jbrowse-plugin-msaview 2.8.2 → 2.10.0

package/src/utils/ncbiTaxonomy.ts

@@ -0,0 +1,37 @@
+import { NCBI_EMAIL, NCBI_TOOL } from './eutils'
+import { jsonfetch } from './fetch'
+
+const EUTILS = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils'
+
+/**
+ * Free text -> NCBI taxon id. A bare number is taken as the id itself; anything
+ * else is searched against db=taxonomy, which resolves a scientific name
+ * (`Danio rerio`), a common name (`zebrafish`) and a genus alike.
+ *
+ * This replaces a fixed list of species the dialog used to offer. The query
+ * taxon has to match the assembly the user is browsing -- `resolveGeneId`
+ * searches `SYMBOL[Gene Name] AND <taxid>[taxid]` -- so a list that stops at 23
+ * species silently resolves the wrong organism's gene for anyone outside it.
+ */
+export async function resolveTaxId(query: string) {
+  const term = query.trim()
+  if (!term) {
+    return undefined
+  }
+  if (/^\d+$/.test(term)) {
+    return Number(term)
+  }
+  const search = new URLSearchParams({
+    db: 'taxonomy',
+    term,
+    retmode: 'json',
+    retmax: '1',
+    tool: NCBI_TOOL,
+    email: NCBI_EMAIL,
+  })
+  const json = await jsonfetch<{ esearchresult?: { idlist?: string[] } }>(
+    `${EUTILS}/esearch.fcgi?${search.toString()}`,
+  )
+  const id = json.esearchresult?.idlist?.[0]
+  return id ? Number(id) : undefined
+}

package/src/utils/types.ts

@@ -6,17 +6,12 @@ export interface BlastHitDescription {
   title?: string
 }
 
-export interface BlastResults {
-  BlastOutput2: {
-    report: {
-      results: {
-        search: {
-          hits: {
-            description: BlastHitDescription[]
-            hsps: { hseq: string }[]
-          }[]
-        }
-      }
-    }
-  }[]
+/**
+ * The shape utils/ebiBlast.ts normalizes EBI's hits into. It keeps the field
+ * names NCBI's JSON2 used, so everything downstream of the search — row naming,
+ * taxonomy lookup, the MSA — was left untouched when the backend moved.
+ */
+export interface BlastHit {
+  description: BlastHitDescription[]
+  hsps: { hseq: string }[]
 }

package/src/utils/useLocalStorage.ts

@@ -5,7 +5,7 @@ import { useState } from 'react'
 // throw "(0, PR.useLocalStorage) is not a function" on hosts built during that
 // window. Same failure mode as `defaultCodonTable`; keeping our own copy takes
 // this plugin out of the whack-a-mole.
-function readLocalStorage<T>(key: string, initialValue: T): T {
+export function readLocalStorage<T>(key: string, initialValue: T): T {
   try {
     const item = globalThis.localStorage.getItem(key)
     return item === null ? initialValue : (JSON.parse(item) as T)

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.8.2'
+export const version = '2.10.0'

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.d.ts

@@ -1,10 +0,0 @@
-import React from 'react';
-import type { AbstractTrackModel, Feature } from '@jbrowse/core/util';
-declare const NCBIBlastAutomaticPanel: ({ handleClose, feature, model, children, baseUrl, }: {
-    model: AbstractTrackModel;
-    feature: Feature;
-    baseUrl: string;
-    handleClose: () => void;
-    children: React.ReactNode;
-}) => React.JSX.Element;
-export default NCBIBlastAutomaticPanel;

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.js

@@ -1,74 +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';
-const useStyles = makeStyles()({
-    marginBottom: {
-        marginBottom: 16,
-    },
-    ridField: {
-        width: 150,
-    },
-    infoText: {
-        marginTop: 20,
-    },
-});
-const NCBIBlastRIDPanel = observer(function ({ handleClose, feature, model, children, baseUrl, }) {
-    const { classes } = useStyles();
-    const view = getLinearGenomeView(model);
-    const [launchViewError, setLaunchViewError] = useState();
-    const [rid, setRid] = useState('');
-    const [selectedMsaAlgorithm, setSelectedMsaAlgorithm] = useState('clustalo');
-    const transcriptSelection = useTranscriptSelection({ feature, view });
-    const { selectedTranscript, proteinSequence } = transcriptSelection;
-    const e = transcriptSelection.error ?? launchViewError;
-    const trimmedRid = rid.trim();
-    return (React.createElement(React.Fragment, null,
-        React.createElement(LaunchPanelContent, { error: e },
-            children,
-            React.createElement(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."),
-            React.createElement(TextField2, { variant: "outlined", label: "BLAST RID", placeholder: "e.g., ABC12345", fullWidth: true, className: classes.marginBottom, value: rid, onChange: event => {
-                    setRid(event.target.value);
-                } }),
-            trimmedRid ? (React.createElement(Typography, { variant: "body2", className: classes.marginBottom },
-                React.createElement(ExternalLink, { href: `${baseUrl}?CMD=Get&RID=${trimmedRid}` }, "View BLAST results on NCBI"))) : null,
-            React.createElement(MsaAlgorithmSelect, { className: classes.ridField, value: selectedMsaAlgorithm, onChange: setSelectedMsaAlgorithm }),
-            React.createElement(TranscriptSelector, { feature: feature, ...transcriptSelection }),
-            React.createElement(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.")),
-        React.createElement(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/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.d.ts

