async def upload_reads_to_cache(request):
name = request.match_info["name"]
sample_id = request.match_info["sample_id"]
key = request.match_info["key"]
if name not in ["reads_1.fq.gz", "reads_2.fq.gz"]:
return not_found()
if sample_id != TEST_SAMPLE_ID or key != TEST_CACHE["key"]:
return not_found()
document = await read_file_from_request(request, name, "fastq")
return json_response(document, status=201)
async def create_mock_cache(request):
sample_id = request.match_info["sample_id"]
if sample_id != TEST_SAMPLE_ID:
return not_found()
_json = await request.json()
key = _json["key"]
if key == TEST_CACHE["key"]:
return json_response(TEST_CACHE, status=201)
else:
return not_found()
async def get_sample(request):
sample_id = request.match_info["sample_id"]
if sample_id != TEST_SAMPLE_ID:
return not_found()
return json_response(TEST_SAMPLE, status=200)
async def get_cache(request):
sample_id = request.match_info["sample_id"]
key = request.match_info["key"]
if sample_id != TEST_SAMPLE_ID or key != TEST_CACHE["key"]:
return not_found()
return json_response(TEST_CACHE)
async def download_reads_file(request):
sample_id = request.match_info["sample_id"]
filename = request.match_info["filename"]
if sample_id != TEST_SAMPLE_ID or filename not in ("reads_1.fq.gz",
"reads_2.fq.gz"):
return not_found()
file_name = "paired_small_1.fq.gz" if filename == "reads_1.fq.gz" else "paired_small_2.fq.gz"
return FileResponse(ANALYSIS_TEST_FILES_DIR / file_name)
async def delete_cache(request):
sample_id = request.match_info["sample_id"]
key = request.match_info["key"]
if sample_id != TEST_SAMPLE_ID or key != TEST_CACHE["key"]:
return not_found()
if TEST_CACHE["ready"] is True:
return json_response({"message": "Cache is finalized."}, status=409)
return Response(status=204)
async def upload_read_files(request):
sample_id = request.match_info["sample_id"]
if sample_id != TEST_SAMPLE_ID:
return not_found()
name = request.query.get("name")
type = request.query.get("type")
file = await read_file_from_request(request, name, type)
return json_response(file, status=201)
async def finalize(request):
sample_id = request.match_info["sample_id"]
if sample_id != TEST_SAMPLE_ID:
return not_found()
response_json = await request.json()
TEST_SAMPLE["quality"] = response_json["quality"]
TEST_SAMPLE["ready"] = True
return json_response(TEST_SAMPLE)
async def upload_artifact_to_cache(request):
sample_id = request.match_info["sample_id"]
key = request.match_info["key"]
type = request.query.get("type")
name = request.query.get("name")
if sample_id != TEST_SAMPLE_ID or key != TEST_CACHE["key"]:
return not_found()
document = await read_file_from_request(request, name, type)
return json_response(document, status=201)
async def delete(request):
sample_id = request.match_info["sample_id"]
if sample_id != TEST_SAMPLE_ID:
return not_found()
if "ready" in TEST_SAMPLE and TEST_SAMPLE["ready"] is True:
return json_response(
{"message": "Already Finalized"},
status=400,
)
return Response(status=204)
async def download_artifact(request):
sample_id = request.match_info["sample_id"]
filename = request.match_info["filename"]
if sample_id != TEST_SAMPLE_ID:
return not_found()
tempdir = Path(tempfile.mkdtemp())
file = tempdir / filename
file.touch()
return FileResponse(file)
async def finalize_cache(request):
sample_id = request.match_info["sample_id"]
key = request.match_info["key"]
if sample_id != TEST_SAMPLE_ID or key != TEST_CACHE["key"]:
return not_found()
_json = await request.json()
quality = _json["quality"]
TEST_CACHE["quality"] = quality
TEST_CACHE["ready"] = True
return json_response(TEST_CACHE)