@apollo-annotation/jbrowse-plugin-apollo 1.0.0 → 1.1.0

package/src/components/AddCodingSequence.tsx

@@ -0,0 +1,255 @@
+/* eslint-disable @typescript-eslint/unbound-method */
+import type {
+  AnnotationFeature,
+  AnnotationFeatureSnapshot,
+} from '@apollo-annotation/mst'
+import { AddFeatureChange } from '@apollo-annotation/shared'
+import type { AbstractSessionModel } from '@jbrowse/core/util'
+import { revcom } from '@jbrowse/core/util'
+import {
+  Button,
+  DialogActions,
+  DialogContent,
+  DialogContentText,
+  FormControl,
+  FormControlLabel,
+  Radio,
+  RadioGroup,
+  TextField,
+} from '@mui/material'
+import ObjectID from 'bson-objectid'
+import React, { useState } from 'react'
+
+import type { ChangeManager } from '../ChangeManager'
+import type { ApolloSessionModel } from '../session'
+import { findLongestOrf } from '../util/sequenceUtils'
+
+import { Dialog } from './Dialog'
+
+interface AddCodingSequenceProps {
+  session: ApolloSessionModel
+  handleClose(): void
+  sourceFeature: AnnotationFeature
+  sourceAssemblyId: string
+  changeManager: ChangeManager
+  refName: string
+}
+
+// Returns the genomic half-open boundary for stitched position `pos`.
+// For strand +1: the inclusive start (min) of the nucleotide.
+// For strand -1: the exclusive end (max) of the nucleotide.
+// Symmetric usage:
+//   plus:  cdsMin = helper(orf[0]), cdsMax = helper(orf[1]+3)
+//   minus: cdsMax = helper(orf[0]), cdsMin = helper(orf[1]+3)
+function stitchedToGenomicBound(
+  pos: number,
+  exons: { min: number; max: number }[],
+  strand: 1 | -1,
+): number {
+  let cum = 0
+  for (const exon of exons) {
+    const len = exon.max - exon.min
+    if (pos <= cum + len) {
+      const off = pos - cum
+      return strand === 1 ? exon.min + off : exon.max - off
+    }
+    cum += len
+  }
+  const last = exons.at(-1)
+  if (!last) {
+    throw new Error('No exons found')
+  }
+  return strand === 1 ? last.max : last.min
+}
+
+export function AddCodingSequence({
+  changeManager,
+  handleClose,
+  refName,
+  session,
+  sourceAssemblyId,
+  sourceFeature,
+}: AddCodingSequenceProps) {
+  const [method, setMethod] = useState<'longest-orf' | 'manual'>('longest-orf')
+  const [minInput, setMinInput] = useState('')
+  const [maxInput, setMaxInput] = useState('')
+  const [errorMessage, setErrorMessage] = useState('')
+
+  async function onSubmit(event: React.FormEvent<HTMLFormElement>) {
+    event.preventDefault()
+    setErrorMessage('')
+
+    let cdsMin: number
+    let cdsMax: number
+
+    try {
+      if (method === 'longest-orf') {
+        const exonParts = sourceFeature.transcriptExonParts.filter(
+          (p) => p.type === 'exon',
+        )
+        if (exonParts.length === 0) {
+          setErrorMessage('No exons found in this transcript')
+          return
+        }
+
+        const backendDriver =
+          session.apolloDataStore.getBackendDriver(sourceAssemblyId)
+        if (!backendDriver) {
+          setErrorMessage('No backend driver found for this assembly')
+          return
+        }
+
+        let stitchedSequence = ''
+        for (const exon of exonParts) {
+          const { seq } = await backendDriver.getSequence({
+            assemblyName: sourceAssemblyId,
+            refName,
+            start: exon.min,
+            end: exon.max,
+          })
+          stitchedSequence += sourceFeature.strand === -1 ? revcom(seq) : seq
+        }
+
+        const orf = findLongestOrf(stitchedSequence)
+        if (!orf) {
+          ;(session as unknown as AbstractSessionModel).notify(
+            'No open reading frame found in this transcript',
+            'error',
+          )
+          handleClose()
+          return
+        }
+
+        const strand = sourceFeature.strand ?? 1
+        if (strand === 1) {
+          cdsMin = stitchedToGenomicBound(orf[0], exonParts, 1)
