@apollo-annotation/shared 0.3.13 → 1.0.0

package/dist/Changes/{DeleteFeatureChange.d.ts → AddAndDeleteFeatureChanges.d.ts}

@@ -1,7 +1,21 @@
-import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
+import { type ChangeOptions, FeatureChange, type SerializedFeatureChange } from '@apollo-annotation/common';
 import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
 import type { Feature } from '@apollo-annotation/schemas';
-import { AddFeatureChange } from './AddFeatureChange.js';
+interface SerializedAddFeatureChangeBase extends SerializedFeatureChange {
+    typeName: 'AddFeatureChange';
+}
+export interface AddFeatureChangeDetails {
+    addedFeature: AnnotationFeatureSnapshot;
+    parentFeatureId?: string;
+    copyFeature?: boolean;
+    allIds?: string[];
+}
+interface SerializedAddFeatureChangeSingle extends SerializedAddFeatureChangeBase, AddFeatureChangeDetails {
+}
+interface SerializedAddFeatureChangeMultiple extends SerializedAddFeatureChangeBase {
+    changes: AddFeatureChangeDetails[];
+}
+export type SerializedAddFeatureChange = SerializedAddFeatureChangeSingle | SerializedAddFeatureChangeMultiple;
 interface SerializedDeleteFeatureChangeBase extends SerializedFeatureChange {
     typeName: 'DeleteFeatureChange';
 }
@@ -15,20 +29,21 @@ interface SerializedDeleteFeatureChangeMultiple extends SerializedDeleteFeatureC
     changes: DeleteFeatureChangeDetails[];
 }
 export type SerializedDeleteFeatureChange = SerializedDeleteFeatureChangeSingle | SerializedDeleteFeatureChangeMultiple;
+export declare class AddFeatureChange extends FeatureChange {
+    typeName: "AddFeatureChange";
+    changes: AddFeatureChangeDetails[];
+    constructor(json: SerializedAddFeatureChange, options?: ChangeOptions);
+    get notification(): string;
+    toJSON(): SerializedAddFeatureChange;
+    getInverse(): DeleteFeatureChange;
+}
+export declare function isAddFeatureChange(change: unknown): change is AddFeatureChange;
 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
-     * @param backend - parameters from backend
-     * @returns
-     */
-    executeOnServer(backend: ServerDataStore): Promise<void>;
-    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
-    executeOnClient(dataStore: ClientDataStore): Promise<void>;
     getInverse(): AddFeatureChange;
 }
 /**
@@ -41,4 +56,4 @@ export declare class DeleteFeatureChange extends FeatureChange {
 export declare function findAndDeleteChildFeature(feature: Feature, featureIdToDelete: string, change: FeatureChange): string[];
 export declare function isDeleteFeatureChange(change: unknown): change is DeleteFeatureChange;
 export {};
-//# sourceMappingURL=DeleteFeatureChange.d.ts.map
+//# sourceMappingURL=AddAndDeleteFeatureChanges.d.ts.map

package/dist/Changes/AddAndDeleteFeatureChanges.d.ts.map

@@ -0,0 +1 @@
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package/dist/Changes/AddAndDeleteFeatureChanges.js

