add a normals feature
This commit is contained in:
Ross
@@ -46,6 +46,9 @@
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<li>
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<a class="dropdown-item" href="{% url 'atlas:case_create' %}"><i class="bi bi-plus-square me-1" aria-hidden="true"></i>Create Case</a>
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</li>
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<li>
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<a class="dropdown-item" href="{% url 'atlas:normals_list' %}"><i class="bi bi-file-earmark-check me-1" aria-hidden="true"></i>Normals</a>
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</li>
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</ul>
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</li>
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<li class="nav-item dropdown">
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@@ -69,6 +72,7 @@
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<li class="nav-item">
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<a class="nav-link" href="{% url 'atlas:resource_view' %}" title="Resources"><i class="bi bi-folder2-open me-1" aria-hidden="true"></i>Resources</a>
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</li>
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<li class="nav-item">
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<a class="nav-link" href="{% url 'atlas:user_uploads' %}" title="View unimported uploads"><i class="bi bi-upload me-1" aria-hidden="true"></i>Uploads</a>
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</li>
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@@ -147,6 +147,10 @@
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{# Diagnostic certainty as a badge #}
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Diagnostic certainty: <span class="badge bg-info text-dark ms-2">{{ case.get_diagnostic_certainty_display }}</span>
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{# Normal toggle HTMX block #}
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<div class="mt-1">
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{% include "atlas/partials/_normal_toggle.html" %}
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</div>
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</div>
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</div>
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@@ -1,5 +1,6 @@
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{% extends "atlas/base.html" %}
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{% load static %}
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{% load crispy_forms_tags %}
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{% block content %}
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<div class="container">
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@@ -12,7 +13,7 @@
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<div class="mb-2">
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{{ field.label_tag }}
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{{ field }}
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+ </div>
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</div>
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{% endfor %}
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<div class="mb-2">
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<button class="btn btn-primary" type="submit">Filter</button>
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@@ -22,13 +23,18 @@
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</div>
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</div>
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<div class="list-group">
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{% for normal in page_obj.object_list %}
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{% include "atlas/partials/_normal_row.html" with normal=normal %}
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{% empty %}
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<div class="list-group-item">No normal cases found.</div>
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{% endfor %}
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</div>
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{% if page_obj.object_list %}
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<div class="list-group">
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{% for normal in page_obj.object_list %}
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<a class="list-group-item list-group-item-action" href="{% url 'atlas:case_detail' normal.case.pk %}">
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{{ normal.case.title }}{% if normal.age_years %} — {{ normal.age_years }} yrs{% endif %}
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<div class="small text-muted">Added {{ normal.added_date }}</div>
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</a>
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{% endfor %}
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</div>
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{% else %}
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<div class="list-group-item">No normal cases found.</div>
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{% endif %}
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<nav aria-label="Page navigation">
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<ul class="pagination mt-3">
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@@ -0,0 +1,28 @@
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{% load static %}
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<div id="normal-toggle-block">
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{% if case.normal_case %}
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<span class="badge bg-success">Normal</span>
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<small class="text-muted">{% if case.normal_case.age_years %}{{ case.normal_case.age_years }}y{% else %}age unknown{% endif %}</small>
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{% if is_atlas_editor %}
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<button class="btn btn-sm btn-outline-danger ms-2"
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hx-post="{% url 'atlas:case_toggle_normal' case.pk %}"
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hx-target="#normal-toggle-block"
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hx-swap="outerHTML"
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hx-confirm="Unmark this case as normal?">
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Unmark normal
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</button>
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{% endif %}
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{% else %}
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{% if is_atlas_editor %}
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<button class="btn btn-sm btn-outline-primary"
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hx-post="{% url 'atlas:case_toggle_normal' case.pk %}"
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hx-target="#normal-toggle-block"
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hx-swap="outerHTML">
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Mark as normal
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</button>
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{% else %}
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<span class="text-muted">Normal status only editable by atlas editors</span>
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{% endif %}
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{% endif %}
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</div>
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@@ -455,6 +455,7 @@ urlpatterns = [
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# path("unchecked/", views.unchecked_list, name="unchecked_list"),
