staff and analysis setup

src/config/settings/base.py

@@ -119,6 +119,7 @@
     "apps.users",
     "apps.core",
     "genlab_bestilling",
+    "genlab_bestilling.staff",
     "theme",
     "frontend",
     "nina",

src/config/urls.py

@@ -20,6 +20,7 @@ def get_redirect_url(self, *args: Any, **kwargs: Any) -> str | None:
     path("api/", include("config.routers")),
     path("accounts/", include("allauth.urls")),
     path("", include("genlab_bestilling.urls")),
+    path("staff/", include("genlab_bestilling.staff.urls", namespace="staff")),
 ]
 
 

src/genlab_bestilling/migrations/0007_analysis_extractionplate_extractplateposition_and_more.py

@@ -0,0 +1,147 @@
+# Generated by Django 5.1.1 on 2024-12-02 08:36
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        (
+            "genlab_bestilling",
+            "0006_genrequest_created_at_genrequest_last_modified_at_and_more",
+        ),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="Analysis",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("name", models.CharField()),
+                ("created_at", models.DateTimeField(auto_now_add=True)),
+                ("last_modified_at", models.DateTimeField(auto_now=True)),
+                ("analysis_date", models.DateTimeField(blank=True, null=True)),
+                ("result_file", models.FileField(blank=True, null=True, upload_to="")),
+                ("extra", models.JSONField(blank=True, null=True)),
+            ],
+        ),
+        migrations.CreateModel(
+            name="ExtractionPlate",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("name", models.CharField()),
+                ("created_at", models.DateTimeField(auto_now_add=True)),
+                ("last_modified_at", models.DateTimeField(auto_now=True)),
+            ],
+        ),
+        migrations.CreateModel(
+            name="ExtractPlatePosition",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("position", models.IntegerField()),
+            ],
+        ),
+        migrations.AddField(
+            model_name="sample",
+            name="desired_extractions",
+            field=models.IntegerField(default=1),
+        ),
+        migrations.AddField(
+            model_name="sample",
+            name="genlab_id",
+            field=models.CharField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="sample",
+            name="parent",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.PROTECT,
+                to="genlab_bestilling.sample",
+            ),
+        ),
+        migrations.AddField(
+            model_name="sample",
+            name="replica_number",
+            field=models.IntegerField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="sample",
+            name="running_number",
+            field=models.IntegerField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="species",
+            name="code",
+            field=models.CharField(blank=True, null=True),
+        ),
+        migrations.AddConstraint(
+            model_name="species",
+            constraint=models.UniqueConstraint(
+                fields=("code",), name="unique species code"
+            ),
+        ),
+        migrations.AddField(
+            model_name="analysis",
+            name="marker",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.DO_NOTHING,
+                to="genlab_bestilling.marker",
+            ),
+        ),
+        migrations.AddField(
+            model_name="analysis",
+            name="samples",
+            field=models.ManyToManyField(blank=True, to="genlab_bestilling.sample"),
+        ),
+        migrations.AddField(
+            model_name="sample",
+            name="extractions",
+            field=models.ManyToManyField(
+                blank=True, to="genlab_bestilling.extractionplate"
+            ),
+        ),
+        migrations.AddField(
+            model_name="extractplateposition",
+            name="plate",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.DO_NOTHING,
+                related_name="sample_positions",
+                to="genlab_bestilling.extractionplate",
+            ),
+        ),
+        migrations.AddField(
+            model_name="extractplateposition",
+            name="sample",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.PROTECT,
+                related_name="plate_positions",
+                to="genlab_bestilling.sample",
+            ),
+        ),
+    ]

src/genlab_bestilling/migrations/0008_alter_order_status.py

@@ -0,0 +1,30 @@
+# Generated by Django 5.1.1 on 2024-12-02 09:44
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        (
+            "genlab_bestilling",
+            "0007_analysis_extractionplate_extractplateposition_and_more",
+        ),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="order",
+            name="status",
+            field=models.CharField(
+                choices=[
+                    ("draft", "Draft"),
+                    ("confirmed", "Confirmed"),
+                    ("processing", "Processing"),
+                    ("completed", "Completed"),
+                    ("checked", "Checked"),
+                    ("extracted", "Extracted"),
+                ],
+                default="draft",
+            ),
+        ),
+    ]

src/genlab_bestilling/models.py

@@ -36,19 +36,22 @@ def __str__(self) -> str:
 
 
 class Species(models.Model):
-    # TODO: use IDs from Artsdatabanken?
     name = models.CharField(max_length=255)
     area = models.ForeignKey("Area", on_delete=models.CASCADE)
     markers = models.ManyToManyField("Marker")
     location_type = models.ForeignKey(
         "LocationType", null=True, blank=True, on_delete=models.CASCADE
     )
+    code = models.CharField(null=True, blank=True)
 
     def __str__(self) -> str:
         return self.name
 
     class Meta:
         verbose_name_plural = "Species"
+        constraints = [
+            models.UniqueConstraint(name="unique species code", fields=["code"])
+        ]
 
