@apollo-annotation/jbrowse-plugin-apollo 0.1.18 → 0.1.20

package/src/components/CopyFeature.tsx

@@ -1,8 +1,9 @@
+/* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 /* eslint-disable @typescript-eslint/no-misused-promises */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import {
-  AnnotationFeatureI,
+  AnnotationFeature,
   AnnotationFeatureSnapshot,
 } from '@apollo-annotation/mst'
 import { AddFeatureChange } from '@apollo-annotation/shared'
@@ -30,7 +31,7 @@ import { Dialog } from './Dialog'
 interface CopyFeatureProps {
   session: ApolloSessionModel
   handleClose(): void
-  sourceFeature: AnnotationFeatureI
+  sourceFeature: AnnotationFeature
   sourceAssemblyId: string
   changeManager: ChangeManager
 }
@@ -88,7 +89,7 @@ export function CopyFeature({
   >(assemblies.find((a) => a.name !== sourceAssemblyId)?.name)
   const [refNames, setRefNames] = useState<Collection[]>([])
   const [selectedRefSeqId, setSelectedRefSeqId] = useState('')
-  const [start, setStart] = useState(sourceFeature.start)
+  const [start, setStart] = useState(sourceFeature.min)
   const [errorMessage, setErrorMessage] = useState('')
 
   function handleChangeAssembly(e: SelectChangeEvent) {
@@ -173,22 +174,12 @@ export function CopyFeature({
       delete attributeMap.Parent
     }
 
-    // Update gffId value if it's ObjectId
-    if (
-      newFeatureLine.gffId &&
-      ObjectID.isValid(newFeatureLine.gffId.toString())
-    ) {
-      newFeatureLine.gffId = newFeatureLine._id
-    }
     newFeatureLine.refSeq = selectedRefSeqId
-    const locationMove = start - newFeatureLine.start
-    newFeatureLine.start = start
-    newFeatureLine.end = start + featureLength
-    // Updates children start, end and gffId values
-    const updatedChildren = updateRefSeqStartEndAndGffId(
-      newFeatureLine,
-      locationMove,
-    )
+    const locationMove = start - newFeatureLine.min
+    newFeatureLine.min = start
+    newFeatureLine.max = start + featureLength
+    // Updates children start and end values
+    const updatedChildren = updateRefSeqStartEnd(newFeatureLine, locationMove)
 
     const change = new AddFeatureChange({
       changedIds: [newFeatureLine._id],
@@ -197,18 +188,15 @@ export function CopyFeature({
       addedFeature: {
         _id: newFeatureLine._id,
         refSeq: newFeatureLine.refSeq,
-        start: newFeatureLine.start,
-        end: newFeatureLine.end,
+        min: newFeatureLine.min,
+        max: newFeatureLine.max,
         type: newFeatureLine.type,
         children: updatedChildren.children as unknown as Record<
           string,
           AnnotationFeatureSnapshot
         >,
         attributes: attributeMap,
-        discontinuousLocations: newFeatureLine.discontinuousLocations,
         strand: newFeatureLine.strand,
-        score: newFeatureLine.score,
-        phase: newFeatureLine.phase,
       },
       copyFeature: true,
       allIds: featureIds,
@@ -221,27 +209,22 @@ export function CopyFeature({
   }
 
   /**
-   * Recursively loop children and update refSeq, start, end and gffId values
+   * Recursively loop children and update refSeq, start, and end values
    * @param feature - parent feature
    * @param locationMove - how much location has been moved from original
    * @returns
    */
-  function updateRefSeqStartEndAndGffId(
+  function updateRefSeqStartEnd(
     feature: AnnotationFeatureSnapshot,
     locationMove: number,
   ): AnnotationFeatureSnapshot {
     const children: Record<string, AnnotationFeatureSnapshot> = {}
     if (feature.children) {
       for (const child of Object.values(feature.children)) {
-        const newChild = updateRefSeqStartEndAndGffId(child, locationMove)
-        // Update gffId value if it's ObjectId
-        // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
-        if (ObjectID.isValid(newChild.gffId!.toString())) {
-          newChild.gffId = newChild._id
-        }
+        const newChild = updateRefSeqStartEnd(child, locationMove)
         newChild.refSeq = selectedRefSeqId
-        newChild.start = newChild.start + locationMove
-        newChild.end = newChild.end + locationMove
+        newChild.min = newChild.min + locationMove
+        newChild.max = newChild.max + locationMove
         children[newChild._id] = newChild
       }
     }