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# path("verified/<int:pk>/", views.verified_detail, name="verified_detail"),
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path("case/<int:pk>/", views.case_detail, name="case_detail"),
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path("case/<int:pk>/toggle_normal/", views.toggle_case_normal, name="case_toggle_normal"),
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# path("case/<int:pk>/collection-form", views.AddCollectionToCaseView.as_view(), name="case_collection_form"),
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path(
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"case/<int:case_id>/collection-form",
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@@ -456,6 +456,8 @@ def case_detail(request, pk):
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case = get_case_for_case_detail(pk)
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can_edit = case.check_user_can_edit(request.user)
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is_atlas_editor = request.user.is_superuser or request.user.groups.filter(name="atlas_editor").exists()
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return render(
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request,
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"atlas/case_detail.html",
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@@ -463,9 +465,98 @@ def case_detail(request, pk):
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"case": case,
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"cimar_sid": request.user.userprofile.cimar_sid,
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"can_edit": can_edit,
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"is_atlas_editor": is_atlas_editor,
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},
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)
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@login_required
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@require_POST
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def toggle_case_normal(request, pk):
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"""HTMX endpoint to toggle the NormalCase mark for a Case.
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- Only users in the 'atlas_editor' group or superusers may toggle.
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- On create, attempt to auto-extract age_years from DICOM metadata.
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- Returns an HTML fragment that replaces the toggle block.
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"""
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case = get_case_for_case_detail(pk)
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# Permission: atlas editors or superusers
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if not (request.user.is_superuser or request.user.groups.filter(name="atlas_editor").exists()):
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return HttpResponse(status=403)
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# If already marked normal, unmark (delete the NormalCase)
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try:
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normal = case.normal_case
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except Exception:
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normal = None
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if normal is not None:
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normal.delete()
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else:
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# Attempt to auto-extract age from DICOM
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age = None
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try:
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from datetime import datetime
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import re
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# Iterate series then images to find first usable DICOM
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for series in case.series.all():
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img = series.images.filter(removed=False).first()
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if not img:
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continue
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ds = img.get_dicom_data()
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if not ds:
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continue
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# Try PatientAge (format often like '045Y' or '45Y')
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try:
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pa = getattr(ds, "PatientAge", None)
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except Exception:
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pa = None
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if pa:
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s = str(pa)
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m = re.search(r"(\d+)", s)
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if m:
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age = int(m.group(1))
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break
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# Try birthdate + studydate
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try:
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pbd = getattr(ds, "PatientBirthDate", None)
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sdate = getattr(ds, "StudyDate", None) or getattr(ds, "AcquisitionDate", None) or getattr(ds, "SeriesDate", None)
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except Exception:
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pbd = None
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sdate = None
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if pbd and sdate:
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try:
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bd = datetime.strptime(str(pbd), "%Y%m%d")
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sd = datetime.strptime(str(sdate), "%Y%m%d")
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years = round((sd - bd).days / 365.25)
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age = int(years)
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break
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except Exception:
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pass
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except Exception:
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age = None
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# Create NormalCase
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from .models import NormalCase
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NormalCase.objects.create(case=case, age_years=age, added_by=request.user)
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# Render the updated fragment
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is_atlas_editor = request.user.is_superuser or request.user.groups.filter(name="atlas_editor").exists()
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html = render_to_string(
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"atlas/partials/_normal_toggle.html",
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{"case": case, "user": request.user, "is_atlas_editor": is_atlas_editor},
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request=request,
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)
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return HttpResponse(html)
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@login_required
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@user_is_author_or_atlas_series_checker_or_atlas_marker_or_open_access
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def series_thumbnail_fail(request, pk):
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