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

package/src/session/ClientDataStore.ts

@@ -1,14 +1,15 @@
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
-/* eslint-disable @typescript-eslint/no-unsafe-call */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 import { ClientDataStore as ClientDataStoreType } from '@apollo-annotation/common'
 import {
-  AnnotationFeature,
+  AnnotationFeatureModel,
   AnnotationFeatureSnapshot,
   ApolloAssembly,
+  ApolloAssemblySnapshot,
   ApolloRefSeq,
+  BackendDriverType,
   CheckResult,
   CheckResultSnapshot,
 } from '@apollo-annotation/mst'
@@ -18,7 +19,7 @@ import { Region, getSession, isElectron } from '@jbrowse/core/util'
 import { LocalPathLocation, UriLocation } from '@jbrowse/core/util/types/mst'
 import {
   Instance,
-  SnapshotOut,
+  addDisposer,
   flow,
   getParentOfType,
   getRoot,
@@ -40,11 +41,12 @@ import {
   TextIndexFieldDefinition,
 } from '../OntologyManager'
 import { ApolloRootModel } from '../types'
+import { autorun } from 'mobx'
 
 export function clientDataStoreFactory(
-  AnnotationFeatureExtended: typeof AnnotationFeature,
+  AnnotationFeatureExtended: typeof AnnotationFeatureModel,
 ) {
-  const clientStoreType = types
+  return types
     .model('ClientDataStore', {
       typeName: types.optional(types.literal('Client'), 'Client'),
       assemblies: types.map(ApolloAssembly),
@@ -68,8 +70,15 @@ export function clientDataStoreFactory(
       },
     }))
     .actions((self) => ({
-      addAssembly(assemblyId: string) {
-        return self.assemblies.put({ _id: assemblyId, refSeqs: {} })
+      addAssembly(assemblyId: string, backendDriverType?: BackendDriverType) {
+        const assemblySnapshot: ApolloAssemblySnapshot = {
+          _id: assemblyId,
+          refSeqs: {},
+        }
+        if (backendDriverType) {
+          assemblySnapshot.backendDriverType = backendDriverType
+        }
+        return self.assemblies.put(assemblySnapshot)
       },
       addFeature(assemblyId: string, feature: AnnotationFeatureSnapshot) {
         const assembly = self.assemblies.get(assemblyId)
@@ -131,36 +140,39 @@ export function clientDataStoreFactory(
     }))
     .actions((self) => ({
       afterCreate() {
-        // Merge in the ontologies from our plugin configuration.
-        // Ontologies of a given name that are already in the session
-        // take precedence over the ontologies in the configuration.
-        const { ontologyManager, pluginConfiguration } = self
-        const configuredOntologies =
-          pluginConfiguration.ontologies as ConfigurationModel<
-            typeof OntologyRecordConfiguration
-          >[]
-
-        for (const ont of configuredOntologies || []) {
-          const [name, version, source, indexFields] = [
-            readConfObject(ont, 'name') as string,
-            readConfObject(ont, 'version') as string,
-            readConfObject(ont, 'source') as
-              | Instance<typeof LocalPathLocation>
-              | Instance<typeof UriLocation>,
-            readConfObject(
-              ont,
-              'textIndexFields',
-            ) as TextIndexFieldDefinition[],
-          ]
-          if (!ontologyManager.findOntology(name)) {
-            ontologyManager.addOntology(name, version, source, {
-              textIndexing: { indexFields },
-            })
-          }
-        }
-
-        // TODO: add in any configured ontology prefixes that we don't already
-        // have in the session (or hardcoded in the model)
+        addDisposer(
+          self,
+          autorun(() => {
+            // Merge in the ontologies from our plugin configuration.
+            // Ontologies of a given name that are already in the session
+            // take precedence over the ontologies in the configuration.
+            const { ontologyManager, pluginConfiguration } = self
+            const configuredOntologies =
+              pluginConfiguration.ontologies as ConfigurationModel<
+                typeof OntologyRecordConfiguration
+              >[]
+            for (const ont of configuredOntologies || []) {
+              const [name, version, source, indexFields] = [
+                readConfObject(ont, 'name') as string,
+                readConfObject(ont, 'version') as string,
+                readConfObject(ont, 'source') as
+                  | Instance<typeof LocalPathLocation>
+                  | Instance<typeof UriLocation>,
+                readConfObject(
+                  ont,
+                  'textIndexFields',
+                ) as TextIndexFieldDefinition[],
+              ]
+              if (!ontologyManager.findOntology(name)) {
+                ontologyManager.addOntology(name, version, source, {
+                  textIndexing: { indexFields },
+                })
+              }
+            }
+            // TODO: add in any configured ontology prefixes that we don't already
+            // have in the session (or hardcoded in the model)
+          }),
+        )
       },
     }))
     .views((self) => ({
@@ -275,13 +287,4 @@ export function clientDataStoreFactory(
         }
       }),
     }))
-
-  // assembly and feature data isn't actually reloaded on reload unless we delete it from the snap
-  return types.snapshotProcessor(clientStoreType, {
-    postProcessor(snap: SnapshotOut<typeof clientStoreType>) {
-      snap.assemblies = {}
-      snap.checkResults = {}
-      return snap
-    },
-  })
 }

