@apollo-annotation/shared 0.1.19 → 0.1.20

package/dist/Changes/ImportJBrowseConfigChange.js

@@ -0,0 +1,67 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ImportJBrowseConfigChange = void 0;
+exports.filterJBrowseConfig = filterJBrowseConfig;
+/* eslint-disable @typescript-eslint/require-await */
+const common_1 = require("@apollo-annotation/common");
+function filterJBrowseConfig(config) {
+    const { 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 filteredConfig = rest;
+    if (filteredAssemblies) {
+        filteredConfig.assemblies = filteredAssemblies;
+    }
+    if (filteredTracks) {
+        filteredConfig.tracks = filteredTracks;
+    }
+    if (filteredPlugins) {
+        filteredConfig.plugins = filteredPlugins;
+    }
+    if (filteredInternetAccounts) {
+        filteredConfig.internetAccounts = filteredInternetAccounts;
+    }
+    return filteredConfig;
+}
+class ImportJBrowseConfigChange extends common_1.Change {
+    typeName = 'ImportJBrowseConfigChange';
+    oldJBrowseConfig;
+    newJBrowseConfig;
+    constructor(json, options) {
+        super(json, options);
+        this.oldJBrowseConfig = json.oldJBrowseConfig;
+        this.newJBrowseConfig = json.newJBrowseConfig;
+    }
+    toJSON() {
+        const { newJBrowseConfig, oldJBrowseConfig, typeName } = this;
+        return { typeName, oldJBrowseConfig, newJBrowseConfig };
+    }
+    async executeOnServer(backend) {
+        const { jbrowseConfigModel } = backend;
+        const { logger, newJBrowseConfig } = this;
+        await jbrowseConfigModel.deleteMany();
+        if (!newJBrowseConfig) {
+            return;
+        }
+        const filteredConfig = filterJBrowseConfig(newJBrowseConfig);
+        await jbrowseConfigModel.create(filteredConfig);
+        logger.debug?.('Stored new JBrowse Config');
+    }
+    async executeOnLocalGFF3(_backend) {
+        throw new Error('executeOnLocalGFF3 not implemented');
+    }
+    // eslint-disable-next-line @typescript-eslint/no-empty-function
+    async executeOnClient(_dataStore) { }
+    getInverse() {
+        const { logger, newJBrowseConfig, oldJBrowseConfig } = this;
+        return new ImportJBrowseConfigChange({
+            typeName: 'ImportJBrowseConfigChange',
+            oldJBrowseConfig: newJBrowseConfig,
+            newJBrowseConfig: oldJBrowseConfig,
+        }, { logger });
+    }
+}
+exports.ImportJBrowseConfigChange = ImportJBrowseConfigChange;
+//# sourceMappingURL=ImportJBrowseConfigChange.js.map

package/dist/Changes/ImportJBrowseConfigChange.js.map

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

@@ -0,0 +1,32 @@
+import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
+interface SerializedLocationEndChangeBase extends SerializedFeatureChange {
+    typeName: 'LocationEndChange';
+}
+export interface LocationEndChangeDetails {
+    featureId: string;
+    oldEnd: number;
+    newEnd: number;
+}
+interface SerializedLocationEndChangeSingle extends SerializedLocationEndChangeBase, LocationEndChangeDetails {
+}
+interface SerializedLocationEndChangeMultiple extends SerializedLocationEndChangeBase {
+    changes: LocationEndChangeDetails[];
+}
+export type SerializedLocationEndChange = SerializedLocationEndChangeSingle | SerializedLocationEndChangeMultiple;
+export declare class LocationEndChange extends FeatureChange {
+    typeName: "LocationEndChange";
+    changes: LocationEndChangeDetails[];
+    constructor(json: SerializedLocationEndChange, options?: ChangeOptions);
+    toJSON(): SerializedLocationEndChange;
+    /**
+     * 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(): LocationEndChange;
+}
+export declare function isLocationEndChange(change: unknown): change is LocationEndChange;
+export {};