package/src/components/DeleteFeature.tsx

@@ -1,7 +1,5 @@
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-misused-promises */
-import { AnnotationFeatureI } from '@apollo-annotation/mst'
+import { AnnotationFeature } from '@apollo-annotation/mst'
 import { DeleteFeatureChange } from '@apollo-annotation/shared'
 import { AbstractSessionModel } from '@jbrowse/core/util'
 import {
@@ -20,11 +18,11 @@ import { Dialog } from './Dialog'
 interface DeleteFeatureProps {
   session: ApolloSessionModel
   handleClose(): void
-  sourceFeature: AnnotationFeatureI
+  sourceFeature: AnnotationFeature
   sourceAssemblyId: string
   changeManager: ChangeManager
-  selectedFeature?: AnnotationFeatureI
-  setSelectedFeature(feature?: AnnotationFeatureI): void
+  selectedFeature?: AnnotationFeature
+  setSelectedFeature(feature?: AnnotationFeature): void
 }
 
 export function DeleteFeature({

package/src/components/ImportFeatures.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 /* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
@@ -158,14 +159,16 @@ export function ImportFeatures({
     const { baseURL } = apolloInternetAccount
 
     // First upload file
-    const url = new URL('files', baseURL).href
+    const url = new URL('files', baseURL)
+    url.searchParams.set('type', 'text/x-gff3')
+    const uri = url.href
     const formData = new FormData()
     formData.append('file', file)
     formData.append('fileName', file.name)
     formData.append('type', 'text/x-gff3')
     const apolloFetchFile = apolloInternetAccount.getFetcher({
       locationType: 'UriLocation',
-      uri: url,
+      uri,
     })
 
     handleClose()
@@ -187,7 +190,7 @@ export function ImportFeatures({
 
     if (apolloFetchFile) {
       const { signal } = controller
-      const response = await apolloFetchFile(url, {
+      const response = await apolloFetchFile(uri, {
         method: 'POST',
         body: formData,
         signal,

package/src/components/LogOut.tsx

@@ -0,0 +1,105 @@
+import {
+  Button,
+  DialogActions,
+  DialogContent,
+  DialogContentText,
+  MenuItem,
+  Select,
+  SelectChangeEvent,
+} from '@mui/material'
+import { getRoot } from 'mobx-state-tree'
+import React, { useState } from 'react'
+
+import { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import { ApolloSessionModel } from '../session'
+import { ApolloRootModel } from '../types'
+import { Dialog } from './Dialog'
+
+interface DeleteAssemblyProps {
+  session: ApolloSessionModel
+  handleClose(): void
+}
+
+export function LogOut({ handleClose, session }: DeleteAssemblyProps) {
+  const { internetAccounts } = getRoot<ApolloRootModel>(session)
+  const [errorMessage, setErrorMessage] = useState('')
+  const apolloInternetAccounts = internetAccounts.filter(
+    (ia) => ia.type === 'ApolloInternetAccount',
+  ) as ApolloInternetAccountModel[]
+  if (apolloInternetAccounts.length === 0) {
+    throw new Error('No Apollo internet account found')
+  }
+  const [selectedInternetAccount, setSelectedInternetAccount] = useState(
+    apolloInternetAccounts[0],
+  )
+
+  function handleChangeInternetAccount(e: SelectChangeEvent) {
+    const newlySelectedInternetAccount = apolloInternetAccounts.find(
+      (ia) => ia.internetAccountId === e.target.value,
+    )
+    if (!newlySelectedInternetAccount) {
+      throw new Error(
+        `Could not find internetAccount with ID "${e.target.value}"`,
+      )
+    }
+    setSelectedInternetAccount(newlySelectedInternetAccount)
+  }
+
+  function onSubmit(event: React.FormEvent<HTMLFormElement>) {
+    event.preventDefault()
+    setErrorMessage('')
+    selectedInternetAccount.removeToken()
+    window.location.reload()
+  }
+
+  return (
+    <Dialog
+      open
+      title="Log out"
+      handleClose={handleClose}
+      maxWidth={false}
+      data-testid="log-out"
+    >
+      <form onSubmit={onSubmit}>
+        <DialogContent style={{ display: 'flex', flexDirection: 'column' }}>
+          {apolloInternetAccounts.length > 1 ? (
+            <>
+              <DialogContentText>Select account</DialogContentText>
+              <Select
+                value={selectedInternetAccount.internetAccountId}
+                onChange={handleChangeInternetAccount}
+              >
+                {internetAccounts.map((option) => (
+                  <MenuItem key={option.id} value={option.internetAccountId}>
+                    {option.name}
+                  </MenuItem>
+                ))}
+              </Select>
+            </>
+          ) : null}
+          <DialogContentText>
+            Are you sure you want to log out?
+          </DialogContentText>
+        </DialogContent>
+
+        <DialogActions>
+          <Button
+            disabled={!selectedInternetAccount}
+            variant="contained"
+            type="submit"
+          >
+            Log Out
+          </Button>
+          <Button variant="outlined" type="submit" onClick={handleClose}>
+            Cancel
+          </Button>
+        </DialogActions>
+      </form>
+      {errorMessage ? (
+        <DialogContent>
+          <DialogContentText color="error">{errorMessage}</DialogContentText>
+        </DialogContent>
+      ) : null}
+    </Dialog>
+  )
+}

