Merge pull request #537 from UW-GAC/main

Deploy to stage

.github/workflows/ci.yml

@@ -19,27 +19,6 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  linter:
-    runs-on: ubuntu-latest
-    steps:
-
-      - name: Checkout Code Repository
-        uses: actions/checkout@v4
-
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.9
-          cache: pip
-          cache-dependency-path: |
-            requirements/requirements.txt
-            requirements/test-requirements.txt
-
-      # Run all pre-commit hooks on all the files.
-      # Getting only staged files can be tricky in case a new PR is opened
-      # since the action is run on a branch in detached head state
-      - name: Install and Run Pre-commit
-        uses: pre-commit/[email protected]
 
   pytest-mariadb:
     runs-on: ubuntu-latest
@@ -50,7 +29,7 @@ jobs:
         # ahead of planned upgrades we can add versions as
         # needed
         python-version: [3.8]
-        mariadb-version: ["10.4"]
+        mariadb-version: ["10.4", "10.5"]
 
     services:
       mysql:

.pre-commit-config.yaml

@@ -10,22 +10,15 @@ repos:
       - id: end-of-file-fixer
       - id: check-yaml
 
-  - repo: https://github.com/psf/black
-    rev: 22.3.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.4.2
     hooks:
-      - id: black
-
-  - repo: https://github.com/timothycrosley/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-
-  - repo: https://github.com/PyCQA/flake8
-    rev: 3.9.2
-    hooks:
-      - id: flake8
-        args: ['--config=setup.cfg']
-        additional_dependencies: [flake8-isort]
+      # Run the linter.
+      - id: ruff
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
 
   - repo: https://github.com/gitleaks/gitleaks
     rev: v8.16.1

.ruff.toml

@@ -0,0 +1,20 @@
+line-length = 120
+exclude = [
+    "**/migrations/**",
+    "*/static/CACHE/*",
+    "venv",
+    "docs",
+]
+
+[lint]
+extend-select = [
+    "E",
+    "F",
+    "W", # pycodestyle warnings
+    "I", # isort
+    "DJ", # flake8-django
+    "E501", # line-too-long
+]
+
+[lint.isort]
+known-first-party = ["gregor_django", "config", ]

README.md

@@ -4,6 +4,8 @@ GREGoR Dynamic Web Apps Oauth Client Site
 
 [![Black code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/UW-GAC/gregor-django/main.svg)](https://results.pre-commit.ci/latest/github/UW-GAC/gregor-django/main)
+
 [![image](https://img.shields.io/badge/License-MIT-blue.svg)](https://lbesson.mit-license.org/)
 
 [![Built with Cookiecutter Django](https://img.shields.io/badge/built%20with-Cookiecutter%20Django-ff69b4.svg?logo=cookiecutter)](https://github.com/pydanny/cookiecutter-django/)

config/settings/base.py

@@ -1,6 +1,7 @@
 """
 Base settings to build other settings files upon.
 """
+
 from pathlib import Path
 
 import environ
@@ -129,9 +130,7 @@
 ]
 # https://docs.djangoproject.com/en/dev/ref/settings/#auth-password-validators
 AUTH_PASSWORD_VALIDATORS = [
-    {
-        "NAME": "django.contrib.auth.password_validation.UserAttributeSimilarityValidator"
-    },
+    {"NAME": "django.contrib.auth.password_validation.UserAttributeSimilarityValidator"},
     {"NAME": "django.contrib.auth.password_validation.MinimumLengthValidator"},
     {"NAME": "django.contrib.auth.password_validation.CommonPasswordValidator"},
     {"NAME": "django.contrib.auth.password_validation.NumericPasswordValidator"},
@@ -257,12 +256,7 @@
 LOGGING = {
     "version": 1,
     "disable_existing_loggers": False,
-    "formatters": {
-        "verbose": {
-            "format": "%(levelname)s %(asctime)s %(module)s "
-            "%(process)d %(thread)d %(message)s"
-        }
-    },
+    "formatters": {"verbose": {"format": "%(levelname)s %(asctime)s %(module)s " "%(process)d %(thread)d %(message)s"}},
     "handlers": {
         "console": {
             "level": "DEBUG",
@@ -380,7 +374,7 @@
 # Specify the path to the service account to use for managing access on AnVIL.
 ANVIL_API_SERVICE_ACCOUNT_FILE = env("ANVIL_API_SERVICE_ACCOUNT_FILE")
 ANVIL_WORKSPACE_ADAPTERS = [
-    "gregor_django.gregor_anvil.adapters.ExampleWorkspaceAdapter",
+    "gregor_django.gregor_anvil.adapters.ResourceWorkspaceAdapter",
     "gregor_django.gregor_anvil.adapters.TemplateWorkspaceAdapter",
     "gregor_django.gregor_anvil.adapters.UploadWorkspaceAdapter",
     "gregor_django.gregor_anvil.adapters.PartnerUploadWorkspaceAdapter",

