@apollo-annotation/shared 0.3.5 → 0.3.7

package/dist/Changes/AddAssemblyAliasesChange.d.ts

@@ -0,0 +1,16 @@
+import { AssemblySpecificChange, type Change, type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
+export interface SerializedAssemblyAliasesChange extends SerializedAssemblySpecificChange {
+    typeName: 'AddAssemblyAliasesChange';
+    aliases: string[];
+}
+export declare class AddAssemblyAliasesChange extends AssemblySpecificChange {
+    typeName: "AddAssemblyAliasesChange";
+    aliases: string[];
+    constructor(json: SerializedAssemblyAliasesChange, options?: ChangeOptions);
+    executeOnClient(clientDataStore: ClientDataStore): Promise<void>;
+    getInverse(): Change;
+    toJSON(): SerializedAssemblyAliasesChange;
+    executeOnServer(backend: ServerDataStore): Promise<void>;
+    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<unknown>;
+    get notification(): string;
+}

package/dist/Changes/AddAssemblyAliasesChange.js

@@ -0,0 +1,50 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.AddAssemblyAliasesChange = void 0;
+const common_1 = require("@apollo-annotation/common");
+const util_1 = require("@jbrowse/core/util");
+class AddAssemblyAliasesChange extends common_1.AssemblySpecificChange {
+    typeName = 'AddAssemblyAliasesChange';
+    aliases;
+    constructor(json, options) {
+        super(json, options);
+        this.aliases = json.aliases;
+    }
+    executeOnClient(clientDataStore) {
+        const { assemblyManager } = (0, util_1.getSession)(clientDataStore);
+        const assembly = assemblyManager.get(this.assembly);
+        if (!assembly) {
+            throw new Error(`assembly ${this.assembly} not found`);
+        }
+        // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+        assembly.configuration.aliases.set(this.aliases);
+        return Promise.resolve();
+    }
+    getInverse() {
+        throw new Error('Method not implemented.');
+    }
+    toJSON() {
+        const { assembly, aliases, typeName } = this;
+        return { assembly, typeName, aliases };
+    }
+    async executeOnServer(backend) {
+        const { assemblyModel } = backend;
+        const { assembly, logger, aliases } = this;
+        logger.debug?.(`Updating assembly aliases for assembly: ${assembly}, aliases: ${JSON.stringify(aliases)}`);
+        const asm = await assemblyModel.findById(assembly);
+        if (!asm) {
+            throw new Error(`Assembly with ID ${assembly} not found`);
+        }
+        asm.aliases = aliases;
+        await asm.save();
+    }
+    executeOnLocalGFF3(_backend) {
+        throw new Error('Method not implemented.');
+    }
+    // eslint-disable-next-line @typescript-eslint/class-literal-property-style
+    get notification() {
+        return 'Assembly aliases have been added.';
+    }
+}
+exports.AddAssemblyAliasesChange = AddAssemblyAliasesChange;
+//# sourceMappingURL=AddAssemblyAliasesChange.js.map

package/dist/Changes/AddAssemblyAliasesChange.js.map

@@ -0,0 +1 @@
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package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.d.ts

@@ -1,4 +1,4 @@
-import { ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
+import { type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
 import { FromFileBaseChange } from './FromFileBaseChange';
 export interface SerializedAddAssemblyAndFeaturesFromFileChangeBase extends SerializedAssemblySpecificChange {
     typeName: 'AddAssemblyAndFeaturesFromFileChange';

package/dist/Changes/AddAssemblyFromExternalChange.d.ts

@@ -1,4 +1,4 @@
-import { AssemblySpecificChange, ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
+import { AssemblySpecificChange, type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
 export interface SerializedAddAssemblyFromExternalChangeBase extends SerializedAssemblySpecificChange {
     typeName: 'AddAssemblyFromExternalChange';
 }

package/dist/Changes/AddAssemblyFromFileChange.d.ts

@@ -1,4 +1,4 @@
-import { ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
+import { type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
 import { FromFileBaseChange } from './FromFileBaseChange';
 export interface SerializedAddAssemblyFromFileChangeBase extends SerializedAssemblySpecificChange {
     typeName: 'AddAssemblyFromFileChange';

