@apollo-annotation/shared 0.1.18 → 0.1.20

package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.d.ts

@@ -0,0 +1,33 @@
+import { ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
+import { FromFileBaseChange } from './FromFileBaseChange';
+export interface SerializedAddAssemblyAndFeaturesFromFileChangeBase extends SerializedAssemblySpecificChange {
+    typeName: 'AddAssemblyAndFeaturesFromFileChange';
+}
+export interface AddAssemblyAndFeaturesFromFileChangeDetails {
+    assemblyName: string;
+    fileIds: {
+        fa: string;
+    };
+}
+export interface SerializedAddAssemblyAndFeaturesFromFileChangeSingle extends SerializedAddAssemblyAndFeaturesFromFileChangeBase, AddAssemblyAndFeaturesFromFileChangeDetails {
+}
+export interface SerializedAddAssemblyAndFeaturesFromFileChangeMultiple extends SerializedAddAssemblyAndFeaturesFromFileChangeBase {
+    changes: AddAssemblyAndFeaturesFromFileChangeDetails[];
+}
+export type SerializedAddAssemblyAndFeaturesFromFileChange = SerializedAddAssemblyAndFeaturesFromFileChangeSingle | SerializedAddAssemblyAndFeaturesFromFileChangeMultiple;
+export declare class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange {
+    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;
+}

package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js

@@ -0,0 +1,83 @@
+"use strict";
+/* eslint-disable @typescript-eslint/require-await */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.AddAssemblyAndFeaturesFromFileChange = void 0;
+const FromFileBaseChange_1 = require("./FromFileBaseChange");
+class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange_1.FromFileBaseChange {
+    typeName = 'AddAssemblyAndFeaturesFromFileChange';
+    changes;
+    constructor(json, options) {
+        super(json, options);
+        this.changes = 'changes' in json ? json.changes : [json];
+    }
+    get notification() {
+        return `Assembly "${this.changes[0].assemblyName}" added successfully. To use it, please refresh the page.`;
+    }
+    toJSON() {
+        const { assembly, changes, typeName } = this;
+        if (changes.length === 1) {
+            const [{ assemblyName, fileIds }] = changes;
+            return { typeName, assembly, assemblyName, fileIds };
+        }
+        return { typeName, assembly, changes };
+    }
+    /**
+     * Applies the required change to database
+     * @param backend - parameters from backend
+     * @returns
+     */
+    async executeOnServer(backend) {
+        const { assemblyModel, fileModel, filesService, user } = backend;
+        const { assembly, changes, logger } = this;
+        for (const change of changes) {
+            const { assemblyName, fileIds } = change;
+            const fileId = fileIds.fa;
+            const { FILE_UPLOAD_FOLDER } = process.env;
+            if (!FILE_UPLOAD_FOLDER) {
+                throw new Error('No FILE_UPLOAD_FOLDER found in .env file');
+            }
+            // Get file checksum
+            const fileDoc = await fileModel.findById(fileId).exec();
+            if (!fileDoc) {
+                throw new Error(`File "${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 "${assemblyName}" already exists`);
+            }
+            // Add assembly
+            const [newAssemblyDoc] = await assemblyModel.create([
+                { _id: assembly, name: assemblyName, user, status: -1, fileId },
+            ]);
+            logger.debug?.(`Added new assembly "${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);
+            // Loop all features
+            logger.debug?.(`**************** LOOPATAAN KAIKKI FEATURET SEURAAVAKSI File type: "${fileDoc.type}"`);
+            const featureStream = filesService.parseGFF3(filesService.getFileStream(fileDoc));
+            for await (const f of featureStream) {
+                const gff3Feature = f;
+                logger.verbose?.(`ENTRY=${JSON.stringify(gff3Feature)}`);
+                // Add new feature into database
+                await this.addFeatureIntoDb(gff3Feature, backend);
+            }
+        }
+    }
+    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 });
+    }
+}
+exports.AddAssemblyAndFeaturesFromFileChange = AddAssemblyAndFeaturesFromFileChange;
+//# sourceMappingURL=AddAssemblyAndFeaturesFromFileChange.js.map

