def export(self, out_dir):
'''export results'''
util.make_dir(out_dir)
io.dict2csv(self.code2manifestation_of,
out_dir + 'manifestationof.csv')
io.dict2csv(self.code2association, out_dir + 'association.csv')
def export(self, out_dir):
'''export results'''
util.make_dir(out_dir)
io.dict2csv(self.code2indications, out_dir + 'indication.csv')
io.dict2csv(self.code2effects, out_dir + 'effect.csv')
io.dict2csv(self.code2ingredients, out_dir + 'ingredient.csv')
def export(self, out_dir): '''export results''' util.make_dir(out_dir) io.dict2csv(self.code2indications, out_dir + 'indication.csv') io.dict2csv(self.code2effects, out_dir + 'effect.csv') io.dict2csv(self.code2ingredients, out_dir + 'ingredient.csv')
code2uri_sider = self.merge_dicts(code2uri, uri2uri)
# print u'J05AB01', code2uri_sider[u'J05AB01']
code2ingredients = self.merge_dicts(code2uri_sider, uri2ingredient)
# print u'J05AB01', code2uri_sider[u'J05AB01']
return code2ingredients
if __name__ == '__main__':
# in terminal: python integrate.py ../Desktop/indication.csv ../Desktop/effects.csv ../Desktop/ingredients.csv
# ... or import from SQL (uncomment)
import cx_Oracle
rows = cx_Oracle.connect('datamart', 'datamart',
'10.67.201.10:1521/XE').cursor()
rows.execute('''SELECT med.atc_code
FROM AA_KOP_patient_dates dts
LEFT JOIN medicaties med ON dts.patientnummer = med.patientnummer''')
idx = 0 # we only query atc codes
# enrich
indications, effects, ingredients = atc_enrichment(rows, idx)
# export
io.dict2csv(indications, sys.argv[1])
io.dict2csv(effects, sys.argv[2])
io.dict2csv(ingredients, sys.argv[3])
def export(self, out_dir): '''export results''' util.make_dir(out_dir) io.dict2csv(self.code2manifestation_of, out_dir + 'manifestationof.csv') io.dict2csv(self.code2association, out_dir + 'association.csv')
code2uri_sider = self.merge_dicts(code2uri, uri2uri)
# print u'J05AB01', code2uri_sider[u'J05AB01']
code2ingredients = self.merge_dicts(code2uri_sider, uri2ingredient)
# print u'J05AB01', code2uri_sider[u'J05AB01']
return code2ingredients
if __name__ == '__main__':
# in terminal: python integrate.py ../Desktop/indication.csv ../Desktop/effects.csv ../Desktop/ingredients.csv
# ... or import from SQL (uncomment)
import cx_Oracle
rows = cx_Oracle.connect('datamart', 'datamart', '10.67.201.10:1521/XE').cursor()
rows.execute('''SELECT med.atc_code
FROM AA_KOP_patient_dates dts
LEFT JOIN medicaties med ON dts.patientnummer = med.patientnummer''')
idx = 0 # we only query atc codes
# enrich
indications, effects, ingredients = atc_enrichment(rows, idx)
# export
io.dict2csv(indications, sys.argv[1])
io.dict2csv(effects, sys.argv[2])
io.dict2csv(ingredients, sys.argv[3])