-
- {% for order in delivered_orders %}
- {% if order.polymorphic_ctype.model == 'analysisorder' %}
-
- {% elif order.polymorphic_ctype.model == 'equipmentorder' %}
-
- {% elif order.polymorphic_ctype.model == 'extractionorder' %}
-
+
+ {% urgent_orders_table area=area %}
+ {% new_unseen_orders_table area=area %}
+ {% new_seen_orders_table area=area %}
- {% endif %}
- {% if urgent_orders|length > 0 %}
-
-
Urgent orders
+
- {% else %}
-
-
Urgent orders
-
No urgent orders found.
-
- {% endif %}
+
{% endblock %}
diff --git a/src/staff/templates/staff/equipmentorder_detail.html b/src/staff/templates/staff/equipmentorder_detail.html
index bb7bb54a..7f76f07b 100644
--- a/src/staff/templates/staff/equipmentorder_detail.html
+++ b/src/staff/templates/staff/equipmentorder_detail.html
@@ -33,6 +33,8 @@
Requested Equipment
{% /table %}
+
+
Assign staff
{% comment %}
{% if object.status == 'draft' %}
Edit
diff --git a/src/staff/templates/staff/equipmentorder_filter.html b/src/staff/templates/staff/equipmentorder_filter.html
index 25b2704d..434f0c13 100644
--- a/src/staff/templates/staff/equipmentorder_filter.html
+++ b/src/staff/templates/staff/equipmentorder_filter.html
@@ -1,5 +1,19 @@
{% extends "staff/base_filter.html" %}
+{% load crispy_forms_tags static %}
+{% load render_table from django_tables2 %}
{% block page-title %}
Equipment Orders
{% endblock page-title %}
+
+{% block page-inner %}
+
+
+{% render_table table %}
+
+{% endblock page-inner %}
diff --git a/src/staff/templates/staff/extractionorder_detail.html b/src/staff/templates/staff/extractionorder_detail.html
index 08ae63cc..cf21b4c0 100644
--- a/src/staff/templates/staff/extractionorder_detail.html
+++ b/src/staff/templates/staff/extractionorder_detail.html
@@ -3,36 +3,55 @@
{% block content %}
- {% fragment as table_header %}
- {% #table-cell header=True %}GUID{% /table-cell %}
- {% #table-cell header=True %}Type{% /table-cell %}
- {% #table-cell header=True %}Species{% /table-cell %}
- {% #table-cell header=True %}Markers{% /table-cell %}
- {% #table-cell header=True %}Location{% /table-cell %}
- {% #table-cell header=True %}Date{% /table-cell %}
- {% #table-cell header=True %}Volume{% /table-cell %}
- {% endfragment %}
Order {{ object }}
-
-
-
- {% object-detail object=object %}
-
-
-
Delivered Samples
-
-
{{ object.samples.count }} samples were delivered
-
+
Samples
+ {% if analysis_orders|length > 1 %}
+
+
+ Go to Analysis Order
+
+
+
+ {% for ao in analysis_orders %}
+
+ {{ ao }}
+
+ {% endfor %}
+
+
+ {% elif analysis_orders|length == 1 %}
+
Go to {{ analysis_orders.first}}
+ {% endif %}
+
Assign staff
+
+
+
+ {% if not object.is_seen %}
+
+ {% endif %}
+
{% if object.status == object.OrderStatus.DELIVERED %}
-
{% url 'staff:order-manually-checked' pk=object.id as confirm_check_url %}
- {% url 'staff:order-to-draft' pk=object.id as to_draft_url %}
-
{% action-button action=confirm_check_url class="bg-secondary text-white" submit_text="Confirm - Order checked" csrf_token=csrf_token %}
+ {% endif %}
+
+ {% if object.status != object.OrderStatus.DRAFT %}
+ {% url 'staff:order-to-draft' pk=object.id as to_draft_url %}
{% action-button action=to_draft_url class="bg-secondary text-white" submit_text="Convert to draft" csrf_token=csrf_token %}
{% endif %}
@@ -43,4 +62,21 @@
Delivered Samples
{% endwith %}
{% endif %}
+
+ {% fragment as table_header %}
+ {% #table-cell header=True %}GUID{% /table-cell %}
+ {% #table-cell header=True %}Type{% /table-cell %}
+ {% #table-cell header=True %}Species{% /table-cell %}
+ {% #table-cell header=True %}Markers{% /table-cell %}
+ {% #table-cell header=True %}Location{% /table-cell %}
+ {% #table-cell header=True %}Date{% /table-cell %}
+ {% #table-cell header=True %}Volume{% /table-cell %}
+ {% endfragment %}
+
+ {% object-detail object=object %}
+
+
Delivered Samples
+
+
{{ object.samples.count }} samples were delivered
+
{% endblock %}
diff --git a/src/staff/templates/staff/extractionorder_filter.html b/src/staff/templates/staff/extractionorder_filter.html
index f0ff30b7..e2c1e8d9 100644
--- a/src/staff/templates/staff/extractionorder_filter.html
+++ b/src/staff/templates/staff/extractionorder_filter.html
@@ -1,5 +1,19 @@
