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 save(body_entity):
"""
Check whether the body entity warEra and morbidities exist or not.
Then save it to the local file system.
:param body_entity: the request dataset configuration entity
:return: the same fully populated dataset configuration entity
"""
# make sure war era exists
war_era = get_war_era_by_name(body_entity['warEra']['warEra'])
# update request war era
body_entity['warEra'] = convert_raw_war(war_era)
total_morbidities = get_morbidities_from_war_code(war_era['war_code'])
for request_morbidity in body_entity['morbiditiesData']:
morbidity_code = request_morbidity['icd10Code']
# check whether morbidity exists in CSV file of the specified war
morbidity_exists = False
for morbidity in total_morbidities:
if morbidity_code == morbidity['icd10Code']:
# set or update morbidity name in request
request_morbidity['name'] = morbidity['name']
morbidity_exists = True
break
# if not found, try to find morbidity in ICD-10 datasource
if not morbidity_exists:
morbidity_name = get_icd_morbidity_name_by_code(morbidity_code)
if morbidity_name:
# set or update morbidity name in request
request_morbidity['name'] = morbidity_name
morbidity_exists = True
if not morbidity_exists:
raise EntityNotFoundError(
'Morbidity with ICD-10 code {0} is unknown'.format(
morbidity_code))
# set default output folder to the configuration
output_folder = GENERATED_DATASETS_DIR
# try to use short relative to the current directory path if possible
try:
output_folder = relpath(output_folder)
except ValueError:
pass
body_entity['outputFolder'] = output_folder
configuration_file = DATASET_CONFIGURATIONS_DIR + '/' + CONFIGURATION_PREFIX + '.' + body_entity[
'title'] + '.json'
try:
with open(configuration_file, 'w') as f:
f.write(dumps(body_entity, indent=2))
return body_entity
except Exception as e:
raise InnerServerError('Cannot save file {0}. Error: {1}'.format(
configuration_file, e))
def delete_dataset_by_title(title):
"""
Delete dateset by title
It raises EntityNotFoundError if dataset not found
:param title: the dataset title
"""
dataset_path = join(GENERATED_DATASETS_DIR, title)
if not exists(dataset_path):
raise EntityNotFoundError("Dataset not found where name = " + title)
rmtree(dataset_path)
def generate(title):
"""
Generate a dataset according to dataset configuration file with the specified title.
It raises EntityNotFoundError if file cannot be found.
:param title: the dataset configuration title
:return: the number of generated report files
"""
configurations = dataset_configuration_service.get(title) # the length will be 1
if len(configurations) <= 0:
raise EntityNotFoundError('Cannot find configuration with title ' + title)
return generate_from_config(configurations[0])
def get_war_era_by_name(name):
"""
Get war era by its name. Raises EntityNotFoundError if not found.
:param name: the war name
:return: the war era details
"""
wars = get_wars_from_file()
filter_wars = list(filter(lambda w: w['war_name'] == name, wars))
if len(filter_wars) <= 0:
raise EntityNotFoundError('Cannot find war era with name ' + name)
return filter_wars[0]
def get_configuration_by_title(title):
"""
Get single configuration with the specified title
:param title: the configuration title
:return: the dataset configuration instance
"""
configuration_file_path = DATASET_CONFIGURATIONS_DIR + '/' + CONFIGURATION_PREFIX + '.' + title + '.json'
if isfile(configuration_file_path):
return read_configuration_from_file(configuration_file_path)
else:
raise EntityNotFoundError('Cannot find configuration file for title ' +
title)
def get_study_profile_by_name(name):
"""
Get study profile by its name. Raises EntityNotFoundError if not found.
:param name: the study profile name
:return: the study profile details
"""
study_profiles = get_study_profiles_from_file()
filter_study_profiles = list(
filter(lambda w: w['study_profile_name'] == name, study_profiles))
if len(filter_study_profiles) <= 0:
raise EntityNotFoundError('Cannot find study profile with name ' +
name)
return filter_study_profiles[0]
def delete_config_by_title(title):
"""
Delete dateset Config by title
It raises EntityNotFoundError if dataset config not found
:param title: the dataset Config title
"""
config_file = join(
DATASET_CONFIGURATIONS_DIR,
'{0}.{1}.{2}'.format(CONFIGURATION_PREFIX, title, 'json'))
if not exists(config_file):
raise EntityNotFoundError("Dataset config not found where title = " +
title)
remove(config_file)
def delete_config_by_title(title):
"""
Delete dateset Config by title
It raises EntityNotFoundError if dataset config not found
:param title: the dataset Config title
"""
config_file = join(
DATASET_CONFIGURATIONS_DIR,
'{0}.{1}.{2}'.format(CONFIGURATION_PREFIX, title, 'json'))
if not exists(config_file):
raise EntityNotFoundError("Dataset config not found where title = " +
title)
remove(config_file)
if get_cache_map().get(title) is not None: # delete from cache
get_cache_map().pop(title, None)
from rest.services.dataset_generation_service import remove_dateset_by_config_title
remove_dateset_by_config_title(title)