output = re.sub(r'(^|[^%])((?:%%)*)%p', r'\1\2foo',
output).replace('%%', '%')
elif arg == '-p':
if not args or args[0] == '--':
print('no id specified', file=sys.stderr)
usage()
pid = args.pop(0)
elif arg == '-l':
if not args or args[0] == '--':
print('no file specified', file=sys.stderr)
usage()
lineFile = args.pop(0)
elif arg == '-c':
if not args or args[0] == '--':
print('no file specified', file=sys.stderr)
usage()
classFile = args.pop(0)
else:
print('unrecognized argument: ' + arg, file=sys.stderr)
usage()
if pid is None:
print('need to specify id with -p', file=sys.stderr)
usage()
allPaths = []
util.convert_paths(args, allPaths)
obj = process(allPaths, lineFile, classFile, pid)
if output != '-' and not os.path.exists(os.path.dirname(output)):
os.makedirs(os.path.dirname(output))
with util.OutWrapper(output) as out:
print(json.dumps(obj, indent=2, sort_keys=True), file=out)
def start_server(max_num, settings_file, format_file, class_file, line_file, cms_path, addr, port, debug):
settings = {}
util.read_config(settings, settings_file, True)
use_cache = settings.get('use_cache', True)
all_paths = []
input_format = {}
use_db = False
omop = None
if settings.get('omop_use_db', False):
use_db = True
omop = OMOP(settings, True)
else:
util.convert_paths([ cms_path ], all_paths)
util.read_format(format_file, input_format, usage)
cms_analyze.input_format = input_format
cms_get_patient.input_format = input_format
build_dictionary.debugOutput = True
build_dictionary.init(settings, settings_file)
dictionary_file = os.path.join(json_dir, dictionary_bind)
patients = set()
def save_patients():
if not use_cache:
return
with open(patients_list, 'w') as pf:
pf.write('\n'.join(sorted(list(patients))))
pf.flush()
if not os.path.isfile(patients_list) or not use_cache:
if use_db:
omop.list_patients(patients, prefix=json_dir, limit=max_num, show_old_ids=True)
else:
tf = StringIO()
cms_analyze.compute(all_paths, {}, False, tf, filter_zero=True)
tf.flush()
tf.seek(0)
lines = tf.readlines()[-max_num:] if max_num is not None else tf.readlines()
for line in lines:
patients.add(json_dir + line.strip() + '.json')
save_patients()
dict = {}
if use_cache:
if os.path.isfile(dictionary_file):
with open(dictionary_file, 'r') as input:
dict = json.loads(input.read())
else:
os.makedirs(json_dir)
# write the initial empty dictionary
# also ensures that the folder is writeable
with open(dictionary_file, 'w') as output:
output.write("{}")
server = create_server((addr, port))
server.bind_path('/', '..')
prefix = '/' + os.path.basename(os.path.normpath(server.base_path))
server.add_default_white_list()
server.add_file_patterns([
prefix + '/' + json_dir + '*',
prefix + '/' + patients_list
], True)
server.favicon_fallback = 'favicon.ico'
server.report_slow_requests = True
if debug:
server.suppress_noise = True
@server.text_get(prefix + '/' + patients_list, 0)
def get_list(req, args):
return '\n'.join(sorted(list(patients)))
@server.json_get(prefix + '/' + json_dir, 1)
def get_patient(req, args):
pid = args['paths'][0]
if pid.endswith('.json') and use_db:
pid = pid[:-len('.json')]
pid = omop.get_person_id(pid)
cache_file = os.path.join(json_dir, pid)
p_name = json_dir + pid.strip()
if p_name not in patients:
patients.add(p_name)
save_patients()
if pid.endswith('.json'):
pid = pid[:-len('.json')]
if not os.path.isfile(cache_file) or not use_cache:
if use_db:
patient = omop.get_patient(pid, dict, line_file, class_file)
else:
patient = cms_get_patient.process(all_paths, line_file, class_file, pid)
build_dictionary.extractEntries(dict, patient)
if use_cache:
with open(cache_file, 'w') as pf:
pf.write(json_dumps(patient))
pf.flush()
if use_cache:
with open(dictionary_file, 'w') as output:
output.write(json_dumps(dict))
output.flush()
return patient
with open(cache_file, 'r') as pf:
return json.loads(pf.read())
@server.json_get(prefix + '/' + dictionary_file)
def get_dictionary(req, args):
return dict
msg("starting server at {0}:{1}", addr if addr else 'localhost', port)
server.serve_forever()
msg("shutting down..")
server.server_close()
output = args.pop(0)
output = re.sub(r'(^|[^%])((?:%%)*)%p', r'\1\2foo', output).replace('%%', '%')
elif arg == '-p':
if not args or args[0] == '--':
print('no id specified', file=sys.stderr)
usage()
id = args.pop(0)
elif arg == '-l':
if not args or args[0] == '--':
print('no file specified', file=sys.stderr)
usage()
lineFile = args.pop(0)
elif arg == '-c':
if not args or args[0] == '--':
print('no file specified', file=sys.stderr)
usage()
classFile = args.pop(0)
else:
print('unrecognized argument: ' + arg, file=sys.stderr)
usage()
if id is None:
print('need to specify id with -p', file=sys.stderr)
usage()
allPaths = []
util.convert_paths(args, allPaths)
obj = process(allPaths, lineFile, classFile, id)
if output != '-' and not os.path.exists(os.path.dirname(output)):
os.makedirs(os.path.dirname(output))
with util.OutWrapper(output) as out:
print(json.dumps(obj, indent=2, sort_keys=True), file=out)
