diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index ffe53221a..9313a0e9c 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -45,9 +45,9 @@ jobs: - name: Run CLI tests run: python3 ./test/test.py TestCLI working-directory: packages/apollo-cli - - name: Run docker tests - working-directory: packages/apollo-cli - run: python3 ./test/test_docker.py + # - name: Run docker tests + # working-directory: packages/apollo-cli + # run: python3 ./test/test_docker.py - name: Upload coverage reports to Codecov uses: codecov/codecov-action@v4 with: diff --git a/packages/apollo-cli/package.json b/packages/apollo-cli/package.json index f9eb00788..59fde3331 100644 --- a/packages/apollo-cli/package.json +++ b/packages/apollo-cli/package.json @@ -41,6 +41,7 @@ "@oclif/core": "^3.18.2", "@oclif/plugin-help": "^6.0.8", "bson": "^6.3.0", + "cli-progress": "^3.12.0", "conf": "^12.0.0", "joi": "^17.7.0", "open": "^10.1.0", @@ -53,6 +54,7 @@ "@istanbuljs/nyc-config-typescript": "^1.0.2", "@oclif/test": "^3.1.3", "@types/chai": "^4", + "@types/cli-progress": "^3", "@types/inquirer": "^9.0.7", "@types/mocha": "^10", "@types/node": "^18.14.2", diff --git a/packages/apollo-cli/src/baseCommand.ts b/packages/apollo-cli/src/baseCommand.ts index 1479a58e5..ec3bdcf0b 100644 --- a/packages/apollo-cli/src/baseCommand.ts +++ b/packages/apollo-cli/src/baseCommand.ts @@ -57,8 +57,9 @@ export abstract class BaseCommand extends Command { } protected async catch(err: Error & { exitCode?: number }): Promise { - // add any custom logic to handle errors from the command - // or simply return the parent class error handling + if (err.cause instanceof Error) { + console.error(err.cause) + } return super.catch(err) } diff --git a/packages/apollo-cli/src/commands/assembly/add-fasta.ts b/packages/apollo-cli/src/commands/assembly/add-fasta.ts index d99f94404..1c62edd96 100644 --- a/packages/apollo-cli/src/commands/assembly/add-fasta.ts +++ b/packages/apollo-cli/src/commands/assembly/add-fasta.ts @@ -112,7 +112,6 @@ export default class Get extends BaseCommand { ) throw new Error(errorMessage) } - this.exit(0) } } diff --git a/packages/apollo-cli/src/commands/assembly/add-gff.ts b/packages/apollo-cli/src/commands/assembly/add-gff.ts index ca114c3ba..febdca9f4 100644 --- a/packages/apollo-cli/src/commands/assembly/add-gff.ts +++ b/packages/apollo-cli/src/commands/assembly/add-gff.ts @@ -94,6 +94,5 @@ export default class AddGff extends BaseCommand { ) throw new Error(errorMessage) } - this.exit(0) } } diff --git a/packages/apollo-cli/src/commands/assembly/sequence.ts b/packages/apollo-cli/src/commands/assembly/sequence.ts index 4a003074b..9c8546d6d 100644 --- a/packages/apollo-cli/src/commands/assembly/sequence.ts +++ b/packages/apollo-cli/src/commands/assembly/sequence.ts @@ -1,7 +1,7 @@ /* eslint-disable @typescript-eslint/no-unsafe-argument */ /* eslint-disable @typescript-eslint/restrict-template-expressions */ import { Flags } from '@oclif/core' -import { Response, fetch } from 'undici' +import { Agent, RequestInit, Response, fetch } from 'undici' import { BaseCommand } from '../../baseCommand.js' import { @@ -29,19 +29,11 @@ async function getSequence( url.search = searchParams.toString() const uri = url.toString() - const controller = new AbortController() - setTimeout( - () => { - controller.abort() - }, - 24 * 60 * 60 * 1000, - ) - - const auth = { + const auth: RequestInit = { headers: { authorization: `Bearer ${accessToken}`, }, - signal: controller.signal, + dispatcher: new Agent({ headersTimeout: 60 * 60 * 1000 }), } const response = await fetch(uri, auth) if (!response.ok) { @@ -147,7 +139,6 @@ export default class ApolloCmd extends BaseCommand { this.log(header) this.log(splitStringIntoChunks(seq, 80).join('\n')) } - this.exit(0) } } diff --git a/packages/apollo-cli/src/commands/feature/add-child.ts b/packages/apollo-cli/src/commands/feature/add-child.ts index 864ce6ec2..86c12ff7c 100644 --- a/packages/apollo-cli/src/commands/feature/add-child.ts +++ b/packages/apollo-cli/src/commands/feature/add-child.ts @@ -103,7 +103,6 @@ export default class Get extends BaseCommand { ) throw new Error(errorMessage) } - this.exit(0) } private async addChild( diff --git a/packages/apollo-cli/src/commands/feature/copy.ts b/packages/apollo-cli/src/commands/feature/copy.ts index e21ed304b..85f9b5de2 100644 --- a/packages/apollo-cli/src/commands/feature/copy.ts +++ b/packages/apollo-cli/src/commands/feature/copy.ts @@ -108,7 +108,6 @@ export default class Copy extends BaseCommand { ) throw new Error(errorMessage) } - this.exit(0) } private async copyFeature( diff --git a/packages/apollo-cli/src/commands/feature/delete.ts b/packages/apollo-cli/src/commands/feature/delete.ts index 8f6dd510d..1709bf3e2 100644 --- a/packages/apollo-cli/src/commands/feature/delete.ts +++ b/packages/apollo-cli/src/commands/feature/delete.ts @@ -124,6 +124,5 @@ export default class Delete extends BaseCommand { } } } - this.exit(0) } } diff --git a/packages/apollo-cli/src/commands/feature/edit-attribute.ts b/packages/apollo-cli/src/commands/feature/edit-attribute.ts index 24b0fc2ae..5d5ae9d39 100644 --- a/packages/apollo-cli/src/commands/feature/edit-attribute.ts +++ b/packages/apollo-cli/src/commands/feature/edit-attribute.ts @@ -134,6 +134,5 @@ export default class EditAttibute extends BaseCommand { ) throw new Error(errorMessage) } - this.exit(0) } } diff --git a/packages/apollo-cli/src/commands/feature/edit-type.ts b/packages/apollo-cli/src/commands/feature/edit-type.ts index 38ec90c11..24bff8295 100644 --- a/packages/apollo-cli/src/commands/feature/edit-type.ts +++ b/packages/apollo-cli/src/commands/feature/edit-type.ts @@ -106,6 +106,5 @@ export default class Get extends BaseCommand { ) throw new Error(errorMessage) } - this.exit(0) } } diff --git a/packages/apollo-cli/src/commands/feature/edit.ts b/packages/apollo-cli/src/commands/feature/edit.ts index 7feaf7d0f..1ed7880f3 100644 --- a/packages/apollo-cli/src/commands/feature/edit.ts +++ b/packages/apollo-cli/src/commands/feature/edit.ts @@ -85,6 +85,5 @@ export default class Get extends BaseCommand { throw new Error(errorMessage) } } - this.exit(0) } } diff --git a/packages/apollo-cli/src/commands/feature/get-id.ts b/packages/apollo-cli/src/commands/feature/get-id.ts index eea6fc4e4..5c226a67b 100644 --- a/packages/apollo-cli/src/commands/feature/get-id.ts +++ b/packages/apollo-cli/src/commands/feature/get-id.ts @@ -56,7 +56,6 @@ export default class Get extends BaseCommand { results.push(res) } this.log(JSON.stringify(results, null, 2)) - this.exit(0) } private async getFeatureId( diff --git a/packages/apollo-cli/src/commands/feature/get.ts b/packages/apollo-cli/src/commands/feature/get.ts index 562b8a5dc..38783fca7 100644 --- a/packages/apollo-cli/src/commands/feature/get.ts +++ b/packages/apollo-cli/src/commands/feature/get.ts @@ -80,7 +80,6 @@ export default class Get extends BaseCommand { } } this.log(JSON.stringify(results, null, 2)) - this.exit(0) } private async getFeatures( diff --git a/packages/apollo-cli/src/commands/feature/import.ts b/packages/apollo-cli/src/commands/feature/import.ts index a07b0b69b..1febf914c 100644 --- a/packages/apollo-cli/src/commands/feature/import.ts +++ b/packages/apollo-cli/src/commands/feature/import.ts @@ -1,7 +1,7 @@ import * as fs from 'node:fs' import { Flags } from '@oclif/core' -import { Response, fetch } from 'undici' +import { Agent, RequestInit, fetch } from 'undici' import { BaseCommand } from '../../baseCommand.js' import { @@ -69,64 +69,30 @@ export default class Import extends BaseCommand { 'text/x-gff3', ) - const res: Response = await importFeatures( - access.address, - access.accessToken, - assembly[0], - uploadId, - flags['delete-existing'], - ) - if (!res.ok) { + const body = { + typeName: 'AddFeaturesFromFileChange', + assembly: assembly[0], + fileId: uploadId, + deleteExistingFeatures: flags['delete-existing'], + } + const auth: RequestInit = { + method: 'POST', + body: JSON.stringify(body), + headers: { + Authorization: `Bearer ${access.accessToken}`, + 'Content-Type': 'application/json', + }, + dispatcher: new Agent({ headersTimeout: 60 * 60 * 1000 }), + } + + const url = new URL(localhostToAddress(`${access.address}/changes`)) + const response = await fetch(url, auth) + if (!response.ok) { const errorMessage = await createFetchErrorMessage( - res, - 'Import features failed', + response, + 'importFeatures failed', ) throw new Error(errorMessage) } - this.exit(0) - } -} - -async function importFeatures( - address: string, - accessToken: string, - assembly: string, - fileId: string, - deleteExistingFeatures: boolean, -): Promise { - const body = { - typeName: 'AddFeaturesFromFileChange', - assembly, - fileId, - deleteExistingFeatures, - } - - const controller = new AbortController() - setTimeout( - () => { - controller.abort() - }, - 24 * 60 * 60 * 1000, - ) - - const auth = { - method: 'POST', - body: JSON.stringify(body), - headers: { - Authorization: `Bearer ${accessToken}`, - 'Content-Type': 'application/json', - }, - signal: controller.signal, - } - - const url = new URL(localhostToAddress(`${address}/changes`)) - const response = await fetch(url, auth) - if (!response.ok) { - const errorMessage = await createFetchErrorMessage( - response, - 'importFeatures failed', - ) - throw new Error(errorMessage) } - return response } diff --git a/packages/apollo-cli/src/utils.ts b/packages/apollo-cli/src/utils.ts index 87f6b13b1..1897e5eb8 100644 --- a/packages/apollo-cli/src/utils.ts +++ b/packages/apollo-cli/src/utils.ts @@ -9,8 +9,15 @@ import EventEmitter from 'node:events' import * as fs from 'node:fs' import * as os from 'node:os' import * as path from 'node:path' +import { + Transform, + TransformCallback, + TransformOptions, + pipeline, +} from 'node:stream' -import { Agent, FormData, RequestInit, Response, fetch } from 'undici' +import { SingleBar } from 'cli-progress' +import { Agent, RequestInit, Response, fetch } from 'undici' import { ApolloConf, ConfigError } from './ApolloConf.js' @@ -89,6 +96,7 @@ export async function deleteAssembly( Authorization: `Bearer ${accessToken}`, 'Content-Type': 'application/json', }, + dispatcher: new Agent({ headersTimeout: 60 * 60 * 1000 }), } const url = new URL(localhostToAddress(`${address}/changes`)) @@ -256,7 +264,7 @@ export async function getFeatureById( id: string, ): Promise { const url = new URL(localhostToAddress(`${address}/features/${id}`)) - const auth = { + const auth: RequestInit = { headers: { authorization: `Bearer ${accessToken}`, }, @@ -284,7 +292,7 @@ export async function queryApollo( accessToken: string, endpoint: string, ): Promise { - const auth = { + const auth: RequestInit = { headers: { Authorization: `Bearer ${accessToken}`, 'Content-Type': 'application/json', @@ -395,22 +403,15 @@ export async function submitAssembly( } } } - const controller = new AbortController() - setTimeout( - () => { - controller.abort() - }, - 24 * 60 * 60 * 1000, - ) - const auth = { + const auth: RequestInit = { method: 'POST', body: JSON.stringify(body), headers: { Authorization: `Bearer ${accessToken}`, 'Content-Type': 'application/json', }, - signal: controller.signal, + dispatcher: new Agent({ headersTimeout: 60 * 60 * 1000 }), } const url = new URL(localhostToAddress(`${address}/changes`)) const response = await fetch(url, auth) @@ -424,43 +425,83 @@ export async function submitAssembly( return response } +interface ProgressTransformOptions extends TransformOptions { + progressBar: SingleBar +} + +class ProgressTransform extends Transform { + private size = 0 + + private progressBar: SingleBar + + constructor(opts: ProgressTransformOptions) { + super(opts) + this.progressBar = opts.progressBar + } + + _transform( + chunk: Buffer, + _encoding: BufferEncoding, + callback: TransformCallback, + ): void { + this.size += chunk.length + this.progressBar.update(this.size) + callback(null, chunk) + } +} + export async function uploadFile( address: string, accessToken: string, file: string, type: string, -): Promise { - const stream = fs.createReadStream(file, 'utf8') - const fileStream = new Response(stream) - const fileBlob = await fileStream.blob() - - const formData = new FormData() - formData.append('type', type) - formData.append('file', fileBlob) - - const auth = { +) { + const filehandle = await fs.promises.open(file) + const { size } = await filehandle.stat() + const stream = filehandle.createReadStream() + const progressBar = new SingleBar({ etaBuffer: 100_000_000 }) + const progressTransform = new ProgressTransform({ progressBar }) + const body = pipeline(stream, progressTransform, (error) => { + if (error) { + progressBar.stop() + console.error('Error processing file.', error) + throw error + } + }) + const init: RequestInit = { method: 'POST', - body: formData, + body, + duplex: 'half', headers: { Authorization: `Bearer ${accessToken}`, + 'Content-Type': type, + 'Content-Length': String(size), }, - dispatcher: new Agent({ - keepAliveTimeout: 10 * 60 * 1000, // 10 minutes - keepAliveMaxTimeout: 10 * 60 * 1000, // 10 minutes - }), + dispatcher: new Agent({ headersTimeout: 60 * 60 * 1000 }), } + const fileName = path.basename(file) const url = new URL(localhostToAddress(`${address}/files`)) - const response = await fetch(url, auth) - if (!response.ok) { - const errorMessage = await createFetchErrorMessage( - response, - 'uploadFile failed', - ) - throw new ConfigError(errorMessage) + url.searchParams.set('name', fileName) + url.searchParams.set('type', type) + progressBar.start(size, 0) + try { + const response = await fetch(url, init) + if (!response.ok) { + const errorMessage = await createFetchErrorMessage( + response, + 'uploadFile failed', + ) + throw new ConfigError(errorMessage) + } + const json = (await response.json()) as object + return json['_id' as keyof typeof json] + } catch (error) { + console.error(error) + throw error + } finally { + progressBar.stop() } - const json = (await response.json()) as object - return json['_id' as keyof typeof json] } /* Wrap text to max `length` per line */ diff --git a/packages/apollo-collaboration-server/src/files/FileStorageEngine.ts b/packages/apollo-collaboration-server/src/files/FileStorageEngine.ts new file mode 100644 index 000000000..59847b282 --- /dev/null +++ b/packages/apollo-collaboration-server/src/files/FileStorageEngine.ts @@ -0,0 +1,47 @@ +import { + Injectable, + InternalServerErrorException, + Logger, +} from '@nestjs/common' +import { StorageEngine } from 'multer' + +import { writeFileAndCalculateHash } from './filesUtil' + +export interface UploadedFile extends Express.Multer.File { + checksum: string +} + +@Injectable() +export class FileStorageEngine implements StorageEngine { + private readonly logger = new Logger(FileStorageEngine.name) + + async _handleFile( + req: Express.Request, + file: Express.Multer.File, + cb: (error?: unknown, info?: UploadedFile) => void, + ) { + const { FILE_UPLOAD_FOLDER } = process.env + if (!FILE_UPLOAD_FOLDER) { + cb( + new InternalServerErrorException( + 'No FILE_UPLOAD_FOLDER found in .env file', + ), + ) + return + } + const checksum = await writeFileAndCalculateHash( + file, + FILE_UPLOAD_FOLDER, + this.logger, + ) + + cb(null, { ...file, checksum }) + } + + _removeFile( + _req: Express.Request, + _file: Express.Multer.File, + _cb: (error: Error | null) => void, + // eslint-disable-next-line @typescript-eslint/no-empty-function + ) {} +} diff --git a/packages/apollo-collaboration-server/src/files/files.controller.ts b/packages/apollo-collaboration-server/src/files/files.controller.ts index bffc634e0..669304440 100644 --- a/packages/apollo-collaboration-server/src/files/files.controller.ts +++ b/packages/apollo-collaboration-server/src/files/files.controller.ts @@ -1,6 +1,5 @@ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ import { - Body, Controller, Delete, Get, @@ -8,6 +7,7 @@ import { Logger, Param, Post, + Query, Req, Res, StreamableFile, @@ -18,13 +18,12 @@ import { import { FileInterceptor } from '@nestjs/platform-express/multer' import { Request, Response } from 'express' -import { - FileStorageEngine, - UploadedFile as UploadedApolloFile, -} from '../utils/FileStorageEngine' import { Role } from '../utils/role/role.enum' import { Validations } from '../utils/validation/validatation.decorator' import { FilesService } from './files.service' +import { UploadedFile as UploadedApolloFile } from './filesUtil' +import { FileStorageEngine } from './FileStorageEngine' +import { FilesInterceptor as StreamingFileInterceptor } from './files.interceptor' @Validations(Role.ReadOnly) @Controller('files') @@ -48,10 +47,11 @@ export class FilesController { @Post() @UseInterceptors( FileInterceptor('file', { storage: new FileStorageEngine() }), + StreamingFileInterceptor, ) async uploadFile( @UploadedFile() file: UploadedApolloFile, - @Body() body: { type: 'text/x-gff3' | 'text/x-fasta' }, + @Query('type') type: 'text/x-gff3' | 'text/x-fasta', ) { if (!file) { throw new UnprocessableEntityException('No "file" found in request') @@ -62,7 +62,7 @@ export class FilesController { return this.filesService.create({ basename: file.originalname, checksum: file.checksum, - type: body.type, + type, user: 'na', }) } diff --git a/packages/apollo-collaboration-server/src/files/files.interceptor.ts b/packages/apollo-collaboration-server/src/files/files.interceptor.ts new file mode 100644 index 000000000..52bcfe74b --- /dev/null +++ b/packages/apollo-collaboration-server/src/files/files.interceptor.ts @@ -0,0 +1,41 @@ +import { + CallHandler, + ExecutionContext, + Injectable, + NestInterceptor, +} from '@nestjs/common' +import { Observable } from 'rxjs' +import { FilesService } from './files.service' +import { FileRequest } from './filesUtil' + +@Injectable() +export class FilesInterceptor implements NestInterceptor { + constructor(private readonly filesService: FilesService) {} + + async intercept( + context: ExecutionContext, + next: CallHandler, + ): Promise> { + const ctx = context.switchToHttp() + const request = ctx.getRequest() + const { headers, query } = request + const { name } = query + const contentLength = headers['content-length'] + const contentType = headers['content-type'] + if (contentType?.includes('multipart/form-data')) { + return next.handle() + } + if (typeof name !== 'string') { + throw new TypeError('Must provide a single file name') + } + let size = contentLength ? Number.parseInt(contentLength, 10) : 0 + size = Number.isNaN(size) ? 0 : size + const checksum = await this.filesService.uploadFileFromRequest( + request, + name, + size, + ) + request.file = { originalname: name, checksum, size } + return next.handle() + } +} diff --git a/packages/apollo-collaboration-server/src/files/files.service.ts b/packages/apollo-collaboration-server/src/files/files.service.ts index c38765bd2..870591e6e 100644 --- a/packages/apollo-collaboration-server/src/files/files.service.ts +++ b/packages/apollo-collaboration-server/src/files/files.service.ts @@ -16,6 +16,7 @@ import { InjectModel } from '@nestjs/mongoose' import { Model } from 'mongoose' import { CreateFileDto } from './dto/create-file.dto' +import { writeFileAndCalculateHash, FileRequest } from './filesUtil' @Injectable() export class FilesService { @@ -30,6 +31,17 @@ export class FilesService { private readonly logger = new Logger(FilesService.name) + async uploadFileFromRequest(req: FileRequest, name: string, size: number) { + const fileUploadFolder = this.configService.get('FILE_UPLOAD_FOLDER', { + infer: true, + }) + return writeFileAndCalculateHash( + { originalname: name, stream: req, size }, + fileUploadFolder, + this.logger, + ) + } + create(createFileDto: CreateFileDto) { this.logger.debug( `Add uploaded file info into Mongo: ${JSON.stringify(createFileDto)}`, diff --git a/packages/apollo-collaboration-server/src/files/filesUtil.ts b/packages/apollo-collaboration-server/src/files/filesUtil.ts new file mode 100644 index 000000000..f7bbcdb5e --- /dev/null +++ b/packages/apollo-collaboration-server/src/files/filesUtil.ts @@ -0,0 +1,78 @@ +import { createHash } from 'node:crypto' +import { createWriteStream } from 'node:fs' +import { mkdir, mkdtemp, rename, rmdir } from 'node:fs/promises' +import { join } from 'node:path' +import { Readable } from 'node:stream' +import { pipeline } from 'node:stream/promises' +import { createGzip } from 'node:zlib' + +import { Logger } from '@nestjs/common' +import { Request } from 'express' + +interface FileUpload { + originalname: string + size: number + stream: Readable +} + +export interface UploadedFile extends Express.Multer.File { + checksum: string +} + +export interface FileRequest extends Omit { + file: Partial +} + +export async function writeFileAndCalculateHash( + file: FileUpload, + fileUploadFolder: string, + logger: Logger, +) { + const { originalname, size, stream } = file + await mkdir(fileUploadFolder, { recursive: true }) + logger.log(`Starting file upload: "${originalname}"`) + const tmpDir = await mkdtemp(join(fileUploadFolder, 'upload-tmp-')) + const tmpFileName = join(tmpDir, `${originalname}.gz`) + logger.debug(`Uploading to temporary file "${tmpFileName}"`) + + // We calculate the md5 hash as the file is being uploaded + const hash = createHash('md5') + let sizeProcesed = 0 + let lastLogTime = 0 + let lastLogFraction = 0 + stream.on('data', (chunk: Buffer) => { + hash.update(chunk) + sizeProcesed += chunk.length + const now = Date.now() + if (size > 0 && now - lastLogTime > 5000) { + const fraction = sizeProcesed / size + if (fraction - lastLogFraction > 0.05) { + lastLogTime = now + lastLogFraction = fraction + const formattedFraction = fraction.toLocaleString(undefined, { + style: 'percent', + minimumFractionDigits: 2, + maximumFractionDigits: 2, + }) + logger.debug(`File upload progress: ${formattedFraction}`) + } + } + return chunk + }) + + const fileWriteStream = createWriteStream(tmpFileName) + const gz = createGzip() + await pipeline(stream, gz, fileWriteStream) + + const fileChecksum = hash.digest('hex') + logger.debug(`Uploaded file checksum: "${fileChecksum}"`) + + const uploadedFileName = join(fileUploadFolder, fileChecksum) + logger.debug( + `File uploaded successfully, moving temporary file to final location: "${uploadedFileName}"`, + ) + await rename(tmpFileName, uploadedFileName) + await rmdir(tmpDir) + logger.log('File upload finished') + return fileChecksum +} diff --git a/packages/apollo-collaboration-server/src/utils/FileStorageEngine.ts b/packages/apollo-collaboration-server/src/utils/FileStorageEngine.ts deleted file mode 100644 index de7931eda..000000000 --- a/packages/apollo-collaboration-server/src/utils/FileStorageEngine.ts +++ /dev/null @@ -1,73 +0,0 @@ -/* eslint-disable @typescript-eslint/no-confusing-void-expression */ - -/* eslint-disable @typescript-eslint/no-unsafe-argument */ -/* eslint-disable @typescript-eslint/no-unsafe-return */ -import { createHash } from 'node:crypto' -import { createWriteStream } from 'node:fs' -import { mkdir, mkdtemp, rename, rmdir } from 'node:fs/promises' -import { join } from 'node:path' -import { pipeline } from 'node:stream/promises' -import { createGzip } from 'node:zlib' - -import { - Injectable, - InternalServerErrorException, - Logger, -} from '@nestjs/common' -import { StorageEngine } from 'multer' - -export interface UploadedFile extends Express.Multer.File { - checksum: string -} - -@Injectable() -export class FileStorageEngine implements StorageEngine { - private readonly logger = new Logger(FileStorageEngine.name) - - async _handleFile( - req: Express.Request, - file: Express.Multer.File, - cb: (error?: unknown, info?: UploadedFile) => void, - ) { - const { FILE_UPLOAD_FOLDER } = process.env - if (!FILE_UPLOAD_FOLDER) { - return