enable ruff checks; resolve ruff errors

.github/workflows/main.yml

@@ -67,10 +67,10 @@ jobs:
           cd server
           poetry install --with dev
 
-      # - name: Run Ruff check
-      #   run: |
-      #     cd server
-      #     poetry run ruff check --output-format=github .
+      - name: Run Ruff check
+        run: |
+          cd server
+          poetry run ruff check --output-format=github .
 
       - name: Run Ruff format check
         run: |

.pre-commit-config.yaml

@@ -2,8 +2,8 @@ repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.16.5
     hooks:
-      # - id: ruff-check
-      #   args: [--fix]
-      #   files: ^server/
+      - id: ruff-check
+        args: [--fix]
+        files: ^server/
       - id: ruff-format
         files: ^server/

README.md

@@ -179,7 +179,7 @@ pre-commit run --all-files
     python3 manage.py migrate
     python3 manage.py collectstatic --noinput
     python3 manage.py createsuperuser  # Unless you will only login with your TACC account
-    python3 manage.py import-apps # Add set of example apps used in Frontera portal (optional)
+    python3 manage.py import_apps # Add set of example apps used in Frontera portal (optional)
 
 #### Initialize the CMS in the `core_portal_cms` container:
 

server/conftest.py

@@ -1,12 +1,14 @@
-import pytest
-from mock import MagicMock
 import json
 import os
 import tempfile
-from portal.apps.auth.models import TapisOAuthToken
-from portal.apps.accounts.models import PortalProfile
+from unittest.mock import MagicMock
+
+import pytest
 from django.conf import settings
 
+from portal.apps.accounts.models import PortalProfile
+from portal.apps.auth.models import TapisOAuthToken
+
 
 @pytest.fixture
 def mock_tapis_client(mocker):

server/portal/apps/_custom/drp/models.py

@@ -1,10 +1,11 @@
-from typing import Optional, Literal
-from pydantic import ConfigDict, NonNegativeInt, NonNegativeFloat
+from typing import Literal
+
+from pydantic import ConfigDict, NonNegativeFloat, NonNegativeInt
 
 from portal.apps.projects.schema_models.base_metadata import (
+    BaseFileMetadata,
     BaseMetadataModel,
     BaseProjectMetadata,
-    BaseFileMetadata,
     FileObj,
 )
 
@@ -20,8 +21,8 @@ class DrpFileMetadata(BaseFileMetadata):
         extra="forbid",
     )
 
-    is_advanced_image_file: Optional[bool] = False
-    image_type: Optional[
+    is_advanced_image_file: bool | None = False
+    image_type: (
         Literal[
             "8_bit",
             "16_bit_signed",
@@ -38,18 +39,19 @@ class DrpFileMetadata(BaseFileMetadata):
             "32_bit_abgr",
             "1_bit_bitmap",
         ]
-    ] = None
-    height: Optional[NonNegativeInt] = None
-    width: Optional[NonNegativeInt] = None
-    number_of_images: Optional[NonNegativeInt] = None
-    offset_to_first_image: Optional[int] = None
-    gap_between_images: Optional[int] = None
-    byte_order: Optional[Literal["big_endian", "little_endian"]] = None
-    use_binary_correction: Optional[bool] = None
+        | None
+    ) = None
+    height: NonNegativeInt | None = None
+    width: NonNegativeInt | None = None
+    number_of_images: NonNegativeInt | None = None
+    offset_to_first_image: int | None = None
+    gap_between_images: int | None = None
+    byte_order: Literal["big_endian", "little_endian"] | None = None
+    use_binary_correction: bool | None = None
 
 
 class DrpProjectMetadata(BaseProjectMetadata):
-    license: Optional[str] = "ODC-BY 1.0"
+    license: str | None = "ODC-BY 1.0"
 
 
 class DrpDatasetMetadata(BaseMetadataModel):
@@ -60,8 +62,8 @@ class DrpDatasetMetadata(BaseMetadataModel):
     )
 
     name: str
-    description: Optional[str] = None
-    uuid: Optional[str] = None
+    description: str | None = None
+    uuid: str | None = None
     data_type: Literal["sample", "origin_data", "digital_dataset", "analysis_data", "file"]
     file_objs: list[FileObj] = []
 
@@ -70,66 +72,79 @@ class DrpSampleMetadata(DrpDatasetMetadata):
     """Model for DRP Sample Metadata"""
 
     porous_media_type: Literal[
-        "sandstone", "soil", "carbonate", "granite", "beads", "fibrous_media", "coal", "energy_storage", "other"
+        "sandstone",
+        "soil",
+        "carbonate",
+        "granite",
+        "beads",
+        "fibrous_media",
+        "coal",
+        "energy_storage",
+        "other",
     ]
 
