Add patient grouping and selection functionality to user uploads

atlas/models.py

@@ -2802,6 +2802,7 @@ class UncategorisedDicom(models.Model):
                 "SliceThickness",
                 "SeriesNumber",
                 "StudyDate",
+                "PatientID",
             )
 
             tags = {}

atlas/templates/atlas/user_uploads.html

@@ -17,7 +17,97 @@
 
     {% if series_list %}
         <div id="series-list">
-            {% if grouped_series %}
+            {% if grouped_patients %}
+                {% for patient in grouped_patients %}
+                    <div class="patient-block mb-4 p-3 border rounded" style="background: rgba(255,255,255,0.015); border-color: rgba(255,255,255,0.08) !important;">
+                        <div class="patient-header d-flex flex-wrap align-items-center justify-content-between pb-2 mb-3 border-bottom border-secondary">
+                            <span>
+                                <i class="bi bi-person-badge me-2 text-info"></i>
+                                <strong>Patient ID:</strong> <span class="badge bg-secondary font-monospace">{{ patient.patient_id }}</span>
+                            </span>
+                            <div class="btn-group">
+                                <button type="button" class="btn btn-sm btn-outline-primary select-all-patient-btn" title="Select all series for this patient">Select Patient Series</button>
+                                <button type="button" class="btn btn-sm btn-outline-secondary deselect-all-patient-btn" title="Deselect all series for this patient">Deselect all</button>
+                            </div>
+                        </div>
+                        
+                        {% for study_uid, study in patient.studies %}
+                            <details class="study-block {% if study.partial_imported_uids %}study-block--partial-import{% endif %}" open>
+                                <summary>
+                                    <strong>{{ study.description|default:"(no description)" }}</strong>
+                                    <small class="text-muted"> ({{ study_uid }}) — {{ study.series|length }} series</small>
+                                    <span class="ms-2">
+                                        <button type="button" class="btn btn-sm btn-outline-secondary select-all-btn" title="Select all in study">Select all</button>
+                                        <button type="button" class="btn btn-sm btn-outline-secondary deselect-all-btn" title="Deselect all in study">Deselect all</button>
+                                    </span>
+                                </summary>
+                                {% if study.partial_imported_uids %}
+                                    <div class="alert alert-warning py-2 mt-2 mb-2 d-flex flex-wrap align-items-center justify-content-between gap-2">
+                                        <div>
+                                            <strong>Partial import detected:</strong>
+                                            {{ study.partial_imported_count }} series in this study already exist.
+                                            The highlighted rows can finish importing the remaining images.
+                                            {% if study.matched_existing_series %}
+                                                <div class="small mt-1">
+                                                    Existing series in Atlas:
+                                                    {% for existing_series in study.matched_existing_series %}
+                                                        <a href="{% url 'atlas:series_detail' existing_series.pk %}">{{ existing_series }}</a>{% if not forloop.last %}, {% endif %}
+                                                    {% endfor %}
+                                                </div>
+                                            {% endif %}
+                                        </div>
+                                        <button
+                                            type="button"
+                                            class="btn btn-sm btn-warning import-partial-series-btn"
+                                            data-series-uids="{{ study.partial_imported_uids|join:',' }}"
+                                            {% if study.preferred_case_id %}data-case-id="{{ study.preferred_case_id }}"{% endif %}
+                                        >Finish these imports</button>
+                                    </div>
+                                {% endif %}
+                                {% if study.import_suggestions %}
+                                    <div class="alert alert-info py-2 mt-2 mb-2">
+                                        <strong>Study already imported:</strong>
+                                        {% for suggestion in study.import_suggestions %}
+                                            <div class="d-flex flex-wrap align-items-center gap-2 mt-1">
+                                                <span>
+                                                    Case:
+                                                    <a href="{% url 'atlas:case_detail' suggestion.case.pk %}">{{ suggestion.case }}</a>
+                                                    ({{ suggestion.already_imported_count }} series already imported)
+                                                </span>
+                                                <button
+                                                    type="button"
+                                                    class="btn btn-sm btn-outline-primary import-missing-series-btn"
+                                                    data-case-id="{{ suggestion.case.pk }}"
+                                                    data-series-uids="{{ suggestion.missing_uids|join:',' }}"
+                                                >
+                                                    Import remaining {{ suggestion.missing_uids|length }} series
+                                                </button>
+                                            </div>
+                                        {% endfor %}
+                                    </div>
+                                {% endif %}
+                                <ul class="study-series-list">
+                                    {% for series, n, tags, date in study.series %}
+                                        {% if series in study.partial_imported_uids %}
+                                            {% if case %}
+                                                {% include 'atlas/partials/_series_item.html' with show_tags_link=True series_is_partial=True series_item_classes='series-item--partial-import' import_case_id=case.pk %}
+                                            {% else %}
+                                                {% include 'atlas/partials/_series_item.html' with show_tags_link=True series_is_partial=True series_item_classes='series-item--partial-import' import_case_id=study.preferred_case_id %}
+                                            {% endif %}
+                                        {% else %}
+                                            {% if case %}
+                                                {% include 'atlas/partials/_series_item.html' with show_tags_link=True series_is_partial=False series_item_classes='' import_case_id=case.pk %}
+                                            {% else %}
+                                                {% include 'atlas/partials/_series_item.html' with show_tags_link=True series_is_partial=False series_item_classes='' %}
+                                            {% endif %}
+                                        {% endif %}
+                                    {% endfor %}
+                                </ul>
+                            </details>
+                        {% endfor %}
+                    </div>
+                {% endfor %}
+            {% elif grouped_series %}
                 {% for study_uid, study in grouped_series %}
                     <details class="study-block {% if study.partial_imported_uids %}study-block--partial-import{% endif %}" open>
                         <summary>
@@ -233,7 +323,7 @@
         </div>
     </div>
 
