Column for isolation method sample status

src/genlab_bestilling/admin.py

@@ -15,13 +15,13 @@
     ExtractionPlate,
     ExtractPlatePosition,
     Genrequest,
+    IsolationMethod,
     Location,
     LocationType,
     Marker,
     Organization,
     Sample,
     SampleMarkerAnalysis,
-    SampleStatus,
     SampleStatusAssignment,
     SampleType,
     Species,
@@ -526,9 +526,9 @@ class AnalysisResultAdmin(ModelAdmin):
     ]
 
 
-@admin.register(SampleStatus)
-class SampleStatusAdmin(ModelAdmin): ...
-
-
 @admin.register(SampleStatusAssignment)
 class SampleStatusAssignmentAdmin(ModelAdmin): ...
+
+
+@admin.register(IsolationMethod)
+class IsolationMethodAdmin(ModelAdmin): ...

src/genlab_bestilling/migrations/0026_alter_samplestatusassignment_status_and_more.py

@@ -0,0 +1,90 @@
+# Generated by Django 5.2.3 on 2025-07-11 10:16
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("genlab_bestilling", "0025_genrequest_responsible_staff"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="samplestatusassignment",
+            name="status",
+            field=models.CharField(
+                blank=True,
+                choices=[
+                    ("marked", "Marked"),
+                    ("plucked", "Plucked"),
+                    ("isolated", "Isolated"),
+                ],
+                help_text="The status of the sample in the lab",
+                null=True,
+                verbose_name="Sample status",
+            ),
+        ),
+        migrations.RemoveField(
+            model_name="sample",
+            name="assigned_statuses",
+        ),
+        migrations.AddField(
+            model_name="isolationmethod",
+            name="species",
+            field=models.ForeignKey(
+                default=None,
+                help_text="The species this isolation method is related to.",
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="species_isolation_methods",
+                to="genlab_bestilling.species",
+            ),
+        ),
+        migrations.CreateModel(
+            name="SampleIsolationMethod",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                (
+                    "isolation_method",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="sample_isolation_methods",
+                        to="genlab_bestilling.isolationmethod",
+                    ),
+                ),
+                (
+                    "sample",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="isolation_methods",
+                        to="genlab_bestilling.sample",
+                    ),
+                ),
+            ],
+            options={
+                "unique_together": {("sample", "isolation_method")},
+            },
+        ),
+        migrations.AddField(
+            model_name="sample",
+            name="isolation_method",
+            field=models.ManyToManyField(
+                blank=True,
+                help_text="The isolation method used for this sample",
+                related_name="samples",
+                through="genlab_bestilling.SampleIsolationMethod",
+                to="genlab_bestilling.isolationmethod",
+            ),
+        ),
+        migrations.DeleteModel(
+            name="SampleStatus",
+        ),
+    ]

src/genlab_bestilling/models.py

@@ -657,11 +657,13 @@ class Sample(models.Model):
 
     extractions = models.ManyToManyField(f"{an}.ExtractionPlate", blank=True)
     parent = models.ForeignKey("self", on_delete=models.PROTECT, null=True, blank=True)
-    assigned_statuses = models.ManyToManyField(
-        f"{an}.SampleStatus",
-        through=f"{an}.SampleStatusAssignment",
+
+    isolation_method = models.ManyToManyField(
+        f"{an}.IsolationMethod",
         related_name="samples",
+        through=f"{an}.SampleIsolationMethod",
         blank=True,
+        help_text="The isolation method used for this sample",
     )
 
     objects = managers.SampleQuerySet.as_manager()
@@ -776,29 +778,23 @@ def generate_genlab_id(self, commit: bool = True) -> str:
 # assignee (one or plus?)
 
