def build_custom(tag, gene_signatures, report_name, category):
"""Builds a custom report.
"""
with session_scope() as session:
report = Report(tag, _gene_signatures=gene_signatures,
is_approved=False, name=report_name,
category=category)
session.add(report)
session.commit()
_build(report.id, category)
return report.id
def rebuild(tag, category, wait_till_done=False):
"""Rebuild report for a tag. Used when the report is not complete
"""
print('Rebuilding report.')
report = tag.approved_report
with session_scope() as session:
report.reset(reanalyze=False)
report.category = category
session.merge(report)
session.commit()
_build(report.id, category, wait_till_done=wait_till_done)
return
def get_rx_age_kde(self):
'''Get the KDE smoothened age distribution for the prescription of this drug.
'''
with session_scope() as session:
query_results = session\
.execute("""SELECT age_years, density
FROM rx_age_kde
WHERE ingredient_id=:ingredient_id
""", params={'ingredient_id': self.ingredient_id})
if query_results.rowcount == 0:
return None
else:
results = query_results.fetchall()
age_years = [item[0] for item in results]
density = [item[1] for item in results]
results = {'density': density, 'age_years':age_years, 'name': self.pert_iname}
return json.dumps(results)
def build(tag, category, reanalyze=False):
"""Creates a new report in a separate thread.
"""
if tag.approved_report:
report = tag.approved_report
# print('Resetting report.')
# with session_scope() as session:
# report.reset(reanalyze=reanalyze)
# report.category = category
# session.merge(report)
# session.commit()
else:
print('Creating new report.')
with session_scope() as session:
report = Report(tag, is_approved=True, category=category)
session.add(report)
session.flush()
_build(report.id, category)
def get_rx_counts(self, nrows=20):
with session_scope() as session:
query_results = session\
.execute("""SELECT co_rx.count AS z,
co_rx.normed_count AS x,
rx_counts.count AS y, rx_counts.ingredient AS name
FROM co_rx
LEFT JOIN rx_counts ON rx_counts.`id`=co_rx.`co_prescribed_drug_id`
WHERE ingredient_id=:ingredient_id
ORDER BY x DESC
LIMIT :nrows;
""", params={'ingredient_id': self.ingredient_id, 'nrows':nrows})
if query_results.rowcount == 0:
return None
else:
field_names = query_results.keys()
rx_counts = query_results.fetchall()
rx_counts = [dict(zip(field_names, row)) for row in rx_counts]
results = {'data': rx_counts, 'name': 'co_prescribed_drug'}
return json.dumps(results)
def get_dx_counts(self, nrows=20):
with session_scope() as session:
query_results = session\
.execute("""SELECT co_dx.count AS z,
co_dx.normed_count AS x,
dx_counts.count AS y, dx_counts.ICD9,
dx_counts.diagnosis AS name
FROM co_dx
LEFT JOIN dx_counts ON dx_counts.`id`=co_dx.`diagnosis_id`
WHERE ingredient_id=:ingredient_id
ORDER BY x DESC
LIMIT :nrows
""", params={'ingredient_id': self.ingredient_id, 'nrows':nrows})
if query_results.rowcount == 0:
return None
else:
field_names = query_results.keys()
dx_counts = query_results.fetchall()
dx_counts = [dict(zip(field_names, row)) for row in dx_counts]
results = {'data': dx_counts, 'name': 'diagnoses'}
return json.dumps(results)