@apollo-annotation/jbrowse-plugin-apollo 0.3.12 → 1.0.0

package/src/components/ViewCheckResults.tsx

@@ -1,55 +1,36 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 /* 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 */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
-import { getRoot } from '@jbrowse/mobx-state-tree'
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
 import {
   Button,
   DialogActions,
   DialogContent,
   DialogContentText,
-  MenuItem,
-  Select,
-  type SelectChangeEvent,
 } from '@mui/material'
-import {
-  DataGrid,
-  type GridColDef,
-  type GridRowsProp,
-  GridToolbar,
-} from '@mui/x-data-grid'
+import { DataGrid, type GridColDef, type GridRowsProp } from '@mui/x-data-grid'
 import React, { useEffect, useState } from 'react'
 
-import type { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
 import type { ApolloSessionModel } from '../session'
-import type { ApolloRootModel } from '../types'
-import { createFetchErrorMessage } from '../util'
 
 import { Dialog } from './Dialog'
 
 interface ViewCheckResultsProps {
   session: ApolloSessionModel
   handleClose(): void
+  assembly: string
 }
 
 export function ViewCheckResults({
   handleClose,
   session,
+  assembly: assemblyName,
 }: ViewCheckResultsProps) {
-  const { internetAccounts } = getRoot<ApolloRootModel>(session)
-  const { collaborationServerDriver } = session.apolloDataStore
-  const apolloInternetAccount = internetAccounts.find(
-    (ia) => ia.type === 'ApolloInternetAccount',
-  ) as ApolloInternetAccountModel | undefined
-  if (!apolloInternetAccount) {
-    throw new Error('No Apollo internet account found')
-  }
-  const { baseURL } = apolloInternetAccount
   const [errorMessage, setErrorMessage] = useState<string>()
   const [displayGridData, setDisplayGridData] = useState<GridRowsProp[]>([])
 
+  const { apolloDataStore } = session
+
   const gridColumns: GridColDef[] = [
     { field: '_id', headerName: 'id', width: 50 },
     {
@@ -62,48 +43,21 @@ export function ViewCheckResults({
     { field: 'message', headerName: 'Message', flex: 1 },
   ]
 
-  const assemblies = collaborationServerDriver.getAssemblies()
-  const [selectedAssembly, setSelectedAssembly] = useState(assemblies.at(0))
-
   useEffect(() => {
     async function getGridData() {
-      const assemblyId: string | undefined = selectedAssembly?.name
-      if (!assemblyId) {
+      const backendDriver = apolloDataStore.getBackendDriver(assemblyName)
+      if (!backendDriver) {
+        setErrorMessage(`No driver found for assembly "${assemblyName}"`)
         return
       }
-      const url = new URL('checks', baseURL)
-      const searchParams = new URLSearchParams({ assembly: assemblyId })
-      url.search = searchParams.toString()
-      const uri = url.toString()
-      const apolloFetch = apolloInternetAccount?.getFetcher({
-        locationType: 'UriLocation',
-        uri,
-      })
-      if (apolloFetch) {
-        const response = await apolloFetch(uri, {
-          headers: new Headers({ 'Content-Type': 'application/json' }),
-        })
-        if (!response.ok) {
-          const newErrorMessage = await createFetchErrorMessage(
-            response,
-            'Error when retrieving checks',
-          )
-          setErrorMessage(newErrorMessage)
-          return
-        }
-        const data = await response.json()
-        setDisplayGridData(data)
-      }
+      const data = await backendDriver.getCheckResults(assemblyName)
+      // @ts-expect-error not sure how to type this
+      setDisplayGridData(data)
     }
     getGridData().catch((error) => {
       setErrorMessage(String(error))
     })
-  }, [selectedAssembly, apolloInternetAccount, baseURL])
-
-  function handleChangeAssembly(e: SelectChangeEvent) {
-    const newAssembly = assemblies.find((asm) => asm.name === e.target.value)
-    setSelectedAssembly(newAssembly)
-  }
+  }, [apolloDataStore, assemblyName])
 
