@apollo-annotation/jbrowse-plugin-apollo 0.3.11 → 0.3.13

package/src/components/DuplicateTranscript.tsx

@@ -0,0 +1,132 @@
+/* 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/types'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
+import {
+  Button,
+  DialogActions,
+  DialogContent,
+  DialogContentText,
+} from '@mui/material'
+import ObjectID from 'bson-objectid'
+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="button" onClick={handleClose}>
+            Cancel
+          </Button>
+        </DialogActions>
+      </form>
+      {errorMessage ? (
+        <DialogContent>
+          <DialogContentText color="error">{errorMessage}</DialogContentText>
+        </DialogContent>
+      ) : null}
+    </Dialog>
+  )
+}

package/src/components/FilterFeatures.tsx

@@ -11,7 +11,7 @@ import { observer } from 'mobx-react'
 import React, { useState } from 'react'
 
 import { isOntologyClass } from '../OntologyManager'
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 
 import { Dialog } from './Dialog'
 import { OntologyTermAutocomplete } from './OntologyTermAutocomplete'

package/src/components/FilterTranscripts.tsx

@@ -1,4 +1,4 @@
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import {
   Checkbox,
   DialogContent,

package/src/components/ImportFeatures.tsx

@@ -6,28 +6,29 @@
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-misused-promises */
 import { AddFeaturesFromFileChange } from '@apollo-annotation/shared'
-import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { getConf } from '@jbrowse/core/configuration'
 import {
   Button,
+  Checkbox,
   DialogActions,
   DialogContent,
   DialogContentText,
+  FormControlLabel,
+  FormHelperText,
+  LinearProgress,
   MenuItem,
   Select,
   type SelectChangeEvent,
 } from '@mui/material'
-import Checkbox from '@mui/material/Checkbox'
-import FormControlLabel from '@mui/material/FormControlLabel'
-import LinearProgress from '@mui/material/LinearProgress'
 import React, { useEffect, useState } from 'react'
 
-import {
-  type ApolloInternetAccount,
-  type CollaborationServerDriver,
+import type {
+  ApolloInternetAccount,
+  CollaborationServerDriver,
 } from '../BackendDrivers'
-import { type ChangeManager } from '../ChangeManager'
-import { type ApolloSessionModel } from '../session'
+import type { ChangeManager } from '../ChangeManager'
+import type { ApolloSessionModel } from '../session'
 import { createFetchErrorMessage } from '../util'
 
 import { Dialog } from './Dialog'
@@ -52,6 +53,7 @@ export function ImportFeatures({
   // default is -1, submit button should be disabled until count is set
   const [featuresCount, setFeaturesCount] = useState<number | undefined>()
   const [deleteFeatures, setDeleteFeatures] = useState(false)
+  const [strict, setStrict] = useState(true)
   const [loading, setLoading] = useState(false)
 
   const { collaborationServerDriver, getInternetAccount } = apolloDataStore as {
@@ -73,6 +75,10 @@ export function ImportFeatures({
     setDeleteFeatures(e.target.checked)
   }
 
+  function handleSetStrict(e: React.ChangeEvent<HTMLInputElement>) {
+    setStrict(e.target.checked)
+  }
+
   // fetch and set features count for selected assembly
   useEffect(() => {
     if (!selectedAssembly) {
@@ -182,7 +188,12 @@ export function ImportFeatures({
       statusMessage: 'Uploading file, this may take awhile',
       progressPct: 0,
       cancelCallback: () => {
-        controller.abort('ImportFeatures')
+        controller.abort(
+          new DOMException(
+            `Canceling importing of features to ${selectedAssembly.displayName}`,
+            'AbortError',
+          ),
+        )
         jobsManager.abortJob(job.name)
       },
     }
@@ -215,6 +226,7 @@ export function ImportFeatures({
       typeName: 'AddFeaturesFromFileChange',
       assembly: selectedAssembly.name,
       fileId,
+      parseOptions: { strict },
       deleteExistingFeatures: deleteFeatures,
     })
 
