@apollo-annotation/shared 0.3.6 → 0.3.8

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.js

@@ -50,7 +50,7 @@ class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange_1.FromFile
                 throw new Error(`Assembly "${assemblyName}" already exists`);
             }
             // get checks
-            const checkDocs = await checkModel.find({ default: true }).exec();
+            const checkDocs = await checkModel.find({ isDefault: true }).exec();
             const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString());
             // Add assembly
             const [newAssemblyDoc] = await assemblyModel.create([

package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js.map

@@ -1 +1 @@
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package/dist/Changes/AddAssemblyFromFileChange.js

@@ -71,7 +71,7 @@ class AddAssemblyFromFileChange extends FromFileBaseChange_1.FromFileBaseChange
         if (assemblyDoc) {
             throw new Error(`Assembly "${assemblyName}" already exists`);
         }
-        const checkDocs = await checkModel.find({ default: true }).exec();
+        const checkDocs = await checkModel.find({ isDefault: true }).exec();
         const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString());
         const [newAssemblyDoc] = await assemblyModel.create([
             {

package/dist/Changes/AddAssemblyFromFileChange.js.map

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

@@ -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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+{"version":3,"file":"AddFeatureChange.js","sourceRoot":"","sources":["../../src/Changes/AddFeatureChange.ts"],"names":[],"mappings":";;;AA4MA,gDAIC;AAhND,qEAAqE;AACrE,qDAAqD;AACrD,gEAAgE;AAChE,sDAOkC;AAGlC,+DAA2D;AA0B3D,MAAa,gBAAiB,SAAQ,sBAAa;IACjD,QAAQ,GAAG,kBAA2B,CAAA;IACtC,OAAO,CAA2B;IAElC,YAAY,IAAgC,EAAE,OAAuB;QACnE,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;QACpB,IAAI,CAAC,OAAO,GAAG,SAAS,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IAC1D,CAAC;IACD,2EAA2E;IAC3E,IAAI,YAAY;QACd,OAAO,4BAA4B,CAAA;IACrC,CAAC;IAED,MAAM;QACJ,MAAM,EAAE,QAAQ,EAAE,UAAU,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QACxD,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACzB,MAAM,CAAC,EAAE,YAAY,EAAE,MAAM,EAAE,WAAW,EAAE,eAAe,EAAE,CAAC,GAAG,OAAO,CAAA;YACxE,OAAO;gBACL,QAAQ;gBACR,UAAU;gBACV,QAAQ;gBACR,YAAY;gBACZ,eAAe;gBACf,WAAW;gBACX,MAAM;aACP,CAAA;QACH,CAAC;QACD,OAAO,EAAE,QAAQ,EAAE,UAAU,EAAE,QAAQ,EAAE,OAAO,EAAE,CAAA;IACpD,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,eAAe,CAAC,OAAwB;QAC5C,MAAM,EAAE,aAAa,EAAE,YAAY,EAAE,WAAW,EAAE,OAAO,EAAE,IAAI,EAAE,GAAG,OAAO,CAAA;QAC3E,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QAE1C,MAAM,WAAW,GAAG,MAAM,aAAa;aACpC,QAAQ,CAAC,QAAQ,CAAC;aAClB,OAAO,CAAC,OAAO,CAAC;aAChB,IAAI,EAAE,CAAA;QACT,IAAI,CAAC,WAAW,EAAE,CAAC;YACjB,MAAM,MAAM,GAAG,gCAAgC,QAAQ,aAAa,CAAA;YACpE,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;YACpB,MAAM,IAAI,KAAK,CAAC,MAAM,CAAC,CAAA;QACzB,CAAC;QAED,IAAI,UAAU,GAAG,CAAC,CAAA;QAClB,MAAM,CAAC,KAAK,EAAE,CAAC,YAAY,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;QAErD,mBAAmB;QACnB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,CAAC,KAAK,EAAE,CAAC,WAAW,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,EAAE,CAAC,CAAA;YACnD,MAAM,EAAE,YAAY,EAAE,MAAM,EAAE,WAAW,EAAE,eAAe,EAAE,GAAG,MAAM,CAAA;YACrE,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,GAAG,YAAY,CAAA;YACpC,MAAM,SAAS,GAAG,MAAM,WAAW;iBAChC,QAAQ,CAAC,MAAM,CAAC;iBAChB,OAAO,CAAC,OAAO,CAAC;iBAChB,IAAI,EAAE,CAAA;YACT,IAAI,CAAC,SAAS,EAAE,CAAC;gBACf,MAAM,IAAI,KAAK,CACb,qCAAqC,QAAQ,iBAAiB,MAAM,aAAa,CAClF,CAAA;YACH,CAAC;YAED,6CAA6C;YAC7C,IAAI,WAAW,EAAE,CAAC;gBAChB,iBAAiB;gBACjB,MAAM,CAAC,aAAa,CAAC,GAAG,MAAM,YAAY,CAAC,MAAM,CAC/C,CAAC,EAAE,GAAG,YAAY,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAC,EAAE,IAAI,EAAE,CAAC,EAC/C,EAAE,OAAO,EAAE,CACZ,CAAA;gBACD,MAAM,CAAC,KAAK,EAAE,CACZ,0BAA0B,aAAa,CAAC,GAAG,kBAAkB,QAAQ,GAAG,CACzE,CAAA;gBACD,UAAU,EAAE,CAAA;YACd,CAAC;iBAAM,CAAC;gBACN,2BAA2B;gBAC3B,IAAI,eAAe,EAAE,CAAC;oBACpB,MAAM,eAAe,GAAG,MAAM,YAAY;yBACvC,OAAO,CAAC,EAAE,MAAM,EAAE,eAAe,EAAE,CAAC;yBACpC,OAAO,CAAC,OAAO,CAAC;yBAChB,IAAI,EAAE,CAAA;oBACT,IAAI,CAAC,eAAe,EAAE,CAAC;wBACrB,MAAM,IAAI,KAAK,CACb,mCAAmC,eAAe,GAAG,CACtD,CAAA;oBACH,CAAC;oBACD,MAAM,aAAa,GAAG,IAAI,CAAC,gBAAgB,CACzC,eAAe,EACf,eAAe,CAChB,CAAA;oBACD,IAAI,CAAC,aAAa,EAAE,CAAC;wBACnB,MAAM,IAAI,KAAK,CACb,mCAAmC,eAAe,iBAAiB,eAAe,CAAC,GAAG,GAAG,CAC1F,CAAA;oBACH,CAAC;oBACD,IAAI,CAAC,QAAQ,CAAC,aAAa,EAAE,YAAY,CAAC,CAAA;oBAC1C,MAAM,QAAQ,GAAG,IAAI,CAAC,kBAAkB,CAAC,YAAY,CAAC,CAAA;oBACtD,eAAe,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,EAAE,GAAG,QAAQ,CAAC,CAAA;oBAC7C,MAAM,eAAe,CAAC,IAAI,EAAE,CAAA;gBAC9B,CAAC;qBAAM,CAAC;oBACN,MAAM,QAAQ,GAAG,IAAI,CAAC,kBAAkB,CAAC,YAAY,CAAC,CAAA;oBACtD,MAAM,QAAQ,GAAG,CAAC,GAAG,EAAE,GAAG,QAAQ,CAAC,CAAA;oBACnC,MAAM,CAAC,aAAa,CAAC,GAAG,MAAM,YAAY,CAAC,MAAM,CAC/C,CAAC,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAC,EAAE,GAAG,YAAY,EAAE,CAAC,EAClD,EAAE,OAAO,EAAE,CACZ,CAAA;oBACD,MAAM,CAAC,OAAO,EAAE,CAAC,gBAAgB,aAAa,CAAC,GAAG,GAAG,CAAC,CAAA;gBACxD,CAAC;YACH,CAAC;YACD,UAAU,EAAE,CAAA;QACd,CAAC;QACD,MAAM,CAAC,KAAK,EAAE,CAAC,SAAS,UAAU,gCAAgC,CAAC,CAAA;IACrE,CAAC;IAED,KAAK,CAAC,kBAAkB,CAAC,QAA4B;QACnD,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAA;IACvD,CAAC;IAED,KAAK,CAAC,eAAe,CAAC,SAA0B;QAC9C,IAAI,CAAC,SAAS,EAAE,CAAC;YACf,MAAM,IAAI,KAAK,CAAC,eAAe,CAAC,CAAA;QAClC,CAAC;QACD,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,GAAG,IAAI,CAAA;QAClC,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,EAAE,YAAY,EAAE,eAAe,EAAE,GAAG,MAAM,CAAA;YAChD,IAAI,eAAe,EAAE,CAAC;gBACpB,MAAM,aAAa,GAAG,SAAS,CAAC,UAAU,CAAC,eAAe,CAAC,CAAA;gBAC3D,IAAI,CAAC,aAAa,EAAE,CAAC;oBACnB,MAAM,IAAI,KAAK,CAAC,kCAAkC,eAAe,GAAG,CAAC,CAAA;gBACvE,CAAC;gBACD,8DAA8D;gBAC9D,IAAI,CAAC,aAAa,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;oBACzC,aAAa,CAAC,YAAY,CAAC,KAAK,EAAE,CAAC,aAAa,CAAC,GAAG,CAAC,CAAC,CAAA;gBACxD,CAAC;gBACD,aAAa,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAA;YACtC,CAAC;iBAAM,CAAC;gBACN,SAAS,CAAC,UAAU,CAAC,QAAQ,EAAE,YAAY,CAAC,CAAA;YAC9C,CAAC;QACH,CAAC;IACH,CAAC;IAED,UAAU;QACR,MAAM,EAAE,QAAQ,EAAE,UAAU,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QACtD,MAAM,iBAAiB,GAAG,CAAC,GAAG,UAAU,CAAC,CAAC,OAAO,EAAE,CAAA;QACnD,MAAM,cAAc,GAAG,CAAC,GAAG,OAAO,CAAC,CAAC,OAAO,EAAE,CAAC,GAAG,CAAC,CAAC,gBAAgB,EAAE,EAAE,CAAC,CAAC;YACvE,cAAc,EAAE,gBAAgB,CAAC,YAAY;YAC7C,eAAe,EAAE,gBAAgB,CAAC,eAAe;SAClD,CAAC,CAAC,CAAA;QAEH,OAAO,IAAI,yCAAmB,CAC5B;YACE,UAAU,EAAE,iBAAiB;YAC7B,QAAQ,EAAE,qBAAqB;YAC/B,OAAO,EAAE,cAAc;YACvB,QAAQ;SACT,EACD,EAAE,MAAM,EAAE,CACX,CAAA;IACH,CAAC;CACF;AAnKD,4CAmKC;AAED,SAAgB,kBAAkB,CAChC,MAAe;IAEf,OAAQ,MAA2B,CAAC,QAAQ,KAAK,kBAAkB,CAAA;AACrE,CAAC"}

