diff --git a/isocor/ui/isocorcli.py b/isocor/ui/isocorcli.py index 0785da3..291553c 100644 --- a/isocor/ui/isocorcli.py +++ b/isocor/ui/isocorcli.py @@ -2,6 +2,7 @@ import isocor as hr import isocor.ui.isocordb import pandas as pd +import numpy as np import io import logging from pathlib import Path @@ -148,7 +149,6 @@ def process(args): dictMetabolites[label] = None errors['labels'] = errors['labels'] + [label] logger.error("cannot construct {}: {}".format(label, err)) - sys.exit(2) logger.info('------------------------------------------------') logger.info('Correcting raw MS data...') @@ -170,15 +170,15 @@ def process(args): logger.info("{} - {}: processed".format(serie[0], label)) except Exception as err: isotopic_inchi = ['']*len(serie[1]) - valuesCorrected = ([pd.np.nan]*len(serie[1]), [pd.np.nan] - * len(serie[1]), [pd.np.nan]*len(serie[1]), pd.np.nan) + valuesCorrected = ([np.nan]*len(serie[1]), [np.nan] + * len(serie[1]), [np.nan]*len(serie[1]), np.nan) logger.error("{} - {}: {}".format(serie[0], label, err)) errors['measurements'] = errors['measurements'] + \ ["{} - {}".format(serie[0], label)] else: isotopic_inchi = ['']*len(serie[1]) - valuesCorrected = ([pd.np.nan]*len(serie[1]), [pd.np.nan] - * len(serie[1]), [pd.np.nan]*len(serie[1]), pd.np.nan) + valuesCorrected = ([np.nan]*len(serie[1]), [np.nan] + * len(serie[1]), [np.nan]*len(serie[1]), np.nan) errors['measurements'] = errors['measurements'] + \ ["{} - {}".format(serie[0], label)] logger.error(