@apollo-annotation/shared 0.1.19 → 0.1.21

package/dist/Changes/DeleteFeatureChange.js

@@ -0,0 +1,143 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.DeleteFeatureChange = void 0;
+exports.isDeleteFeatureChange = isDeleteFeatureChange;
+/* eslint-disable @typescript-eslint/restrict-template-expressions */
+/* eslint-disable @typescript-eslint/require-await */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+const common_1 = require("@apollo-annotation/common");
+const AddFeatureChange_1 = require("./AddFeatureChange");
+class DeleteFeatureChange extends common_1.FeatureChange {
+    typeName = 'DeleteFeatureChange';
+    changes;
+    constructor(json, options) {
+        super(json, options);
+        this.changes = 'changes' in json ? json.changes : [json];
+    }
+    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 };
+    }
+    /**
+     * Applies the required change to database
+     * @param backend - parameters from backend
+     * @returns
+     */
+    async executeOnServer(backend) {
+        const { featureModel, session } = backend;
+        const { changes, logger } = this;
+        // Loop the changes
+        for (const change of changes) {
+            const { deletedFeature, parentFeatureId } = change;
+            // Search feature
+            const featureDoc = await featureModel
+                .findOne({ allIds: deletedFeature._id })
+                .session(session)
+                .exec();
+            if (!featureDoc) {
+                const errMsg = `*** ERROR: The following featureId was not found in database ='${deletedFeature._id}'`;
+                logger.error(errMsg);
+                throw new Error(errMsg);
+            }
+            // Check if feature is on top level, then simply delete the whole document (i.e. not just sub-feature inside document)
+            if (featureDoc._id.equals(deletedFeature._id)) {
+                if (parentFeatureId) {
+                    throw new Error(`Feature "${deletedFeature._id}" is top-level, but received a parent feature ID`);
+                }
+                await featureModel.findByIdAndDelete(featureDoc._id);
+                logger.debug?.(`Feature "${deletedFeature._id}" deleted from document "${featureDoc._id}". Whole document deleted.`);
+                continue;
+            }
+            const deletedIds = this.findAndDeleteChildFeature(featureDoc, deletedFeature._id);
+            deletedIds.push(deletedFeature._id);
+            featureDoc.allIds = featureDoc.allIds.filter((id) => !deletedIds.includes(id));
+            // Save updated document in Mongo
+            featureDoc.markModified('children'); // Mark as modified. Without this save() -method is not updating data in database
+            try {
+                await featureDoc.save();
+            }
+            catch (error) {
+                logger.debug?.(`*** FAILED: ${error}`);
+                throw error;
+            }
+            logger.debug?.(`Feature "${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 ${_id}`);
+    }
+    async executeOnLocalGFF3(_backend) {
+        throw new Error('executeOnLocalGFF3 not implemented');
+    }
+    async executeOnClient(dataStore) {
+        if (!dataStore) {
+            throw new Error('No data store');
+        }
+        for (const change of this.changes) {
+            const { deletedFeature, parentFeatureId } = change;
+            if (parentFeatureId) {
+                const parentFeature = dataStore.getFeature(parentFeatureId);
+                if (!parentFeature) {
+                    throw new Error(`Could not find parent feature "${parentFeatureId}"`);
+                }
+                parentFeature.deleteChild(deletedFeature._id);
+            }
+            else {
+                if (dataStore.getFeature(deletedFeature._id)) {
+                    dataStore.deleteFeature(deletedFeature._id);
+                }
+            }
+        }
+    }
+    getInverse() {
+        const { assembly, changedIds, changes, logger } = this;
+        const inverseChangedIds = [...changedIds].reverse();
+        const inverseChanges = [...changes]
+            .reverse()
+            .map((deleteFeatuerChange) => ({
+            addedFeature: deleteFeatuerChange.deletedFeature,
+            parentFeatureId: deleteFeatuerChange.parentFeatureId,
+        }));
+        logger.debug?.(`INVERSE CHANGE '${JSON.stringify(inverseChanges)}'`);
+        return new AddFeatureChange_1.AddFeatureChange({
+            changedIds: inverseChangedIds,
+            typeName: 'AddFeatureChange',
+            changes: inverseChanges,
+            assembly,
+        }, { logger });
+    }
+}
+exports.DeleteFeatureChange = DeleteFeatureChange;
+function isDeleteFeatureChange(change) {
+    return change.typeName === 'DeleteFeatureChange';
+}
+//# sourceMappingURL=DeleteFeatureChange.js.map