@@ -248,37 +260,43 @@ export function ImportFeatures({
               </MenuItem>
             ))}
           </Select>
-        </DialogContent>
-        <DialogContent style={{ display: 'flex', flexDirection: 'column' }}>
           <DialogContentText>Upload GFF3 to load features</DialogContentText>
           <input
             type="file"
             onChange={handleChangeFile}
             disabled={submitted && !errorMessage}
           />
+          <FormControlLabel
+            label="Strict parsing"
+            disabled={submitted && !errorMessage}
+            control={<Checkbox checked={strict} onChange={handleSetStrict} />}
+          />
+          <FormHelperText>
+            Don&apos;t import any features if any lines in the GFF3 are unable
+            to be processed
+          </FormHelperText>
+
+          {featuresCount && featuresCount > 0 ? (
+            <>
+              <FormControlLabel
+                label="Delete existing features"
+                disabled={submitted && !errorMessage}
+                control={
+                  <Checkbox
+                    checked={deleteFeatures}
+                    onChange={handleDeleteFeatures}
+                    slotProps={{ input: { 'aria-label': 'controlled' } }}
+                    color="warning"
+                  />
+                }
+              />
+              <FormHelperText>
+                This assembly has {featuresCount} features that will be deleted
+              </FormHelperText>
+            </>
+          ) : null}
         </DialogContent>
 
-        {featuresCount && featuresCount > 0 ? (
-          <DialogContent>
-            <DialogContentText>
-              This assembly already has {featuresCount} features, would you like
-              to delete the existing features before importing new ones?
-            </DialogContentText>
-            <FormControlLabel
-              label="Yes, delete existing features"
-              disabled={submitted && !errorMessage}
-              control={
-                <Checkbox
-                  checked={deleteFeatures}
-                  onChange={handleDeleteFeatures}
-                  slotProps={{ input: { 'aria-label': 'controlled' } }}
-                  color="warning"
-                />
-              }
-            />
-          </DialogContent>
-        ) : null}
-
         <DialogActions>
           <Button
             disabled={

package/src/components/LogOut.tsx

@@ -1,4 +1,5 @@
 /* eslint-disable @typescript-eslint/unbound-method */
+import { getRoot } from '@jbrowse/mobx-state-tree'
 import {
   Button,
   DialogActions,
@@ -8,12 +9,11 @@ import {
   Select,
   type SelectChangeEvent,
 } from '@mui/material'
-import { getRoot } from 'mobx-state-tree'
 import React, { useState } from 'react'
 
-import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
-import { type ApolloSessionModel } from '../session'
-import { type ApolloRootModel } from '../types'
+import type { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import type { ApolloSessionModel } from '../session'
+import type { ApolloRootModel } from '../types'
 
 import { Dialog } from './Dialog'
 

package/src/components/ManageChecks.tsx

@@ -1,7 +1,8 @@
 /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 /* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/no-misused-promises */
-import { type AbstractSessionModel } from '@jbrowse/core/util'
+import type { AbstractSessionModel } from '@jbrowse/core/util'
+import { getRoot } from '@jbrowse/mobx-state-tree'
 import {
   Button,
   Checkbox,
@@ -19,16 +20,15 @@ import {
   TableHead,
   TableRow,
 } from '@mui/material'
-import { getRoot } from 'mobx-state-tree'
 import React, { useEffect, useState } from 'react'
 
-import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
-import {
-  type ApolloInternetAccount,
-  type CollaborationServerDriver,
+import type { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import type {
+  ApolloInternetAccount,
+  CollaborationServerDriver,
 } from '../BackendDrivers'
-import { type ApolloSessionModel } from '../session'
-import { type ApolloRootModel } from '../types'
+import type { ApolloSessionModel } from '../session'
+import type { ApolloRootModel } from '../types'
 import { createFetchErrorMessage } from '../util'
 
 import { Dialog } from './Dialog'

package/src/components/ManageUsers.tsx

@@ -1,12 +1,12 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+
 /* eslint-disable @typescript-eslint/no-misused-promises */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
 import { DeleteUserChange, UserChange } from '@apollo-annotation/shared'
-import { type AbstractRootModel } from '@jbrowse/core/util'
+import { getRoot } from '@jbrowse/mobx-state-tree'
 import DeleteIcon from '@mui/icons-material/Delete'
 import {
   Button,
@@ -27,12 +27,12 @@ import {
   type GridRowParams,
   GridToolbar,
 } from '@mui/x-data-grid'
-import { getRoot } from 'mobx-state-tree'
 import React, { useEffect, useState } from 'react'
 
-import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
-import { type ChangeManager } from '../ChangeManager'
-import { type ApolloSessionModel } from '../session'
+import type { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import type { ChangeManager } from '../ChangeManager'
+import type { ApolloSessionModel } from '../session'
+import { type ApolloRootModel, isApolloInternetAccount } from '../types'
 import { createFetchErrorMessage } from '../util'
 
 import { Dialog } from './Dialog'
@@ -50,19 +50,15 @@ interface ManageUsersProps {
   changeManager: ChangeManager
 }
 
