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 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 process_semehr(config_file):
"""
a pipeline to process all SemEHR related processes:
0. ES doc copy from one index to another;
1. bio-yodie NLP pipeline annotation on docs;
2. entity centric SemEHR ES indexing
:param config_file:
:return:
"""
# read the configuration
ps = ProcessSetting(config_file)
# setting log configuration
log_level = 'INFO' if ps.get_attr(
['logging', 'level']) is None else ps.get_attr(['logging', 'level'])
log_format = '%(name)s %(asctime)s %(levelname)s %(message)s' if ps.get_attr(['logging', 'format']) is None \
else ps.get_attr(['logging', 'format'])
log_file = None if ps.get_attr(
['logging', 'file']) is None else ps.get_attr(['logging', 'file'])
logging.basicConfig(level=log_level, format=log_format)
if log_file is not None:
formatter = logging.Formatter(log_format)
file_handler = logging.FileHandler(log_file)
file_handler.setLevel(log_level)
file_handler.setFormatter(formatter)
logging.getLogger().addHandler(file_handler)
logging.info('logging to %s' % log_file)
# initialise the jobstatus class instance
job_file = join(
ps.get_attr(['job', 'job_status_file_path']),
'semehr_job_status_%s.json' % ps.get_attr(['job', 'job_id']))
logging.info('[SemEHR-step] using job status file %s' % job_file)
job_status = JobStatus(job_file)
job_status.job_start()
# preload: load documents to es
if ps.get_attr(['job', 'epr_index']) == 'yes':
logging.info('[SemEHR-step]load documents to elasticsearch...')
load_document_to_es(settings=ps)
logging.info('[SemEHR-step-end] epr_index step done')
data_rows = []
doc2pid = {}
pids = []
if ps.get_attr(['job', 'load_docs']) == 'yes':
sql_template = ps.get_attr(['new_docs', 'sql_query'])
logging.info(
'[SemEHR-step] retrieving docs by using the template [%s]' %
sql_template)
data_rows = get_docs_for_processing(
job_status, sql_template,
ps.get_attr(['new_docs', 'dbconn_setting_file']))
logging.info('total docs num is %s' % len(data_rows))
elif ps.get_attr(['job', 'cohort_docs']) == 'yes':
logging.info('[SemEHR-step] retrieving docs by cohort [%s]' %
ps.get_attr(['cohort_docs', 'es_cohort_file']))
data_rows, doc2pid, pids = es_get_cohort_docs(ps)
logging.info('total docs num is %s' % len(data_rows))
try:
# if True:
# 0. copy docs
if ps.get_attr(['job', 'copy_docs']) == 'yes':
logging.info('[SemEHR-step] copy docs')
docs = [str(r['docid']) for r in data_rows]
utils.multi_thread_tasking(
docs,
ps.get_attr(['doc_copy', 'thread_num']),
do_copy_doc,
args=[
EntityCentricES(ps.get_attr(['doc_copy', 'es_host'])),
ps.get_attr(['doc_copy', 'src_index']),
ps.get_attr(['doc_copy', 'src_doc_type']),
ps.get_attr(['doc_copy', 'dest_index']),
ps.get_attr(['doc_copy', 'dest_doc_type'])
])
logging.info('[SemEHR-step-end]copying docs done')
if ps.get_attr(['job', 'yodie']) == 'yes':
docid_path = '%s/%s_docids.txt' % (ps.get_attr([
'yodie', 'input_doc_file_path'
]), ps.get_attr(['job', 'job_id']))
logging.info('[SemEHR-step] doing yodie')
# 1. do bio-yodie pipeline
# 1.1 prepare the configuration file
num_docs = produce_yodie_config(ps, data_rows, docid_path)
if num_docs == 0:
logging.info(
'[SemEHR-step-end] nothing to process, NLP step done')
else:
logging.info('total number of docs %s' % num_docs)
# 1.2 set the env variables
set_sys_env(ps)
# 1.3 clear ann output folder
logging.info('clearing %s ...' %
ps.get_attr(['yodie', 'output_file_path']))
clear_folder(ps.get_attr(['yodie', 'output_file_path']))
# 1.3 run bio-yodie
os.chdir(ps.get_attr(['yodie', 'gcp_run_path']))
if ps.get_attr(['yodie', 'os']) == 'win':
cmd = ' '.join([
'java',
"-Dgate.home=%s" % ps.get_attr(['env', 'gate_home']),
"-Dgcp.home=%s" % ps.get_attr(['env', 'gcp_home']),
"-Djava.protocol.handler.pkgs=gate.cloud.util.protocols",
"-cp .;{SCRIPTDIR}/conf;{SCRIPTDIR}/gcp.jar;{SCRIPTDIR}/lib/*;"
"{GATE_HOME}/bin/gate.jar;{GATE_HOME}/lib/*".format(
**{
"SCRIPTDIR": ps.get_attr(['env', 'gcp_home']),
"GATE_HOME": ps.get_attr(['env', 'gate_home'])
}),
'-Dat.ofai.gate.modularpipelines.configFile="%s/bio-yodie-1-2-1/main-bio/main-bio.config.yaml" '
% ps.get_attr(['env', 'yodie_path']),
"-Xmx%s" % ps.get_attr(['yodie', 'memory']),
"gate.cloud.batch.BatchRunner",
"-t %s" % ps.get_attr(['yodie', 'thread_num']),
"-b %s" % ps.get_attr(['yodie', 'config_xml_path'])
])
else:
cmd = ' '.join([
'gcp-direct.sh',
"-t %s" % ps.get_attr(['yodie', 'thread_num']),
"-Xmx%s" % ps.get_attr(['yodie', 'memory']),
"-b %s" % ps.get_attr(['yodie', 'config_xml_path']),
'-Dat.ofai.gate.modularpipelines.configFile="%s/bio-yodie-1-2-1/main-bio/main-bio.config.yaml" '
% ps.get_attr(['env', 'yodie_path']),
])
logging.debug(
'executing the following command to start NLP...')
