Fix more mypy.

src/genlab_bestilling/admin.py

@@ -279,7 +279,7 @@ class EquipmentOrderAdmin(ModelAdmin):
     search_help_text = "Search for equipment name or id"
     search_fields = [
         EO.name.field.name,
-        EO.id.field.name,
+        EO.id.field.name,  # type: ignore[attr-defined]
     ]
     list_filter = [
         (EO.sample_types.field.name, unfold_filters.AutocompleteSelectMultipleFilter),
@@ -320,7 +320,7 @@ class ExtractionOrderAdmin(ModelAdmin):
     search_help_text = "Search for extraction name or id"
     search_fields = [
         EO.name.field.name,
-        EO.id.field.name,
+        EO.id.field.name,  # type: ignore[attr-defined]
     ]
     list_filter = [
         (EO.species.field.name, unfold_filters.AutocompleteSelectMultipleFilter),

src/genlab_bestilling/api/serializers.py

@@ -73,7 +73,7 @@ def get_has_error(self, obj: Sample) -> bool:
         try:
             return obj.has_error
         except exceptions.ValidationError as e:
-            return e.detail[0]
+            return e.detail[0]  # type: ignore[return-value,index]  # TODO: check if this is actually bool.
 
     class Meta:
         model = Sample
@@ -186,7 +186,7 @@ def get_has_error(self, obj: Sample) -> bool:
         try:
             return obj.has_error
         except exceptions.ValidationError as e:
-            return e.detail[0]
+            return e.detail[0]  # type: ignore[return-value,index] # TODO: check if this is actually bool.
 
     class Meta:
         model = Sample

src/genlab_bestilling/api/views.py

@@ -1,6 +1,7 @@
 import contextlib
 import re
 import uuid
+from typing import Any
 
 from django.db import transaction
 from django.db.models import QuerySet
@@ -104,7 +105,7 @@ def get_csv_fields_and_labels(
         labels = [self.FIELD_LABELS.get(f, f) for f in fields]
         return fields, labels
 
-    def get_nested(self, obj: dict, dotted: str) -> str | None:
+    def get_nested(self, obj: Any, dotted: str) -> Any:
         for part in dotted.split("."):
             obj = obj.get(part) if isinstance(obj, dict) else None
         return obj

src/genlab_bestilling/forms.py

@@ -35,7 +35,7 @@ def __init__(self, *args, user: User | None = None, project: Any = None, **kwarg
         self.user = user
 
         if "project" in self.fields:
-            self.fields[
+            self.fields[  # type: ignore[attr-defined]
                 "project"
             ].queryset = Project.objects.filter_selectable().filter(
                 memberships=user,
@@ -121,7 +121,7 @@ def __init__(self, *args, genrequest: Genrequest, **kwargs):
         self.genrequest = genrequest
 
         # self.fields["species"].queryset = genrequest.species.all()
-        self.fields["sample_types"].queryset = genrequest.sample_types.all()
+        self.fields["sample_types"].queryset = genrequest.sample_types.all()  # type: ignore[attr-defined]
 
     def save(self, commit: bool = True) -> EquipmentOrder:
         obj = super().save(commit=False)
@@ -167,9 +167,9 @@ def save(self, commit: bool = True) -> EquipmentOrder:
         return obj
 
     def clean(self) -> None:
-        cleaned_data = super().clean()
+        cleaned_data = super().clean() or {}
 
-        if not cleaned_data["equipment"] and not cleaned_data["buffer"]:
+        if not cleaned_data.get("equipment") and not cleaned_data.get("buffer"):
             msg = "Equipment and/or Buffer should be filled"
             raise ValidationError(msg)
 
@@ -249,8 +249,8 @@ def __init__(self, *args, genrequest: Genrequest, **kwargs):
             "for this order to help you find it later"
         )
 
-        self.fields["species"].queryset = genrequest.species.all()
-        self.fields["sample_types"].queryset = genrequest.sample_types.all()
+        self.fields["species"].queryset = genrequest.species.all()  # type: ignore[attr-defined]
+        self.fields["sample_types"].queryset = genrequest.sample_types.all()  # type: ignore[attr-defined]
         # self.fields["markers"].queryset = Marker.objects.filter(
         #     species__genrequests__id=genrequest.id
         # ).distinct()
@@ -307,12 +307,12 @@ def __init__(self, *args, genrequest: Genrequest, **kwargs):
             "for this order to help you find it later"
         )
 