+          cdsMax = stitchedToGenomicBound(orf[1] + 3, exonParts, 1)
+        } else {
+          cdsMax = stitchedToGenomicBound(orf[0], exonParts, -1)
+          cdsMin = stitchedToGenomicBound(orf[1] + 3, exonParts, -1)
+        }
+      } else {
+        cdsMin = Number(minInput) - 1
+        cdsMax = Number(maxInput)
+      }
+
+      const _id = new ObjectID().toHexString()
+      const addedFeature: AnnotationFeatureSnapshot = {
+        _id,
+        refSeq: sourceFeature.refSeq,
+        min: cdsMin,
+        max: cdsMax,
+        type: 'CDS',
+      }
+      if (sourceFeature.strand) {
+        addedFeature.strand = sourceFeature.strand
+      }
+      const change = new AddFeatureChange({
+        changedIds: [sourceFeature._id],
+        typeName: 'AddFeatureChange',
+        assembly: sourceAssemblyId,
+        addedFeature,
+        parentFeatureId: sourceFeature._id,
+      })
+      await changeManager.submit(change)
+      session.apolloSetSelectedFeature(_id)
+      handleClose()
+    } catch (error) {
+      setErrorMessage(
+        error instanceof Error ? error.message : 'An unknown error occurred',
+      )
+    }
+  }
+
+  const manualError =
+    method === 'manual' &&
+    Boolean(minInput) &&
+    Boolean(maxInput) &&
+    Number(maxInput) <= Number(minInput)
+
+  const submitDisabled =
+    method === 'manual' ? !(minInput && maxInput) || manualError : false
+
+  return (
+    <Dialog
+      open
+      title="Add coding sequence"
+      handleClose={handleClose}
+      maxWidth={false}
+      data-testid="add-coding-sequence"
+    >
+      <form
+        onSubmit={(event) => {
+          void onSubmit(event)
+        }}
+      >
+        <DialogContent style={{ display: 'flex', flexDirection: 'column' }}>
+          <FormControl>
+            <RadioGroup
+              value={method}
+              onChange={(e) => {
+                setMethod(e.target.value as 'longest-orf' | 'manual')
+              }}
+            >
+              <FormControlLabel
+                value="longest-orf"
+                control={<Radio />}
+                label="Calculate longest open reading frame"
+              />
+              <FormControlLabel
+                value="manual"
+                control={<Radio />}
+                label="Manual"
+              />
+            </RadioGroup>
+          </FormControl>
+          {method === 'manual' ? (
+            <>
+              <TextField
+                margin="dense"
+                id="cds-min"
+                label="Min"
+                type="number"
+                fullWidth
+                variant="outlined"
+                value={minInput}
+                onChange={(e) => {
+                  setMinInput(e.target.value)
+                }}
+              />
+              <TextField
+                margin="dense"
+                id="cds-max"
+                label="Max"
+                type="number"
+                fullWidth
+                variant="outlined"
+                value={maxInput}
+                onChange={(e) => {
+                  setMaxInput(e.target.value)
+                }}
+                error={manualError}
+                helperText={
+                  manualError ? '"Max" must be greater than "Min"' : null
+                }
+              />
+            </>
+          ) : null}
+        </DialogContent>
+        <DialogActions>
+          <Button variant="contained" type="submit" disabled={submitDisabled}>
+            Submit
+          </Button>
+          <Button variant="outlined" type="button" onClick={handleClose}>
+            Cancel
+          </Button>
+        </DialogActions>
+      </form>
+      {errorMessage ? (
+        <DialogContent>
+          <DialogContentText color="error">{errorMessage}</DialogContentText>
+        </DialogContent>
+      ) : null}
+    </Dialog>
+  )
+}

