More blast stuff

Author: cmdcolin

config.json

@@ -32,6 +32,42 @@
     }
   ],
   "tracks": [
+    {
+      "type": "FeatureTrack",
+      "trackId": "hg38-ncbiRefSeq",
+      "name": "NCBI RefSeq - RefSeq All",
+      "assemblyNames": ["hg38"],
+      "description": "NCBI RefSeq genes, curated and predicted (NM_*, XM_*, NR_*, XR_*, NP_*, YP_*)",
+      "category": ["Genes and Gene Predictions"],
+      "metadata": {
+        "ucsc": {
+          "baseColorDefault": "genomicCodons",
+          "baseColorUseCds": "given",
+          "color": "12,12,120",
+          "idXref": "ncbiRefSeqLink mrnaAcc name",
+          "longLabel": "NCBI RefSeq genes, curated and predicted (NM_*, XM_*, NR_*, XR_*, NP_*, YP_*)",
+          "parent": "refSeqComposite off",
+          "priority": "1",
+          "shortLabel": "RefSeq All",
+          "track": "ncbiRefSeq",
+          "html": ""
+        }
+      },
+      "adapter": {
+        "type": "Gff3TabixAdapter",
+        "gffGzLocation": {
+          "locationType": "UriLocation",
+          "uri": "https://jbrowse.org/ucsc/hg38/ncbiRefSeq.gff.gz"
+        },
+        "index": {
+          "indexType": "CSI",
+          "location": {
+            "locationType": "UriLocation",
+            "uri": "https://jbrowse.org/ucsc/hg38/ncbiRefSeq.gff.gz.csi"
+          }
+        }
+      }
+    },
     {
       "type": "FeatureTrack",
       "trackId": "hg38-knownGene",

src/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.tsx

@@ -1,4 +1,4 @@
-import React, { useEffect, useState } from 'react'
+import React, { useEffect, useMemo, useState } from 'react'
 
 import { Feature, getContainingView } from '@jbrowse/core/util'
 import DeleteIcon from '@mui/icons-material/Delete'
@@ -24,6 +24,31 @@ import type { CachedBlastResult } from '../../../utils/blastCache'
 import type { AbstractTrackModel } from '@jbrowse/core/util'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
+function getGeneIdentifiers(feature: Feature): string[] {
+  const ids = [
+    feature.id(),
+    feature.get('id'),
+    feature.get('name'),
+    feature.get('gene_id'),
+    feature.get('gene_name'),
+  ].filter((id): id is string => !!id)
+  return [...new Set(ids)]
+}
+
+function getResultDisplayName(result: CachedBlastResult): string {
+  const parts = []
+  if (result.geneName) {
+    parts.push(result.geneName)
+  }
+  if (result.transcriptName && result.transcriptName !== result.geneName) {
+    parts.push(result.transcriptName)
+  }
+  if (parts.length === 0) {
+    parts.push(result.geneId ?? result.transcriptId ?? 'Unknown')
+  }
+  return parts.join(' - ')
+}
+
 const CachedBlastResults = observer(function ({
   model,
   handleClose,
@@ -37,19 +62,20 @@ const CachedBlastResults = observer(function ({
   const [loading, setLoading] = useState(true)
   const view = getContainingView(model) as LinearGenomeViewModel
 
-  const geneId = feature.get('id')
+  const geneIds = useMemo(() => getGeneIdentifiers(feature), [feature])
+
   useEffect(() => {
     // eslint-disable-next-line @typescript-eslint/no-floating-promises
     ;(async () => {
       try {
         const cached = await getAllCachedResults()
-        setResults(cached.filter(r => r.geneId === geneId))
+        setResults(cached.filter(r => r.geneId && geneIds.includes(r.geneId)))
         setLoading(false)
       } catch (e) {
         console.error(e)
       }
     })()
-  }, [geneId])
+  }, [geneIds])
 
