def setUpClass(cls):
''' Retrieve the publication list for each disease from NCBI. '''
ini = IniParser()
config = ini.read_ini('publications.ini')
res = Search(ElasticQuery(Query.match_all(), sources=['code']), idx=ElasticSettings.idx('DISEASE')).search()
sections = ''
for doc in res.docs:
sections += 'DISEASE::'+getattr(doc, 'code').upper()+','
# sections = 'DISEASE::T1D,DISEASE::MS,DISEASE::SLE'
# download ncbi publication lists for each disease
for section_name in config.sections():
if sections is not None and not ini._is_section_match(section_name, sections):
continue
ini._inherit_section(section_name, config)
logger.debug(section_name)
section = config[section_name]
disease = section_name.split('::')[1]
file_name = 'disease_pub_'+disease+'.tmp'
HTTPDownload().download(section['location']+"?"+section['http_params'],
cls.TEST_DATA_DIR, file_name=file_name)
DiseasePublicationTest.DISEASES.append(disease)
print()