package/dist/Changes/AddFeatureChange.d.ts

@@ -1,5 +1,5 @@
-import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
-import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
 import { DeleteFeatureChange } from './DeleteFeatureChange';
 interface SerializedAddFeatureChangeBase extends SerializedFeatureChange {
     typeName: 'AddFeatureChange';
@@ -20,6 +20,7 @@ export declare class AddFeatureChange extends FeatureChange {
     typeName: "AddFeatureChange";
     changes: AddFeatureChangeDetails[];
     constructor(json: SerializedAddFeatureChange, options?: ChangeOptions);
+    get notification(): string;
     toJSON(): SerializedAddFeatureChange;
     /**
      * Applies the required change to database

package/dist/Changes/AddFeatureChange.js

@@ -3,7 +3,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.AddFeatureChange = void 0;
 exports.isAddFeatureChange = isAddFeatureChange;
 /* eslint-disable @typescript-eslint/restrict-template-expressions */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/require-await */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 const common_1 = require("@apollo-annotation/common");
@@ -15,6 +14,10 @@ class AddFeatureChange extends common_1.FeatureChange {
         super(json, options);
         this.changes = 'changes' in json ? json.changes : [json];
     }
+    // eslint-disable-next-line @typescript-eslint/class-literal-property-style
+    get notification() {
+        return 'Feature added successfully';
+    }
     toJSON() {
         const { assembly, changedIds, changes, typeName } = this;
         if (changes.length === 1) {
@@ -83,30 +86,7 @@ class AddFeatureChange extends common_1.FeatureChange {
                     if (!parentFeature) {
                         throw new Error(`Could not find feature with ID "${parentFeatureId}" in feature "${topLevelFeature._id}"`);
                     }
-                    if (!parentFeature.children) {
-                        parentFeature.children = new Map();
-                    }
-                    if (!parentFeature.attributes?._id) {
-                        let { attributes } = parentFeature;
-                        if (!attributes) {
-                            attributes = {};
-                        }
-                        attributes = {
-                            _id: [parentFeature._id.toString()],
-                            // eslint-disable-next-line unicorn/prefer-structured-clone
-                            ...JSON.parse(JSON.stringify(attributes)),
-                        };
-                        parentFeature.attributes = attributes;
-                    }
-                    parentFeature.children.set(_id, {
-                        allIds: [],
-                        ...addedFeature,
-                        // eslint-disable-next-line @typescript-eslint/ban-ts-comment
-                        // @ts-expect-error
-                        _id,
-                    });
-                    // Child features should be sorted for click and drag of gene glyphs to work properly
-                    parentFeature.children = new Map([...parentFeature.children.entries()].sort((a, b) => a[1].min - b[1].min));
+                    this.addChild(parentFeature, addedFeature);
                     const childIds = this.getChildFeatureIds(addedFeature);
                     topLevelFeature.allIds.push(_id, ...childIds);
                     await topLevelFeature.save();

package/dist/Changes/AddFeatureChange.js.map

@@ -1 +1 @@
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package/dist/Changes/AddFeaturesFromFileChange.d.ts

@@ -1,4 +1,4 @@
-import { ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
+import { type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
 import { FromFileBaseChange } from './FromFileBaseChange';
 export interface SerializedAddFeaturesFromFileChangeBase extends SerializedAssemblySpecificChange {
     typeName: 'AddFeaturesFromFileChange';

package/dist/Changes/AddRefSeqAliasesChange.d.ts

@@ -1,4 +1,4 @@
-import { AssemblySpecificChange, Change, ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
+import { AssemblySpecificChange, type Change, type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
 export interface SerializedRefSeqAliases {
     refName: string;
     aliases: string[];

package/dist/Changes/DeleteAssemblyChange.d.ts

@@ -1,4 +1,4 @@
-import { AssemblySpecificChange, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
+import { AssemblySpecificChange, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
 export interface SerializedDeleteAssemblyChange extends SerializedAssemblySpecificChange {
     typeName: 'DeleteAssemblyChange';
 }