package/dist/Changes/DeleteFeatureChange.js.map

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

@@ -0,0 +1,25 @@
+import { Change, ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedChange, ServerDataStore } from '@apollo-annotation/common';
+export interface SerializedDeleteUserChangeBase extends SerializedChange {
+    typeName: 'DeleteUserChange';
+    userId: string;
+}
+export interface DeleteUserChangeDetails {
+}
+interface SerializedDeleteUserChangeSingle extends SerializedDeleteUserChangeBase, DeleteUserChangeDetails {
+}
+interface SerializedDeleteUserChangeMultiple extends SerializedDeleteUserChangeBase {
+    changes: DeleteUserChangeDetails[];
+}
+export type SerializedDeleteUserChange = SerializedDeleteUserChangeSingle | SerializedDeleteUserChangeMultiple;
+export declare class DeleteUserChange extends Change {
+    typeName: "DeleteUserChange";
+    changes: DeleteUserChangeDetails[];
+    userId: string;
+    constructor(json: SerializedDeleteUserChange, options?: ChangeOptions);
+    toJSON(): SerializedDeleteUserChange;
+    executeOnServer(backend: ServerDataStore): Promise<void>;
+    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
+    executeOnClient(_dataStore: ClientDataStore): Promise<void>;
+    getInverse(): DeleteUserChange;
+}
+export {};

package/dist/Changes/DeleteUserChange.js

@@ -0,0 +1,53 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.DeleteUserChange = void 0;
+/* eslint-disable @typescript-eslint/require-await */
+const common_1 = require("@apollo-annotation/common");
+class DeleteUserChange extends common_1.Change {
+    typeName = 'DeleteUserChange';
+    changes;
+    userId;
+    constructor(json, options) {
+        super(json, options);
+        this.changes = 'changes' in json ? json.changes : [json];
+        this.userId = json.userId;
+    }
+    toJSON() {
+        const { typeName, userId } = this;
+        return { typeName, userId };
+    }
+    async executeOnServer(backend) {
+        const { session, userModel } = backend;
+        const { logger, userId } = this;
+        const user = await userModel
+            .findOneAndDelete({ _id: userId })
+            .session(session)
+            .exec();
+        if (!user) {
+            const errMsg = `*** ERROR: User with id "${userId}" not found`;
+            logger.error(errMsg);
+            throw new Error(errMsg);
+        }
+    }
+    async executeOnLocalGFF3(_backend) {
+        throw new Error('executeOnLocalGFF3 not implemented');
+    }
+    // eslint-disable-next-line @typescript-eslint/no-empty-function
+    async executeOnClient(_dataStore) { }
+    getInverse() {
+        const { logger, typeName, userId } = this;
+        return new DeleteUserChange({ typeName, userId }, { logger });
+        //   const inverseChangedIds = this.changedIds.slice().reverse()
+        //   const inverseChanges = this.changes
+        //     .slice()
+        //     .reverse()
+        //     .map((deleteUserChange) => ({
+        //       addedUser: deleteUserChange.userId,
+        //     }))
+        //   this.logger.debug?.(`INVERSE CHANGE '${JSON.stringify(inverseChanges)}'`)
+        //   // return new AddUserChange()
+        // }
+    }
+}
+exports.DeleteUserChange = DeleteUserChange;
+//# sourceMappingURL=DeleteUserChange.js.map