@@ -0,0 +1,117 @@
+/* eslint-disable @typescript-eslint/restrict-template-expressions */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+import { FeatureChange, } from '@apollo-annotation/common';
+export class AddFeatureChange extends FeatureChange {
+    typeName = 'AddFeatureChange';
+    changes;
+    constructor(json, options) {
+        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) {
+            const [{ addedFeature, allIds, copyFeature, parentFeatureId }] = changes;
+            return {
+                typeName,
+                changedIds,
+                assembly,
+                addedFeature,
+                parentFeatureId,
+                copyFeature,
+                allIds,
+            };
+        }
+        return { typeName, changedIds, assembly, changes };
+    }
+    getInverse() {
+        const { assembly, changedIds, changes, logger } = this;
+        const inverseChangedIds = [...changedIds].reverse();
+        const inverseChanges = [...changes].reverse().map((addFeatureChange) => ({
+            deletedFeature: addFeatureChange.addedFeature,
+            parentFeatureId: addFeatureChange.parentFeatureId,
+        }));
+        return new DeleteFeatureChange({
+            changedIds: inverseChangedIds,
+            typeName: 'DeleteFeatureChange',
+            changes: inverseChanges,
+            assembly,
+        }, { logger });
+    }
+}
+export function isAddFeatureChange(change) {
+    return change.typeName === 'AddFeatureChange';
+}
+export class DeleteFeatureChange extends FeatureChange {
+    typeName = 'DeleteFeatureChange';
+    changes;
+    constructor(json, options) {
+        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) {
+            const [{ deletedFeature, parentFeatureId }] = changes;
+            return { typeName, changedIds, assembly, deletedFeature, parentFeatureId };
+        }
+        return { typeName, changedIds, assembly, changes };
+    }
+    getInverse() {
+        const { assembly, changedIds, changes, logger } = this;
+        const inverseChangedIds = [...changedIds].reverse();
+        const inverseChanges = [...changes]
+            .reverse()
+            .map((deleteFeatureChange) => ({
+            addedFeature: deleteFeatureChange.deletedFeature,
+            parentFeatureId: deleteFeatureChange.parentFeatureId,
+        }));
+        logger.debug?.(`INVERSE CHANGE '${JSON.stringify(inverseChanges)}'`);
+        return new AddFeatureChange({
+            changedIds: inverseChangedIds,
+            typeName: 'AddFeatureChange',
+            changes: inverseChanges,
+            assembly,
+        }, { logger });
+    }
+}
+/**
+ * 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 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}`);
+}
+export function isDeleteFeatureChange(change) {
+    return change.typeName === 'DeleteFeatureChange';
+}
+//# sourceMappingURL=AddAndDeleteFeatureChanges.js.map

package/dist/Changes/AddAndDeleteFeatureChanges.js.map

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

@@ -1,4 +1,4 @@
-import { AssemblySpecificChange, type Change, type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
+import { AssemblySpecificChange, type Change, type ChangeOptions, type SerializedAssemblySpecificChange } from '@apollo-annotation/common';
 export interface SerializedAssemblyAliasesChange extends SerializedAssemblySpecificChange {
     typeName: 'AddAssemblyAliasesChange';
     aliases: string[];
@@ -7,11 +7,8 @@ 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;
 }
 //# sourceMappingURL=AddAssemblyAliasesChange.d.ts.map

package/dist/Changes/AddAssemblyAliasesChange.d.ts.map

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

@@ -1,8 +1,4 @@
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-/* eslint-disable @typescript-eslint/no-unsafe-call */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import { AssemblySpecificChange, } from '@apollo-annotation/common';
-import { getSession } from '@jbrowse/core/util';
 export class AddAssemblyAliasesChange extends AssemblySpecificChange {
     typeName = 'AddAssemblyAliasesChange';
     aliases;
@@ -10,15 +6,6 @@ export class AddAssemblyAliasesChange extends AssemblySpecificChange {
         super(json, options);
         this.aliases = json.aliases;
     }
-    executeOnClient(clientDataStore) {
-        const { assemblyManager } = getSession(clientDataStore);
-        const assembly = assemblyManager.get(this.assembly);
-        if (!assembly) {
-            throw new Error(`assembly ${this.assembly} not found`);
-        }
-        assembly.configuration.aliases.set(this.aliases);
-        return Promise.resolve();
-    }
     getInverse() {
         throw new Error('Method not implemented.');
     }
@@ -26,20 +13,6 @@ export class AddAssemblyAliasesChange extends AssemblySpecificChange {
         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.';

package/dist/Changes/AddAssemblyAliasesChange.js.map

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

@@ -1,5 +1,4 @@
-import type { ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
-import { FromFileBaseChange } from './FromFileBaseChange.js';
+import { AssemblySpecificChange, type ChangeOptions, type SerializedAssemblySpecificChange } from '@apollo-annotation/common';
 export interface SerializedAddAssemblyAndFeaturesFromFileChangeBase extends SerializedAssemblySpecificChange {
     typeName: 'AddAssemblyAndFeaturesFromFileChange';
 }
@@ -19,20 +18,12 @@ export interface SerializedAddAssemblyAndFeaturesFromFileChangeMultiple extends
     changes: AddAssemblyAndFeaturesFromFileChangeDetails[];
 }
 export type SerializedAddAssemblyAndFeaturesFromFileChange = SerializedAddAssemblyAndFeaturesFromFileChangeSingle | SerializedAddAssemblyAndFeaturesFromFileChangeMultiple;
-export declare class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange {
+export declare class AddAssemblyAndFeaturesFromFileChange extends AssemblySpecificChange {
     typeName: "AddAssemblyAndFeaturesFromFileChange";
     changes: AddAssemblyAndFeaturesFromFileChangeDetails[];
     constructor(json: SerializedAddAssemblyAndFeaturesFromFileChange, options?: ChangeOptions);
     get notification(): string;
     toJSON(): SerializedAddAssemblyAndFeaturesFromFileChange;
-    /**
-     * Applies the required change to database
-     * @param backend - parameters from backend
-     * @returns
-     */
-    executeOnServer(backend: ServerDataStore): Promise<void>;
-    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
-    executeOnClient(_dataStore: ClientDataStore): Promise<void>;
     getInverse(): AddAssemblyAndFeaturesFromFileChange;
 }
 //# sourceMappingURL=AddAssemblyAndFeaturesFromFileChange.d.ts.map

