fix flake8

backend/metagenedb/utils/parsers.py

@@ -29,7 +29,7 @@ class KEGGLineParser(object):
                 'long_name': names[1].lstrip(),
                 'ec_number': ec_number
             }
-        except:
+        except Exception:
             _LOGGER.error(f"Could not parse: {line.rstrip()}. Are you sure it comes from KEGG KO list?")
             raise
 
@@ -61,23 +61,24 @@ class NCBITaxonomyLineParser(object):
             comments                                -- free-text comments and citations
         """
         elements = line.rstrip().split('|')
+        elements = [element.strip() for element in elements]
         try:
             return {
-                    "tax_id": elements[0].strip(),
-                    "parent_tax_id": elements[1].strip(),
-                    "rank": elements[2].strip(),
-                    "embl_code": elements[3].strip(),
-                    "division_id": elements[4].strip(),
-                    "inherited_div_flag": elements[5].strip(),
-                    "genetic_code_id": elements[6].strip(),
-                    "inherited_GC_flag": elements[7].strip(),
-                    "mitochondrial_genetic_code_id": elements[8].strip(),
-                    "inherited_MGC_flag": elements[9].strip(),
-                    "GenBank_hidden_flag": elements[10].strip(),
-                    "hidden_subtree_root_flag": elements[11].strip(),
-                    "comments": elements[12].strip()
+                    "tax_id": elements[0],
+                    "parent_tax_id": elements[1],
+                    "rank": elements[2].replace(' ', '_'),
+                    "embl_code": elements[3],
+                    "division_id": elements[4],
+                    "inherited_div_flag": elements[5],
+                    "genetic_code_id": elements[6],
+                    "inherited_GC_flag": elements[7],
+                    "mitochondrial_genetic_code_id": elements[8],
+                    "inherited_MGC_flag": elements[9],
+                    "GenBank_hidden_flag": elements[10],
+                    "hidden_subtree_root_flag": elements[11],
+                    "comments": elements[12]
                 }
-        except:
+        except Exception:
             _LOGGER.error(f"Could not parse: {line.rstrip()}. Are you sure it comes from nodes.dmp file?")
             raise
 
@@ -102,6 +103,6 @@ class NCBITaxonomyLineParser(object):
                     "unique_name": elements[2].strip(),
                     "name_class": elements[3].strip(),
                 }
-        except:
+        except Exception:
             _LOGGER.error(f"Could not parse: {line.rstrip()}. Are you sure it comes from nodes.dmp file?")
             raise