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Create a duplicate transcript #756

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66 changes: 46 additions & 20 deletions packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@ import { alpha } from '@mui/material'

import { type OntologyRecord } from '../../OntologyManager'
import { MergeExons, MergeTranscripts, SplitExon } from '../../components'
import { DuplicateTranscript } from '../../components/DuplicateTranscript'
import {
type MousePosition,
type MousePositionWithFeature,
Expand Down Expand Up @@ -950,29 +951,54 @@ function getContextMenuItems(
)
}
if (isTranscriptFeature(feature, session)) {
contextMenuItemsForFeature.push({
label: 'Merge transcript',
onClick: () => {
;(session as unknown as AbstractSessionModel).queueDialog(
(doneCallback) => [
MergeTranscripts,
{
session,
handleClose: () => {
doneCallback()
contextMenuItemsForFeature.push(
{
label: 'Merge transcript',
onClick: () => {
;(session as unknown as AbstractSessionModel).queueDialog(
(doneCallback) => [
MergeTranscripts,
{
session,
handleClose: () => {
doneCallback()
},
changeManager,
sourceFeature: feature,
sourceAssemblyId: currentAssemblyId,
selectedFeature,
setSelectedFeature: (feature?: AnnotationFeature) => {
display.setSelectedFeature(feature)
},
},
changeManager,
sourceFeature: feature,
sourceAssemblyId: currentAssemblyId,
selectedFeature,
setSelectedFeature: (feature?: AnnotationFeature) => {
display.setSelectedFeature(feature)
],
)
},
},
{
label: 'Duplicate transcript',
onClick: () => {
;(session as unknown as AbstractSessionModel).queueDialog(
(doneCallback) => [
DuplicateTranscript,
{
session,
handleClose: () => {
doneCallback()
},
changeManager,
sourceFeature: feature,
sourceAssemblyId: currentAssemblyId,
selectedFeature,
setSelectedFeature: (feature?: AnnotationFeature) => {
display.setSelectedFeature(feature)
},
},
},
],
)
],
)
},
},
})
)
if (isSessionModelWithWidgets(session)) {
contextMenuItemsForFeature.splice(1, 0, {
label: 'Open transcript editor',
Expand Down
132 changes: 132 additions & 0 deletions packages/jbrowse-plugin-apollo/src/components/DuplicateTranscript.tsx
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Original file line number Diff line number Diff line change
@@ -0,0 +1,132 @@
/* eslint-disable @typescript-eslint/unbound-method */
import {
type AnnotationFeature,
type AnnotationFeatureSnapshot,
} from '@apollo-annotation/mst'
import { AddFeatureChange } from '@apollo-annotation/shared'
import { type AbstractSessionModel } from '@jbrowse/core/util/types'
import {
Button,
DialogActions,
DialogContent,
DialogContentText,
} from '@mui/material'
import ObjectID from 'bson-objectid'
import { getSnapshot } from 'mobx-state-tree'
import React, { useState } from 'react'

import { type ChangeManager } from '../ChangeManager'
import { type ApolloSessionModel } from '../session'

import { Dialog } from './Dialog'

interface DuplicateTranscriptProps {
session: ApolloSessionModel
handleClose(): void
sourceFeature: AnnotationFeature
sourceAssemblyId: string
changeManager: ChangeManager
selectedFeature?: AnnotationFeature
setSelectedFeature(feature?: AnnotationFeature): void
}

export function DuplicateTranscript({
changeManager,
handleClose,
session,
sourceAssemblyId,
sourceFeature,
setSelectedFeature,
}: DuplicateTranscriptProps) {
const [errorMessage, setErrorMessage] = useState('')
const { notify } = session as unknown as AbstractSessionModel

async function onSubmit(event: React.FormEvent<HTMLFormElement>) {
event.preventDefault()
setErrorMessage('')

try {
const parentGene = sourceFeature.parent
if (!parentGene) {
setErrorMessage('No parent gene found for this transcript')
return
}

const transcriptSnapshot = getSnapshot(sourceFeature)
const newTranscriptId = new ObjectID().toHexString()
const duplicateTranscript = {
...transcriptSnapshot,
_id: newTranscriptId,
} as AnnotationFeatureSnapshot

if (duplicateTranscript.children) {
const newChildren: Record<string, AnnotationFeatureSnapshot> = {}
for (const [, child] of Object.entries(duplicateTranscript.children)) {
const newChildId = new ObjectID().toHexString()
newChildren[newChildId] = {
...child,
_id: newChildId,
} as AnnotationFeatureSnapshot
}
duplicateTranscript.children = newChildren
}

const change = new AddFeatureChange({
parentFeatureId: parentGene._id,
changedIds: [parentGene._id],
typeName: 'AddFeatureChange',
assembly: sourceAssemblyId,
addedFeature: duplicateTranscript,
})

await changeManager.submit(change).then(() => {
setSelectedFeature(undefined)
session.apolloSetSelectedFeature(newTranscriptId)
notify('Successfully duplicated transcript', 'success')
})

handleClose()
} catch (error) {
setErrorMessage(
error instanceof Error
? error.message
: 'Failed to duplicate transcript',
)
}
}

return (
<Dialog
open
title="Duplicate transcript"
handleClose={handleClose}
maxWidth={false}
data-testid="duplicate-transcript"
>
<form
onSubmit={(event) => {
void onSubmit(event)
}}
>
<DialogContent style={{ display: 'flex', flexDirection: 'column' }}>
<DialogContentText>
Are you sure you want to create a duplicate of this transcript?
</DialogContentText>
</DialogContent>
<DialogActions>
<Button variant="contained" type="submit">
Yes
</Button>
<Button variant="outlined" type="submit" onClick={handleClose}>
Cancel
</Button>
</DialogActions>
</form>
{errorMessage ? (
<DialogContent>
<DialogContentText color="error">{errorMessage}</DialogContentText>
</DialogContent>
) : null}
</Dialog>
)
}