package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"AddAssemblyAndFeaturesFromFileChange.d.ts","sourceRoot":"","sources":["../../src/Changes/AddAssemblyAndFeaturesFromFileChange.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,EACtB,KAAK,aAAa,EAClB,KAAK,gCAAgC,EACtC,MAAM,2BAA2B,CAAA;AAElC,MAAM,WAAW,kDACf,SAAQ,gCAAgC;IACxC,QAAQ,EAAE,sCAAsC,CAAA;CACjD;AAED,MAAM,WAAW,2CAA2C;IAC1D,YAAY,EAAE,MAAM,CAAA;IACpB,OAAO,EAAE;QAAE,EAAE,EAAE,MAAM,CAAA;KAAE,CAAA;IACvB,YAAY,CAAC,EAAE;QAAE,UAAU,CAAC,EAAE,MAAM,CAAC;QAAC,MAAM,CAAC,EAAE,OAAO,CAAA;KAAE,CAAA;CACzD;AAED,MAAM,WAAW,oDACf,SAAQ,kDAAkD,EACxD,2CAA2C;CAAG;AAElD,MAAM,WAAW,sDACf,SAAQ,kDAAkD;IAC1D,OAAO,EAAE,2CAA2C,EAAE,CAAA;CACvD;AAED,MAAM,MAAM,8CAA8C,GACtD,oDAAoD,GACpD,sDAAsD,CAAA;AAE1D,qBAAa,oCAAqC,SAAQ,sBAAsB;IAC9E,QAAQ,yCAAkD;IAC1D,OAAO,EAAE,2CAA2C,EAAE,CAAA;gBAGpD,IAAI,EAAE,8CAA8C,EACpD,OAAO,CAAC,EAAE,aAAa;IAMzB,IAAI,YAAY,IAAI,MAAM,CAEzB;IAED,MAAM,IAAI,8CAA8C;IASxD,UAAU;CAOX"}

