def run_trials(run_id):
""" Returns the trials from a given run-id.
You can filter the returned trias by supplying 'intv' for intervention
types to be included and 'phases' for trial phases to be active """
# from pycallgraph import PyCallGraph
# from pycallgraph.output import GraphvizOutput
# with PyCallGraph(output=GraphvizOutput()):
runner = Runner.get(run_id)
if runner is None:
bottle.abort(404)
if not runner.done:
bottle.abort(400, "Trials are not yet available")
# get request vars
intv = bottle.request.query.intv
intv = intv.split('|') if intv else []
phases = bottle.request.query.phases
phases = phases.split('|') if phases else []
reload_phases = bottle.request.query.reload_phases
ret_dict = {
'trials': runner.trials_json(intv, phases)
}
if reload_phases:
ret_dict['drug_phases'] = runner.trial_phases(intv)
return json.dumps(ret_dict)
def run_trials(run_id):
""" Returns the trials from a given run-id.
You can filter the returned trias by supplying 'intv' for intervention
types to be included and 'phases' for trial phases to be active """
# from pycallgraph import PyCallGraph
# from pycallgraph.output import GraphvizOutput
# with PyCallGraph(output=GraphvizOutput()):
runner = Runner.get(run_id)
if runner is None:
bottle.abort(404)
if not runner.done:
bottle.abort(400, "Trials are not yet available")
# get request vars
intv = bottle.request.query.intv
intv = intv.split('|') if intv else []
phases = bottle.request.query.phases
phases = phases.split('|') if phases else []
reload_phases = bottle.request.query.reload_phases
ret_dict = {'trials': runner.trials_json(intv, phases)}
if reload_phases:
ret_dict['drug_phases'] = runner.trial_phases(intv)
return json.dumps(ret_dict)
def trial_progress(run_id):
""" Returns text status from the file corresponding to the given run-id, if
it's missing returns a 404. """
runner = Runner.get(run_id)
if runner is None:
bottle.abort(404)
return runner.status
def trial_progress(run_id): """ Returns text status from the file corresponding to the given run-id, if it's missing returns a 404. """ runner = Runner.get(run_id) if runner is None: bottle.abort(404) return runner.status
def run_overview(run_id):
""" Overview results for a run. """
runner = Runner.get(run_id)
if runner is None:
bottle.abort(404)
try:
overview = runner.overview()
except Exception as e:
bottle.abort(400, e)
return json.dumps(overview)
def run_overview(run_id): """ Overview results for a run. """ runner = Runner.get(run_id) if runner is None: bottle.abort(404) try: overview = runner.overview() except Exception as e: bottle.abort(400, e) return json.dumps(overview)
#!/usr/bin/python
# -*- coding: utf-8 -*-
import logging
from ClinicalTrials.runner import Runner
logging.basicConfig(level=logging.DEBUG)
# setup the runner
run = Runner(666, 'run-alternative')
run.catch_exceptions = False
#run.limit = 3
run.discard_cached = False
run.term = "pulmonary arterial hypertension"
# run.term = "juvenile rheumatoid arthritis"
run.analyze_eligibility = False
run.analyze_keypaths = set([
'condition_browse', 'intervention_browse', 'intervention', 'keyword',
'primary_outcome', 'arm_group'
])
# create a callback
def cb(success, trials):
if success:
# loop trials
for trial in trials:
doc = trial.doc or {}
print 'Trial "%s" [ %s ]' % (trial.title, trial.nct)
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 find_trials():
""" Initiates the chain to find trials for the given condition or search-
term. Supply with parameters:
- "cond" or "term", the prior taking precedence
- "gender" ('male' or 'female')
- "age" (in years)
- "latlng", comma-separated latitude and longituted of the patient
- "remember_input" if the condition or term should be stored in the session
This method forks off and prints the status to a file which can be read by
calling /trials_status/<run-id>. "run-id" is returned from this call.
