def _get_sample_by_id(self, sample_id):
""" Do not use from api layer, you must validate account and source."""
with self._transaction.cursor() as cur:
cur.execute(
"SELECT "
"ag.ag_kit_barcodes.sample_date, "
"ag.ag_kit_barcodes.sample_time, "
"ag.ag_kit_barcodes.site_sampled, "
"ag.ag_kit_barcodes.notes, "
"barcodes.barcode.barcode, "
"barcodes.barcode.scan_date "
"FROM "
"ag.ag_kit_barcodes "
"LEFT JOIN barcodes.barcode "
"ON "
"ag.ag_kit_barcodes.barcode = barcodes.barcode.barcode "
"LEFT JOIN source "
"ON "
"ag.ag_kit_barcodes.source_id = source.id "
"WHERE "
"ag_kit_barcodes.ag_kit_barcode_id = %s", (sample_id, ))
sample_row = cur.fetchone()
if sample_row is None:
return None
sample_barcode = sample_row[4]
sample_projects = self._retrieve_projects(sample_barcode)
return Sample.from_db(sample_id, *sample_row, sample_projects)
def get_sample(self, account_id, source_id, sample_id):
with self._transaction.cursor() as cur:
cur.execute(
"SELECT "
"ag.ag_kit_barcodes.sample_date, "
"ag.ag_kit_barcodes.sample_time, "
"ag.ag_kit_barcodes.site_sampled, "
"ag.ag_kit_barcodes.notes, "
"barcodes.barcode.barcode, "
"barcodes.barcode.scan_date "
"FROM "
"ag.ag_kit_barcodes "
"LEFT JOIN barcodes.barcode "
"ON "
"ag.ag_kit_barcodes.barcode = barcodes.barcode.barcode "
"LEFT JOIN source "
"ON "
"ag.ag_kit_barcodes.source_id = source.id "
"WHERE "
"ag_kit_barcodes.ag_kit_barcode_id = %s AND "
"source.id = %s AND "
"source.account_id = %s", (sample_id, source_id, account_id))
sample_row = cur.fetchone()
if sample_row is None:
return None
sample_barcode = sample_row[4]
sample_projects = self._retrieve_projects(sample_barcode)
return Sample.from_db(sample_id, *sample_row, sample_projects)
def _create_sample_obj(self, sample_row):
if sample_row is None:
return None
sample_barcode = sample_row[5]
sample_projects = self._retrieve_projects(sample_barcode)
return Sample.from_db(*sample_row, sample_projects)
def _create_sample_obj(self, sample_row):
if sample_row is None:
return None
sample_barcode = sample_row[5]
scan_timestamp = sample_row[6]
sample_projects = self._retrieve_projects(sample_barcode)
sample_status = self.get_sample_status(sample_barcode, scan_timestamp)
return Sample.from_db(*sample_row, sample_projects, sample_status)
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
def get_samples_by_source(self, account_id, source_id):
with self._transaction.cursor() as cur:
acct_repo = AccountRepo(self._transaction)
if acct_repo.get_account(account_id) is None:
raise NotFound("No such account")
source_repo = SourceRepo(self._transaction)
if source_repo.get_source(account_id, source_id) is None:
raise NotFound("No such source")
cur.execute(
"SELECT "
"ag_kit_barcodes.ag_kit_barcode_id, "
"ag_kit_barcodes.sample_date, "
"ag_kit_barcodes.sample_time, "
"ag_kit_barcodes.site_sampled, "
"ag_kit_barcodes.notes, "
"ag_kit_barcodes.barcode, "
"barcode.scan_date "
"FROM ag_kit_barcodes "
"LEFT JOIN barcode "
"USING (barcode) "
"LEFT JOIN source "
"ON ag_kit_barcodes.source_id = source.id "
"WHERE "
"source.account_id = %s AND "
"source.id = %s "
"ORDER BY barcode.barcode asc", (account_id, source_id))
samples = []
for sample_row in cur.fetchall():
barcode = sample_row[5]
sample_projects = self._retrieve_projects(barcode)
s = Sample.from_db(*sample_row, sample_projects)
samples.append(s)
return samples