Show new fields analysis samples 2

src/genlab_bestilling/migrations/0030_samplemarkeranalysis_has_pcr_and_more.py

@@ -0,0 +1,30 @@
+# Generated by Django 5.2.3 on 2025-07-22 13:00
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        (
+            "genlab_bestilling",
+            "0029_alter_order_contact_email_alter_order_contact_person",
+        ),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="samplemarkeranalysis",
+            name="has_pcr",
+            field=models.BooleanField(default=False),
+        ),
+        migrations.AddField(
+            model_name="samplemarkeranalysis",
+            name="is_analysed",
+            field=models.BooleanField(default=False),
+        ),
+        migrations.AddField(
+            model_name="samplemarkeranalysis",
+            name="is_outputted",
+            field=models.BooleanField(default=False),
+        ),
+    ]

src/genlab_bestilling/models.py

@@ -614,6 +614,11 @@ class SampleMarkerAnalysis(models.Model):
     marker = models.ForeignKey(f"{an}.Marker", on_delete=models.PROTECT)
     transaction = models.UUIDField(blank=True, null=True)
 
+    # Fields for status tracking
+    has_pcr = models.BooleanField(default=False)
+    is_analysed = models.BooleanField(default=False)
+    is_outputted = models.BooleanField(default=False)
+
     objects = managers.SampleAnalysisMarkerQuerySet.as_manager()
 
     class Meta:

src/staff/tables.py

@@ -401,10 +401,6 @@ class Meta(SampleBaseTable.Meta):
 
 
 class OrderAnalysisSampleTable(tables.Table):
-    sample__plate_positions = tables.Column(
-        empty_values=(), orderable=False, verbose_name="Extraction position"
-    )
-
     checked = tables.CheckBoxColumn(
         accessor="pk",
         orderable=False,
@@ -424,29 +420,22 @@ class Meta:
         model = SampleMarkerAnalysis
         fields = [
             "checked",
-            "sample__genlab_id",
-            "sample__type",
+            "sample.genlab_id",
+            "sample.type",
             "marker",
-            "sample__plate_positions",
-            "sample__isolation_method",
-            # "sample__pcr",
-            # "sample__analysis",
-            # "sample__output",
-            "sample__notes",
-            "sample__order",
+            "has_pcr",
+            "is_analysed",
+            "is_outputted",
+            "sample.internal_note",
+            "sample.order",
         ]
         attrs = {"class": "w-full table-auto tailwind-table table-sm"}
         empty_text = "No Samples"
 
-    def render_sample__plate_positions(self, value: Any) -> str:
-        if value:
-            return ", ".join([str(v) for v in value.all()])
-
-        return ""
-
     def render_checked(self, record: Any) -> str:
+        order_pk = getattr(self, "order_pk", None)
         return mark_safe(  # noqa: S308
-            f'<input type="checkbox" name="checked-{record.order.id}" value="{record.id}">'  # noqa: E501
+            f'<input type="checkbox" name="checked-analysis-{order_pk}" value="{record.id}">'  # noqa: E501
         )
 
 

src/staff/templates/staff/samplemarkeranalysis_filter.html

@@ -21,20 +21,54 @@
     </div>
 </form>
 
-{% render_table table %}
+<form method="post" action="{% url 'staff:order-analysis-samples' order.pk %}">
+    {% csrf_token %}
+    {% for status in statuses %}
+        <button class="btn custom_order_button_green" type="submit" name="status" value="{{ status }}">
+            {% if status == "pcr" %}
+                PCR
+            {% else %}
+            {{ status|capfirst }}
+            {% endif %}
+        </button>
+    {% endfor %}
+
+    {% render_table table %}
+</form>
 
 <script>
     document.addEventListener("DOMContentLoaded", function () {
         const selectAll = document.getElementById('select-all-checkbox');
         const noteInputs = document.querySelectorAll('.internal_note-input');
 
         selectAll?.addEventListener('change', function() {
-            const checkboxes = document.querySelectorAll(`input[name="checked-{{ order.pk }}"]`);
+            const checkboxes = document.querySelectorAll(`input[name="checked-analysis-{{ order.pk }}"]`);
             checkboxes.forEach((cb) => {
                 cb.checked = selectAll.checked;
             })
         });
-    })
+
+        let debounceTimeout;
+        noteInputs.forEach(function (noteInput) {
+            noteInput.addEventListener("input", function (event) {
+                const sampleId = event.target.dataset.sampleId;
+                const value = event.target.value;
+                const formData = new FormData();
+                formData.append("sample_id", sampleId);
+                formData.append("field_name", "internal_note-input");
+                formData.append("field_value", value);
+                formData.append("csrfmiddlewaretoken", "{{ csrf_token }}");
+
+                clearTimeout(debounceTimeout);
+                debounceTimeout = setTimeout(function () {
+                    fetch("{% url 'staff:update-internal-note' %}", {
+                        method: "POST",
+                        body: formData
+                    });
+                }, 500);
+            });
+        });
+    });
 </script>
 
 {% endblock page-inner %}

src/staff/views.py

@@ -355,11 +355,19 @@ def post(self, request: HttpRequest, *args, **kwargs) -> HttpResponse:
 
 
 class OrderAnalysisSamplesListView(StaffMixin, SingleTableMixin, FilterView):
-    table_pagination = False
+    PCR = "pcr"
+    ANALYSED = "analysed"
+    OUTPUT = "output"
+    VALID_STATUSES = [PCR, ANALYSED, OUTPUT]
 