-interface ApolloRootModel extends AbstractRootModel {
-  internetAccounts: ApolloInternetAccountModel[]
-}
-
 export function ManageUsers({
   changeManager,
   handleClose,
   session,
 }: ManageUsersProps) {
   const { internetAccounts } = getRoot<ApolloRootModel>(session)
-  const apolloInternetAccounts = internetAccounts.filter(
-    (ia) => ia.type === 'ApolloInternetAccount' && ia.role?.includes('admin'),
-  )
+  const apolloInternetAccounts: ApolloInternetAccountModel[] = internetAccounts
+    .filter((ia) => isApolloInternetAccount(ia))
+    .filter((ia) => ia.role?.includes('admin'))
   if (apolloInternetAccounts.length === 0) {
     throw new Error('No Apollo internet account found')
   }
@@ -80,21 +76,17 @@ export function ManageUsers({
         locationType: 'UriLocation',
         uri,
       })
-      if (apolloFetch) {
-        const response = await apolloFetch(uri, { method: 'GET' })
-        if (!response.ok) {
-          const newErrorMessage = await createFetchErrorMessage(
-            response,
-            'Error when getting user data from db',
-          )
-          setErrorMessage(newErrorMessage)
-          return
-        }
-        const data = (await response.json()) as UserResponse[]
-        setUsers(
-          data.map((u) => (u.role === undefined ? { ...u, role: '' } : u)),
+      const response = await apolloFetch(uri, { method: 'GET' })
+      if (!response.ok) {
+        const newErrorMessage = await createFetchErrorMessage(
+          response,
+          'Error when getting user data from db',
         )
+        setErrorMessage(newErrorMessage)
+        return
       }
+      const data = (await response.json()) as UserResponse[]
+      setUsers(data.map((u) => (u.role === undefined ? { ...u, role: '' } : u)))
     }
     getUsers().catch((error) => {
       setErrorMessage(String(error))

package/src/components/MergeExons.tsx

@@ -1,7 +1,8 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import { MergeExonsChange } from '@apollo-annotation/shared'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 import {
   Box,
   Button,
@@ -14,11 +15,10 @@ import {
   RadioGroup,
   type SelectChangeEvent,
 } from '@mui/material'
-import { getSnapshot } from 'mobx-state-tree'
 import React, { useState } from 'react'
 
-import { type ChangeManager } from '../ChangeManager'
-import { type ApolloSessionModel } from '../session'
+import type { ChangeManager } from '../ChangeManager'
+import type { ApolloSessionModel } from '../session'
 
 import { Dialog } from './Dialog'
 

package/src/components/MergeTranscripts.tsx

@@ -1,6 +1,7 @@
 /* eslint-disable @typescript-eslint/unbound-method */
-import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
 import { MergeTranscriptsChange } from '@apollo-annotation/shared'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 import {
   Box,
   Button,
@@ -13,11 +14,10 @@ import {
   RadioGroup,
   type SelectChangeEvent,
 } from '@mui/material'
-import { getSnapshot } from 'mobx-state-tree'
 import React, { useState } from 'react'
 
-import { type ChangeManager } from '../ChangeManager'
-import { type ApolloSessionModel } from '../session'
+import type { ChangeManager } from '../ChangeManager'
+import type { ApolloSessionModel } from '../session'
 
 import { Dialog } from './Dialog'
 

package/src/components/OntologyTermAutocomplete.tsx

@@ -1,6 +1,6 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 
-import { type AbstractSessionModel } from '@jbrowse/core/util'
+import type { AbstractSessionModel } from '@jbrowse/core/util'
 import { isAbortException } from '@jbrowse/core/util/aborting'
 import {
   Autocomplete,
@@ -11,7 +11,7 @@ import React, { useCallback, useEffect, useState } from 'react'
 
 import { type OntologyTerm, isDeprecated } from '../OntologyManager'
 import type OntologyStore from '../OntologyManager/OntologyStore'
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 
 interface OntologyTermAutocompleteProps {
   session: ApolloSessionModel
@@ -93,7 +93,12 @@ export function OntologyTermAutocomplete({
       )
     }
     return () => {
-      controller.abort('OntologyTermAutocomplete matcher')
+      controller.abort(
+        new DOMException(
+          'Cancel getting current term from ontology store',
+          'AbortError',
+        ),
+      )
     }
   }, [session, valueString, filterTerms, ontologyStore, needToLoadCurrentTerm])
 
