def get_all_datasets():
"""
Get all dataset by scan output folder, if folder name start begin DATASET_PREFIX, that's mean this dataset generate
by rest api, it should be returned.
If get configuration by title failed, then this api will skip the dataset
:return: the rest api generated datasets
"""
datasets_folders = [f for f in listdir(GENERATED_DATASETS_DIR) if isdir(join(GENERATED_DATASETS_DIR, f))]
datasets = []
for dataset_name in datasets_folders:
if not dataset_name.startswith(DATASET_PREFIX): # not generate by rest api
continue
dataset_parts = dataset_name.split('.')
name = len(dataset_parts) > 1 and dataset_parts[1] or 'ERROR TO GET NAME'
output_format = len(dataset_parts) > 3 and dataset_parts[3] or 'CCDA'
try:
configurations = dataset_configuration_service.get_configuration_by_title(name)
datasets.append({
'title': name,
'completedOn': datetime.fromtimestamp(
stat(join(GENERATED_DATASETS_DIR, dataset_name)).st_mtime).isoformat(),
'configuration': configurations,
'outputFormat': output_format,
'datasetName': dataset_name
})
except Exception as e:
# if get configuration error, then skip this dataset, so we don't need raise error here
logger.error(e)
if len(datasets) > 0:
datasets = sorted(datasets, key=lambda k: k['completedOn'], reverse=True)
return datasets
def get_morbidities_from_war_code(war_code, include_percentage=False):
"""
Get morbidities by war code. If the result is already cached, then return the cached result.
If not found raise EntityNotFoundError
:param war_code: the war code
:param include_percentage: True if percentage of morbidity should be added to output, False otherwise
:return: the list with morbidities data
"""
global morbidity_map
if morbidity_map.get(war_code) is not None: # return cached data
return morbidity_map.get(war_code)
file_path = DATASOURCES_DIR + '/morbidity_' + war_code + '.csv'
try:
with open(file_path, 'rU') as csv_file:
morbidity_raw_list = csv.reader(csv_file, delimiter=',', quotechar='"')
morbidity_list = []
first = True
for row in morbidity_raw_list:
if first: # skip first row with header
first = False
continue
item = {'name': row[0], 'icd10Code': row[1]}
if include_percentage:
item['percentOfProbabilityToAcquireDiagnosis'] = float(row[2])
morbidity_list.append(item)
morbidity_map[war_code] = morbidity_list
return morbidity_list
except Exception as e:
logger.error(e)
raise EntityNotFoundError('Could not open {0}. Error: {1}'.format(file_path, e))
def get_wars_from_file():
"""
Get war eras from file. Return cache result if data is already cached.
:return: the war eras
"""
global military_eras
if military_eras is not None:
# return cached data
return military_eras
wars_data_path = DATASOURCES_DIR + '/military_eras.csv'
try:
# load the military_eras datasource
with open(wars_data_path, 'rU') as csv_file:
military_eras_list = csv.reader(csv_file, delimiter=',', quotechar='"')
military_eras = []
for row in military_eras_list:
if row[0] == 'war_code': # skip first element (titles row)
continue
war_code = row[0]
war_name = row[1]
percentage = float(row[2])
start_date = str_to_datetime(row[3])
end_date = str_to_datetime(row[4])
military_eras.append({"war_code": war_code,
"war_name": war_name,
"percentage": percentage,
"start_date": start_date,
"end_date": end_date})
return military_eras
except Exception as e:
logger.error('Could not open {0}. Error: {1}'.format(wars_data_path, e))
def get_all_datasets():
"""
get all datasets from cache
:return: the rest api generated datasets
"""
datasets = []
global dataset_manager
keys = dataset_manager.get_all_keys()
for dataset_name in keys:
dataset = dataset_manager.get_by_name(dataset_name)
if dataset is None:
continue
dataset_parts = dataset_name.split('.')