package/dist/Changes/LocationEndChange.js

@@ -0,0 +1,129 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.LocationEndChange = void 0;
+exports.isLocationEndChange = isLocationEndChange;
+/* 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 LocationEndChange extends common_1.FeatureChange {
+    typeName = 'LocationEndChange';
+    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 [{ featureId, newEnd, oldEnd }] = changes;
+            return { typeName, changedIds, assembly, featureId, oldEnd, newEnd };
+        }
+        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 = [];
+        // Let's first check that all features are found and those old values match with expected ones. We do this just to be sure that all changes can be done.
+        for (const change of changes) {
+            const { featureId, oldEnd } = 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?.(`*** TOP level 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)}`);
+            if (foundFeature.max === oldEnd) {
+                featuresForChanges.push({ feature: foundFeature, topLevelFeature });
+            }
+            else {
+                if (foundFeature.children) {
+                    for (const [, childFeature] of foundFeature.children) {
+                        if (childFeature.max === oldEnd) {
+                            logger.debug?.(`*************** UPDATE CHILD FEATURE ID= ${featureId}, CHILD: ${JSON.stringify(childFeature)}`);
+                            featuresForChanges.push({
+                                feature: childFeature,
+                                topLevelFeature,
+                            });
+                            break;
+                        }
+                    }
+                }
+            }
+        }
+        // Let's update objects.
+        for (const [idx, change] of changes.entries()) {
+            const { newEnd } = change;
+            const { feature, topLevelFeature } = featuresForChanges[idx];
+            feature.max = newEnd;
+            if (topLevelFeature._id.equals(feature._id)) {
+                topLevelFeature.markModified('end'); // 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?.(`*** Object updated in Mongo. New object: ${JSON.stringify(topLevelFeature)}`);
+        }
+    }
+    async executeOnLocalGFF3(_backend) {
+        throw new Error('executeOnLocalGFF3 not implemented');
+    }
+    async executeOnClient(dataStore) {
+        if (!dataStore) {
+            throw new Error('No data store');
+        }
+        for (const [idx, changedId] of this.changedIds.entries()) {
+            const feature = dataStore.getFeature(changedId);
+            if (!feature) {
+                throw new Error(`Could not find feature with identifier "${changedId}"`);
+            }
+            feature.setMax(this.changes[idx].newEnd);
+        }
+    }
+    getInverse() {
+        const { assembly, changedIds, changes, logger, typeName } = this;
+        const inverseChangedIds = [...changedIds].reverse();
+        const inverseChanges = [...changes].reverse().map((endChange) => ({
+            featureId: endChange.featureId,
+            oldEnd: endChange.newEnd,
+            newEnd: endChange.oldEnd,
+        }));
+        return new LocationEndChange({
+            changedIds: inverseChangedIds,
+            typeName,
+            changes: inverseChanges,
+            assembly,
+        }, { logger });
+    }
+}
+exports.LocationEndChange = LocationEndChange;
+function isLocationEndChange(change) {
+    return change.typeName === 'LocationEndChange';
+}
+//# sourceMappingURL=LocationEndChange.js.map

package/dist/Changes/LocationEndChange.js.map

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package/dist/Changes/LocationStartChange.d.ts

@@ -0,0 +1,32 @@
+import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
+interface SerializedLocationStartChangeBase extends SerializedFeatureChange {
+    typeName: 'LocationStartChange';
+}
+interface LocationStartChangeDetails {
+    featureId: string;
+    oldStart: number;
+    newStart: number;
+}
+interface SerializedLocationStartChangeSingle extends SerializedLocationStartChangeBase, LocationStartChangeDetails {
+}
+interface SerializedLocationStartChangeMultiple extends SerializedLocationStartChangeBase {
+    changes: LocationStartChangeDetails[];
+}
+export type SerializedLocationStartChange = SerializedLocationStartChangeSingle | SerializedLocationStartChangeMultiple;
+export declare class LocationStartChange extends FeatureChange {
+    typeName: "LocationStartChange";
+    changes: LocationStartChangeDetails[];
+    constructor(json: SerializedLocationStartChange, options?: ChangeOptions);
+    toJSON(): SerializedLocationStartChange;
+    /**
+     * 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(): LocationStartChange;
+}
+export declare function isLocationStartChange(change: unknown): change is LocationStartChange;
+export {};