-        self.fields["markers"].queryset = Marker.objects.filter(
+        self.fields["markers"].queryset = Marker.objects.filter(  # type: ignore[attr-defined]
             genrequest__id=genrequest.id
         ).distinct()
         self.fields["markers"].required = True
         if "from_order" in self.fields:
-            self.fields["from_order"].queryset = ExtractionOrder.objects.filter(
+            self.fields["from_order"].queryset = ExtractionOrder.objects.filter(  # type: ignore[attr-defined]
                 genrequest_id=genrequest.id,
             ).exclude(status=Order.OrderStatus.DRAFT)
             self.fields["from_order"].help_text = (

src/genlab_bestilling/libs/isolation.py

@@ -27,6 +27,8 @@ def isolate(order_id: int | str) -> None:
                     position = 0
 
                 ExtractPlatePosition.objects.create(
-                    plate=plate, sample=sample, position=position
+                    plate=plate,
+                    sample=sample,
+                    position=position,  # type: ignore[misc]
                 )
                 position += 1

src/genlab_bestilling/managers.py

@@ -8,6 +8,8 @@
 from shared.db import assert_is_in_atomic_block
 
 if TYPE_CHECKING:
+    from collections.abc import Sequence
+
     from django.db.models import QuerySet
 
     from capps.users.models import User
@@ -75,7 +77,7 @@ def filter_in_draft(self) -> QuerySet:
     def generate_genlab_ids(
         self,
         order_id: int,
-        selected_samples: list[int] | None = None,
+        selected_samples: Sequence[int | str] | None = None,
     ) -> None:
         """
         genlab ids given a certain order_id, sorting order and sample ids

src/genlab_bestilling/models.py

@@ -1,4 +1,5 @@
 import uuid
+from collections.abc import Sequence
 from datetime import timedelta
 from typing import Any
 
@@ -508,7 +509,7 @@ def confirm_order(self, persist: bool = True) -> None:
     @transaction.atomic
     def order_selected_checked(
         self,
-        selected_samples: list[int] | None = None,
+        selected_samples: Sequence[int | str] | None = None,
     ) -> None:
         """
         Partially set the order as checked by the lab staff,
@@ -522,7 +523,7 @@ def order_selected_checked(
             return
 
         Sample.objects.generate_genlab_ids(
-            order_id=self.id,
+            order_id=self.id,  # type: ignore[arg-type] # `self` has been saved first, so id is known to exists.
             selected_samples=selected_samples,
         )
 
@@ -741,7 +742,7 @@ def has_error(self) -> bool:
             ):
                 msg = "Invalid location for the selected species"
                 raise ValidationError(msg)
-        elif self.location_id and self.species.location_type_id:
+        elif self.species.location_type_id and self.location:
             # if the location is optional, but it's provided,
             # check it is compatible with the species
             if self.species.location_type_id not in self.location.types.values_list(
@@ -752,12 +753,21 @@ def has_error(self) -> bool:
 
         return False
 
+    class MissingOrder(Exception):
+        """
+        Exception raised when trying to generate a genlab_id without an ExtractionOrder.
+        """
+
     def generate_genlab_id(self, commit: bool = True) -> str:
         assert_is_in_atomic_block()
 
         if self.genlab_id:
             return self.genlab_id
         species = self.species
+
+        if not self.order:
+            raise self.MissingOrder
+
         year = self.order.confirmed_at.year
 
         sequence = GIDSequence.objects.get_sequence_for_species_year(

src/nina/views.py

@@ -93,7 +93,7 @@ def get_form_kwargs(self) -> dict[str, Any]:
     def get_success_url(self) -> str:
         return reverse(
             "nina:project-detail",
-            kwargs={"pk": self.object.pk},
+            kwargs={"pk": self.object.pk},  # type: ignore[union-attr]
         )
 
 

src/shared/forms.py

@@ -30,7 +30,7 @@ def __init__(
         bound_field_class=None,
         **kwargs,
     ) -> None:
-        super().__init__(
+        super().__init__(  # type: ignore[call-arg]
             data=data,
             files=files,
             auto_id=auto_id,

src/shared/sentry.py

@@ -7,7 +7,7 @@
 def report_errors(err: Exception, app_name: str = __name__) -> None:
     logger = logging.getLogger(app_name)
 