config/settings/local.py

@@ -26,9 +26,7 @@
 # EMAIL
 # ------------------------------------------------------------------------------
 # https://docs.djangoproject.com/en/dev/ref/settings/#email-backend
-EMAIL_BACKEND = env(
-    "DJANGO_EMAIL_BACKEND", default="django.core.mail.backends.console.EmailBackend"
-)
+EMAIL_BACKEND = env("DJANGO_EMAIL_BACKEND", default="django.core.mail.backends.console.EmailBackend")
 
 # WhiteNoise
 # ------------------------------------------------------------------------------

config/settings/production.py

@@ -57,15 +57,11 @@
 # in our apache configuration. Having in both places causes duplicate header
 SECURE_HSTS_SECONDS = 0
 # https://docs.djangoproject.com/en/dev/ref/settings/#secure-hsts-include-subdomains
-SECURE_HSTS_INCLUDE_SUBDOMAINS = env.bool(
-    "DJANGO_SECURE_HSTS_INCLUDE_SUBDOMAINS", default=True
-)
+SECURE_HSTS_INCLUDE_SUBDOMAINS = env.bool("DJANGO_SECURE_HSTS_INCLUDE_SUBDOMAINS", default=True)
 # https://docs.djangoproject.com/en/dev/ref/settings/#secure-hsts-preload
 SECURE_HSTS_PRELOAD = env.bool("DJANGO_SECURE_HSTS_PRELOAD", default=True)
 # https://docs.djangoproject.com/en/dev/ref/middleware/#x-content-type-options-nosniff
-SECURE_CONTENT_TYPE_NOSNIFF = env.bool(
-    "DJANGO_SECURE_CONTENT_TYPE_NOSNIFF", default=True
-)
+SECURE_CONTENT_TYPE_NOSNIFF = env.bool("DJANGO_SECURE_CONTENT_TYPE_NOSNIFF", default=True)
 # Since we have disabled HSTS above we get a warning when running check --deploy
 # we are manually silencing this as we have verified apache is enforcing
 # https://docs.djangoproject.com/en/dev/ref/checks/#security
@@ -79,9 +75,7 @@
 # EMAIL
 # ------------------------------------------------------------------------------
 # https://docs.djangoproject.com/en/dev/ref/settings/#default-from-email
-DEFAULT_FROM_EMAIL = env(
-    "DJANGO_DEFAULT_FROM_EMAIL", default="gac-django <[email protected]>"
-)
+DEFAULT_FROM_EMAIL = env("DJANGO_DEFAULT_FROM_EMAIL", default="gac-django <[email protected]>")
 # https://docs.djangoproject.com/en/dev/ref/settings/#server-email
 SERVER_EMAIL = env("DJANGO_SERVER_EMAIL", default=DEFAULT_FROM_EMAIL)
 # https://docs.djangoproject.com/en/dev/ref/settings/#email-subject-prefix
@@ -130,12 +124,7 @@
             "()": "maintenance_mode.logging.RequireNotMaintenanceMode503",
         },
     },
-    "formatters": {
-        "verbose": {
-            "format": "%(levelname)s %(asctime)s %(module)s "
-            "%(process)d %(thread)d %(message)s"
-        }
-    },
+    "formatters": {"verbose": {"format": "%(levelname)s %(asctime)s %(module)s " "%(process)d %(thread)d %(message)s"}},
     "handlers": {
         "mail_admins": {
             "level": "ERROR",