"""
# get the runner
run_id = datetime.now().isoformat()
runner = Runner.get(run_id)
if runner is None:
runner = Runner(run_id, "run-server")
runner.in_background = True
# configure
cond = bottle.request.query.get('cond')
term = bottle.request.query.get('term')
if cond:
cond = re.sub(r'\s+\((disorder|finding)\)', '', cond)
runner.condition = cond
elif term:
term = re.sub(r'\s+-(\w+)', r' NOT \1', term)
term = re.sub(r'\s*([^\w\d])\s+([^-])', r' AND \2', term)
runner.term = term
else:
bottle.abort(400, 'You need to specify "cond" or "term"')
# latitude and longitude
latlng = bottle.request.query.get('latlng')
if latlng is None or 0 == len(latlng):
latlng = '42.358,-71.06' # default to Boston
parts = latlng.split(',', 2)
if parts is None or 2 != len(parts):
bottle.abort(400, '"latlng" must be two numbers separated by a comma')
lat = parts[0]
lng = parts[1]
runner.reference_location = (lat, lng)
# store in session
age = bottle.request.query.get('age')
sess = _get_session()
runs = sess.get('runs', {})
runs[run_id] = {
'cond': cond,
'gender': bottle.request.query.get('gender'),
'age': int(age) if age else None,
'latlng': latlng
}
sess['runs'] = runs
if 'true' == bottle.request.query.get('remember_input'):
if cond or term:
sess['last_manual_input'] = cond or term
elif 'last_manual_input' in sess:
del sess['last_manual_input']
# launch and return id
runner.run([
'id', 'acronym', 'keyword', 'brief_title', 'official_title',
'brief_summary', 'overall_contact', 'eligibility', 'location',
'attributes', 'intervention', 'intervention_browse', 'phase',
'study_design', 'primary_outcome'
])
return run_id
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 find_trials():
""" Initiates the chain to find trials for the given condition or search-
term. Supply with parameters:
- "cond" or "term", the prior taking precedence
- "gender" ('male' or 'female')
- "age" (in years)
- "latlng", comma-separated latitude and longituted of the patient
- "remember_input" if the condition or term should be stored in the session
This method forks off and prints the status to a file which can be read by
calling /trials_status/<run-id>. "run-id" is returned from this call.
"""
# get the runner
run_id = datetime.now().isoformat()
runner = Runner.get(run_id)
if runner is None:
runner = Runner(run_id, "run-server")
runner.in_background = True
# configure
cond = bottle.request.query.get('cond')
term = bottle.request.query.get('term')
if cond:
cond = re.sub(r'\s+\((disorder|finding)\)', '', cond)
runner.condition = cond
elif term:
term = re.sub(r'\s+-(\w+)', r' NOT \1', term)
term = re.sub(r'\s*([^\w\d])\s+([^-])', r' AND \2', term)
runner.term = term
else:
bottle.abort(400, 'You need to specify "cond" or "term"')
# latitude and longitude
latlng = bottle.request.query.get('latlng')
if latlng is None or 0 == len(latlng):
latlng = '42.358,-71.06' # default to Boston
parts = latlng.split(',', 2)
if parts is None or 2 != len(parts):
bottle.abort(400, '"latlng" must be two numbers separated by a comma')
lat = parts[0]
lng = parts[1]
runner.reference_location = (lat, lng)
# store in session
age = bottle.request.query.get('age')
sess = _get_session()
runs = sess.get('runs', {})
runs[run_id] = {
'cond': cond,
'gender': bottle.request.query.get('gender'),
'age': int(age) if age else None,
'latlng': latlng
}
sess['runs'] = runs
if 'true' == bottle.request.query.get('remember_input'):
if cond or term:
sess['last_manual_input'] = cond or term
elif 'last_manual_input' in sess:
del sess['last_manual_input']