   return (
     <Dialog
@@ -113,26 +67,14 @@ export function ViewCheckResults({
       handleClose={handleClose}
       data-testid="view-check-results"
     >
-      <Select
-        style={{ width: 200, marginLeft: 40 }}
-        value={selectedAssembly?.name ?? ''}
-        onChange={handleChangeAssembly}
-        disabled={assemblies.length === 0}
-      >
-        {assemblies.map((option) => (
-          <MenuItem key={option.name} value={option.name}>
-            {option.displayName}
-          </MenuItem>
-        ))}
-      </Select>
-
       <DialogContent>
+        <DialogContentText>Check results for {assemblyName}</DialogContentText>
         <DataGrid
           pagination
           rows={displayGridData}
           columns={gridColumns}
           getRowId={(row) => row._id}
-          slots={{ toolbar: GridToolbar }}
+          showToolbar
           initialState={{
             sorting: { sortModel: [{ field: 'name', sort: 'asc' }] },
             columns: { columnVisibilityModel: { name: true } },

package/src/components/index.ts

@@ -2,6 +2,7 @@ export * from './AddAssembly'
 export * from './AddAssemblyAliases'
 export * from './AddChildFeature'
 export * from './AddFeature'
+export * from './ColorFeature'
 export * from './CopyFeature'
 export * from './DeleteAssembly'
 export * from './DeleteFeature'
@@ -12,7 +13,6 @@ export * from './ManageChecks'
 export * from './ManageUsers'
 export * from './MergeExons'
 export * from './MergeTranscripts'
-export * from './OpenLocalFile'
 export * from './ViewChangeLog'
 export * from './AddRefSeqAliases'
 export * from './ViewCheckResults'

package/src/config.ts

@@ -3,24 +3,42 @@ import { types } from '@jbrowse/mobx-state-tree'
 
 import { OntologyRecordConfiguration } from './OntologyManager'
 
-const ApolloPluginConfigurationSchema = ConfigurationSchema('ApolloPlugin', {
-  ontologies: types.array(OntologyRecordConfiguration),
-  featureTypeOntologyName: {
-    description: 'Name of the feature type ontology',
-    type: 'string',
-    defaultValue: 'Sequence Ontology',
-  },
-  hasRole: {
-    description: 'Flag used internally by jbrowse-plugin-apollo',
-    type: 'boolean',
-    defaultValue: false,
-  },
-  geneBackgroundColor: {
-    description: 'Color for feature background',
-    type: 'string',
-    defaultValue: 'jexl:geneBackgroundColor(featureType)',
-    contextVariable: ['featureType'],
-  },
-})
+const ApolloPluginConfigurationSchema: ReturnType<typeof ConfigurationSchema> =
+  ConfigurationSchema(
+    'ApolloPlugin',
+    {
+      ontologies: types.array(OntologyRecordConfiguration),
+      featureTypeOntologyName: {
+        description: 'Name of the feature type ontology',
+        type: 'string',
+        defaultValue: 'Sequence Ontology',
+      },
+      hasRole: {
+        description: 'Flag used internally by jbrowse-plugin-apollo',
+        type: 'boolean',
+        defaultValue: false,
+      },
+      skippedAttributesOnCopy: {
+        description: 'Feature attribute keys to skip when copying features',
+        type: 'stringArray',
+        defaultValue: [],
+      },
+      geneBackgroundColor: {
+        description: 'Color for feature background',
+        type: 'string',
+        defaultValue: 'jexl:geneBackgroundColor(featureType)',
+        contextVariable: ['featureType'],
+      },
+    },
+    {
+      // eslint-disable-next-line @typescript-eslint/no-explicit-any
+      actions: (self: any) => ({
+        addOntology(ontologySnapshot: { name: string }) {
+          // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+          self.ontologies.push(ontologySnapshot)
+        },
+      }),
+    },
+  )
 
