def get_instrument_info(self):
logger.info('Getting message instrument info...')
instrument_info = namedtuple('Instrument', 'id model sn sw_version')
model = self.msg.oul_r22_specimen[0].oul_r22_order[
0].oul_r22_obxtcdsidnte_suppgrp[0].obx.obx_18.ei_1.value
sn = self.msg.msh.msh_3.msh_3_2.value
sw = self.msg.msh.msh_3.msh_3_1.value
pattern = '.*(\d\.\d\.\d\.\d{4})$'
match = re.search(pattern, sw)
sw_version = match.group(1)
with CursorFromPool() as cur:
cur.execute(
"""
SELECT id, model, sn, sw_version FROM instruments
WHERE model = %s AND sn = %s AND sw_version = %s;
""", (model, sn, sw_version))
result = cur.fetchone()
if result is None:
with CursorFromPool() as cur:
cur.execute(
"""
INSERT INTO instruments (model, sn, sw_version)
VALUES (%s, %s, %s)
RETURNING id, model, sn, sw_version;
""", (model, sn, sw_version))
update_result = cur.fetchone()
self.instrument_info = instrument_info(*update_result)
else:
self.instrument_info = instrument_info(*result)
logger.debug('Message instrument_info: {}'.format(
self.instrument_info))
def get_assay_info(self):
"""
Parses assay from HL7 message and queries assays table for relevant information.
:return: namedtuple of assay information (id, instrument_id, lis_code, name)
"""
logger.debug('Getting sample assay info...')
assay = namedtuple('Assay', 'id instrument_id lis_code assay_name')
lis_code = self.msg.oul_r22_specimen[0].oul_r22_order[
0].obr.obr_4.obr_4_1.value
with CursorFromPool() as cur:
cur.execute(
"""
SELECT * FROM assays WHERE instrument_id = %s AND lis_code =%s;
""", (self.instrument_info.id, lis_code))
result = cur.fetchone()
if result is None:
with CursorFromPool() as cur:
cur.execute(
"""
INSERT INTO assays (instrument_id, lis_code, assay_name)
VALUES (%s, %s, %s)
RETURNING id, instrument_id, lis_code, assay_name;
""", (self.instrument_info.id, lis_code, 'temp'))
update_result = cur.fetchone()
return assay(*update_result)
return assay(*result)
def load_from_db(cls, customer):
with CursorFromPool() as cursor:
cursor.execute('select * from reservation where name = %s', (customer,))
customer_data = cursor.fetchone()
if customer_data:
return cls(customer_data[0], customer_data[1], customer_data[2], customer_data[3])
def availability(room):
with CursorFromPool() as cursor:
if room == "Presidential" or room == "Suite":
cursor.execute('select count(*) from reservation where room = %s', (room,))
for row in cursor:
if row[0] >= 2:
print("NO more rooms available")
else:
print("Welcome!")
elif room == "Double":
cursor.execute('select count(*) from reservation where room = %s', (room,))
for row in cursor:
if row[0] >= 5:
print("NO more rooms available")
else:
print("Welcome!")
elif room == "Standard":
cursor.execute('select count(*) from reservation where room = %s', (room,))
for row in cursor:
if row[0] >= 5:
print("NO more rooms available")
else:
print("Welcome!")
def fetch_results():
global results
global runid
runid = request.args.get('run')
logger.info('Fetching results for run {}...'.format(runid))
with CursorFromPool() as cur:
cur.execute("SELECT * FROM results_file(%s)", (str(runid),))
results = [result for result in cur.fetchall()]
logger.info('Run {} results fetched'.format(runid))
return render_template('index.html', run_list=runs, results=results, runid=runid)
def load_from_db_by_screen_name(cls, screen_name):
with CursorFromPool() as cursor:
cursor.execute('SELECT * from users WHERE screen_name=%s',
(screen_name, ))
user_data = cursor.fetchone()
if user_data is not None:
return cls(screen_name=user_data[1],
oauth_token=user_data[2],
oauth_token_secret=user_data[3],
id=user_data[0])
else:
return None
def save_run_info(self):
logger.info('Getting message run info...')
run_info = namedtuple('Run', 'id instrument_id msg_ts msg_guid')
msg_ts = datetime.strptime(self.msg.msh.msh_7.value, '%Y%m%d%H%M%S%z')
msg_guid = self.msg.msh.msh_10.value
with CursorFromPool() as cur:
cur.execute(
"""
INSERT INTO runs (instrument_id, msg_ts, msg_guid)
VALUES (%s, %s, %s)
RETURNING id, instrument_id, msg_ts, msg_guid;
""", (self.instrument_info.id, msg_ts, msg_guid))
result = cur.fetchone()
self.run_info = run_info(*result)
def save_results(self):
"""
Inserts results into database
"""
with CursorFromPool() as cur:
for i, result in enumerate(self._parse_results(), start=1):
logger.info(
'Inserting run {} - sample {} into results table...'.
format(result.run_id, i))
cur.execute(
"""
INSERT INTO results (run_id, assay_id, sample_role, sample_type, sample_id, result, units,
result_status, username, flags, cntrl_cts, comments, dwp_id, mwp_id, mwp_position, start_ts,
end_ts)
VALUES (%s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s);
""", result)
def update(customer):
with CursorFromPool() as cursor:
cursor.execute('delete from reservation where name = %s cascade', (customer,))
def check(customer):
with CursorFromPool() as cursor:
cursor.execute('select * from net where name = %s', (customer,))
def insert_to_db(self):
with CursorFromPool() as cursor:
cursor.execute('insert into reservation values(%s, %s, %s, %s)',
(self.customer, self.room, self.check_in, self.check_out))
def index():
global runs
with CursorFromPool() as cur:
cur.execute("SELECT * FROM runs;")
runs = [run for run in cur.fetchall()]
return render_template('index.html', run_list=runs, results=None, runid=None)
def save_to_db(self):
with CursorFromPool() as cursor:
cursor.execute(
'INSERT INTO users (screen_name, oauth_token, oauth_token_secret) '
'VALUES (%s,%s,%s)',
(self.screen_name, self.oauth_token, self.oauth_token_secret))