196 make a user interface for generating genlab ids

src/genlab_bestilling/libs/genlabid.py

@@ -63,7 +63,11 @@ def get_current_sequences(order_id: int | str) -> Any:
         return sequences
 
 
-def generate(order_id: int | str) -> None:
+def generate(
+    order_id: int | str,
+    sorting_order: list[str] | None = None,
+    selected_samples: list[Any] | None = None,
+) -> None:
     """
     wrapper to handle errors and reset the sequence to the current sequence value
     """

src/genlab_bestilling/models.py

@@ -301,6 +301,10 @@ def to_draft(self) -> None:
     def get_type(self) -> str:
         return "order"
 
+    @property
+    def filled_genlab_count(self) -> int:
+        return self.samples.filter(genlab_id__isnull=False).count()
+
     @property
     def next_status(self) -> OrderStatus | None:
         current_index = self.STATUS_ORDER.index(self.status)
@@ -461,6 +465,27 @@ def order_manually_checked(self) -> None:
         self.save()
         app.configure_task(name="generate-genlab-ids").defer(order_id=self.id)
 
+    def order_selected_checked(
+        self,
+        sorting_order: list[str] | None = None,
+        selected_samples: list[str] | None = None,
+    ) -> None:
+        """
+        Partially set the order as checked by the lab staff,
+        generate a genlab id for the samples selected
+        """
+        self.internal_status = self.Status.CHECKED
+        self.status = self.OrderStatus.PROCESSING
+        self.save()
+
+        selected_sample_names = list(selected_samples.values_list("id", flat=True))
+
+        app.configure_task(name="generate-genlab-ids").defer(
+            order_id=self.id,
+            sorting_order=sorting_order,
+            selected_samples=selected_sample_names,
+        )
+
 
 class AnalysisOrder(Order):
     samples = models.ManyToManyField(

src/genlab_bestilling/tasks.py

@@ -1,4 +1,6 @@
 # from .libs.isolation import isolate
+from typing import Any
+
 from django.db.utils import OperationalError
 from procrastinate import RetryStrategy
 from procrastinate.contrib.django import app
@@ -12,6 +14,14 @@
         max_attempts=5, linear_wait=5, retry_exceptions={OperationalError}
     ),
 )
-def generate_ids(order_id: str | int) -> None:
-    generate_genlab_id(order_id=order_id)
+def generate_ids(
+    order_id: int | str,
+    sorting_order: list[str] | None = None,
+    selected_samples: list[Any] | None = None,
+) -> None:
+    generate_genlab_id(
+        order_id=order_id,
+        sorting_order=sorting_order,
+        selected_samples=selected_samples,
+    )
     # isolate(order_id=order_id)

src/staff/tables.py

@@ -1,6 +1,8 @@
 from typing import Any
 
 import django_tables2 as tables
+from django.db.models import IntegerField
+from django.db.models.functions import Cast
 from django.utils.safestring import mark_safe
 
 from genlab_bestilling.models import (
@@ -139,6 +141,17 @@ class SampleBaseTable(tables.Table):
         verbose_name="",
     )
 
+    checked = tables.CheckBoxColumn(
+        attrs={
+            "th__input": {"type": "checkbox", "id": "select-all-checkbox"},
+        },
+        accessor="pk",
+        orderable=False,
+        empty_values=(),
+    )
+
+    name = tables.Column(order_by=("name_as_int",))
+
     class Meta:
         model = Sample
         fields = [
@@ -154,17 +167,41 @@ class Meta:
             "plate_positions",
         ]
         attrs = {"class": "w-full table-auto tailwind-table table-sm"}
-        sequence = ("is_prioritised", "genlab_id", "guid", "name", "species", "type")
-        order_by = ("-is_prioritised", "species", "genlab_id", "name")
+        sequence = (
+            "checked",
+            "is_prioritised",
+            "genlab_id",
+            "guid",
+            "name",
+            "species",
+            "type",
+        )
+        order_by = (
+            "-is_prioritised",
+            "species",
+            "genlab_id",
+            "name_as_int",
+        )
 
         empty_text = "No Samples"
 
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+
+        if hasattr(self.data, "data"):
+            self.data.data = self.data.data.annotate(
+                name_as_int=Cast("name", output_field=IntegerField())
+            )
+
     def render_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:
+        return mark_safe(f'<input type="checkbox" name="checked" value="{record.id}">')  # noqa: S308
+
 
 def create_sample_table(base_fields: list[str] | None = None) -> type[tables.Table]:
     class CustomSampleTable(tables.Table):

src/staff/templates/staff/analysisorder_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 %}
 Analysis Orders
 {% endblock page-title %}
+
+{% block page-inner %}
+<form method="get" class="py-3 px-4 border mb-3 ">
+    <div class="flex flex-wrap gap-4">
+        {{ filter.form | crispy }}
+    </div>
+    <button class="btn bg-primary" type="submit">Search</button>
+</form>
+
+{% render_table table %}
+
+{% endblock page-inner %}

src/staff/templates/staff/base_filter.html

@@ -5,19 +5,23 @@
 {% block content %}
     <h3 class="text-4xl mb-5">{% block page-title %}{% endblock page-title %}</h3>
     {% block page-inner %}{% endblock page-inner %}
-
-    <form method="get" class="py-3 px-4 border mb-3 ">
-        <div class="flex flex-wrap gap-4">
-            {{ filter.form | crispy }}
-        </div>
-        <button class="btn bg-primary" type="submit">Search</button>
-    </form>
-
-    {% render_table table %}
 {% endblock %}
 