package/src/session/session.ts

@@ -1,21 +1,36 @@
-/* eslint-disable @typescript-eslint/no-unused-vars */
+/* eslint-disable @typescript-eslint/no-unsafe-return */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
-/* eslint-disable @typescript-eslint/no-unsafe-argument */
 import { ClientDataStore as ClientDataStoreType } from '@apollo-annotation/common'
-import { AnnotationFeature, AnnotationFeatureI } from '@apollo-annotation/mst'
-import { UserLocation } from '@apollo-annotation/shared'
-import { AssemblyModel } from '@jbrowse/core/assemblyManager/assembly'
-import { getConf } from '@jbrowse/core/configuration'
-import { BaseInternetAccountModel } from '@jbrowse/core/pluggableElementTypes'
+import {
+  AnnotationFeature,
+  AnnotationFeatureModel,
+} from '@apollo-annotation/mst'
+import {
+  filterJBrowseConfig,
+  ImportJBrowseConfigChange,
+  JBrowseConfig,
+  UserLocation,
+} from '@apollo-annotation/shared'
+import { readConfObject, getConf } from '@jbrowse/core/configuration'
+import { BaseTrackConfig } from '@jbrowse/core/pluggableElementTypes'
 import PluginManager from '@jbrowse/core/PluginManager'
 import {
   AbstractSessionModel,
   SessionWithConfigEditing,
 } from '@jbrowse/core/util'
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import SaveIcon from '@mui/icons-material/Save'
 import { autorun, observable } from 'mobx'
-import { Instance, flow, getRoot, types } from 'mobx-state-tree'
+import {
+  Instance,
+  SnapshotOut,
+  applySnapshot,
+  flow,
+  getRoot,
+  getSnapshot,
+  types,
+} from 'mobx-state-tree'
 
 import { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
 import { ApolloJobModel } from '../ApolloJobModel'
@@ -23,27 +38,12 @@ import { ChangeManager } from '../ChangeManager'
 import { ApolloRootModel } from '../types'
 import { createFetchErrorMessage } from '../util'
 import { clientDataStoreFactory } from './ClientDataStore'
+import { AssemblyModel } from '@jbrowse/core/assemblyManager/assembly'
 
 export interface ApolloSession extends AbstractSessionModel {
   apolloDataStore: ClientDataStoreType & { changeManager: ChangeManager }
-  apolloSelectedFeature?: AnnotationFeatureI
-  apolloSetSelectedFeature(feature?: AnnotationFeatureI): void
-}
-
-interface ApolloAssemblyResponse {
-  _id: string
-  name: string
-  displayName?: string
-  description?: string
-  aliases?: string[]
-}
-
-export interface ApolloRefSeqResponse {
-  _id: string
-  name: string
-  description?: string
-  length: string
-  assembly: string
+  apolloSelectedFeature?: AnnotationFeature
+  apolloSetSelectedFeature(feature?: AnnotationFeature): void
 }
 
