Temp commit to fix buffer

GMOD · Sep 18, 2024 · f46e7a5 · f46e7a5
1 parent b01ad2a
commit f46e7a5
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Showing 4 changed files with 17 additions and 9 deletions.
diff --git a/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts b/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts
@@ -137,7 +137,7 @@ Indexes should be named <my.fasta.gz>.gzi and <my.fasta.gz>.fai unless options -
             access.accessToken,
             fai,
             'text/x-fai',
-            true,
+            false,
           )
 
       const gziId = gziIsFileId
@@ -147,7 +147,7 @@ Indexes should be named <my.fasta.gz>.gzi and <my.fasta.gz>.fai unless options -
             access.accessToken,
             gzi,
             'application/x-gzi',
-            true,
+            false,
           )
 
       body = {

diff --git a/packages/apollo-collaboration-server/src/files/files.service.ts b/packages/apollo-collaboration-server/src/files/files.service.ts
@@ -87,13 +87,13 @@ export class FilesService {
     })
     const fileName = join(fileUploadFolder, file.checksum)
     switch (file.type) {
-      case 'application/x-bgzip-fasta':
+      case 'text/x-fai':
       case 'application/x-gzi': {
         return new LocalFileGzip(fileName)
       }
+      case 'application/x-bgzip-fasta':
       case 'text/x-gff3':
-      case 'text/x-fasta':
-      case 'text/x-fai': {
+      case 'text/x-fasta': {
         return new LocalFile(fileName)
       }
     }

diff --git a/packages/apollo-collaboration-server/src/sequence/sequence.service.ts b/packages/apollo-collaboration-server/src/sequence/sequence.service.ts
@@ -19,6 +19,7 @@ import { Model } from 'mongoose'
 import { AssembliesService } from '../assemblies/assemblies.service'
 import { GetSequenceDto } from './dto/get-sequence.dto'
 import path from 'node:path'
+import { LocalFileGzip } from '@apollo-annotation/shared'
 
 @Injectable()
 export class SequenceService {
@@ -96,7 +97,9 @@ export class SequenceService {
       const sequenceAdapter = gzi
         ? new BgzipIndexedFasta({
             fasta: new LocalFile(path.join(FILE_UPLOAD_FOLDER, faChecksum)),
-            fai: new LocalFile(path.join(FILE_UPLOAD_FOLDER, faiChecksum)),
+            fai: new LocalFileGzip(path.join(FILE_UPLOAD_FOLDER, faiChecksum), {
+              encoding: 'utf8',
+            }),
             gzi: new LocalFile(path.join(FILE_UPLOAD_FOLDER, gziChecksum)),
           })
         : new IndexedFasta({

diff --git a/packages/apollo-shared/src/util.ts b/packages/apollo-shared/src/util.ts
@@ -36,9 +36,12 @@ export class LocalFileGzip implements GenericFilehandle {
   ): Promise<{ bytesRead: number; buffer: Buffer }> {
     const fileHandle = await this.getFileHandle()
     const unzippedContents = await unzip(fileHandle)
-    const str = unzippedContents.toString()
-    const substr = str.slice(position, position + length)
-    const bytesRead = buffer.write(substr, offset)
+    const bytesRead = unzippedContents.copy(
+      buffer,
+      position,
+      offset,
+      offset + length,
+    )
     return { bytesRead, buffer }
   }
 
@@ -59,8 +62,10 @@ export class LocalFileGzip implements GenericFilehandle {
     const fileHandle = await this.getFileHandle()
     const unzippedContents = await unzip(fileHandle)
     if (this.opts.encoding) {
+      console.log(`IN: ${this.filename}`)
       return unzippedContents.toString(this.opts.encoding)
     }
+    console.log(`OUT: ${this.filename}`)
     return unzippedContents
   }