@apollo-annotation/shared 0.1.18 → 0.1.20

package/dist/Changes/AddFeatureChange.js

@@ -0,0 +1,169 @@
+"use strict";
+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");
+const DeleteFeatureChange_1 = require("./DeleteFeatureChange");
+class AddFeatureChange extends common_1.FeatureChange {
+    typeName = 'AddFeatureChange';
+    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 [{ addedFeature, allIds, copyFeature, parentFeatureId }] = changes;
+            return {
+                typeName,
+                changedIds,
+                assembly,
+                addedFeature,
+                parentFeatureId,
+                copyFeature,
+                allIds,
+            };
+        }
+        return { typeName, changedIds, assembly, changes };
+    }
+    /**
+     * Applies the required change to database
+     * @param backend - parameters from backend
+     * @returns
+     */
+    async executeOnServer(backend) {
+        const { assemblyModel, featureModel, refSeqModel, session, user } = backend;
+        const { assembly, changes, logger } = this;
+        const assemblyDoc = await assemblyModel
+            .findById(assembly)
+            .session(session)
+            .exec();
+        if (!assemblyDoc) {
+            const errMsg = `*** ERROR: Assembly with id "${assembly}" not found`;
+            logger.error(errMsg);
+            throw new Error(errMsg);
+        }
+        let featureCnt = 0;
+        logger.debug?.(`changes: ${JSON.stringify(changes)}`);
+        // Loop the changes
+        for (const change of changes) {
+            logger.debug?.(`change: ${JSON.stringify(change)}`);
+            const { addedFeature, allIds, copyFeature, parentFeatureId } = change;
+            const { _id, refSeq } = addedFeature;
+            const refSeqDoc = await refSeqModel
+                .findById(refSeq)
+                .session(session)
+                .exec();
+            if (!refSeqDoc) {
+                throw new Error(`RefSeq was not found by assembly "${assembly}" and seq_id "${refSeq}" not found`);
+            }
+            // CopyFeature is called from CopyFeature.tsx
+            if (copyFeature) {
+                // Add into Mongo
+                const [newFeatureDoc] = await featureModel.create([{ ...addedFeature, allIds, status: -1, user }], { session });
+                logger.debug?.(`Copied feature, docId "${newFeatureDoc._id}" to assembly "${assembly}"`);
+                featureCnt++;
+            }
+            else {
+                // Adding new child feature
+                if (parentFeatureId) {
+                    const topLevelFeature = await featureModel
+                        .findOne({ allIds: parentFeatureId })
+                        .session(session)
+                        .exec();
+                    if (!topLevelFeature) {
+                        throw new Error(`Could not find feature with ID "${parentFeatureId}"`);
+                    }
+                    const parentFeature = this.getFeatureFromId(topLevelFeature, parentFeatureId);
+                    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()],
+                            ...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));
+                    const childIds = this.getChildFeatureIds(addedFeature);
+                    topLevelFeature.allIds.push(_id, ...childIds);
+                    await topLevelFeature.save();
+                }
+                else {
+                    const childIds = this.getChildFeatureIds(addedFeature);
+                    const allIdsV2 = [_id, ...childIds];
+                    const [newFeatureDoc] = await featureModel.create([{ allIds: allIdsV2, status: 0, ...addedFeature }], { session });
+                    logger.verbose?.(`Added docId "${newFeatureDoc._id}"`);
+                }
+            }
+            featureCnt++;
+        }
+        logger.debug?.(`Added ${featureCnt} new feature(s) into database.`);
+    }
+    async executeOnLocalGFF3(_backend) {
+        throw new Error('executeOnLocalGFF3 not implemented');
+    }
+    async executeOnClient(dataStore) {
+        if (!dataStore) {
+            throw new Error('No data store');
+        }
+        const { assembly, changes } = this;
+        for (const change of changes) {
+            const { addedFeature, parentFeatureId } = change;
+            if (parentFeatureId) {
+                const parentFeature = dataStore.getFeature(parentFeatureId);
+                if (!parentFeature) {
+                    throw new Error(`Could not find parent feature "${parentFeatureId}"`);
+                }
+                // create an ID for the parent feature if it does not have one
+                if (!parentFeature.attributes.get('_id')) {
+                    parentFeature.setAttribute('_id', [parentFeature._id]);
+                }
+                parentFeature.addChild(addedFeature);
+            }
+            else {
+                dataStore.addFeature(assembly, addedFeature);
+            }
+        }
+    }
+    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_1.DeleteFeatureChange({
+            changedIds: inverseChangedIds,
+            typeName: 'DeleteFeatureChange',
+            changes: inverseChanges,
+            assembly,
+        }, { logger });
+    }
+}
+exports.AddFeatureChange = AddFeatureChange;
+function isAddFeatureChange(change) {
+    return change.typeName === 'AddFeatureChange';
+}
+//# sourceMappingURL=AddFeatureChange.js.map