 export interface Collaborator {
@@ -60,10 +60,10 @@ export function extendSession(
   const { signal } = aborter
   const AnnotationFeatureExtended = pluginManager.evaluateExtensionPoint(
     'Apollo-extendAnnotationFeature',
-    AnnotationFeature,
-  ) as typeof AnnotationFeature
+    AnnotationFeatureModel,
+  ) as typeof AnnotationFeatureModel
   const ClientDataStore = clientDataStoreFactory(AnnotationFeatureExtended)
-  return sessionModel
+  const sm = sessionModel
     .props({
       apolloDataStore: types.optional(ClientDataStore, { typeName: 'Client' }),
       apolloSelectedFeature: types.safeReference(AnnotationFeatureExtended),
@@ -93,7 +93,8 @@ export function extendSession(
       }
     })
     .actions((self) => ({
-      apolloSetSelectedFeature(feature?: AnnotationFeatureI) {
+      apolloSetSelectedFeature(feature?: AnnotationFeature) {
+        // @ts-expect-error Not sure why TS thinks these MST types don't match
         self.apolloSelectedFeature = feature
       },
       addApolloTrackConfig(assembly: AssemblyModel, baseURL?: string) {
@@ -186,7 +187,15 @@ export function extendSession(
     }))
     .actions((self) => ({
       afterCreate: flow(function* afterCreate() {
-        const { internetAccounts } = getRoot<ApolloRootModel>(self)
+        // When the initial config.json loads, it doesn't include the Apollo
+        // tracks, which would result in a potentially invalid session snapshot
+        // if any tracks are open. Here we copy the session snapshot, apply an
+        // empty session snapshot, and then restore the original session
+        // snapshot after the updated config.json loads.
+        const sessionSnapshot = getSnapshot(self)
+        const { id, name } = sessionSnapshot
+        applySnapshot(self, { name, id })
+        const { internetAccounts, jbrowse } = getRoot<ApolloRootModel>(self)
         autorun(
           () => {
             // broadcastLocations() // **** This is not working and therefore we need to duplicate broadcastLocations() -method code here because autorun() does not observe changes otherwise
@@ -248,8 +257,8 @@ export function extendSession(
             continue
           }
 
