Merge pull request #156 from hubmapconsortium/jpuerto/r-investigation

Jpuerto/r investigation
hubmapconsortium · Feb 29, 2024 · faf6ab1 · faf6ab1
2 parents cd0f903 + 6f1eda5
commit faf6ab1
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Showing 31 changed files with 397 additions and 381 deletions.
diff --git a/.github/workflows/linters.yml b/.github/workflows/linters.yml
@@ -20,13 +20,13 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 black isort
+        pip install flake8==7.0.0 black==24.2.0 isort==5.13.2
     - name: Flake8 Lint
       run: |
         flake8 --ignore=E501,W503 src
     - name: Black Lint
       run: |
-        black --line-length 88 --check --diff src
+        black --line-length 99 --check --diff src
     - name: isort Lint
       run: |
         isort --profile black --check-only --diff src
diff --git a/src/example_config.json b/src/example_config.json
@@ -40,8 +40,11 @@
         "main_resource": {
           "python_version": "python3.8",
           "module_manager": "virtualenv",
-          "modules": ["jupyterlab"],
-          "time_limit": "60"
+          "modules": [
+            "jupyterlab"
+          ],
+          "time_limit": "60",
+          "environment_name": "JupyterLabJob"
         }
       }
     },

diff --git a/src/example_django_config.json b/src/example_django_config.json
@@ -28,7 +28,9 @@
     "default": {
       "BACKEND": "channels_redis.core.RedisChannelLayer",
       "CONFIG": {
-        "hosts": ["redis://127.0.0.1:6379/0?"]
+        "hosts": [
+          "redis://127.0.0.1:6379/0?"
+        ]
       }
     }
   },
@@ -41,47 +43,52 @@
   "LOGGING": {
     "version": 1,
     "formatters": {
-        "django-q": {
-            "format": "{asctime} [Q] {levelname} {message}",
-            "style": "{"
-        },
-        "user_workspaces_server": {
-            "format": "{asctime} [UWS] {levelname} {message}",
-            "style": "{"
-        }
+      "django-q": {
+        "format": "{asctime} [Q] {levelname} {message}",
+        "style": "{"
+      },
+      "user_workspaces_server": {
+        "format": "{asctime} [UWS] {levelname} {message}",
+        "style": "{"
+      }
     },
     "handlers": {
-        "discard": {
-            "class": "logging.NullHandler"
-        },
-        "django-q-console": {
-            "class": "logging.StreamHandler",
-            "formatter": "django-q"
-        },
-        "user_workspaces_server_console": {
-            "class": "logging.StreamHandler",
-            "formatter": "user_workspaces_server"
-        },
-        "mail": {
-            "class": "user_workspaces_server.logging.AsyncEmailHandler",
-            "formatter": "user_workspaces_server",
-            "level": "ERROR",
-            "subject": "UWS Log",
-            "from_email": "[email protected]",
-            "email_list": []
-        }
+      "discard": {
+        "class": "logging.NullHandler"
+      },
+      "django-q-console": {
+        "class": "logging.StreamHandler",
+        "formatter": "django-q"
+      },
+      "user_workspaces_server_console": {
+        "class": "logging.StreamHandler",
+        "formatter": "user_workspaces_server"
+      },
+      "mail": {
+        "class": "user_workspaces_server.logging.AsyncEmailHandler",
+        "formatter": "user_workspaces_server",
+        "level": "ERROR",
+        "subject": "UWS Log",
+        "from_email": "[email protected]",
+        "email_list": []
+      }
     },
     "loggers": {
-        "django-q": {
-            "level": "INFO",
-            "propagate": true,
-            "handlers": ["django-q-console"]
-        },
-        "user_workspaces_server": {
-            "level": "DEBUG",
-            "propagate": false,
-            "handlers": ["user_workspaces_server_console", "mail"]
-        }
+      "django-q": {
+        "level": "INFO",
+        "propagate": true,
+        "handlers": [
+          "django-q-console"
+        ]
+      },
+      "user_workspaces_server": {
+        "level": "DEBUG",
+        "propagate": false,
+        "handlers": [
+          "user_workspaces_server_console",
+          "mail"
+        ]
+      }
     }
   }
 }
diff --git a/src/manage.py b/src/manage.py
@@ -6,9 +6,7 @@
 
 def main():
     """Run administrative tasks."""
-    os.environ.setdefault(
-        "DJANGO_SETTINGS_MODULE", "user_workspaces_server_project.settings"
-    )
+    os.environ.setdefault("DJANGO_SETTINGS_MODULE", "user_workspaces_server_project.settings")
     argv = sys.argv
     cmd = argv[1] if len(argv) > 1 else ""
     os.environ["SUBCOMMAND"] = cmd

diff --git a/src/tests/controllers/userauthenticationmethods/test_user_authentication.py b/src/tests/controllers/userauthenticationmethods/test_user_authentication.py
@@ -38,14 +38,10 @@ def api_authenticate(self, request):
             raise ParseError(repr(e))
 
         if "client_token" not in body:
-            raise ParseError(
-                "Missing client_token. Please have admin generate a token for you."
-            )
+            raise ParseError("Missing client_token. Please have admin generate a token for you.")
 
         if "user_info" not in body:
-            raise ParseError(
-                "Missing user_info. Please provide user_info to get user_token."
-            )
+            raise ParseError("Missing user_info. Please provide user_info to get user_token.")
 