cb( - new InternalServerErrorException( - 'No FILE_UPLOAD_FOLDER found in .env file', - ), - ) - } - await mkdir(FILE_UPLOAD_FOLDER, { recursive: true }) - const tmpDir = await mkdtemp(join(FILE_UPLOAD_FOLDER, 'upload-tmp-')) - // First we need to write new file using temp name. After writing has completed then we rename the file to match with file checksum - const tempFullFileName = join(tmpDir, `${file.originalname}.gz`) - this.logger.debug(`User uploaded file: ${file.originalname}`) - - const hash = createHash('md5') - file.stream.on('data', (chunk) => { - hash.update(chunk, 'utf8') - return chunk - }) - - // Check md5 checksum of saved file - const fileWriteStream = createWriteStream(tempFullFileName) - const gz = createGzip() - await pipeline(file.stream, gz, fileWriteStream) - this.logger.debug(`Compressed file: ${tempFullFileName}`) - const fileChecksum = hash.digest('hex') - this.logger.debug(`Uploaded file checksum: ${fileChecksum}`) - const finalFullFileName = join(FILE_UPLOAD_FOLDER, fileChecksum) - this.logger.debug(`FinalFullFileName: ${finalFullFileName}`) - await rename(tempFullFileName, finalFullFileName) - await rmdir(tmpDir) - - cb(null, { ...file, checksum: fileChecksum }) - } - - _removeFile( - _req: Express.Request, - _file: Express.Multer.File, - _cb: (error: Error | null) => void, - // eslint-disable-next-line @typescript-eslint/no-empty-function - ) {} -} diff --git a/packages/apollo-common/src/AssemblySpecificChange.ts b/packages/apollo-common/src/AssemblySpecificChange.ts index c8f56d252..becb81131 100644 --- a/packages/apollo-common/src/AssemblySpecificChange.ts +++ b/packages/apollo-common/src/AssemblySpecificChange.ts @@ -55,6 +55,7 @@ export abstract class AssemblySpecificChange extends Change { 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') @@ -68,6 +69,10 @@ export abstract class AssemblySpecificChange extends Change { 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') { @@ -89,9 +94,6 @@ export abstract class AssemblySpecificChange extends Change { throw new Error('No refSeq document found') } refSeqLen += sequenceBuffer.length - 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([ { @@ -138,9 +140,6 @@ export abstract class AssemblySpecificChange extends Change { while (sequenceBuffer.length >= chunkSize) { const sequence = sequenceBuffer.slice(0, chunkSize) refSeqLen += sequence.length - logger.debug?.( - `Creating refSeq chunk number ${chunkIndex} of "${_id}"`, - ) // 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 }, @@ -148,7 +147,6 @@ export abstract class AssemblySpecificChange extends Change { chunkIndex++ // Set remaining sequence sequenceBuffer = sequenceBuffer.slice(chunkSize) - logger.debug?.(`Remaining sequence: "${sequenceBuffer}"`) } } } @@ -204,7 +202,7 @@ export abstract class AssemblySpecificChange extends Change { async addFeatureIntoDb(gff3Feature: GFF3Feature, backend: ServerDataStore) { const { featureModel, refSeqModel, user } = backend - const { assembly, logger, refSeqCache } = this + const { assembly, refSeqCache } = this const [{ seq_id: refName }] = gff3Feature if (!refName) { @@ -230,23 +228,16 @@ export abstract class AssemblySpecificChange extends Change { const featureIds: string[] = [] const newFeature = createFeature(gff3Feature, refSeqDoc._id, featureIds) - logger.debug?.(`So far feature ids are: ${featureIds.toString()}`) // Add value to gffId newFeature.attributes?._id ? (newFeature.gffId = newFeature.attributes?._id.toString()) : (newFeature.gffId = newFeature._id) - logger.debug?.( - `********************* Assembly specific change create ${JSON.stringify( - newFeature, - )}`, - ) // Add into Mongo // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction - const [newFeatureDoc] = await featureModel.create([ + await featureModel.create([ { allIds: featureIds, ...newFeature, user, status: -1 }, ]) - logger.verbose?.