Move LocalFileGzip to collab server package

GMOD · Sep 20, 2024 · db455a3 · db455a3
1 parent 9d149dc
commit db455a3
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Showing 4 changed files with 93 additions and 89 deletions.
diff --git a/packages/apollo-collaboration-server/src/files/files.service.ts b/packages/apollo-collaboration-server/src/files/files.service.ts
@@ -16,9 +16,12 @@ import { InjectModel } from '@nestjs/mongoose'
 import { Model } from 'mongoose'
 
 import { CreateFileDto } from './dto/create-file.dto'
-import { writeFileAndCalculateHash, FileRequest } from './filesUtil'
+import {
+  writeFileAndCalculateHash,
+  FileRequest,
+  LocalFileGzip,
+} from './filesUtil'
 import { GenericFilehandle, LocalFile } from 'generic-filehandle'
-import { LocalFileGzip } from '@apollo-annotation/shared'
 
 @Injectable()
 export class FilesService {

diff --git a/packages/apollo-collaboration-server/src/files/filesUtil.ts b/packages/apollo-collaboration-server/src/files/filesUtil.ts
@@ -1,13 +1,22 @@
 import { createHash } from 'node:crypto'
-import { createWriteStream } from 'node:fs'
-import { mkdir, mkdtemp, rename, rmdir } from 'node:fs/promises'
+import { createWriteStream, Stats } from 'node:fs'
+import {
+  FileHandle,
+  mkdir,
+  mkdtemp,
+  open,
+  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 { promisify } from 'node:util'
+import { createGzip, gunzip } from 'node:zlib'
 
 import { Logger } from '@nestjs/common'
 import { Request } from 'express'
+import { GenericFilehandle, FilehandleOptions } from 'generic-filehandle'
 
 interface FileUpload {
   originalname: string
@@ -81,3 +90,78 @@ export async function writeFileAndCalculateHash(
   logger.log('File upload finished')
   return fileChecksum
 }
+
+async function unzip(input: FileHandle): Promise<Buffer> {
+  const gunzipP = promisify(gunzip)
+  const fileContents = await input.readFile()
+  const unzippedContents = await gunzipP(fileContents)
+  return unzippedContents
+}
+
+export class LocalFileGzip implements GenericFilehandle {
+  private fileHandle: Promise<FileHandle> | undefined
+  private filename: string
+  private opts: FilehandleOptions
+
+  public constructor(source: string, opts: FilehandleOptions = {}) {
+    this.filename = source
+    this.opts = opts
+  }
+
+  private getFileHandle(): Promise<FileHandle> {
+    if (!this.fileHandle) {
+      this.fileHandle = open(this.filename)
+    }
+    return this.fileHandle
+  }
+
+  public async read(
+    buffer: Buffer,
+    offset = 0,
+    length: number,
+    position = 0,
+  ): Promise<{ bytesRead: number; buffer: Buffer }> {
+    const fileHandle = await this.getFileHandle()
+    const unzippedContents = await unzip(fileHandle)
+    const bytesRead = unzippedContents.copy(
+      buffer,
+      position,
+      offset,
+      offset + length,
+    )
+    return { bytesRead, buffer }
+  }
+
+  public async readFile(): Promise<Buffer>
+  public async readFile(options: BufferEncoding): Promise<string>
+  public async readFile<T extends undefined>(
+    options:
+      | Omit<FilehandleOptions, 'encoding'>
+      | (Omit<FilehandleOptions, 'encoding'> & { encoding: T }),
+  ): Promise<Buffer>
+  public async readFile<T extends BufferEncoding>(
+    options: Omit<FilehandleOptions, 'encoding'> & { encoding: T },
+  ): Promise<string>
+
+  public async readFile(
+    _options?: FilehandleOptions | BufferEncoding,
+  ): Promise<Buffer | string> {
+    const fileHandle = await this.getFileHandle()
+    const unzippedContents = await unzip(fileHandle)
+    if (this.opts.encoding) {
+      return unzippedContents.toString(this.opts.encoding)
+    }
+    return unzippedContents
+  }
+
+  // todo memoize
+  public async stat(): Promise<Stats> {
+    const fh = await this.getFileHandle()
+    return fh.stat()
+  }
+
+  public async close(): Promise<void> {
+    const fh = await this.getFileHandle()
+    return fh.close()
+  }
+}
diff --git a/packages/apollo-shared/src/util.ts b/packages/apollo-shared/src/util.ts
@@ -3,89 +3,6 @@
 import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 import { GFF3Feature } from '@gmod/gff'
 