package/src/components/AddFeature.tsx

@@ -233,7 +233,7 @@ export function AddFeature({
     }
   }
 
-  let submitDisabled: boolean = Boolean(error) || !(start && end && type)
+  let submitDisabled: boolean = error || !(start && end && type)
   if (
     (type === NewFeature.CUSTOM && !customType) ||
     (!strand && type === NewFeature.GENE_AND_SUBFEATURES) ||

package/src/components/AddRefSeqAliases.tsx

@@ -68,7 +68,7 @@ export const AddRefSeqAliases = observer(function AddRefSeqAliases({
     }[]
   >([])
   const [refNameAliasMap, setRefNameAliasMap] = useState<Map<string, string[]>>(
-    new Map(),
+    () => new Map(),
   )
 
   const { apolloDataStore } = session
@@ -83,6 +83,7 @@ export const AddRefSeqAliases = observer(function AddRefSeqAliases({
 
   useEffect(() => {
     if (assemblies.length > 0) {
+      // eslint-disable-next-line @eslint-react/set-state-in-effect
       setSelectedAssembly(assemblies[0])
       collaborationServerDriver
         .getRefNameAliases(assemblies[0].name)
@@ -94,7 +95,7 @@ export const AddRefSeqAliases = observer(function AddRefSeqAliases({
           setErrorMessage('Error fetching refName aliases for assembly')
         })
     }
-    // eslint-disable-next-line react-hooks/exhaustive-deps
+    // eslint-disable-next-line @eslint-react/exhaustive-deps
   }, [])
 
   const initializeRefNameAliasMap = (refNameAliasesList: RefNameAliases[]) => {

package/src/components/CopyFeature.tsx

@@ -8,6 +8,7 @@ import type {
   AnnotationFeatureSnapshot,
 } from '@apollo-annotation/mst'
 import { AddFeatureChange } from '@apollo-annotation/shared'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { readConfObject } from '@jbrowse/core/configuration'
 import type { AbstractSessionModel } from '@jbrowse/core/util'
 import { getSnapshot } from '@jbrowse/mobx-state-tree'
@@ -105,7 +106,9 @@ export function CopyFeature({
         setErrorMessage('No assemblies to copy to')
         return
       }
-      const assembly = await assemblyManager.waitForAssembly(selectedAssemblyId)
+      const assembly = (await assemblyManager.waitForAssembly(
+        selectedAssemblyId,
+      )) as Assembly | undefined
       if (!assembly) {
         return
       }
@@ -136,7 +139,9 @@ export function CopyFeature({
     event.preventDefault()
     setErrorMessage('')
     const featureLength = sourceFeature.length
-    const assembly = await assemblyManager.waitForAssembly(selectedAssemblyId)
+    const assembly = (await assemblyManager.waitForAssembly(
+      selectedAssemblyId,
+    )) as Assembly | undefined
     if (!assembly) {
       setErrorMessage(`Assembly not found: ${selectedAssemblyId}.`)
       return
@@ -165,7 +170,7 @@ export function CopyFeature({
     const featureIds: string[] = []
     // Let's add featureId to each child recursively
     const newFeatureLine = generateNewIds(
-      getSnapshot(sourceFeature) as unknown as AnnotationFeatureSnapshot,
+      getSnapshot(sourceFeature),
       featureIds,
     )
     // Clear possible parentId -attribute.
@@ -193,10 +198,7 @@ export function CopyFeature({
         min: newFeatureLine.min,
         max: newFeatureLine.max,
         type: newFeatureLine.type,
-        children: updatedChildren.children as unknown as Record<
-          string,
-          AnnotationFeatureSnapshot
-        >,
+        children: updatedChildren.children,
         attributes: attributeMap,
         strand: newFeatureLine.strand,
       },

package/src/components/CreateApolloAnnotation.tsx

@@ -1,4 +1,4 @@
-/* eslint-disable react-hooks/exhaustive-deps */
+/* eslint-disable @eslint-react/set-state-in-effect */
 /* eslint-disable @typescript-eslint/no-misused-promises */
 /* eslint-disable @typescript-eslint/unbound-method */
 