   const handleDelete = async (id: string) => {
     await deleteCachedResult(id)
@@ -65,7 +91,7 @@ const CachedBlastResults = observer(function ({
     blastLaunchViewFromCache({
       view,
       cached,
-      newViewTitle: `BLAST - ${cached.geneId ?? cached.transcriptId ?? 'Unknown gene'}`,
+      newViewTitle: `BLAST - ${getResultDisplayName(cached)}`,
     })
     handleClose()
   }
@@ -132,7 +158,7 @@ const CachedBlastResults = observer(function ({
               }}
             >
               <ListItemText
-                primary={`${result.geneId ?? result.transcriptId ?? 'Unknown'} - ${result.blastDatabase}/${result.blastProgram} (${result.msaAlgorithm})`}
+                primary={`${getResultDisplayName(result)} - ${result.blastDatabase}/${result.blastProgram} (${result.msaAlgorithm})`}
                 secondary={`${new Date(result.timestamp).toLocaleString()} - Seq: ${result.proteinSequence.slice(0, 30)}...`}
               />
             </ListItemButton>

src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx

@@ -1,4 +1,4 @@
-import React, { useEffect, useState } from 'react'
+import React, { useEffect, useMemo, useState } from 'react'
 
 import { ErrorMessage } from '@jbrowse/core/ui'
 import {
@@ -30,6 +30,17 @@ import { useTranscriptSelection } from '../useTranscriptSelection'
 
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
+function getGeneIdentifiers(feature: Feature): string[] {
+  const ids = [
+    feature.id(),
+    feature.get('id'),
+    feature.get('name'),
+    feature.get('gene_id'),
+    feature.get('gene_name'),
+  ].filter((id): id is string => !!id)
+  return [...new Set(ids)]
+}
+
 const useStyles = makeStyles()({
   dialogContent: {
     width: '80em',
@@ -72,19 +83,21 @@ const NCBIBlastAutomaticPanel = observer(function ({
   const [hasCachedResults, setHasCachedResults] = useState(false)
   const [error, setError] = useState<unknown>()
 
-  const geneId = feature.get('id')
+  const geneIds = useMemo(() => getGeneIdentifiers(feature), [feature])
   useEffect(() => {
     // eslint-disable-next-line @typescript-eslint/no-floating-promises
     ;(async () => {
       try {
         const results = await getAllCachedResults()
-        setHasCachedResults(results.some(r => r.geneId === geneId))
+        setHasCachedResults(
+          results.some(r => r.geneId && geneIds.includes(r.geneId)),
+        )
       } catch (e) {
         console.error(e)
         setError(e)
       }
     })()
-  }, [geneId])
+  }, [geneIds])
 
   const {
     options,

src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastMethodSelector.tsx

@@ -21,13 +21,14 @@ export default function NCBIBlastMethodSelector({
         <FormControlLabel
           value="automatic"
           control={<Radio />}
-          label="Run NCBI BLAST and load results automatically"
+          label="Automatic"
         />
         <FormControlLabel
-          value="manual"
+          value="rid"
           control={<Radio />}
-          label="Link to NCBI BLAST and import results manually"
+          label="Load from RID"
         />
+        <FormControlLabel value="manual" control={<Radio />} label="Manual" />
       </RadioGroup>
     </FormControl>
   )

src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.tsx

@@ -7,11 +7,18 @@ import { IconButton } from '@mui/material'
 import NCBIBlastAutomaticPanel from './NCBIBlastAutomaticPanel'
 import NCBIBlastManualPanel from './NCBIBlastManualPanel'
 import NCBIBlastMethodSelector from './NCBIBlastMethodSelector'
+import NCBIBlastRIDPanel from './NCBIBlastRIDPanel'
 import NCBISettingsDialog from './NCBISettingsDialog'
 import { BASE_BLAST_URL } from './consts'
 
 import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
 
+const panelMap = {
+  automatic: NCBIBlastAutomaticPanel,
+  rid: NCBIBlastRIDPanel,
+  manual: NCBIBlastManualPanel,
+} as const
+
 export default function NCBIBlastPanel({
   handleClose,
   model,
@@ -28,10 +35,7 @@ export default function NCBIBlastPanel({
   )
   const [settingsOpen, setSettingsOpen] = useState(false)
 
-  const Panel =
-    lookupMethod === 'automatic'
-      ? NCBIBlastAutomaticPanel
-      : NCBIBlastManualPanel
+  const Panel = panelMap[lookupMethod as keyof typeof panelMap]
 
   return (
     <>