package/dist/Changes/AddFeatureChange.js.map

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

@@ -0,0 +1,32 @@
+import { ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
+import { FromFileBaseChange } from './FromFileBaseChange';
+export interface SerializedAddFeaturesFromFileChangeBase extends SerializedAssemblySpecificChange {
+    typeName: 'AddFeaturesFromFileChange';
+    deleteExistingFeatures?: boolean;
+}
+export interface AddFeaturesFromFileChangeDetails {
+    fileId: string;
+}
+export interface SerializedAddFeaturesFromFileChangeSingle extends SerializedAddFeaturesFromFileChangeBase, AddFeaturesFromFileChangeDetails {
+}
+export interface SerializedAddFeaturesFromFileChangeMultiple extends SerializedAddFeaturesFromFileChangeBase {
+    changes: AddFeaturesFromFileChangeDetails[];
+}
+export type SerializedAddFeaturesFromFileChange = SerializedAddFeaturesFromFileChangeSingle | SerializedAddFeaturesFromFileChangeMultiple;
+export declare class AddFeaturesFromFileChange extends FromFileBaseChange {
+    typeName: "AddFeaturesFromFileChange";
+    changes: AddFeaturesFromFileChangeDetails[];
+    deleteExistingFeatures: boolean;
+    constructor(json: SerializedAddFeaturesFromFileChange, options?: ChangeOptions);
+    get notification(): string;
+    toJSON(): SerializedAddFeaturesFromFileChange;
+    /**
+     * 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(): AddFeaturesFromFileChange;
+}

package/dist/Changes/AddFeaturesFromFileChange.js

@@ -0,0 +1,76 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.AddFeaturesFromFileChange = void 0;
+const FromFileBaseChange_1 = require("./FromFileBaseChange");
+class AddFeaturesFromFileChange extends FromFileBaseChange_1.FromFileBaseChange {
+    typeName = 'AddFeaturesFromFileChange';
+    changes;
+    deleteExistingFeatures = false;
+    constructor(json, options) {
+        super(json, options);
+        this.deleteExistingFeatures = json.deleteExistingFeatures ?? false;
+        this.changes = 'changes' in json ? json.changes : [json];
+    }
+    // eslint-disable-next-line @typescript-eslint/class-literal-property-style
+    get notification() {
+        return 'Features have been added. To see them, please refresh the page.';
+    }
+    toJSON() {
+        const { assembly, changes, deleteExistingFeatures, typeName } = this;
+        if (changes.length === 1) {
+            const [{ fileId }] = changes;
+            return { typeName, assembly, fileId, deleteExistingFeatures };
+        }
+        return { typeName, assembly, changes, deleteExistingFeatures };
+    }
+    /**
+     * Applies the required change to database
+     * @param backend - parameters from backend
+     * @returns
+     */
+    async executeOnServer(backend) {
+        const { fileModel, filesService } = backend;
+        const { changes, deleteExistingFeatures, logger } = this;
+        if (deleteExistingFeatures) {
+            await this.removeExistingFeatures(backend);
+        }
+        for (const change of changes) {
+            const { fileId } = change;
+            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}"`);
+            // Read data from compressed file and parse the content
+            const featureStream = filesService.parseGFF3(filesService.getFileStream(fileDoc));
+            let featureCount = 0;
+            for await (const f of featureStream) {
+                const gff3Feature = f;
+                // Add new feature into database
+                // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
+                await this.addFeatureIntoDb(gff3Feature, backend);
+                featureCount++;
+                if (featureCount % 1000 === 0) {
+                    logger.debug?.(`Processed ${featureCount} features`);
+                }
+            }
+        }
+        logger.debug?.('New features added into database!');
+    }
+    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 AddFeaturesFromFileChange({ typeName, changes, assembly }, { logger });
+    }
+}
+exports.AddFeaturesFromFileChange = AddFeaturesFromFileChange;
+//# sourceMappingURL=AddFeaturesFromFileChange.js.map

