# look for the list
if not os.path.exists(_list_path):
print 'x> The list file at %s does not exist' % _list_path
sys.exit(1)
# read list
with codecs.open(_list_path, 'r') as handle:
ncts = [nct.strip() if len(nct.strip()) > 0 else None for nct in handle.readlines()]
assert len(ncts) > 0
trials = {}
rows_and_years = []
lilly = LillyCOI()
# retrieve from our database
if not _force_update:
existing = Study.retrieve(ncts)
for ex in existing:
trials[ex.nct] = ex
# loop trials
for nct in ncts:
if not nct:
continue
# get the trial fresh via web
if nct in trials:
trial = trials[nct]
else:
trial = lilly.get_trial(nct)
if trial is None:
raise Exception("No trial for %s" % nct)
sys.exit(1)
# read list
with codecs.open(_list_path, 'r') as handle:
ncts = [
nct.strip() if len(nct.strip()) > 0 else None
for nct in handle.readlines()
]
assert len(ncts) > 0
trials = {}
rows_and_years = []
lilly = LillyCOI()
# retrieve from our database
if not _force_update:
existing = Study.retrieve(ncts)
for ex in existing:
trials[ex.nct] = ex
# loop trials
for nct in ncts:
if not nct:
continue
# get the trial fresh via web
if nct in trials:
trial = trials[nct]
else:
trial = lilly.get_trial(nct)
if trial is None:
raise Exception("No trial for %s" % nct)
from ClinicalTrials.lillycoi import LillyCOI
from ClinicalTrials.sqlite import SQLite
from ClinicalTrials.study import Study
from ClinicalTrials.umls import UMLS
CTAKES = {
'INPUT': './ctakes_input',
'OUTPUT': './ctakes_output'
}
UMLS_FILE = 'SnomedCT_Release_INT_20120731/RF2Release/Full/Terminology/sct2_Description_Full-en_INT_20120731.txt'
# main
if __name__ == "__main__":
Study.setup_ctakes(CTAKES)
Study.setup_tables()
UMLS.setup_umls(UMLS_FILE)
UMLS.setup_tables()
# ask for a condition
condition = raw_input("Condition: ")
if condition is None or len(condition) < 1:
condition = 'spondylitis'
# search for studies
print "Fetching %s studies..." % condition
lilly = LillyCOI()
results = lilly.search_for(condition)
# process all studies
#!/usr/bin/python
# -*- coding: utf-8 -*-
# NCT01954979
from ClinicalTrials.study import Study
# loop trials
trials = Study.retrieve(['NCT01954979'])
for trial in trials:
print '-> ', trial.title
codifieds = trial.codified_properties()
if codifieds is None or 0 == len(codifieds):
print 'xx> No codified data'
continue
# look at codified data
for prop, codified in codifieds.iteritems():
if len(codified) > 0:
for nlp_name, res in codified.iteritems():
# MetaMap
if 'metamap' == nlp_name:
codes = res.get('codes')
if codes:
text = codes.get('text')
cuis = codes.get('cui')
# sort cuis by location
sorted_cuis = []