package/dist/Changes/DeleteUserChange.js.map

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

@@ -0,0 +1,31 @@
+import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
+interface SerializedFeatureAttributeChangeBase extends SerializedFeatureChange {
+    typeName: 'FeatureAttributeChange';
+}
+export interface FeatureAttributeChangeDetails {
+    featureId: string;
+    attributes: Record<string, string[]>;
+}
+interface SerializedFeatureAttributeChangeSingle extends SerializedFeatureAttributeChangeBase, FeatureAttributeChangeDetails {
+}
+interface SerializedFeatureAttributeChangeMultiple extends SerializedFeatureAttributeChangeBase {
+    changes: FeatureAttributeChangeDetails[];
+}
+export type SerializedFeatureAttributeChange = SerializedFeatureAttributeChangeSingle | SerializedFeatureAttributeChangeMultiple;
+export declare class FeatureAttributeChange extends FeatureChange {
+    typeName: "FeatureAttributeChange";
+    changes: FeatureAttributeChangeDetails[];
+    constructor(json: SerializedFeatureAttributeChange, options?: ChangeOptions);
+    toJSON(): SerializedFeatureAttributeChange;
+    /**
+     * 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(): FeatureAttributeChange;
+}
+export declare function isFeatureAttributeChange(change: unknown): change is FeatureAttributeChange;
+export {};

package/dist/Changes/FeatureAttributeChange.js

@@ -0,0 +1,112 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.FeatureAttributeChange = void 0;
+exports.isFeatureAttributeChange = isFeatureAttributeChange;
+/* eslint-disable @typescript-eslint/restrict-template-expressions */
+/* eslint-disable @typescript-eslint/require-await */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+const common_1 = require("@apollo-annotation/common");
+class FeatureAttributeChange extends common_1.FeatureChange {
+    typeName = 'FeatureAttributeChange';
+    changes;
+    constructor(json, options) {
+        super(json, options);
+        this.changes = 'changes' in json ? json.changes : [json];
+    }
+    toJSON() {
+        const { assembly, changedIds, changes, typeName } = this;
+        if (changes.length === 1) {
+            const [{ attributes, featureId }] = changes;
+            return { typeName, changedIds, assembly, featureId, attributes };
+        }
+        return { typeName, changedIds, assembly, changes };
+    }
+    /**
+     * Applies the required change to database
+     * @param backend - parameters from backend
+     * @returns
+     */
+    async executeOnServer(backend) {
+        const { featureModel, session } = backend;
+        const { changes, logger } = this;
+        const featuresForChanges = [];
+        // Loop the changes and check that all features are found
+        for (const change of changes) {
+            const { featureId } = change;
+            // Search correct feature
+            const topLevelFeature = await featureModel
+                .findOne({ allIds: featureId })
+                .session(session)
+                .exec();
+            if (!topLevelFeature) {
+                const errMsg = `*** ERROR: The following featureId was not found in database ='${featureId}'`;
+                logger.error(errMsg);
+                throw new Error(errMsg);
+                // throw new NotFoundException(errMsg)  -- This is causing runtime error because Exception comes from @nestjs/common!!!
+            }
+            logger.debug?.(`*** Feature found: ${JSON.stringify(topLevelFeature)}`);
+            const foundFeature = this.getFeatureFromId(topLevelFeature, featureId);
+            if (!foundFeature) {
+                const errMsg = 'ERROR when searching feature by featureId';
+                logger.error(errMsg);
+                throw new Error(errMsg);
+            }
+            logger.debug?.(`*** Found feature: ${JSON.stringify(foundFeature)}`);
+            featuresForChanges.push({ feature: foundFeature, topLevelFeature });
+        }
+        // Let's update objects
+        for (const [idx, change] of changes.entries()) {
+            const { attributes } = change;
+            const { feature, topLevelFeature } = featuresForChanges[idx];
+            feature.attributes = attributes;
+            if (topLevelFeature._id.equals(feature._id)) {
+                topLevelFeature.markModified('attributes'); // Mark as modified. Without this save() -method is not updating data in database
+            }
+            else {
+                topLevelFeature.markModified('children'); // Mark as modified. Without this save() -method is not updating data in database
+            }
+            try {
+                await topLevelFeature.save();
+            }
+            catch (error) {
+                logger.debug?.(`*** FAILED: ${error}`);
+                throw error;
+            }
+            logger.debug?.(`*** Feature attributes modified (added, edited or deleted), docId: ${JSON.stringify(topLevelFeature)}`);
+        }
+    }
+    async executeOnLocalGFF3(_backend) {
+        throw new Error('applyToLocalGFF3 not implemented');
+    }
+    async executeOnClient(dataStore) {
+        if (!dataStore) {
+            throw new Error('No data store');
+        }
+        for (const [idx, changedId] of this.changedIds.entries()) {
+            const feature = dataStore.getFeature(changedId);
+            if (!feature) {
+                throw new Error(`Could not find feature with identifier "${changedId}"`);
+            }
+            feature.setAttributes(new Map(Object.entries(this.changes[idx].attributes)));
+        }
+    }
+    getInverse() {
+        const { assembly, changedIds, changes, logger } = this;
+        const inverseChangedIds = [...changedIds].reverse();
+        const inverseChanges = [...changes].reverse().map((oneChange) => ({
+            featureId: oneChange.featureId,
+            attributes: oneChange.attributes,
+        }));
+        return new FeatureAttributeChange({
+            changedIds: inverseChangedIds,
+            typeName: 'FeatureAttributeChange',
+            changes: inverseChanges,
+            assembly,
+        }, { logger });
+    }
+}
+exports.FeatureAttributeChange = FeatureAttributeChange;
+function isFeatureAttributeChange(change) {
+    return (change.typeName === 'FeatureAttributeChange');
+}
+//# sourceMappingURL=FeatureAttributeChange.js.map

