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 read_sample_association(account_id, source_id, sample_id, token_info):
_validate_account_access(token_info, account_id)
with Transaction() as t:
sample_repo = SampleRepo(t)
sample = sample_repo.get_sample(account_id, source_id, sample_id)
if sample is None:
return jsonify(code=404, message="Sample not found"), 404
return jsonify(sample.to_api()), 200
def dissociate_answered_survey_from_sample(self, account_id, source_id,
sample_id, survey_id):
sample_repo = SampleRepo(self._transaction)
if not self._acct_source_owns_survey(account_id, source_id, survey_id):
raise werkzeug.exceptions.NotFound("No survey ID: %s" % survey_id)
s = sample_repo.get_sample(account_id, source_id, sample_id)
if s is None:
raise werkzeug.exceptions.NotFound("No sample ID: %s" % sample_id)
with self._transaction.cursor() as cur:
cur.execute(
"DELETE FROM source_barcodes_surveys "
"WHERE "
"barcode = %s AND "
"survey_id = %s", (s.barcode, survey_id))
# Also delete from vioscreen, myfoodrepo and polyphenol registries
cur.execute(
"UPDATE vioscreen_registry "
"SET deleted=true "
"WHERE "
"account_id = %s AND "
"source_id = %s AND "
"sample_id = %s AND "
"vio_id = %s", (account_id, source_id, sample_id, survey_id))
cur.execute(
"UPDATE myfoodrepo_registry "
"SET deleted=true "
"WHERE "
"account_id = %s AND "
"source_id = %s AND "
"myfoodrepo_id = %s", (account_id, source_id, survey_id))
try:
uuid.UUID(survey_id)
cur.execute(
"UPDATE polyphenol_ffq_registry "
"SET deleted = true "
"WHERE "
"account_id = %s AND "
"source_id = %s AND "
"polyphenol_ffq_id = %s",
(account_id, source_id, survey_id))
except ValueError:
# Note: we don't care about the error, just means it's not
# the Polyphenol FFQ
pass
def associate_answered_survey_with_sample(self, account_id, source_id,
sample_id, survey_id):
sample_repo = SampleRepo(self._transaction)
if not self._acct_owns_survey(account_id, survey_id):
raise werkzeug.exceptions.NotFound("No survey ID: %s" % survey_id)
s = sample_repo.get_sample(account_id, source_id, sample_id)
if s is None:
raise werkzeug.exceptions.NotFound("No sample ID: %s" % sample_id)
with self._transaction.cursor() as cur:
cur.execute("INSERT INTO source_barcodes_surveys "
"(barcode, survey_id) "
"VALUES(%s, %s)", (s.barcode, survey_id))
def dissociate_answered_survey_from_sample(self, account_id, source_id,
sample_id, survey_id):
sample_repo = SampleRepo(self._transaction)
if not self._acct_source_owns_survey(account_id, source_id, survey_id):
raise werkzeug.exceptions.NotFound("No survey ID: %s" % survey_id)
s = sample_repo.get_sample(account_id, source_id, sample_id)
if s is None:
raise werkzeug.exceptions.NotFound("No sample ID: %s" % sample_id)
with self._transaction.cursor() as cur:
cur.execute(
"DELETE FROM source_barcodes_surveys "
"WHERE "
"barcode = %s AND "
"survey_id = %s", (s.barcode, survey_id))
def list_answered_surveys_by_sample(self, account_id, source_id,
sample_id):
sample_repo = SampleRepo(self._transaction)
# Note: Retrieving sample in this way validates permissions.
sample = sample_repo.get_sample(account_id, source_id, sample_id)
if sample is None:
raise werkzeug.exceptions.NotFound("No sample ID: %s" % sample.id)
with self._transaction.cursor() as cur:
cur.execute(
"SELECT "
"survey_id "
"FROM "
"ag_kit_barcodes "
"LEFT JOIN source_barcodes_surveys "
"USING (barcode)"
"WHERE "
"ag_kit_barcode_id = %s", (sample_id, ))
rows = cur.fetchall()
answered_surveys = [r[0] for r in rows if r[0] is not None]
return answered_surveys
def read_sample_association(account_id, source_id, sample_id, token_info):
_validate_account_access(token_info, account_id)
with Transaction() as t:
sample_repo = SampleRepo(t)
sample = sample_repo.get_sample(account_id, source_id, sample_id)
if sample is None:
return jsonify(code=404, message="Sample not found"), 404
qiita_body = {'sample_ids': ["10317." + str(sample.barcode)]}
try:
qiita_data = qclient.post('/api/v1/study/10317/samples/status',
json=qiita_body)
accession_urls = []
for barcode_info in qiita_data:
experiment_accession = barcode_info.get("ebi_experiment_accession")
if experiment_accession is None:
continue
accession_urls.append("https://www.ebi.ac.uk/ena/browser/view/" +
experiment_accession + "?show=reads")
sample.set_accession_urls(accession_urls)
except NotFoundError:
# I guess qiita doesn't know about this barcode,
# so probably no ebi accession info
pass
except BadRequestError:
# How do I log these to gunicorn??
app.logger.warning("Couldn't communicate with qiita", exc_info=True)
except ForbiddenError:
# How do I log these to gunicorn??
app.logger.warning("Couldn't communicate with qiita", exc_info=True)
except RuntimeError:
# How do I log these to gunicorn??
app.logger.warning("Couldn't communicate with qiita", exc_info=True)
raise
return jsonify(sample.to_api()),
def associate_answered_survey_with_sample(self, account_id, source_id,
sample_id, survey_id):
sample_repo = SampleRepo(self._transaction)
if not self._acct_owns_survey(account_id, survey_id):
raise werkzeug.exceptions.NotFound("No survey ID: %s" % survey_id)
s = sample_repo.get_sample(account_id, source_id, sample_id)
if s is None:
raise werkzeug.exceptions.NotFound("No sample ID: %s" % sample_id)
# Switching to insert if not exists semantics since vioscreen IDs will
# be associated with samples prior to being filled out.
with self._transaction.cursor() as cur:
cur.execute(
"SELECT * FROM source_barcodes_surveys "
"WHERE barcode=%s AND survey_id=%s", (s.barcode, survey_id))
if cur.fetchone() is None:
cur.execute(
"INSERT INTO source_barcodes_surveys "
"(barcode, survey_id) "
"VALUES(%s, %s)", (s.barcode, survey_id))