Fix additional Ruff issues

bats_ai/core/admin/recording.py

@@ -1,14 +1,18 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 from django.contrib import admin, messages
-from django.db.models import QuerySet
-from django.http import HttpRequest
 from django.urls import reverse
 from django.utils.html import format_html
 
 from bats_ai.core.models import Recording
 from bats_ai.core.tasks.tasks import recording_compute_spectrogram
 
+if TYPE_CHECKING:
+    from django.db.models import QuerySet
+    from django.http import HttpRequest
+
 
 @admin.register(Recording)
 class RecordingAdmin(admin.ModelAdmin):

bats_ai/core/api.py

@@ -0,0 +1,42 @@
+from __future__ import annotations
+
+import logging
+
+from ninja import NinjaAPI
+from oauth2_provider.models import AccessToken
+
+from bats_ai.core import views
+from bats_ai.core.views import nabat
+
+logger = logging.getLogger(__name__)
+
+
+def global_auth(request):
+    if request.user.is_anonymous:
+        token = request.headers.get("Authorization", "").replace("Bearer ", "")
+        if len(token) > 0:
+            try:
+                access_token = AccessToken.objects.get(token=token)
+            except AccessToken.DoesNotExist:
+                access_token = None
+            if access_token and access_token.user and not access_token.user.is_anonymous:
+                request.user = access_token.user
+    user = request.user
+    return (not user.is_anonymous) and (user.profile.verified or user.is_superuser)
+
+
+api = NinjaAPI(auth=global_auth)
+
+api.add_router("/recording/", views.recording_router)
+api.add_router("/species/", views.species_router)
+api.add_router("/grts/", views.grts_cells_router)
+api.add_router("/guano/", views.guano_metadata_router)
+api.add_router("/recording-annotation/", views.recording_annotation_router)
+api.add_router("/export-annotation/", views.export_annotation_router)
+api.add_router("/configuration/", views.configuration_router)
+api.add_router("/processing-task/", views.processing_task_router)
+api.add_router("/recording-tag/", views.recording_tag_router)
+api.add_router("/vetting/", views.vetting_router)
+
+api.add_router("/nabat/recording/", nabat.nabat_recording_router)
+api.add_router("/nabat/configuration/", nabat.nabat_configuration_router)

bats_ai/core/management/commands/copy_recordings.py

@@ -205,7 +205,7 @@ def handle(self, *args, **options):
                     new_recording.save()
 
                     # Apply a random subset of tags to this recording
-                    k = random.randint(1, len(tag_texts))
+                    k = random.randint(1, len(tag_texts))  # noqa: S311
                     chosen = random.sample(tag_texts, k=k)
                     for text in chosen:
                         tag, _ = RecordingTag.objects.get_or_create(user=owner, text=text)

bats_ai/core/management/commands/loadGRTS.py

@@ -2,14 +2,14 @@
 
 import logging
 import os
+from pathlib import Path
 import tempfile
-import urllib
-from urllib.request import urlretrieve
 import zipfile
 
 from django.core.management.base import BaseCommand, CommandError
 from django.db import transaction
 import geopandas as gpd
+import requests
 from tqdm import tqdm  # progress bar
 
 from bats_ai.core.models import GRTSCells
@@ -56,6 +56,12 @@ def add_arguments(self, parser):
             "--batch-size", type=int, default=5000, help="Batch size for database insertion"
         )
 
+    def _download_file(self, url: str, zip_path: Path) -> None:
+        response = requests.get(url, timeout=120)
+        response.raise_for_status()
+        with zip_path.open("wb") as f:
+            f.write(response.content)
+
     def handle(self, *args, **options):
         batch_size = options["batch_size"]
 