package/src/components/ManageChecks.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 /* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/no-misused-promises */
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly'

package/src/components/ManageUsers.tsx

@@ -1,3 +1,4 @@
+/* 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 */
@@ -123,7 +124,26 @@ export function ManageUsers({
       headerName: 'Role',
       width: 140,
       type: 'singleSelect',
-      valueOptions: ['', 'readOnly', 'user', 'admin'],
+      valueOptions: ['readOnly', 'user', 'admin', 'none'],
+      getOptionLabel(value) {
+        switch (value) {
+          case 'readOnly': {
+            return 'Read-only'
+          }
+          case 'user': {
+            return 'User'
+          }
+          case 'admin': {
+            return 'Admin'
+          }
+          case 'none': {
+            return 'None'
+          }
+          default: {
+            return 'unknown'
+          }
+        }
+      },
       editable: true,
     },
     {

package/src/components/ModifyFeatureAttribute.tsx

@@ -1,7 +1,7 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-misused-promises */
-import { AnnotationFeatureI } from '@apollo-annotation/mst'
+import { AnnotationFeature } from '@apollo-annotation/mst'
 import { FeatureAttributeChange } from '@apollo-annotation/shared'
 import { AbstractSessionModel } from '@jbrowse/core/util'
 import DeleteIcon from '@mui/icons-material/Delete'
@@ -35,7 +35,7 @@ import { OntologyTermMultiSelect } from './OntologyTermMultiSelect'
 interface ModifyFeatureAttributeProps {
   session: ApolloSessionModel
   handleClose(): void
-  sourceFeature: AnnotationFeatureI
+  sourceFeature: AnnotationFeature
   sourceAssemblyId: string
   changeManager: ChangeManager
 }

package/src/components/OntologyTermAutocomplete.tsx

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-unused-vars */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
@@ -10,7 +9,6 @@ import {
 } from '@mui/material'
 import React, { useCallback, useEffect, useState } from 'react'
 
-import type { OntologyManager } from '../OntologyManager'
 import { OntologyTerm, isDeprecated } from '../OntologyManager'
 import OntologyStore from '../OntologyManager/OntologyStore'
 import { ApolloSessionModel } from '../session'

package/src/components/OntologyTermMultiSelect.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { isAbortException } from '@jbrowse/core/util'
 import {

package/src/components/OpenLocalFile.tsx

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-misused-promises */
 import { AbstractSessionModel, isElectron } from '@jbrowse/core/util'
@@ -33,7 +32,7 @@ export interface RefSeqInterface {
 }
 