package/dist/Changes/LocationStartChange.js

@@ -0,0 +1,129 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.LocationStartChange = void 0;
+exports.isLocationStartChange = isLocationStartChange;
+/* 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 LocationStartChange extends common_1.FeatureChange {
+    typeName = 'LocationStartChange';
+    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 [{ featureId, newStart, oldStart }] = changes;
+            return { typeName, changedIds, assembly, featureId, oldStart, newStart };
+        }
+        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 = [];
+        // Let's first check that all features are found and those old values match with expected ones. We do this just to be sure that all changes can be done.
+        for (const change of changes) {
+            const { featureId, oldStart } = 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?.(`*** TOP level 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)}`);
+            if (foundFeature.min === oldStart) {
+                featuresForChanges.push({ feature: foundFeature, topLevelFeature });
+            }
+            else {
+                if (foundFeature.children) {
+                    for (const [, childFeature] of foundFeature.children) {
+                        if (childFeature.min === oldStart) {
+                            logger.debug?.(`*** UPDATE CHILD FEATURE ID= ${featureId}, CHILD: ${JSON.stringify(childFeature)}`);
+                            featuresForChanges.push({
+                                feature: childFeature,
+                                topLevelFeature,
+                            });
+                            break;
+                        }
+                    }
+                }
+            }
+        }
+        // Let's update objects.
+        for (const [idx, change] of changes.entries()) {
+            const { newStart } = change;
+            const { feature, topLevelFeature } = featuresForChanges[idx];
+            feature.min = newStart;
+            if (topLevelFeature._id.equals(feature._id)) {
+                topLevelFeature.markModified('start'); // 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?.(`*** Object updated in Mongo. New object: ${JSON.stringify(topLevelFeature)}`);
+        }
+    }
+    async executeOnLocalGFF3(_backend) {
+        throw new Error('executeOnLocalGFF3 not implemented');
+    }
+    async executeOnClient(dataStore) {
+        if (!dataStore) {
+            throw new Error('No data store');
+        }
+        for (const [idx, changedId] of this.changedIds.entries()) {
+            const feature = dataStore.getFeature(changedId);
+            if (!feature) {
+                throw new Error(`Could not find feature with identifier "${changedId}"`);
+            }
+            feature.setMin(this.changes[idx].newStart);
+        }
+    }
+    getInverse() {
+        const { assembly, changedIds, changes, logger, typeName } = this;
+        const inverseChangedIds = [...changedIds].reverse();
+        const inverseChanges = [...changes].reverse().map((startChange) => ({
+            featureId: startChange.featureId,
+            oldStart: startChange.newStart,
+            newStart: startChange.oldStart,
+        }));
+        return new LocationStartChange({
+            changedIds: inverseChangedIds,
+            typeName,
+            changes: inverseChanges,
+            assembly,
+        }, { logger });
+    }
+}
+exports.LocationStartChange = LocationStartChange;
+function isLocationStartChange(change) {
+    return change.typeName === 'LocationStartChange';
+}
+//# sourceMappingURL=LocationStartChange.js.map

package/dist/Changes/LocationStartChange.js.map

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package/dist/Changes/StrandChange.d.ts

@@ -0,0 +1,31 @@
+import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
+interface SerializedStrandChangeBase extends SerializedFeatureChange {
+    typeName: 'StrandChange';
+}
+interface StrandChangeDetails {
+    featureId: string;
+    oldStrand: -1 | 1 | undefined;
+    newStrand: -1 | 1 | undefined;
+}
+interface SerializedStrandChangeSingle extends SerializedStrandChangeBase, StrandChangeDetails {
+}
+interface SerializedStrandChangeMultiple extends SerializedStrandChangeBase {
+    changes: StrandChangeDetails[];
+}
+type SerializedStrandChange = SerializedStrandChangeSingle | SerializedStrandChangeMultiple;
+export declare class StrandChange extends FeatureChange {
+    typeName: "StrandChange";
+    changes: StrandChangeDetails[];
+    constructor(json: SerializedStrandChange, options?: ChangeOptions);
+    toJSON(): SerializedStrandChange;
+    /**
+     * 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(): StrandChange;
+}
+export {};