{% extends "staff/base_filter.html" %}
+{% load crispy_forms_tags static %}
+{% load render_table from django_tables2 %}
{% block page-title %}
Extraction Orders
{% endblock page-title %}
+
+{% block page-inner %}
+
+
+{% render_table table %}
+
+{% endblock page-inner %}
diff --git a/src/staff/templates/staff/extractionplate_filter.html b/src/staff/templates/staff/extractionplate_filter.html
index 877fca41..26e046dd 100644
--- a/src/staff/templates/staff/extractionplate_filter.html
+++ b/src/staff/templates/staff/extractionplate_filter.html
@@ -1,4 +1,6 @@
{% extends "staff/base_filter.html" %}
+{% load crispy_forms_tags static %}
+{% load render_table from django_tables2 %}
{% block page-title %}
Extraction plates
@@ -8,4 +10,13 @@
+
+
+
+{% render_table table %}
{% endblock page-inner %}
diff --git a/src/staff/templates/staff/note_input_column.html b/src/staff/templates/staff/note_input_column.html
new file mode 100644
index 00000000..c98206c3
--- /dev/null
+++ b/src/staff/templates/staff/note_input_column.html
@@ -0,0 +1,7 @@
+
diff --git a/src/staff/templates/staff/order_staff_edit.html b/src/staff/templates/staff/order_staff_edit.html
new file mode 100644
index 00000000..efeab57b
--- /dev/null
+++ b/src/staff/templates/staff/order_staff_edit.html
@@ -0,0 +1,50 @@
+{% extends 'base.html' %}
+{% load crispy_forms_tags core %}
+
+{% block css %}
+
+{% endblock %}
+
+{% block content %}
+
Manage Responsible Staff - {{ object }}
+
+
+
+
+
Assign Staff to Order
+
+
+{% endblock %}
diff --git a/src/staff/templates/staff/prioritise_flag.html b/src/staff/templates/staff/prioritise_flag.html
new file mode 100644
index 00000000..36eb56ca
--- /dev/null
+++ b/src/staff/templates/staff/prioritise_flag.html
@@ -0,0 +1,3 @@
+
+
diff --git a/src/staff/templates/staff/project_detail.html b/src/staff/templates/staff/project_detail.html
index bcd80534..1a6b19e3 100644
--- a/src/staff/templates/staff/project_detail.html
+++ b/src/staff/templates/staff/project_detail.html
@@ -4,14 +4,16 @@
{% block content %}
Project {{ object }}
-
-
-
- {% object-detail object=object %}
+
{% url 'staff:projects-verify' pk=object.pk as verify_url %}
- {% action-button action=verify_url class="btn-secondary text-white" submit_text="Mark as verified" csrf_token=csrf_token %}
+ {% if object.verified_at is null %}
+ {% action-button action=verify_url class="btn-secondary text-white" submit_text="Mark as verified" csrf_token=csrf_token %}
+ {% endif %}
+
+ {% object-detail object=object %}
+
{% endblock %}
diff --git a/src/staff/templates/staff/project_filter.html b/src/staff/templates/staff/project_filter.html
index 22279374..b0434b4c 100644
--- a/src/staff/templates/staff/project_filter.html
+++ b/src/staff/templates/staff/project_filter.html
@@ -1,5 +1,19 @@
{% extends "staff/base_filter.html" %}
+{% load crispy_forms_tags static %}
+{% load render_table from django_tables2 %}
{% block page-title %}
Projects
{% endblock page-title %}
+
+{% block page-inner %}
+
+
+{% render_table table %}
+
+{% endblock page-inner %}
diff --git a/src/staff/templates/staff/sample_filter.html b/src/staff/templates/staff/sample_filter.html
index 7fc5448f..430cc1b9 100644
--- a/src/staff/templates/staff/sample_filter.html
+++ b/src/staff/templates/staff/sample_filter.html
@@ -1,7 +1,22 @@
{% extends "staff/base_filter.html" %}
+{% load crispy_forms_tags static %}
+{% load render_table from django_tables2 %}
{% block page-title %}
-{% if order %}{{ order }} - Samples{% else %}Samples{% endif %}
+
+
+ {% if order %}
+ {{ order }} - Samples
+ {% else %}
+ Samples
+ {% endif %}
+
+ {% if order %}
+
+ {{ order.filled_genlab_count }} / {{ order.samples.count }} Genlabs generated
+
+ {% endif %}
+
{% endblock page-title %}
{% block page-inner %}
@@ -9,6 +24,36 @@
+
+
+
+
{% endif %}
+
{% endblock page-inner %}
diff --git a/src/staff/templates/staff/sample_lab.html b/src/staff/templates/staff/sample_lab.html
new file mode 100644
index 00000000..47368e3c
--- /dev/null
+++ b/src/staff/templates/staff/sample_lab.html
@@ -0,0 +1,85 @@
+{% extends "staff/base.html" %}
+{% load render_table from django_tables2 %}
+
+{% block content %}
+
