Add formatFields and formatFieldsNested

packages/core/BaseFeatureWidget/BaseFeatureDetail.tsx

@@ -40,6 +40,9 @@ const MAX_FIELD_NAME_WIDTH = 170
 
 // these are always omitted as too detailed
 const globalOmit = [
+  'origId',
+  'origName',
+  'origType',
   'length',
   'position',
   'subfeatures',
@@ -131,8 +134,8 @@ export function BaseCard({
 export const FieldName = ({
   description,
   name,
-  prefix = [],
   width,
+  prefix = [],
 }: {
   description?: React.ReactNode
   name: string
@@ -343,10 +346,9 @@ const DataGridDetails = ({
     const columns = colNames.map(val => ({
       field: val,
       width: Math.max(
-        ...rows.map(row => {
-          const result = String(row[val])
-          return Math.min(Math.max(measureText(result, 14) + 50, 80), 1000)
-        }),
+        ...rows.map(row =>
+          Math.min(Math.max(measureText(String(row[val]), 14) + 50, 80), 1000),
+        ),
       ),
     }))
 
@@ -526,22 +528,30 @@ function isEmpty(obj: Record<string, unknown>) {
   return Object.keys(obj).length === 0
 }
 
+function generateTitle(name: string, id: string, type: string) {
+  return [ellipses(name || id), type].filter(f => !!f).join(' - ')
+}
+
 export const FeatureDetails = (props: {
   model: IAnyStateTreeNode
-  feature: SimpleFeatureSerialized & { name?: string; id?: string }
+  feature: SimpleFeatureSerialized & {
+    origName?: string
+    origId?: string
+    origType?: string
+  }
   depth?: number
   omit?: string[]
   formatter?: (val: unknown, key: string) => React.ReactElement
 }) => {
   const { omit = [], model, feature, depth = 0 } = props
-  const { name = '', id = '', type = '', subfeatures } = feature
+  const { origName = '', origId = '', origType = '', subfeatures } = feature
   const session = getSession(model)
   const defaultSeqTypes = ['mRNA', 'transcript']
   const sequenceTypes =
     getConf(session, ['featureDetails', 'sequenceTypes']) || defaultSeqTypes
 
   return (
-    <BaseCard title={[ellipses(name || id), type].filter(f => !!f).join(' - ')}>
+    <BaseCard title={generateTitle(origName, origId, origType)}>
       <Typography>Core details</Typography>
       <CoreDetails {...props} />
       <Divider />
@@ -585,8 +595,7 @@ export const FeatureDetails = (props: {
 
 const BaseFeatureDetails = observer((props: BaseInputProps) => {
   const { model } = props
-  const { featureData, track } = model
-  const session = getSession(model)
+  const { featureData } = model
 
   if (!featureData) {
     return null
@@ -596,24 +605,7 @@ const BaseFeatureDetails = observer((props: BaseInputProps) => {
     return null
   }
 
-  const sessionExtra = session
-    ? getConf(session, ['featureDetails', 'extraFields'], {
-        feature,
-      })
-    : {}
-  const trackExtra = track
-    ? getConf(track, ['extraFields'], {
-        feature,
-      })
-    : {}
-
-
-  return (
-    <FeatureDetails
-      model={model}
-      feature={{ ...feature, ...sessionExtra, ...trackExtra }}
-    />
-  )
+  return <FeatureDetails model={model} feature={feature} />
 })
 
 export default BaseFeatureDetails

packages/core/BaseFeatureWidget/index.ts

@@ -1,10 +1,41 @@
 import { types } from 'mobx-state-tree'
 import PluginManager from '../PluginManager'
-import { ConfigurationSchema } from '../configuration'
+import { getConf, ConfigurationSchema } from '../configuration'
 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 (var 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,
+) {
+  if (obj.subfeatures) {
+    //@ts-ignore
+    obj.subfeatures = obj.subfeatures.map(sub => {
+      iterateSubfeatures(sub, parse)
+      return parse(sub)
+    })
+  }
+}
+
 export default function stateModelFactory(pluginManager: PluginManager) {
   return types
     .model('BaseFeatureWidget', {
@@ -22,8 +53,36 @@ export default function stateModelFactory(pluginManager: PluginManager) {
       ),
     })
     .actions(self => ({
-      setFeatureData(data: Record<string, unknown>) {
-        self.featureData = data
+      setFeatureData(feature: Record<string, unknown>) {
+        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) {
+            trackExtra = ret
+          }
+
+          iterateSubfeatures(feature, obj => {
+            const r = getConf(self.track, ['formatFieldsNested'], {
+              feature: obj,
+            })
+            return r ? { ...obj, ...r } : obj
+          })
+        }
+
+        self.featureData = { ...feature, ...trackExtra }
       },
       clearFeatureData() {
         self.featureData = undefined

