def trials_filter_by(run_id, filter_by):
runner = Runner.get(run_id)
if runner is None:
bottle.abort(404)
if not runner.done:
bottle.abort(400, "Trial results are not available")
ncts = runner.get_ncts(restrict='none')
sess = _get_session()
run_data = sess.get('runs', {}).get(run_id, {})
# demographics - get age and gender
if 'demographics' == filter_by:
f_gender = run_data.get('gender')
f_age = int(run_data.get('age', 0))
for tpl in ncts:
nct = tpl[0]
reason = tpl[1] if len(tpl) > 1 else None
if not reason:
trial = Trial(nct)
trial.load()
# filter gender
if f_gender:
if 'male' == f_gender:
if trial.eligibility.gender == 2:
reason = "Limited to women"
else:
if trial.eligibility.gender == 1:
reason = "Limited to men"
# filter age
if f_age > 0:
if trial.eligibility.min_age and trial.eligibility.min_age > f_age:
reason = "Patient is too young (min age %d)" % trial.eligibility.min_age
elif trial.eligibility.max_age and trial.eligibility.max_age < f_age:
reason = "Patient is too old (max age %d)" % trial.eligibility.max_age
# TODO: REFACTOR into runner class!
if reason:
runner.write_trial_reason(nct, reason)
runner.commit_transactions()
# problems (only if NLP is on)
elif 'problems' == filter_by:
if USE_NLP:
probs = problems().get('problems', [])
# extract snomed codes from patient's problem list
snomed = SNOMEDLookup()
exclusion_codes = []
for problem in probs:
snomed_url = problem.get('sp:problemName',
{}).get('sp:code', {}).get('@id')
if snomed_url is not None:
snomed_code = os.path.basename(snomed_url)
exclusion_codes.append(snomed_code)
# look at trial criteria
for tpl in ncts:
nct = tpl[0]
reason = tpl[1] if len(tpl) > 1 else None
# if we already have a reason, this trial has already been filtered
if not reason:
trial = Trial(nct)
trial.load()
# exclusion criterion matched
if trial.filter_snomed(exclusion_codes) is not None:
reason = 'Matches exclusion criterium "%s" (SNOMED %s)' % (
snomed.lookup_code_meaning(match, True,
True), match)
break
# TODO: REFACTOR
# runner.write_trial_reason(nct, reason)
# unknown filtering property
else:
return '{"error": "We can not filter by %s"}' % filter_by
return '{"status": "ok"}'
def trials_filter_by(run_id, filter_by):
runner = Runner.get(run_id)
if runner is None:
bottle.abort(404)
if not runner.done:
bottle.abort(400, "Trial results are not available")
ncts = runner.get_ncts(restrict='none')
sess = _get_session()
run_data = sess.get('runs', {}).get(run_id, {})
# demographics - get age and gender
if 'demographics' == filter_by:
f_gender = run_data.get('gender')
f_age = int(run_data.get('age', 0))
for tpl in ncts:
nct = tpl[0]
reason = tpl[1] if len(tpl) > 1 else None
if not reason:
trial = Trial(nct)
trial.load()
# filter gender
if f_gender:
if 'male' == f_gender:
if trial.eligibility.gender == 2:
reason = "Limited to women"
else:
if trial.eligibility.gender == 1:
reason = "Limited to men"
# filter age
if f_age > 0:
if trial.eligibility.min_age and trial.eligibility.min_age > f_age:
reason = "Patient is too young (min age %d)" % trial.eligibility.min_age
elif trial.eligibility.max_age and trial.eligibility.max_age < f_age:
reason = "Patient is too old (max age %d)" % trial.eligibility.max_age
# TODO: REFACTOR into runner class!
if reason:
runner.write_trial_reason(nct, reason)
runner.commit_transactions()
# problems (only if NLP is on)
elif 'problems' == filter_by:
if USE_NLP:
probs = problems().get('problems', [])
# extract snomed codes from patient's problem list
snomed = SNOMEDLookup()
exclusion_codes = []
for problem in probs:
snomed_url = problem.get('sp:problemName', {}).get('sp:code', {}).get('@id')
if snomed_url is not None:
snomed_code = os.path.basename(snomed_url)
exclusion_codes.append(snomed_code)
# look at trial criteria
for tpl in ncts:
nct = tpl[0]
reason = tpl[1] if len(tpl) > 1 else None
# if we already have a reason, this trial has already been filtered
if not reason:
trial = Trial(nct)
trial.load()
# exclusion criterion matched
if trial.filter_snomed(exclusion_codes) is not None:
reason = 'Matches exclusion criterium "%s" (SNOMED %s)' % (snomed.lookup_code_meaning(match, True, True), match)
break
# TODO: REFACTOR
# runner.write_trial_reason(nct, reason)
# unknown filtering property
else:
return '{"error": "We can not filter by %s"}' % filter_by
return '{"status": "ok"}'