 export function OpenLocalFile({ handleClose, session }: OpenLocalFileProps) {
-  const { addApolloTrackConfig, apolloDataStore } = session
+  const { apolloDataStore } = session
   const { addAssembly, addSessionAssembly, assemblyManager, notify } =
     session as unknown as AbstractSessionModel & {
       // eslint-disable-next-line @typescript-eslint/ban-types
@@ -79,8 +78,10 @@ export function OpenLocalFile({ handleClose, session }: OpenLocalFileProps) {
     try {
       await loadAssemblyIntoClient(assemblyId, fileData, apolloDataStore)
     } catch (error) {
-      setErrorMessage(String(error))
-      setSubmitted(false)
+      console.error(error)
+      notify(`Error loading GFF3 ${file.name}, ${String(error)}`, 'error')
+      handleClose()
+      return
     }
 
     const assemblyConfig = {
@@ -105,7 +106,7 @@ export function OpenLocalFile({ handleClose, session }: OpenLocalFileProps) {
     const a = await assemblyManager.waitForAssembly(assemblyConfig.name)
     if (a) {
       // @ts-expect-error MST type coercion problem?
-      addApolloTrackConfig(a)
+      session.addApolloTrackConfig(a)
       notify(`Loaded GFF3 ${file.name}`, 'success')
     } else {
       notify(`Error loading GFF3 ${file.name}`, 'error')

package/src/components/ViewChangeLog.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */

package/src/components/ViewCheckResults.tsx

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */

package/src/components/index.ts

@@ -1,12 +1,16 @@
 export * from './AddAssembly'
 export * from './AddChildFeature'
+export * from './AddFeature'
 export * from './CopyFeature'
 export * from './DeleteAssembly'
 export * from './DeleteFeature'
 export * from './DownloadGFF3'
 export * from './ImportFeatures'
+export * from './LogOut'
 export * from './ManageChecks'
 export * from './ManageUsers'
 export * from './ModifyFeatureAttribute'
 export * from './OpenLocalFile'
 export * from './ViewChangeLog'
+export * from './AddRefSeqAliases'
+export * from './ViewCheckResults'

package/src/extensions/annotationFromPileup.ts

@@ -106,10 +106,9 @@ export function annotationFromPileup(pluggableElement: PluggableElementBase) {
 
         const newFeature: AnnotationFeatureSnapshot = {
           _id: ObjectID().toHexString(),
-          gffId: '',
           refSeq: refSeqId,
-          start: feature.get('start'),
-          end: feature.get('end'),
+          min: feature.get('start'),
+          max: feature.get('end'),
           type: 'mRNA',
           strand: feature.get('strand'),
         }
@@ -122,22 +121,19 @@ export function annotationFromPileup(pluggableElement: PluggableElementBase) {
         const [firstExon] = exons
         const cdsFeature: AnnotationFeatureSnapshot = {
           _id: ObjectID().toHexString(),
-          gffId: '',
           refSeq: refSeqId,
-          start: firstExon.start,
-          end: firstExon.end,
+          min: firstExon.start,
+          max: firstExon.end,
           type: 'CDS',
           strand: feature.get('strand'),
-          phase: 0,
         }
         newFeature.children[cdsFeature._id] = cdsFeature
         if (exons.length === 1) {
           const exon: AnnotationFeatureSnapshot = {
             _id: ObjectID().toHexString(),
-            gffId: '',
             refSeq: refSeqId,
-            start: firstExon.start,
-            end: firstExon.end,
+            min: firstExon.start,
+            max: firstExon.end,
             type: 'exon',
             strand: feature.get('strand'),
           }
@@ -152,24 +148,22 @@ export function annotationFromPileup(pluggableElement: PluggableElementBase) {
         }[] = []
         let phase: 0 | 1 | 2 = 0
         for (const exon of exons) {
-          cdsFeature.start = Math.min(cdsFeature.start, exon.start)
-          cdsFeature.end = Math.max(cdsFeature.end, exon.end)
+          cdsFeature.min = Math.min(cdsFeature.min, exon.start)
+          cdsFeature.max = Math.max(cdsFeature.max, exon.end)
           const { end, start } = exon
           discontinuousLocations.push({ start, end, phase })
           const localPhase = (end - start) % 3
           phase = ((phase + localPhase) % 3) as 0 | 1 | 2
           const newExon: AnnotationFeatureSnapshot = {
             _id: ObjectID().toHexString(),
-            gffId: '',
             refSeq: refSeqId,
-            start,
-            end,
+            min: start,
+            max: end,
             type: 'exon',
             strand: feature.get('strand'),
           }
           newFeature.children[newExon._id] = newExon
         }
-        cdsFeature.discontinuousLocations = discontinuousLocations
         return newFeature
       },
       async onPileupFeatureContext() {