-    <div class="modal fade" id="caseSeriesModal" tabindex="-1" aria-hidden="true">
+    <div class="modal fade" id="caseSeriesModal" aria-hidden="true">
         <div class="modal-dialog modal-xl modal-dialog-centered modal-dialog-scrollable">
             <div class="modal-content">
                 <div class="modal-header">
@@ -531,7 +621,7 @@
             });
         }
 
-        // Select / Deselect all series within a study block
+        // Select / Deselect all series within a study block or patient block
         document.addEventListener('click', function (e) {
             const target = e.target;
             if (target.matches('.select-all-btn')) {
@@ -562,6 +652,34 @@
                 });
                 if (typeof updateSelectionCount === 'function') updateSelectionCount();
             }
+            if (target.matches('.select-all-patient-btn')) {
+                const patientBlock = target.closest('.patient-block');
+                if (!patientBlock) return;
+                const inputs = patientBlock.querySelectorAll('input[name="selection"]');
+                inputs.forEach(cb => {
+                    if (!cb.disabled) {
+                        cb.checked = true;
+                        const li = cb.closest('.series-item');
+                        if (li) li.classList.add('selected');
+                        cb.dispatchEvent(new Event('change', { bubbles: true }));
+                    }
+                });
+                if (typeof updateSelectionCount === 'function') updateSelectionCount();
+            }
+            if (target.matches('.deselect-all-patient-btn')) {
+                const patientBlock = target.closest('.patient-block');
+                if (!patientBlock) return;
+                const inputs = patientBlock.querySelectorAll('input[name="selection"]');
+                inputs.forEach(cb => {
+                    if (!cb.disabled) {
+                        cb.checked = false;
+                        const li = cb.closest('.series-item');
+                        if (li) li.classList.remove('selected');
+                        cb.dispatchEvent(new Event('change', { bubbles: true }));
+                    }
+                });
+                if (typeof updateSelectionCount === 'function') updateSelectionCount();
+            }
         });
 
         // Listen for `case:selected` events dispatched by the case-search widget and perform the import
@@ -884,6 +1002,10 @@
             color: #ffffff;
         }
 