{% block page-title %}{% if order %}{{ order }} - Samples{% else %}Samples{% endif %}{% endblock page-title %}
+{% block page-inner %}
+
+
+{% endblock page-inner %}
+
+
+{% endblock content %}
diff --git a/src/staff/templates/staff/samplemarkeranalysis_filter.html b/src/staff/templates/staff/samplemarkeranalysis_filter.html
index 4f81078d..227e0a18 100644
--- a/src/staff/templates/staff/samplemarkeranalysis_filter.html
+++ b/src/staff/templates/staff/samplemarkeranalysis_filter.html
@@ -1,4 +1,6 @@
{% extends "staff/base_filter.html" %}
+{% load crispy_forms_tags static %}
+{% load render_table from django_tables2 %}
{% block page-title %}
{% if order %}{{ order }} - Samples{% else %}Samples{% endif %}
@@ -10,4 +12,14 @@
{% endif %}
+
+
+
+{% render_table table %}
+
{% endblock page-inner %}
diff --git a/src/staff/templatetags/__init__.py b/src/staff/templatetags/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/staff/templatetags/order_tags.py b/src/staff/templatetags/order_tags.py
new file mode 100644
index 00000000..77f63f48
--- /dev/null
+++ b/src/staff/templatetags/order_tags.py
@@ -0,0 +1,188 @@
+from django import template
+from django.db import models
+
+from genlab_bestilling.models import Area, Order
+
+from ..tables import (
+ AssignedOrderTable,
+ DraftOrderTable,
+ NewSeenOrderTable,
+ NewUnseenOrderTable,
+ UrgentOrderTable,
+)
+
+register = template.Library()
+
+
+@register.inclusion_tag("staff/components/order_table.html", takes_context=True)
+def urgent_orders_table(context: dict, area: Area | None = None) -> dict:
+ urgent_orders = (
+ Order.objects.filter(
+ is_urgent=True,
+ )
+ .exclude(status=Order.OrderStatus.DRAFT)
+ .select_related("genrequest")
+ )
+
+ if area:
+ urgent_orders = urgent_orders.filter(genrequest__area=area)
+
+ urgent_orders = urgent_orders.order_by(
+ models.Case(
+ models.When(status=Order.OrderStatus.PROCESSING, then=0),
+ models.When(status=Order.OrderStatus.DELIVERED, then=1),
+ models.When(status=Order.OrderStatus.COMPLETED, then=2),
+ default=3,
+ output_field=models.IntegerField(),
+ ),
+ "-created_at",
+ )
+
+ return {
+ "title": "Urgent orders",
+ "table": UrgentOrderTable(urgent_orders),
+ "count": urgent_orders.count(),
+ "request": context.get("request"),
+ }
+
+
+@register.inclusion_tag("staff/components/order_table.html", takes_context=True)
+def new_seen_orders_table(context: dict, area: Area | None = None) -> dict:
+ new_orders = (
+ Order.objects.filter(status=Order.OrderStatus.DELIVERED, is_seen=True)
+ .exclude(is_urgent=True)
+ .select_related("genrequest")
+ .annotate(
+ sample_count=models.Case(
+ models.When(
+ extractionorder__isnull=False,
+ then=models.Count("extractionorder__samples", distinct=True),
+ ),
+ models.When(
+ analysisorder__isnull=False,
+ then=models.Count("analysisorder__samples", distinct=True),
+ ),
+ default=0,
+ ),
+ priority=models.Case(
+ models.When(is_urgent=True, then=Order.OrderPriority.URGENT),
+ models.When(is_prioritized=True, then=Order.OrderPriority.PRIORITIZED),
+ default=1,
+ ),
+ )
+ )
+
+ if area:
+ new_orders = new_orders.filter(genrequest__area=area)
+
+ new_orders = new_orders.order_by("-priority", "-created_at")
+
+ return {
+ "title": "New seen orders",
+ "table": NewSeenOrderTable(new_orders),
+ "count": new_orders.count(),
+ "request": context.get("request"),
+ }
+
+
+@register.inclusion_tag("staff/components/order_table.html", takes_context=True)
+def new_unseen_orders_table(context: dict, area: Area | None = None) -> dict:
+ new_orders = (
+ Order.objects.filter(status=Order.OrderStatus.DELIVERED, is_seen=False)
+ .exclude(is_urgent=True)
+ .select_related("genrequest")
+ .annotate(
+ sample_count=models.Case(
+ models.When(
+ extractionorder__isnull=False,
+ then=models.Count("extractionorder__samples", distinct=True),
+ ),
+ models.When(
+ analysisorder__isnull=False,
+ then=models.Count("analysisorder__samples", distinct=True),
+ ),
+ default=0,
+ )
+ )
+ )
+
+ if area:
+ new_orders = new_orders.filter(genrequest__area=area)
+
+ new_orders = new_orders.order_by("-created_at")
+
+ return {
+ "title": "New unseen orders",
+ "table": NewUnseenOrderTable(new_orders),
+ "count": new_orders.count(),
+ "request": context.get("request"),
+ }
+
+
