start working on case_study bulk editiing and add relative dates to the model

atlas/forms.py

@@ -746,7 +746,8 @@ class CaseForm(ModelForm):
                 "open_access",
                 "previous_case",
                 "diagnostic_certainty",
-                "cimar_uuid",
+                #cimar_uuid",
+                "study_date",
             ),
         )
 
@@ -779,7 +780,8 @@ class CaseForm(ModelForm):
             "open_access",
             "previous_case",
             "diagnostic_certainty",
-            "cimar_uuid",
+            #cimar_uuid",
+            "study_date",
         ]
         # fields = ['question', 'findings', 'subspecialty', 'references']
         widgets = {

atlas/migrations/0105_case_study_date.py

@@ -0,0 +1,18 @@
+# Generated by Django 6.0.1 on 2026-06-01 09:01
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0104_series_source_series_instance_uid'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='case',
+            name='study_date',
+            field=models.DateField(blank=True, help_text='Optional manually overridden study date for linked case series.', null=True),
+        ),
+    ]

atlas/models.py

@@ -840,6 +840,12 @@ class Case(models.Model, AuthorMixin, QuestionMixin):
 
     cimar_uuid = models.CharField(max_length=255, null=True, blank=True)
 
+    study_date = models.DateField(
+        null=True,
+        blank=True,
+        help_text="Optional manually overridden study date for linked case series.",
+    )
+
     def get_ordered_series_details(self):
         cached = getattr(self, "_ordered_series_details_cache", None)
         if cached is not None:
@@ -873,6 +879,41 @@ class Case(models.Model, AuthorMixin, QuestionMixin):
         self._ordered_series_cache = ordered
         return ordered
 
+    @staticmethod
+    def _parse_dicom_date(value):
+        if not value:
+            return None
+        try:
+            return datetime.datetime.strptime(str(value), "%Y%m%d").date()
+        except (TypeError, ValueError):
+            return None
+
+    def get_effective_study_date(self):
+        if self.study_date:
+            return self.study_date
+
+        for series in self.get_ordered_series():
+            image = series.images.filter(removed=False).first()
+            if not image:
+                continue
+            try:
+                ds = image.get_dicom_data()
+            except Exception:
+                ds = None
+            if not ds:
+                continue
+
+            raw_date = (
+                getattr(ds, "StudyDate", None)
+                or getattr(ds, "AcquisitionDate", None)
+                or getattr(ds, "SeriesDate", None)
+            )
+            parsed = self._parse_dicom_date(raw_date)
+            if parsed:
+                return parsed
+
+        return None
+
     def get_app_name(self):
         return "atlas"
 

atlas/templates/atlas/linked_cases_overview.html

@@ -18,6 +18,84 @@
             </div>
         </div>
 
+        {% if can_edit_chain %}
+            <div class="card border-secondary-subtle shadow-sm mb-4">
+                <div class="card-body">
+                    <div class="d-flex flex-wrap justify-content-between align-items-start gap-3 mb-3">
+                        <div>
+                            <h2 class="h5 mb-1">Study Dates</h2>
+                            <p class="text-muted mb-0">Edit each case date directly, or use the copy action to apply one case date to the rest of the linked chain.</p>
+                        </div>
+                        {% if anchor_date %}
+                            <div class="small text-muted">Relative offsets are measured from {{ anchor_date|date:"Y-m-d" }}.</div>
+                        {% endif %}
+                    </div>
+
+                    <form method="post">
+                        {% csrf_token %}
+                        <div class="table-responsive">
+                            <table class="table table-dark table-hover align-middle mb-0">
+                                <thead>
+                                    <tr>
+                                        <th scope="col">Case</th>
+                                        <th scope="col" class="text-nowrap">Study date</th>
+                                        <th scope="col" class="text-nowrap">Relative</th>
+                                        <th scope="col" class="text-nowrap">Actions</th>
+                                    </tr>
+                                </thead>
+                                <tbody>
+                                    {% for row in linked_case_rows %}
+                                        <tr class="{% if row.is_current %}table-primary{% endif %}">
+                                            <td>
+                                                <div class="fw-semibold">{{ row.case.title|default:"Untitled case" }}</div>
+                                                <div class="small text-muted">Case {{ row.case.pk }}{% if row.is_current %} · current{% endif %}</div>
+                                            </td>
+                                            <td style="min-width: 14rem;">
+                                                <input
+                                                    type="date"
+                                                    class="form-control form-control-sm"
+                                                    name="study_date_{{ row.case.pk }}"
+                                                    value="{% if row.study_date %}{{ row.study_date|date:'Y-m-d' }}{% endif %}"
+                                                    {% if not row.can_edit %}disabled{% endif %}
+                                                >
+                                            </td>
+                                            <td class="text-nowrap">
+                                                {% if row.relative_days is not None %}
+                                                    {% if row.relative_days == 0 %}
+                                                        Day 0
+                                                    {% elif row.relative_days > 0 %}
+                                                        +{{ row.relative_days }} day{{ row.relative_days|pluralize }}
+                                                    {% else %}
+                                                        {{ row.relative_days }} day{{ row.relative_days|pluralize }}
+                                                    {% endif %}
+                                                {% else %}
+                                                    <span class="text-muted">No anchor</span>
+                                                {% endif %}
+                                            </td>
+                                            <td class="text-nowrap">
+                                                <button
+                                                    type="submit"
+                                                    class="btn btn-sm btn-outline-info"
+                                                    name="apply_to_all_from"
+                                                    value="{{ row.case.pk }}"
+                                                    {% if not row.can_edit %}disabled{% endif %}
+                                                >
+                                                    Copy to others
+                                                </button>
+                                            </td>
+                                        </tr>
+                                    {% endfor %}
+                                </tbody>
+                            </table>
+                        </div>
+                        <div class="d-flex flex-wrap justify-content-end gap-2 mt-3">
+                            <button type="submit" class="btn btn-primary">Save study dates</button>
+                        </div>
+                    </form>
+                </div>
+            </div>
+        {% endif %}
+
         <div class="row g-3 mb-4">
             <div class="col-lg-8">
                 <div class="card border-secondary-subtle shadow-sm h-100">

