refactor: More style changes (to comply with mypy)

api/security.py

@@ -1,9 +1,9 @@
+# pylint: skip-file
 import logging
 import os
 import time
 
 from pathlib import Path
-from typing import Any
 
 from wsgiref.util import FileWrapper
 from django.http import Http404
@@ -102,12 +102,6 @@ def get_conn():
 
 
 class ISpyBSafeQuerySet(viewsets.ReadOnlyModelViewSet):
-    def __init__(self, **kwargs: Any) -> None:
-        super().__init__(**kwargs)
-        self.request = None
-        self.filter_permissions = None
-        self.queryset = None
-
     def get_queryset(self):
         """
         Optionally restricts the returned purchases to a given proposals

docs/source/conf.py

@@ -43,7 +43,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = []
+exclude_patterns = []  # type: ignore
 
 
 # -- Options for HTML output -------------------------------------------------

fragalysis/settings.py

@@ -280,11 +280,11 @@
 if os.environ.get("BUILD_XCDB") == 'yes':
     DATABASES["xchem_db"] = {
         "ENGINE": 'django.db.backends.postgresql',
-        "NAME": os.environ.get("XCHEM_NAME"),
-        "USER": os.environ.get("XCHEM_USER"),
-        "PASSWORD": os.environ.get("XCHEM_PASSWORD"),
-        "HOST": os.environ.get("XCHEM_HOST"),
-        "PORT": os.environ.get("XCHEM_PORT"),
+        "NAME": os.environ.get("XCHEM_NAME", ""),
+        "USER": os.environ.get("XCHEM_USER", ""),
+        "PASSWORD": os.environ.get("XCHEM_PASSWORD", ""),
+        "HOST": os.environ.get("XCHEM_HOST", ""),
+        "PORT": os.environ.get("XCHEM_PORT", ""),
     }
 
 if CHEMCENTRAL_DB_NAME != "UNKOWN":

viewer/cset_upload.py

@@ -37,16 +37,13 @@
 
 def dataType(a_str: str) -> str:
     lean_str = a_str.strip()
-    if len(lean_str) == 0:
+    if not lean_str:
         return 'BLANK'
+
     try:
         t = ast.literal_eval(lean_str)
-
-    except ValueError:
-        return 'TEXT'
-    except SyntaxError:
+    except (ValueError, SyntaxError):
         return 'TEXT'
-
     else:
         if type(t) in [int, int, float, bool]:
             if t in [
@@ -72,6 +69,9 @@ def dataType(a_str: str) -> str:
                 return 'INT'
             if type(t) is float:
                 return 'FLOAT'
+
+            # Can't get here?
+            assert False
         else:
             return 'TEXT'
 

viewer/discourse.py

@@ -2,6 +2,8 @@
 discourse.py Functions for to send and retrieve posts to/fraom the discourse platform.
 """
 import os
+from typing import Tuple
+
 from pydiscourse import DiscourseClient
 from django.conf import settings
 from viewer.models import DiscourseCategory, DiscourseTopic
@@ -10,15 +12,16 @@
 logger = logging.getLogger(__name__)
 
 
-def get_user(client, username):
-    """Call discourse API users to retreive user by username."""
+def get_user(client, username) -> Tuple[bool, str, int]:
+    """Call discourse API users to retrieve user by username."""
     logger.info('+ discourse.get_user')
-    error = False
-    error_message = ''
-    user = 0
+
+    error: bool = False
+    error_message: str = ''
+    user: int = 0
 
     try:
-        user = client.user(username)
+        user_record = client.user(username)
     except Exception as e:
         # User is not known in Discourse or there is a failure accessing Discourse.
         logger.error('discourse.get_user', exc_info=e)
@@ -33,7 +36,7 @@ def get_user(client, username):
         else:
             error_message = 'Please check Discourse Host parameter for Fragalysis'
     else:
-        user = user['id']
+        user = user_record['id']
 
     logger.info('- discourse.get_user')
     return error, error_message, user

viewer/migrations/0018_merge_20231109_1252.py

@@ -8,4 +8,4 @@ class Migration(migrations.Migration):
         ('viewer', '0017_alter_experimentupload_message'),
     ]
 
-    operations = []
+    operations = []  # type: ignore

viewer/models.py

@@ -1,6 +1,7 @@
 from dataclasses import dataclass
 import uuid
 import logging
+from typing import List
 
 from django.contrib.auth.models import User
 from django.db import models
@@ -457,13 +458,13 @@ def get_vectors(
         cmpd_id=None,
         vector_type=None,
         number=None,
-    ):
+    ) -> List[Vector3d]:
         """Get the vectors for a given molecule
 
         :param mols: the Django molecules to get them from
         :return: None
         """
-        result = []
+        result: List[Vector3d] = []
         # pk checks and later continure statements are doing filtering
         # - as this is not going through the usual django_filter
         # machinery, it needs a different approach

viewer/squonk_job_file_transfer.py

@@ -3,6 +3,7 @@
 """
 import urllib.parse
 import os
+from typing import Dict, List, Tuple
 
 from django.conf import settings
 from rest_framework import status
@@ -109,7 +110,9 @@ def process_file_transfer(auth_token, job_transfer_id):
             raise RuntimeError(msg)
 
 
-def validate_file_transfer_files(request):
+def validate_file_transfer_files(
+    request,
+) -> Tuple[Dict[str, str], List[SiteObservation], List[ComputedMolecule]]:
     """Check the request and return a list of proteins and/or computed molecule objects
 
     Args:
@@ -119,9 +122,9 @@ def validate_file_transfer_files(request):
         list of validated proteins (SiteObservation)
         list of validated computed molecules (ComputedMolecule)
     """
-    error = {}
-    proteins = []
-    compounds = []
+    error: Dict[str, str] = {}
+    proteins: List[SiteObservation] = []
+    compounds: List[ComputedMolecule] = []
 
     if request.data['proteins']:
         # Get first part of protein code

viewer/target_set_upload.py

@@ -7,6 +7,7 @@
 """
 import logging
 import sys
+from typing import Any, Dict
 
 # import json
 import os
@@ -801,7 +802,7 @@ def validate_target(new_data_folder, target_name, proposal_ref):
     # Don't need
     del proposal_ref
 
-    validate_dict = {'Location': [], 'Error': [], 'Line number': []}
+    validate_dict: Dict[str, Any] = {'Location': [], 'Error': [], 'Line number': []}
 
     # Check if there is any data to process
     target_path = os.path.join(new_data_folder, target_name)

viewer/tests/test_loader.py

@@ -19,8 +19,8 @@
 from viewer.models import QuatAssembly
 
 
-test_mpro_v1 = Path(__file__).absolute().parent.joinpath("Mpro-v1-zero.tgz")
-test_mpro_v2 = Path(__file__).absolute().parent.joinpath("Mpro-v2-zero.tgz")
+test_mpro_v1 = str(Path(__file__).absolute().parent.joinpath("Mpro-v1-zero.tgz"))
+test_mpro_v2 = str(Path(__file__).absolute().parent.joinpath("Mpro-v2-zero.tgz"))
 
 
 class LoaderTests(TestCase):