-    porous_media_other_description: Optional[str] = None
+    porous_media_other_description: str | None = None
 
     source: Literal[
         "natural",
         "natural_extraterrestrial",
         "artificial",
         "computer_generated",
     ]
-    collection_method: Optional[str] = None
-    onshore_offshore: Optional[Literal["onshore", "offshore"]] = None
-    depth: Optional[str] = None
-    total_vertical_depth: Optional[str] = None
-    water_depth: Optional[str] = None
-    geographic_origin: Optional[str] = None
-    procedure: Optional[str] = None
-    equipment: Optional[str] = None
-    algorithm_description: Optional[str] = None
-    grain_size_min: Optional[NonNegativeFloat] = None
-    grain_size_max: Optional[NonNegativeFloat] = None
-    grain_size_avg: Optional[NonNegativeFloat] = None
-    grain_size_units: Optional[Literal["nanometer", "micrometer", "millimeter", "other"]] = None
-    porosity: Optional[float] = None
-    geographical_location: Optional[str] = None
-    date_of_collection: Optional[str] = None
-    date_of_creation: Optional[str] = None
-    identifier: Optional[str] = None
-    location: Optional[str] = None  # TODO_DRP: Remove in new model
+    collection_method: str | None = None
+    onshore_offshore: Literal["onshore", "offshore"] | None = None
+    depth: str | None = None
+    total_vertical_depth: str | None = None
+    water_depth: str | None = None
+    geographic_origin: str | None = None
+    procedure: str | None = None
+    equipment: str | None = None
+    algorithm_description: str | None = None
+    grain_size_min: NonNegativeFloat | None = None
+    grain_size_max: NonNegativeFloat | None = None
+    grain_size_avg: NonNegativeFloat | None = None
+    grain_size_units: Literal["nanometer", "micrometer", "millimeter", "other"] | None = None
+    porosity: float | None = None
+    geographical_location: str | None = None
+    date_of_collection: str | None = None
+    date_of_creation: str | None = None
+    identifier: str | None = None
+    location: str | None = None  # TODO_DRP: Remove in new model
 
 
 class DrpOriginDatasetMetadata(DrpDatasetMetadata):
     """Model for DRP Origin Dataset Metadata"""
 
     is_segmented: Literal["yes", "no"]
     sample: str
-    imaging_center: Optional[str] = None
-    imaging_equipment_and_model: Optional[str] = None
-    image_format: Optional[str] = None
-    image_dimensions: Optional[str] = None
-    image_byte_order: Optional[str] = None
-    voxel_x: Optional[NonNegativeFloat] = None
-    voxel_y: Optional[NonNegativeFloat] = None
-    voxel_z: Optional[NonNegativeFloat] = None
-    voxel_units: Optional[Literal["nanometer", "micrometer", "millimeter", "other"]] = None
-    dimensionality: Optional[str] = None
-    digital_dataset: Optional[str] = None
-    external_uri: Optional[str] = None  # TODO_DRP: Remove in new model
+    imaging_center: str | None = None
+    imaging_equipment_and_model: str | None = None
+    image_format: str | None = None
+    image_dimensions: str | None = None
+    image_byte_order: str | None = None
+    voxel_x: NonNegativeFloat | None = None
+    voxel_y: NonNegativeFloat | None = None
+    voxel_z: NonNegativeFloat | None = None
+    voxel_units: Literal["nanometer", "micrometer", "millimeter", "other"] | None = None
+    dimensionality: str | None = None
+    digital_dataset: str | None = None
+    external_uri: str | None = None  # TODO_DRP: Remove in new model
 
 
 class DrpAnalysisDatasetMetadata(DrpDatasetMetadata):
     """Model for DRP Analysis Dataset Metadata"""
 
     is_segmented: Literal["yes", "no"]
     dataset_type: Literal[
-        "machine_learning", "simulation", "geometric_analysis", "experimental", "characterization", "other"
+        "machine_learning",
+        "simulation",
+        "geometric_analysis",
+        "experimental",
+        "characterization",
+        "other",
     ]
-    external_uri: Optional[str] = None
+    external_uri: str | None = None
     sample: str
     # base_origin_data: Optional[str] = None
-    digital_dataset: Optional[str] = None
-    digital_dataset_other_information: Optional[str] = None
+    digital_dataset: str | None = None
+    digital_dataset_other_information: str | None = None

server/portal/apps/_custom/drp/schema.py

@@ -1,13 +1,13 @@
 """DRP schema extension."""
 