@@ -192,30 +192,35 @@ export function CreateApolloAnnotation({
   const refSeq = apolloAssembly?.refSeqs.get(refSeqId)
   const features = refSeq?.getFeatures(region.start, region.end)
 
-  const getDestinationFeatures = () => {
-    const filteredFeatures: AnnotationFeatureSnapshot[] = []
+  useEffect(() => {
+    const getDestinationFeatures = () => {
+      const filteredFeatures: AnnotationFeatureSnapshot[] = []
 
-    for (const f of features ?? []) {
-      if (f.min > region.end || f.max < region.start) {
-        continue
-      }
+      for (const f of features ?? []) {
+        if (f.min > region.end || f.max < region.start) {
+          continue
+        }
 
-      // Destination feature should be of type gene
-      if (featureTypeOntology?.isTypeOf(f.type, 'gene')) {
-        const featureSnapshot = getSnapshot(f)
-        filteredFeatures.push(featureSnapshot)
+        // Destination feature should be of type gene
+        if (featureTypeOntology?.isTypeOf(f.type, 'gene')) {
+          const featureSnapshot = getSnapshot(f)
+          filteredFeatures.push(featureSnapshot)
+        }
       }
-    }
 
-    return filteredFeatures
-  }
-
-  useEffect(() => {
+      return filteredFeatures
+    }
     setErrorMessage('')
-    const features = getDestinationFeatures()
-    setDestinationFeatures(features)
-    setSelectedDestinationFeature(features[0])
-  }, [checkedChildrens, parentFeatureChecked, region])
+    const destinationFeatures = getDestinationFeatures()
+    setDestinationFeatures(destinationFeatures)
+    setSelectedDestinationFeature(destinationFeatures[0])
+  }, [
+    checkedChildrens,
+    featureTypeOntology,
+    features,
+    parentFeatureChecked,
+    region,
+  ])
 
   const handleParentFeatureCheck = (
     event: React.ChangeEvent<HTMLInputElement>,
@@ -349,7 +354,7 @@ export function CreateApolloAnnotation({
   const copyGeneFeature = async () => {
     const copiedAnnotationFeature = {
       ...annotationFeature,
-    } as AnnotationFeatureSnapshot
+    }
     removeSkippedAttributes(copiedAnnotationFeature, skippedAttributesOnCopy)
 
     let change
@@ -394,7 +399,7 @@ export function CreateApolloAnnotation({
     for (const transcriptId of Object.keys(transcripts)) {
       const transcript = {
         ...transcripts[transcriptId],
-      } as AnnotationFeatureSnapshot
+      }
       removeSkippedAttributes(transcript, skippedAttributesOnCopy)
       transcript.strand = selectedDestinationFeature.strand
 
@@ -422,7 +427,7 @@ export function CreateApolloAnnotation({
   ) => {
     const copiedChildrens: Record<string, AnnotationFeatureSnapshot> = {}
     for (const [childId, child] of Object.entries(childrens)) {
-      const copiedChild = { ...child } as AnnotationFeatureSnapshot
+      const copiedChild = { ...child }
       removeSkippedAttributes(copiedChild, skippedAttributesOnCopy)
       copiedChildrens[childId] = copiedChild
     }

package/src/components/DeleteAssembly.tsx

@@ -40,7 +40,7 @@ export function DeleteAssembly({
 }: DeleteAssemblyProps) {
   const { internetAccounts } = getRoot<ApolloRootModel>(session)
   const [errorMessage, setErrorMessage] = useState('')
-  const [confirmDelete, setconfirmDelete] = useState(false)
+  const [confirmDelete, setConfirmDelete] = useState(false)
   const [submitted, setSubmitted] = useState(false)
   const apolloInternetAccounts = internetAccounts.filter(
     (ia) => ia.type === 'ApolloInternetAccount',
@@ -151,7 +151,7 @@ export function DeleteAssembly({
                 <Checkbox
                   checked={confirmDelete}
                   onChange={() => {
-                    setconfirmDelete(!confirmDelete)
+                    setConfirmDelete(!confirmDelete)
                   }}
                 />
               }

