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Add ability to get refNames for a track in the "About track" panel (#…
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,126 @@ | ||
| import React, { useState, useEffect } from 'react' | ||
| import { Button, DialogContent, Typography } from '@mui/material' | ||
| import { | ||
| readConfObject, | ||
| AnyConfigurationModel, | ||
| } from '@jbrowse/core/configuration' | ||
| import { Dialog, LoadingEllipses } from '@jbrowse/core/ui' | ||
| import { getSession } from '@jbrowse/core/util' | ||
| import { observer } from 'mobx-react' | ||
| import { makeStyles } from 'tss-react/mui' | ||
| import copy from 'copy-to-clipboard' | ||
|
|
||
| const MAX_REF_NAMES = 10_000 | ||
|
|
||
| const useStyles = makeStyles()(theme => ({ | ||
| container: { | ||
| minWidth: 800, | ||
| }, | ||
| refNames: { | ||
| maxHeight: 300, | ||
| width: '100%', | ||
| overflow: 'auto', | ||
| flexGrow: 1, | ||
| background: theme.palette.background.default, | ||
| }, | ||
| })) | ||
|
|
||
| const RefNameInfoDialog = observer(function ({ | ||
| config, | ||
| onClose, | ||
| }: { | ||
| config: AnyConfigurationModel | ||
| onClose: () => void | ||
| }) { | ||
| const [error, setError] = useState<unknown>() | ||
| const [refNames, setRefNames] = useState<Record<string, string[]>>() | ||
| const [copied, setCopied] = useState(false) | ||
| const { classes } = useStyles() | ||
| const session = getSession(config) | ||
| const { rpcManager } = session | ||
|
|
||
| useEffect(() => { | ||
| // eslint-disable-next-line @typescript-eslint/no-floating-promises | ||
| ;(async () => { | ||
| try { | ||
| const assemblyNames = [ | ||
| ...new Set(readConfObject(config, 'assemblyNames') as string[]), | ||
| ] | ||
| const map = await Promise.all( | ||
| assemblyNames.map(async assemblyName => { | ||
| const adapterConfig = readConfObject(config, 'adapter') | ||
| return [ | ||
| assemblyName, | ||
| (await rpcManager.call(config.trackId, 'CoreGetRefNames', { | ||
| adapterConfig, | ||
| // hack for synteny adapters | ||
| regions: [{ assemblyName }], | ||
| })) as string[], | ||
| ] as const | ||
| }), | ||
| ) | ||
| setRefNames(Object.fromEntries(map)) | ||
| } catch (e) { | ||
| console.error(e) | ||
| setError(e) | ||
| } | ||
| })() | ||
| }, [config, rpcManager]) | ||
|
|
||
| const names = refNames ? Object.entries(refNames) : [] | ||
| const result = names | ||
| .flatMap(([assemblyName, refNames]) => { | ||
| return [ | ||
| `--- ${assemblyName} ---`, | ||
| ...refNames.slice(0, MAX_REF_NAMES), | ||
| `${ | ||
| refNames.length > MAX_REF_NAMES | ||
| ? `\nToo many refNames to show in browser for ${assemblyName}, use "Copy ref names" button to copy to clipboard` | ||
| : '' | ||
| }`, | ||
| ] | ||
| }) | ||
| .filter(f => !!f) | ||
| .join('\n') | ||
|
|
||
| return ( | ||
| <Dialog | ||
| open | ||
| title="Reference sequence names used in track" | ||
| onClose={onClose} | ||
| > | ||
| <DialogContent className={classes.container}> | ||
| {error ? ( | ||
| <Typography color="error">{`${error}`}</Typography> | ||
| ) : refNames === undefined ? ( | ||
| <LoadingEllipses message="Loading refNames" /> | ||
| ) : ( | ||
| <> | ||
| <Button | ||
| variant="contained" | ||
| onClick={() => { | ||
| copy( | ||
| names | ||
| .flatMap(([assemblyName, refNames]) => [ | ||
| `--- ${assemblyName} ---`, | ||
| ...refNames, | ||
| ]) | ||
| .filter(f => !!f) | ||
| .join('\n'), | ||
| ) | ||
| setCopied(true) | ||
| setTimeout(() => setCopied(false), 1000) | ||
| }} | ||
| > | ||
| {copied ? 'Copied to clipboard!' : 'Copy ref names'} | ||
| </Button> | ||
|
|
||
| <pre className={classes.refNames}>{result}</pre> | ||
| </> | ||
| )} | ||
| </DialogContent> | ||
| </Dialog> | ||
| ) | ||
| }) | ||
|
|
||
| export default RefNameInfoDialog |
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