-          const { baseURL, configuration } = internetAccount
-          const uri = new URL('assemblies', baseURL).href
+          const { baseURL } = internetAccount
+          const uri = new URL('jbrowse/config.json', baseURL).href
           const fetch = internetAccount.getFetcher({
             locationType: 'UriLocation',
             uri,
@@ -259,7 +268,6 @@ export function extendSession(
             response = yield fetch(uri, { signal })
           } catch (error) {
             console.error(error)
-            // setError(e instanceof Error ? e : new Error(String(e)))
             continue
           }
           if (!response.ok) {
@@ -270,96 +278,160 @@ export function extendSession(
             console.error(errorMessage)
             continue
           }
-          let fetchedAssemblies
+          let jbrowseConfig
           try {
-            fetchedAssemblies =
-              (yield response.json()) as ApolloAssemblyResponse[]
+            jbrowseConfig = yield response.json()
           } catch (error) {
             console.error(error)
             continue
           }
-          for (const assembly of fetchedAssemblies) {
-            const { addAssembly, addSessionAssembly, assemblyManager } =
-              self as unknown as AbstractSessionModel & {
-                // eslint-disable-next-line @typescript-eslint/ban-types
-                addSessionAssembly: Function
-              }
-            const selectedAssembly = assemblyManager.get(assembly.name)
-            if (selectedAssembly) {
-              // @ts-expect-error MST type coercion problem?
-              self.addApolloTrackConfig(selectedAssembly, baseURL)
-              continue
-            }
-            const url = new URL('refSeqs', baseURL)
-            const searchParams = new URLSearchParams({ assembly: assembly._id })
-            url.search = searchParams.toString()
-            const uri2 = url.toString()
-            const fetch2 = internetAccount.getFetcher({
-              locationType: 'UriLocation',
-              uri: uri2,
-            })
-            const response2 = (yield fetch2(uri2, {
-              signal,
-            })) as unknown as Response
-            if (!response2.ok) {
-              let errorMessage
-              try {
-                errorMessage = yield response2.text()
-              } catch {
-                errorMessage = ''
-              }
-              throw new Error(
-                `Failed to fetch fasta info — ${response2.status} (${
-                  response2.statusText
-                })${errorMessage ? ` (${errorMessage})` : ''}`,
-              )
-            }
-            const f = (yield response2.json()) as ApolloRefSeqResponse[]
-            const ids: Record<string, string> = {}
-            const refNameAliasesFeatures = f.map((contig) => {
-              ids[contig.name] = contig._id
-              return {
-                refName: contig.name,
-                aliases: [contig._id],
-                uniqueId: `alias-${contig._id}`,
-              }
-            })
-            const assemblyConfig = {
-              name: assembly._id,
-              aliases: [assembly.name, ...(assembly.aliases ?? [])],
-              displayName: assembly.displayName ?? assembly.name,
-              sequence: {
-                trackId: `sequenceConfigId-${assembly.name}`,
-                type: 'ReferenceSequenceTrack',
-                adapter: {
-                  type: 'ApolloSequenceAdapter',
-                  assemblyId: assembly._id,
-                  baseURL: { uri: baseURL, locationType: 'UriLocation' },
-                },
-                metadata: {
-                  apollo: true,
-                  internetAccountConfigId: configuration.internetAccountId,
-                  ids,
-                },
-              },
-              refNameAliases: {
-                adapter: {
-                  type: 'FromConfigAdapter',
-                  features: refNameAliasesFeatures,
-                },
-              },
-            }
-            ;(addSessionAssembly || addAssembly)(assemblyConfig)
-            const a = yield assemblyManager.waitForAssembly(assemblyConfig.name)
-            self.addApolloTrackConfig(a, baseURL)
-          }
+          applySnapshot(jbrowse, jbrowseConfig)
+          applySnapshot(self, sessionSnapshot)
         }
       }),
       beforeDestroy() {
-        aborter.abort()
+        aborter.abort('destroying session model')
       },
     }))
+
+    .views((self) => {
+      const superTrackActionMenuItems = (
+        self as unknown as AbstractSessionModel
+      ).getTrackActionMenuItems
+      return {
+        getTrackActionMenuItems(conf: BaseTrackConfig) {
+          if (
+            conf.type === 'ApolloTrack' ||
+            conf.type === 'ReferenceSequenceTrack'
+          ) {
+            return superTrackActionMenuItems?.(conf)
+          }
+          const trackId = readConfObject(conf, 'trackId') as string
+          const sessionTrackIdentifier = '-sessionTrack'
+          const isSessionTrack = trackId.endsWith(sessionTrackIdentifier)
+          return isSessionTrack
+            ? [
+                ...(superTrackActionMenuItems?.(conf) ?? []),
+                {
+                  label: 'Save track to Apollo',
+                  onClick: async () => {
+                    const { internetAccounts, jbrowse } =
+                      getRoot<ApolloRootModel>(self)
+                    const currentConfig = getSnapshot<JBrowseConfig>(jbrowse)