+@register.inclusion_tag("staff/components/order_table.html", takes_context=True)
+def assigned_orders_table(context: dict) -> dict:
+ user = context.get("user")
+
+ assigned_orders = (
+ Order.objects.filter(
+ status__in=[
+ Order.OrderStatus.PROCESSING,
+ Order.OrderStatus.DELIVERED,
+ Order.OrderStatus.COMPLETED,
+ ],
+ responsible_staff=user,
+ )
+ .select_related("genrequest")
+ .annotate(
+ sample_count=models.Count("extractionorder__samples", distinct=True),
+ priority=models.Case(
+ models.When(is_urgent=True, then=Order.OrderPriority.URGENT),
+ models.When(is_prioritized=True, then=Order.OrderPriority.PRIORITIZED),
+ default=1,
+ ),
+ )
+ .order_by(
+ models.Case(
+ models.When(status=Order.OrderStatus.PROCESSING, then=0),
+ models.When(status=Order.OrderStatus.DELIVERED, then=1),
+ models.When(status=Order.OrderStatus.COMPLETED, then=2),
+ default=3,
+ output_field=models.IntegerField(),
+ ),
+ "-priority",
+ "-created_at",
+ )
+ )
+
+ return {
+ "title": "My orders",
+ "table": AssignedOrderTable(assigned_orders),
+ "count": assigned_orders.count(),
+ "request": context.get("request"),
+ }
+
+
+@register.inclusion_tag("staff/components/order_table.html", takes_context=True)
+def draft_orders_table(context: dict, area: Area) -> dict:
+ draft_orders = (
+ Order.objects.filter(status=Order.OrderStatus.DRAFT)
+ .select_related("genrequest")
+ .annotate(
+ sample_count=models.Count("extractionorder__samples", distinct=True),
+ priority=models.Case(
+ models.When(is_urgent=True, then=Order.OrderPriority.URGENT),
+ default=1,
+ ),
+ )
+ .order_by("-priority", "-created_at")
+ )
+
+ if area:
+ draft_orders = draft_orders.filter(genrequest__area=area)
+
+ return {
+ "title": "Draft orders",
+ "table": DraftOrderTable(draft_orders),
+ "count": draft_orders.count(),
+ "request": context.get("request"),
+ }
diff --git a/src/staff/urls.py b/src/staff/urls.py
index a3dbf599..b43c512e 100644
--- a/src/staff/urls.py
+++ b/src/staff/urls.py
@@ -11,17 +11,23 @@
ExtractionPlateCreateView,
ExtractionPlateDetailView,
ExtractionPlateListView,
+ GenerateGenlabIDsView,
ManaullyCheckedOrderActionView,
+ MarkAsSeenView,
OrderAnalysisSamplesListView,
OrderExtractionSamplesListView,
+ OrderPrioritizedAdminView,
OrderToDraftActionView,
OrderToNextStatusActionView,
ProjectDetailView,
ProjectListView,
ProjectValidateActionView,
SampleDetailView,
+ SampleLabView,
SampleReplicaActionView,
SamplesListView,
+ StaffEditView,
+ UpdateInternalNote,
)
app_name = "staff"
@@ -68,11 +74,31 @@
ManaullyCheckedOrderActionView.as_view(),
name="order-manually-checked",
),
+ path(
+ "
//add-staff/",
+ StaffEditView.as_view(),
+ name="add-staff",
+ ),
path(
"orders/extraction//samples/",
OrderExtractionSamplesListView.as_view(),
name="order-extraction-samples",
),
+ path(
+ "orders/extraction//samples/lab",
+ SampleLabView.as_view(),
+ name="order-extraction-samples-lab",
+ ),
+ path(
+ "orders/extraction//samples/generate-genlab-ids/",
+ GenerateGenlabIDsView.as_view(),
+ name="generate-genlab-ids",
+ ),
+ path(
+ "orders/samples/update/internal-note/",
+ UpdateInternalNote.as_view(),
+ name="update-internal-note",
+ ),
path(
"orders/analysis//samples/",
OrderAnalysisSamplesListView.as_view(),
@@ -98,6 +124,11 @@
EquipmentOrderDetailView.as_view(),
name="order-equipment-detail",
),
+ path(
+ "order/mark-as-seen//",
+ MarkAsSeenView.as_view(),
+ name="mark-as-seen",
+ ),
path(
"orders/extraction//",
ExtractionOrderDetailView.as_view(),
@@ -118,4 +149,9 @@
ExtractionPlateDetailView.as_view(),
name="plates-detail",
),
+ path(
+ "orders//priority/",
+ OrderPrioritizedAdminView.as_view(),
+ name="order-priority",
+ ),
]
diff --git a/src/staff/views.py b/src/staff/views.py
index 5bf21248..7b44831f 100644
--- a/src/staff/views.py
+++ b/src/staff/views.py
@@ -1,11 +1,14 @@
+from collections import defaultdict
from typing import Any
from django.contrib import messages
from django.contrib.auth.mixins import LoginRequiredMixin, UserPassesTestMixin
from django.db import models
+from django.db.models import Count
from django.forms import Form
-from django.http import HttpRequest, HttpResponse, HttpResponseRedirect
-from django.urls import reverse_lazy