-    if settings.SENTRY_DSN:
+    if settings.SENTRY_DSN:  # type: ignore[misc]
         from sentry_sdk import capture_exception  # noqa: PLC0415
 
         capture_exception(err)

src/staff/forms.py

@@ -25,7 +25,7 @@ class OrderStaffForm(forms.Form):
     def __init__(self, *args, order: Order | Genrequest | None = None, **kwargs):
         super().__init__(*args, **kwargs)
 
-        self.fields["responsible_staff"].choices = self.get_all_staff()
+        self.fields["responsible_staff"].choices = self.get_all_staff()  # type: ignore[attr-defined]
 
         if order:
             self.fields["responsible_staff"].initial = [

src/staff/tables.py

@@ -215,9 +215,9 @@ class Meta(OrderTable.Meta):
             "needs_guid",
             "sample_types",
         ]
-        sequence = ("is_seen", "is_urgent", "status", "id", "name")
+        sequence = ["is_seen", "is_urgent", "status", "id", "name"]
         empty_text = "No Orders"
-        order_by = ("-is_urgent", "last_modified_at", "created_at")
+        order_by = ["-is_urgent", "last_modified_at", "created_at"]
 
     def render_id(self, record: Any) -> str:
         return str(record)

src/staff/views.py

@@ -66,7 +66,7 @@ def get_template_names(self) -> list[str]:
         ]
 
     def test_func(self) -> bool:
-        return self.request.user.is_superuser or self.request.user.is_genlab_staff()
+        return self.request.user.is_superuser or self.request.user.is_genlab_staff()  # type: ignore[attr-defined]
 
 
 class DashboardView(StaffMixin, TemplateView):
@@ -261,35 +261,41 @@ def get_return_url(self, return_to: str | None) -> str:
 class ExtractionOrderDetailView(StaffMixin, DetailView):
     model = ExtractionOrder
 
-    # Retrieves analysis orders associated with the samples in the extraction order
     def get_analysis_orders_for_samples(
         self, samples: QuerySet[Sample]
     ) -> QuerySet[AnalysisOrder]:
+        """
+        Retrieves analysis orders associated with the samples in the extraction order.
+        """
         return AnalysisOrder.objects.filter(samples__in=samples).distinct()
 
-    # Checks if the analysis orders have multiple extraction orders
-    # This is used to determine which type of link to show in the template
     def analysis_has_multiple_extraction_orders(
-        self, analysis_orders: QuerySet[AnalysisOrder]
+        self, *, analysis_orders: QuerySet[AnalysisOrder]
     ) -> bool:
-        if len(analysis_orders) == 1:
-            analysis_order = get_object_or_404(
-                AnalysisOrder, pk=analysis_orders.first().id
-            )
-            extraction_order_ids = analysis_order.samples.values_list(
-                "order_id", flat=True
-            ).distinct()
-            return extraction_order_ids.count() > 1
-        return False
+        """
+        Checks if the analysis orders have multiple extraction orders.
+        This is used to determine which type of link to show in the template.
+        """
+        if analysis_orders.count() != 1:
+            return False
+
+        analysis_order = analysis_orders.first()
+
+        extraction_order_ids = analysis_order.samples.values_list(  # type: ignore[union-attr] # We have already checked for existance.
+            "order_id", flat=True
+        ).distinct()
+        return extraction_order_ids.count() > 1
 
     def get_context_data(self, **kwargs: Any) -> dict[str, Any]:
         context = super().get_context_data(**kwargs)
         extraction_order = self.object
         samples = extraction_order.samples.all()
-        analysis_orders = self.get_analysis_orders_for_samples(samples)
+        analysis_orders = self.get_analysis_orders_for_samples(samples=samples)
         context["analysis_orders"] = analysis_orders
         context["analysis_has_multiple_extraction_orders"] = (
-            self.analysis_has_multiple_extraction_orders(analysis_orders)
+            self.analysis_has_multiple_extraction_orders(
+                analysis_orders=analysis_orders
+            )
         )
         return context