atlas/templates/atlas/partials/_linked_case_card.html

@@ -29,7 +29,9 @@
                 {% endif %}
             </div>
             <div class="text-sm-end small text-muted">
-                {% if linked_case.published_date %}
+                {% if linked_case.get_effective_study_date %}
+                    <div>Study date {{ linked_case.get_effective_study_date|date:"Y-m-d" }}</div>
+                {% elif linked_case.published_date %}
                     <div>Published {{ linked_case.published_date|date:"Y-m-d" }}</div>
                 {% else %}
                     <div>Created {{ linked_case.created_date|date:"Y-m-d" }}</div>

atlas/tests/test_cases.py

@@ -1,15 +1,181 @@
-
 import json
-import pytest
 
-# from django.contrib.auth.models import User
+from django.http import HttpResponse
 from django.urls import reverse
+import pytest
+from atlas.models import CaseCollection, Finding, Condition
+#from atlas.views import GenericExamViews
+from pytest_django.asserts import assertRedirects, assertContains, assertQuerySetEqual
+from django.test import TestCase
 
-from rich.pretty import pprint
 
-from bs4 import BeautifulSoup
+#@pytest.mark.django_db
+def test_create_condition(db):
+    abnormality = Condition.objects.create(name="Abnorm")
+    assert abnormality.name == "Abnorm"
 
-from django.contrib.auth.models import Group
+
+def test_condition_tree_structure(db):
+    parent = Condition.objects.create(name="parent")
+
+    child1 = Condition.objects.create(name="child1")
+    child2 = Condition.objects.create(name="child2")
+
+    parent.child.set([child1, child2])
+
+    child1_1 = Condition.objects.create(name="child1_1")
+    child1_2 = Condition.objects.create(name="child1_2")
+
+    child1.child.set([child1_1, child1_2])
+
+    assert len(parent.get_children()) == 2
+    assert len(child1.get_children()) == 2
+
+    assert len(child1.get_parents()) == 1
+    assert parent in child1.get_parents()
+
+    assert len(child2.get_parents()) == 1
+    assert parent in child2.get_parents()
+
+
+#@pytest.fixture
+#def create_basic_user(db, django_user_model):
+#    return django_user_model.objects.create_superuser("basicuser", "ross@xkjq.uk", "password")
+#
+#@pytest.fixture
+#def create_exam(db):
+#    return Exam.objects.create(name="test exam", exam_mode=True)
+#
+#def test_exam_creation(create_exam):
+#    exams = Exam.objects.filter(name="test exam")
+#    assert exams.exists()
+#
+#    exam = exams.first()
+#
+#    assert exam.time_limit == 35 * 60
+#
+#def test_exam_list(rf, admin_user, create_exam):
+#    request = rf.get('/rapids/exam/')
+#    # Remember that when using RequestFactory, the request does not pass
+#    # through middleware. If your view expects fields such as request.user to be
+#    # set, you need to set them explicitly.
+#    # The following line sets request.user to an admin user.
+#    request.user = admin_user
+#    response = GenericExamViews.exam_list(request)
+#    #print(response)
+#    assert response.status_code == 200
+#
+#def test_exam_active_admin(rf, admin_user, create_exam, client):
+#    request = rf.get(reverse('rapids:active_exams'))
+#    request.user = admin_user
+#    response = GenericExamViews.active_exams(request)
+#    print(response.content)
+#    assert response.status_code == 200
+#
+#def test_exam_active_basic_user(create_basic_user, create_exam, client):
+#    client.login(username="basicuser", password="password")
+#    response = client.get(reverse('rapids:active_exams'))
+#    print(response.content)
+#    assert response.status_code == 200
+
+def test_create_case(db, create_case):
+    case = create_case
+    assert case.title == "Sample Case"
+
+def test_create_series(db, create_series):
+    series = create_series
+    assert series
 