package/src/components/DeleteFeature.tsx

@@ -330,10 +330,7 @@ export function DeleteFeature({
       }
     }
 
-    if (
-      featureTypeOntology &&
-      featureTypeOntology.isTypeOf(sourceFeature.type, 'exon')
-    ) {
+    if (featureTypeOntology?.isTypeOf(sourceFeature.type, 'exon')) {
       const cdsChange = trimCDS(sourceFeature)
       if (cdsChange) {
         if (cdsChange.typeName === 'DeleteFeatureChange') {

package/src/components/DownloadGFF3.tsx

@@ -3,6 +3,7 @@
 /* eslint-disable @typescript-eslint/no-misused-promises */
 import { annotationFeatureToGFF3 } from '@apollo-annotation/shared'
 import { GFFFormattingTransformer } from '@gmod/gff'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { getConf } from '@jbrowse/core/configuration'
 import type { AbstractSessionModel } from '@jbrowse/core/util'
 import {
@@ -49,7 +50,7 @@ export function DownloadGFF3({
   session,
   assembly: assemblyName,
 }: DownloadGFF3Props) {
-  const [includeFASTA, setincludeFASTA] = useState(false)
+  const [includeFASTA, setIncludeFASTA] = useState(false)
   const [errorMessage, setErrorMessage] = useState('')
 
   const { getInternetAccount } = session.apolloDataStore as {
@@ -61,7 +62,7 @@ export function DownloadGFF3({
   }
 
   const { assemblyManager } = session as unknown as AbstractSessionModel
-  const assembly = assemblyManager.get(assemblyName)
+  const assembly = assemblyManager.get(assemblyName) as Assembly | undefined
   if (!assembly) {
     setErrorMessage(`Assembly "${assemblyName}" not found`)
     return
@@ -140,7 +141,7 @@ export function DownloadGFF3({
                 <Checkbox
                   checked={includeFASTA}
                   onChange={() => {
-                    setincludeFASTA(!includeFASTA)
+                    setIncludeFASTA(!includeFASTA)
                   }}
                   disabled={!internetAccountConfigId}
                 />