package/dist/Changes/FeatureAttributeChange.js.map

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package/dist/Changes/FromFileBaseChange.d.ts

@@ -0,0 +1,9 @@
+import { AssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
+import { FileDocument } from '@apollo-annotation/schemas';
+import { GFF3Feature } from '@gmod/gff';
+export declare abstract class FromFileBaseChange extends AssemblySpecificChange {
+    addRefSeqIntoDb(fileDoc: FileDocument, assembly: string, backend: ServerDataStore): Promise<void>;
+    private refSeqCache;
+    removeExistingFeatures(backend: ServerDataStore): Promise<void>;
+    addFeatureIntoDb(gff3Feature: GFF3Feature, backend: ServerDataStore): Promise<void>;
+}

package/dist/Changes/FromFileBaseChange.js

@@ -0,0 +1,187 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.FromFileBaseChange = void 0;
+/* eslint-disable @typescript-eslint/restrict-plus-operands */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+const common_1 = require("@apollo-annotation/common");
+const GFF3_1 = require("../GFF3");
+class FromFileBaseChange extends common_1.AssemblySpecificChange {
+    async addRefSeqIntoDb(fileDoc, assembly, backend) {
+        const { logger } = this;
+        const { filesService, refSeqChunkModel, refSeqModel, user } = backend;
+        const { CHUNK_SIZE } = process.env;
+        const customChunkSize = CHUNK_SIZE && Number(CHUNK_SIZE);
+        let chunkIndex = 0;
+        let refSeqLen = 0;
+        let refSeqDoc;
+        let fastaInfoStarted = fileDoc.type !== 'text/x-gff3';
+        // Read data from compressed file and parse the content
+        const sequenceStream = filesService.getFileStream(fileDoc);
+        let sequenceBuffer = '';
+        let incompleteLine = '';
+        let lastLineIsIncomplete = true;
+        let parsingStarted = false;
+        logger.debug?.('starting sequence stream');
+        let lineCount = 0;
+        for await (const data of sequenceStream) {
+            const chunk = data.toString();
+            lastLineIsIncomplete = !chunk.endsWith('\n');
+            // chunk is small enough that you can split the whole thing into lines without having to make it into smaller chunks first.
+            const lines = chunk.split(/\r?\n/);
+            if (incompleteLine) {
+                lines[0] = `${incompleteLine}${lines[0]}`;
+                incompleteLine = '';
+            }
+            if (lastLineIsIncomplete) {
+                incompleteLine = lines.pop() || '';
+            }
+            for await (const line of lines) {
+                lineCount++;
+                if (lineCount % 1_000_000 === 0) {
+                    logger.debug?.(`Processed ${lineCount} lines`);
+                }
+                // In case of GFF3 file we start to read sequence after '##FASTA' is found
+                if (!fastaInfoStarted) {
+                    if (line.trim() === '##FASTA') {
+                        fastaInfoStarted = true;
+                    }
+                    continue;
+                }
+                const refSeqInfoLine = /^>\s*(\S+)\s*(.*)/.exec(line);
+                // Add new ref sequence info if we are reference seq info line
+                if (refSeqInfoLine) {
+                    parsingStarted = true;
+                    logger.debug?.(`Reference sequence information line "${refSeqInfoLine[0]}"`);
+                    // If there is sequence from previous reference sequence then we need to add it to previous ref seq
+                    if (sequenceBuffer !== '') {
+                        if (!refSeqDoc) {
+                            throw new Error('No refSeq document found');
+                        }
+                        refSeqLen += sequenceBuffer.length;
+                        // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
+                        await refSeqChunkModel.create([
+                            {
+                                refSeq: refSeqDoc._id,
+                                n: chunkIndex,
+                                sequence: sequenceBuffer,
+                                user,
+                                status: -1,
+                            },
+                        ]);
+                        sequenceBuffer = '';
+                    }
+                    await refSeqDoc?.updateOne({ length: refSeqLen });
+                    // await refSeqDoc?.updateOne({ length: refSeqLen }, { session })
+                    refSeqLen = 0;
+                    chunkIndex = 0;
+                    const name = refSeqInfoLine[1].trim();
+                    const description = refSeqInfoLine[2] ? refSeqInfoLine[2].trim() : '';
+                    // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