 
-class SampleStatus(models.Model):
-    name = models.CharField(max_length=255)
-    weight = models.IntegerField(
-        default=0,
-    )
-    area = models.ForeignKey(
-        f"{an}.Area",
-        on_delete=models.CASCADE,
-        related_name="area_statuses",
-        help_text="The area this status is related to.",
-    )
-
-
 class SampleStatusAssignment(models.Model):
+    class SampleStatus(models.TextChoices):
+        MARKED = "marked", _("Marked")
+        PLUCKED = "plucked", _("Plucked")
+        ISOLATED = "isolated", _("Isolated")
+
     sample = models.ForeignKey(
         f"{an}.Sample",
         on_delete=models.CASCADE,
         related_name="sample_status_assignments",
     )
-    status = models.ForeignKey(
-        f"{an}.SampleStatus",
-        on_delete=models.CASCADE,
-        related_name="status_assignments",
+    status = models.CharField(
+        choices=SampleStatus.choices,
+        null=True,
+        blank=True,
+        verbose_name="Sample status",
+        help_text="The status of the sample in the lab",
     )
     order = models.ForeignKey(
         f"{an}.Order",
@@ -814,8 +810,31 @@ class Meta:
         unique_together = ("sample", "status", "order")
 
 
+class SampleIsolationMethod(models.Model):
+    sample = models.ForeignKey(
+        f"{an}.Sample",
+        on_delete=models.CASCADE,
+        related_name="isolation_methods",
+    )
+    isolation_method = models.ForeignKey(
+        f"{an}.IsolationMethod",
+        on_delete=models.CASCADE,
+        related_name="sample_isolation_methods",
+    )
+
+    class Meta:
+        unique_together = ("sample", "isolation_method")
+
+
 class IsolationMethod(models.Model):
     name = models.CharField(max_length=255, unique=True)
+    species = models.ForeignKey(
+        f"{an}.Species",
+        on_delete=models.CASCADE,
+        related_name="species_isolation_methods",
+        help_text="The species this isolation method is related to.",
+        default=None,
+    )
 
     def __str__(self) -> str:
         return self.name

src/staff/tables.py

@@ -219,47 +219,68 @@ 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):
-        """
-        This shows a checkbox in the header.
-        To display text in the header alongside the checkbox
-        override the header-property in the CheckBoxColumn class.
-        """
-
-        checked = tables.CheckBoxColumn(
-            accessor="pk",
-            orderable=True,
-            attrs={
-                "th__input": {
-                    "id": "select-all-checkbox",
-                },
-                "td__input": {
-                    "name": "checked",
-                },
-            },
-            empty_values=(),
-            verbose_name="Mark",
-        )
+class SampleStatusTable(tables.Table):
+    """
+    This shows a checkbox in the header.
+    To display text in the header alongside the checkbox
+    override the header-property in the CheckBoxColumn class.
+    """
 
-        for field in base_fields:
-            locals()[field] = tables.BooleanColumn(
-                verbose_name=field.capitalize(),
-                orderable=True,
-                yesno="✔,-",
-                default=False,
-            )
+    checked = tables.CheckBoxColumn(
+        accessor="pk",
+        orderable=False,
+        attrs={
+            "th__input": {
+                "id": "select-all-checkbox",
+            },
+            "td__input": {
+                "name": "checked",
+            },
+        },
+        empty_values=(),
+        verbose_name="Mark",
+    )
 
-        internal_note = tables.TemplateColumn(
-            template_name="staff/note_input_column.html", orderable=False
-        )
+    internal_note = tables.TemplateColumn(
+        template_name="staff/note_input_column.html", orderable=False
+    )
 
-        class Meta:
-            model = Sample
-            fields = ["checked", "genlab_id", "internal_note"] + list(base_fields)
-            sequence = ["checked", "genlab_id"] + list(base_fields) + ["internal_note"]
+    marked = tables.BooleanColumn(
+        verbose_name="Marked",
+        orderable=True,
+        yesno="✔,-",
+        default=False,
+    )
+    plucked = tables.BooleanColumn(
+        verbose_name="Plucked",
+        orderable=True,
+        yesno="✔,-",
+        default=False,
+    )
+    isolated = tables.BooleanColumn(
+        verbose_name="Isolated",
+        orderable=True,
+        yesno="✔,-",
+        default=False,
+    )
 