 {% block body_javascript %}
 {{ block.super }}
 <script type="text/javascript" src="{% static 'admin/js/vendor/jquery/jquery.js' %}"></script>
 {{ filter.form.media }}
+<script>
+    document.addEventListener('DOMContentLoaded', function () {
+      const selectAll = document.getElementById('select-all-checkbox');
+      if (selectAll) {
+        selectAll.addEventListener('change', function () {
+          const checkboxes = document.querySelectorAll('input[name="checked"]');
+          checkboxes.forEach(cb => {
+            cb.checked = selectAll.checked;
+          });
+        });
+      }
+    });
+</script>
 {% endblock body_javascript %}

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 %}
+<form method="get" class="py-3 px-4 border mb-3 ">
+    <div class="flex flex-wrap gap-4">
+        {{ filter.form | crispy }}
+    </div>
+    <button class="btn bg-primary" type="submit">Search</button>
+</form>
+
+{% render_table table %}
+
+{% endblock page-inner %}

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 %}
+<form method="get" class="py-3 px-4 border mb-3 ">
+    <div class="flex flex-wrap gap-4">
+        {{ filter.form | crispy }}
+    </div>
+    <button class="btn bg-primary" type="submit">Search</button>
+</form>
+
+{% render_table table %}
+
+{% endblock page-inner %}

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 @@
 <div class="flex justify-end my-3">
     <a class="btn bg-primary" href="{% url 'staff:plates-create' %}">Create</a>
 </div>
+
+<form method="get" class="py-3 px-4 border mb-3 ">
+    <div class="flex flex-wrap gap-4">
+        {{ filter.form | crispy }}
+    </div>
+    <button class="btn bg-primary" type="submit">Search</button>
+</form>
+
+{% render_table table %}
 {% endblock page-inner %}

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 %}
+<form method="get" class="py-3 px-4 border mb-3 ">
+    <div class="flex flex-wrap gap-4">
+        {{ filter.form | crispy }}
+    </div>
+    <button class="btn bg-primary" type="submit">Search</button>
+</form>
+
+{% render_table table %}
+
+{% endblock page-inner %}

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 %}
+<div class="flex justify-between items-center w-full">
+    <div>
+        {% if order %}
+            {{ order }} - Samples
+        {% else %}
+            Samples
+        {% endif %}
+    </div>
+    {% if order %}
+        <div>
+            {{ order.filled_genlab_count }} / {{ order.samples.count }} Genlabs generated
+        </div>
+    {% endif %}
+</div>
 {% endblock page-title %}
 
 {% block page-inner %}
@@ -11,5 +26,17 @@
     <a class="btn bg-yellow-500" href="{% url 'samples-csv' %}?order={{ order.pk }}"><i class="fas fa-download"></i> Download CSV</a>
     <a class="btn bg-primary" href="{% url 'staff:order-extraction-samples-lab' order.pk %}"><i class="fas fa-flask"></i> Lab</a>
 </div>
+
+<form method="post" action="{% url 'staff:generate-genlab-ids' pk=order.pk %}">
+    {% csrf_token %}
+    <input type="hidden" name="sort" value="{{ request.GET.sort|default:'' }}">
+    <button class="btn bg-blue-500 text-white mt-4" type="submit" name="generate_genlab_ids">
+        <i class="fa-solid fa-id-badge"></i> Generate genlab IDs
+    </button>
+
+    <div class="text-right text-sm text-red-500"> This page is under development. The genlab IDs will generate for all, and without sorting as per now. </div>
+
+    {% render_table table %}
+  </form>
 {% endif %}
 {% endblock page-inner %}

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 @@
     <a class="btn bg-primary" href="../"><i class="fas fa-arrow-left"></i> back</a>
 </div>
 {% endif %}
+
+<form method="get" class="py-3 px-4 border mb-3 ">
+    <div class="flex flex-wrap gap-4">
+        {{ filter.form | crispy }}
+    </div>
+    <button class="btn bg-primary" type="submit">Search</button>
+</form>
+
+{% render_table table %}
+
 {% endblock page-inner %}

src/staff/urls.py

@@ -11,6 +11,7 @@
     ExtractionPlateCreateView,
     ExtractionPlateDetailView,
     ExtractionPlateListView,
+    GenerateGenlabIDsView,
     ManaullyCheckedOrderActionView,
     OrderAnalysisSamplesListView,
     OrderExtractionSamplesListView,
@@ -85,6 +86,11 @@
         SampleLabView.as_view(),
         name="order-extraction-samples-lab",
     ),
+    path(
+        "orders/extraction/<int:pk>/samples/generate-genlab-ids/",
+        GenerateGenlabIDsView.as_view(),
+        name="generate-genlab-ids",
+    ),
     path(
         "orders/analysis/<int:pk>/samples/",
         OrderAnalysisSamplesListView.as_view(),