def get_kit_all_samples_by_kit_id(self, kit_id):
sample_repo = SampleRepo(self._transaction)
with self._transaction.cursor() as cur:
cur.execute("SELECT "
"ag_kit.ag_kit_id, "
"ag_kit_barcodes.ag_kit_barcode_id "
"FROM ag_kit LEFT JOIN ag_kit_barcodes ON "
"ag_kit.ag_kit_id = ag_kit_barcodes.ag_kit_id "
"WHERE "
"ag_kit.ag_kit_id = %s",
(kit_id,))
rows = cur.fetchall()
if len(rows) == 0:
return None
else:
samples = [sample_repo._get_sample_by_id(r[1]) for r in rows]
return Kit(rows[0][0], samples)
def test_dissociate_sample_from_source_success(self):
dummy_acct_id, dummy_source_id = create_dummy_source(
"Bo", Source.SOURCE_TYPE_HUMAN, DUMMY_HUMAN_SOURCE,
create_dummy_1=True)
create_dummy_kit(dummy_acct_id, dummy_source_id)
dummy_answered_survey_id = create_dummy_answered_survey(
dummy_acct_id, dummy_source_id, dummy_sample_id=MOCK_SAMPLE_ID)
base_url = '/api/accounts/{0}/sources/{1}/samples'.format(
dummy_acct_id, dummy_source_id)
sample_url = "{0}/{1}".format(base_url, MOCK_SAMPLE_ID)
delete_resp = self.client.delete(
'%s?%s' % (sample_url, self.default_lang_querystring),
headers=self.dummy_auth
)
# check response code
self.assertEqual(204, delete_resp.status_code)
# load the samples associated to this source
get_response = self.client.get(
'%s?%s' % (base_url, self.default_lang_querystring),
headers=self.dummy_auth)
# check response code
self.assertEqual(200, get_response.status_code)
# ensure there are zero samples associated with this source
get_resp_obj = json.loads(get_response.data)
self.assertEqual(get_resp_obj, [])
# load the sample info
_, expected_sample = create_dummy_sample_objects(False)
with Transaction() as t:
# make sure the sample's collection info is wiped
sample_repo = SampleRepo(t)
obs_sample = sample_repo._get_sample_by_id(MOCK_SAMPLE_ID)
self.assertEqual(expected_sample.__dict__, obs_sample.__dict__)
# make sure answered survey no longer associated with any samples
answered_survey_repo = SurveyAnswersRepo(t)
answered_survey_ids = answered_survey_repo.\
_get_survey_sample_associations(dummy_answered_survey_id)
self.assertEqual([], answered_survey_ids)
def get_kit_unused_samples(self, supplied_kit_id):
sample_repo = SampleRepo(self._transaction)
# Business Logic: We now define an unclaimed sample as a sample with
# a null source_id in ag_kit_barcodes
with self._transaction.cursor() as cur:
cur.execute("SELECT "
"ag_kit.ag_kit_id, "
"ag_kit_barcodes.ag_kit_barcode_id "
"FROM ag_kit LEFT JOIN ag_kit_barcodes ON "
"ag_kit.ag_kit_id = ag_kit_barcodes.ag_kit_id "
"WHERE "
"ag_kit.supplied_kit_id = %s AND "
"ag_kit_barcodes.source_id is null",
(supplied_kit_id,))
rows = cur.fetchall()
if len(rows) == 0:
return None
else:
samples = [sample_repo._get_sample_by_id(r[1]) for r in rows]
return Kit(rows[0][0], samples)
def get_survey_metadata(self, sample_barcode, survey_template_id=None):
ids = self._get_ids_relevant_to_barcode(sample_barcode)
if ids is None:
raise NotFound("No such barcode")
account_id = ids.get('account_id')
source_id = ids.get('source_id')
sample_id = ids.get('sample_id')
account = None
source = None
sample = None
if sample_id is not None:
sample_repo = SampleRepo(self._transaction)
sample = sample_repo._get_sample_by_id(sample_id)
if source_id is not None and account_id is not None:
source_repo = SourceRepo(self._transaction)
account_repo = AccountRepo(self._transaction)
account = account_repo.get_account(account_id)
source = source_repo.get_source(account_id, source_id)
if source is None:
raise RepoException("Barcode is not associated with a source")
# TODO: This is my best understanding of how the data must be
# transformed to get the host_subject_id, needs verification that it
# generates the expected values for preexisting samples.
prehash = account_id + source.name.lower()
host_subject_id = sha512(prehash.encode()).hexdigest()
survey_answers_repo = SurveyAnswersRepo(self._transaction)
answer_ids = survey_answers_repo.list_answered_surveys_by_sample(
account_id, source_id, sample_id)
answer_to_template_map = {}
for answer_id in answer_ids:
template_id = survey_answers_repo.find_survey_template_id(
answer_id)
answer_to_template_map[answer_id] = template_id
# if a survey template is specified, filter the returned surveys
if survey_template_id is not None:
