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247 changes: 247 additions & 0 deletions
247
packages/jbrowse-plugin-apollo/src/components/AddChildFeature.tsx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,247 @@ | ||
| import { AbstractSessionModel } from '@jbrowse/core/util' | ||
| import { | ||
| Button, | ||
| DialogActions, | ||
| DialogContent, | ||
| DialogContentText, | ||
| FormControl, | ||
| InputLabel, | ||
| MenuItem, | ||
| Select, | ||
| SelectChangeEvent, | ||
| TextField, | ||
| } from '@mui/material' | ||
| import { AnnotationFeatureI } from 'apollo-mst' | ||
| import { AddFeatureChange } from 'apollo-shared' | ||
| import ObjectID from 'bson-objectid' | ||
| import React, { useState } from 'react' | ||
|
|
||
| import { ChangeManager } from '../ChangeManager' | ||
| import { isOntologyClass } from '../OntologyManager' | ||
| import OntologyStore from '../OntologyManager/OntologyStore' | ||
| import { ApolloSessionModel } from '../session' | ||
| import { Dialog } from './Dialog' | ||
| import { OntologyTermAutocomplete } from './OntologyTermAutocomplete' | ||
|
|
||
| interface AddChildFeatureProps { | ||
| session: ApolloSessionModel | ||
| handleClose(): void | ||
| sourceFeature: AnnotationFeatureI | ||
| sourceAssemblyId: string | ||
| changeManager: ChangeManager | ||
| } | ||
|
|
||
| enum PhaseEnum { | ||
| zero = 0, | ||
| one = 1, | ||
| two = 2, | ||
| } | ||
|
|
||
| export function AddChildFeature({ | ||
| changeManager, | ||
| handleClose, | ||
| session, | ||
| sourceAssemblyId, | ||
| sourceFeature, | ||
| }: AddChildFeatureProps) { | ||
| const { notify } = session as unknown as AbstractSessionModel | ||
| const [end, setEnd] = useState(String(sourceFeature.end)) | ||
| const [start, setStart] = useState(String(sourceFeature.start)) | ||
| const [type, setType] = useState('') | ||
| const [phase, setPhase] = useState('') | ||
| const [phaseAsNumber, setPhaseAsNumber] = useState<PhaseEnum>() | ||
| const [showPhase, setShowPhase] = useState<boolean>(false) | ||
| const [errorMessage, setErrorMessage] = useState('') | ||
| const [typeWarningText, setTypeWarningText] = useState('') | ||
|
|
||
| async function fetchValidDescendantTerms( | ||
| parentFeature: AnnotationFeatureI | undefined, | ||
| ontologyStore: OntologyStore, | ||
| _signal: AbortSignal, | ||
| ) { | ||
| if (!parentFeature) { | ||
| return | ||
| } | ||
| // since this is a child of an existing feature, restrict the autocomplete choices to valid | ||
| // parts of that feature | ||
| const parentTypeTerms = await ontologyStore.getTermsWithLabelOrSynonym( | ||
| parentFeature.type, | ||
| { includeSubclasses: false }, | ||
| ) | ||
| // eslint-disable-next-line unicorn/no-array-callback-reference | ||
| const parentTypeClassTerms = parentTypeTerms.filter(isOntologyClass) | ||
| if (parentTypeTerms.length === 0) { | ||
| return | ||
| } | ||
| const subpartTerms = await ontologyStore.getClassesThat( | ||
| 'part_of', | ||
| parentTypeClassTerms, | ||
| ) | ||
| if (subpartTerms.length > 0) { | ||
| setTypeWarningText('') | ||
| } else { | ||
| setTypeWarningText( | ||
| `Type "${parentFeature.type}" does not have any children in the ontology`, | ||
| ) | ||
| } | ||
| return subpartTerms | ||
| } | ||
|
|
||
| async function onSubmit(event: React.FormEvent<HTMLFormElement>) { | ||
| event.preventDefault() | ||
| setErrorMessage('') | ||
| if (showPhase && phase === '') { | ||
| setErrorMessage('The phase is REQUIRED for all CDS features.') | ||
| return | ||
| } | ||
| const change = new AddFeatureChange({ | ||
| changedIds: [sourceFeature._id], | ||
| typeName: 'AddFeatureChange', | ||
| assembly: sourceAssemblyId, | ||
| addedFeature: { | ||
| _id: new ObjectID().toHexString(), | ||
| gffId: '', | ||
| refSeq: sourceFeature.refSeq, | ||
