Fixed Codacy issues.

adapters/glioma.py

@@ -21,8 +21,8 @@ def __init__(self):
         self.cleanup_fields.append('SRA_accession')
 
     @staticmethod
-    def _dash_to_underscore(input):
-        return input.replace('-', '_')
+    def _dash_to_underscore(org):
+        return org.replace('-', '_')
 
     def get_org_url(self):
         """

file_copier.py

@@ -14,13 +14,12 @@
 if LOG_PREFIX not in os.environ:
     os.environ[LOG_PREFIX] = 'File_Loader'
 
-""""
-This script copies (stream in memory) files from an URL to specified S3 bucket
 
-Inputs:
-  pre-manifest: TSV file that contains all information of original files
-  target bucket: 
-"""
+# This script copies (stream in memory) files from an URL to specified S3 bucket
+#
+# Inputs:
+#   pre-manifest: TSV file that contains all information of original files
+#   target bucket:
 
 
 class FileLoader:
@@ -195,15 +194,17 @@ def populate_neo4j_record(self, record, result):
         record[Copier.ACL] = result[Copier.ACL]
         return record
 
-    def _clean_up_field_names(self, headers):
+    @staticmethod
+    def _clean_up_field_names(headers):
         '''
         Removes leading and trailing spaces from header names
         :param headers:
         :return:
         '''
         return [header.strip() for header in headers]
 
-    def _clean_up_record(self, record):
+    @staticmethod
+    def _clean_up_record(record):
         '''
         Removes leading and trailing spaces from keys in org_record
         :param record:
@@ -216,7 +217,7 @@ def _read_pre_manifest(self):
         with open(self.pre_manifest) as pre_m:
             reader = csv.DictReader(pre_m, delimiter='\t')
             self.field_names = self._clean_up_field_names(reader.fieldnames)
-            for i in range(self.skip):
+            for _ in range(self.skip):
                 next(reader)
                 self.files_skipped += 1
 

loader.py

@@ -272,10 +272,10 @@ def main():
             log.info('No files to load.')
 
 
-    except ServiceUnavailable as err:
+    except ServiceUnavailable:
         log.critical("Neo4j service not available at: \"{}\"".format(config.neo4j_uri))
         return
-    except AuthError as err:
+    except AuthError:
         log.error("Wrong Neo4j username or password!")
         return