From c229c568269e33ad537fb45250caf3c0b792f03d Mon Sep 17 00:00:00 2001
From: alapendr <audrey.lapendry@ens-lyon.fr>
Date: Tue, 10 Mar 2020 10:40:51 +0100
Subject: [PATCH] get_fill_metadata.py: problems solving
---
.../projects_metadata/get_fill_metadata.py | 25 +++++++++++--------
1 file changed, 15 insertions(+), 10 deletions(-)
diff --git a/src/db_utils/projects_metadata/get_fill_metadata.py b/src/db_utils/projects_metadata/get_fill_metadata.py
index 0afb89ea..1886020d 100644
--- a/src/db_utils/projects_metadata/get_fill_metadata.py
+++ b/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')
--
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