name = len(
dataset_parts) > 1 and dataset_parts[1] or 'ERROR TO GET NAME'
try:
configurations = dataset_configuration_service.get_configuration_by_title(
name)
dataset['configuration'] = configurations
datasets.append(dataset)
except Exception as e:
# if get configuration error, then skip this dataset, so we don't need raise error here
logger.error(e)
if len(datasets) > 0:
datasets = sorted(datasets,
key=lambda k: k['completedOn'],
reverse=True)
return datasets
def load_datasources():
"""
Load datasource.json, military eras and ICD-10 code/name pairs, terminate if error occurs
"""
global data_source
global military_eras
# load datasource.json with generation rules for patient fields
data_source_file = DATASOURCES_DIR + '/datasource.json'
try:
with open(data_source_file) as data_file:
data_source = json.load(data_file, object_pairs_hook=OrderedDict)
except Exception as e:
logger.error('Could not open {0}. Error: {1}'.format(
data_source_file, e))
if data_source is None or len(data_source) == 0:
logger.error('Datasource not defined. Cannot continue.')
exit(1)
# load all war eras
military_eras = get_wars_from_file()
# load ICD-10 code/name pairs
load_icd10_codes()
def preload_datasets():
"""
preload all datasets into manager
Get all dataset by scan output folder, if folder name start begin DATASET_PREFIX, that's mean this dataset generate
by rest api
If get configuration by title failed, then this api will skip the dataset
:return: None
"""
datasets_folders = [
f for f in listdir(GENERATED_DATASETS_DIR)
if isdir(join(GENERATED_DATASETS_DIR, f))
]
for dataset_name in datasets_folders:
if not dataset_name.startswith(
DATASET_PREFIX): # not generate by rest api
continue
dataset_parts = dataset_name.split('.')
name = len(
dataset_parts) > 1 and dataset_parts[1] or 'ERROR TO GET NAME'
output_format = len(dataset_parts) > 3 and dataset_parts[3] or 'CCDA'
try:
configurations = dataset_configuration_service.get_configuration_by_title(
name)
dataset = {
'title':
name,
'completedOn':
datetime.fromtimestamp(
stat(join(GENERATED_DATASETS_DIR,
dataset_name)).st_mtime).isoformat(),
'configuration':
configurations,
'status':
DATASET_COMPLETED,
'progress':
100,
'outputFormat':
output_format,
'datasetName':
dataset_name
}
dataset_manager.push_entity(dataset_name, dataset)
logger.info("succeed load dataset = " + dataset_name)
except Exception as e:
# if get configuration error, then skip this dataset, so we don't need raise error here
logger.error(e)
def load_icd10_codes():
"""
Read icd10cm_codes_2018.txt file, extract code/name pairs of known morbidities from it.
The result is saved to the global icd_morbidity_name_by_code variable.
:return: None
"""
global icd_morbidity_name_by_code
icd_morbidity_name_by_code = {}
# load the ICD-10 datasource
try:
logger.info('Reading ICD-10 datasource...')
lines_num = 0
for line in open(ICD_10_CODES_FILE_PATH):
code = line[:8].strip()
name = line[8:].strip()
icd_morbidity_name_by_code[code] = name
lines_num += 1
logger.info('Loaded {0} records from ICD-10 datasource'.format(lines_num))
except Exception as e:
logger.error('Could not open {0}. Error: {1}'.format(ICD_10_CODES_FILE_PATH, e))
raise
from rest.services.dataset_configuration_service import read_configuration_from_file
from rest.services.dataset_configuration_service import get_configuration_by_title
from rest.services.datasources_service import get_morbidities_from_study_profile_code
if __name__ == '__main__':
# parse command line options
options = docopt(__doc__, version='1.0.0')
# check configuration file parameters and read configuration file if required
config_path = options['-c']
config_title = options['-t']
config = None
if config_path and config_title:
logger.error(
'Both configuration file path and configuration title were specified. '
+ 'Only one of them can be provided at a time')
exit(1)
if config_path is not None:
if not isfile(config_path):
logger.error(
"Configuration file {0} doesn't exist".format(config_path))
exit(1)
try:
config = read_configuration_from_file(config_path)
except Exception as e:
logger.error(
"Error occurred while reading configuration file: {0}".format(
e))
exit(1)
