def run_refresh(filename):
proj_filter = []
with dax.XnatUtils.get_interface() as xnat:
proj_filter = utils.get_user_favorites(xnat)
df = get_data(xnat, proj_filter)
save_data(df, filename)
return df
def run_refresh(filename):
proj_filter = []
proc_filter = []
scan_filter = []
# force a requery
with dax.XnatUtils.get_interface() as xnat:
proj_filter = utils.get_user_favorites(xnat)
df = get_data(xnat, proj_filter, proc_filter, scan_filter)
save_data(df, filename)
return df
def load_stats_data():
my_redcaps = []
df = pd.DataFrame()
# Load assr data
logging.debug('loading stats data')
try:
# Read inputs yaml as dictionary
with open(REDCAP_FILE, 'rt') as file:
redcap_data = yaml.load(file, yaml.SafeLoader)
except EnvironmentError:
logging.info('REDCap settings file not found, not loading stats')
df = pd.DataFrame(columns=static_columns())
return df
api_url = redcap_data['api_url']
with dax.XnatUtils.get_interface() as xnat:
my_projects = utils.get_user_favorites(xnat)
# Filter the list of redcaps based on our project access
for r in redcap_data['projects']:
name = r['name']
try:
(proj, proc, res) = parse_redcap_name(name)
except ValueError:
continue
if (proj in my_projects):
my_redcaps.append(r)
# Load data from each redcap
icount = len(my_redcaps)
for i, r in enumerate(my_redcaps):
name = r['name']
api_key = r['key']
(proj, proc, res) = parse_redcap_name(name)
logging.info('{}/{} loading redcap:{}'.format(i+1, icount, name))
try:
cur_df = load_redcap_stats(api_url, api_key)
df = pd.concat([df, cur_df], ignore_index=True, sort=False)
except Exception as err:
logging.error('error exporting redcap:{}:{}'.format(name, err))
import traceback
traceback.print_exc()
continue
# Rename columns
df.rename(columns=STATS_RENAME, inplace=True)
# Filter out columns we don't want by keeping intersection
_static = static_columns()
_var = get_vars()
_keep = df.columns
_keep = [x for x in _keep if (x in _var or x in _static)]
#print('_keep', _keep)
df = df[_keep]
# return the stats data
logging.info('loaded {} stats'.format(len(df)))
return df