package/src/index.ts

@@ -46,18 +46,21 @@ import {
 import { installApolloTextSearchAdapter } from './ApolloTextSearchAdapter'
 import { BackendDriver } from './BackendDrivers'
 import {
+  AddFeature,
   DownloadGFF3,
+  LogOut,
   ManageChecks,
   OpenLocalFile,
   ViewChangeLog,
+  ViewCheckResults,
 } from './components'
-import { AddFeature } from './components/AddFeature'
-import { ViewCheckResults } from './components/ViewCheckResults'
 import ApolloPluginConfigurationSchema from './config'
 import { annotationFromPileup } from './extensions'
 import {
   ApolloFeatureDetailsWidget,
   ApolloFeatureDetailsWidgetModel,
+  ApolloTranscriptDetailsModel,
+  ApolloTranscriptDetailsWidget,
 } from './FeatureDetailsWidget'
 import {
   stateModelFactory as LinearApolloDisplayStateModelFactory,
@@ -72,6 +75,7 @@ import {
   stateModelFactory as SixFrameFeatureDisplayStateModelFactory,
   configSchemaFactory as sixFrameFeatureDisplayConfigSchemaFactory,
 } from './SixFrameFeatureDisplay'
+import { installApolloRefNameAliasAdapter } from './ApolloRefNameAliasAdapter'
 
 interface RpcHandle {
   on(event: string, listener: (event: MessageEvent) => void): this
@@ -114,6 +118,7 @@ export default class ApolloPlugin extends Plugin {
 
   install(pluginManager: PluginManager) {
     installApolloSequenceAdapter(pluginManager)
+    installApolloRefNameAliasAdapter(pluginManager)
     installApolloTextSearchAdapter(pluginManager)
 
     pluginManager.addWidgetType(() => {
@@ -127,7 +132,17 @@ export default class ApolloPlugin extends Plugin {
       })
       return widgetType
     })
-
+    pluginManager.addWidgetType(() => {
+      const configSchema = ConfigurationSchema('ApolloTranscriptDetails', {})
+      const widgetType = new WidgetType({
+        name: 'ApolloTranscriptDetails',
+        heading: 'Apollo transcript details',
+        configSchema,
+        stateModel: ApolloTranscriptDetailsModel,
+        ReactComponent: ApolloTranscriptDetailsWidget,
+      })
+      return widgetType
+    })
     pluginManager.addTrackType(() => {
       const configSchema = ConfigurationSchema(
         'ApolloTrack',
@@ -203,6 +218,7 @@ export default class ApolloPlugin extends Plugin {
 
     pluginManager.addToExtensionPoint(
       'Core-extendSession',
+      // @ts-expect-error not sure how to deal with snapshot model types
       extendSession.bind(this, pluginManager),
     )
 
@@ -317,6 +333,28 @@ export default class ApolloPlugin extends Plugin {
                 })
                 break
               }
+              case 'getRefNameAliases': {
+                const { assembly } = event
+                const dataStore = (
+                  pluginManager.rootModel?.session as
+                    | ApolloSessionModel
+                    | undefined
+                )?.apolloDataStore
+                if (!dataStore) {
+                  break
+                }
+                const backendDriver = dataStore.getBackendDriver(
+                  assembly,
+                ) as BackendDriver
+                const refNameAliases =
+                  await backendDriver.getRefNameAliases(assembly)
+                handle.workers[0].postMessage({
+                  apollo,
+                  messageId,
+                  refNameAliases,
+                })
+                break
+              }
               default: {
                 break
               }
@@ -411,6 +449,22 @@ export default class ApolloPlugin extends Plugin {
           )
         },
       })
+      pluginManager.rootModel.appendToMenu('Apollo', {
+        label: 'Log out',
+        onClick: (session: ApolloSessionModel) => {
+          ;(session as unknown as AbstractSessionModel).queueDialog(
+            (doneCallback) => [
+              LogOut,
+              {
+                session,
+                handleClose: () => {
+                  doneCallback()
+                },
+              },
+            ],
+          )
+        },
+      })
     }
   }
 }