def index_cris_cohort():
f_patient_doc = './hepc_pos_doc_brcid.txt'
f_yodie_anns = 'U:/kconnect/hepc_output/'
print 'loading all docs at a time...'
docs = load_all_docs()
print 'docs read'
doc_dict = {}
for d in docs:
doc_dict[d['CN_Doc_ID']] = d
es = EntityCentricES.get_instance('./index_settings/es_cris_setting.json')
lines = utils.read_text_file(f_patient_doc, encoding='utf-8-sig')
doc_to_patient = {}
for l in lines:
arr = l.split('\t')
doc_to_patient[arr[1]] = arr[0]
container = []
ann_files = [
f for f in listdir(f_yodie_anns) if isfile(join(f_yodie_anns, f))
]
for ann in ann_files:
utils.multi_thread_large_file_tasking(
join(f_yodie_anns, ann),
20,
do_index_cris,
args=[es, doc_to_patient, doc_dict, container],
file_encoding='iso-8859-1')
print 'file %s [%s] done' % (ann, len(container))
print 'num done %s' % len(container)
print 'done'
def do_semehr_index(settings, patients, doc_to_patient):
"""
do SemEHR index
:param settings:
:param patients:
:param doc_to_patient:
:return:
"""
es = EntityCentricES(settings.get_attr(['semehr', 'es_host']))
es.index_name = settings.get_attr(['semehr', 'index'])
es.concept_doc_type = settings.get_attr(['semehr', 'concept_doc_type'])
es.entity_doc_type = settings.get_attr(['semehr', 'entity_doc_type'])
es.doc_level_index = settings.get_attr(['semehr', 'doc_level_index'])
f_yodie_anns = settings.get_attr(['yodie', 'output_file_path'])
ann_files = [
f for f in listdir(f_yodie_anns) if isfile(join(f_yodie_anns, f))
]
if settings.get_attr(['job', 'semehr-concept']) == 'yes':
logging.info('[SemEHR-step] starting semehr-concept process')
logging.debug('working on files : %s' % ann_files)
# index concepts
concept_index = settings.get_attr(['semehr', 'concept_index'])
for ann in ann_files:
utils.multi_thread_large_file_tasking(
join(f_yodie_anns, ann),
10,
do_index_100k_anns,
args=[es, doc_to_patient, concept_index])
logging.info('[SemEHR-step-end]concept/document level indexing done')
if settings.get_attr(['job', 'semehr-patients']) == 'yes':
logging.info('[SemEHR-step] indexing annotations at patient level')
# index patients
es_doc_url = settings.get_attr(['semehr', 'es_doc_url'])
es_full_text = Elasticsearch([es_doc_url],
serializer=JSONSerializerPython2(),
verify_certs=False)
ft_index_name = settings.get_attr(['semehr', 'full_text_index'])
ft_doc_type = settings.get_attr(['semehr', 'full_text_doc_type'])
ft_entity_field = settings.get_attr(
['semehr', 'full_text_patient_field'])
ft_fulltext_field = settings.get_attr(
['semehr', 'full_text_text_field'])
utils.multi_thread_tasking(patients,
10,
do_index_100k_patients,
args=[
es, es_full_text, ft_index_name,
ft_doc_type, ft_entity_field,
ft_fulltext_field
])
logging.info('[SemEHR-step-end]patient level indexing done')
def index_mimic_notes():
es = EntityCentricES.get_instance('./index_settings/es_mimic_setting.json')
ann_files = [
f for f in listdir(_f_yodie_anns) if isfile(join(_f_yodie_anns, f))
]
patients = []
for ann in ann_files:
print 'indexing %s ...' % ann
utils.multi_thread_large_file_tasking(join(_f_yodie_anns, ann),
20,
do_index_mimic,
args=[es, patients])
print 'full text and annotations done.'
patients = list(set(patients))
index_patients(patients, es)
def do_semehr_index(settings, patients, doc_to_patient):
"""
do SemEHR index
:param settings:
:param patients:
:param doc_to_patient:
:return:
"""
es = EntityCentricES(settings.get_attr(['semehr', 'es_host']))
es.index_name = settings.get_attr(['semehr', 'index'])
es.concept_doc_type = settings.get_attr(['semehr', 'concept_doc_type'])
es.entity_doc_type = settings.get_attr(['semehr', 'entity_doc_type'])
f_yodie_anns = settings.get_attr(['yodie', 'output_file_path'])
ann_files = [
f for f in listdir(f_yodie_anns) if isfile(join(f_yodie_anns, f))
]
if settings.get_attr(['job', 'semehr-concept']) == 'yes':
print 'working on files : %s' % ann_files
# index concepts
for ann in ann_files:
utils.multi_thread_large_file_tasking(join(f_yodie_anns, ann),
10,
do_index_100k_anns,
args=[es, doc_to_patient])
if settings.get_attr(['job', 'semehr-patients']) == 'yes':
# index patients
es_doc_url = settings.get_attr(['semehr', 'es_doc_url'])
es_full_text = Elasticsearch([es_doc_url],
serializer=JSONSerializerPython2())
ft_index_name = settings.get_attr(['semehr', 'full_text_index'])
ft_doc_type = settings.get_attr(['semehr', 'full_text_doc_type'])
ft_entity_field = settings.get_attr(
['semehr', 'full_text_patient_field'])
ft_fulltext_field = settings.get_attr(
['semehr', 'full_text_text_field'])
utils.multi_thread_tasking(patients,
10,
do_index_100k_patients,
args=[
es, es_full_text, ft_index_name,
ft_doc_type, ft_entity_field,
ft_fulltext_field
])
def index_100k(index_setting_file, patient_index_only=None):
es = EntityCentricES.get_instance(index_setting_file)
f_patient_doc = es.customise_settings['patient_doc_mapping_file']
f_yodie_anns = es.customise_settings['yodie_output_folder']
es_epr_full_text = es.customise_settings['es_ft']
ft_index_name = es.customise_settings['ft_index_name']
ft_doc_type = es.customise_settings['ft_doc_type']
ft_entity_field = es.customise_settings['ft_entity_field']
ft_fulltext_field = es.customise_settings['ft_fulltext_field']
lines = utils.read_text_file(f_patient_doc)
doc_to_patient = {}
patients = set()
for l in lines:
arr = l.split('\t')
doc_to_patient[arr[1]] = arr[0]
patients.add(arr[0])
patients = list(patients)
# epr full text index api
es_full_text = Elasticsearch([es_epr_full_text],
serializer=JSONSerializerPython2())
# es_full_text.get()
if patient_index_only is None:
ann_files = [
f for f in listdir(f_yodie_anns) if isfile(join(f_yodie_anns, f))
]
for ann in ann_files:
utils.multi_thread_large_file_tasking(join(f_yodie_anns, ann),
10,
do_index_100k_anns,
args=[es, doc_to_patient])
print 'anns done, indexing patients...'
else:
print 'skipping concept indexing'
utils.multi_thread_tasking(patients,
10,
do_index_100k_patients,
args=[
es, es_full_text, ft_index_name,
ft_doc_type, ft_entity_field,
ft_fulltext_field
])
print 'all done'