 export default ApolloPluginConfigurationSchema

package/src/extensions/annotationFromJBrowseFeature.test.ts

@@ -110,7 +110,7 @@ describe('Convert JBrowse feature to annotation feature', () => {
       expect(xcds?.type).toStrictEqual('CDS')
       expect(xcds?.min).toStrictEqual(15)
       expect(xcds?.max).toStrictEqual(27)
-      expect(xcds?.attributes?.name?.at(0)).toStrictEqual('XYZ')
+      expect(xcds?.attributes?.gff_name?.at(0)).toStrictEqual('XYZ')
       expect(xcds?.attributes?.gff_score?.at(0)).toStrictEqual('0')
       expect(xcds?.attributes?.gff_source?.at(0)).toStrictEqual('mySource')
     } else {

package/src/extensions/annotationFromJBrowseFeature.ts

@@ -6,19 +6,16 @@
 import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 import { gff3ToAnnotationFeature } from '@apollo-annotation/shared'
 import type { GFF3Feature } from '@gmod/gff'
-import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import type { PluggableElementType } from '@jbrowse/core/pluggableElementTypes'
 import type DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
-import {
-  type AbstractSessionModel,
-  getContainingView,
-  getSession,
-} from '@jbrowse/core/util'
+import { getContainingView, getSession } from '@jbrowse/core/util'
 import type { Feature } from '@jbrowse/core/util/simpleFeature'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-import AddIcon from '@mui/icons-material/Add'
 
+import { CollaborationServerDriver } from '../BackendDrivers'
 import { CreateApolloAnnotation } from '../components/CreateApolloAnnotation'
+import { Apollo as ApolloIcon } from '../menus/Icons'
+import type { ApolloSessionModel } from '../session'
 
 function simpleFeatureToGFF3Feature(
   feature: Feature,
@@ -60,29 +57,67 @@ export function jbrowseFeatureToAnnotationFeature(
   return gff3ToAnnotationFeature(simpleFeatureToGFF3Feature(feature, refSeqId))
 }
 
+const fieldsToSkip = new Set([
+  'start',
+  'end',
+  'type',
+  'strand',
+  'refName',
+  'subfeatures',
+  'derived_features',
+  'phase',
+  'source',
+  'score',
+  'parent',
+  // From https://github.com/GMOD/jbrowse-components/blob/ab3126374367f43d01038d6d2e86d8db03c4d8d8/packages/core/src/BaseFeatureWidget/BaseFeatureDetail/Attributes.tsx#L12-L24
+  '__jbrowsefmt',
+  'length',
+  'position',
+  'uniqueId',
+  'exonFrames',
+  'parentId',
+  'thickStart',
+  'thickEnd',
+  '_lineHash',
+])
+
+const fieldsToRename: Record<string, string | undefined> = {
+  id: 'gff_id',
+  name: 'gff_name',
+  alias: 'gff_alias',
+  target: 'gff_target',
+  gap: 'gff_gap',
+  derives_from: 'gff_derives_from',
+  note: 'gff_note',
+  dbxref: 'gff_dbxref',
+  ontology_term: 'gff_ontology_term',
+  is_circular: 'gff_is_circular',
+}
+
 function convertFeatureAttributes(feature: Feature): Record<string, string[]> {
   const attributes: Record<string, string[]> = {}
-  const defaultFields = new Set([
-    'start',
-    'end',
-    'type',
-    'strand',
-    'refName',
-    'subfeatures',
-    'derived_features',
-    'phase',
-    'source',
-    'score',
-  ])
-  for (const [key, value] of Object.entries(feature.toJSON())) {
-    if (defaultFields.has(key)) {
+
+  for (const [originalKey, value] of Object.entries(feature.toJSON())) {
+    if (fieldsToSkip.has(originalKey)) {
       continue
     }
+    const renamedKey = fieldsToRename[originalKey]
+    const key = renamedKey ?? originalKey
     attributes[key] = Array.isArray(value) ? value.map(String) : [String(value)]
   }
   return attributes
 }
 
