Download CSV of samples

.gitignore

@@ -335,3 +335,6 @@ staticfiles/
 
 # Local History for devcontainer
 .devcontainer/bash_history
+
+### macOS ###
+.DS_Store

src/genlab_bestilling/api/serializers.py

@@ -1,7 +1,3 @@
-from collections.abc import Mapping
-from typing import Any
-
-from django.forms import Field
 from rest_framework import exceptions, serializers
 
 from ..models import (
@@ -103,10 +99,15 @@ class SampleCSVSerializer(serializers.ModelSerializer):
     species = SpeciesSerializer()
     location = LocationSerializer(allow_null=True, required=False)
     fish_id = serializers.SerializerMethodField()
+    analysis_orders = serializers.SerializerMethodField()
+    project = serializers.SerializerMethodField()
+    isolation_method = serializers.SerializerMethodField()
+    marked = serializers.SerializerMethodField()
+    plucked = serializers.SerializerMethodField()
+    isolated = serializers.SerializerMethodField()
 
     class Meta:
         model = Sample
-        # Make fields as a list to enable the removal of fish_id dynamically
         fields = [
             "order",
             "guid",
@@ -119,20 +120,43 @@ class Meta:
             "notes",
             "genlab_id",
             "fish_id",
+            "analysis_orders",
+            "project",
+            "isolation_method",
+            "marked",
+            "plucked",
+            "isolated",
         ]
 
-    def get_field_names(
-        self, declared_fields: Mapping[str, Field], info: Any
-    ) -> list[str]:
-        field_names = super().get_field_names(declared_fields, info)
-        if not self.context.get("include_fish_id", False):
-            # Remove fish_id if the area is not aquatic (only relevant for aquatic area)
-            field_names.remove("fish_id")
-        return field_names
-
     def get_fish_id(self, obj: Sample) -> str:
         return obj.fish_id or "-"
 
+    def get_analysis_orders(self, obj: Sample) -> list[str]:
+        if obj.order and obj.order.analysis_orders.exists():
+            return [str(anl.id) for anl in obj.order.analysis_orders.all()]
+        return []
+
+    def get_project(self, obj: Sample) -> str:
+        if obj.order and obj.order.genrequest and obj.order.genrequest.project:
+            return str(obj.order.genrequest.project)
+        return ""
+
+    def get_isolation_method(self, obj: Sample) -> str:
+        method = obj.isolation_method.first()
+        return method.name if method else ""
+
+    def _flag(self, value: bool) -> str:
+        return "x" if value else ""
+
+    def get_marked(self, obj: Sample) -> str:
+        return self._flag(obj.is_marked)
+
+    def get_plucked(self, obj: Sample) -> str:
+        return self._flag(obj.is_plucked)
+
+    def get_isolated(self, obj: Sample) -> str:
+        return self._flag(obj.is_isolated)
+
 
 class SampleUpdateSerializer(serializers.ModelSerializer):
     has_error = serializers.SerializerMethodField()

src/genlab_bestilling/api/views.py

@@ -1,8 +1,8 @@
 import uuid
-from typing import Any
 
 from django.db import transaction
-from django.db.models import QuerySet
+from django.db.models import Exists, OuterRef, QuerySet
+from django.http import HttpResponse
 from django.views import View
 from drf_spectacular.utils import extend_schema
 from rest_framework.decorators import action
@@ -33,6 +33,7 @@
     Marker,
     Sample,
     SampleMarkerAnalysis,
+    SampleStatusAssignment,
     SampleType,
     Species,
 )
@@ -77,6 +78,115 @@ class SampleViewset(ModelViewSet):
     pagination_class = IDCursorPagination
     permission_classes = [AllowSampleDraft, IsAuthenticated]
 