# TODO: This schema is so awkward for this type of query...
answers = []
for answer_id in answer_ids:
if answer_to_template_map[answer_id] == survey_template_id:
answers.append(answer_id)
if len(answers) == 0:
raise NotFound("This barcode is not associated with any "
"surveys matching this template id")
if len(answers) > 1:
# I really hope this can't happen. (x . x)
raise RepoException("This barcode is associated with more "
"than one survey matching this template"
" id")
answer_ids = answers
metadata_map = survey_answers_repo.build_metadata_map()
all_survey_answers = []
for answer_id in answer_ids:
answer_model = survey_answers_repo.get_answered_survey(
account_id, source_id, answer_id, "en-US")
survey_answers = {}
for k in answer_model:
new_k = metadata_map[int(k)]
survey_answers[k] = [new_k, answer_model[k]]
all_survey_answers.append({
"template":
answer_to_template_map[answer_id],
"response":
survey_answers
})
pulldown = {
"sample_barcode": sample_barcode,
"host_subject_id": host_subject_id,
"account": account,
"source": source,
"sample": sample,
"survey_answers": all_survey_answers
}
return pulldown
def retrieve_diagnostics_by_barcode(self, sample_barcode, grab_kit=True):
def _rows_to_dicts_list(rows):
return [dict(x) for x in rows]
with self._transaction.dict_cursor() as cur:
ids = self._get_ids_relevant_to_barcode(sample_barcode)
if ids is None:
ids = {}
# default for not found is None
sample_id = ids.get("sample_id")
source_id = ids.get("source_id")
account_id = ids.get("account_id")
# NB: this is the true UUID kit id (the primary key of
# ag.ag_kit), NOT the kit's participant-facing string "id"
kit_id = ids.get("kit_id")
account = None
source = None
sample = None
kit = None
# get sample object for this barcode, if any
if sample_id is not None:
sample_repo = SampleRepo(self._transaction)
sample = sample_repo._get_sample_by_id(sample_id)
# get account object for this barcode, if any
if account_id is not None:
account_repo = AccountRepo(self._transaction)
account = account_repo.get_account(account_id)
# and source object for this barcode, if any
if source_id is not None:
source_repo = SourceRepo(self._transaction)
source = source_repo.get_source(account_id, source_id)
# get (partial) projects_info list for this barcode
query = f"""
SELECT {p.DB_PROJ_NAME_KEY}, {p.IS_MICROSETTA_KEY},
{p.BANK_SAMPLES_KEY}, {p.PLATING_START_DATE_KEY}
FROM barcodes.project
INNER JOIN barcodes.project_barcode
USING (project_id)
WHERE barcode=%s;"""
cur.execute(query, (sample_barcode, ))
# this can't be None; worst-case is an empty list
projects_info = _rows_to_dicts_list(cur.fetchall())
# get scans_info list for this barcode
# NB: ORDER MATTERS here. Do not change the order unless you
# are positive you know what already depends on it.
cur.execute(
"SELECT barcode_scan_id, barcode, "
"scan_timestamp, sample_status, "
"technician_notes "
"FROM barcodes.barcode_scans "
"WHERE barcode=%s "
"ORDER BY scan_timestamp asc", (sample_barcode, ))
# this can't be None; worst-case is an empty list
scans_info = _rows_to_dicts_list(cur.fetchall())
latest_scan = None
if len(scans_info) > 0:
# NB: the correctness of this depends on the scans (queried
# right above) being in ascending order by timestamp
latest_scan = scans_info[len(scans_info) - 1]
# get details about this barcode itself; CAN be None if the
# barcode doesn't exist in db
barcode_info = None
cur.execute(
"SELECT barcode, assigned_on, status, "
"sample_postmark_date, biomass_remaining, "
"sequencing_status, obsolete, "
"create_date_time, kit_id "
"FROM barcodes.barcode "
"WHERE barcode = %s", (sample_barcode, ))
barcode_row = cur.fetchone()
if barcode_row is not None:
barcode_info = dict(barcode_row)
if account is None and source is None and sample is None and \
len(projects_info) == 0 and len(scans_info) == 0 \
and barcode_info is None:
return None
diagnostic = {
"account": account,
"source": source,
"sample": sample,
"latest_scan": latest_scan,
"scans_info": scans_info,
"barcode_info": barcode_info,
"projects_info": projects_info
}
if grab_kit:
# get kit object
if kit_id is not None:
kit_repo = KitRepo(self._transaction)
kit = kit_repo.get_kit_all_samples_by_kit_id(kit_id)
diagnostic["kit"] = kit
return diagnostic
def retrieve_diagnostics_by_barcode(self, sample_barcode, grab_kit=True):
def _rows_to_dicts_list(rows):
return [dict(x) for x in rows]
with self._transaction.dict_cursor() as cur:
ids = self._get_ids_relevant_to_barcode(sample_barcode)
if ids is None:
sample_id = None
source_id = None
account_id = None
kit_id = None
else:
sample_id = ids["sample_id"]
source_id = ids["source_id"]
account_id = ids["account_id"]
kit_id = ids["kit_id"]
account = None
source = None
sample = None
kit = None
# get sample object for this barcode
if sample_id is not None:
sample_repo = SampleRepo(self._transaction)
sample = sample_repo._get_sample_by_id(sample_id)
# get account and source objects for this barcode
if source_id is not None and account_id is not None:
account_repo = AccountRepo(self._transaction)
source_repo = SourceRepo(self._transaction)
account = account_repo.get_account(account_id)
source = source_repo.get_source(account_id, source_id)
# get projects_info list for this barcode
cur.execute("SELECT project, is_microsetta, "
"bank_samples, plating_start_date "
"FROM barcodes.project "
"INNER JOIN barcodes.project_barcode "
"USING (project_id) "
"WHERE barcode=%s",
(sample_barcode,))
# this can't be None; worst-case is an empty list
projects_info = _rows_to_dicts_list(cur.fetchall())
