Staging API¶

The staging area holds uploaded files before they are linked to samples via bulk submission.

Upload a file¶

POST /api/v1/staging/upload

Requires authentication. Upload files directly — MD5 is computed server-side.

curl -X POST http://localhost:8000/api/v1/staging/upload \
  -H "Authorization: Bearer $TOKEN" \
  -F "file=@SAMPLE_001_R1.fastq.gz"

Response:

{
  "id": 1,
  "filename": "SAMPLE_001_R1.fastq.gz",
  "file_size": 1234567890,
  "checksum_md5": "d41d8cd98f00b204e9800998ecf8427e",
  "status": "VERIFIED",
  "upload_method": "direct",
  "created_at": "2026-01-15T10:30:00"
}

List staged files¶

GET /api/v1/staging/files

Returns all files staged by the authenticated user.

curl -H "Authorization: Bearer $TOKEN" \
  http://localhost:8000/api/v1/staging/files

Delete a staged file¶

DELETE /api/v1/staging/files/{file_id}

curl -X DELETE http://localhost:8000/api/v1/staging/files/42 \
  -H "Authorization: Bearer $TOKEN"

Presigned upload (alternative)¶

For large files or S3-compatible clients:

Initiate¶

curl -X POST http://localhost:8000/api/v1/staging/initiate \
  -H "Authorization: Bearer $TOKEN" \
  -H "Content-Type: application/json" \
  -d '{"filename": "SAMPLE_001_R1.fastq.gz", "file_size": 1234567890}'

Response:

{
  "staged_file_id": 1,
  "presigned_url": "http://minio:9000/nfdp-staging/...",
  "staging_path": "user_1/1/SAMPLE_001_R1.fastq.gz",
  "expires_in": 86400
}

Upload to presigned URL¶

curl -X PUT "$PRESIGNED_URL" \
  --upload-file SAMPLE_001_R1.fastq.gz

Complete¶

curl -X POST http://localhost:8000/api/v1/staging/complete/1 \
  -H "Authorization: Bearer $TOKEN"

Lifecycle¶

Upload — File stored in staging bucket
Validation — Bulk submit matches staged files to sample sheet
Confirmation — Files linked to runs, marked as "linked"
Cleanup — Linked files moved to raw storage

Info

Staged files persist across sessions until used or deleted.