# 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 = []