# launch and return id
runner.run(['id', 'acronym', 'keyword', 'brief_title', 'official_title', 'brief_summary', 'overall_contact', 'eligibility', 'location', 'attributes', 'intervention', 'intervention_browse', 'phase', 'study_design', 'primary_outcome'])
return run_id
#!/usr/bin/python
# -*- coding: utf-8 -*-
import logging
from ClinicalTrials.runner import Runner
logging.basicConfig(level=logging.DEBUG)
# setup the runner
run = Runner(666, 'run-alternative')
run.catch_exceptions = False
#run.limit = 3
run.discard_cached = False
run.term = "pulmonary arterial hypertension"
# run.term = "juvenile rheumatoid arthritis"
run.analyze_eligibility = False
run.analyze_keypaths = set(['condition_browse', 'intervention_browse', 'intervention', 'keyword', 'primary_outcome', 'arm_group'])
# create a callback
def cb(success, trials):
if success:
# loop trials
for trial in trials:
doc = trial.doc or {}
print 'Trial "%s" [ %s ]' % (trial.title, trial.nct)
print ' keyw: %s' % '; '.join(doc.get('keyword') or [])
print ' cond: %s' % '; '.join(doc.get('condition_browse', {}).get('mesh_term', []))
print ' intr: %s' % '; '.join(doc.get('intervention_browse', {}).get('mesh_term', []))
print ' intn: %s' % "\n ----> ".join([p.get('intervention_name') or '' for p in doc.get('intervention', [])])
from ClinicalTrials.runner import Runner from ClinicalTrials.umls import UMLSLookup from ClinicalTrials.ctakes import cTAKES from ClinicalTrials.metamap import MetaMap from ClinicalTrials.nltktags import NLTKTags logging.basicConfig(level=logging.DEBUG) # setup NLP pipelines nlp_ctakes = cTAKES() nlp_metamap = MetaMap() nlp_nltkt = NLTKTags() #nlp_nltkt.cleanup = False # setup the runner run = Runner(666, 'run-test') run.catch_exceptions = False #run.limit = 3 run.discard_cached = False run.term = "juvenile rheumatoid arthritis" run.analyze_eligibility = False run.analyze_keypaths = set(['brief_summary']) # run.analyze_keypaths = set(['eligibility_inclusion', 'eligibility_exclusion', 'brief_summary', 'detailed_description']) run.add_pipeline(nlp_metamap) # run.add_pipeline(nlp_nltkt) # create a callback def cb(success, trials): if success:
if term is None or len(term) < 1:
term = "diabetic cardiomyopathy"
# recruiting = None
# if _use_recruiting:
# recruiting = raw_input("Recruiting: [no] ")
# if recruiting is None or len(recruiting) < 1:
# recruiting = False
# else:
# recruiting = recruiting[:1] is 'y' or recruiting[:1] is 'Y'
# run the runner
now = date.today()
run_id = now.isoformat()
run_dir = "run-%s-%s" % (re.sub(r"[^\w\d\-]+", "_", term.lower()), run_id)
runner = Runner(run_id, run_dir)
runner.run_ctakes = True
runner.run_metamap = True
runner.term = term
runner.log_status = True
runner.run()
# generate HTML report
if _generate_report:
print "Generating report..."
recr_status = ""
if _use_recruiting:
recr_status = ", recruiting" if recruiting else ", not recruiting"
html = """<html>
<head>
if term is None or len(term) < 1:
term = 'diabetic cardiomyopathy'
# recruiting = None
# if _use_recruiting:
# recruiting = raw_input("Recruiting: [no] ")
# if recruiting is None or len(recruiting) < 1:
# recruiting = False
# else:
# recruiting = recruiting[:1] is 'y' or recruiting[:1] is 'Y'
# run the runner
now = date.today()
run_id = now.isoformat()
run_dir = "run-%s-%s" % (re.sub(r'[^\w\d\-]+', '_', term.lower()), run_id)
runner = Runner(run_id, run_dir)
runner.run_ctakes = True
runner.run_metamap = True
runner.term = term
runner.log_status = True
runner.run()
# generate HTML report
if _generate_report:
print 'Generating report...'
recr_status = ''
if _use_recruiting:
recr_status = ', recruiting' if recruiting else ', not recruiting'
html = """<html>
<head>