Use files service to get filehandles

GMOD · Sep 18, 2024 · 3d78eeb · 3d78eeb
1 parent e7bbb2f
commit 3d78eeb
Showing 1 changed file with 14 additions and 23 deletions.
diff --git a/packages/apollo-collaboration-server/src/sequence/sequence.service.ts b/packages/apollo-collaboration-server/src/sequence/sequence.service.ts
@@ -13,19 +13,19 @@ import {
 import { BgzipIndexedFasta, IndexedFasta } from '@gmod/indexedfasta'
 import { Injectable, Logger } from '@nestjs/common'
 import { InjectModel } from '@nestjs/mongoose'
-import { LocalFile, RemoteFile } from 'generic-filehandle'
+import { RemoteFile } from 'generic-filehandle'
 import { Model } from 'mongoose'
 
 import { AssembliesService } from '../assemblies/assemblies.service'
+import { FilesService } from '../files/files.service'
 import { GetSequenceDto } from './dto/get-sequence.dto'
-import path from 'node:path'
-import { LocalFileGzip } from '@apollo-annotation/shared'
 
 @Injectable()
 export class SequenceService {
   constructor(
     @InjectModel(File.name)
     private readonly fileModel: Model<FileDocument>,
+    private readonly filesService: FilesService,
     @InjectModel(RefSeqChunk.name)
     private readonly refSeqChunkModel: Model<RefSeqChunkDocument>,
     @InjectModel(RefSeq.name)
@@ -72,39 +72,30 @@ export class SequenceService {
       this.logger.debug(
         `Local fasta file = ${fa}, Local fasta index file = ${fai}`,
       )
-      const { FILE_UPLOAD_FOLDER } = process.env
-      if (!FILE_UPLOAD_FOLDER) {
-        throw new Error('No FILE_UPLOAD_FOLDER found in .env file')
-      }
       const faDoc = await this.fileModel.findById(fa)
-      const faChecksum = faDoc?.checksum
-      if (!faChecksum) {
-        throw new Error(`No checksum for file document ${faDoc}`)
+      if (!faDoc) {
+        throw new Error(`No checksum for file document ${fa}`)
       }
 
       const faiDoc = await this.fileModel.findById(fai)
-      const faiChecksum = faiDoc?.checksum
-      if (!faiChecksum) {
-        throw new Error(`No checksum for file document ${faiDoc}`)
+      if (!faiDoc) {
+        throw new Error(`File document not found for ${fai}`)
       }
 
       const gziDoc = await this.fileModel.findById(gzi)
-      const gziChecksum = gziDoc?.checksum
-      if (!gziChecksum) {
-        throw new Error(`No checksum for file document ${gziDoc}`)
+      if (!gziDoc) {
+        throw new Error(`File document not found for ${gzi}`)
       }
 
       const sequenceAdapter = gzi
         ? new BgzipIndexedFasta({
-            fasta: new LocalFile(path.join(FILE_UPLOAD_FOLDER, faChecksum)),
-            fai: new LocalFileGzip(path.join(FILE_UPLOAD_FOLDER, faiChecksum), {
-              encoding: 'utf8',
-            }),
-            gzi: new LocalFileGzip(path.join(FILE_UPLOAD_FOLDER, gziChecksum)),
+            fasta: this.filesService.getFileHandle(faDoc),
+            fai: this.filesService.getFileHandle(faiDoc),
+            gzi: this.filesService.getFileHandle(gziDoc),
           })
         : new IndexedFasta({
-            fasta: new LocalFile(fa),
-            fai: new LocalFile(fai),
+            fasta: this.filesService.getFileHandle(faDoc),
+            fai: this.filesService.getFileHandle(faiDoc),
           })
       const sequence = await sequenceAdapter.getSequence(name, start, end)
       if (sequence === undefined) {