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Fix collaboration server running out of memory on GFF3 import #719

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Merged
garrettjstevens merged 1 commit into from
Oct 23, 2025
Merged

Fix collaboration server running out of memory on GFF3 import #719

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6 changes: 5 additions & 1 deletion 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 @@ -103,14 +103,18 @@ export class FilesService {
}
}

parseGFF3(stream: ReadableStream<Uint8Array>): ReadableStream<GFF3Feature> {
parseGFF3(
stream: ReadableStream<Uint8Array>,
options?: { bufferSize?: number },
): ReadableStream<GFF3Feature> {
return stream.pipeThrough(
new TransformStream(
new GFFTransformer({
parseSequences: false,
parseComments: false,
parseDirectives: false,
parseFeatures: true,
...options,
}),
),
)
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5 changes: 4 additions & 1 deletion packages/apollo-common/src/Operation.ts
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Expand Up @@ -45,7 +45,10 @@ export interface ServerDataStore {
filesService: {
getFileStream(file: FileDocument): ReadableStream<Uint8Array>
getFileHandle(file: FileDocument): GenericFilehandle
parseGFF3(stream: ReadableStream<Uint8Array>): ReadableStream<GFF3Feature>
parseGFF3(
stream: ReadableStream<Uint8Array>,
parseOptions?: { bufferSize?: number },
): ReadableStream<GFF3Feature>
create(createFileDto: CreateFileDto): void
remove(id: string): void
}
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9 changes: 4 additions & 5 deletions packages/apollo-shared/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts
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Expand Up @@ -19,6 +19,7 @@ export interface SerializedAddAssemblyAndFeaturesFromFileChangeBase
export interface AddAssemblyAndFeaturesFromFileChangeDetails {
assemblyName: string
fileIds: { fa: string }
parseOptions?: { bufferSize: number }
}

export interface SerializedAddAssemblyAndFeaturesFromFileChangeSingle
Expand Down Expand Up @@ -68,7 +69,7 @@ export class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange {
const { assemblyModel, checkModel, fileModel, filesService, user } = backend
const { assembly, changes, logger } = this
for (const change of changes) {
const { assemblyName, fileIds } = change
const { assemblyName, fileIds, parseOptions } = change
const fileId = fileIds.fa

const { FILE_UPLOAD_FOLDER } = process.env
Expand Down Expand Up @@ -110,12 +111,10 @@ export class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange {
backend,
)

// Loop all features
logger.debug?.(
`**************** LOOPATAAN KAIKKI FEATURET SEURAAVAKSI File type: "${fileDoc.type}"`,
)
const { bufferSize = 10_000 } = parseOptions ?? {}
const featureStream = filesService.parseGFF3(
filesService.getFileStream(fileDoc),
{ bufferSize },
)
// @ts-expect-error type is wrong here
// eslint-disable-next-line @typescript-eslint/await-thenable
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5 changes: 4 additions & 1 deletion packages/apollo-shared/src/Changes/AddFeaturesFromFileChange.ts
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Expand Up @@ -18,6 +18,7 @@ export interface SerializedAddFeaturesFromFileChangeBase

export interface AddFeaturesFromFileChangeDetails {
fileId: string
parseOptions?: { bufferSize: number }
}

export interface SerializedAddFeaturesFromFileChangeSingle
Expand Down Expand Up @@ -75,7 +76,7 @@ export class AddFeaturesFromFileChange extends FromFileBaseChange {
}

for (const change of changes) {
const { fileId } = change
const { fileId, parseOptions } = change

const { FILE_UPLOAD_FOLDER } = process.env
if (!FILE_UPLOAD_FOLDER) {
Expand All @@ -89,8 +90,10 @@ export class AddFeaturesFromFileChange extends FromFileBaseChange {
logger.debug?.(`FileId "${fileId}", checksum "${fileDoc.checksum}"`)

// Read data from compressed file and parse the content
const { bufferSize = 10_000 } = parseOptions ?? {}
const featureStream = filesService.parseGFF3(
filesService.getFileStream(fileDoc),
{ bufferSize },
)
let featureCount = 0
// @ts-expect-error type is wrong here
Expand Down