package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js.map

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

@@ -0,0 +1,34 @@
+import { AssemblySpecificChange, ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
+export interface SerializedAddAssemblyFromExternalChangeBase extends SerializedAssemblySpecificChange {
+    typeName: 'AddAssemblyFromExternalChange';
+}
+export interface AddAssemblyFromExternalChangeDetails {
+    assemblyName: string;
+    externalLocation: {
+        fa: string;
+        fai: string;
+        gzi?: string;
+    };
+}
+export interface SerializedAddAssemblyFromExternalChangeSingle extends SerializedAddAssemblyFromExternalChangeBase, AddAssemblyFromExternalChangeDetails {
+}
+export interface SerializedAddAssemblyFromExternalChangeMultiple extends SerializedAddAssemblyFromExternalChangeBase {
+    changes: AddAssemblyFromExternalChangeDetails[];
+}
+export type SerializedAddAssemblyFromExternalChange = SerializedAddAssemblyFromExternalChangeSingle | SerializedAddAssemblyFromExternalChangeMultiple;
+export declare class AddAssemblyFromExternalChange extends AssemblySpecificChange {
+    typeName: "AddAssemblyFromExternalChange";
+    changes: AddAssemblyFromExternalChangeDetails[];
+    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;
+}

package/dist/Changes/AddAssemblyFromExternalChange.js

@@ -0,0 +1,97 @@
+"use strict";
+/* eslint-disable @typescript-eslint/restrict-template-expressions */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.AddAssemblyFromExternalChange = void 0;
+/* eslint-disable @typescript-eslint/require-await */
+const common_1 = require("@apollo-annotation/common");
+const indexedfasta_1 = require("@gmod/indexedfasta");
+const generic_filehandle_1 = require("generic-filehandle");
+class AddAssemblyFromExternalChange extends common_1.AssemblySpecificChange {
+    typeName = 'AddAssemblyFromExternalChange';
+    changes;
+    constructor(json, options) {
+        super(json, options);
+        this.changes = 'changes' in json ? json.changes : [json];
+    }
+    get notification() {
+        return `Assembly "${this.changes[0].assemblyName}" added successfully. To use it, please refresh the page.`;
+    }
+    toJSON() {
+        const { assembly, changes, typeName } = this;
+        if (changes.length === 1) {
+            const [{ assemblyName, externalLocation }] = changes;
+            return { typeName, assembly, assemblyName, externalLocation };
+        }
+        return { typeName, assembly, changes };
+    }
+    /**
+     * Applies the required change to database
+     * @param backend - parameters from backend
+     * @returns
+     */
+    async executeOnServer(backend) {
+        const { assemblyModel, refSeqModel, user } = backend;
+        const { assembly, changes, logger } = this;
+        const { CHUNK_SIZE } = process.env;
+        const customChunkSize = CHUNK_SIZE && Number(CHUNK_SIZE);
+        for (const change of changes) {
+            const { assemblyName, externalLocation } = change;
+            const { fa, fai, gzi } = externalLocation;
+            const sequenceAdapter = gzi
+                ? new indexedfasta_1.BgzipIndexedFasta({
+                    fasta: new generic_filehandle_1.RemoteFile(fa, { fetch }),
+                    fai: new generic_filehandle_1.RemoteFile(fai, { fetch }),
+                    gzi: new generic_filehandle_1.RemoteFile(gzi, { fetch }),
+                })
+                : new indexedfasta_1.IndexedFasta({
+                    fasta: new generic_filehandle_1.RemoteFile(fa, { fetch }),
+                    fai: new generic_filehandle_1.RemoteFile(fai, { fetch }),
+                });
+            const allSequenceSizes = await sequenceAdapter.getSequenceSizes();
+            if (!allSequenceSizes) {
+                throw new Error('No data read from indexed fasta getSequenceSizes');
+            }
+            const assemblyDoc = await assemblyModel
+                .findOne({ name: assemblyName })
+                .exec();
+            if (assemblyDoc) {
+                throw new Error(`Assembly "${assemblyName}" already exists`);
+            }
+            const [newAssemblyDoc] = await assemblyModel.create([
+                {
+                    _id: assembly,
+                    name: assemblyName,
+                    user,
+                    status: -1,
+                    externalLocation,
+                },
+            ]);
+            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 });
+    }
+}
+exports.AddAssemblyFromExternalChange = AddAssemblyFromExternalChange;
+//# sourceMappingURL=AddAssemblyFromExternalChange.js.map