# get scans_info list for this barcode
# NB: ORDER MATTERS here. Do not change the order unless you
# are positive you know what already depends on it.
cur.execute("SELECT barcode_scan_id, barcode, "
"scan_timestamp, sample_status, "
"technician_notes "
"FROM barcodes.barcode_scans "
"WHERE barcode=%s "
"ORDER BY scan_timestamp asc",
(sample_barcode,))
# this can't be None; worst-case is an empty list
scans_info = _rows_to_dicts_list(cur.fetchall())
latest_scan = None
if len(scans_info) > 0:
# NB: the correctness of this depends on the scans (queried
# right above) being in ascending order by timestamp
latest_scan = scans_info[len(scans_info)-1]
# get details about this barcode itself; CAN be None if the
# barcode doesn't exist in db
barcode_info = None
cur.execute("SELECT barcode, assigned_on, status, "
"sample_postmark_date, biomass_remaining, "
"sequencing_status, obsolete, "
"create_date_time, kit_id "
"FROM barcodes.barcode "
"WHERE barcode = %s",
(sample_barcode,))
barcode_row = cur.fetchone()
if barcode_row is not None:
barcode_info = dict(barcode_row)
if account is None and source is None and sample is None and \
len(projects_info) == 0 and len(scans_info) == 0 \
and barcode_info is None:
return None
diagnostic = {
"account": account,
"source": source,
"sample": sample,
"latest_scan": latest_scan,
"scans_info": scans_info,
"barcode_info": barcode_info,
"projects_info": projects_info
}
if grab_kit:
# get kit object
if kit_id is not None:
kit_repo = KitRepo(self._transaction)
kit = kit_repo.get_kit_all_samples_by_kit_id(kit_id)
diagnostic["kit"] = kit
return diagnostic
def retrieve_diagnostics_by_barcode(self, sample_barcode, grab_kit=True):
with self._transaction.dict_cursor() as cur:
ids = self._get_ids_relevant_to_barcode(sample_barcode)
if ids is None:
sample_id = None
source_id = None
account_id = None
kit_id = None
else:
sample_id = ids["sample_id"]
source_id = ids["source_id"]
account_id = ids["account_id"]
kit_id = ids["kit_id"]
account = None
source = None
sample = None
kit = None
if sample_id is not None:
sample_repo = SampleRepo(self._transaction)
sample = sample_repo._get_sample_by_id(sample_id)
if source_id is not None and account_id is not None:
account_repo = AccountRepo(self._transaction)
source_repo = SourceRepo(self._transaction)
account = account_repo.get_account(account_id)
source = source_repo.get_source(account_id, source_id)
if kit_id is not None and grab_kit:
kit_repo = KitRepo(self._transaction)
kit = kit_repo.get_kit_all_samples_by_kit_id(kit_id)
cur.execute("SELECT * from barcodes.barcode "
"LEFT OUTER JOIN barcodes.project_barcode "
"USING (barcode) "
"LEFT OUTER JOIN barcodes.project "
"USING (project_id) "
"where barcode=%s",
(sample_barcode,))
barcode_info = cur.fetchall()
# How to unwrap a psycopg2 DictRow. I feel dirty.
barcode_info = [{k: v for k, v in x.items()}
for x in barcode_info] # Get Inceptioned!!
# Collapse info from joined project_barcode and project tables
# into array within barcode_info
if barcode_info:
first = barcode_info[0]
first['projects'] = [
{
'project_id': r['project_id'],
'project': r['project']
}
for r in barcode_info]
del first['project_id']
del first['project']
barcode_info = first
else:
barcode_info = None
if account is None and \
source is None and \
sample is None and \
barcode_info is None:
return None
diagnostic = {
"barcode": sample_barcode,
"account": account,
"source": source,
"sample": sample,
"barcode_info": barcode_info
}
if grab_kit:
diagnostic["kit"] = kit
return diagnostic
