jbrowse-plugin-msaview 2.8.2 → 2.9.0

package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.tsx

@@ -1,137 +0,0 @@
-import React, { useState } from 'react'
-
-import { Typography } from '@mui/material'
-import { observer } from 'mobx-react'
-import { makeStyles } from 'tss-react/mui'
-
-import MsaAlgorithmSelect from './MsaAlgorithmSelect'
-import { blastLaunchView } from './blastLaunchView'
-import ExternalLink from '../../../components/ExternalLink'
-import TextField2 from '../../../components/TextField2'
-import { getBlastViewTitle, getLinearGenomeView } from '../../util'
-import LaunchPanelContent from '../LaunchPanelContent'
-import SubmitCancelActions from '../SubmitCancelActions'
-import TranscriptSelector from '../TranscriptSelector'
-import { useTranscriptSelection } from '../useTranscriptSelection'
-
-import type { MsaAlgorithm } from './consts'
-import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
-
-const useStyles = makeStyles()({
-  marginBottom: {
-    marginBottom: 16,
-  },
-  ridField: {
-    width: 150,
-  },
-  infoText: {
-    marginTop: 20,
-  },
-})
-
-const NCBIBlastRIDPanel = observer(function ({
-  handleClose,
-  feature,
-  model,
-  children,
-  baseUrl,
-}: {
-  model: AbstractTrackModel
-  feature: Feature
-  baseUrl: string
-  handleClose: () => void
-  children: React.ReactNode
-}) {
-  const { classes } = useStyles()
-  const view = getLinearGenomeView(model)
-  const [launchViewError, setLaunchViewError] = useState<unknown>()
-  const [rid, setRid] = useState('')
-  const [selectedMsaAlgorithm, setSelectedMsaAlgorithm] =
-    useState<MsaAlgorithm>('clustalo')
-
-  const transcriptSelection = useTranscriptSelection({ feature, view })
-  const { selectedTranscript, proteinSequence } = transcriptSelection
-
-  const e = transcriptSelection.error ?? launchViewError
-  const trimmedRid = rid.trim()
-
-  return (
-    <>
-      <LaunchPanelContent error={e}>
-        {children}
-
-        <Typography variant="body2" className={classes.marginBottom}>
-          Enter the RID (Request ID) from a previously submitted NCBI BLAST
-          query. You can find the RID in the BLAST results page URL or at the
-          top of the results page. RIDs are typically valid for 24-36 hours
-          after submission.
-        </Typography>
-
-        <TextField2
-          variant="outlined"
-          label="BLAST RID"
-          placeholder="e.g., ABC12345"
-          fullWidth
-          className={classes.marginBottom}
-          value={rid}
-          onChange={event => {
-            setRid(event.target.value)
-          }}
-        />
-
-        {trimmedRid ? (
-          <Typography variant="body2" className={classes.marginBottom}>
-            <ExternalLink href={`${baseUrl}?CMD=Get&RID=${trimmedRid}`}>
-              View BLAST results on NCBI
-            </ExternalLink>
-          </Typography>
-        ) : null}
-
-        <MsaAlgorithmSelect
-          className={classes.ridField}
-          value={selectedMsaAlgorithm}
-          onChange={setSelectedMsaAlgorithm}
-        />
-
-        <TranscriptSelector feature={feature} {...transcriptSelection} />
-
-        <Typography className={classes.infoText}>
-          This will fetch the BLAST results for the provided RID and run them
-          through a multiple sequence alignment. The protein sequence from the
-          selected transcript will be added as the query sequence in the MSA.
-        </Typography>
-      </LaunchPanelContent>
-      <SubmitCancelActions
-        submitDisabled={!proteinSequence || !trimmedRid}
-        onSubmit={() => {
-          try {
-            if (selectedTranscript && trimmedRid) {
-              setLaunchViewError(undefined)
-              blastLaunchView({
-                feature: selectedTranscript,
-                view,
-                newViewTitle: getBlastViewTitle(feature, selectedTranscript),
-                blastParams: {
-                  baseUrl,
-                  blastProgram: 'blastp',
-                  blastDatabase: 'nr',
-                  msaAlgorithm: selectedMsaAlgorithm,
-                  selectedTranscript,
-                  proteinSequence,
-                  rid: trimmedRid,
-                },
-              })
-              handleClose()
-            }
-          } catch (e) {
-            console.error(e)
-            setLaunchViewError(e)
-          }
-        }}
-        onCancel={handleClose}
-      />
-    </>
-  )
-})
-
-export default NCBIBlastRIDPanel

package/src/LaunchMsaView/components/NCBIBlastQuery/consts.ts

@@ -1,10 +0,0 @@
-export const BASE_BLAST_URL = 'https://blast.ncbi.nlm.nih.gov/Blast.cgi'
-
-export const msaAlgorithms = ['clustalo', 'muscle', 'kalign', 'mafft'] as const
-export type MsaAlgorithm = (typeof msaAlgorithms)[number]
-
-export const blastDatabaseOptions = ['nr', 'nr_cluster_seq'] as const
-export type BlastDatabase = (typeof blastDatabaseOptions)[number]
-
-export const blastPrograms = ['blastp', 'quick-blastp'] as const
-export type BlastProgram = (typeof blastPrograms)[number]

