@apollo-annotation/jbrowse-plugin-apollo 0.2.0 → 0.2.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/jbrowse-plugin-apollo",
-  "version": "0.2.0",
+  "version": "0.2.2",
   "description": "Apollo plugin for JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -48,9 +48,9 @@
     }
   },
   "dependencies": {
-    "@apollo-annotation/common": "^0.2.0",
-    "@apollo-annotation/mst": "^0.2.0",
-    "@apollo-annotation/shared": "^0.2.0",
+    "@apollo-annotation/common": "^0.2.2",
+    "@apollo-annotation/mst": "^0.2.2",
+    "@apollo-annotation/shared": "^0.2.2",
     "@emotion/react": "^11.10.6",
     "@emotion/styled": "^11.10.6",
     "@gmod/gff": "1.2.0",
@@ -91,7 +91,7 @@
     "librpc-web-mod": "^1.1.9",
     "mobx": "^6.6.1",
     "mobx-react": "^7.2.1",
-    "mobx-state-tree": "^5.1.7",
+    "mobx-state-tree": "^5.4.0",
     "npm-run-all": "^4.1.5",
     "prop-types": "^15.8.1",
     "react": "^18.2.0",
@@ -112,7 +112,7 @@
     "@mui/material": "^5.11.14",
     "mobx": "^6.6.1",
     "mobx-react": "^7.2.1",
-    "mobx-state-tree": "^5.1.7",
+    "mobx-state-tree": "^5.4.0",
     "prop-types": "^15.8.1",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",

package/src/BackendDrivers/DesktopFileDriver.ts

@@ -9,8 +9,8 @@ import {
   CheckResultSnapshot,
 } from '@apollo-annotation/mst'
 import {
+  annotationFeatureToGFF3,
   ValidationResultSet,
-  makeGFF3Feature,
   splitStringIntoChunks,
 } from '@apollo-annotation/shared'
 import gff, { GFF3Item } from '@gmod/gff'
@@ -148,7 +148,7 @@ export class DesktopFileDriver extends BackendDriver {
     for (const [, refSeq] of clientAssembly.refSeqs) {
       const { features } = refSeq
       for (const [, feature] of features) {
-        gff3Items.push(makeGFF3Feature(getSnapshot(feature)))
+        gff3Items.push(annotationFeatureToGFF3(getSnapshot(feature)))
       }
     }
     for (const [, refSeq] of clientAssembly.refSeqs) {

package/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()
   }
 

package/src/OntologyManager/OntologyStore/prefixes.ts

@@ -13,10 +13,13 @@
 /**
  * compact the given URI using the given prefixes
  */
-export function applyPrefixes(uri: string, prefixes: Map<string, string>) {
+export function applyPrefixes(
+  uri: string,
+  prefixes: Map<string | number, string>,
+) {
   for (const [prefix, uriBase] of prefixes.entries()) {
     if (uri.startsWith(uriBase)) {
-      return uri.replace(uriBase, prefix)
+      return uri.replace(uriBase, String(prefix))
     }
   }
   return uri
@@ -25,10 +28,13 @@ export function applyPrefixes(uri: string, prefixes: Map<string, string>) {
 /**
  * expand the given compacted URI using given prefixes
  */
-export function expandPrefixes(uri: string, prefixes: Map<string, string>) {
+export function expandPrefixes(
+  uri: string,
+  prefixes: Map<string | number, string>,
+) {
   for (const [prefix, uriBase] of prefixes.entries()) {
-    if (uri.startsWith(prefix)) {
-      return uri.replace(prefix, uriBase)
+    if (uri.startsWith(String(prefix))) {
+      return uri.replace(String(prefix), uriBase)
     }
   }
   return uri

package/src/components/DownloadGFF3.tsx

@@ -4,7 +4,6 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-misused-promises */
 import { ApolloAssembly } from '@apollo-annotation/mst'
-import { makeGFF3Feature } from '@apollo-annotation/shared'
 import gff, { GFF3Item } from '@gmod/gff'
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { getConf } from '@jbrowse/core/configuration'
@@ -29,6 +28,7 @@ import {
 import { ApolloSessionModel } from '../session'
 import { createFetchErrorMessage } from '../util'
 import { Dialog } from './Dialog'
+import { annotationFeatureToGFF3 } from '@apollo-annotation/shared'
 
 interface DownloadGFF3Props {
   session: ApolloSessionModel
@@ -153,7 +153,7 @@ export function DownloadGFF3({ handleClose, session }: DownloadGFF3Props) {
         continue
       }
       for (const [, feature] of features) {
-        gff3Items.push(makeGFF3Feature(getSnapshot(feature)))
+        gff3Items.push(annotationFeatureToGFF3(getSnapshot(feature)))
       }
     }
     for (const sequenceFeature of sequenceFeatures) {

package/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),

package/src/session/session.ts

@@ -154,7 +154,14 @@ export function extendSession(
             dynamicBlocks.forEach((block) => {
               if (block.regionNumber !== undefined) {
                 const { assemblyName, end, refName, start } = block
-                locations.push({ assemblyName, refName, start, end })
+                const assembly =
+                  self.apolloDataStore.assemblies.get(assemblyName)
+                if (
+                  assembly &&
+                  assembly.backendDriverType === 'CollaborationServerDriver'
+                ) {
+                  locations.push({ assemblyName, refName, start, end })
+                }
               }
             })
           }
@@ -217,7 +224,14 @@ export function extendSession(
                 dynamicBlocks.forEach((block) => {
                   if (block.regionNumber !== undefined) {
                     const { assemblyName, end, refName, start } = block
-                    locations.push({ assemblyName, refName, start, end })
+                    const assembly =
+                      self.apolloDataStore.assemblies.get(assemblyName)
+                    if (
+                      assembly &&
+                      assembly.backendDriverType === 'CollaborationServerDriver'
+                    ) {
+                      locations.push({ assemblyName, refName, start, end })
+                    }
                   }
                 })
               }
@@ -286,6 +300,7 @@ export function extendSession(
             continue
           }
           applySnapshot(jbrowse, jbrowseConfig)
+          // @ts-expect-error snapshot seems to get wrong type?
           applySnapshot(self, sessionSnapshot)
         }
       }),
@@ -412,7 +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(
@@ -425,6 +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
     },
   })