+                    const [newRefSeqDoc] = await refSeqModel.create([
+                        {
+                            name,
+                            description,
+                            assembly,
+                            length: 0,
+                            ...(customChunkSize ? { chunkSize: customChunkSize } : null),
+                            user,
+                            status: -1,
+                        },
+                    ]);
+                    logger.debug?.(`Added new refSeq "${name}", desc "${description}", docId "${newRefSeqDoc._id}"`);
+                    refSeqDoc = newRefSeqDoc;
+                }
+                else if (/\S/.test(line)) {
+                    if (!refSeqDoc) {
+                        throw new Error('No refSeq document found');
+                    }
+                    const { _id, chunkSize } = refSeqDoc;
+                    sequenceBuffer += line.replaceAll(/\s/g, '');
+                    // If sequence block > chunk size then save chunk into Mongo
+                    while (sequenceBuffer.length >= chunkSize) {
+                        const sequence = sequenceBuffer.slice(0, chunkSize);
+                        refSeqLen += sequence.length;
+                        // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
+                        await refSeqChunkModel.create([
+                            { refSeq: _id, n: chunkIndex, sequence, user, status: -1 },
+                        ]);
+                        chunkIndex++;
+                        // Set remaining sequence
+                        sequenceBuffer = sequenceBuffer.slice(chunkSize);
+                    }
+                }
+            }
+        }
+        if (!parsingStarted) {
+            throw new Error('No reference sequences found in file');
+        }
+        if (sequenceBuffer || lastLineIsIncomplete) {
+            if (!refSeqDoc) {
+                throw new Error('No refSeq document found');
+            }
+            // If the file did not end with line break so the last line is incomplete
+            if (lastLineIsIncomplete) {
+                sequenceBuffer += incompleteLine;
+            }
+            refSeqLen += sequenceBuffer.length;
+            logger.verbose?.(`*** Add the very last chunk to ref seq ("${refSeqDoc._id}", index ${chunkIndex} and total length for ref seq is ${refSeqLen}): "${sequenceBuffer}"`);
+            logger.debug?.(`Creating refSeq chunk number ${chunkIndex} of "${refSeqDoc._id}"`);
+            // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
+            await refSeqChunkModel.create([
+                {
+                    refSeq: refSeqDoc._id,
+                    n: chunkIndex,
+                    sequence: sequenceBuffer,
+                    user,
+                    status: -1,
+                },
+            ]);
+            await refSeqDoc.updateOne({ length: refSeqLen });
+        }
+    }
+    refSeqCache = new Map();
+    async removeExistingFeatures(backend) {
+        const { featureModel, refSeqModel } = backend;
+        const { assembly, logger } = this;
+        logger.debug?.(`Removing existing features for assembly = ${assembly}`);
+        const refSeqs = await refSeqModel
+            .find({ assembly })
+            .exec();
+        for (const refSeq of refSeqs) {
+            await featureModel.deleteMany({ refSeq: refSeq._id });
+        }
+    }
+    async addFeatureIntoDb(gff3Feature, backend) {
+        const { featureModel, refSeqModel, user } = backend;
+        const { assembly, refSeqCache } = this;
+        const [{ seq_id: refName }] = gff3Feature;
+        if (!refName) {
+            throw new Error(`Valid seq_id not found in feature ${JSON.stringify(gff3Feature)}`);
+        }
+        let refSeqDoc = refSeqCache.get(refName);
+        if (!refSeqDoc) {
+            refSeqDoc =
+                (await refSeqModel.findOne({ assembly, name: refName }).exec()) ??
+                    undefined;
+            if (refSeqDoc) {
+                refSeqCache.set(refName, refSeqDoc);
+            }
+        }
+        if (!refSeqDoc) {
+            throw new Error(`RefSeq was not found by assembly "${assembly}" and seq_id "${refName}" not found`);
+        }
+        // Let's add featureId to parent feature
+        const featureIds = [];
+        const newFeature = (0, GFF3_1.gff3ToAnnotationFeature)(gff3Feature, refSeqDoc._id, featureIds);
+        // Add into Mongo
+        // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
+        await featureModel.create([
+            { allIds: featureIds, ...newFeature, user, status: -1 },
+        ]);
+    }
+}
+exports.FromFileBaseChange = FromFileBaseChange;
+//# sourceMappingURL=FromFileBaseChange.js.map