@@ -65,19 +71,21 @@ def handle(self, *args, **options):
         for url, sample_frame_id, name, backup_url in SHAPEFILES:
             logger.info("Downloading shapefile for Location %s...", name)
             with tempfile.TemporaryDirectory() as tmpdir:
-                zip_path = os.path.join(tmpdir, "file.zip")
+                tmpdir = Path(tmpdir)
+
+                zip_path = tmpdir / "file.zip"
                 try:
-                    urlretrieve(url, zip_path)
-                except urllib.error.URLError as e:
+                    self._download_file(url, zip_path)
+                except requests.RequestException as e:
                     logger.warning(
                         "Failed to download from primary URL: %s. Attempting backup URL...", e
                     )
                     if backup_url is None:
                         logger.warning("No backup URL provided, skipping this shapefile.")
                         continue
                     try:
-                        urlretrieve(backup_url, zip_path)
-                    except urllib.error.URLError as e2:
+                        self._download_file(backup_url, zip_path)
+                    except requests.RequestException as e2:
                         raise CommandError(
                             f"Failed to download from backup URL as well: {e2}"
                         ) from e2

bats_ai/core/management/commands/load_public_dataset.py

@@ -106,6 +106,7 @@ def _try_start_spectrogram_generation(recording_id: int):
 
 
 def _ingest_files_from_manifest(
+    *,
     s3_client,
     bucket: str,
     manifest: Path,
@@ -268,12 +269,12 @@ def handle(self, *args, **options):
         if limit:
             self.stdout.write(f"Ingesting the first {limit} files from {manifest}...")
         _ingest_files_from_manifest(
-            s3_client,
-            bucket,
-            manifest,
-            owner,
-            public,
-            limit,
+            s3_client=s3_client,
+            bucket=bucket,
+            manifest=manifest,
+            owner=owner,
+            public=public,
+            limit=limit,
             file_key=file_key,
             tag_keys=tag_keys,
         )

bats_ai/core/models/grts_cells.py

@@ -26,7 +26,7 @@ class GRTSCells(models.Model):
     geom_4326 = models.GeometryField()
 
     @property
-    def sampleFrameMapping(self):
+    def sample_frame_mapping(self):
         return sample_frame_map[self.sample_frame_id]
 
     @staticmethod

bats_ai/core/tasks/export_task.py

@@ -18,7 +18,7 @@
 )
 
 
-def build_filters(filters, has_confidence=False):
+def build_filters(filters, *, has_confidence=False):
     conditions = {}
     if filters.get("start_date"):
         conditions["created__date__gte"] = filters["start_date"]
@@ -37,7 +37,7 @@ def build_filters(filters, has_confidence=False):
 
 
 def annotation_to_dict(
-    annotation, include_times=False, include_freqs=False, include_confidence=False
+    annotation, *, include_times=False, include_freqs=False, include_confidence=False
 ):
     data = {
         "id": annotation.id,
@@ -67,7 +67,13 @@ def annotation_to_dict(
 
 
 def write_csv_and_json(
-    zipf, name_prefix, queryset, include_times=False, include_freqs=False, include_confidence=False
+    zipf,
+    name_prefix,
+    queryset,
+    *,
+    include_times=False,
+    include_freqs=False,
+    include_confidence=False,
 ):
     rows = [
         annotation_to_dict(

bats_ai/core/tests/conftest.py

@@ -4,7 +4,7 @@
 from ninja.testing import TestClient
 import pytest
 
-from bats_ai.api import api
+from bats_ai.core.api import api
 
 
 @pytest.fixture

bats_ai/core/utils/contour_utils.py

@@ -279,6 +279,7 @@ def extract_contours(
 
 def process_spectrogram_assets_for_contours(
     assets: dict[str, Any],
+    *,
     levels_mode: str = "percentile",
     percentile_values: list[float] | None = None,
     min_area: float = 30.0,

bats_ai/core/utils/guano_utils.py

@@ -84,7 +84,7 @@ def extract_metadata_from_filename(filename: str) -> dict:
     return metadata
 
 
-def extract_guano_metadata(file_path: str | Path, check_filename: bool = False) -> dict:
+def extract_guano_metadata(file_path: str | Path, *, check_filename: bool = False) -> dict:
     """Extract GUANO metadata from a WAV file.
 
