def dissociate_sample(self,
account_id,
source_id,
sample_id,
override_locked=False):
existing_sample = self.get_sample(account_id, source_id, sample_id)
if existing_sample is None:
raise werkzeug.exceptions.NotFound("No sample ID: %s" % sample_id)
if existing_sample.edit_locked and not override_locked:
raise RepoException(
"Sample information locked: Sample already evaluated for "
"processing")
# Wipe any user entered fields from the sample:
self.update_info(account_id,
source_id,
SampleInfo(sample_id, None, None, None),
override_locked=override_locked)
if existing_sample.remove_locked and not override_locked:
raise RepoException(
"Sample association locked: Sample already received")
# And detach the sample from the source
self._update_sample_association(sample_id,
None,
override_locked=override_locked)
def update_sample_association(account_id, source_id, sample_id, body,
token_info):
_validate_account_access(token_info, account_id)
# TODO: API layer doesn't understand that BadRequest can be thrown,
# but that looks to be the right result if sample_site bad.
# Need to update the api layer if we want to specify 400s.
# (Or we leave api as is and say 400's can always be thrown if your
# request is bad)
with Transaction() as t:
sample_repo = SampleRepo(t)
source_repo = SourceRepo(t)
source = source_repo.get_source(account_id, source_id)
if source is None:
return jsonify(code=404, message="No such source"), 404
needs_sample_site = source.source_type in [
Source.SOURCE_TYPE_HUMAN, Source.SOURCE_TYPE_ANIMAL
]
precludes_sample_site = source.source_type == \
Source.SOURCE_TYPE_ENVIRONMENT
sample_site_present = "sample_site" in body and \
body["sample_site"] is not None
if needs_sample_site and not sample_site_present:
# Human/Animal sources require sample_site to be set
raise BadRequest("human/animal samples require sample_site")
if precludes_sample_site and sample_site_present:
raise BadRequest("environmental samples cannot specify "
"sample_site")
sample_datetime = body['sample_datetime']
try:
sample_datetime = fromisotime(sample_datetime)
except ValueError:
raise BadRequest("Invalid sample_datetime")
curdate = datetime.now(sample_datetime.tzinfo)
lower_limit = curdate + relativedelta(years=-10)
upper_limit = curdate + relativedelta(months=+1)
if sample_datetime < lower_limit or sample_datetime > upper_limit:
raise BadRequest('Invalid sample date')
# sample_site will not be present if its environmental. this will
# default to None if the key is not present
sample_site = body.get('sample_site')
sample_info = SampleInfo(sample_id, sample_datetime, sample_site,
body["sample_notes"])
is_admin = token_grants_admin_access(token_info)
sample_repo.update_info(account_id,
source_id,
sample_info,
override_locked=is_admin)
final_sample = sample_repo.get_sample(account_id, source_id, sample_id)
t.commit()
return jsonify(final_sample), 200
def dissociate_sample(self, account_id, source_id, sample_id):
existing_sample = self.get_sample(account_id, source_id, sample_id)
if existing_sample is None:
raise werkzeug.exceptions.NotFound("No sample ID: %s" % sample_id)
if existing_sample.is_locked:
raise RepoException("Sample edits locked: Sample already received")
# Wipe any user entered fields from the sample:
self.update_info(account_id, source_id,
SampleInfo(sample_id, None, None, None))
# And detach the sample from the source
self._update_sample_association(sample_id, None)
def create_dummy_sample_objects(filled=False):
info_dict = DUMMY_FILLED_SAMPLE_INFO if filled else DUMMY_EMPTY_SAMPLE_INFO
datetime_str = info_dict["sample_datetime"]
datetime_obj = None if datetime_str is None else isoparse(datetime_str)
sample_info = SampleInfo(
info_dict["sample_id"],
datetime_obj,
info_dict["sample_site"],
info_dict["sample_notes"]
)
sample = Sample(info_dict["sample_id"],
datetime_obj,
info_dict["sample_site"],
info_dict["sample_notes"],
info_dict["sample_barcode"],
None,
info_dict["sample_projects"])
return sample_info, sample