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

package/dist/index.esm.js

@@ -1,5 +1,5 @@
 import { checkRegistry, changeRegistry, Change, isAssemblySpecificChange } from '@apollo-annotation/common';
-import { gff3ToAnnotationFeature, AddAssemblyFromExternalChange, AddAssemblyAndFeaturesFromFileChange, AddAssemblyFromFileChange, AddFeatureChange, DeleteAssemblyChange, DeleteFeatureChange, makeGFF3Feature, AddFeaturesFromFileChange, UserChange, DeleteUserChange, FeatureAttributeChange, AddRefSeqAliasesChange, getDecodedToken, makeUserSessionId, LocationEndChange, LocationStartChange, TypeChange, StrandChange, splitStringIntoChunks, validationRegistry, ValidationResultSet, filterJBrowseConfig, ImportJBrowseConfigChange, changes, CDSCheck, CoreValidation, ParentChildValidation } from '@apollo-annotation/shared';
+import { gff3ToAnnotationFeature, AddAssemblyFromExternalChange, AddAssemblyAndFeaturesFromFileChange, AddAssemblyFromFileChange, AddFeatureChange, DeleteAssemblyChange, DeleteFeatureChange, annotationFeatureToGFF3, AddFeaturesFromFileChange, UserChange, DeleteUserChange, FeatureAttributeChange, AddRefSeqAliasesChange, getDecodedToken, makeUserSessionId, LocationEndChange, LocationStartChange, TypeChange, StrandChange, splitStringIntoChunks, validationRegistry, ValidationResultSet, filterJBrowseConfig, ImportJBrowseConfigChange, changes, CDSCheck, CoreValidation, ParentChildValidation } from '@apollo-annotation/shared';
 import { ConfigurationSchema, readConfObject, getConf, ConfigurationReference } from '@jbrowse/core/configuration';
 import { BaseInternetAccountConfig, InternetAccount, RendererType, TextSearchAdapterType, BaseDisplay, WidgetType, createBaseTrackConfig, TrackType, createBaseTrackModel, InternetAccountType, DisplayType } from '@jbrowse/core/pluggableElementTypes';
 import Plugin from '@jbrowse/core/Plugin';
@@ -50,7 +50,7 @@ import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
 import ErrorIcon from '@mui/icons-material/Error';
 import SaveIcon from '@mui/icons-material/Save';
 
-var version = "0.2.0";
+var version = "0.2.2";
 
 const ApolloConfigSchema = ConfigurationSchema('ApolloInternetAccount', {
     baseURL: {
@@ -576,7 +576,7 @@ const stopwords = genericEnglishStopwords;
 function applyPrefixes(uri, prefixes) {
     for (const [prefix, uriBase] of prefixes.entries()) {
         if (uri.startsWith(uriBase)) {
-            return uri.replace(uriBase, prefix);
+            return uri.replace(uriBase, String(prefix));
         }
     }
     return uri;
@@ -586,8 +586,8 @@ function applyPrefixes(uri, prefixes) {
  */
 function expandPrefixes(uri, prefixes) {
     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;
@@ -2006,7 +2006,7 @@ function DownloadGFF3({ handleClose, session }) {
                 continue;
             }
             for (const [, feature] of features) {
-                gff3Items.push(makeGFF3Feature(getSnapshot(feature)));
+                gff3Items.push(annotationFeatureToGFF3(getSnapshot(feature)));
             }
         }
         for (const sequenceFeature of sequenceFeatures) {
@@ -9022,6 +9022,15 @@ class InMemoryFileDriver extends BackendDriver {
         });
     }
     async submitChange(_change, _opts = {}) {
+        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();
     }
     async searchFeatures(_term, _assemblies) {
@@ -9135,7 +9144,7 @@ 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) {
@@ -9231,6 +9240,9 @@ function clientDataStoreFactory(AnnotationFeatureExtended) {
         deleteCheckResult(checkResultId) {
             self.checkResults.delete(checkResultId);
         },
+        clearCheckResults() {
+            self.checkResults.clear();
+        },
     }))
         .volatile((self) => ({
         changeManager: new ChangeManager(self),
@@ -9458,7 +9470,11 @@ function extendSession(pluginManager, sessionModel) {
                     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 });
+                            }
                         }
                     });
                 }
@@ -9514,7 +9530,11 @@ function extendSession(pluginManager, sessionModel) {
                         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 });
+                                }
                             }
                         });
                     }
@@ -9577,6 +9597,7 @@ function extendSession(pluginManager, sessionModel) {
                     continue;
                 }
                 applySnapshot(jbrowse, jbrowseConfig);
+                // @ts-expect-error snapshot seems to get wrong type?
                 applySnapshot(self, sessionSnapshot);
             }
         }),
@@ -9688,7 +9709,7 @@ function extendSession(pluginManager, sessionModel) {
         };
     });
     return types.snapshotProcessor(sm, {
-        postProcessor(snap) {
+        postProcessor(snap, node) {
             snap.apolloSelectedFeature = undefined;
             const assemblies = Object.fromEntries(Object.entries(snap.apolloDataStore.assemblies).filter(([, assembly]) => assembly.backendDriverType === 'InMemoryFileDriver'));
             // @ts-expect-error ontologyManager isn't actually required
@@ -9697,6 +9718,21 @@ function extendSession(pluginManager, sessionModel) {
                 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;
         },
     });