logging.info(cmd)
p = Popen(cmd, shell=True, stderr=STDOUT)
p.wait()
if 0 != p.returncode:
job_status.set_status(False)
job_status.save()
logging.error(
'ERROR doing the NLP, stopped with a coide [%s]' %
p.returncode)
exit(p.returncode)
else:
logging.info('[SemEHR-step-end] NLP step done')
if 'semehr_path' in os.environ:
logging.info('changing back to semehr_path: %s' %
os.environ['semehr_path'])
os.chdir(os.environ['semehr_path'])
# 2. do SemEHR concept/entity indexing
if ps.get_attr(['job', 'semehr-concept']) == 'yes' or ps.get_attr(
['job', 'semehr-patients']) == 'yes':
patients = []
doc_to_patient = {}
for r in data_rows:
patients.append(str(r['patientid']))
doc_to_patient[str(r['docid'])] = str(r['patientid'])
patients = list(set(patients))
do_semehr_index(ps, patients, doc_to_patient)
# 3. do SemEHR actionable transparency
if ps.get_attr(['job', 'action_trans']) == 'yes':
logging.info('[SemEHR-step]doing transparency...')
actionable_transparise(settings=ps)
# 4. do SemEHR document annotation analysis (post processing)
if ps.get_attr(['job', 'doc_analysis']) == 'yes':
logging.info('[SemEHR-step]doing SemEHR annotation analysis...')
do_semehr_doc_anns_analysis(settings=ps)
logging.info('[SemEHR-step-end] doc_analysis step done')
# 4.5 do SemEHR patient level index
if ps.get_attr(['job', 'patient_index']) == 'yes':
logging.info('[SemEHR-step]doing patient level indexing...')
patient_level_indexing(settings=ps, pids=pids)
logging.info('[SemEHR-step-end] patient level indexing done')
# 5. do populate results for a research study
if ps.get_attr(['job', 'populate_cohort_result']) == 'yes':
logging.info(
'[SemEHR-step]doing SemEHR cohort result extraction...')
populate_cohort_results(settings=ps)
logging.info('[SemEHR-step-end] populate_cohort_result step done')
# 6. do collect cohort doc based results for a research study
if ps.get_attr(['job', 'cohort_doc_collection']) == 'yes':
logging.info(
'[SemEHR-step]doing SemEHR cohort doc based collection...')