+function getTopLevelSimpleFeature(feature: Feature) {
+  let topLevel = feature
+  let parent = feature.get('parent')
+  while (parent) {
+    topLevel = parent
+    parent = parent.get('parent')
+  }
+  return topLevel
+}
+
 export function annotationFromJBrowseFeature(
   pluggableElement: PluggableElementType,
 ) {
@@ -108,29 +143,6 @@ export function annotationFromJBrowseFeature(
         }
         return assembly
       },
-      getRefSeqId(assembly: Assembly) {
-        const firstRegion = self.getFirstRegion()
-        const { refName } = firstRegion
-        const { refNameAliases } = assembly
-        if (!refNameAliases) {
-          throw new Error(`Could not find aliases for ${assembly.name}`)
-        }
-        const newRefNames = [...Object.entries(refNameAliases)]
-          .filter(([id, refName]) => id !== refName)
-          .map(([id, refName]) => ({
-            _id: id,
-            name: refName,
-          }))
-        const refSeqId = newRefNames.find((item) => item.name === refName)?._id
-        if (!refSeqId) {
-          throw new Error(`Could not find refSeqId named ${refName}`)
-        }
-        return refSeqId
-      },
-      getAnnotationFeature(assembly: Assembly, feature: Feature) {
-        const refSeqId = self.getRefSeqId(assembly)
-        return jbrowseFeatureToAnnotationFeature(feature, refSeqId)
-      },
     }))
     .views((self) => {
       const superContextMenuItems = self.contextMenuItems
@@ -144,30 +156,46 @@ export function annotationFromJBrowseFeature(
           if (!feature) {
             return superContextMenuItems()
           }
+          const topLevelFeature = getTopLevelSimpleFeature(feature)
           return [
             ...superContextMenuItems(),
             {
               label: 'Create Apollo annotation',
-              icon: AddIcon,
-              onClick: () => {
-                ;(session as unknown as AbstractSessionModel).queueDialog(
-                  (doneCallback) => [
-                    CreateApolloAnnotation,
-                    {
-                      session,
-                      handleClose: () => {
-                        doneCallback()
-                      },
-                      annotationFeature: self.getAnnotationFeature(
-                        assembly,
-                        feature,
-                      ),
-                      assembly,
-                      refSeqId: self.getRefSeqId(assembly),
-                      region,
-                    },
-                  ],
+              icon: ApolloIcon,
+              onClick: async () => {
+                const backendDriver = (
+                  session as unknown as ApolloSessionModel
+                ).apolloDataStore.getBackendDriver(region.assemblyName)
+                let refSeqId = region.refName
+                if (backendDriver instanceof CollaborationServerDriver) {
+                  const backendRefSeqId = await backendDriver.getRefSeqId(
+                    region.assemblyName,
+                    region.refName,
+                  )
+                  if (!backendRefSeqId) {
+                    throw new Error(
+                      `Could not find refSeq for "${region.refName}"`,
+                    )
+                  }
+                  refSeqId = backendRefSeqId
+                }
+                const annotationFeature = jbrowseFeatureToAnnotationFeature(
+                  topLevelFeature,
+                  refSeqId,
                 )
+                session.queueDialog((doneCallback) => [
+                  CreateApolloAnnotation,
+                  {
+                    session,
+                    handleClose: () => {
+                      doneCallback()
+                    },
+                    annotationFeature,
+                    assembly,
+                    refSeqId,
+                    region,
+                  },
+                ])
               },
             },
           ]

package/src/extensions/annotationFromPileup.ts

@@ -4,7 +4,6 @@
 /* eslint-disable @typescript-eslint/no-unsafe-call */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
 import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
-import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import type {
   DisplayType,
   PluggableElementType,
@@ -14,11 +13,14 @@ import {
   getContainingView,
   getSession,
 } from '@jbrowse/core/util'
+import type { Feature } from '@jbrowse/core/util/simpleFeature'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-import AddIcon from '@mui/icons-material/Add'
 import ObjectID from 'bson-objectid'
 