package/dist/Changes/DeleteFeatureChange.d.ts

@@ -1,6 +1,6 @@
-import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
-import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
-import { Feature } from '@apollo-annotation/schemas';
+import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+import { type Feature } from '@apollo-annotation/schemas';
 import { AddFeatureChange } from './AddFeatureChange';
 interface SerializedDeleteFeatureChangeBase extends SerializedFeatureChange {
     typeName: 'DeleteFeatureChange';
@@ -19,6 +19,7 @@ export declare class DeleteFeatureChange extends FeatureChange {
     typeName: "DeleteFeatureChange";
     changes: DeleteFeatureChangeDetails[];
     constructor(json: SerializedDeleteFeatureChange, options?: ChangeOptions);
+    get notification(): string;
     toJSON(): SerializedDeleteFeatureChange;
     /**
      * Applies the required change to database
@@ -26,17 +27,17 @@ export declare class DeleteFeatureChange extends FeatureChange {
      * @returns
      */
     executeOnServer(backend: ServerDataStore): Promise<void>;
-    /**
-     * Delete feature's subfeatures that match an ID and return the IDs of any
-     * sub-subfeatures that were deleted
-     * @param feature -
-     * @param featureIdToDelete -
-     * @returns - list of deleted feature IDs
-     */
-    findAndDeleteChildFeature(feature: Feature, featureIdToDelete: string): string[];
     executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
     executeOnClient(dataStore: ClientDataStore): Promise<void>;
     getInverse(): AddFeatureChange;
 }
+/**
+ * Delete feature's subfeatures that match an ID and return the IDs of any
+ * sub-subfeatures that were deleted
+ * @param feature -
+ * @param featureIdToDelete -
+ * @returns - list of deleted feature IDs
+ */
+export declare function findAndDeleteChildFeature(feature: Feature, featureIdToDelete: string, change: FeatureChange): string[];
 export declare function isDeleteFeatureChange(change: unknown): change is DeleteFeatureChange;
 export {};

package/dist/Changes/DeleteFeatureChange.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.DeleteFeatureChange = void 0;
+exports.findAndDeleteChildFeature = findAndDeleteChildFeature;
 exports.isDeleteFeatureChange = isDeleteFeatureChange;
 /* eslint-disable @typescript-eslint/restrict-template-expressions */
 /* eslint-disable @typescript-eslint/require-await */
@@ -14,6 +15,10 @@ class DeleteFeatureChange extends common_1.FeatureChange {
         super(json, options);
         this.changes = 'changes' in json ? json.changes : [json];
     }
+    // eslint-disable-next-line @typescript-eslint/class-literal-property-style
+    get notification() {
+        return 'Feature deleted successfully';
+    }
     toJSON() {
         const { assembly, changedIds, changes, typeName } = this;
         if (changes.length === 1) {
@@ -52,7 +57,7 @@ class DeleteFeatureChange extends common_1.FeatureChange {
                 logger.debug?.(`Feature "${deletedFeature._id}" deleted from document "${featureDoc._id}". Whole document deleted.`);
                 continue;
             }
-            const deletedIds = this.findAndDeleteChildFeature(featureDoc, deletedFeature._id);
+            const deletedIds = findAndDeleteChildFeature(featureDoc, deletedFeature._id, this);
             deletedIds.push(deletedFeature._id);
             featureDoc.allIds = featureDoc.allIds.filter((id) => !deletedIds.includes(id));
             // Save updated document in Mongo
@@ -67,34 +72,6 @@ class DeleteFeatureChange extends common_1.FeatureChange {
             logger.debug?.(`Feature "${deletedFeature._id}" deleted from document "${featureDoc._id}"`);
         }
     }
-    /**
-     * Delete feature's subfeatures that match an ID and return the IDs of any
-     * sub-subfeatures that were deleted
-     * @param feature -
-     * @param featureIdToDelete -
-     * @returns - list of deleted feature IDs
-     */
-    findAndDeleteChildFeature(feature, featureIdToDelete) {
-        if (!feature.children) {
-            throw new Error(`Feature ${feature._id} has no children`);
-        }
-        const { _id, children } = feature;
-        const child = children.get(featureIdToDelete);
-        if (child) {
-            const deletedIds = this.getChildFeatureIds(child);
-            children.delete(featureIdToDelete);
-            return deletedIds;
-        }
-        for (const [, childFeature] of children) {
-            try {
-                return this.findAndDeleteChildFeature(childFeature, featureIdToDelete);
-            }
-            catch {
-                // pass
-            }
-        }
-        throw new Error(`Feature "${featureIdToDelete}" not found in ${_id}`);
-    }
     async executeOnLocalGFF3(_backend) {
         throw new Error('executeOnLocalGFF3 not implemented');
     }
@@ -123,9 +100,9 @@ class DeleteFeatureChange extends common_1.FeatureChange {
         const inverseChangedIds = [...changedIds].reverse();
         const inverseChanges = [...changes]
             .reverse()
-            .map((deleteFeatuerChange) => ({
-            addedFeature: deleteFeatuerChange.deletedFeature,
-            parentFeatureId: deleteFeatuerChange.parentFeatureId,
+            .map((deleteFeatureChange) => ({
+            addedFeature: deleteFeatureChange.deletedFeature,
+            parentFeatureId: deleteFeatureChange.parentFeatureId,
         }));
         logger.debug?.(`INVERSE CHANGE '${JSON.stringify(inverseChanges)}'`);
         return new AddFeatureChange_1.AddFeatureChange({
@@ -137,6 +114,34 @@ class DeleteFeatureChange extends common_1.FeatureChange {
     }
 }
 exports.DeleteFeatureChange = DeleteFeatureChange;
+/**
+ * Delete feature's subfeatures that match an ID and return the IDs of any
+ * sub-subfeatures that were deleted
+ * @param feature -
+ * @param featureIdToDelete -
+ * @returns - list of deleted feature IDs
+ */
+function findAndDeleteChildFeature(feature, featureIdToDelete, change) {
+    if (!feature.children) {
+        throw new Error(`Feature ${feature._id} has no children`);
+    }
+    const { _id, children } = feature;
+    const child = children.get(featureIdToDelete);
+    if (child) {
+        const deletedIds = change.getChildFeatureIds(child);
+        children.delete(featureIdToDelete);
+        return deletedIds;
+    }
+    for (const [, childFeature] of children) {
+        try {
+            return findAndDeleteChildFeature(childFeature, featureIdToDelete, change);
+        }
+        catch {
+            // pass
+        }
+    }
+    throw new Error(`Feature "${featureIdToDelete}" not found in ${_id}`);
+}
 function isDeleteFeatureChange(change) {
     return change.typeName === 'DeleteFeatureChange';
 }

