Summer25 week 30 2

src/genlab_bestilling/api/serializers.py

@@ -102,9 +102,10 @@ class SampleCSVSerializer(serializers.ModelSerializer):
     analysis_orders = serializers.SerializerMethodField()
     project = serializers.SerializerMethodField()
     isolation_method = serializers.SerializerMethodField()
-    marked = serializers.SerializerMethodField()
-    plucked = serializers.SerializerMethodField()
-    isolated = serializers.SerializerMethodField()
+    is_marked = serializers.SerializerMethodField()
+    is_plucked = serializers.SerializerMethodField()
+    is_isolated = serializers.SerializerMethodField()
+    internal_note = serializers.SerializerMethodField()
 
     class Meta:
         model = Sample
@@ -123,9 +124,10 @@ class Meta:
             "analysis_orders",
             "project",
             "isolation_method",
-            "marked",
-            "plucked",
-            "isolated",
+            "is_marked",
+            "is_plucked",
+            "is_isolated",
+            "internal_note",
         ]
 
     def get_fish_id(self, obj: Sample) -> str:
@@ -148,15 +150,20 @@ def get_isolation_method(self, obj: Sample) -> str:
     def _flag(self, value: bool) -> str:
         return "x" if value else ""
 
-    def get_marked(self, obj: Sample) -> str:
+    def get_is_marked(self, obj: Sample) -> str:
         return self._flag(obj.is_marked)
 
-    def get_plucked(self, obj: Sample) -> str:
+    def get_is_plucked(self, obj: Sample) -> str:
         return self._flag(obj.is_plucked)
 
-    def get_isolated(self, obj: Sample) -> str:
+    def get_is_isolated(self, obj: Sample) -> str:
         return self._flag(obj.is_isolated)
 
+    def get_internal_note(self, obj: Sample) -> str:
+        if obj.internal_note:
+            return obj.internal_note
+        return ""
+
 
 class SampleUpdateSerializer(serializers.ModelSerializer):
     has_error = serializers.SerializerMethodField()

src/genlab_bestilling/api/views.py

@@ -1,3 +1,4 @@
+import re
 import uuid
 
 from django.db import transaction
@@ -92,30 +93,64 @@ class SampleViewset(ModelViewSet):
         "length": "Length",
         "weight": "Weight",
         "classification": "Classification",
-        "year": "Date",
-        "notes": "Remarks",
-        "project": "Projectnumber",
+        "year": "Year",
+        "notes": "Notes",
+        "project": "Project Number",
         "isolation_method": "Isolation Method",
         "qiagen_number": "Qiagen#",
         "is_marked": "Marked",
         "is_plucked": "Plucked",
         "is_isolated": "Isolated",
         "station": "Station",
-        "placement_in_fridge": "Placement in fridge",
-        "delivered_to_lab": "Delivered to lab",
+        "placement_in_fridge": "Placement in Fridge",
+        "delivered_to_lab": "Delivered to Lab",
+        "fluidigm#": "Fluidigm#",
+        "laksov_species": "LaksOV + Species",
+        "species_date": "Species Date",
+        "pcr": "PCR",
+        "fluidigm": "Fluidigm",
+        "output": "Output",
+        "analysis_note": "Analysis Note",
+        "rerun": "Rerun",
+        "rerun_qiagen": "Rerun Qiagen",
+        "river": "River",
+        "str_date": "STR Date",
+        "rerun_date": "Rerun Date",
+        "watercourse_number": "Watercourse Number",
+        "under_locality": "Sub-locality",
+        "county": "County",
+        "snp_assay_1": "SNP Assay 1",
+        "snp_assay_2": "SNP Assay 2",
+        "str_mixab": "STR Mix AB",
+        "str_mixc": "STR Mix C",
+        "str_mixy": "STR Mix Y",
+        "internal_note": "Internal Note",
+        "bb#": "BB#",
+        "output_bb": "Output",
+        "bba2#": "BBA2#",
+        "output_bba2": "Output",
+        "mixab": "Mix AB",
+        "ab_rep#": "AB Rep#",
+        "mixc": "Mix C",
+        "c_rep#": "C Rep#",
+        "re_extracted_date": "Re-extracted Date",
+        "re_extracted_qiagen#": "Re-extracted Qiagen#",
+        "weight_g_for_diet_analysis": "Weight (g) for Diet Analysis",
+        "position": "Position",
     }
 