+import { CollaborationServerDriver } from '../BackendDrivers'
 import { CreateApolloAnnotation } from '../components/CreateApolloAnnotation'
+import { Apollo as ApolloIcon } from '../menus/Icons'
+import type { ApolloSessionModel } from '../session'
 
 function parseCigar(cigar: string): [string, number][] {
   const regex = /(\d+)([MIDNSHPX=])/g
@@ -44,7 +46,7 @@ export function annotationFromPileup(pluggableElement: PluggableElementType) {
         return lgv.dynamicBlocks.contentBlocks[0]
       },
       getAssembly() {
-        const firstRegion = self.getFirstRegion()
+        const firstRegion = this.getFirstRegion()
         const session = getSession(self)
         const { assemblyManager } = session
         const { assemblyName } = firstRegion
@@ -54,35 +56,13 @@ export function annotationFromPileup(pluggableElement: PluggableElementType) {
         }
         return assembly
       },
-      getRefSeqId(assembly: Assembly) {
-        const firstRegion = self.getFirstRegion()
-        const { refName } = firstRegion
-        const { refNameAliases } = assembly
-        if (!refNameAliases) {
-          throw new Error(`Could not find aliases for ${assembly.name}`)
-        }
-        const newRefNames = [...Object.entries(refNameAliases)]
-          .filter(([id, refName]) => id !== refName)
-          .map(([id, refName]) => ({
-            _id: id,
-            name: refName,
-          }))
-        const refSeqId = newRefNames.find((item) => item.name === refName)?._id
-        if (!refSeqId) {
-          throw new Error(`Could not find refSeqId named ${refName}`)
-        }
-        return refSeqId
-      },
-      getAnnotationFeature() {
-        const feature = self.contextMenuFeature
-        const assembly = self.getAssembly()
-        const refSeqId = self.getRefSeqId(assembly)
-        const start: number = feature.get('start')
-        const end: number = feature.get('end')
-        const strand = feature.get('strand')
-        const name = feature.get('name')
+      getAnnotationFeature(jbrowseFeature: Feature, refSeqId: string) {
+        const start: number = jbrowseFeature.get('start')
+        const end: number = jbrowseFeature.get('end')
+        const strand = jbrowseFeature.get('strand') as 1 | -1 | undefined
+        const name = jbrowseFeature.get('name') as string | undefined
 
-        const cigarData: string = feature.get('CIGAR')
+        const cigarData = jbrowseFeature.get('CIGAR') as string
         const ops = parseCigar(cigarData)
         let position = start
         let currentExonStart: number | undefined
@@ -151,9 +131,10 @@ export function annotationFromPileup(pluggableElement: PluggableElementType) {
           max: end,
           type: 'mRNA',
           strand,
-          attributes: {
-            name: [name],
-          },
+        }
+        if (name) {
+          newFeature.attributes = {}
+          newFeature.attributes.gff_name = [name]
         }
         if (exons.length === 0) {
           return newFeature
@@ -183,16 +164,32 @@ export function annotationFromPileup(pluggableElement: PluggableElementType) {
           const session = getSession(self)
           const assembly = self.getAssembly()
           const region = self.getFirstRegion()
-          const feature = self.contextMenuFeature
-          if (!feature) {
+          const jbrowseFeature = self.contextMenuFeature
+          if (!jbrowseFeature) {
             return superContextMenuItems()
           }
           return [
             ...superContextMenuItems(),
             {
               label: 'Create Apollo annotation',
-              icon: AddIcon,
-              onClick: () => {
+              icon: ApolloIcon,
+              onClick: async () => {
+                const backendDriver = (
+                  session as unknown as ApolloSessionModel
+                ).apolloDataStore.getBackendDriver(region.assemblyName)
+                let refSeqId = region.refName
+                if (backendDriver instanceof CollaborationServerDriver) {
+                  const backendRefSeqId = await backendDriver.getRefSeqId(
+                    region.assemblyName,
+                    region.refName,
+                  )
+                  if (!backendRefSeqId) {
+                    throw new Error(
+                      `Could not find refSeq for "${region.refName}"`,
+                    )
+                  }
+                  refSeqId = backendRefSeqId
+                }
                 ;(session as unknown as AbstractSessionModel).queueDialog(
                   (doneCallback) => [
                     CreateApolloAnnotation,
@@ -201,9 +198,12 @@ export function annotationFromPileup(pluggableElement: PluggableElementType) {
                       handleClose: () => {
                         doneCallback()
                       },
-                      annotationFeature: self.getAnnotationFeature(assembly),
+                      annotationFeature: self.getAnnotationFeature(
+                        jbrowseFeature,
+                        refSeqId,
+                      ),
                       assembly,
-                      refSeqId: self.getRefSeqId(assembly),
+                      refSeqId,
                       region,
                     },
                   ],