| start: Number(start), | ||
| end: Number(end), | ||
| type, | ||
| phase: phaseAsNumber, | ||
| }, | ||
| parentFeatureId: sourceFeature._id, | ||
| }) | ||
| await changeManager.submit?.(change) | ||
| notify('Feature added successfully', 'success') | ||
| handleClose() | ||
| event.preventDefault() | ||
| } | ||
| function handleChangeType(newType: string) { | ||
| setErrorMessage('') | ||
| setType(newType) | ||
| if (newType.startsWith('CDS')) { | ||
| setShowPhase(true) | ||
| setPhase('') | ||
| } else { | ||
| setShowPhase(false) | ||
| } | ||
| } | ||
| async function handleChangePhase(e: SelectChangeEvent<string>) { | ||
| setErrorMessage('') | ||
| setPhase(e.target.value) | ||
|
|
||
| switch (Number(e.target.value)) { | ||
| case 0: { | ||
| setPhaseAsNumber(PhaseEnum.zero) | ||
| break | ||
| } | ||
| case 1: { | ||
| setPhaseAsNumber(PhaseEnum.one) | ||
| break | ||
| } | ||
| case 2: { | ||
| setPhaseAsNumber(PhaseEnum.two) | ||
| break | ||
| } | ||
| default: { | ||
| // eslint-disable-next-line unicorn/no-useless-undefined | ||
| setPhaseAsNumber(undefined) | ||
| } | ||
| } | ||
| } | ||
| const error = Number(end) <= Number(start) | ||
| return ( | ||
| <Dialog | ||
| open | ||
| title="Add new child feature" | ||
| handleClose={handleClose} | ||
| maxWidth={false} | ||
| data-testid="add-feature-dialog" | ||
| > | ||
| <form onSubmit={onSubmit}> | ||
| <DialogContent style={{ display: 'flex', flexDirection: 'column' }}> | ||
| <TextField | ||
| margin="dense" | ||
| id="start" | ||
| label="Start" | ||
| type="number" | ||
| fullWidth | ||
| variant="outlined" | ||
| value={start} | ||
| onChange={(e) => setStart(e.target.value)} | ||
| /> | ||
| <TextField | ||
| margin="dense" | ||
| id="end" | ||
| label="End" | ||
| type="number" | ||
| fullWidth | ||
| variant="outlined" | ||
| value={end} | ||
| onChange={(e) => setEnd(e.target.value)} | ||
| error={error} | ||
| helperText={error ? '"End" must be greater than "Start"' : null} | ||
| /> | ||
| {/* <Select value={type} onChange={handleChangeType} label="Type"> | ||
| {(possibleChildTypes ?? []).map((option) => ( | ||
| <MenuItem key={option} value={option}> | ||
| {option} | ||
| </MenuItem> | ||
| ))} | ||
| </Select> */} | ||
| <OntologyTermAutocomplete | ||
| session={session} | ||
| ontologyName="Sequence Ontology" | ||
| style={{ width: 170 }} | ||
| value={type} | ||
| filterTerms={isOntologyClass} | ||
| fetchValidTerms={fetchValidDescendantTerms.bind( | ||
| null, | ||
| sourceFeature, | ||
| )} | ||
| renderInput={(params) => ( | ||
| <TextField | ||
| {...params} | ||
| label="Type" | ||
| variant="outlined" | ||
| fullWidth | ||
| error={Boolean(typeWarningText)} | ||
| helperText={typeWarningText} | ||
| /> | ||
| )} | ||
| onChange={(oldValue, newValue) => { | ||
| if (newValue) { | ||
| handleChangeType(newValue) | ||
| } | ||
| }} | ||
| /> | ||
| {showPhase ? ( | ||
| <FormControl> | ||
| <InputLabel>Phase</InputLabel> | ||
| <Select value={phase} onChange={handleChangePhase}> | ||
| <MenuItem value={0}>0</MenuItem> | ||
| <MenuItem value={1}>1</MenuItem> | ||
| <MenuItem value={2}>2</MenuItem> | ||
| </Select> | ||
| </FormControl> | ||
| ) : null} | ||
| </DialogContent> | ||
| <DialogActions> | ||
| <Button | ||
| variant="contained" | ||
| type="submit" | ||
| disabled={error || !(start && end && type)} | ||
| > | ||
| Submit | ||
| </Button> | ||
| <Button variant="outlined" type="submit" onClick={handleClose}> | ||
| Cancel | ||
| </Button> | ||
| </DialogActions> | ||
| </form> | ||
| {errorMessage ? ( | ||
| <DialogContent> | ||
| <DialogContentText color="error">{errorMessage}</DialogContentText> | ||
| </DialogContent> | ||
| ) : null} | ||
| </Dialog> | ||
| ) | ||
| } |
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