+                    let filteredConfig: JBrowseConfig | undefined
+                    filteredConfig = filterJBrowseConfig(currentConfig)
+                    if (Object.keys(filteredConfig).length === 0) {
+                      filteredConfig = undefined
+                    }
+                    const trackConfigSnapshot = getSnapshot(conf) as {
+                      trackId: string
+                      type: string
+                    }
+                    const newTrackId = trackId.slice(
+                      0,
+                      trackId.length - sessionTrackIdentifier.length,
+                    )
+                    const newTrackConfigSnapshot = {
+                      ...trackConfigSnapshot,
+                      trackId: newTrackId,
+                    }
+                    for (const internetAccount of internetAccounts as ApolloInternetAccountModel[]) {
+                      if (internetAccount.type !== 'ApolloInternetAccount') {
+                        continue
+                      }
+                      const change = new ImportJBrowseConfigChange({
+                        typeName: 'ImportJBrowseConfigChange',
+                        oldJBrowseConfig: filteredConfig,
+                        newJBrowseConfig: {
+                          ...filteredConfig,
+                          tracks: filteredConfig?.tracks && [
+                            ...filteredConfig.tracks,
+                            newTrackConfigSnapshot,
+                          ],
+                        },
+                      })
+                      const { internetAccountId } = internetAccount
+                      await self.apolloDataStore.changeManager.submit(change, {
+                        internetAccountId,
+                      })
+                      const { notify } = self as unknown as AbstractSessionModel
+                      notify('Track added', 'success')
+                    }
+                    // @ts-expect-error This method is missing in the JB types
+                    self.deleteTrackConf(conf)
+                    // eslint-disable-next-line @typescript-eslint/no-unsafe-call
+                    jbrowse.addTrackConf(newTrackConfigSnapshot)
+                  },
+                  icon: SaveIcon,
+                },
+              ]
+            : [
+                ...(superTrackActionMenuItems?.(conf) ?? []),
+                {
+                  label: 'Remove track from Apollo',
+                  onClick: async () => {
+                    const { internetAccounts, jbrowse } =
+                      getRoot<ApolloRootModel>(self)
+                    const currentConfig = getSnapshot<JBrowseConfig>(jbrowse)
+                    let filteredConfig: JBrowseConfig | undefined
+                    filteredConfig = filterJBrowseConfig(currentConfig)
+                    if (Object.keys(filteredConfig).length === 0) {
+                      filteredConfig = undefined
+                    }
+                    const filteredTracks = filteredConfig?.tracks?.filter(
+                      (t) => t.trackId !== trackId,
+                    )
+                    for (const internetAccount of internetAccounts as ApolloInternetAccountModel[]) {
+                      if (internetAccount.type !== 'ApolloInternetAccount') {
+                        continue
+                      }
+                      const change = new ImportJBrowseConfigChange({
+                        typeName: 'ImportJBrowseConfigChange',
+                        oldJBrowseConfig: filteredConfig,
+                        newJBrowseConfig: {
+                          ...filteredConfig,
+                          tracks: filteredTracks,
+                        },
+                      })
+                      const { internetAccountId } = internetAccount
+                      await self.apolloDataStore.changeManager.submit(change, {
+                        internetAccountId,
+                      })
+                      const { notify } = self as unknown as AbstractSessionModel
+                      notify('Track removed', 'success')
+                    }
+                    // @ts-expect-error This method is missing in the JB types
+                    self.deleteTrackConf(conf)
+                    // eslint-disable-next-line @typescript-eslint/no-unsafe-call
+                    jbrowse.deleteTrackConf(conf)
+                  },
+                  icon: SaveIcon,
+                },
+              ]
+        },
+      }
+    })
+  return types.snapshotProcessor(sm, {
+    postProcessor(snap: SnapshotOut<typeof sm>) {
+      snap.apolloSelectedFeature = undefined
+      const assemblies = Object.fromEntries(
+        Object.entries(snap.apolloDataStore.assemblies).filter(
+          ([, assembly]) => assembly.backendDriverType === 'InMemoryFileDriver',
+        ),
+      )
+      snap.apolloDataStore = {
+        typeName: 'Client',
+        assemblies,
+        checkResults: {},
+      }
+      return snap
+    },
+  })
 }
 
 export type ApolloSessionStateModel = ReturnType<typeof extendSession>
-export type ApolloSessionModel = Instance<ApolloSessionStateModel>
+// @ts-expect-error Snapshots seem to mess up types here
+// eslint disable because of
+// https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time
+// eslint-disable-next-line @typescript-eslint/no-empty-interface
+export interface ApolloSessionModel extends Instance<ApolloSessionStateModel> {}