packages/core/pluggableElementTypes/models/baseTrackConfig.ts

@@ -50,22 +50,19 @@ export function createBaseTrackConfig(pluginManager: PluginManager) {
         ),
       }),
       displays: types.array(pluginManager.pluggableConfigSchemaType('display')),
-      // see corresponding entry in circular-view ChordTrack
-      // no config slot editor exists for this at the time being
-      // configRelationships: {
-      //   type: 'configRelationships',
-      //   model: types.array(
-      //     types.model('Relationship', {
-      //       type: types.string,
-      //       target: types.maybe(types.reference(base)),
-      //     }),
-      //   ),
-      //   defaultValue: [],
-      // },
-      extraFields: {
-        type: 'string',
-        description: 'modifies on the base feature details',
-        defaultValue: `jexl:{}`,
+
+      formatFields: {
+        type: 'frozen',
+        description: 'adds extra fields to the base feature details',
+        defaultValue: {},
+        contextVariable: ['feature'],
+      },
+
+      formatFieldsNested: {
+        type: 'frozen',
+        description:
+          'adds extra fields to the base feature details, applied across nested subfeatures',
+        defaultValue: {},
         contextVariable: ['feature'],
       },
     },

packages/core/util/jexl.ts

@@ -102,9 +102,7 @@ export default function (/* config?: any*/): JexlNonBuildable {
   )
   j.addFunction('toLowerCase', (str: string) => str.toLowerCase())
   j.addFunction('toUpperCase', (str: string) => str.toUpperCase())
-  j.addFunction('trim', (str: string) => {
-    str.trim()
-  })
+  j.addFunction('trim', (str: string) => str.trim())
   j.addFunction('trimEnd', (str: string) => str.trimEnd())
   j.addFunction('trimStart', (str: string) => str.trimStart())
 

plugins/linear-genome-view/src/BaseLinearDisplay/models/BaseLinearDisplayModel.tsx

@@ -335,12 +335,14 @@ export const BaseLinearDisplay = types
           'BaseFeatureWidget',
           'baseFeature',
           {
-            featureData: feature.toJSON(),
             view: getContainingView(self),
             display: self,
             track: getContainingTrack(self),
           },
         )
+
+        // @ts-ignore
+        featureWidget.setFeatureData(feature.toJSON())
         session.showWidget(featureWidget)
       }
       if (isSelectionContainer(session)) {

test_data/config_demo.json

@@ -80,7 +80,31 @@
     {
       "type": "FeatureTrack",
       "trackId": "ncbi_gff_hg19",
-      "name": "NCBI RefSeq (GFF3Tabix)",
+      "name": "NCBI RefSeq w/ nested feature details",
+      "formatFieldsNested": "jexl:{name:\"https://google.com/?q=\"+feature.id}",
+      "assemblyNames": ["hg19"],
+      "category": ["Annotation"],
+      "metadata": {
+        "source": "https://www.ncbi.nlm.nih.gov/genome/guide/human/",
+        "dateaccessed": "12/03/2020"
+      },
+      "adapter": {
+        "type": "Gff3TabixAdapter",
+        "gffGzLocation": {
+          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/ncbi_refseq/GRCh37_latest_genomic.sort.gff.gz"
+        },
+        "index": {
+          "location": {
+            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/ncbi_refseq/GRCh37_latest_genomic.sort.gff.gz.tbi"
+          }
+        }
+      }
+    },
+    {
+      "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\"}",
       "assemblyNames": ["hg19"],
       "category": ["Annotation"],
       "metadata": {
@@ -116,6 +140,9 @@
       "type": "FeatureTrack",
       "trackId": "nclist_genes_hg19",
       "name": "Gencode v19",
+      "formatFields": "jexl:{name:\"https://civicdb.org/events/genes/\"+feature.gene_id+\"/summary/variants/\"+feature.id+\"/summary\"}",
+      "formatFieldsNested": "jexl:{name:\"https://civicdb.org/events/genes/\"+feature.gene_id+\"/summary/variants/\"+feature.id+\"/summary\"}",
+
       "assemblyNames": ["hg19"],
       "category": ["Annotation"],
       "adapter": {