get_fill_metadata.py: problems solving

src/db_utils/projects_metadata/get_fill_metadata.py

@@ -15,6 +15,8 @@ import pandas as pd
 from io import StringIO
 from ..populate_database import populate_df
 import re
+import logging
+from ...logging_conf import logging_def
 
 
 def launch_PmagicGEO_script() -> None:
@@ -25,8 +27,8 @@ def launch_PmagicGEO_script() -> None:
     :param GSM_file: A file with the list of GSM or GSE for which we want to \
         obtain metadata.
     """
-    subprocess.check_output(f"PmagicGEO.pl -i {Config.geo_id_file} " \
-                            f"-p {Config.output} " f"-o {Config.outfile}", \
+    subprocess.check_output(f"PmagicGEO.pl -i {Config.geo_id_file} "
+                            f"-p {Config.output} " f"-o {Config.outfile}",
                             shell=True, stderr=subprocess.STDOUT)
 
 
@@ -67,24 +69,27 @@ def merge_metadata() -> pd.DataFrame:
     """
     Merging of metadata obtained through PmagicGEO.pl and manually.
     """
-    projects = load_metadata().merge(load_manual_metadata(), left_on = "gsm", \
-                                                       right_on = "GSM")
+    projects = load_metadata().merge(load_manual_metadata(), left_on = "gsm",
+                                     right_on = "GSM")
     projects = projects.drop(["gsm", "GSM"], axis=1)
-    projects.rename(columns={"GSM-GSE": "id_project", "GSM-Title": "name", \
-                   "GSM-Characteristics": "description", \
-                   "GSM_FAMILYSOFT-contact_institute": "institute", \
-                   "GSEA-Citation(s)": "citation", "Cell line": "cell_line", \
-                   "Real source": "database", "Kept GSM": "id_sample", \
+    projects.rename(columns={"GSM-GSE": "id_project", "GSM-Title": "name",
+                   "GSM-Characteristics": "description",
+                   "GSM_FAMILYSOFT-contact_institute": "institute",
+                   "GSEA-Citation(s)": "citation", "Cell line": "cell_line",
+                   "Real source": "database", "Kept GSM": "id_sample",
                    "Antibody": "antibody"}, inplace=True)
     projects = projects.reset_index().rename(columns={"index":"id"})
     logging.debug(projects.head())
     return projects
 
 
-def fill_projects_table() -> None:
+def fill_projects_table(logging_level: str = "DISABLE",) -> None:
     """
     Fill the table projects
+
+    :param logging_level: The level of data to display.
     """
+    logging_def(Config.output, __file__, logging_level)
     logging.debug('Filling cin_projects')
     populate_df(table='cin_projects', df=merge_metadata(), clean='y')