     Args:

bats_ai/core/views/__init__.py

@@ -1,29 +1,29 @@
 from __future__ import annotations
 
-from .annotations import router as AnnotationRouter
-from .configuration import router as ConfigurationRouter
-from .export_annotation import router as ExportAnnotationRouter
-from .grts_cells import router as GRTSCellsRouter
-from .guanometadata import router as GuanoMetadataRouter
-from .processing_tasks import router as ProcessingTaskRouter
-from .recording import router as RecordingRouter
-from .recording_annotation import router as RecordingAnnotationRouter
-from .recording_tag import router as RecordingTagRouter
-from .sequence_annotations import router as SequenceAnnotationRouter
-from .species import router as SpeciesRouter
-from .vetting_details import router as VettingRouter
+from .annotations import router as annotation_router
+from .configuration import router as configuration_router
+from .export_annotation import router as export_annotation_router
+from .grts_cells import router as grts_cells_router
+from .guanometadata import router as guano_metadata_router
+from .processing_tasks import router as processing_task_router
+from .recording import router as recording_router
+from .recording_annotation import router as recording_annotation_router
+from .recording_tag import router as recording_tag_router
+from .sequence_annotations import router as sequence_annotation_router
+from .species import router as species_router
+from .vetting_details import router as vetting_router
 
 __all__ = [
-    "AnnotationRouter",
-    "ConfigurationRouter",
-    "ExportAnnotationRouter",
-    "GRTSCellsRouter",
-    "GuanoMetadataRouter",
-    "ProcessingTaskRouter",
-    "RecordingAnnotationRouter",
-    "RecordingRouter",
-    "RecordingTagRouter",
-    "SequenceAnnotationRouter",
-    "SpeciesRouter",
-    "VettingRouter",
+    "annotation_router",
+    "configuration_router",
+    "export_annotation_router",
+    "grts_cells_router",
+    "guano_metadata_router",
+    "processing_task_router",
+    "recording_annotation_router",
+    "recording_router",
+    "recording_tag_router",
+    "sequence_annotation_router",
+    "species_router",
+    "vetting_router",
 ]

bats_ai/core/views/annotations.py

@@ -1,13 +1,16 @@
 from __future__ import annotations
 
 import logging
+from typing import TYPE_CHECKING
 
-from django.http import HttpRequest
 from ninja import Schema
 from ninja.pagination import RouterPaginated
 
 from bats_ai.core.models import Annotations, Recording
 
+if TYPE_CHECKING:
+    from django.http import HttpRequest
+
 logger = logging.getLogger(__name__)
 
 

bats_ai/core/views/export_annotation.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
-from datetime import datetime
 import logging
+from typing import TYPE_CHECKING
 
 from django.http import JsonResponse
 from django.shortcuts import get_object_or_404
@@ -10,6 +10,9 @@
 
 from bats_ai.core.models import ExportedAnnotationFile
 
+if TYPE_CHECKING:
+    from datetime import datetime
+
 logger = logging.getLogger(__name__)
 
 router = Router()

bats_ai/core/views/guanometadata.py

@@ -1,15 +1,19 @@
 from __future__ import annotations
 
-from datetime import datetime
 import logging
+from typing import TYPE_CHECKING
 
 from django.http import HttpRequest, JsonResponse
 from ninja import File, Schema
-from ninja.files import UploadedFile
 from ninja.pagination import RouterPaginated
 
 from bats_ai.core.utils.guano_utils import extract_guano_metadata
 
+if TYPE_CHECKING:
+    from datetime import datetime
+
+    from ninja.files import UploadedFile
+
 router = RouterPaginated()
 logger = logging.getLogger(__name__)