Summer25 Week 28

aliases.sh

@@ -6,6 +6,8 @@ alias dpcli_prod="docker compose --profile prod"
 alias djcli_dev="docker compose exec -it django-dev ./src/manage.py"
 alias djcli_prod="docker compose exec -it django ./src/manage.py"
 
+alias run-mypy="uv run mypy ."
+
 alias deps-sync="uv sync"
 alias deps-sync-prod="uv sync --profile prod --no-dev"
 alias deps-outdated="uv tree --outdated --depth 1"

src/fixtures/users.json

@@ -15,5 +15,41 @@
         "groups": [1],
         "user_permissions": []
       }
+  },
+  {
+    "model": "users.user",
+    "pk": 2,
+    "fields": {
+      "password": "pbkdf2_sha256$180000$10jDVElGx6nr$0o2RbVZhcE/BAHG6pCvAX4DI8V4mjIHgnN0pdNOKkr8=",
+      "last_login": "2023-05-27T09:22:46.831Z",
+      "is_superuser": false,
+      "first_name": "Kari",
+      "last_name": "Nordmann",
+      "email": "kari.nordmann@norge.no",
+      "is_staff": true,
+      "is_active": true,
+      "date_joined": "2023-05-27T08:35:08.845Z",
+      "groups": [
+        1
+      ],
+      "user_permissions": []
     }
-  ]
+  },
+  {
+    "model": "users.user",
+    "pk": 3,
+    "fields": {
+      "password": "pbkdf2_sha256$180000$10jDVElGx6nr$0o2RbVZhcE/BAHG6pCvAX4DI8V4mjIHgnN0pdNOKkr8=",
+      "last_login": "2023-05-27T09:22:46.831Z",
+      "is_superuser": false,
+      "first_name": "Ola",
+      "last_name": "Nordmann",
+      "email": "ola.nordmann@norge.no",
+      "is_staff": true,
+      "is_active": true,
+      "date_joined": "2023-05-27T08:35:08.845Z",
+      "groups": [],
+      "user_permissions": []
+    }
+  }
+]

src/genlab_bestilling/admin.py

@@ -15,12 +15,14 @@
     ExtractionPlate,
     ExtractPlatePosition,
     Genrequest,
+    IsolationMethod,
     Location,
     LocationType,
     Marker,
     Organization,
     Sample,
     SampleMarkerAnalysis,
+    SampleStatusAssignment,
     SampleType,
     Species,
 )
@@ -200,9 +202,18 @@ class EquipmentTypeAdmin(ModelAdmin):
 
 @admin.register(EquipmentBuffer)
 class EquipmentBufferAdmin(ModelAdmin):
-    list_display = ["name", "unit"]
-    list_filter = ["unit"]
-    search_fields = ["name"]
+    M = EquipmentBuffer
+    list_display = [M.name.field.name, M.unit.field.name]
+
+    search_help_text = "Search for equipment buffer name"
+    search_fields = [M.name.field.name]
+
+    list_filter = [
+        (M.name.field.name, unfold_filters.FieldTextFilter),
+        (M.unit.field.name, unfold_filters.FieldTextFilter),
+    ]
+    list_filter_submit = True
+    list_filter_sheet = False
 
 
 @admin.register(EquimentOrderQuantity)
@@ -513,3 +524,11 @@ class AnalysisResultAdmin(ModelAdmin):
         M.last_modified_at.field.name,
         M.created_at.field.name,
     ]
+
+
+@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