+from django.http import HttpRequest, HttpResponse, HttpResponseRedirect, JsonResponse
+from django.shortcuts import get_object_or_404
+from django.urls import reverse, reverse_lazy
from django.utils.timezone import now
from django.utils.translation import gettext as _
from django.views.generic import CreateView, DetailView, TemplateView
@@ -15,12 +18,17 @@
from genlab_bestilling.models import (
AnalysisOrder,
+ Area,
EquipmentOrder,
ExtractionOrder,
ExtractionPlate,
+ Genrequest,
+ IsolationMethod,
Order,
Sample,
+ SampleIsolationMethod,
SampleMarkerAnalysis,
+ SampleStatusAssignment,
)
from nina.models import Project
from shared.views import ActionView
@@ -32,7 +40,7 @@
SampleFilter,
SampleMarkerOrderFilter,
)
-from .forms import ExtractionPlateForm
+from .forms import ExtractionPlateForm, OrderStaffForm
from .tables import (
AnalysisOrderTable,
EquipmentOrderTable,
@@ -41,6 +49,7 @@
OrderExtractionSampleTable,
PlateTable,
ProjectTable,
+ SampleStatusTable,
SampleTable,
)
@@ -61,19 +70,25 @@ def test_func(self) -> bool:
class DashboardView(StaffMixin, TemplateView):
template_name = "staff/dashboard.html"
- def get_context_data(self, **kwargs) -> dict[str, Any]:
- context = super().get_context_data(**kwargs)
+ def get_area_from_query(self) -> Area | None:
+ area_id = self.request.GET.get("area")
+ if area_id:
+ try:
+ return Area.objects.get(pk=area_id)
+ except Area.DoesNotExist:
+ return None
+ return None
- urgent_orders = Order.objects.filter(
- is_urgent=True,
- status__in=[Order.OrderStatus.PROCESSING, Order.OrderStatus.DELIVERED],
- ).order_by("-created_at")
- context["urgent_orders"] = urgent_orders
+ def get_areas(self) -> models.QuerySet[Area]:
+ return Area.objects.all().order_by("name")
- delivered_orders = Order.objects.filter(status=Order.OrderStatus.DELIVERED)
+ def get_context_data(self, **kwargs) -> dict[str, Any]:
+ context = super().get_context_data(**kwargs)
- context["delivered_orders"] = delivered_orders
context["now"] = now()
+ context["areas"] = self.get_areas()
+ context["area"] = self.get_area_from_query()
+
return context
@@ -113,6 +128,7 @@ def get_queryset(self) -> models.QuerySet[ExtractionOrder]:
"genrequest__area",
)
.prefetch_related("species", "sample_types")
+ .annotate(sample_count=Count("samples"))
)
@@ -154,14 +170,50 @@ def get_queryset(self) -> models.QuerySet[EquipmentOrder]:
class AnalysisOrderDetailView(StaffMixin, DetailView):
model = AnalysisOrder
+ def get_context_data(self, **kwargs: Any) -> dict[str, Any]:
+ context = super().get_context_data(**kwargs)
+ analysis_order = self.object
+ context["extraction_order"] = analysis_order.from_order
+ return context
+
class EquipmentOrderDetailView(StaffMixin, DetailView):
model = EquipmentOrder
+class MarkAsSeenView(StaffMixin, DetailView):
+ model = Order
+
+ def get_object(self) -> Order:
+ return Order.objects.get(pk=self.kwargs["pk"])
+
+ def post(self, request: HttpRequest, *args, **kwargs) -> HttpResponse:
+ try:
+ order = self.get_object()
+ order.toggle_seen()
+ messages.success(request, _("Order is marked as seen"))
+ except Exception as e:
+ messages.error(request, f"Error: {str(e)}")
+
+ return_to = request.POST.get("return_to")
+ return HttpResponseRedirect(self.get_return_url(return_to))
+
+ def get_return_url(self, return_to: str) -> str:
+ if return_to == "dashboard":
+ return reverse("staff:dashboard")
+ else:
+ return self.get_object().get_absolute_staff_url()
+
+
class ExtractionOrderDetailView(StaffMixin, DetailView):
model = ExtractionOrder
+ def get_context_data(self, **kwargs: Any) -> dict[str, Any]:
+ context = super().get_context_data(**kwargs)
+ extraction_order = self.object
+ context["analysis_orders"] = extraction_order.analysis_orders.all()
+ return context
+
class OrderExtractionSamplesListView(StaffMixin, SingleTableMixin, FilterView):
table_pagination = False
@@ -185,6 +237,18 @@ def get_context_data(self, **kwargs) -> dict[str, Any]:
context["order"] = ExtractionOrder.objects.get(pk=self.kwargs.get("pk"))
return context
+ def post(self, request: HttpRequest, *args, **kwargs) -> HttpResponse:
+ sample_id = request.POST.get("sample_id")
+
+ if sample_id:
+ sample = get_object_or_404(Sample, pk=sample_id)
+ sample.is_prioritised = not sample.is_prioritised
