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Slight refactor
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@cmdcolin
cmdcolin committed Nov 29, 2023
1 parent 8ec1d22 commit 8d44ad1
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Showing 2 changed files with 88 additions and 81 deletions.
113 changes: 32 additions & 81 deletions plugins/linear-genome-view/src/LinearGenomeView/components/ImportForm.tsx
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,9 +16,9 @@ import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
import CloseIcon from '@mui/icons-material/Close'

// locals
import RefNameAutocomplete from './RefNameAutocomplete'
import { fetchResults, splitLast } from './util'
import { LinearGenomeViewModel } from '..'
import { handleSelectedRegion, navToOption } from '../../searchUtils'
import ImportFormRefNameAutocomplete from './ImportFormRefNameAutocomplete'

const useStyles = makeStyles()(theme => ({
importFormContainer: {
Expand All @@ -41,11 +41,10 @@ const LinearGenomeViewImportForm = observer(function ({
}) {
const { classes } = useStyles()
const session = getSession(model)
const { assemblyNames, assemblyManager, textSearchManager } = session
const { rankSearchResults, error } = model
const { assemblyNames, assemblyManager } = session
const { error } = model
const [selectedAsm, setSelectedAsm] = useState(assemblyNames[0])
const [option, setOption] = useState<BaseResult>()
const searchScope = model.searchScope(selectedAsm)
const assembly = assemblyManager.get(selectedAsm)
const assemblyError = assemblyNames.length
? assembly?.error
Expand All @@ -65,61 +64,6 @@ const LinearGenomeViewImportForm = observer(function ({
setValue(r0)
}, [r0, selectedAsm])

async function navToOption(option: BaseResult) {
const location = option.getLocation()
const trackId = option.getTrackId()
if (location) {
await model.navToLocString(location, selectedAsm)
if (trackId) {
model.showTrack(trackId)
}
}
}

// gets a string as input, or use stored option results from previous query,
// then re-query and
// 1) if it has multiple results: pop a dialog
// 2) if it's a single result navigate to it
// 3) else assume it's a locstring and navigate to it
async function handleSelectedRegion(input: string) {
try {
if (option?.getDisplayString() === input && option.hasLocation()) {
await navToOption(option)
} else if (option?.results?.length) {
model.setSearchResults(option.results, option.getLabel(), selectedAsm)
} else {
const [ref, rest] = splitLast(input, ':')
const allRefs = assembly?.allRefNamesWithLowerCase || []
if (
allRefs.includes(input) ||
(allRefs.includes(ref) && !Number.isNaN(Number.parseInt(rest, 10)))
) {
await model.navToLocString(input, selectedAsm)
} else {
const results = await fetchResults({
queryString: input,
searchType: 'exact',
searchScope,
rankSearchResults,
textSearchManager,
assembly,
})

if (results.length > 1) {
model.setSearchResults(results, input.toLowerCase(), selectedAsm)
} else if (results.length === 1) {
await navToOption(results[0])
} else {
await model.navToLocString(input, selectedAsm)
}
}
}
} catch (e) {
console.error(e)
session.notify(`${e}`, 'warning')
}
}

// implementation notes:
// having this wrapped in a form allows intuitive use of enter key to submit
return (
Expand All @@ -132,7 +76,29 @@ const LinearGenomeViewImportForm = observer(function ({
model.setError(undefined)
if (value) {
// has it's own error handling
await handleSelectedRegion(value)
try {
if (
option?.getDisplayString() === value &&
option.hasLocation()
) {
await navToOption({
option,
model,
assemblyName: selectedAsm,
})
} else if (option?.results?.length) {
model.setSearchResults(
option.results,
option.getLabel(),
selectedAsm,
)
} else if (assembly) {
await handleSelectedRegion({ input: value, assembly, model })
}
} catch (e) {
console.error(e)
session.notify(`${e}`, 'warning')
}
}
}}
>
Expand All @@ -158,27 +124,12 @@ const LinearGenomeViewImportForm = observer(function ({
<CloseIcon style={{ color: 'red' }} />
) : assemblyLoaded ? (
<FormControl>
<RefNameAutocomplete
fetchResults={queryString =>
fetchResults({
queryString,
assembly,
textSearchManager,
rankSearchResults,
searchScope,
})
}
model={model}
assemblyName={selectedAsm}
<ImportFormRefNameAutocomplete
value={value}
minWidth={270}
onChange={str => setValue(str)}
onSelect={val => setOption(val)}
TextFieldProps={{
variant: 'outlined',
helperText:
'Enter sequence name, feature name, or location',
}}
setValue={setValue}
selectedAsm={selectedAsm}
setOption={setOption}
model={model}
/>
</FormControl>
) : (
Expand Down
56 changes: 56 additions & 0 deletions plugins/linear-genome-view/src/LinearGenomeView/components/ImportFormRefNameAutocomplete.tsx
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Original file line number Diff line number Diff line change
@@ -0,0 +1,56 @@
import React from 'react'
import { observer } from 'mobx-react'
import { getSession } from '@jbrowse/core/util'
import BaseResult from '@jbrowse/core/TextSearch/BaseResults'

// locals
import RefNameAutocomplete from './RefNameAutocomplete'
import { fetchResults } from './util'
import { LinearGenomeViewModel } from '..'

type LGV = LinearGenomeViewModel

const ImportFormRefNameAutocomplete = observer(function ({
model,
selectedAsm,
value,
setValue,
setOption,
}: {
value: string
setValue: (arg: string) => void
model: LGV
selectedAsm: string
setOption: (arg: BaseResult) => void
}) {
const session = getSession(model)
const { assemblyManager, textSearchManager } = session
const { rankSearchResults } = model
const searchScope = model.searchScope(selectedAsm)
const assembly = assemblyManager.get(selectedAsm)
return (
<RefNameAutocomplete
fetchResults={queryString =>
fetchResults({
queryString,
assembly,
textSearchManager,
rankSearchResults,
searchScope,
})
}
model={model}
assemblyName={selectedAsm}
value={value}
minWidth={270}
onChange={str => setValue(str)}
onSelect={val => setOption(val)}
TextFieldProps={{
variant: 'outlined',
helperText: 'Enter sequence name, feature name, or location',
}}
/>
)
})

export default ImportFormRefNameAutocomplete

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