src/db_utils/projects_metadata/get_fill_metadata.py: fix fill_projects_table...

src/db_utils/projects_metadata/get_fill_metadata.py: fix fill_projects_table to make it launch launch_pmagicGEO_script + pep8 modifications

src/db_utils/projects_metadata/get_fill_metadata.py

@@ -9,7 +9,6 @@ Then it allows to get data to fill the projects table in the ChIA-PET database.
 """
 
 import subprocess
-from pathlib import Path
 from .config_metadata_chiapet import Config_metadata as Config
 import pandas as pd
 from io import StringIO
@@ -19,13 +18,11 @@ import logging
 from ...logging_conf import logging_def
 
 
-def launch_PmagicGEO_script() -> None:
+def launch_pmagicGEO_script() -> None:
     """
     Launch PmagicGEO.pl to obtain metadata associated to a list of projects \
         that we want to study.
 
-    :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}",
@@ -52,8 +49,8 @@ def load_metadata() -> pd.DataFrame:
         new_cols[0] = 'gsm'
     df.columns = new_cols
     logging.debug(df.head())
-    return df[["gsm", "GSM-GSE", "GSM-Title", "GSM-Characteristics", \
-        "GSM_FAMILYSOFT-contact_institute", "GSEA-Citation(s)"]]
+    return df[["gsm", "GSM-GSE", "GSM-Title", "GSM-Characteristics",
+               "GSM_FAMILYSOFT-contact_institute", "GSEA-Citation(s)"]]
 
 
 def load_manual_metadata() -> pd.DataFrame:
@@ -62,23 +59,25 @@ def load_manual_metadata() -> pd.DataFrame:
     These informations were retrieved manually.
     """
     mfile = Config.metadata_file
-    return pd.read_csv(mfile, sep = "\t")
+    return pd.read_csv(mfile, sep="\t")
 
 
 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",
-                   "Antibody": "antibody"}, inplace=True)
-    projects = projects.reset_index().rename(columns={"index":"id"})
+                             "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
 
@@ -90,9 +89,11 @@ def fill_projects_table(logging_level: str = "DISABLE",) -> None:
     :param logging_level: The level of data to display.
     """
     logging_def(Config.output, __file__, logging_level)
+    logging.debug('Launching Pmagicgeo ...')
+    launch_pmagicGEO_script()
     logging.debug('Filling cin_projects')
     populate_df(table='cin_projects', df=merge_metadata(), clean='y')
 
 
 if __name__ == "__main__":
-    fill_projects_table('DEBUG')
\ No newline at end of file
+    fill_projects_table('DEBUG')