package/dist/Changes/AddFeaturesFromFileChange.js.map

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

@@ -0,0 +1,20 @@
+import { AssemblySpecificChange, Change, ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
+export interface SerializedRefSeqAliases {
+    refName: string;
+    aliases: string[];
+}
+export interface SerializedRefSeqAliasesChange extends SerializedAssemblySpecificChange {
+    typeName: 'AddRefSeqAliasesChange';
+    refSeqAliases: SerializedRefSeqAliases[];
+}
+export declare class AddRefSeqAliasesChange extends AssemblySpecificChange {
+    typeName: "AddRefSeqAliasesChange";
+    refSeqAliases: SerializedRefSeqAliases[];
+    constructor(json: SerializedRefSeqAliasesChange, options?: ChangeOptions);
+    executeOnClient(clientDataStore: ClientDataStore): Promise<void>;
+    getInverse(): Change;
+    toJSON(): SerializedRefSeqAliasesChange;
+    executeOnServer(backend: ServerDataStore): Promise<void>;
+    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<unknown>;
+    get notification(): string;
+}

package/dist/Changes/AddRefSeqAliasesChange.js

@@ -0,0 +1,61 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.AddRefSeqAliasesChange = void 0;
+const common_1 = require("@apollo-annotation/common");
+const util_1 = require("@jbrowse/core/util");
+class AddRefSeqAliasesChange extends common_1.AssemblySpecificChange {
+    typeName = 'AddRefSeqAliasesChange';
+    refSeqAliases;
+    constructor(json, options) {
+        super(json, options);
+        this.refSeqAliases = json.refSeqAliases;
+    }
+    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`);
+        }
+        const sessionAliases = assembly.refNameAliases;
+        const sessionLCAliases = assembly.lowerCaseRefNameAliases;
+        if (!sessionAliases || !sessionLCAliases) {
+            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);
+        return Promise.resolve();
+    }
+    getInverse() {
+        throw new Error('Method not implemented.');
+    }
+    toJSON() {
+        const { assembly, refSeqAliases, typeName } = this;
+        return { assembly, typeName, refSeqAliases };
+    }
+    async executeOnServer(backend) {
+        const { refSeqModel, session } = backend;
+        const { assembly, logger, refSeqAliases } = this;
+        for (const refSeqAlias of refSeqAliases) {
+            logger.debug?.(`Updating Refname alias for assembly: ${assembly}, refSeqAlias: ${JSON.stringify(refSeqAlias)}`);
+            const { aliases, refName } = refSeqAlias;
+            await refSeqModel
+                .updateOne({ assembly, name: refName }, { $set: { aliases } })
+                .session(session);
+        }
+    }
+    executeOnLocalGFF3(_backend) {
+        throw new Error('Method not implemented.');
+    }
+    // eslint-disable-next-line @typescript-eslint/class-literal-property-style
+    get notification() {
+        return 'RefSeq aliases have been added.';
+    }
+}
+exports.AddRefSeqAliasesChange = AddRefSeqAliasesChange;
+//# sourceMappingURL=AddRefSeqAliasesChange.js.map

package/dist/Changes/AddRefSeqAliasesChange.js.map

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

@@ -0,0 +1,18 @@
+import { AssemblySpecificChange, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
+export interface SerializedDeleteAssemblyChange extends SerializedAssemblySpecificChange {
+    typeName: 'DeleteAssemblyChange';
+}
+export declare class DeleteAssemblyChange extends AssemblySpecificChange {
+    typeName: "DeleteAssemblyChange";
+    get notification(): string;
+    toJSON(): SerializedDeleteAssemblyChange;
+    /**
+     * 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(): DeleteAssemblyChange;
+}

