def request_handler(request, func, *args):
try:
record_timing(request, note="before")
msg = {'result': str(func(*args))}
record_timing(request, note="after")
except InvalidNumber:
msg = {'message': 'Invalid number'}
return msg
async def get_with_intermediate_timing(request: Request) -> None:
await asyncio.sleep(0.1)
record_timing(request, note="halfway")
await asyncio.sleep(0.1)
def get_with_intermediate_timing(request: Request) -> None:
record_timing(request, note="hello")
def fail_to_record(request: Request) -> None:
record_timing(request)
async def patch_run(
request: Request,
run_id: int,
patch: list,
enforcer: casbin.Enforcer = Depends(get_enforcer),
db: Session = Depends(get_db),
current_user: Auth0ClaimsPatched = Depends(get_current_user)):
if not check_access(enforcer,
user=current_user.username,
path=f"/run/{str(run_id)}",
method="PUT"):
raise HTTPException(status_code=403, detail='Insufficient Permissions')
new_run = db.query(Run).get(run_id)
original_run_version = new_run.current
if not new_run or new_run.is_deleted:
raise HTTPException(status_code=404, detail='Run Not Found')
record_timing(request, note=f"Fetched run {run_id}")
run_dict = versioned_row_to_dict(new_run, new_run.current)
run_dict.pop('protocol', None)
json_patch = jsonpatch.JsonPatch(patch)
run_dict.pop('protocol', None)
run_dict = json_patch.apply(run_dict)
if not change_allowed(run_to_dict(new_run, new_run.current), run_dict):
raise HTTPException(status_code=403, detail='Insufficient Permissions')
new_run_version = RunVersion(data=strip_metadata(run_dict),
server_version=settings.server_version)
new_run_version.run = new_run
add_updator(new_run_version, current_user.username)
original_run_version = new_run.current
new_run.current = new_run_version
db.add(new_run_version)
db.commit()
record_timing(request, note=f"Saved changes to run {run_id}")
samples_dirty = False
for operation in patch:
operation_path = operation.get('path', '')
# Check for changes to the path: /sections/*/blocks/*/plates
if re.search(
"^/(sections/([^/]+/(blocks/([^/]+/(plates(/.*)?)?)?)?)?)?$",
operation_path):
samples_dirty = True
break
# Check for changes to the path: /sections/*/blocks/*/plateSequencingResults
if re.search(
"^/(sections/([^/]+/(blocks/([^/]+/(plateSequencingResults(/.*)?)?)?)?)?)?$",
operation_path):
samples_dirty = True
break
# Check for changes to the path: /protocol/sections/*/blocks/*/plateMarkers
if re.search(
"^/(protocol/(sections/([^/]+/(blocks/([^/]+/(plateMarkers(/.*)?)?)?)?)?)?)?$",
operation_path):
samples_dirty = True
break
if samples_dirty:
logger.info("======================================")
logger.info(
f"Regenerating samples for run_version: ({new_run.id}, {new_run_version.id})"
)
samples = get_samples(new_run_version, new_run.protocol_version)
record_timing(
request,
note=f"Regenerated run {new_run.id} samples (len: {len(samples)})")
if samples:
for sample in samples:
db.merge(sample)
logger.info(
f"Generated {len(samples)} samples for run_version: ({new_run.id}, {new_run_version.id})"
)
logger.info("======================================")
record_timing(
request,
note=f"Saved {len(samples)} regenerated samples to run {new_run.id}"
)
else:
logger.info("======================================")
logger.info(
f"Using old samples for run_version: ({new_run.id}, {new_run_version.id})"
)
samples = db.query(Sample)\
.filter(Sample.run_version_id == original_run_version.id)\
.distinct()
sample_count = 0
for sample in samples:
new_sample_version = clone_model(db,
sample.current,
run_version_id=new_run_version.id)
new_sample = clone_model(db,
sample,
current=new_sample_version,
run_version_id=new_run_version.id)
db.merge(new_sample)
sample_count += 1
logger.info(
f"Attached {sample_count} existing samples to run_version: ({new_run.id}, {new_run_version.id})"
)
logger.info("======================================")
record_timing(
request,
note=f"Attached {sample_count} existing samples to run {new_run.id}"
)
db.commit()
return run_to_dict(new_run, new_run.current)