package/src/MsaViewPanel/components/RIDLink.tsx

@@ -1,19 +0,0 @@
-import React from 'react'
-
-import { Typography } from '@mui/material'
-
-import ExternalLink from '../../components/ExternalLink'
-
-function RIDLink({ baseUrl, rid }: { rid: string; baseUrl: string }) {
-  return (
-    <Typography>
-      RID {rid} (
-      <ExternalLink href={`${baseUrl}?CMD=Get&RID=${rid}`}>
-        see status
-      </ExternalLink>
-      )
-    </Typography>
-  )
-}
-
-export default RIDLink

package/src/utils/ncbiBlast.ts

@@ -1,143 +0,0 @@
-import { jsonfetch, textfetch } from './fetch'
-import { pollLoop } from './poll'
-
-import type { BlastResults } from './types'
-import type {
-  BlastDatabase,
-  BlastProgram,
-} from '../LaunchMsaView/components/NCBIBlastQuery/consts'
-
-export async function queryBlastFromRid({
-  rid,
-  baseUrl,
-  onProgress,
-}: {
-  rid: string
-  baseUrl: string
-  onProgress: (arg: string) => void
-}) {
-  onProgress(`Checking BLAST status for RID: ${rid}...`)
-  await waitForRid({
-    rid,
-    onProgress,
-    baseUrl,
-  })
-  const ret = await jsonfetch<BlastResults>(
-    `${baseUrl}?CMD=Get&RID=${rid}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`,
-  )
-  return {
-    rid,
-    hits: ret.BlastOutput2[0]?.report.results.search.hits ?? [],
-  }
-}
-
-export async function queryBlast({
-  query,
-  blastDatabase,
-  blastProgram,
-  baseUrl,
-  onProgress,
-  onRid,
-}: {
-  query: string
-  blastDatabase: BlastDatabase
-  blastProgram: BlastProgram
-  baseUrl: string
-  onProgress: (arg: string) => void
-  onRid: (arg: string) => void
-}) {
-  onProgress('Submitting to NCBI BLAST...')
-  const { rid } = await initialQuery({
-    query,
-    blastDatabase,
-    blastProgram,
-    baseUrl,
-  })
-  onRid(rid)
-  return queryBlastFromRid({ rid, baseUrl, onProgress })
-}
-
-async function initialQuery({
-  query,
-  blastProgram,
-  blastDatabase,
-  baseUrl,
-}: {
-  query: string
-  blastProgram: BlastProgram
-  blastDatabase: BlastDatabase
-  baseUrl: string
-}) {
-  const res = await textfetch(baseUrl, {
-    method: 'POST',
-    body: new URLSearchParams({
-      CMD: 'Put',
-      PROGRAM: blastProgram === 'quick-blastp' ? 'blastp' : blastProgram,
-      DATABASE: blastDatabase,
-      QUERY: query,
-      ...(blastDatabase === 'nr_cluster_seq'
-        ? {
-            CLUSTERED_DB: 'on',
-            DB_TYPE: 'Experimental Databases',
-          }
-        : {}),
-      ...(blastProgram === 'quick-blastp'
-        ? { BLAST_PROGRAMS: 'kmerBlastp' }
-        : {}),
-    }),
-  })
-
-  // the initial submission/query to the BLAST "REST API" does not return JSON
-  // as a response (e.g. FORMAT_TYPE=JSON does not work), so the RID is
-  // literally parsed from the text of the HTML that is returned
-  const rid = /^ {4}RID = (.*$)/m.exec(res)?.[1]
-  const rtoe = /^ {4}RTOE = (.*$)/m.exec(res)?.[1]
-
-  if (!rid) {
-    throw new Error('Failed to get RID from BLAST request')
-  }
-  return {
-    rid,
-    rtoe,
-  }
-}
-
-async function waitForRid({
-  rid,
-  onProgress,
-  baseUrl,
-}: {
-  rid: string
-  onProgress: (arg: string) => void
-  baseUrl: string
-}) {
-  await pollLoop({
-    intervalSeconds: 20,
-    onCountdown: s => {
-      onProgress(`Re-checking BLAST status in... ${s}`)
-    },
-    check: async () => {
-      const res = await textfetch(
-        `${baseUrl}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${rid}`,
-      )
-      const status = /\s+Status=(\S+)/m.exec(res)?.[1]
-      const hasHits = /\s+ThereAreHits=yes/m.test(res)
-
-      if (status === 'WAITING') {
-        return false
-      }
-      if (status === 'FAILED') {
-        throw new Error(`BLAST ${rid} failed`)
-      }
-      if (status === 'READY') {
-        if (hasHits) {
-          return true
-        }
-        throw new Error('No hits found')
-      }
-      throw new Error(
-        `BLAST ${rid} returned unexpected status: ${status ?? 'unknown'}`,
-      )
-    },
-  })
-}