package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js

@@ -1,10 +1,5 @@
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-/* eslint-disable @typescript-eslint/no-unsafe-argument */
-/* eslint-disable @typescript-eslint/no-unsafe-call */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
-/* eslint-disable @typescript-eslint/require-await */
-import { FromFileBaseChange } from './FromFileBaseChange.js';
-export class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange {
+import { AssemblySpecificChange, } from '@apollo-annotation/common';
+export class AddAssemblyAndFeaturesFromFileChange extends AssemblySpecificChange {
     typeName = 'AddAssemblyAndFeaturesFromFileChange';
     changes;
     constructor(json, options) {
@@ -22,81 +17,6 @@ export class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange {
         }
         return { typeName, assembly, changes };
     }
-    /**
-     * Applies the required change to database
-     * @param backend - parameters from backend
-     * @returns
-     */
-    async executeOnServer(backend) {
-        const { assemblyModel, checkModel, fileModel, filesService, user } = backend;
-        const { assembly, changes, logger } = this;
-        for (const change of changes) {
-            const { assemblyName, fileIds, parseOptions } = change;
-            const fileId = fileIds.fa;
-            const { FILE_UPLOAD_FOLDER } = process.env;
-            if (!FILE_UPLOAD_FOLDER) {
-                throw new Error('No FILE_UPLOAD_FOLDER found in .env file');
-            }
-            // Get file checksum
-            const fileDoc = await fileModel.findById(fileId).exec();
-            if (!fileDoc) {
-                throw new Error(`File "${fileId}" not found in Mongo`);
-            }
-            logger.debug?.(`FileId "${fileId}", checksum "${fileDoc.checksum}"`);
-            // Check and add new assembly
-            const assemblyDoc = await assemblyModel
-                .findOne({ name: assemblyName })
-                .exec();
-            if (assemblyDoc) {
-                throw new Error(`Assembly "${assemblyName}" already exists`);
-            }
-            // get checks
-            const checkDocs = await checkModel.find({ isDefault: true }).exec();
-            const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString());
-            // Add assembly
-            const [newAssemblyDoc] = await assemblyModel.create([
-                { _id: assembly, name: assemblyName, user, status: -1, fileId, checks },
-            ]);
-            logger.debug?.(`Added new assembly "${assemblyName}", docId "${newAssemblyDoc._id.toHexString()}"`);
-            logger.debug?.(`File type: "${fileDoc.type}"`);
-            // Add refSeqs
-            // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
-            await this.addRefSeqIntoDb(fileDoc, newAssemblyDoc._id.toString(), backend);
-            const { bufferSize = 10_000, strict = true } = parseOptions ?? {};
-            const featureStream = filesService.parseGFF3(filesService.getFileStream(fileDoc), { bufferSize });
-            let featureCount = 0;
-            let errorCount = 0;
-            for await (const gff3Feature of featureStream) {
-                // Add new feature into database
-                try {
-                    await this.addFeatureIntoDb(gff3Feature, backend);
-                }
-                catch (error) {
-                    // if the first feature is an error, assume the file isn't valid and throw
-                    if (strict || featureCount === 0) {
-                        throw error;
-                    }
-                    if (errorCount <= 99) {
-                        logger.warn('Error parsing feature');
-                        logger.warn(error);
-                        if (errorCount === 99) {
-                            logger.warn('Reached 100 parsing errors, omitting further warnings from log');
-                        }
-                    }
-                    errorCount++;
-                }
-                featureCount++;
-                if (featureCount % 1000 === 0) {
-                    logger.debug?.(`Processed ${featureCount} features`);
-                }
-            }
-        }
-    }
-    async executeOnLocalGFF3(_backend) {
-        throw new Error('executeOnLocalGFF3 not implemented');
-    }
-    // eslint-disable-next-line @typescript-eslint/no-empty-function
-    async executeOnClient(_dataStore) { }
     getInverse() {
         const { assembly, changes, logger, typeName } = this;
         return new AddAssemblyAndFeaturesFromFileChange({ typeName, changes, assembly }, { logger });

package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js.map

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package/dist/Changes/AddAssemblyFromExternalChange.d.ts

@@ -1,4 +1,4 @@
-import { AssemblySpecificChange, type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
+import { AssemblySpecificChange, type ChangeOptions, type SerializedAssemblySpecificChange } from '@apollo-annotation/common';
 export interface SerializedAddAssemblyFromExternalChangeBase extends SerializedAssemblySpecificChange {
     typeName: 'AddAssemblyFromExternalChange';
 }
@@ -22,14 +22,6 @@ export declare class AddAssemblyFromExternalChange extends AssemblySpecificChang
     constructor(json: SerializedAddAssemblyFromExternalChange, options?: ChangeOptions);
     get notification(): string;
     toJSON(): SerializedAddAssemblyFromExternalChange;
-    /**
-     * Applies the required change to database
-     * @param backend - parameters from backend
-     * @returns
-     */
-    executeOnServer(backend: ServerDataStore): Promise<void>;
-    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
-    executeOnClient(_dataStore: ClientDataStore): Promise<void>;
     getInverse(): AddAssemblyFromExternalChange;
 }
 //# sourceMappingURL=AddAssemblyFromExternalChange.d.ts.map

