+}
 function generateTitle(name: string, id: string, type: string) {
-  return [ellipses(name || id), type].filter(f => !!f).join(' - ')
+  console.log({ name, id }, clean(name || id))
+  return [ellipses(clean(name || id)), type].filter(f => !!f).join(' - ')
 }
 
 export const FeatureDetails = (props: {
   model: IAnyStateTreeNode
-  feature: SimpleFeatureSerialized & {
-    origName?: string
-    origId?: string
-    origType?: string
-  }
+  feature: SimpleFeatureSerialized
   depth?: number
   omit?: string[]
   formatter?: (val: unknown, key: string) => React.ReactElement
 }) => {
   const { omit = [], model, feature, depth = 0 } = props
-  const { origName = '', origId = '', origType = '', subfeatures } = feature
+  const { name = '', id = '', type = '', subfeatures } = feature
   const session = getSession(model)
   const defaultSeqTypes = ['mRNA', 'transcript']
   const sequenceTypes =
     getConf(session, ['featureDetails', 'sequenceTypes']) || defaultSeqTypes
 
   return (
-    <BaseCard title={generateTitle(origName, origId, origType)}>
+    <BaseCard title={generateTitle(name, id, type)}>
       <Typography>Core details</Typography>
       <CoreDetails {...props} />
       <Divider />

diff --git a/packages/core/BaseFeatureWidget/index.ts b/packages/core/BaseFeatureWidget/index.ts
@@ -7,24 +7,6 @@ import { ElementId } from '../util/types/mst'
 
 const configSchema = ConfigurationSchema('BaseFeatureWidget', {})
 
-function isObject(obj: unknown): obj is Record<string, unknown> {
-  return typeof obj === 'object' && obj !== null
-}
-
-function iterate(
-  obj: Record<string, unknown>,
-  parse: (key: string, value: unknown, obj: Record<string, unknown>) => void,
-) {
-  for (const k in obj) {
-    const r = obj[k]
-    if (isObject(r)) {
-      iterate(r, parse)
-    } else if (obj.hasOwnProperty(k)) {
-      parse(k, r, obj)
-    }
-  }
-}
-
 function iterateSubfeatures(
   obj: Record<string, unknown>,
   parse: (obj: Record<string, unknown>) => void,
@@ -76,18 +58,6 @@ export default function stateModelFactory(pluginManager: PluginManager) {
               const feature = clone(self.unformattedFeatureData)
               let trackExtra = {}
 
-              iterate(feature, (key, val, obj) => {
-                if (key === 'id') {
-                  obj.origId = val
-                }
-                if (key === 'name') {
-                  obj.origName = val
-                }
-                if (key === 'type') {
-                  obj.origType = val
-                }
-              })
-
               if (self.track) {
                 const ret = getConf(self.track, ['formatFields'], { feature })
                 if (ret) {
@@ -109,12 +79,19 @@ export default function stateModelFactory(pluginManager: PluginManager) {
       },
     }))
     .preProcessSnapshot(snap => {
-      const { featureData, ...rest } = snap
-      return { unformattedFeatureData: featureData, ...rest }
+      // @ts-ignore
+      const { featureData, finalizedFeatureData, ...rest } = snap
+      return {
+        unformattedFeatureData: featureData,
+        featureData: finalizedFeatureData,
+        ...rest,
+      }
     })
     .postProcessSnapshot(snap => {
-      const { unformattedFeatureData, ...rest } = snap
-      return rest
+      const { unformattedFeatureData, featureData, ...rest } = snap
+      // finalizedFeatureData avoids running formatter twice if loading from
+      // snapshot
+      return { finalizedFeatureData: featureData, ...rest }
     })
 }
 

diff --git a/packages/core/pluggableElementTypes/models/baseTrackConfig.ts b/packages/core/pluggableElementTypes/models/baseTrackConfig.ts
@@ -53,15 +53,14 @@ export function createBaseTrackConfig(pluginManager: PluginManager) {
 
       formatFields: {
         type: 'frozen',
-        description: 'adds extra fields to the base feature details',
+        description: 'adds extra fields to the feature details',
         defaultValue: {},
         contextVariable: ['feature'],
       },
 
-      formatFieldsNested: {
+      formatSubfeatureFields: {
         type: 'frozen',
-        description:
-          'adds extra fields to the base feature details, applied across nested subfeatures',
+        description: 'adds extra fields to the subfeatures of a feature',
         defaultValue: {},
         contextVariable: ['feature'],
       },

diff --git a/test_data/config_demo.json b/test_data/config_demo.json
@@ -139,7 +139,7 @@
       "type": "FeatureTrack",
       "trackId": "ncbi_gff_hg19_2",
       "name": "NCBI RefSeq w/ top-level feature details",
-      "formatFields": "jexl:{name:\"https://google.com/?q=\"+feature.name,random:\"Wow\"}",
+      "formatFields": "jexl:{name:\"https://google.com/?q=\"+feature.name,random:\"Wow \"+feature.name}",
       "assemblyNames": ["hg19"],
       "category": ["Annotation"],
       "metadata": {