package/dist/Changes/DeleteFeatureChange.js.map

@@ -1 +1 @@
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package/dist/Changes/DeleteUserChange.d.ts

@@ -1,4 +1,4 @@
-import { Change, ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedChange, ServerDataStore } from '@apollo-annotation/common';
+import { Change, type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedChange, type ServerDataStore } from '@apollo-annotation/common';
 export interface SerializedDeleteUserChangeBase extends SerializedChange {
     typeName: 'DeleteUserChange';
     userId: string;

package/dist/Changes/FeatureAttributeChange.d.ts

@@ -1,10 +1,11 @@
-import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
+import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
 interface SerializedFeatureAttributeChangeBase extends SerializedFeatureChange {
     typeName: 'FeatureAttributeChange';
 }
 export interface FeatureAttributeChangeDetails {
     featureId: string;
-    attributes: Record<string, string[]>;
+    oldAttributes: Record<string, string[]>;
+    newAttributes: Record<string, string[]>;
 }
 interface SerializedFeatureAttributeChangeSingle extends SerializedFeatureAttributeChangeBase, FeatureAttributeChangeDetails {
 }

package/dist/Changes/FeatureAttributeChange.js

@@ -16,8 +16,15 @@ class FeatureAttributeChange extends common_1.FeatureChange {
     toJSON() {
         const { assembly, changedIds, changes, typeName } = this;
         if (changes.length === 1) {
-            const [{ attributes, featureId }] = changes;
-            return { typeName, changedIds, assembly, featureId, attributes };
+            const [{ oldAttributes, newAttributes, featureId }] = changes;
+            return {
+                typeName,
+                changedIds,
+                assembly,
+                featureId,
+                oldAttributes,
+                newAttributes,
+            };
         }
         return { typeName, changedIds, assembly, changes };
     }
@@ -56,9 +63,9 @@ class FeatureAttributeChange extends common_1.FeatureChange {
         }
         // Let's update objects
         for (const [idx, change] of changes.entries()) {
-            const { attributes } = change;
+            const { newAttributes } = change;
             const { feature, topLevelFeature } = featuresForChanges[idx];
-            feature.attributes = attributes;
+            feature.attributes = newAttributes;
             if (topLevelFeature._id.equals(feature._id)) {
                 topLevelFeature.markModified('attributes'); // Mark as modified. Without this save() -method is not updating data in database
             }
@@ -87,7 +94,7 @@ class FeatureAttributeChange extends common_1.FeatureChange {
             if (!feature) {
                 throw new Error(`Could not find feature with identifier "${changedId}"`);
             }
-            feature.setAttributes(new Map(Object.entries(this.changes[idx].attributes)));
+            feature.setAttributes(new Map(Object.entries(this.changes[idx].newAttributes)));
         }
     }
     getInverse() {
@@ -95,7 +102,8 @@ class FeatureAttributeChange extends common_1.FeatureChange {
         const inverseChangedIds = [...changedIds].reverse();
         const inverseChanges = [...changes].reverse().map((oneChange) => ({
             featureId: oneChange.featureId,
-            attributes: oneChange.attributes,
+            oldAttributes: oneChange.newAttributes,
+            newAttributes: oneChange.oldAttributes,
         }));
         return new FeatureAttributeChange({
             changedIds: inverseChangedIds,

package/dist/Changes/FeatureAttributeChange.js.map

@@ -1 +1 @@
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package/dist/Changes/FromFileBaseChange.d.ts