 
 # TODO: better understand "other" case. should the user be able to insert new orws?
@@ -145,6 +148,9 @@ class OrderStatus(models.TextChoices):
         PROCESSING = "processing", _("Processing")
         COMPLETED = "completed", _("Completed")
 
+        CHECKED = "checked", _("Checked")
+        EXTRACTED = "extracted", _("Extracted")
+
     name = models.CharField(null=True, blank=True)
     genrequest = models.ForeignKey(
         "Genrequest", on_delete=models.CASCADE, related_name="orders"
@@ -175,6 +181,18 @@ def clone(self):
         self.species.add(*species)
         self.sample_types.add(*sample_types)
 
+    def order_manually_checked(self):
+        self.status = Order.OrderStatus.CHECKED
+        self.save()
+
+    def to_draft(self):
+        self.status = Order.OrderStatus.DRAFT
+        self.confirmed_at = None
+        self.save()
+
+    def get_type(self):
+        return "order"
+
     def __str__(self):
         return f"#ORD_{self.id}"
 
@@ -216,6 +234,9 @@ def confirm_order(self):
             raise Order.CannotConfirm(_("No equipments found"))
         return super().confirm_order()
 
+    def get_type(self):
+        return "equipment"
+
 
 class AnalysisOrder(Order):
     needs_guid = models.BooleanField(default=False)  # TODO: default?
@@ -232,6 +253,9 @@ def get_absolute_url(self):
             kwargs={"pk": self.pk, "genrequest_id": self.genrequest_id},
         )
 
+    def get_type(self):
+        return "analysis"
+
     def clone(self):
         markers = self.markers.all()
         super().clone()
@@ -276,10 +300,17 @@ class Sample(models.Model):
     )
     volume = models.FloatField(null=True, blank=True)
 
+    extractions = models.ManyToManyField("ExtractionPlate", blank=True)
+    desired_extractions = models.IntegerField(default=1)
+    genlab_id = models.CharField(null=True, blank=True)
+    parent = models.ForeignKey("self", on_delete=models.PROTECT, null=True, blank=True)
+    running_number = models.IntegerField(blank=True, null=True)
+    replica_number = models.IntegerField(blank=True, null=True)
+
     objects = managers.SampleQuerySet.as_manager()
 
     def __str__(self) -> str:
-        return f"#SMP_{self.id}"
+        return self.genlab_id or f"#SMP_{self.id}"
 
     @property
     def has_error(self):
@@ -308,9 +339,6 @@ def has_error(self):
         else:
             return False
 
-    # plate
-    # coordinates on plate
-
 
 # class Analysis(models.Model):
 # type =
@@ -320,3 +348,35 @@ def has_error(self):
 # result
 # status
 # assignee (one or plus?)
+
+
+# Some extracts can be placed in multiple wells
+class ExtractPlatePosition(models.Model):
+    plate = models.ForeignKey(
+        "ExtractionPlate", on_delete=models.DO_NOTHING, related_name="sample_positions"
+    )
+    sample = models.ForeignKey(
+        "Sample", on_delete=models.PROTECT, related_name="plate_positions"
+    )
+    position = models.IntegerField()
+
+    # TODO: unique position per plate
+
+
+class ExtractionPlate(models.Model):
+    name = models.CharField()
+    created_at = models.DateTimeField(auto_now_add=True)
+    last_modified_at = models.DateTimeField(auto_now=True)
+    # freezer
+    # shelf
+
+
+class Analysis(models.Model):
+    name = models.CharField()
+    created_at = models.DateTimeField(auto_now_add=True)
+    last_modified_at = models.DateTimeField(auto_now=True)
+    analysis_date = models.DateTimeField(null=True, blank=True)
+    marker = models.ForeignKey("Marker", on_delete=models.DO_NOTHING)
+    result_file = models.FileField(null=True, blank=True)
+    samples = models.ManyToManyField("Sample", blank=True)
+    extra = models.JSONField(null=True, blank=True)

src/genlab_bestilling/staff/apps.py

@@ -0,0 +1,15 @@
+from typing import Self
+
+from django.apps import AppConfig as DjangoAppConfig
+from django.utils.translation import gettext_lazy as _
+
+
+class AppConfig(DjangoAppConfig):
+    name = "genlab_bestilling.staff"
+    verbose_name = _("GenLab staff")
+
+    def ready(self: Self) -> None:
+        try:
+            import genlab_bestilling.signals  # noqa: F401
+        except ImportError:
+            pass

src/genlab_bestilling/staff/filters.py

@@ -0,0 +1,32 @@
+import django_filters as filters
+
+from ..models import AnalysisOrder, Sample
+
+
+class AnalysisOrderFilter(filters.FilterSet):
+    class Meta:
+        model = AnalysisOrder
+        fields = [
+            "id",
+            "status",
+            "genrequest",
+            "genrequest__project",
+        ]
+
+
+class SampleFilter(filters.FilterSet):
+    class Meta:
+        model = Sample
+        fields = [
+            "order",
+            "guid",
+            "name",
+            "genlab_id",
+            "species",
+            "type",
+            "year",
+            "location",
+            "pop_id",
+            "type",
+            "desired_extractions",
+        ]