package/src/index.ts

@@ -91,6 +91,12 @@ interface ApolloMessageData {
   assembly: string
 }
 
+interface JBrowseTrackConfig {
+  trackId: string
+  type: string
+  displays?: { type: string; displayId: string }[]
+}
+
 function isApolloMessageData(data?: unknown): data is ApolloMessageData {
   return (
     typeof data === 'object' &&
@@ -118,7 +124,8 @@ validationRegistry.registerValidation(new ParentChildValidation())
 export default class ApolloPlugin extends Plugin {
   name = 'ApolloPlugin'
   version = version
-  configurationSchema = ApolloPluginConfigurationSchema
+  configurationSchema: ReturnType<typeof ConfigurationSchema> =
+    ApolloPluginConfigurationSchema
 
   install(pluginManager: PluginManager) {
     installApolloSequenceAdapter(pluginManager)
@@ -288,6 +295,43 @@ export default class ApolloPlugin extends Plugin {
       annotationFromJBrowseFeature,
     )
 
+    pluginManager.addToExtensionPoint(
+      'Core-preProcessTrackConfig',
+      (snap: JBrowseTrackConfig): JBrowseTrackConfig => {
+        if (snap.type !== 'ReferenceSequenceTrack') {
+          return snap
+        }
+        const displays = snap.displays ?? []
+        const apolloDisplayIdx = displays.findIndex(
+          (d) => d.type === 'LinearApolloReferenceSequenceDisplay',
+        )
+        if (apolloDisplayIdx === 0) {
+          return snap
+        }
+        if (apolloDisplayIdx === -1) {
+          return {
+            ...snap,
+            displays: [
+              {
+                type: 'LinearApolloReferenceSequenceDisplay',
+                displayId: `${snap.trackId}-LinearApolloReferenceSequenceDisplay`,
+              },
+              ...displays,
+            ],
+          }
+        }
+        const reorderedDisplays = displays.toSpliced(apolloDisplayIdx, 1)
+        reorderedDisplays.unshift({
+          type: 'LinearApolloReferenceSequenceDisplay',
+          displayId: `${snap.trackId}-LinearApolloReferenceSequenceDisplay`,
+        })
+        return {
+          ...snap,
+          displays: reorderedDisplays,
+        }
+      },
+    )
+
     pluginManager.addToExtensionPoint(
       'LinearGenomeView-searchResultSelected',
       (_: any, props: Record<string, unknown>) => {

package/src/makeDisplayComponent.tsx

@@ -65,9 +65,16 @@ function scrollSelectedFeatureIntoView(
 ) {
   const { apolloRowHeight, selectedFeature } = model
   if (scrollContainerRef.current && selectedFeature) {
-    const position = model.getFeatureLayoutPosition(selectedFeature)
-    if (position) {
-      const row = position.layoutRow + position.featureRow
+    let row: number | undefined
+    if ('getFeatureLayoutPosition' in model) {
+      const position = model.getFeatureLayoutPosition(selectedFeature)
+      if (position) {
+        row = position.layoutRow + position.featureRow
+      }
+    } else {
+      row = model.getRowForFeature(selectedFeature)
+    }
+    if (row !== undefined) {
       const top = row * apolloRowHeight
       scrollContainerRef.current.scroll({ top, behavior: 'smooth' })
     }