+    CSV_FIELD_LABELS: dict[str, str] = {
+        "genlab_id": "Genlab ID",
+        "fish_id": "Old Genlab ID",
+        "guid": "GUID",
+        "name": "Name",
+        "species.name": "Species",
+        "location.name": "Location",
+        "order": "EXT_order",
+        "analysis_orders": "ANL_order",
+        "pop_id": "PopID",
+        "type.name": "Sample Type",
+        "gender": "Gender",
+        "length": "Length",
+        "weight": "Weight",
+        "classification": "Classification",
+        "year": "Date",
+        "notes": "Remarks",
+        "project": "Projectnumber",
+        "isolation_method": "Isolation Method",
+        "qiagen_number": "Qiagen#",
+        "marked": "Marked",
+        "plucked": "Plucked",
+        "isolated": "Isolated",
+        "station": "Station",
+        "placement_in_fridge": "Placement in fridge",
+        "delivered_to_lab": "Delivered to lab",
+    }
+
+    # NOTE: This can be modified to include more fields based on species or area.
+    CSV_FIELDS_BY_AREA: dict[str, list[str]] = {
+        "Akvatisk": [
+            "genlab_id",
+            "fish_id",
+            "guid",
+            "order",
+            "analysis_orders",
+            "location.name",
+            "pop_id",
+            "name",
+            "species.name",
+            "gender",
+            "length",
+            "weight",
+            "classification",
+            "year",
+            "notes",
+            "project",
+            "type.name",
+            "isolation_method",
+            "qiagen_number",
+            "marked",
+            "plucked",
+            "isolated",
+        ],
+        "Elvemusling": [
+            "genlab_id",
+            "fish_id",
+            "guid",
+            "location.name",
+            "year",
+            "name",
+            "station",
+            "type.name",
+            "length",
+            "notes",
+            "isolation_method",
+            "qiagen_number",
+            "placement_in_fridge",
+            "marked",
+            "plucked",
+            "isolated",
+        ],
+        "Terrestrisk": [
+            "genlab_id",
+            "guid",
+            "name",
+            "type.name",
+            "species.name",
+            "location.name",
+            "delivered_to_lab",
+            "order",
+            "analysis_orders",
+            "notes",
+            "marked",
+            "plucked",
+            "isolated",
+            "isolation_method",
+            "qiagen_number",
+        ],
+        # Same as "Terrestrisk" for now, can be modified later if needed.
+        "default": [
+            "genlab_id",
+            "guid",
+            "name",
+            "type.name",
+            "species.name",
+            "location.name",
+            "delivered_to_lab",
+            "order",
+            "analysis_orders",
+            "notes",
+            "marked",
+            "plucked",
+            "isolated",
+            "isolation_method",
+            "qiagen_number",
+        ],
+    }
+
     def get_queryset(self) -> QuerySet:
         return (
             super()
@@ -89,7 +199,24 @@ def get_queryset(self) -> QuerySet:
                 "order__genrequest__area",
                 "location",
             )
-            .order_by("id")
+            .annotate(
+                is_marked=Exists(
+                    SampleStatusAssignment.objects.filter(
+                        sample=OuterRef("pk"), status="marked"
+                    )
+                ),
+                is_plucked=Exists(
+                    SampleStatusAssignment.objects.filter(
+                        sample=OuterRef("pk"), status="plucked"
+                    )
+                ),
+                is_isolated=Exists(
+                    SampleStatusAssignment.objects.filter(
+                        sample=OuterRef("pk"), status="isolated"
+                    )
+                ),
+            )
+            .order_by("genlab_id", "type")
         )
 
     def get_serializer_class(self) -> type[BaseSerializer]:
@@ -99,21 +226,78 @@ def get_serializer_class(self) -> type[BaseSerializer]:
             return SampleCSVSerializer
         return super().get_serializer_class()
 