 
 
+def test_collection(db, create_case_collection, create_case, make_case, client, create_user):
+    collection: CaseCollection = create_case_collection
+
+    # create some cases
+    case1 = create_case
+    case2 = make_case()
+    case3 = make_case(title="Case 3")
+    case4 = make_case(title="Case 4")
+
+    collection.cases.set([case1, case2, case3, case4])
+
+    case5 = make_case(title="Case 5")
+
+    assert collection.cases.all().count() == 4
+
+    collection.add_case(case5)
+
+    assert collection.cases.all().count() == 5
+
+    assert collection.get_case_by_index(0) == case1
+    assert collection.get_case_by_index(1) == case2
+    assert collection.get_case_by_index(2) == case3
+    assert collection.get_case_by_index(3) == case4
+    assert collection.get_case_by_index(4) == case5
+
+    assert collection.get_absolute_url() == reverse("atlas:collection_detail", kwargs={"pk": collection.pk})
+
+    assert collection.get_take_url() == reverse("atlas:collection_take_start", kwargs={"pk": collection.pk})
+
+    start_order = collection.get_cases()
+
+    new_order = [
+        case5.pk,
+        case1.pk,
+        case2.pk,
+        case3.pk,
+        case4.pk
+    ]
+    response: HttpResponse = client.post(reverse("atlas:exam_json_edit", kwargs={"pk":collection.pk} ), json=new_order, follow=True)
+    # Check that sorting the exam works
+
+    # First attempt is not logged in
+    assertRedirects(response, f"{reverse('login')}?next=%2Fatlas%2Fcollection%2F1%2Fjson_edit")
+
+    client.force_login(create_user)
+
+    # Random user cannot modify order
+    response: HttpResponse = client.post(reverse("atlas:exam_json_edit", kwargs={"pk":collection.pk} ), json=new_order, follow=True)
+    assert response.status_code == 403
+
+    assertQuerySetEqual(start_order , collection.get_cases())
+
+    # Once the user has been made an author, they can modify the order
+    collection.add_author(create_user)
+    response: HttpResponse = client.post(reverse("atlas:exam_json_edit", kwargs={"pk":collection.pk} ), data={"set_exam_order" : json.dumps(new_order)}, follow=True)
+    assert response.status_code == 200
+
+    assert collection.get_cases().count() == 5
+    assert collection.get_case_by_index(0) == case5
+    assert collection.get_case_by_index(1) == case1
+
+
+@pytest.mark.django_db
+def test_linked_cases_overview_can_copy_study_date_to_chain(client, create_user, make_case):
+    user = create_user
+    case1 = make_case(title="Case 1")
+    case2 = make_case(title="Case 2")
+    case2.previous_case = case1
+    case2.save(update_fields=["previous_case"])
+
+    case1.author.add(user)
+    case2.author.add(user)
+
+    client.force_login(user)
+
+    response = client.post(
+        reverse("atlas:linked_cases_overview", kwargs={"case_id": case1.pk}),
+        data={
+            f"study_date_{case1.pk}": "2026-01-10",
+            f"study_date_{case2.pk}": "2026-01-12",
+            "apply_to_all_from": str(case1.pk),
+        },
+        follow=True,
+    )
+
+    assert response.status_code == 200
+    case1.refresh_from_db()
+    case2.refresh_from_db()
+
+    assert str(case1.study_date) == "2026-01-10"
+    assert str(case2.study_date) == "2026-01-10"

atlas/views.py

@@ -4,6 +4,7 @@ import csv
 import random
 import copy
 import io
+import datetime
 from datetime import timedelta
 from typing import Any
 from dal import autocomplete
@@ -168,6 +169,31 @@ from .filters import (
     NormalCaseFilter,
 )
 
