From 27a2b926036211469eccbf8c3d9580182482bdc2 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Wed, 6 Jan 2021 14:13:13 +0100
Subject: cleaned utils.py

---
 workflows/pull-data/genbank/utils.py | 22 +++++++++++++++-------
 1 file changed, 15 insertions(+), 7 deletions(-)

(limited to 'workflows')

diff --git a/workflows/pull-data/genbank/utils.py b/workflows/pull-data/genbank/utils.py
index 3efc67a..96920a5 100644
--- a/workflows/pull-data/genbank/utils.py
+++ b/workflows/pull-data/genbank/utils.py
@@ -1,5 +1,6 @@
 import os
 
+
 def is_integer(string_to_check):
     try:
         int(string_to_check)
@@ -7,19 +8,26 @@ def is_integer(string_to_check):
     except ValueError:
         return False
 
+
 def chunks(lst, n):
     for i in range(0, len(lst), n):
         yield lst[i:i + n]
 
+
 def check_and_get_ontology_dictionaries(dir_ontology_dictionaries):
-    # Check duplicated entry looking at all dictionaries
+    """
+    Check duplicated entry by looking in all dictionaries
+    """
+
     field_to_term_to_uri_dict = {}
 
-    path_dict_xxx_csv_list = [os.path.join(dir_ontology_dictionaries, name_xxx_csv) for name_xxx_csv in
-                              os.listdir(dir_ontology_dictionaries) if name_xxx_csv.endswith('.csv')]
+    path_dict_xxx_csv_list = [
+        os.path.join(dir_ontology_dictionaries, name_xxx_csv) for name_xxx_csv in
+        os.listdir(dir_ontology_dictionaries) if name_xxx_csv.endswith('.csv')
+    ]
 
     for path_dict_xxx_csv in path_dict_xxx_csv_list:
-        print('Read {}'.format(path_dict_xxx_csv))
+        print(f'Read {path_dict_xxx_csv}')
 
         with open(path_dict_xxx_csv) as f:
             for line in f:
@@ -31,7 +39,7 @@ def check_and_get_ontology_dictionaries(dir_ontology_dictionaries):
                 term = term.strip('"')
 
                 if term in field_to_term_to_uri_dict:
-                    print('Warning: in the dictionaries there are more entries for the same term ({}).'.format(term))
+                    print(f'Warning: in the dictionaries there are more entries for the same term ({term}).')
                     continue
 
                 field_to_term_to_uri_dict[term] = uri
@@ -54,9 +62,9 @@ def check_and_get_ontology_dictionaries(dir_ontology_dictionaries):
                 term = term.strip('"')
 
                 if term in field_to_term_to_uri_dict[field]:
-                    print('Warning: in the {} dictionary there are more entries for the same term ({}).'.format(field, term))
+                    print(f'Warning: in the {field} dictionary there are more entries for the same term ({term}).')
                     continue
 
                 field_to_term_to_uri_dict[field][term] = uri
 
-    return field_to_term_to_uri_dict
\ No newline at end of file
+    return field_to_term_to_uri_dict
-- 
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