-    def get_serializer_context(self, *args, **kwargs) -> dict[str, Any]:
-        context = super().get_serializer_context(*args, **kwargs)
-        queryset = self.filter_queryset(self.get_queryset())
-        is_aquatic = queryset.filter(order__genrequest__area__name="Akvatisk").exists()
-        context["include_fish_id"] = is_aquatic
-        return context
+    def get_area_name(self, queryset: QuerySet) -> str:
+        return (
+            queryset.values_list("order__genrequest__area__name", flat=True).first()
+            or "default"
+        )
+
+    # NOTE: If the headers differ from species to species, we can add more headers
+    # to the CSV_FIELDS_BY_AREA dict, and then use the species name to determine
+    # which headers to use.
+    def get_csv_fields_and_labels(
+        self, area_name: str, queryset: QuerySet
+    ) -> tuple[list[str], list[str]]:
+        get_fields = area_name
+        if area_name == "Akvatisk":
+            species = queryset.values_list("species__name", flat=True).distinct()
+            if species.first() == "Elvemusling":
+                get_fields = "Elvemusling"
+
+        fields = self.CSV_FIELDS_BY_AREA.get(
+            get_fields, self.CSV_FIELDS_BY_AREA["default"]
+        )
+        labels = [self.CSV_FIELD_LABELS.get(f, f) for f in fields]
+        return fields, labels
+
+    # Helper function to get nested values from a dict using dotted notation.
+    def get_nested(self, obj: dict, dotted: str) -> str | None:
+        for part in dotted.split("."):
+            obj = obj.get(part) if isinstance(obj, dict) else None
+        return obj
+
+    def build_csv_data(
+        self, serialized_data: list[dict], fields: list[str]
+    ) -> list[dict[str, str]]:
+        return [
+            {
+                self.CSV_FIELD_LABELS[f]: (
+                    ", ".join(v)
+                    if isinstance(v := self.get_nested(item, f), list)
+                    else v or ""
+                )
+                for f in fields
+            }
+            for item in serialized_data
+        ]
 
     @action(
-        methods=["GET"], url_path="csv", detail=False, renderer_classes=[CSVRenderer]
+        methods=["GET"],
+        url_path="csv",
+        detail=False,
+        renderer_classes=[CSVRenderer],
     )
-    def csv(self, request: Request) -> Response:
+    def csv(self, request: Request) -> HttpResponse:
         queryset = self.filter_queryset(self.get_queryset())
-        serializer = self.get_serializer(queryset, many=True)
-        return Response(
-            serializer.data,
+        area_name = self.get_area_name(queryset)
+
+        serializer = self.get_serializer(
+            queryset,
+            many=True,
+        )
+
+        fields, headers = self.get_csv_fields_and_labels(area_name, queryset)
+        data = self.build_csv_data(serializer.data, fields)
+
+        csv_data = CSVRenderer().render(
+            data,
+            media_type="text/csv",
+            renderer_context={"header": headers},
+        )
+
+        return HttpResponse(
+            csv_data,
+            content_type="text/csv; charset=utf-8",
             headers={"Content-Disposition": "attachment; filename=samples.csv"},
         )
 

src/genlab_bestilling/migrations/0027_alter_isolationmethod_name.py

@@ -0,0 +1,17 @@
+# Generated by Django 5.2.3 on 2025-07-15 07:00
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("genlab_bestilling", "0026_alter_samplestatusassignment_status_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="isolationmethod",
+            name="name",
+            field=models.CharField(max_length=255),
+        ),
+    ]

src/genlab_bestilling/models.py

@@ -819,7 +819,7 @@ class Meta:
 
 
 class IsolationMethod(models.Model):
-    name = models.CharField(max_length=255, unique=True)
+    name = models.CharField(max_length=255, unique=False)
     species = models.ForeignKey(
         f"{an}.Species",
         on_delete=models.CASCADE,

src/staff/views.py

@@ -364,8 +364,10 @@ def get_isolation_methods(self) -> list[str]:
         samples = Sample.objects.filter(order=order)
         species_ids = samples.values_list("species_id", flat=True).distinct()
 
-        return IsolationMethod.objects.filter(species_id__in=species_ids).values_list(
-            "name", flat=True
+        return (
+            IsolationMethod.objects.filter(species_id__in=species_ids)
+            .values_list("name", flat=True)
+            .distinct()
         )
 
     def get_base_fields(self) -> list[str]:
@@ -478,7 +480,9 @@ def update_isolation_methods(
         ).first()
 
         try:
-            im = IsolationMethod.objects.get(name=selected_isolation_method.name)
+            im = IsolationMethod.objects.filter(
+                name=selected_isolation_method.name
+            ).first()
         except IsolationMethod.DoesNotExist:
             messages.error(
                 request,