package/dist/Changes/AddAssemblyFromExternalChange.d.ts.map

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

@@ -1,10 +1,4 @@
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
-/* eslint-disable @typescript-eslint/require-await */
 import { AssemblySpecificChange, } from '@apollo-annotation/common';
-import { BgzipIndexedFasta, IndexedFasta } from '@gmod/indexedfasta';
-import { RemoteFile } from 'generic-filehandle2';
 export class AddAssemblyFromExternalChange extends AssemblySpecificChange {
     typeName = 'AddAssemblyFromExternalChange';
     changes;
@@ -23,72 +17,6 @@ export class AddAssemblyFromExternalChange extends AssemblySpecificChange {
         }
         return { typeName, assembly, changes };
     }
-    /**
-     * Applies the required change to database
-     * @param backend - parameters from backend
-     * @returns
-     */
-    async executeOnServer(backend) {
-        const { assemblyModel, checkModel, refSeqModel, user } = backend;
-        const { assembly, changes, logger } = this;
-        const { CHUNK_SIZE } = process.env;
-        const customChunkSize = CHUNK_SIZE && Number(CHUNK_SIZE);
-        for (const change of changes) {
-            const { assemblyName, externalLocation } = change;
-            const { fa, fai, gzi } = externalLocation;
-            const sequenceAdapter = gzi
-                ? new BgzipIndexedFasta({
-                    fasta: new RemoteFile(fa, { fetch }),
-                    fai: new RemoteFile(fai, { fetch }),
-                    gzi: new RemoteFile(gzi, { fetch }),
-                })
-                : new IndexedFasta({
-                    fasta: new RemoteFile(fa, { fetch }),
-                    fai: new RemoteFile(fai, { fetch }),
-                });
-            const allSequenceSizes = await sequenceAdapter.getSequenceSizes();
-            if (!allSequenceSizes) {
-                throw new Error('No data read from indexed fasta getSequenceSizes');
-            }
-            const assemblyDoc = await assemblyModel
-                .findOne({ name: assemblyName })
-                .exec();
-            if (assemblyDoc) {
-                throw new Error(`Assembly "${assemblyName}" already exists`);
-            }
-            const checkDocs = await checkModel.find({ default: true }).exec();
-            const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString());
-            const [newAssemblyDoc] = await assemblyModel.create([
-                {
-                    _id: assembly,
-                    name: assemblyName,
-                    user,
-                    status: -1,
-                    externalLocation,
-                    checks,
-                },
-            ]);
-            logger.debug?.(`Added new assembly "${assemblyName}", docId "${newAssemblyDoc._id}"`);
-            for (const sequenceName in allSequenceSizes) {
-                const [newRefSeqDoc] = await refSeqModel.create([
-                    {
-                        name: sequenceName,
-                        assembly: newAssemblyDoc._id,
-                        length: allSequenceSizes[sequenceName],
-                        ...(customChunkSize ? { chunkSize: customChunkSize } : null),
-                        user,
-                        status: -1,
-                    },
-                ]);
-                logger.debug?.(`Added new refSeq "${sequenceName}", docId "${newRefSeqDoc._id}"`);
-            }
-        }
-    }
-    async executeOnLocalGFF3(_backend) {
-        throw new Error('executeOnLocalGFF3 not implemented');
-    }
-    // eslint-disable-next-line @typescript-eslint/no-empty-function
-    async executeOnClient(_dataStore) { }
     getInverse() {
         const { assembly, changes, logger, typeName } = this;
         return new AddAssemblyFromExternalChange({ typeName, changes, assembly }, { logger });

package/dist/Changes/AddAssemblyFromExternalChange.js.map

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package/dist/Changes/AddAssemblyFromFileChange.d.ts

@@ -1,5 +1,4 @@
-import type { ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
-import { FromFileBaseChange } from './FromFileBaseChange.js';
+import { AssemblySpecificChange, type ChangeOptions, type SerializedAssemblySpecificChange } from '@apollo-annotation/common';
 export interface SerializedAddAssemblyFromFileChangeBase extends SerializedAssemblySpecificChange {
     typeName: 'AddAssemblyFromFileChange';
 }
@@ -19,26 +18,12 @@ export interface SerializedAddAssemblyFromFileChangeMultiple extends SerializedA
     changes: AddAssemblyFromFileChangeDetails[];
 }
 export type SerializedAddAssemblyFromFileChange = SerializedAddAssemblyFromFileChangeSingle | SerializedAddAssemblyFromFileChangeMultiple;
-export declare class AddAssemblyFromFileChange extends FromFileBaseChange {
+export declare class AddAssemblyFromFileChange extends AssemblySpecificChange {
     typeName: "AddAssemblyFromFileChange";
     changes: AddAssemblyFromFileChangeDetails[];
     constructor(json: SerializedAddAssemblyFromFileChange, options?: ChangeOptions);
     get notification(): string;
     toJSON(): SerializedAddAssemblyFromFileChange;
-    /**
-     * Applies the required change to database
-     * @param backend - parameters from backend
-     * @returns
-     */
-    executeOnServer(backend: ServerDataStore): Promise<void>;
-    executeOnServerIndexed(backend: ServerDataStore, assemblyName: string, fileIds: {
-        fa: string;
-        fai: string;
-        gzi: string;
-    }): Promise<void>;
-    executeOnServerFasta(backend: ServerDataStore, assemblyName: string, fileId: string): Promise<void>;
-    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
-    executeOnClient(_dataStore: ClientDataStore): Promise<void>;
     getInverse(): AddAssemblyFromFileChange;
 }
 //# sourceMappingURL=AddAssemblyFromFileChange.d.ts.map

package/dist/Changes/AddAssemblyFromFileChange.d.ts.map

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