Keep local file checks on refresh

GMOD · Dec 14, 2024 · 85527e0 · 85527e0
1 parent d0e3c7c
commit 85527e0
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Showing 5 changed files with 31 additions and 2 deletions.
diff --git a/packages/apollo-common/src/Change.ts b/packages/apollo-common/src/Change.ts
@@ -38,6 +38,7 @@ export interface ClientDataStore {
     assemblyId: string,
     backendDriverType?: BackendDriverType,
   ): ApolloAssemblyI
+  clearCheckResults(): void
 }
 
 export type SerializedChange = SerializedOperation

diff --git a/packages/apollo-shared/src/Checks/CDSCheck.ts b/packages/apollo-shared/src/Checks/CDSCheck.ts
@@ -124,7 +124,7 @@ async function checkMRNA(
           refSeq: refSeq.toString(),
           start: max,
           end: max,
-          message: `Feature "${_id}" is missing a stop codon`,
+          message: `Missing stop codon`,
         })
       }
     } else {

diff --git a/packages/jbrowse-plugin-apollo/src/BackendDrivers/InMemoryFileDriver.ts b/packages/jbrowse-plugin-apollo/src/BackendDrivers/InMemoryFileDriver.ts
@@ -10,6 +10,7 @@ import { Region, getSession } from '@jbrowse/core/util'
 
 import { SubmitOpts } from '../ChangeManager'
 import { BackendDriver, RefNameAliases } from './BackendDriver'
+import { checkFeatures } from '../util'
 
 export class InMemoryFileDriver extends BackendDriver {
   async getFeatures(): Promise<
@@ -84,6 +85,15 @@ export class InMemoryFileDriver extends BackendDriver {
     _change: Change | AssemblySpecificChange,
     _opts: SubmitOpts = {},
   ) {
+    const { clientStore } = this
+    const { assemblies } = clientStore
+    clientStore.clearCheckResults()
+    for (const [, assembly] of assemblies) {
+      if (assembly.backendDriverType === 'InMemoryFileDriver') {
+        const checkResults = await checkFeatures(assembly)
+        clientStore.addCheckResults(checkResults)
+      }
+    }
     return new ValidationResultSet()
   }
 

diff --git a/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts b/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts
@@ -125,6 +125,9 @@ export function clientDataStoreFactory(
       deleteCheckResult(checkResultId: string) {
         self.checkResults.delete(checkResultId)
       },
+      clearCheckResults() {
+        self.checkResults.clear()
+      },
     }))
     .volatile((self) => ({
       changeManager: new ChangeManager(self as unknown as ClientDataStoreType),

diff --git a/packages/jbrowse-plugin-apollo/src/session/session.ts b/packages/jbrowse-plugin-apollo/src/session/session.ts
@@ -427,7 +427,7 @@ export function extendSession(
       }
     })
   return types.snapshotProcessor(sm, {
-    postProcessor(snap: SnapshotOut<typeof sm>) {
+    postProcessor(snap: SnapshotOut<typeof sm>, node) {
       snap.apolloSelectedFeature = undefined
       const assemblies = Object.fromEntries(
         Object.entries(snap.apolloDataStore.assemblies).filter(
@@ -440,6 +440,21 @@ export function extendSession(
         assemblies,
         checkResults: {},
       }
+      if (!node) {
+        return snap
+      }
+      const { apolloDataStore } = node
+      const { checkResults } = apolloDataStore
+      for (const [, cr] of checkResults) {
+        const [feature] = cr.ids
+        if (!feature) {
+          continue
+        }
+        const assembly = apolloDataStore.assemblies.get(feature.assemblyId)
+        if (assembly && assembly.backendDriverType === 'InMemoryFileDriver') {
+          snap.apolloDataStore.checkResults[cr._id] = getSnapshot(cr)
+        }
+      }
       return snap
     },
   })