Brought back Sample list page

src/staff/filters.py

@@ -131,17 +131,10 @@ def __init__(
     class Meta:
         model = Sample
         fields = [
-            # "order",
-            # "guid",
             "genlab_id",
             "name",
             "species",
             "type",
-            # "year",
-            # "location",
-            # "pop_id",
-            # "type",
-            # "desired_extractions",
         ]
 
 
@@ -210,10 +203,6 @@ def __init__(
     class Meta:
         model = Sample
         fields = [
-            # "order",
-            # "order__status",
-            # "order__genrequest__project",
-            "guid",
             "name",
             "genlab_id",
             "species",
@@ -222,8 +211,6 @@ class Meta:
             "location",
             "pop_id",
             "type",
-            # "desired_extractions",
-            "plate_positions__plate",
         ]
 
 

src/staff/tables.py

@@ -328,21 +328,6 @@ def render_sample__plate_positions(self, value: Any) -> str:
         return ""
 
 
-class SampleTable(SampleBaseTable):
-    genlab_id = tables.Column(
-        linkify=("staff:samples-detail", {"pk": tables.A("id")}),
-        orderable=False,
-        empty_values=(),
-    )
-
-    class Meta(SampleBaseTable.Meta):
-        fields = SampleBaseTable.Meta.fields + [
-            "order",
-            "order__status",
-            "order__genrequest__project",
-        ]
-
-
 class PlateTable(tables.Table):
     id = tables.Column(
         linkify=("staff:plates-detail", {"pk": tables.A("id")}),
@@ -388,6 +373,126 @@ def render_status(self, value: Order.OrderStatus, record: Order) -> str:
         )
 
 
+class StatusMixinTableSamples(tables.Table):
+    sample_status = tables.Column(
+        verbose_name="Sample Status", empty_values=(), orderable=True
+    )
+
+    order__status = tables.Column(
+        verbose_name="Order Status", empty_values=(), orderable=True
+    )
+
+    def render_order__status(self, value: Order.OrderStatus, record: Order) -> str:
+        status_colors = {
+            "Processing": "bg-yellow-100 text-yellow-800",
+            "Completed": "bg-green-100 text-green-800",
+            "Delivered": "bg-red-100 text-red-800",
+        }
+        status_text = {
+            "Processing": "Processing",
+            "Completed": "Completed",
+            "Delivered": "Not started",
+        }
+        color_class = status_colors.get(value, "bg-gray-100 text-gray-800")
+        status_text = status_text.get(value, "Unknown")
+        return mark_safe(  # noqa: S308
+            f'<span class="px-2 py-1 text-xs font-medium rounded-full whitespace-nowrap {color_class}">{status_text}</span>'  # noqa: E501
+        )
+
+    def render_sample_status(self, value: Any, record: Sample) -> str:
+        order = record.order
+
+        # Determine status label
+        if isinstance(order, ExtractionOrder):
+            if record.is_isolated:
+                status = "Isolated"
+            elif record.is_plucked:
+                status = "Plucked"
+            elif record.is_marked:
+                status = "Marked"
+            else:
+                status = "Not started"
+        else:
+            status = getattr(order, "sample_status", "Unknown")
+
+        # Define color map
+        status_colors = {
+            "Marked": "bg-orange-100 text-orange-800",
+            "Plucked": "bg-yellow-100 text-yellow-800",
+            "Isolated": "bg-green-100 text-green-800",
+            "Not started": "bg-red-100 text-red-800",
+            "Unknown": "bg-gray-100 text-gray-800",
+        }
+
+        # Use computed status, not value
+        color_class = status_colors.get(status, "bg-gray-100 text-gray-800")
+
+        return mark_safe(  # noqa: S308
+            f'<span class="px-2 py-1 text-xs font-medium rounded-full whitespace-nowrap {color_class}">{status}</span>'  # noqa: E501
+        )
+
+
+class SampleTable(SampleBaseTable, StatusMixinTableSamples):
+    STATUS_PRIORITY = {
+        "Not started": 0,
+        "Marked": 1,
+        "Plucked": 2,
+        "Isolated": 3,
+    }
+
+    genlab_id = tables.Column(
+        linkify=("staff:samples-detail", {"pk": tables.A("id")}),
+        orderable=False,
+        empty_values=(),
+    )
+
+    sample_status = tables.Column(
+        verbose_name="Sample Status", empty_values=(), orderable=True
+    )
+
+    order__status = tables.Column(
+        verbose_name="Order Status", empty_values=(), orderable=True
+    )
+
+    class Meta(SampleBaseTable.Meta):
+        fields = SampleBaseTable.Meta.fields + [
+            "order",
+            "order__status",
+            "order__genrequest__project",
+            "order__responsible_staff",
+        ]
+        sequence = SampleBaseTable.Meta.sequence + (
+            "sample_status",
+            "order",
+            "order__status",
+            "order__responsible_staff",
+            "notes",
+        )
+        exclude = ("guid", "plate_positions", "checked", "is_prioritised")
+
+    def order_sample_status(
+        self, records: Sequence[Any], is_descending: bool
+    ) -> tuple[list[Any], bool]:
+        def get_status_value(record: Any) -> int:
+            if isinstance(record.order, ExtractionOrder):
+                if record.is_isolated:
+                    return self.STATUS_PRIORITY["Isolated"]
+                elif record.is_plucked:
+                    return self.STATUS_PRIORITY["Plucked"]
+                elif record.is_marked:
+                    return self.STATUS_PRIORITY["Marked"]
+                else:
+                    return self.STATUS_PRIORITY["Not started"]
+            else:
+                # fallback for other types of orders
+                return self.STATUS_PRIORITY.get(
+                    getattr(record.order, "sample_status", ""), -1
+                )
+
+        sorted_records = sorted(records, key=get_status_value, reverse=is_descending)
+        return (sorted_records, True)
+
+
 class StaffIDMixinTable(tables.Table):
     id = tables.Column(
         orderable=False,