package/src/components/DuplicateFeatureDialog.tsx

@@ -0,0 +1,154 @@
+/* eslint-disable @typescript-eslint/no-misused-promises */
+/* eslint-disable @typescript-eslint/unbound-method */
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import {
+  AddFeatureChange,
+  DeleteFeatureChange,
+} from '@apollo-annotation/shared'
+import {
+  Button,
+  DialogActions,
+  DialogContent,
+  DialogContentText,
+  FormControl,
+  FormControlLabel,
+  FormLabel,
+  Radio,
+  RadioGroup,
+} from '@mui/material'
+import ObjectID from 'bson-objectid'
+import React, { useState } from 'react'
+
+import type { ChangeManager } from '../ChangeManager'
+
+import { Dialog } from './Dialog'
+
+type Choice = 'keepExisting' | 'useNew' | 'keepBoth'
+
+interface DuplicateFeatureDialogProps {
+  featureSnapshot: AnnotationFeatureSnapshot
+  existingFeature: AnnotationFeatureSnapshot
+  assemblyName: string
+  changeManager: ChangeManager
+  handleClose(): void
+}
+
+function reassignIds(
+  feature: AnnotationFeatureSnapshot,
+): AnnotationFeatureSnapshot {
+  const newChildren: Record<string, AnnotationFeatureSnapshot> = {}
+  if (feature.children) {
+    for (const child of Object.values(feature.children)) {
+      const newChild = reassignIds(child)
+      newChildren[newChild._id] = newChild
+    }
+  }
+  return {
+    ...feature,
+    _id: new ObjectID().toHexString(),
+    children: feature.children ? newChildren : undefined,
+  }
+}
+
+export function DuplicateFeatureDialog({
+  assemblyName,
+  changeManager,
+  existingFeature,
+  featureSnapshot,
+  handleClose,
+}: DuplicateFeatureDialogProps) {
+  const [choice, setChoice] = useState<Choice>('keepExisting')
+  const [errorMessage, setErrorMessage] = useState('')
+  const [submitted, setSubmitted] = useState(false)
+
+  const handleSubmit = async () => {
+    setErrorMessage('')
+    setSubmitted(true)
+    try {
+      if (choice === 'useNew') {
+        const deleteChange = new DeleteFeatureChange({
+          typeName: 'DeleteFeatureChange',
+          assembly: assemblyName,
+          changedIds: [existingFeature._id],
+          deletedFeature: existingFeature,
+        })
+        await changeManager.submit(deleteChange)
+        const addChange = new AddFeatureChange({
+          typeName: 'AddFeatureChange',
+          assembly: assemblyName,
+          changedIds: [featureSnapshot._id],
+          addedFeature: featureSnapshot,
+        })
+        await changeManager.submit(addChange)
+      } else if (choice === 'keepBoth') {
+        const newSnapshot = reassignIds(featureSnapshot)
+        const addChange = new AddFeatureChange({
+          typeName: 'AddFeatureChange',
+          assembly: assemblyName,
+          changedIds: [newSnapshot._id],
+          addedFeature: newSnapshot,
+        })
+        await changeManager.submit(addChange)
+      }
+      handleClose()
+    } catch (error) {
+      setErrorMessage(String(error))
+      setSubmitted(false)
+    }
+  }
+
+  return (
+    <Dialog
+      open
+      title="Duplicate Feature Detected"
+      handleClose={handleClose}
+      maxWidth="sm"
+      fullWidth
+    >
+      <DialogContent>
+        <DialogContentText>
+          A feature with ID &ldquo;{featureSnapshot._id}&rdquo; already exists.
+          How would you like to resolve this conflict?
+        </DialogContentText>
+        <FormControl component="fieldset" sx={{ mt: 2 }}>
+          <FormLabel component="legend">Resolution</FormLabel>
+          <RadioGroup
+            value={choice}
+            onChange={(e) => {
+              setChoice(e.target.value as Choice)
+            }}
+          >
+            <FormControlLabel
+              value="keepExisting"
+              control={<Radio />}
+              label="Keep the existing feature"
+            />
+            <FormControlLabel
+              value="useNew"
+              control={<Radio />}
+              label="Replace with the new feature"
+            />
+            <FormControlLabel
+              value="keepBoth"
+              control={<Radio />}
+              label="Keep both (assign new IDs to the incoming feature)"
+            />
+          </RadioGroup>
+        </FormControl>
+        {errorMessage ? (
+          <DialogContentText color="error" sx={{ mt: 1 }}>
+            {errorMessage}
+          </DialogContentText>
+        ) : null}
+      </DialogContent>
+      <DialogActions>
+        <Button variant="contained" onClick={handleSubmit} disabled={submitted}>
+          Confirm
+        </Button>
+        <Button onClick={handleClose} disabled={submitted}>
+          Cancel
+        </Button>
+      </DialogActions>
+    </Dialog>
+  )
+}

package/src/components/DuplicateTranscript.tsx

@@ -68,7 +68,7 @@ export function DuplicateTranscript({
           newChildren[newChildId] = {
             ...child,
             _id: newChildId,
-          } as AnnotationFeatureSnapshot
+          }
         }
         duplicateTranscript.children = newChildren
       }

package/src/components/FilterTranscripts.tsx

@@ -63,8 +63,8 @@ export const FilterTranscripts = observer(function FilterTranscripts({
           <Grid size={8}>
             <FormGroup>
               {allTranscripts.map((item) => (
-                // eslint-disable-next-line react/jsx-key
                 <FormControlLabel
+                  key={item}
                   control={
                     <Checkbox
                       checked={!excludedTranscripts.includes(item)}