+    table_pagination = False
     model = SampleMarkerAnalysis
     table_class = OrderAnalysisSampleTable
     filterset_class = SampleMarkerOrderFilter
+    template_name = "staff/samplemarkeranalysis_filter.html"
+
+    def get_order(self) -> AnalysisOrder:
+        return get_object_or_404(AnalysisOrder, pk=self.kwargs["pk"])
 
     def get_queryset(self) -> QuerySet[SampleMarkerAnalysis]:
         return (
@@ -378,11 +386,132 @@ def get_queryset(self) -> QuerySet[SampleMarkerAnalysis]:
             )
         )
 
+    def get_table_data(self) -> list[Sample]:
+        order = self.get_order()
+        return SampleMarkerAnalysis.objects.filter(order=order).select_related(
+            "sample__type", "sample__location", "sample__species", "marker"
+        )
+
+    def get_table(self, **kwargs) -> Any:
+        table = super().get_table(**kwargs)
+        table.order_pk = self.kwargs["pk"]  # Inject the pk into the table
+        return table
+
+    def get_base_fields(self) -> list[str]:
+        return self.VALID_STATUSES
+
     def get_context_data(self, **kwargs) -> dict[str, Any]:
         context = super().get_context_data(**kwargs)
-        context["order"] = AnalysisOrder.objects.get(pk=self.kwargs.get("pk"))
+        order = self.get_order()
+        samples = self.get_table_data()
+
+        # Instantiate the filter with the current GET parameters
+        filterset = self.filterset_class(self.request.GET, queryset=samples)
+        self.object_list = filterset.qs  # Ensures get_table uses the filtered queryset
+        table = self.get_table()
+
+        context.update(
+            {
+                "order": order,
+                "statuses": self.get_base_fields(),
+                "filter": filterset,
+                "table": table,
+            }
+        )
         return context
 
+    def get_success_url(self) -> str:
+        return reverse(
+            "staff:order-analysis-samples", kwargs={"pk": self.get_order().pk}
+        )
+
+    def post(self, request: HttpRequest, *args, **kwargs) -> HttpResponse:
+        status_name = request.POST.get("status")
+        selected_ids = request.POST.getlist(f"checked-analysis-{self.get_order().pk}")
+
+        if not selected_ids:
+            messages.error(request, "No samples selected.")
+            return HttpResponseRedirect(self.get_success_url())
+
+        order = self.get_order()
+
+        # Get the selected samples
+        analyses = SampleMarkerAnalysis.objects.filter(id__in=selected_ids)
+
+        if status_name:
+            self.assign_status_to_samples(analyses, status_name, request)
+            if status_name == self.OUTPUT:
+                self.check_all_output(SampleMarkerAnalysis.objects.filter(order=order))
+            else:
+                self.get_order().to_processing()
+        return HttpResponseRedirect(self.get_success_url())
+
+    def statuses_with_lower_or_equal_priority(self, status_name: str) -> list[str]:
+        index = self.VALID_STATUSES.index(status_name)
+        return self.VALID_STATUSES[: index + 1]
+
+    def assign_status_to_samples(
+        self,
+        analyses: models.QuerySet,
+        status_name: str,
+        request: HttpRequest,
+    ) -> None:
+        if status_name not in self.VALID_STATUSES:
+            messages.error(request, f"Status '{status_name}' is not valid.")
+            return
+
+        statuses_to_turn_on = self.statuses_with_lower_or_equal_priority(status_name)
+
+        if status_name == self.PCR:
+            field_name = "has_pcr"
+        elif status_name == self.ANALYSED:
+            field_name = "is_analysed"
+        else:
+            field_name = "is_outputted"
+
+        samples_to_turn_off_ids = list(
+            analyses.filter(**{field_name: True}).values_list("id", flat=True)
+        )
+        samples_to_turn_on_ids = list(
+            analyses.filter(**{field_name: False}).values_list("id", flat=True)
+        )
+
+        SampleMarkerAnalysis.objects.filter(id__in=samples_to_turn_off_ids).update(
+            **{field_name: False}
+        )
+
+        update_dict = {}
+        if self.PCR in statuses_to_turn_on:
+            update_dict["has_pcr"] = True
+        if self.ANALYSED in statuses_to_turn_on:
+            update_dict["is_analysed"] = True
+        if self.OUTPUT in statuses_to_turn_on:
+            update_dict["is_outputted"] = True
+
+        SampleMarkerAnalysis.objects.filter(id__in=samples_to_turn_on_ids).update(
+            **update_dict
+        )
+        messages.success(
+            request,
+            f"Set statuses {', '.join(statuses_to_turn_on)} for {analyses.count()} analyses.",  # noqa: E501
+        )
+
+    # Checks if all samples in the order have output
+    # If they are, it updates the order status to completed
+    def check_all_output(self, analyses: models.QuerySet) -> None:
+        if not analyses.filter(is_outputted=False).exists():
+            self.get_order().to_next_status()
+            messages.success(
+                self.request,
+                "All samples have an output. The order status is updated to completed.",
+            )
+        elif self.get_order().status == Order.OrderStatus.COMPLETED:
+            self.get_order().to_processing()
+            messages.success(
+                self.request,
+                "Not all samples have output. The order status is updated to processing.",  # noqa: E501
+            )
+
 
 class SamplesListView(StaffMixin, SingleTableMixin, FilterView):
     table_pagination = False