+
+def _parse_study_date(value):
+    if not value:
+        return None
+    try:
+        parsed_value = str(value)
+        for date_format in ("%Y%m%d", "%Y-%m-%d"):
+            try:
+                return datetime.datetime.strptime(parsed_value, date_format).date()
+            except ValueError:
+                continue
+        return None
+    except (TypeError, ValueError):
+        return None
+
+
+def _extract_study_date_from_dicoms(dicoms):
+    for dicom in dicoms.iterator():
+        tags = dicom.basic_dicom_tags or {}
+        for key in ("StudyDate", "AcquisitionDate", "SeriesDate"):
+            study_date = _parse_study_date(tags.get(key))
+            if study_date:
+                return study_date
+    return None
+
 from .tasks import push_case_to_cimar_task, series_downsample_task, series_reconstruct_task
 try:
     from django_tasks import TaskResultStatus
@@ -3637,14 +3663,15 @@ def uploads_import_case_series_htmx(request):
                 for field_name in case_field_names:
                     setattr(case, field_name, getattr(base_case, field_name))
                 case.previous_case = previous_case
+                study_series_uids = study_groups[study_uid]
+                study_dicoms = dicoms.filter(series_instance_uid__in=study_series_uids)
+                case.study_date = _extract_study_date_from_dicoms(study_dicoms)
                 case.save()
                 case.author.add(request.user)
 
                 for field_name in m2m_field_names:
                     getattr(case, field_name).set(form.cleaned_data.get(field_name, []))
 
-                study_series_uids = study_groups[study_uid]
-                study_dicoms = dicoms.filter(series_instance_uid__in=study_series_uids)
                 imported_rows = import_dicoms_helper(request, case_id=case.pk, dicoms=study_dicoms)
                 created_cases.append(case)
                 import_results.append((case, study_uid, imported_rows))
@@ -9520,20 +9547,17 @@ def linked_cases_overview(request, case_id):
     """
     Display the linked-case chain around a case, including prior and follow-up cases.
     """
-    # Get the current case
     case = get_object_or_404(Case, pk=case_id)
 
-    # Traverse backward to get all previous cases
     previous_cases = []
     try:
         current_case = case.previous_case
         while current_case:
-            previous_cases.insert(0, current_case)  # Insert at the beginning to maintain order
+            previous_cases.insert(0, current_case)
             current_case = current_case.previous_case
     except ObjectDoesNotExist:
         pass
 
-    # Traverse forward to get all next cases
     next_cases = []
     try:
         current_case = case.next_case
@@ -9547,7 +9571,62 @@ def linked_cases_overview(request, case_id):
     direct_previous = previous_cases[-1] if previous_cases else None
     direct_next = next_cases[0] if next_cases else None
 
-    # Render the template with the linked cases
+    if request.method == "POST":
+        if not case.check_user_can_edit(request.user):
+            raise PermissionDenied("You do not have permission to edit this case chain.")
+
+        apply_to_all_from = request.POST.get("apply_to_all_from")
+        updated_cases = 0
+
+        if apply_to_all_from:
+            source_case = next(
+                (linked_case for linked_case in chain_cases if str(linked_case.pk) == apply_to_all_from),
+                None,
+            )
+            if source_case and source_case.check_user_can_edit(request.user):
+                source_date = _parse_study_date(request.POST.get(f"study_date_{source_case.pk}"))
+                for linked_case in chain_cases:
+                    if not linked_case.check_user_can_edit(request.user):
+                        continue
+                    if linked_case.study_date != source_date:
+                        linked_case.study_date = source_date
+                        linked_case.save(update_fields=["study_date"])
+                        updated_cases += 1
+                messages.success(request, f"Applied the study date to {updated_cases} case(s).")
+        else:
+            for linked_case in chain_cases:
+                if not linked_case.check_user_can_edit(request.user):
+                    continue
+                raw_value = request.POST.get(f"study_date_{linked_case.pk}", "").strip()
+                new_date = _parse_study_date(raw_value)
+                if linked_case.study_date != new_date:
+                    linked_case.study_date = new_date
+                    linked_case.save(update_fields=["study_date"])
+                    updated_cases += 1
+            messages.success(request, f"Updated {updated_cases} linked case date(s).")
+
+        return redirect("atlas:linked_cases_overview", case_id=case.pk)
+
+    linked_case_rows = []
+    anchor_date = next(
+        (linked_case.get_effective_study_date() for linked_case in chain_cases if linked_case.get_effective_study_date()),
+        None,
+    )
+    for linked_case in chain_cases:
+        study_date = linked_case.get_effective_study_date()
+        relative_days = None
+        if anchor_date and study_date:
+            relative_days = (study_date - anchor_date).days
+        linked_case_rows.append(
+            {
+                "case": linked_case,
+                "study_date": study_date,
+                "relative_days": relative_days,
+                "can_edit": linked_case.check_user_can_edit(request.user),
+                "is_current": linked_case.pk == case.pk,
+            }
+        )
+
     return render(
         request,
         "atlas/linked_cases_overview.html",
@@ -9556,6 +9635,9 @@ def linked_cases_overview(request, case_id):
             "previous_cases": previous_cases,
             "next_cases": next_cases,
             "chain_cases": chain_cases,
+            "linked_case_rows": linked_case_rows,
+            "anchor_date": anchor_date,
+            "can_edit_chain": any(row["can_edit"] for row in linked_case_rows),
             "chain_total": len(chain_cases),
             "current_index": len(previous_cases) + 1,
             "direct_previous": direct_previous,