-import fs from 'node:fs'
-
-import { Buffer } from 'node:buffer'
-import { promisify } from 'node:util'
-import { GenericFilehandle, FilehandleOptions, Stats } from 'generic-filehandle'
-import { FileHandle } from 'node:fs/promises'
-import { gunzip } from 'node:zlib'
-
-export class LocalFileGzip implements GenericFilehandle {
-  private fileHandle: Promise<FileHandle> | undefined
-  private filename: string
-  private opts: FilehandleOptions
-
-  public constructor(source: string, opts: FilehandleOptions = {}) {
-    this.filename = source
-    this.opts = opts
-  }
-
-  private getFileHandle(): Promise<FileHandle> {
-    if (!this.fileHandle) {
-      this.fileHandle = fs.promises.open(this.filename)
-    }
-    return this.fileHandle
-  }
-
-  public async read(
-    buffer: Buffer,
-    offset = 0,
-    length: number,
-    position = 0,
-  ): Promise<{ bytesRead: number; buffer: Buffer }> {
-    const fileHandle = await this.getFileHandle()
-    const unzippedContents = await unzip(fileHandle)
-    const bytesRead = unzippedContents.copy(
-      buffer,
-      position,
-      offset,
-      offset + length,
-    )
-    return { bytesRead, buffer }
-  }
-
-  public async readFile(): Promise<Buffer>
-  public async readFile(options: BufferEncoding): Promise<string>
-  public async readFile<T extends undefined>(
-    options:
-      | Omit<FilehandleOptions, 'encoding'>
-      | (Omit<FilehandleOptions, 'encoding'> & { encoding: T }),
-  ): Promise<Buffer>
-  public async readFile<T extends BufferEncoding>(
-    options: Omit<FilehandleOptions, 'encoding'> & { encoding: T },
-  ): Promise<string>
-
-  public async readFile(
-    _options?: FilehandleOptions | BufferEncoding,
-  ): Promise<Buffer | string> {
-    const fileHandle = await this.getFileHandle()
-    const unzippedContents = await unzip(fileHandle)
-    if (this.opts.encoding) {
-      return unzippedContents.toString(this.opts.encoding)
-    }
-    return unzippedContents
-  }
-
-  // todo memoize
-  public async stat(): Promise<Stats> {
-    const fh = await this.getFileHandle()
-    return fh.stat()
-  }
-
-  public async close(): Promise<void> {
-    const fh = await this.getFileHandle()
-    return fh.close()
-  }
-}
-
-async function unzip(input: FileHandle): Promise<Buffer> {
-  const gunzipP = promisify(gunzip)
-  const fileContents = await input.readFile()
-  const unzippedContents = await gunzipP(fileContents)
-  return unzippedContents
-}
-
 export function makeGFF3Feature(
   feature: AnnotationFeatureSnapshot,
   parentId?: string,

diff --git a/packages/jbrowse-plugin-apollo/src/components/AddAssembly.tsx b/packages/jbrowse-plugin-apollo/src/components/AddAssembly.tsx
@@ -225,7 +225,7 @@ export function AddAssembly({
       const fileUploadChangeBase = {
         assembly: new ObjectID().toHexString(),
         assemblyName,
-        fileId,
+        fileIds: { fa: fileId },
       }
       change =
         fileType === FileType.GFF3 && importFeatures