package/dist/Changes/DeleteAssemblyChange.js

@@ -0,0 +1,72 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.DeleteAssemblyChange = void 0;
+/* eslint-disable @typescript-eslint/no-unsafe-return */
+/* eslint-disable @typescript-eslint/require-await */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+const common_1 = require("@apollo-annotation/common");
+const util_1 = require("@jbrowse/core/util");
+class DeleteAssemblyChange extends common_1.AssemblySpecificChange {
+    typeName = 'DeleteAssemblyChange';
+    get notification() {
+        return `Assembly "${this.assembly}" deleted successfully.`;
+    }
+    toJSON() {
+        const { assembly, typeName } = this;
+        return { typeName, assembly };
+    }
+    /**
+     * Applies the required change to database
+     * @param backend - parameters from backend
+     * @returns
+     */
+    async executeOnServer(backend) {
+        const { assemblyModel, featureModel, refSeqChunkModel, refSeqModel, session, } = backend;
+        const { assembly, logger } = this;
+        const assemblyDoc = await assemblyModel
+            .findById(assembly)
+            .session(session)
+            .exec();
+        if (!assemblyDoc) {
+            const errMsg = `*** ERROR: Assembly with id "${assembly}" not found`;
+            logger.error(errMsg);
+            throw new Error(errMsg);
+        }
+        // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
+        // Get RefSeqs
+        const refSeqs = await refSeqModel.find({ assembly }).exec();
+        const refSeqIds = refSeqs.map((refSeq) => refSeq._id);
+        // Get and delete RefSeqChunks
+        await refSeqChunkModel.deleteMany({ refSeq: refSeqIds }).exec();
+        // Get and delete Features
+        await featureModel.deleteMany({ refSeq: refSeqIds }).exec();
+        // Delete RefSeqs and Assembly
+        await refSeqModel.deleteMany({ assembly }).exec();
+        await assemblyModel.findByIdAndDelete(assembly).exec();
+        logger.debug?.(`Assembly "${assembly}" deleted from database.`);
+    }
+    async executeOnLocalGFF3(_backend) {
+        throw new Error('executeOnLocalGFF3 not implemented');
+    }
+    async executeOnClient(dataStore) {
+        const { assembly } = this;
+        if (!dataStore) {
+            throw new Error('No data store');
+        }
+        const session = (0, util_1.getSession)(dataStore);
+        // If assemblyId is not present in client data store
+        if (dataStore.assemblies.has(assembly)) {
+            dataStore.deleteAssembly(assembly);
+        }
+        await session.removeAssembly?.(assembly);
+        // @ts-expect-error this isn't on the AbstractSessionModel
+        await session.removeSessionAssembly?.(assembly);
+    }
+    getInverse() {
+        const { assembly, logger } = this;
+        return new DeleteAssemblyChange({ typeName: 'DeleteAssemblyChange', assembly }, { logger });
+    }
+}
+exports.DeleteAssemblyChange = DeleteAssemblyChange;
+//# sourceMappingURL=DeleteAssemblyChange.js.map

package/dist/Changes/DeleteAssemblyChange.js.map

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

@@ -0,0 +1,42 @@
+import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
+import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+import { Feature } from '@apollo-annotation/schemas';
+import { AddFeatureChange } from './AddFeatureChange';
+interface SerializedDeleteFeatureChangeBase extends SerializedFeatureChange {
+    typeName: 'DeleteFeatureChange';
+}
+export interface DeleteFeatureChangeDetails {
+    deletedFeature: AnnotationFeatureSnapshot;
+    parentFeatureId?: string;
+}
+interface SerializedDeleteFeatureChangeSingle extends SerializedDeleteFeatureChangeBase, DeleteFeatureChangeDetails {
+}
+interface SerializedDeleteFeatureChangeMultiple extends SerializedDeleteFeatureChangeBase {
+    changes: DeleteFeatureChangeDetails[];
+}
+export type SerializedDeleteFeatureChange = SerializedDeleteFeatureChangeSingle | SerializedDeleteFeatureChangeMultiple;
+export declare class DeleteFeatureChange extends FeatureChange {
+    typeName: "DeleteFeatureChange";
+    changes: DeleteFeatureChangeDetails[];
+    constructor(json: SerializedDeleteFeatureChange, options?: ChangeOptions);
+    toJSON(): SerializedDeleteFeatureChange;
+    /**
+     * Applies the required change to database
+     * @param backend - parameters from backend
+     * @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;
+}
+export declare function isDeleteFeatureChange(change: unknown): change is DeleteFeatureChange;
+export {};