@@ -1,5 +0,0 @@
-import React from 'react';
-export default function NCBISettingsDialog({ handleClose, baseUrl, }: {
-    handleClose: (arg?: string) => void;
-    baseUrl: string;
-}): React.JSX.Element;

package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.d.ts

@@ -1,7 +0,0 @@
-export declare const BASE_BLAST_URL = "https://blast.ncbi.nlm.nih.gov/Blast.cgi";
-export declare const msaAlgorithms: readonly ["clustalo", "muscle", "kalign", "mafft"];
-export type MsaAlgorithm = (typeof msaAlgorithms)[number];
-export declare const blastDatabaseOptions: readonly ["nr", "nr_cluster_seq"];
-export type BlastDatabase = (typeof blastDatabaseOptions)[number];
-export declare const blastPrograms: readonly ["blastp", "quick-blastp"];
-export type BlastProgram = (typeof blastPrograms)[number];

package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js

@@ -1,4 +0,0 @@
-export const BASE_BLAST_URL = 'https://blast.ncbi.nlm.nih.gov/Blast.cgi';
-export const msaAlgorithms = ['clustalo', 'muscle', 'kalign', 'mafft'];
-export const blastDatabaseOptions = ['nr', 'nr_cluster_seq'];
-export const blastPrograms = ['blastp', 'quick-blastp'];

package/dist/MsaViewPanel/components/RIDLink.d.ts

@@ -1,6 +0,0 @@
-import React from 'react';
-declare function RIDLink({ baseUrl, rid }: {
-    rid: string;
-    baseUrl: string;
-}): React.JSX.Element;
-export default RIDLink;

package/dist/MsaViewPanel/components/RIDLink.js

@@ -1,12 +0,0 @@
-import React from 'react';
-import { Typography } from '@mui/material';
-import ExternalLink from '../../components/ExternalLink';
-function RIDLink({ baseUrl, rid }) {
-    return (React.createElement(Typography, null,
-        "RID ",
-        rid,
-        " (",
-        React.createElement(ExternalLink, { href: `${baseUrl}?CMD=Get&RID=${rid}` }, "see status"),
-        ")"));
-}
-export default RIDLink;

package/dist/utils/ncbiBlast.d.ts

@@ -1,30 +0,0 @@
-import type { BlastDatabase, BlastProgram } from '../LaunchMsaView/components/NCBIBlastQuery/consts';
-export declare function queryBlastFromRid({ rid, baseUrl, onProgress, }: {
-    rid: string;
-    baseUrl: string;
-    onProgress: (arg: string) => void;
-}): Promise<{
-    rid: string;
-    hits: {
-        description: import("./types").BlastHitDescription[];
-        hsps: {
-            hseq: string;
-        }[];
-    }[];
-}>;
-export declare function queryBlast({ query, blastDatabase, blastProgram, baseUrl, onProgress, onRid, }: {
-    query: string;
-    blastDatabase: BlastDatabase;
-    blastProgram: BlastProgram;
-    baseUrl: string;
-    onProgress: (arg: string) => void;
-    onRid: (arg: string) => void;
-}): Promise<{
-    rid: string;
-    hits: {
-        description: import("./types").BlastHitDescription[];
-        hsps: {
-            hseq: string;
-        }[];
-    }[];
-}>;

package/dist/utils/ncbiBlast.js

@@ -1,84 +0,0 @@
-import { jsonfetch, textfetch } from './fetch';
-import { pollLoop } from './poll';
-export async function queryBlastFromRid({ rid, baseUrl, onProgress, }) {
-    onProgress(`Checking BLAST status for RID: ${rid}...`);
-    await waitForRid({
-        rid,
-        onProgress,
-        baseUrl,
-    });
-    const ret = await jsonfetch(`${baseUrl}?CMD=Get&RID=${rid}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`);
-    return {
-        rid,
-        hits: ret.BlastOutput2[0]?.report.results.search.hits ?? [],
-    };
-}
-export async function queryBlast({ query, blastDatabase, blastProgram, baseUrl, onProgress, onRid, }) {
-    onProgress('Submitting to NCBI BLAST...');
-    const { rid } = await initialQuery({
-        query,
-        blastDatabase,
-        blastProgram,
-        baseUrl,
-    });
-    onRid(rid);
-    return queryBlastFromRid({ rid, baseUrl, onProgress });
-}
-async function initialQuery({ query, blastProgram, blastDatabase, baseUrl, }) {
-    const res = await textfetch(baseUrl, {
-        method: 'POST',
-        body: new URLSearchParams({
-            CMD: 'Put',
-            PROGRAM: blastProgram === 'quick-blastp' ? 'blastp' : blastProgram,
-            DATABASE: blastDatabase,
-            QUERY: query,
-            ...(blastDatabase === 'nr_cluster_seq'
-                ? {
-                    CLUSTERED_DB: 'on',
-                    DB_TYPE: 'Experimental Databases',
-                }
-                : {}),
-            ...(blastProgram === 'quick-blastp'
-                ? { BLAST_PROGRAMS: 'kmerBlastp' }
-                : {}),
-        }),
-    });
-    // the initial submission/query to the BLAST "REST API" does not return JSON
-    // as a response (e.g. FORMAT_TYPE=JSON does not work), so the RID is
-    // literally parsed from the text of the HTML that is returned
-    const rid = /^ {4}RID = (.*$)/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, }) {
-    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'}`);
-        },
-    });
-}

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'}`,
-      )
-    },
-  })
-}