+ sample.save()
+
+ return self.get(
+ request, *args, **kwargs
+ ) # Re-render the view with updated data
+
class OrderAnalysisSamplesListView(StaffMixin, SingleTableMixin, FilterView):
table_pagination = False
@@ -243,6 +307,184 @@ class SampleDetailView(StaffMixin, DetailView):
model = Sample
+class SampleLabView(StaffMixin, TemplateView):
+ disable_pagination = False
+ template_name = "staff/sample_lab.html"
+ table_class = SampleStatusTable
+
+ def get_order(self) -> ExtractionOrder:
+ if not hasattr(self, "_order"):
+ self._order = get_object_or_404(ExtractionOrder, pk=self.kwargs["pk"])
+ return self._order
+
+ def get_data(self) -> list[Sample]:
+ order = self.get_order()
+ samples = Sample.objects.filter(order=order, genlab_id__isnull=False)
+ sample_status = SampleStatusAssignment.SampleStatus.choices
+
+ # Fetch all SampleStatusAssignment entries related to the current order
+ sample_assignments = SampleStatusAssignment.objects.filter(order_id=order.id)
+
+ # Build a lookup: {sample_id: set of status names}
+ # This allows us to check status presence without querying per sample
+ sample_status_map = defaultdict(set)
+ for assignment in sample_assignments:
+ name = str(assignment.status)
+
+ sample_status_map[assignment.sample_id].add(name)
+
+ # Annotate each sample instance with boolean flags per status
+ # Equivalent to: sample.status_name = True/False
+ # based on whether the sample has that status
+ for sample in samples:
+ sample.selected_isolation_method = (
+ sample.isolation_method.first()
+ if sample.isolation_method.exists()
+ else None
+ )
+ status_names = sample_status_map.get(sample.id, set())
+ for status, _i in sample_status:
+ setattr(sample, status, status in status_names)
+
+ return samples
+
+ def get_isolation_methods(self) -> list[str]:
+ order = self.get_order()
+ 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
+ )
+
+ def get_base_fields(self) -> list[str]:
+ return [v for v, _ in SampleStatusAssignment.SampleStatus.choices]
+
+ def get_context_data(self, **kwargs: Any) -> dict[str, Any]:
+ context = super().get_context_data(**kwargs)
+ context["order"] = self.get_order()
+ context["statuses"] = self.get_base_fields()
+ context["isolation_methods"] = self.get_isolation_methods()
+ context["table"] = self.table_class(data=self.get_data())
+
+ return context
+
+ def get_success_url(self) -> str:
+ return reverse(
+ "staff:order-extraction-samples-lab", 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("checked")
+ isolation_method = request.POST.get("isolation_method")
+
+ if not selected_ids:
+ messages.error(request, "No samples selected.")
+ return HttpResponseRedirect(self.get_success_url())
+
+ order = self.get_order()
+
+ # Get the selected samples
+ samples = Sample.objects.filter(id__in=selected_ids)
+
+ if status_name:
+ self.assign_status_to_samples(samples, status_name, order, request)
+ if isolation_method:
+ self.update_isolation_methods(samples, isolation_method, request)
+ return HttpResponseRedirect(self.get_success_url())
+
+ def assign_status_to_samples(
+ self,
+ samples: models.QuerySet,
+ status_name: str,
+ order: ExtractionOrder,
+ request: HttpRequest,
+ ) -> None:
+ statuses = SampleStatusAssignment.SampleStatus.choices
+
+ # Check if the provided status exists
+ if status_name not in [k for k, _ in statuses]:
+ messages.error(request, f"Status '{status_name}' is not valid.")
+ return HttpResponseRedirect(self.get_success_url())
+
+ # Get the index of the target status
+ status_weight = next(
+ i for i, (name, _) in enumerate(statuses) if name == status_name
+ )
+
+ # Slice the list up to that index (inclusive) and extract only the names
+ statuses_to_apply = [name for name, _ in statuses[: status_weight + 1]]
+
+ # Apply status assignments
+ assignments = []
+ for sample in samples:
+ for status in statuses_to_apply:
+ assignment = SampleStatusAssignment(
+ sample=sample,
+ status=status,
+ order=order,
+ )
+ assignments.append(assignment)
+
+ SampleStatusAssignment.objects.bulk_create(
+ assignments,
+ ignore_conflicts=True,
+ )
+
+ messages.success(
+ request, f"{samples.count()} samples updated with status '{status_name}'."