config/urls.py

@@ -7,9 +7,7 @@
 
 urlpatterns = [
     path("", TemplateView.as_view(template_name="pages/home.html"), name="home"),
-    path(
-        "about/", TemplateView.as_view(template_name="pages/about.html"), name="about"
-    ),
+    path("about/", TemplateView.as_view(template_name="pages/about.html"), name="about"),
     # Django Admin, use {% url 'admin:index' %}
     path(settings.ADMIN_URL, admin.site.urls),
     # User management

config/wsgi.py

@@ -13,6 +13,7 @@
 framework.
 
 """
+
 import os
 import sys
 from pathlib import Path

gregor_django/__init__.py

@@ -1,7 +1,2 @@
 __version__ = "0.1.0"
-__version_info__ = tuple(
-    [
-        int(num) if num.isdigit() else num
-        for num in __version__.replace("-", ".", 1).split(".")
-    ]
-)
+__version_info__ = tuple([int(num) if num.isdigit() else num for num in __version__.replace("-", ".", 1).split(".")])

gregor_django/drupal_oauth_provider/provider.py

@@ -24,7 +24,6 @@ class CustomAccount(ProviderAccount):
 
 
 class CustomProvider(OAuth2Provider):
-
     id = DRUPAL_PROVIDER_ID
     name = OVERRIDE_NAME
     account_class = CustomAccount

gregor_django/drupal_oauth_provider/tests.py

@@ -167,6 +167,4 @@ def test_custom_provider_has_scope(self):
             }
         ]
         with override_settings(SOCIALACCOUNT_PROVIDERS=custom_provider_settings):
-            CustomProvider(request).get_provider_managed_scope_status(
-                scopes_granted=["X"]
-            )
+            CustomProvider(request).get_provider_managed_scope_status(scopes_granted=["X"])

gregor_django/drupal_oauth_provider/views.py

@@ -50,12 +50,9 @@ def _get_public_key_jwk(self, headers):
             return keys[0]
 
     def get_public_key(self, headers):
-
         public_key_jwk = self._get_public_key_jwk(headers)
         try:
-            public_key = jwt.algorithms.RSAAlgorithm.from_jwk(
-                json.dumps(public_key_jwk)
-            )
+            public_key = jwt.algorithms.RSAAlgorithm.from_jwk(json.dumps(public_key_jwk))
         except Exception as e:
             logger.error(f"[get_public_key] failed to convert jwk to public key {e}")
         else:
@@ -83,9 +80,7 @@ def get_scopes_from_token(self, id_token, headers):
             logger.error(f"Invalid id_token {e} {id_token.token}")
             raise OAuth2Error("Invalid id_token") from e
         except Exception as e:
-            logger.error(
-                f"Other exception parsing token {e} header {unverified_header} token {id_token}"
-            )
+            logger.error(f"Other exception parsing token {e} header {unverified_header} token {id_token}")
             raise OAuth2Error("Error when decoding token {e}")
         else:
             scopes = token_payload.get("scope")
@@ -96,9 +91,7 @@ def complete_login(self, request, app, token, **kwargs):
         headers = {"Authorization": "Bearer {0}".format(token.token)}
 
         scopes_granted = self.get_scopes_from_token(token, headers)
-        managed_scope_status = self.get_provider().get_provider_managed_scope_status(
-            scopes_granted
-        )
+        managed_scope_status = self.get_provider().get_provider_managed_scope_status(scopes_granted)
 
         resp = requests.get(self.profile_url, headers=headers)
         resp.raise_for_status()
@@ -110,9 +103,7 @@ def complete_login(self, request, app, token, **kwargs):
         )
         extra_data["scopes_granted"] = scopes_granted
         extra_data["managed_scope_status"] = managed_scope_status
-        social_login = self.get_provider().sociallogin_from_response(
-            request, extra_data
-        )
+        social_login = self.get_provider().sociallogin_from_response(request, extra_data)
 
         return social_login