         try:
             client_token = body["client_token"]

diff --git a/src/tests/github_test_django_config.json b/src/tests/github_test_django_config.json
@@ -24,7 +24,9 @@
     "default": {
       "BACKEND": "channels_redis.core.RedisChannelLayer",
       "CONFIG": {
-        "hosts": ["redis://127.0.0.1:6379/0?"]
+        "hosts": [
+          "redis://127.0.0.1:6379/0?"
+        ]
       }
     }
   },
@@ -37,47 +39,52 @@
   "LOGGING": {
     "version": 1,
     "formatters": {
-        "django-q": {
-            "format": "{asctime} [Q] {levelname} {message}",
-            "style": "{"
-        },
-        "user_workspaces_server": {
-            "format": "{asctime} [UWS] {levelname} {message}",
-            "style": "{"
-        }
+      "django-q": {
+        "format": "{asctime} [Q] {levelname} {message}",
+        "style": "{"
+      },
+      "user_workspaces_server": {
+        "format": "{asctime} [UWS] {levelname} {message}",
+        "style": "{"
+      }
     },
     "handlers": {
-        "discard": {
-            "class": "logging.NullHandler"
-        },
-        "django-q-console": {
-            "class": "logging.StreamHandler",
-            "formatter": "django-q"
-        },
-        "user_workspaces_server_console": {
-            "class": "logging.StreamHandler",
-            "formatter": "user_workspaces_server"
-        },
-        "mail": {
-            "class": "user_workspaces_server.logging.AsyncEmailHandler",
-            "formatter": "user_workspaces_server",
-            "level": "ERROR",
-            "subject": "UWS Log",
-            "from_email": "[email protected]",
-            "email_list": []
-        }
+      "discard": {
+        "class": "logging.NullHandler"
+      },
+      "django-q-console": {
+        "class": "logging.StreamHandler",
+        "formatter": "django-q"
+      },
+      "user_workspaces_server_console": {
+        "class": "logging.StreamHandler",
+        "formatter": "user_workspaces_server"
+      },
+      "mail": {
+        "class": "user_workspaces_server.logging.AsyncEmailHandler",
+        "formatter": "user_workspaces_server",
+        "level": "ERROR",
+        "subject": "UWS Log",
+        "from_email": "[email protected]",
+        "email_list": []
+      }
     },
     "loggers": {
-        "django-q": {
-            "level": "INFO",
-            "propagate": true,
-            "handlers": ["django-q-console"]
-        },
-        "user_workspaces_server": {
-            "level": "DEBUG",
-            "propagate": false,
-            "handlers": ["user_workspaces_server_console", "mail"]
-        }
+      "django-q": {
+        "level": "INFO",
+        "propagate": true,
+        "handlers": [
+          "django-q-console"
+        ]
+      },
+      "user_workspaces_server": {
+        "level": "DEBUG",
+        "propagate": false,
+        "handlers": [
+          "user_workspaces_server_console",
+          "mail"
+        ]
+      }
     }
   }
 }
diff --git a/src/tests/settings.py b/src/tests/settings.py
@@ -21,11 +21,7 @@
 UWS_CONFIG = json.load(
     open(
         BASE_DIR
-        / (
-            "github_test_config.json"
-            if os.environ.get("GITHUB_WORKFLOW")
-            else "test_config.json"
-        )
+        / ("github_test_config.json" if os.environ.get("GITHUB_WORKFLOW") else "test_config.json")
     )
 )
 
@@ -41,9 +37,7 @@
 )
 
 SECRET_KEY = (
-    get_random_string(12)
-    if not DJANGO_CONFIG["SECRET_KEY"]
-    else DJANGO_CONFIG["SECRET_KEY"]
+    get_random_string(12) if not DJANGO_CONFIG["SECRET_KEY"] else DJANGO_CONFIG["SECRET_KEY"]
 )
 
 DEBUG = DJANGO_CONFIG["DEBUG"]
@@ -93,13 +87,11 @@
 
 WSGI_APPLICATION = "user_workspaces_server_project.wsgi.application"
 
-
 # Database
 # https://docs.djangoproject.com/en/3.2/ref/settings/#databases
 
 DATABASES = DJANGO_CONFIG["DATABASES"]
 
-
 # Password validation
 # https://docs.djangoproject.com/en/3.2/ref/settings/#auth-password-validators
 
@@ -118,7 +110,6 @@
     },
 ]
 
-
 # Internationalization
 # https://docs.djangoproject.com/en/3.2/topics/i18n/
 
@@ -132,7 +123,6 @@
 
 USE_TZ = True
 
-
 # Static files (CSS, JavaScript, Images)
 # https://docs.djangoproject.com/en/3.2/howto/static-files/
 

diff --git a/src/tests/unittests/test_models.py b/src/tests/unittests/test_models.py
@@ -5,11 +5,11 @@
 
 class WorkspaceModelTests(TestCase):
     def test_get_workspace_query_param_fields(self):
-        """Animals that can speak are correctly identified"""
+        """Check Workspace query parameters"""
         assert Workspace.get_query_param_fields() == ["name", "description", "status"]
 
     def test_get_workspace_dict_fields(self):
-        """Animals that can speak are correctly identified"""
+        """Check Workspace dictionary fields"""
         assert Workspace.get_dict_fields() == [
             "id",
             "name",
@@ -18,12 +18,13 @@ def test_get_workspace_dict_fields(self):
             "datetime_created",
             "workspace_details",
             "status",
+            "default_job_type",
         ]
 
 
 class JobModelTests(TestCase):
     def test_get_workspace_query_param_fields(self):
-        """Animals that can speak are correctly identified"""
+        """Check Job query parameters"""
         assert Job.get_query_param_fields() == [
             "workspace_id",
             "resource_job_id",
@@ -32,7 +33,7 @@ def test_get_workspace_query_param_fields(self):
         ]
 
     def test_get_workspace_dict_fields(self):
-        """Animals that can speak are correctly identified"""
+        """Check Job dictionary fields"""
         assert Job.get_dict_fields() == [
             "id",
             "workspace_id",