+ )
+
+ def update_isolation_methods(
+ self, samples: models.QuerySet, isolation_method: str, request: HttpRequest
+ ) -> None:
+ selected_isolation_method = IsolationMethod.objects.filter(
+ name=isolation_method
+ ).first()
+
+ try:
+ im = IsolationMethod.objects.get(name=selected_isolation_method.name)
+ except IsolationMethod.DoesNotExist:
+ messages.error(
+ request,
+ f"Isolation method '{selected_isolation_method.name}' not found.",
+ )
+ return
+
+ for sample in samples:
+ # Remove any existing methods for this sample
+ SampleIsolationMethod.objects.filter(sample=sample).delete()
+
+ # Add the new one
+ SampleIsolationMethod.objects.create(sample=sample, isolation_method=im)
+ messages.success(
+ request,
+ f"{samples.count()} samples updated with isolation method '{isolation_method}'.", # noqa: E501
+ )
+
+
+class UpdateInternalNote(StaffMixin, ActionView):
+ def post(self, request: HttpRequest, *args, **kwargs) -> JsonResponse:
+ sample_id = request.POST.get("sample_id")
+ field_name = request.POST.get("field_name")
+ field_value = request.POST.get("field_value")
+
+ if not sample_id or not field_name or field_value is None:
+ return JsonResponse({"error": "Invalid input"}, status=400)
+
+ try:
+ sample = Sample.objects.get(id=sample_id)
+
+ if field_name == "internal_note-input":
+ sample.internal_note = field_value
+ sample.save()
+
+ return JsonResponse({"success": True})
+ except Sample.DoesNotExist:
+ return JsonResponse({"error": "Sample not found"}, status=404)
+
+
class ManaullyCheckedOrderActionView(SingleObjectMixin, ActionView):
model = ExtractionOrder
@@ -263,11 +505,7 @@ def form_valid(self, form: Form) -> HttpResponse:
_("The order was checked, GenLab IDs will be generated"),
)
except Exception as e:
- messages.add_message(
- self.request,
- messages.ERROR,
- f"Error: {str(e)}",
- )
+ messages.error(self.request, f"Error: {str(e)}")
return super().form_valid(form)
@@ -281,11 +519,68 @@ def form_invalid(self, form: Form) -> HttpResponse:
return HttpResponseRedirect(self.get_success_url())
+class StaffEditView(StaffMixin, SingleObjectMixin, TemplateView):
+ form_class = OrderStaffForm
+ template_name = "staff/order_staff_edit.html"
+
+ def get_queryset(self) -> models.QuerySet[Order] | models.QuerySet[Genrequest]:
+ model_type = self._get_model_type()
+ if model_type == "genrequest":
+ return Genrequest.objects.all()
+ return Order.objects.filter(status=Order.OrderStatus.DELIVERED)
+
+ def _get_model_type(self) -> str:
+ """Returns model type based on request data."""
+ return self.kwargs["model_type"]
+
+ def get(self, request: HttpRequest, *args, **kwargs) -> HttpResponse:
+ self.object = self.get_object()
+ return super().get(request, *args, **kwargs)
+
+ def post(self, request: HttpRequest, *args, **kwargs) -> HttpResponse:
+ self.object = self.get_object()
+ form = self.form_class(request.POST, order=self.object)
+
+ if form.is_valid():
+ responsible_staff = form.cleaned_data.get("responsible_staff", [])
+ self.object.responsible_staff.set(responsible_staff)
+
+ messages.add_message(
+ request,
+ messages.SUCCESS,
+ "Staff assignment updated successfully",
+ )
+ model_type = self._get_model_type()
+ return HttpResponseRedirect(self.get_success_url(model_type))
+
+ return self.render_to_response(self.get_context_data(form=form))
+
+ def get_context_data(self, **kwargs) -> dict[str, Any]:
+ context = super().get_context_data(**kwargs)
+ context["object"] = self.object
+ context["form"] = self.form_class(order=self.object)
+ context["model_type"] = self._get_model_type()
+
+ return context
+
+ def get_success_url(self, model_type: str | None) -> str:
+ if model_type == "genrequest":
+ return reverse(
+ "genrequest-detail",
+ kwargs={"pk": self.object.id},
+ )
+
+ return reverse_lazy(
+ f"staff:order-{model_type}-detail",
+ kwargs={"pk": self.object.pk},
+ )
+
+
class OrderToDraftActionView(SingleObjectMixin, ActionView):
model = Order
def get_queryset(self) -> models.QuerySet[Order]:
- return super().get_queryset().filter(status=Order.OrderStatus.DELIVERED)
+ return super().get_queryset()
def post(self, request: HttpRequest, *args, **kwargs) -> HttpResponse:
self.object: Order = self.get_object()
@@ -351,6 +646,54 @@ def form_invalid(self, form: Form) -> HttpResponse:
return HttpResponseRedirect(self.get_success_url())
+class GenerateGenlabIDsView(
+ SingleObjectMixin, StaffMixin, SingleTableMixin, FilterView
+):
+ model = ExtractionOrder
+
+ def get_object(self) -> ExtractionOrder:
+ return ExtractionOrder.objects.get(pk=self.kwargs["pk"])
+
+ def post(self, request: HttpRequest, *args, **kwargs) -> HttpResponse:
+ self.object = self.get_object()
+ selected_ids = request.POST.getlist("checked")
+
+ if not selected_ids:
+ messages.error(request, "No samples were selected.")