@@ -119,7 +124,12 @@ export function OntologyTermAutocomplete({
       )
     }
     return () => {
-      controller.abort('OntologyTermAutocomplete loader')
+      controller.abort(
+        new DOMException(
+          'Canceling getting valid terms from ontology store',
+          'AbortError',
+        ),
+      )
     }
   }, [
     needToLoadTermChoices,

package/src/components/OntologyTermMultiSelect.tsx

@@ -2,6 +2,7 @@
 /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { isAbortException } from '@jbrowse/core/util/aborting'
+import { getParent } from '@jbrowse/mobx-state-tree'
 import {
   Autocomplete,
   type AutocompleteRenderValueGetItemProps,
@@ -14,7 +15,6 @@ import {
 import { debounce } from '@mui/material/utils'
 import highlightMatch from 'autosuggest-highlight/match'
 import highlightParse from 'autosuggest-highlight/parse'
-import { getParent } from 'mobx-state-tree'
 import * as React from 'react'
 
 import {
@@ -23,9 +23,9 @@ import {
   type OntologyTerm,
   isOntologyClass,
 } from '../OntologyManager'
-import { type Match } from '../OntologyManager/OntologyStore/fulltext'
+import type { Match } from '../OntologyManager/OntologyStore/fulltext'
 import { isDeprecated } from '../OntologyManager/OntologyStore/indexeddb-schema'
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 
 interface TermValue {
   term: OntologyTerm
@@ -89,7 +89,12 @@ function TermTagWithTooltip({
     })
 
     return () => {
-      controller.abort('TermTagWithTooltip ')
+      controller.abort(
+        new DOMException(
+          'Cancel fetching term description from ontology store',
+          'AbortError',
+        ),
+      )
     }
   }, [termId, ontology, manager])
 
@@ -211,7 +216,9 @@ export function OntologyTermMultiSelect({
     })
 
     return () => {
-      aborter.abort('OntologyTermMultiSelect')
+      aborter.abort(
+        new DOMException('Cancel getting ontology terms', 'AbortError'),
+      )
     }
   }, [getOntologyTerms, ontology, includeDeprecated, inputValue, value])
 

package/src/components/OpenLocalFile.tsx

@@ -16,8 +16,8 @@ import {
 import { nanoid } from 'nanoid'
 import React, { useState } from 'react'
 
-import { type InMemoryFileDriver } from '../BackendDrivers'
-import { type ApolloSessionModel } from '../session'
+import type { InMemoryFileDriver } from '../BackendDrivers'
+import type { ApolloSessionModel } from '../session'
 import { loadAssemblyIntoClient } from '../util'
 
 import { Dialog } from './Dialog'

package/src/components/SplitExon.tsx

@@ -1,10 +1,11 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 
-import {
-  type AnnotationFeature,
-  type AnnotationFeatureSnapshot,
+import type {
+  AnnotationFeature,
+  AnnotationFeatureSnapshot,
 } from '@apollo-annotation/mst'
 import { SplitExonChange } from '@apollo-annotation/shared'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 import {
   Button,
   DialogActions,
@@ -12,11 +13,10 @@ import {
   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 type { ChangeManager } from '../ChangeManager'
+import type { ApolloSessionModel } from '../session'
 
 import { Dialog } from './Dialog'
 

package/src/components/ViewChangeLog.tsx

@@ -6,6 +6,8 @@
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
 import { changeRegistry } from '@apollo-annotation/common'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
+import { getRoot } from '@jbrowse/mobx-state-tree'
 import {
   Button,
   DialogActions,
@@ -21,17 +23,15 @@ import {
   type GridRowsProp,
   GridToolbar,
 } from '@mui/x-data-grid'
-import { getRoot } from 'mobx-state-tree'
 import React, { useEffect, useState } from 'react'
-import { makeStyles } from 'tss-react/mui'
 
-import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
-import {
-  type ApolloInternetAccount,
-  type CollaborationServerDriver,
+import type { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import type {
+  ApolloInternetAccount,
+  CollaborationServerDriver,
 } from '../BackendDrivers'
-import { type ApolloSessionModel } from '../session'
-import { type ApolloRootModel } from '../types'
+import type { ApolloSessionModel } from '../session'
+import type { ApolloRootModel } from '../types'
 import { createFetchErrorMessage } from '../util'
 
 import { Dialog } from './Dialog'