-from portal.apps.projects.schema_models import constants
 from portal.apps._custom.drp.models import (
-    DrpProjectMetadata,
-    DrpSampleMetadata,
-    DrpOriginDatasetMetadata,
     DrpAnalysisDatasetMetadata,
     DrpFileMetadata,
+    DrpOriginDatasetMetadata,
+    DrpProjectMetadata,
+    DrpSampleMetadata,
 )
+from portal.apps.projects.schema_models import constants
 
 SCHEMA_MAPPING = {
     constants.PROJECT: DrpProjectMetadata,

server/portal/apps/_custom/drp/urls.py

@@ -4,6 +4,7 @@
 """
 
 from django.urls import re_path
+
 from portal.apps._custom.drp.views import DigitalRocksSampleView, GenerateImagesView
 
 app_name = "custom"

server/portal/apps/_custom/drp/views.py

@@ -1,15 +1,17 @@
 import json
-from portal.views.base import BaseApiView
+import logging
+
+import networkx as nx
 from django.conf import settings
 from django.http import HttpRequest, JsonResponse
-from portal.exceptions.api import ApiException
+
 from portal.apps.projects.models.project_metadata import ProjectMetadata
 from portal.apps.projects.schema_models import constants
-import networkx as nx
-from portal.apps.projects.workspace_operations.project_meta_operations import patch_file_obj_entity
 from portal.apps.projects.tasks import process_file
 from portal.apps.projects.views import get_project_client
-import logging
+from portal.apps.projects.workspace_operations.project_meta_operations import patch_file_obj_entity
+from portal.exceptions.api import ApiException
+from portal.views.base import BaseApiView
 
 logger = logging.getLogger(__name__)
 

server/portal/apps/accounts/api/urls.py

@@ -4,6 +4,7 @@
 """
 
 from django.urls import re_path
+
 from portal.apps.accounts.api.views.systems import SystemKeysView
 
 app_name = "portal_accounts_api"

server/portal/apps/accounts/api/views/systems.py

@@ -3,21 +3,23 @@
    :synopsis: Account's systems views
 """
 
-import logging
 import json
-from django.http import JsonResponse
+import logging
+
 from django.contrib.auth.decorators import login_required
+from django.http import JsonResponse
 from django.utils.decorators import method_decorator
-from portal.views.base import BaseApiView
-from portal.apps.accounts.managers import accounts as AccountsManager
 from tapipy.errors import BaseTapyException
+
+from portal.apps.accounts.managers import accounts as AccountsManager
+from portal.apps.datafiles.utils import evaluate_datafiles_storage_system
 from portal.apps.onboarding.steps.system_access_v3 import (
     create_system_credentials_with_keys,
-    create_system_credentials_with_tms,
     create_system_credentials_with_password,
+    create_system_credentials_with_tms,
 )
 from portal.utils.encryption import createKeyPair
-from portal.apps.datafiles.utils import evaluate_datafiles_storage_system
+from portal.views.base import BaseApiView
 
 logger = logging.getLogger(__name__)
 

server/portal/apps/accounts/integrations.py

@@ -1,7 +1,7 @@
-from importlib import import_module
-from django.conf import settings
 import logging
+from importlib import import_module
 
+from django.conf import settings
 
 logger = logging.getLogger(__name__)
 INTEGRATION_APPS = [s["integration"] for s in settings.PORTAL_DATAFILES_STORAGE_SYSTEMS if "integration" in s]
@@ -12,14 +12,10 @@ def get_integrations(request):
 
     for app in INTEGRATION_APPS:
         try:
-            mod = import_module("{}.integrations".format(app))
+            mod = import_module(f"{app}.integrations")
             app_integrations += mod.provide_integrations(request)
 
         except Exception as exc:
-            logger.warning(
-                "Call to module.provide_integrations fail for module: {app_name}. {exc}".format(
-                    app_name=app, exc=str(exc)
-                )
-            )
+            logger.warning(f"Call to module.provide_integrations fail for module: {app}. {str(exc)}")
 
     return app_integrations

server/portal/apps/accounts/managers/abstract.py

@@ -4,6 +4,7 @@
 """
 
 from abc import ABCMeta, abstractmethod
+
 from six import add_metaclass
 
 

server/portal/apps/accounts/managers/accounts.py

@@ -5,8 +5,10 @@
 
 import logging
 from importlib import import_module
+
 from django.conf import settings
 from paramiko.ssh_exception import AuthenticationException, ChannelException, SSHException
+
 from portal.apps.accounts.managers.ssh_keys import KeyCannotBeAdded
 
 logger = logging.getLogger(__name__)