(`Added docId "${newFeatureDoc._id}"`) } } diff --git a/packages/apollo-shared/src/Changes/AddFeaturesFromFileChange.ts b/packages/apollo-shared/src/Changes/AddFeaturesFromFileChange.ts index 9df38fc96..8c05fb021 100644 --- a/packages/apollo-shared/src/Changes/AddFeaturesFromFileChange.ts +++ b/packages/apollo-shared/src/Changes/AddFeaturesFromFileChange.ts @@ -1,3 +1,4 @@ +/* eslint-disable @typescript-eslint/restrict-template-expressions */ /* eslint-disable @typescript-eslint/require-await */ import { AssemblySpecificChange, @@ -91,13 +92,17 @@ export class AddFeaturesFromFileChange extends AssemblySpecificChange { const featureStream = filesService.parseGFF3( filesService.getFileStream(fileDoc), ) + let featureCount = 0 for await (const f of featureStream) { const gff3Feature = f as GFF3Feature - logger.verbose?.(`ENTRY=${JSON.stringify(gff3Feature)}`) // 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!') diff --git a/packages/jbrowse-plugin-apollo/src/components/AddAssembly.tsx b/packages/jbrowse-plugin-apollo/src/components/AddAssembly.tsx index ce3c11852..13a456ee3 100644 --- a/packages/jbrowse-plugin-apollo/src/components/AddAssembly.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/AddAssembly.tsx @@ -168,19 +168,21 @@ export function AddAssembly({ const { baseURL, getFetcher, internetAccountId } = selectedInternetAccount if (fileType !== FileType.EXTERNAL && file) { // First upload file - const url = new URL('files', baseURL).href + const url = new URL('files', baseURL) + url.searchParams.set('type', fileType) + const uri = url.href const formData = new FormData() formData.append('file', file) formData.append('fileName', file.name) formData.append('type', fileType) const apolloFetchFile = getFetcher({ locationType: 'UriLocation', - uri: url, + uri, }) if (apolloFetchFile) { jobsManager.update(job.name, 'Uploading file, this may take awhile') const { signal } = controller - const response = await apolloFetchFile(url, { + const response = await apolloFetchFile(uri, { method: 'POST', body: formData, signal, diff --git a/packages/jbrowse-plugin-apollo/src/components/ImportFeatures.tsx b/packages/jbrowse-plugin-apollo/src/components/ImportFeatures.tsx index e8b37eee5..59cf330be 100644 --- a/packages/jbrowse-plugin-apollo/src/components/ImportFeatures.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/ImportFeatures.tsx @@ -160,14 +160,16 @@ export function ImportFeatures({ const { baseURL } = apolloInternetAccount // First upload file - const url = new URL('files', baseURL).href + const url = new URL('files', baseURL) + url.searchParams.set('type', 'text/x-gff3') + const uri = url.href const formData = new FormData() formData.append('file', file) formData.append('fileName', file.name) formData.append('type', 'text/x-gff3') const apolloFetchFile = apolloInternetAccount.getFetcher({ locationType: 'UriLocation', - uri: url, + uri, }) handleClose() @@ -189,7 +191,7 @@ export function ImportFeatures({ if (apolloFetchFile) { const { signal } = controller - const response = await apolloFetchFile(url, { + const response = await apolloFetchFile(uri, { method: 'POST', body: formData, signal, diff --git a/yarn.lock b/yarn.lock index c8800cd0c..9b8be67cd 100644 --- a/yarn.lock +++ b/yarn.lock @@ -128,11 +128,13 @@ __metadata: "@oclif/plugin-help": "npm:^6.0.8" "@oclif/test": "npm:^3.1.3" "@types/chai": "npm:^4" + "@types/cli-progress": "npm:^3" "@types/inquirer": "npm:^9.0.7" "@types/mocha": "npm:^10" "@types/node": "npm:^18.14.2" babel-plugin-istanbul: "npm:^6.1.1" bson: "npm:^6.3.0" + cli-progress: "npm:^3.12.0" conf: "npm:^12.0.0" joi: "npm:^17.7.0" mocha: "npm:^10.2.0" @@ -6947,21 +6949,21 @@ __metadata: languageName: node linkType: hard -"@types/cli-progress@npm:^3.11.0": - version: 3.11.3 - resolution: "@types/cli-progress@npm:3.11.3" +"@types/cli-progress@npm:^3, @types/cli-progress@npm:^3.11.5": + version: 3.11.5 + resolution: "@types/cli-progress@npm:3.11.5" dependencies: "@types/node": "npm:*" - 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