src/staff/templates/staff/sample_filter.html

@@ -55,17 +55,35 @@
       {% render_table table %}
   </form>
 
-  <form id="prioritise-form" method="post" action="{% url 'staff:order-extraction-samples' pk=order.pk %}" style="display:none;">
-    {% csrf_token %}
-    <input type="hidden" name="sample_id" id="prioritise-sample-id">
-  </form>
+{% else %}
+
+<form method="get" class="py-3 px-4 border mb-3 ">
+  <div class="flex flex-wrap gap-4">
+      {{ filter.form | crispy }}
+  <button class="btn custom_order_button_blue mt-6" type="submit">Search</button>
+  </div>
+</form>
+<input type="hidden" name="sort" value="{{ request.GET.sort|default:'' }}">
+
+{% render_table table %}
 {% endif %}
+
+<form id="prioritise-form" method="post" style="display:none;">
+  {% csrf_token %}
+  <input type="hidden" name="sample_id" id="prioritise-sample-id">
+  <input type="hidden" name="next" id="prioritise-next-url" value="{{ request.get_full_path }}">
+</form>
+
 <script>
     document.addEventListener("DOMContentLoaded", function () {
       document.querySelectorAll('.toggle-prioritise').forEach(btn => {
         btn.addEventListener('click', function () {
           const sampleId = this.dataset.sampleId;
+          const orderId = this.dataset.orderId;
           const form = document.getElementById('prioritise-form');
+          const actionUrl = `/staff/orders/extraction/${orderId}/samples/`;
+          form.action = actionUrl;
+          form.querySelector('#prioritise-next-url').value = window.location.href;
           form.querySelector('#prioritise-sample-id').value = sampleId;
           form.submit();
         });

src/staff/views.py

@@ -7,7 +7,7 @@
 from django.db.models.functions import Cast
 from django.forms import Form
 from django.http import HttpRequest, HttpResponse, HttpResponseRedirect, JsonResponse
-from django.shortcuts import get_object_or_404
+from django.shortcuts import get_object_or_404, redirect
 from django.urls import reverse, reverse_lazy
 from django.utils.timezone import now
 from django.utils.translation import gettext as _
@@ -275,6 +275,10 @@ def post(self, request: HttpRequest, *args, **kwargs) -> HttpResponse:
             sample.is_prioritised = not sample.is_prioritised
             sample.save()
 
+        next_url = request.POST.get("next")
+        if next_url:
+            return redirect(next_url)
+
         return self.get(
             request, *args, **kwargs
         )  # Re-render the view with updated data
@@ -311,6 +315,8 @@ def get_context_data(self, **kwargs) -> dict[str, Any]:
 
 
 class SamplesListView(StaffMixin, SingleTableMixin, FilterView):
+    table_pagination = False
+
     model = Sample
     table_class = SampleTable
     filterset_class = SampleFilter
@@ -327,7 +333,10 @@ def get_queryset(self) -> models.QuerySet[Sample]:
                 "order__genrequest",
                 "order__genrequest__project",
             )
-            .prefetch_related("plate_positions")
+            .prefetch_related(
+                "plate_positions",
+                "order__responsible_staff",
+            )
             .exclude(order__status=Order.OrderStatus.DRAFT)
             .order_by("species__name", "year", "location__name", "name")
         )