package/dist/Changes/FromFileBaseChange.js.map

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

@@ -0,0 +1,43 @@
+import { Change, ChangeOptions, ClientDataStore, LocalGFF3DataStore, ServerDataStore } from '@apollo-annotation/common';
+interface JBrowseAssembly {
+    sequence: {
+        adapter: {
+            type: string;
+        };
+    };
+}
+interface JBrowseTrack {
+    type: string;
+    trackId: string;
+}
+interface JBrowsePlugin {
+    name: string;
+}
+interface JBrowseInternetAccount {
+    type: string;
+}
+export interface JBrowseConfig {
+    assemblies?: JBrowseAssembly[];
+    tracks?: JBrowseTrack[];
+    plugins?: JBrowsePlugin[];
+    internetAccounts?: JBrowseInternetAccount[];
+    [key: string]: unknown;
+}
+export interface SerializedImportJBrowseConfigChange {
+    typeName: 'ImportJBrowseConfigChange';
+    oldJBrowseConfig?: JBrowseConfig;
+    newJBrowseConfig?: JBrowseConfig;
+}
+export declare function filterJBrowseConfig(config: JBrowseConfig): JBrowseConfig;
+export declare class ImportJBrowseConfigChange extends Change {
+    typeName: "ImportJBrowseConfigChange";
+    oldJBrowseConfig?: JBrowseConfig;
+    newJBrowseConfig?: JBrowseConfig;
+    constructor(json: SerializedImportJBrowseConfigChange, options?: ChangeOptions);
+    toJSON(): SerializedImportJBrowseConfigChange;
+    executeOnServer(backend: ServerDataStore): Promise<void>;
+    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
+    executeOnClient(_dataStore: ClientDataStore): Promise<void>;
+    getInverse(): ImportJBrowseConfigChange;
+}
+export {};