package/dist/Changes/StrandChange.js

@@ -0,0 +1,114 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.StrandChange = void 0;
+/* 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 StrandChange extends common_1.FeatureChange {
+    typeName = 'StrandChange';
+    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 [{ featureId, newStrand, oldStrand }] = changes;
+            return { typeName, changedIds, assembly, featureId, oldStrand, newStrand };
+        }
+        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 = [];
+        // Let's first check that all features are found and those old values match with expected ones. We do this just to be sure that all changes can be done.
+        for (const entry of changes) {
+            const { featureId, oldStrand } = entry;
+            // 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: ${JSON.stringify(foundFeature)}`);
+            if (foundFeature.strand !== oldStrand) {
+                const errMsg = `*** ERROR: Feature's current strand "${topLevelFeature.strand}" doesn't match with expected value "${oldStrand}"`;
+                logger.error(errMsg);
+                throw new Error(errMsg);
+            }
+            featuresForChanges.push({ feature: foundFeature, topLevelFeature });
+        }
+        // Let's update objects.
+        for (const [idx, change] of changes.entries()) {
+            const { newStrand } = change;
+            const { feature, topLevelFeature } = featuresForChanges[idx];
+            feature.strand = newStrand;
+            if (topLevelFeature._id.equals(feature._id)) {
+                topLevelFeature.markModified('strand'); // 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?.(`*** Object updated in Mongo. New object: ${JSON.stringify(topLevelFeature)}`);
+        }
+    }
+    async executeOnLocalGFF3(_backend) {
+        throw new Error('executeOnLocalGFF3 not implemented');
+    }
+    async executeOnClient(dataStore) {
+        if (!dataStore) {
+            throw new Error('No data store');
+        }
+        for (const [idx, changedId] of this.changedIds.entries()) {
+            const feature = dataStore.getFeature(changedId);
+            if (!feature) {
+                throw new Error(`Could not find feature with identifier "${changedId}"`);
+            }
+            feature.setStrand(this.changes[idx].newStrand);
+        }
+    }
+    getInverse() {
+        const { assembly, changedIds, changes, logger, typeName } = this;
+        const inverseChangedIds = [...changedIds].reverse();
+        const inverseChanges = [...changes].reverse().map((endChange) => ({
+            featureId: endChange.featureId,
+            oldStrand: endChange.newStrand,
+            newStrand: endChange.oldStrand,
+        }));
+        return new StrandChange({
+            changedIds: inverseChangedIds,
+            typeName,
+            changes: inverseChanges,
+            assembly,
+        }, { logger });
+    }
+}
+exports.StrandChange = StrandChange;
+//# sourceMappingURL=StrandChange.js.map

package/dist/Changes/StrandChange.js.map

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

@@ -0,0 +1,31 @@
+import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
+interface SerializedTypeChangeBase extends SerializedFeatureChange {
+    typeName: 'TypeChange';
+}
+interface TypeChangeDetails {
+    featureId: string;
+    oldType: string;
+    newType: string;
+}
+interface SerializedTypeChangeSingle extends SerializedTypeChangeBase, TypeChangeDetails {
+}
+interface SerializedTypeChangeMultiple extends SerializedTypeChangeBase {
+    changes: TypeChangeDetails[];
+}
+export type SerializedTypeChange = SerializedTypeChangeSingle | SerializedTypeChangeMultiple;
+export declare class TypeChange extends FeatureChange {
+    typeName: "TypeChange";
+    changes: TypeChangeDetails[];
+    constructor(json: SerializedTypeChange, options?: ChangeOptions);
+    toJSON(): SerializedTypeChange;
+    /**
+     * 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(): TypeChange;
+}
+export {};