package/dist/Changes/AddRefSeqAliasesChange.js

@@ -17,18 +17,16 @@ class AddRefSeqAliasesChange extends common_1.AssemblySpecificChange {
             throw new Error(`assembly ${this.assembly} not found`);
         }
         const sessionAliases = assembly.refNameAliases;
-        const sessionLCAliases = assembly.lowerCaseRefNameAliases;
-        if (!sessionAliases || !sessionLCAliases) {
+        if (!sessionAliases) {
             throw new Error('Session refNameAliases not found in assembly');
         }
         for (const refSeqAlias of this.refSeqAliases) {
             const { aliases, refName } = refSeqAlias;
             for (const alias of aliases) {
                 sessionAliases[alias] = refName;
-                sessionLCAliases[alias.toLowerCase()] = refName;
             }
         }
-        assembly.setRefNameAliases(sessionAliases, sessionLCAliases);
+        assembly.setRefNameAliases(sessionAliases);
         return Promise.resolve();
     }
     getInverse() {

package/dist/Changes/AddRefSeqAliasesChange.js.map

@@ -1 +1 @@
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+{"version":3,"file":"AddRefSeqAliasesChange.js","sourceRoot":"","sources":["../../src/Changes/AddRefSeqAliasesChange.ts"],"names":[],"mappings":";;;AAAA,sDAQkC;AAClC,6CAA+C;AAa/C,MAAa,sBAAuB,SAAQ,+BAAsB;IAChE,QAAQ,GAAG,wBAAiC,CAAA;IAC5C,aAAa,CAA2B;IAExC,YAAY,IAAmC,EAAE,OAAuB;QACtE,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;QACpB,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,aAAa,CAAA;IACzC,CAAC;IAED,eAAe,CAAC,eAAgC;QAC9C,MAAM,EAAE,eAAe,EAAE,GAAG,IAAA,iBAAU,EAAC,eAAe,CAAC,CAAA;QACvD,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;QACnD,IAAI,CAAC,QAAQ,EAAE,CAAC;YACd,MAAM,IAAI,KAAK,CAAC,YAAY,IAAI,CAAC,QAAQ,YAAY,CAAC,CAAA;QACxD,CAAC;QACD,MAAM,cAAc,GAAG,QAAQ,CAAC,cAAc,CAAA;QAE9C,IAAI,CAAC,cAAc,EAAE,CAAC;YACpB,MAAM,IAAI,KAAK,CAAC,8CAA8C,CAAC,CAAA;QACjE,CAAC;QAED,KAAK,MAAM,WAAW,IAAI,IAAI,CAAC,aAAa,EAAE,CAAC;YAC7C,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,WAAW,CAAA;YACxC,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE,CAAC;gBAC5B,cAAc,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;YACjC,CAAC;QACH,CAAC;QACD,QAAQ,CAAC,iBAAiB,CAAC,cAAc,CAAC,CAAA;QAC1C,OAAO,OAAO,CAAC,OAAO,EAAE,CAAA;IAC1B,CAAC;IAED,UAAU;QACR,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAA;IAC5C,CAAC;IAED,MAAM;QACJ,MAAM,EAAE,QAAQ,EAAE,aAAa,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QAClD,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,aAAa,EAAE,CAAA;IAC9C,CAAC;IAED,KAAK,CAAC,eAAe,CAAC,OAAwB;QAC5C,MAAM,EAAE,WAAW,EAAE,OAAO,EAAE,GAAG,OAAO,CAAA;QACxC,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;QAEhD,KAAK,MAAM,WAAW,IAAI,aAAa,EAAE,CAAC;YACxC,MAAM,CAAC,KAAK,EAAE,CACZ,wCAAwC,QAAQ,kBAAkB,IAAI,CAAC,SAAS,CAAC,WAAW,CAAC,EAAE,CAChG,CAAA;YACD,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,WAAW,CAAA;YACxC,MAAM,WAAW;iBACd,SAAS,CAAC,EAAE,QAAQ,EAAE,IAAI,EAAE,OAAO,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,OAAO,EAAE,EAAE,CAAC;iBAC7D,OAAO,CAAC,OAAO,CAAC,CAAA;QACrB,CAAC;IACH,CAAC;IAED,kBAAkB,CAAC,QAA4B;QAC7C,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAA;IAC5C,CAAC;IAED,2EAA2E;IAC3E,IAAI,YAAY;QACd,OAAO,iCAAiC,CAAA;IAC1C,CAAC;CACF;AA/DD,wDA+DC"}

package/dist/Changes/DeleteFeatureChange.d.ts

@@ -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

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package/dist/Changes/FeatureAttributeChange.d.ts

@@ -4,7 +4,8 @@ interface SerializedFeatureAttributeChangeBase extends SerializedFeatureChange {
 }
 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/ImportJBrowseConfigChange.d.ts

@@ -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.tracks = tracks.filter((t) => t.type !== 'ApolloTrack');
     }
     return filteredConfig;
 }

package/dist/Changes/ImportJBrowseConfigChange.js.map

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