-    return CustomSampleTable
+    class Meta:
+        model = Sample
+        fields = [
+            "checked",
+            "genlab_id",
+            "internal_note",
+            "isolation_method",
+        ]
+        sequence = [
+            "checked",
+            "genlab_id",
+            "marked",
+            "plucked",
+            "isolated",
+            "internal_note",
+            "isolation_method",
+        ]
 
 
 class OrderExtractionSampleTable(SampleBaseTable):

src/staff/templates/staff/sample_lab.html

@@ -2,22 +2,51 @@
 {% load render_table from django_tables2 %}
 
 {% block content %}
-<h3 class="text-4xl mb-5">{% if order %}{{ order }} - Samples{% else %}Samples{% endif %}</h3>
-
-<div class="flex gap-5 mb-5">
-    <a class="btn bg-primary" href="../"><i class="fas fa-arrow-left"></i> back</a>
-</div>
-
-<form method="post" action="{% url 'staff:order-extraction-samples-lab' order.pk %}">
-    {% csrf_token %}
-    {% for status in statuses %}
-    <button class="btn bg-blue-500 text-white mt-4 mr-2" type="submit" name="status" value="{{ status.name }}">
-        <i class="fa-solid fa-id-badge"></i> {{ status.name }}
-    </button>
-    {% endfor %}
-
-    {% render_table table %}
-</form>
+<h3 class="text-4xl mb-5">{% block page-title %}{% if order %}{{ order }} - Samples{% else %}Samples{% endif %}{% endblock page-title %}</h3>
+{% block page-inner %}
+    <div class="flex gap-5 mb-5">
+        <a class="btn bg-primary" href="../"><i class="fas fa-arrow-left"></i> back</a>
+    </div>
+    <form method="post" action="{% url 'staff:order-extraction-samples-lab' order.pk %}">
+        {% csrf_token %}
+        {% for status in statuses %}
+            <button class="btn bg-blue-500 text-white mt-4 mr-2" type="submit" name="status" value="{{ status }}">
+                {{ status|capfirst }}
+            </button>
+        {% endfor %}
+        <div class="inline-block text-left">
+            <button type="button"
+                id="parent-dropdown-button"
+                onclick="document.getElementById('parent-dropdown-menu').classList.toggle('hidden')"
+                class="btn bg-slate-100 w-64 h-10 px-4">
+            <span id="selected-method-{{ record.pk }}" class="truncate block w-full text-center">
+                {{ record.selected_isolation_method.name|default:"Isolation method" }}
+                <i class="fa-solid fa-chevron-down ml-2"></i>
+            </span>
+            </button>
+          <div id="parent-dropdown-menu"
+               class="absolute z-10 mt-2 w-100 origin-top-right rounded-md bg-white shadow-lg hidden"
+               role="menu" aria-orientation="vertical" aria-labelledby="parent-dropdown-button">
+            {% if not isolation_methods %}
+              <p class="px-4 py-2 text-sm text-gray-700">No isolation methods available</p>
+            {% else %}
+              {% for im in isolation_methods %}
+                <button
+                  type="submit"
+                  name="isolation_method"
+                  value="{{ im }}"
+                class="update-isolation-button block w-full text-left px-4 py-2 text-sm hover:bg-gray-100 text-gray-700"
+                role="menuitem"
+              >
+                {{ im }}
+              </button>
+            {% endfor %}
+            {% endif %}
+          </div>
+        </div>
+        {% render_table table %}
+    </form>
+{% endblock page-inner %}
 
 <script>
     document.addEventListener("DOMContentLoaded", function () {
@@ -44,7 +73,7 @@ <h3 class="text-4xl mb-5">{% if order %}{{ order }} - Samples{% else %}Samples{%
 
                 clearTimeout(debounceTimeout);
                 debounceTimeout = setTimeout(function () {
-                    fetch("{% url 'staff:update-sample' %}", {
+                    fetch("{% url 'staff:update-internal-note' %}", {
                         method: "POST",
                         body: formData
                     });