collect_cohort_doc_results(settings=ps, doc2pid=doc2pid)
logging.info(
'[SemEHR-step-end] collect_cohort_doc_results step done')
job_status.set_status(True)
job_status.save()
logging.info('[SemEHR-process-end] all done')
except Exception as e:
logging.error('[SemEHR-process-ERROR] Failed to do SemEHR process %s' %
str(e))
job_status.set_status(False)
job_status.save()
def process_semehr(config_file):
"""
a pipeline to process all SemEHR related processes:
0. ES doc copy from one index to another;
1. bio-yodie NLP pipeline annotation on docs;
2. entity centric SemEHR ES indexing
:param config_file:
:return:
"""
# read the configuration
ps = ProcessSetting(config_file)
# initialise the jobstatus class instance
job_file = join(
ps.get_attr(['job', 'job_status_file_path']),
'semehr_job_status_%s.json' % ps.get_attr(['job', 'job_id']))
print 'using job status file %s' % job_file
job_status = JobStatus(job_file)
job_status.job_start()
data_rows = []
if ps.get_attr(['job', 'load_docs']) == 'yes':
sql_template = ps.get_attr(['new_docs', 'sql_query'])
print 'retrieving docs by using the template [%s]' % sql_template
data_rows = get_docs_for_processing(
job_status, sql_template,
ps.get_attr(['new_docs', 'dbconn_setting_file']))
print 'total docs num is %s' % len(data_rows)
# try:
if True:
# 0. copy docs
if ps.get_attr(['job', 'copy_docs']) == 'yes':
docs = [str(r['docid']) for r in data_rows]
utils.multi_thread_tasking(
docs,
ps.get_attr(['doc_copy', 'thread_num']),
do_copy_doc,
args=[
EntityCentricES(ps.get_attr(['doc_copy', 'es_host'])),
ps.get_attr(['doc_copy', 'src_index']),
ps.get_attr(['doc_copy', 'src_doc_type']),
ps.get_attr(['doc_copy', 'dest_index']),
ps.get_attr(['doc_copy', 'dest_doc_type'])
])
if ps.get_attr(['job', 'yodie']) == 'yes':
docid_path = '%s/%s_docids.txt' % (ps.get_attr([
'yodie', 'input_doc_file_path'
]), ps.get_attr(['job', 'job_id']))
print 'working on yodie with %s documents, saved to %s...' % (str(
len(data_rows)), docid_path)
# save doc ids to text file for input to bioyodie
print 'saving doc ids to [%s]' % docid_path
utils.save_string('\n'.join([str(r['docid']) for r in data_rows]),
docid_path)
# 1. do bio-yodie pipeline
# 1.1 prepare the configuration file
produce_yodie_config(ps)
# 1.2 set the env variables
set_sys_env(ps)
# 1.3 clear ann output folder
print 'clearing %s ...' % ps.get_attr(
['yodie', 'output_file_path'])
clear_folder(ps.get_attr(['yodie', 'output_file_path']))
# 1.3 run bio-yodie
os.chdir(ps.get_attr(['yodie', 'gcp_run_path']))
if ps.get_attr(['yodie', 'os']) == 'win':
cmd = ' '.join([
'java',
"-Dgate.home=%s" % ps.get_attr(['env', 'gate_home']),
"-Dgcp.home=%s" % ps.get_attr(['env', 'gcp_home']),
"-Djava.protocol.handler.pkgs=gate.cloud.util.protocols",
"-cp .;{SCRIPTDIR}/conf;{SCRIPTDIR}/gcp.jar;{SCRIPTDIR}/lib/*;"
"{GATE_HOME}/bin/gate.jar;{GATE_HOME}/lib/*".format(
**{
"SCRIPTDIR": ps.get_attr(['env', 'gcp_home']),
"GATE_HOME": ps.get_attr(['env', 'gate_home'])
}),
'-Dat.ofai.gate.modularpipelines.configFile="%s/bio-yodie-1-2-1/main-bio/main-bio.config.yaml" '
% ps.get_attr(['env', 'yodie_path']),
"-Xmx%s" % ps.get_attr(['yodie', 'memory']),
"gate.cloud.batch.BatchRunner",
"-t %s" % ps.get_attr(['yodie', 'thread_num']),
"-b %s" % ps.get_attr(['yodie', 'config_xml_path'])
])
else:
cmd = ' '.join([
'gcp-direct.sh',
"-t %s" % ps.get_attr(['yodie', 'thread_num']),
"-Xmx%s" % ps.get_attr(['yodie', 'memory']),
"-b %s" % ps.get_attr(['yodie', 'config_xml_path']),
'-Dat.ofai.gate.modularpipelines.configFile="%s/bio-yodie-1-2-1/main-bio/main-bio.config.yaml" '
% ps.get_attr(['env', 'yodie_path']),
])
print cmd
p = Popen(cmd, shell=True, stderr=STDOUT)
p.wait()
if 0 != p.returncode:
job_status.set_status(False)
job_status.save()
exit(p.returncode)
# 2. do SemEHR concept/entity indexing
if ps.get_attr(['job', 'semehr-concept']) == 'yes' or ps.get_attr(
['job', 'semehr-patients']) == 'yes':
patients = []
doc_to_patient = {}
for r in data_rows:
patients.append(str(r['patientid']))
doc_to_patient[str(r['docid'])] = str(r['patientid'])
patients = list(set(patients))
do_semehr_index(ps, patients, doc_to_patient)
# 3. do SemEHR actionable transparency
if ps.get_attr(['job', 'action_trans']) == 'yes':
print 'doing transparency...'
actionable_transparise(settings=ps)
job_status.set_status(True)
job_status.save()