package/dist/Changes/AddAssemblyFromExternalChange.js.map

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package/dist/Changes/AddAssemblyFromFileChange.d.ts

@@ -0,0 +1,43 @@
+import { ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
+import { FromFileBaseChange } from './FromFileBaseChange';
+export interface SerializedAddAssemblyFromFileChangeBase extends SerializedAssemblySpecificChange {
+    typeName: 'AddAssemblyFromFileChange';
+}
+export interface AddAssemblyFromFileChangeDetails {
+    assemblyName: string;
+    fileIds: {
+        fa: string;
+    } | {
+        fa: string;
+        fai: string;
+        gzi: string;
+    };
+}
+export interface SerializedAddAssemblyFromFileChangeSingle extends SerializedAddAssemblyFromFileChangeBase, AddAssemblyFromFileChangeDetails {
+}
+export interface SerializedAddAssemblyFromFileChangeMultiple extends SerializedAddAssemblyFromFileChangeBase {
+    changes: AddAssemblyFromFileChangeDetails[];
+}
+export type SerializedAddAssemblyFromFileChange = SerializedAddAssemblyFromFileChangeSingle | SerializedAddAssemblyFromFileChangeMultiple;
+export declare class AddAssemblyFromFileChange extends FromFileBaseChange {
+    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;
+}