+ return HttpResponseRedirect(self.get_return_url())
+
+ sort_param = request.POST.get("sort", "")
+ sorting_order = [s.strip() for s in sort_param.split(",") if s.strip()]
+
+ selected_samples = Sample.objects.filter(pk__in=selected_ids)
+
+ if sorting_order:
+ selected_samples = selected_samples.order_by(*sorting_order)
+
+ try:
+ self.object.order_selected_checked(
+ sorting_order=sorting_order, selected_samples=selected_samples
+ )
+ messages.add_message(
+ request,
+ messages.SUCCESS,
+ _(f"Genlab IDs generated for {selected_samples.count()} samples."),
+ )
+ except Exception as e:
+ messages.add_message(
+ request,
+ messages.ERROR,
+ f"Error: {str(e)}",
+ )
+
+ return HttpResponseRedirect(self.get_return_url())
+
+ def get_return_url(self) -> str:
+ return reverse_lazy(
+ "staff:order-extraction-samples", kwargs={"pk": self.object.pk}
+ )
+
+
class ExtractionPlateCreateView(StaffMixin, CreateView):
model = ExtractionPlate
form_class = ExtractionPlateForm
@@ -444,3 +787,16 @@ def get_success_url(self) -> str:
def form_invalid(self, form: Form) -> HttpResponse:
return HttpResponseRedirect(self.get_success_url())
+
+
+class OrderPrioritizedAdminView(StaffMixin, ActionView):
+ def post(self, request: HttpRequest, *args, **kwargs) -> HttpResponse:
+ pk = kwargs.get("pk")
+ order = Order.objects.get(pk=pk)
+ order.toggle_prioritized()
+
+ return HttpResponseRedirect(
+ reverse(
+ "staff:dashboard",
+ )
+ )
diff --git a/src/templates/django_tables2/tailwind.html b/src/templates/django_tables2/tailwind.html
index 57650799..a322ecb5 100644
--- a/src/templates/django_tables2/tailwind.html
+++ b/src/templates/django_tables2/tailwind.html
@@ -1,126 +1,7 @@
-{% load django_tables2 %}
-{% load i18n %}
{% block table-wrapper %}
-
-
- {% block table %}
-
- {% block table.thead %}
- {% if table.show_header %}
-
-
- {% for column in table.columns %}
-
- {% if column.orderable %}
- {% comment%}
- If the column is orderable, two small arrows will show next to the column name to signal that it can be sorted.
- {% endcomment%}
-
- {{ column.header }}
-
-
- {% else %}
- {{ column.header }}
- {% endif %}
-
- {% endfor %}
-
-
- {% endif %}
- {% endblock table.thead %}
-
-
- {% block table.tbody %}
-
- {% for row in table.paginated_rows %}
- {% block table.tbody.row %}
-
-
- {% for column, cell in row.items %}
-
- {% if column.localize == None %}
- {{ cell }}
- {% else %}
- {% if column.localize %}
- {{ cell|localize }}
- {% else %}
- {{ cell|unlocalize }}
- {% endif %}
- {% endif %}
- {% endfor %}
-
- {% endblock table.tbody.row %}
- {% empty %}
- {% if table.empty_text %}
- {% block table.tbody.empty_text %}
- {{ table.empty_text }}
- {% endblock table.tbody %}
-
-
- {% block table.tfoot %}
- {% if table.has_footer %}
-
-
- {% for column in table.columns %}
- {{ column.footer }}
- {% endfor %}
-
-
- {% endif %}
- {% endblock table.tfoot %}
-
- {% endblock table %}
-
- {% block pagination %}
- {% if table.page and table.paginator.num_pages > 1 %}
-
-
-
- {% endif %}
- {% endblock pagination %}
-
+
+
+ {% include 'django_tables2/tailwind_inner.html' %}
+
{% endblock table-wrapper %}
diff --git a/src/templates/django_tables2/tailwind_inner.html b/src/templates/django_tables2/tailwind_inner.html
new file mode 100644
index 00000000..24485f46
--- /dev/null
+++ b/src/templates/django_tables2/tailwind_inner.html
@@ -0,0 +1,120 @@
+{% load django_tables2 %}
+{% load i18n %}
+
+{% block table %}
+
+ {% block table.thead %}
+ {% if table.show_header %}
+
+
+ {% for column in table.columns %}
+
+ {% if column.orderable %}
+ {% comment%}
+ If the column is orderable, two small arrows will show next to the column name to signal that it can be sorted.
+ {% endcomment%}
+
+ {{ column.header }}
+
+
+ {% else %}
+ {{ column.header }}
+ {% endif %}
+
+ {% endfor %}
+
+
+ {% endif %}
+ {% endblock table.thead %}
+
+
+ {% block table.tbody %}
+
+ {% for row in table.paginated_rows %}
+ {% block table.tbody.row %}
+
+
+ {% for column, cell in row.items %}
+
+ {% if column.localize == None %}
+ {{ cell }}
+ {% else %}
+ {% if column.localize %}
+ {{ cell|localize }}
+ {% else %}
+ {{ cell|unlocalize }}
+ {% endif %}
+ {% endif %}
+ {% endfor %}
+
+ {% endblock table.tbody.row %}
+ {% empty %}
+ {% if table.empty_text %}
+ {% block table.tbody.empty_text %}
+ {{ table.empty_text }}
+ {% endblock table.tbody %}
+
+
+ {% block table.tfoot %}
+ {% if table.has_footer %}
+
+
+ {% for column in table.columns %}
+ {{ column.footer }}
+ {% endfor %}
+
+
+ {% endif %}
+ {% endblock table.tfoot %}
+
+{% endblock table %}
+
+{% block pagination %}
+ {% if table.page and table.paginator.num_pages > 1 %}
+
+
+
+ {% endif %}
+{% endblock pagination %}