     # NOTE: This can be modified to include more fields based on species or area.
     CSV_FIELDS_BY_AREA: dict[str, list[str]] = {
         "Akvatisk": [
+            "name",
             "genlab_id",
             "fish_id",
             "guid",
             "order",
             "analysis_orders",
             "location.name",
+            "watercourse_number",
             "pop_id",
-            "name",
             "species.name",
             "gender",
             "length",
@@ -127,54 +162,89 @@ class SampleViewset(ModelViewSet):
             "type.name",
             "isolation_method",
             "qiagen_number",
+            "fluidigm#",
+            "laksov_species",
+            "species_date",
             "is_marked",
             "is_plucked",
             "is_isolated",
+            "pcr",
+            "fluidigm",
+            "output",
+            "analysis_note",
+            "rerun",
+            "rerun_date",
         ],
         "Elvemusling": [
+            "name",
             "genlab_id",
             "fish_id",
             "guid",
+            "river",
             "location.name",
+            "under_locality",
+            "watercourse_number",
+            "county",
             "year",
-            "name",
             "station",
             "type.name",
             "length",
             "notes",
             "isolation_method",
             "qiagen_number",
+            "position",
             "placement_in_fridge",
             "is_marked",
             "is_plucked",
             "is_isolated",
+            "pcr",
+            "str_date",
+            "output",
+            "analysis_note",
+            "rerun",
+            "rerun_date",
         ],
         "Terrestrisk": [
+            "name",
             "genlab_id",
             "guid",
-            "name",
             "type.name",
             "species.name",
             "location.name",
             "delivered_to_lab",
             "order",
             "analysis_orders",
             "notes",
+            "snp_assay_1",
+            "snp_assay_2",
+            "str_mixab",
+            "str_mixc",
+            "str_mixy",
             "is_marked",
             "is_plucked",
             "is_isolated",
             "isolation_method",
             "qiagen_number",
+            "internal_note",
+            "bb#",
+            "output_bb",
+            "bba2#",
+            "output_bba2",
+            "mixab",
+            "ab_rep#",
+            "mixc",
+            "c_rep#",
+            "re_extracted_date",
+            "re_extracted_qiagen#",
+            "weight_g_for_diet_analysis",
         ],
-        # 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",
@@ -239,19 +309,40 @@ def get_nested(self, obj: dict, dotted: str) -> str | None:
         return obj
 
     def build_csv_data(
-        self, serialized_data: list[dict], fields: list[str]
+        self, serialized_data: list[dict], fields: list[str], area_name: 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
-        ]
+        rows = []
+
+        for item in serialized_data:
+            row = {}
+
+            for f in fields:
+                if area_name in {"Akvatisk", "Elvemusling"} and f == "location.name":
+                    full_location = self.get_nested(item, "location.name")
+
+                    if (
+                        full_location
+                        and re.search(r"\d+", full_location)
+                        and " " in full_location
+                    ):
+                        watercourse, location = full_location.split(" ", 1)
+                    else:
+                        watercourse, location = "", full_location or ""
+
+                    row[self.CSV_FIELD_LABELS["watercourse_number"]] = watercourse
+                    row[self.CSV_FIELD_LABELS["location.name"]] = location
+
+                # We skip "watercourse_number" because it is handled above.
+                elif f != "watercourse_number":
+                    value = self.get_nested(item, f)
+                    if isinstance(value, list):
+                        row[self.CSV_FIELD_LABELS[f]] = ", ".join(value)
+                    else:
+                        row[self.CSV_FIELD_LABELS[f]] = value or ""
+
+            rows.append(row)
+
+        return rows
 
     @action(
         methods=["GET"],
@@ -269,7 +360,7 @@ def csv(self, request: Request) -> HttpResponse:
         )
 
         fields, headers = self.get_csv_fields_and_labels(area_name, queryset)
-        data = self.build_csv_data(serializer.data, fields)
+        data = self.build_csv_data(serializer.data, fields, area_name)
 
         csv_data = CSVRenderer().render(
             data,

src/genlab_bestilling/migrations/0029_alter_order_contact_email_alter_order_contact_person.py

@@ -0,0 +1,28 @@
+# Generated by Django 5.2.3 on 2025-07-18 07:58
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("genlab_bestilling", "0028_sample_is_isolated_sample_is_marked_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="order",
+            name="contact_email",
+            field=models.EmailField(
+                help_text="Email to contact with questions about this order",
+                max_length=254,
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="order",
+            name="contact_person",
+            field=models.CharField(
+                help_text="Person to contact with questions about this order", null=True
+            ),
+        ),
+    ]

src/genlab_bestilling/models.py

@@ -282,12 +282,12 @@ class OrderPriority:
     )
     contact_person = models.CharField(
         null=True,
-        blank=True,
+        blank=False,
         help_text="Person to contact with questions about this order",
     )
     contact_email = models.EmailField(
         null=True,
-        blank=True,
+        blank=False,
         help_text="Email to contact with questions about this order",
     )
     responsible_staff = models.ManyToManyField(
@@ -310,6 +310,8 @@ class OrderPriority:
     def confirm_order(self) -> None:
         self.status = Order.OrderStatus.DELIVERED
         self.confirmed_at = timezone.now()
+        if self.is_urgent:
+            self.is_seen = True
         self.save()
 
     def clone(self) -> None:
@@ -325,6 +327,10 @@ def to_draft(self) -> None:
         self.confirmed_at = None
         self.save()
 
+    def to_processing(self) -> None:
+        self.status = Order.OrderStatus.PROCESSING
+        self.save()
+
     def toggle_seen(self) -> None:
         self.is_seen = not self.is_seen
         self.save()

src/genlab_bestilling/templates/genlab_bestilling/base_filter.html

@@ -10,6 +10,7 @@ <h3 class="text-4xl mb-5">{% block page-title %}{% endblock page-title %}</h3>
         <div class="flex flex-wrap gap-4">
             {{ filter.form | crispy }}
         <button class="btn custom_order_button_blue mt-6" type="submit">Search</button>
+        <a href="{{ request.path }}" class="btn custom_order_button_grey mt-6">Clear Filters</a>
         </div>
     </form>