+        .select2-container {
+            width: 100% !important;
+        }
+
         #series-list li {
         }
         #series-list .selected {

atlas/tests/test_user_uploads.py

@@ -56,3 +56,43 @@ def test_user_uploads_partial_import_button_prefers_case_for_hash_matched_series
     content = response.content.decode("utf-8")
     assert 'class="btn btn-sm btn-warning import-partial-series-btn"' in content
     assert f'data-case-id="{primary_case.pk}"' in content
+
+
+@pytest.mark.django_db
+def test_user_uploads_patient_grouping_and_select2(client, admin_user):
+    client.force_login(admin_user)
+
+    # Create UncategorisedDicom with PatientID tag using bulk_create to avoid reading non-existent file
+    UncategorisedDicom.objects.bulk_create(
+        [
+            UncategorisedDicom(
+                image="pending-upload-patient.dcm",
+                user=admin_user,
+                series_instance_uid="uploaded-series-patient-1",
+                basic_dicom_tags={
+                    "SeriesInstanceUID": "uploaded-series-patient-1",
+                    "StudyInstanceUID": "study-patient-1",
+                    "StudyDescription": "Patient Study 1",
+                    "SeriesDescription": "Uploaded series",
+                    "Modality": "CT",
+                    "PatientID": "PAT-999-XYZ",
+                },
+            )
+        ]
+    )
+
+    response = client.get(reverse("atlas:user_uploads"))
+    assert response.status_code == 200
+    content = response.content.decode("utf-8")
+
+    # Verify patient grouping is rendered
+    assert "PAT-999-XYZ" in content
+    assert "Patient ID:" in content
+    assert "select-all-patient-btn" in content
+
+    # Verify form autocomplete widgets are in context
+    form = response.context["case_series_form"]
+    from dal import autocomplete
+    assert isinstance(form.fields["condition"].widget, autocomplete.ModelSelect2Multiple)
+    assert isinstance(form.fields["presentation"].widget, autocomplete.ModelSelect2Multiple)
+    assert isinstance(form.fields["procedures"].widget, autocomplete.ModelSelect2Multiple)

atlas/views.py

@@ -3343,9 +3343,15 @@ def user_uploads(
     for d in dicoms:
         tags = d.basic_dicom_tags
 
+        if tags is None or "PatientID" not in tags:
+            try:
+                d.save()
+                tags = d.basic_dicom_tags
+            except Exception:
+                pass
+
         if tags is None:
-            d.save()
+            continue
-            tags = d.basic_dicom_tags
 
         series_uid = tags.get("SeriesInstanceUID")
         if not series_uid:
@@ -3569,6 +3575,36 @@ def user_uploads(
                 )
                 study_data["preferred_case_id"] = sorted_suggestions[0]["case"].pk
 
+    # Now group the processed studies by PatientID
+    patient_groups = defaultdict(lambda: {
+        "studies": [],
+        "min_date": "99999999",
+    })
+
+    for study_uid, study_data in grouped_series:
+        patient_id = "Unknown Patient"
+        if study_data["series"]:
+            first_series_tags = study_data["series"][0][2]
+            patient_id = first_series_tags.get("PatientID") or "Unknown Patient"
+
+        pg = patient_groups[patient_id]
+        pg["studies"].append((study_uid, study_data))
+        study_date = study_data.get("date") or ""
+        if study_date and study_date < pg["min_date"]:
+            pg["min_date"] = study_date
+
+    grouped_patients = sorted(
+        [
+            {
+                "patient_id": patient_id,
+                "studies": pg["studies"],
+                "min_date": pg["min_date"],
+            }
+            for patient_id, pg in patient_groups.items()
+        ],
+        key=lambda x: x["min_date"] or ""
+    )
+
     case = False
     if case_id is not None:
         case = get_object_or_404(Case, pk=case_id)
@@ -3576,17 +3612,6 @@ def user_uploads(
     case_series_form = CaseForm(user=request.user)
     case_series_form.fields["previous_case"].required = False
     case_series_form.fields["previous_case"].widget = HiddenInput()
-    for field_name in ("condition", "presentation", "procedures"):
-        field = case_series_form.fields.get(field_name)
-        if field is None:
-            continue
-        field.widget = forms.SelectMultiple(
-            attrs={
-                "class": "form-select",
-                "size": 8,
-            }
-        )
-        field.widget.choices = field.choices
 
     return render(
         request,
@@ -3594,6 +3619,7 @@ def user_uploads(
         {
             "series_list": series_list,
             "grouped_series": grouped_series,
+            "grouped_patients": grouped_patients,
             "uploaded_series_uids": uploaded_series_uids,
             "case": case,
             "user": user,