[Chore] Linted Files (#150)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#150

epdb/management/commands/import_external_identifiers.py

@@ -1,57 +1,58 @@
 from csv import DictReader
 
 from django.core.management.base import BaseCommand
+from django.db import transaction
 
-from epdb.models import *
+from epdb.models import Compound, CompoundStructure, Reaction, ExternalDatabase, ExternalIdentifier
 
 
 class Command(BaseCommand):
     STR_TO_MODEL = {
-        'Compound': Compound,
-        'CompoundStructure': CompoundStructure,
-        'Reaction': Reaction,
+        "Compound": Compound,
+        "CompoundStructure": CompoundStructure,
+        "Reaction": Reaction,
     }
 
     STR_TO_DATABASE = {
-        'ChEBI': ExternalDatabase.objects.get(name='ChEBI'),
-        'RHEA': ExternalDatabase.objects.get(name='RHEA'),
-        'KEGG Reaction': ExternalDatabase.objects.get(name='KEGG Reaction'),
-        'PubChem Compound': ExternalDatabase.objects.get(name='PubChem Compound'),
-        'PubChem Substance': ExternalDatabase.objects.get(name='PubChem Substance'),
+        "ChEBI": ExternalDatabase.objects.get(name="ChEBI"),
+        "RHEA": ExternalDatabase.objects.get(name="RHEA"),
+        "KEGG Reaction": ExternalDatabase.objects.get(name="KEGG Reaction"),
+        "PubChem Compound": ExternalDatabase.objects.get(name="PubChem Compound"),
+        "PubChem Substance": ExternalDatabase.objects.get(name="PubChem Substance"),
     }
 
     def add_arguments(self, parser):
         parser.add_argument(
-            '--data',
+            "--data",
             type=str,
-            help='Path of the ID Mapping file.',
+            help="Path of the ID Mapping file.",
             required=True,
         )
 
         parser.add_argument(
-            '--replace-host',
+            "--replace-host",
             type=str,
-            help='Replace https://envipath.org/ with this host, e.g. http://localhost:8000/',
+            help="Replace https://envipath.org/ with this host, e.g. http://localhost:8000/",
         )
 
     @transaction.atomic
     def handle(self, *args, **options):
-        with open(options['data']) as fh:
+        with open(options["data"]) as fh:
             reader = DictReader(fh)
             for row in reader:
-                clz = self.STR_TO_MODEL[row['model']]
+                clz = self.STR_TO_MODEL[row["model"]]
 
-                url = row['url']
-                if options['replace_host']:
-                    url = url.replace('https://envipath.org/', options['replace_host'])
+                url = row["url"]
+                if options["replace_host"]:
+                    url = url.replace("https://envipath.org/", options["replace_host"])
 
                 instance = clz.objects.get(url=url)
-                db = self.STR_TO_DATABASE[row['identifier_type']]
+                db = self.STR_TO_DATABASE[row["identifier_type"]]
 
                 ExternalIdentifier.objects.create(
                     content_object=instance,
                     database=db,
-                    identifier_value=row['identifier_value'],
-                    url=db.url_pattern.format(id=row['identifier_value']),
-                    is_primary=False
+                    identifier_value=row["identifier_value"],
+                    url=db.url_pattern.format(id=row["identifier_value"]),
+                    is_primary=False,
                 )