Update for 215-column-for-isolation-method-sample-status

src/genlab_bestilling/admin.py

@@ -15,6 +15,7 @@
     ExtractionPlate,
     ExtractPlatePosition,
     Genrequest,
+    IsolationMethod,
     Location,
     LocationType,
     Marker,
@@ -532,3 +533,7 @@ class SampleStatusAdmin(ModelAdmin): ...
 
 @admin.register(SampleStatusAssignment)
 class SampleStatusAssignmentAdmin(ModelAdmin): ...
+
+
+@admin.register(IsolationMethod)
+class IsolationMethodAdmin(ModelAdmin): ...

src/genlab_bestilling/managers.py

@@ -1,9 +1,17 @@
-from django.db import models
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+from django.db import models, transaction
 from django.db.models import QuerySet
+from django.db.models.expressions import RawSQL
 from polymorphic.managers import PolymorphicManager, PolymorphicQuerySet
 
 from capps.users.models import User
 
+if TYPE_CHECKING:
+    from .models import GIDSequence, Species
+
 
 class GenrequestQuerySet(models.QuerySet):
     def filter_allowed(self, user: User) -> QuerySet:
@@ -46,6 +54,9 @@ def filter_in_draft(self) -> QuerySet:
         )
 
 
+DEFAULT_SORTING_FIELDS = ["name_as_int", "name"]
+
+
 class SampleQuerySet(models.QuerySet):
     def filter_allowed(self, user: User) -> QuerySet:
         """
@@ -61,6 +72,48 @@ def filter_in_draft(self) -> QuerySet:
             order__status=self.model.OrderStatus.DRAFT
         )
 
+    @transaction.atomic
+    def generate_genlab_ids(
+        self,
+        order_id: int,
+        sorting_order: list[str] | None = DEFAULT_SORTING_FIELDS,
+        selected_samples: list[int] | None = None,
+    ) -> None:
+        """
+        genlab ids given a certain order_id, sorting order and sample ids
+
+        """
+
+        # Lock the samples
+        samples = (
+            self.select_related("species", "order")
+            .filter(order_id=order_id, genlab_id__isnull=True)
+            .select_for_update()
+        )
+
+        if selected_samples:
+            samples = samples.filter(id__in=selected_samples)
+
+        if sorting_order == DEFAULT_SORTING_FIELDS:
+            # create an annotation containg all integer values
+            # of "name", so that it's possible to sort numerically and alphabetically
+            samples = samples.annotate(
+                name_as_int=RawSQL(
+                    r"substring(%s from '^\d+$')::int",
+                    params=["name"],
+                    output_field=models.IntegerField(),
+                )
+            ).order_by(*sorting_order)
+        else:
+            samples = samples.order_by(*sorting_order)
+
+        updates = []
+        for sample in samples:
+            sample.generate_genlab_id(commit=False)
+            updates.append(sample)
+
+        self.bulk_update(updates, ["genlab_id"])
+
 
 class SampleAnalysisMarkerQuerySet(models.QuerySet):
     def filter_allowed(self, user: User) -> QuerySet:
@@ -76,3 +129,23 @@ def filter_in_draft(self) -> QuerySet:
         return self.select_related("order").filter(
             order__status=self.model.OrderStatus.DRAFT
         )
+
+
+class GIDSequenceQuerySet(models.QuerySet):
+    def get_sequence_for_species_year(
+        self, species: Species, year: int, lock: bool = False
+    ) -> GIDSequence:
+        """
+        Get or creates an ID sequence based on the sample year and species
+        """
+        if lock:
+            s = self.select_for_update()
+        else:
+            s = self
+
+        sequence_id, _ = s.get_or_create(
+            year=year,
+            species=species,
+            defaults={"id": f"G{year % 100}{species.code}"},
+        )
+        return sequence_id

src/genlab_bestilling/migrations/0023_alter_order_responsible_staff.py

@@ -0,0 +1,25 @@
+# Generated by Django 5.2.3 on 2025-07-08 10:19
+
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("genlab_bestilling", "0022_sample_internal_note"),
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="order",
+            name="responsible_staff",
+            field=models.ManyToManyField(
+                blank=True,
+                help_text="Staff members responsible for this order",
+                related_name="responsible_orders",
+                to=settings.AUTH_USER_MODEL,
+                verbose_name="Responsible staff",
+            ),
+        ),
+    ]