package/dist/Changes/AddAssemblyFromFileChange.js

@@ -0,0 +1,140 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.AddAssemblyFromFileChange = void 0;
+const indexedfasta_1 = require("@gmod/indexedfasta");
+const FromFileBaseChange_1 = require("./FromFileBaseChange");
+class AddAssemblyFromFileChange extends FromFileBaseChange_1.FromFileBaseChange {
+    typeName = 'AddAssemblyFromFileChange';
+    changes;
+    constructor(json, options) {
+        super(json, options);
+        this.changes = 'changes' in json ? json.changes : [json];
+    }
+    get notification() {
+        return `Assembly "${this.changes[0].assemblyName}" added successfully. To use it, please refresh the page.`;
+    }
+    toJSON() {
+        const { assembly, changes, typeName } = this;
+        if (changes.length === 1) {
+            const [{ assemblyName, fileIds }] = changes;
+            return { typeName, assembly, assemblyName, fileIds };
+        }
+        return { typeName, assembly, changes };
+    }
+    /**
+     * Applies the required change to database
+     * @param backend - parameters from backend
+     * @returns
+     */
+    async executeOnServer(backend) {
+        const { changes } = this;
+        for (const change of changes) {
+            const { assemblyName, fileIds } = change;
+            await ('gzi' in fileIds
+                ? this.executeOnServerIndexed(backend, assemblyName, fileIds)
+                : this.executeOnServerFasta(backend, assemblyName, fileIds.fa));
+        }
+    }
+    async executeOnServerIndexed(backend, assemblyName, fileIds) {
+        const { CHUNK_SIZE } = process.env;
+        const customChunkSize = CHUNK_SIZE && Number(CHUNK_SIZE);
+        const { FILE_UPLOAD_FOLDER } = process.env;
+        if (!FILE_UPLOAD_FOLDER) {
+            throw new Error('No FILE_UPLOAD_FOLDER found in .env file');
+        }
+        const { fa, fai, gzi } = fileIds;
+        const { assemblyModel, fileModel, filesService, refSeqModel, user } = backend;
+        const faDoc = await fileModel.findById(fa);
+        const faChecksum = faDoc?.checksum;
+        if (!faChecksum) {
+            throw new Error(`No checksum for file document ${faDoc}`);
+        }
+        const faiDoc = await fileModel.findById(fai);
+        const faiChecksum = faiDoc?.checksum;
+        if (!faiChecksum) {
+            throw new Error(`No checksum for file document ${faiDoc}`);
+        }
+        const gziDoc = await fileModel.findById(gzi);
+        const gziChecksum = gziDoc?.checksum;
+        if (!gziChecksum) {
+            throw new Error(`No checksum for file document ${gziDoc}`);
+        }
+        const sequenceAdapter = new indexedfasta_1.BgzipIndexedFasta({
+            fasta: filesService.getFileHandle(faDoc),
+            fai: filesService.getFileHandle(faiDoc),
+            gzi: filesService.getFileHandle(gziDoc),
+        });
+        const allSequenceSizes = await sequenceAdapter.getSequenceSizes();
+        const assemblyDoc = await assemblyModel
+            .findOne({ name: assemblyName })
+            .exec();
+        if (assemblyDoc) {
+            throw new Error(`Assembly "${assemblyName}" already exists`);
+        }
+        const [newAssemblyDoc] = await assemblyModel.create([
+            {
+                _id: this.assembly,
+                name: assemblyName,
+                user,
+                status: -1,
+                fileIds,
+            },
+        ]);
+        this.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,
+                },
+            ]);
+            this.logger.debug?.(`Added new refSeq "${sequenceName}", docId "${newRefSeqDoc._id}"`);
+        }
+    }
+    async executeOnServerFasta(backend, assemblyName, fileId) {
+        const { assemblyModel, fileModel, user } = backend;
+        // Get file checksum
+        const fileDoc = await fileModel.findById(fileId).exec();
+        if (!fileDoc) {
+            throw new Error(`File "${fileId}" not found in Mongo`);
+        }
+        this.logger.debug?.(`FileId "${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`);
+        }
+        // Add assembly
+        const [newAssemblyDoc] = await assemblyModel.create([
+            {
+                _id: this.assembly,
+                name: assemblyName,
+                user,
+                status: -1,
+                fileIds: { fa: fileId },
+            },
+        ]);
+        this.logger.debug?.(`Added new assembly "${assemblyName}", docId "${newAssemblyDoc._id}"`);
+        this.logger.debug?.(`File type: "${fileDoc.type}", assemblyId: "${newAssemblyDoc._id}"`);
+        // 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);
+    }
+    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 AddAssemblyFromFileChange({ typeName, changes, assembly }, { logger });
+    }
+}
+exports.AddAssemblyFromFileChange = AddAssemblyFromFileChange;
+//# sourceMappingURL=AddAssemblyFromFileChange.js.map

package/dist/Changes/AddAssemblyFromFileChange.js.map

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package/dist/Changes/AddFeatureChange.d.ts

@@ -0,0 +1,35 @@
+import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
+import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+import { DeleteFeatureChange } from './DeleteFeatureChange';
+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;
+export declare class AddFeatureChange extends FeatureChange {
+    typeName: "AddFeatureChange";
+    changes: AddFeatureChangeDetails[];
+    constructor(json: SerializedAddFeatureChange, options?: ChangeOptions);
+    toJSON(): SerializedAddFeatureChange;
+    /**
+     * 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(): DeleteFeatureChange;
+}
+export declare function isAddFeatureChange(change: unknown): change is AddFeatureChange;
+export {};