@@ -1,6 +1,6 @@
-import { AssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
-import { FileDocument } from '@apollo-annotation/schemas';
-import { GFF3Feature } from '@gmod/gff';
+import { AssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
+import { type FileDocument } from '@apollo-annotation/schemas';
+import { type GFF3Feature } from '@gmod/gff';
 export declare abstract class FromFileBaseChange extends AssemblySpecificChange {
     addRefSeqIntoDb(fileDoc: FileDocument, assembly: string, backend: ServerDataStore): Promise<void>;
     private refSeqCache;

package/dist/Changes/FromFileBaseChange.js.map

@@ -1 +1 @@
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package/dist/Changes/ImportJBrowseConfigChange.d.ts

@@ -1,4 +1,4 @@
-import { Change, ChangeOptions, ClientDataStore, LocalGFF3DataStore, ServerDataStore } from '@apollo-annotation/common';
+import { Change, type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type ServerDataStore } from '@apollo-annotation/common';
 interface JBrowseAssembly {
     sequence: {
         adapter: {
@@ -18,6 +18,9 @@ interface JBrowseInternetAccount {
 }
 export interface JBrowseConfig {
     assemblies?: JBrowseAssembly[];
+    configuration?: {
+        ApolloPlugin?: Record<string, unknown>;
+    };
     tracks?: JBrowseTrack[];
     plugins?: JBrowsePlugin[];
     internetAccounts?: JBrowseInternetAccount[];

package/dist/Changes/ImportJBrowseConfigChange.js

@@ -5,23 +5,27 @@ exports.filterJBrowseConfig = filterJBrowseConfig;
 /* eslint-disable @typescript-eslint/require-await */
 const common_1 = require("@apollo-annotation/common");
 function filterJBrowseConfig(config) {
-    const { __v, _id, assemblies, internetAccounts, plugins, tracks, ...rest } = config;
-    const filteredAssemblies = assemblies?.filter((a) => a.sequence.adapter.type !== 'ApolloSequenceAdapter');
-    const filteredTracks = tracks?.filter((t) => t.type !== 'ApolloTrack');
-    const filteredPlugins = plugins?.filter((p) => p.name !== 'Apollo');
-    const filteredInternetAccounts = internetAccounts?.filter((i) => i.type !== 'ApolloInternetAccount');
+    const { __v, _id, assemblies, configuration, internetAccounts, plugins, tracks, ...rest } = config;
+    // Need to make sure that configuration.ApolloPlugin.hasRole isn't set
     const filteredConfig = rest;
-    if (filteredAssemblies) {
-        filteredConfig.assemblies = filteredAssemblies;
+    if (assemblies) {
+        filteredConfig.assemblies = assemblies.filter((a) => a.sequence.adapter.type !== 'ApolloSequenceAdapter');
     }
-    if (filteredTracks) {
-        filteredConfig.tracks = filteredTracks;
+    if (configuration?.ApolloPlugin?.hasRole) {
+        const { hasRole, ...apolloPluginRest } = configuration.ApolloPlugin;
+        filteredConfig.configuration = {
+            ...configuration,
+            ApolloPlugin: apolloPluginRest,
+        };
     }
-    if (filteredPlugins) {
-        filteredConfig.plugins = filteredPlugins;
+    if (internetAccounts) {
+        filteredConfig.internetAccounts = internetAccounts.filter((i) => i.type !== 'ApolloInternetAccount');
     }
-    if (filteredInternetAccounts) {
-        filteredConfig.internetAccounts = filteredInternetAccounts;
+    if (plugins) {
+        filteredConfig.plugins = plugins.filter((p) => p.name !== 'Apollo');
+    }
+    if (tracks) {
+        filteredConfig.trackss = tracks.filter((t) => t.type !== 'ApolloTrack');
     }
     return filteredConfig;
 }

package/dist/Changes/ImportJBrowseConfigChange.js.map

@@ -1 +1 @@
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package/dist/Changes/LocationEndChange.d.ts

@@ -1,4 +1,4 @@
-import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
+import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
 interface SerializedLocationEndChangeBase extends SerializedFeatureChange {
     typeName: 'LocationEndChange';
 }