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Make sure LocalFile handles get closed #489

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merged 1 commit into from
Dec 4, 2024
Merged

Make sure LocalFile handles get closed #489

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10 changes: 1 addition & 9 deletions packages/apollo-collaboration-server/src/files/files.service.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -86,8 +86,6 @@ export class FilesService {
return fileStream.pipe(gunzip)
}

private fileHandleCache: Record<string, GenericFilehandle | undefined> = {}

getFileHandle(file: FileDocument): GenericFilehandle {
const fileUploadFolder = this.configService.get('FILE_UPLOAD_FOLDER', {
infer: true,
Expand All @@ -96,13 +94,7 @@ export class FilesService {
switch (file.type) {
case 'text/x-fai':
case 'application/x-gzi': {
const fileHandleCacheHit = this.fileHandleCache[fileName]
if (fileHandleCacheHit) {
return fileHandleCacheHit
}
const fh = new LocalFileGzip(fileName)
this.fileHandleCache[fileName] = fh
return fh
return new LocalFileGzip(fileName)
}
case 'application/x-bgzip-fasta':
case 'text/x-gff3':
Expand Down
34 changes: 14 additions & 20 deletions packages/apollo-collaboration-server/src/sequence/sequence.service.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -66,36 +66,30 @@ export class SequenceService {
}

if (assemblyDoc?.fileIds?.fai) {
const { fa, fai, gzi } = assemblyDoc.fileIds
this.logger.debug(
`Local fasta file = ${fa}, Local fasta index file = ${fai}, Local gzi index file = ${gzi}`,
)
const faDoc = await this.fileModel.findById(fa)
const { fa: faId, fai: faiId, gzi: gziId } = assemblyDoc.fileIds
const faDoc = await this.fileModel.findById(faId)
if (!faDoc) {
throw new Error(`No checksum for file document ${fa}`)
throw new Error(`No checksum for file document ${faId}`)
}

const faiDoc = await this.fileModel.findById(fai)
const faiDoc = await this.fileModel.findById(faiId)
if (!faiDoc) {
throw new Error(`File document not found for ${fai}`)
throw new Error(`File document not found for ${faiId}`)
}

const gziDoc = await this.fileModel.findById(gzi)
const gziDoc = await this.fileModel.findById(gziId)
if (!gziDoc) {
throw new Error(`File document not found for ${gzi}`)
throw new Error(`File document not found for ${gziId}`)
}

const sequenceAdapter = gzi
? new BgzipIndexedFasta({
fasta: this.filesService.getFileHandle(faDoc),
fai: this.filesService.getFileHandle(faiDoc),
gzi: this.filesService.getFileHandle(gziDoc),
})
: new IndexedFasta({
fasta: this.filesService.getFileHandle(faDoc),
fai: this.filesService.getFileHandle(faiDoc),
})
const fasta = this.filesService.getFileHandle(faDoc)
const fai = this.filesService.getFileHandle(faiDoc)
const gzi = gziId ? this.filesService.getFileHandle(gziDoc) : undefined
const sequenceAdapter = gziId
? new BgzipIndexedFasta({ fasta, fai, gzi })
: new IndexedFasta({ fasta, fai })
const sequence = await sequenceAdapter.getSequence(name, start, end)
await Promise.all([fasta.close(), fai.close(), gzi?.close()])
if (sequence === undefined) {
throw new Error('Sequence not found')
}
Expand Down
18 changes: 9 additions & 9 deletions packages/apollo-shared/src/Changes/AddAssemblyFromFileChange.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -87,7 +87,7 @@ export class AddAssemblyFromFileChange extends FromFileBaseChange {
throw new Error('No FILE_UPLOAD_FOLDER found in .env file')
}

const { fa, fai, gzi } = fileIds
const { fa: faId, fai: faiId, gzi: gziId } = fileIds
const {
assemblyModel,
checkModel,
Expand All @@ -97,30 +97,30 @@ export class AddAssemblyFromFileChange extends FromFileBaseChange {
user,
} = backend

const faDoc = await fileModel.findById(fa)
const faDoc = await fileModel.findById(faId)
const faChecksum = faDoc?.checksum
if (!faChecksum) {
throw new Error(`No checksum for file document ${faDoc}`)
}

const faiDoc = await fileModel.findById(fai)
const faiDoc = await fileModel.findById(faiId)
const faiChecksum = faiDoc?.checksum
if (!faiChecksum) {
throw new Error(`No checksum for file document ${faiDoc}`)
}

const gziDoc = await fileModel.findById(gzi)
const gziDoc = await fileModel.findById(gziId)
const gziChecksum = gziDoc?.checksum
if (!gziChecksum) {
throw new Error(`No checksum for file document ${gziDoc}`)
}

const sequenceAdapter = new BgzipIndexedFasta({
fasta: filesService.getFileHandle(faDoc),
fai: filesService.getFileHandle(faiDoc),
gzi: filesService.getFileHandle(gziDoc),
})
const fasta = filesService.getFileHandle(faDoc)
const fai = filesService.getFileHandle(faiDoc)
const gzi = filesService.getFileHandle(gziDoc)
const sequenceAdapter = new BgzipIndexedFasta({ fasta, fai, gzi })
const allSequenceSizes = await sequenceAdapter.getSequenceSizes()
await Promise.all([fasta.close(), fai.close(), gzi.close()])

const assemblyDoc = await assemblyModel
.findOne({ name: assemblyName })
Expand Down
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