.

Dockerfile

@@ -1,5 +1,6 @@
 # pull official base image
 FROM python:3.12.1-slim
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
 
 # set work directory
 WORKDIR /usr/src/rad
@@ -17,9 +18,14 @@ RUN apt-get update && apt-get -y install postgresql postgresql-contrib git libca
 
 
 # install dependencies
-RUN pip install --upgrade pip
+#RUN pip install --upgrade pip
 COPY ./requirements.txt .
-RUN pip install -r requirements.txt
+RUN uv venv /opt/venv
+# Use the virtual environment automatically
+ENV VIRTUAL_ENV=/opt/venv
+# Place entry points in the environment at the front of the path
+ENV PATH="/opt/venv/bin:$PATH"
+RUN uv pip install -r requirements.txt
 
 # copy project
 COPY . .

anatomy/models.py

@@ -22,6 +22,7 @@ from collections import defaultdict
 from helpers.images import image_as_base64
 
 import reversion
+import urllib.parse
 
 image_storage = FileSystemStorage(
     # Physical file location ROOT
@@ -540,6 +541,8 @@ class UserAnswer(UserAnswerBase):
     #     s = self.answer.lower().strip()
     #     s = s.translate(str.maketrans('', '', string.punctuation))
     #     return s
+    def get_answer_url_safe(self):
+        return urllib.parse.quote(self.answer_compare)
 
     def get_answer_string(self):
         return self.answer

anatomy/templates/anatomy/mark.html

@@ -38,22 +38,22 @@
                         {% for answer in user_answers %}
 
                             {% if answer in answer_suggest_incorrect %}
-                                <li><pre><span class="answer incorrect suggest" title="{{answer}}" data-answerurl="{% url 'anatomy:question_user_answers_by_compare' question.pk answer %}">{{ answer }}</span></pre></li>
+                                <li><pre><span class="answer incorrect suggest" title="{{answer}}" data-answerurl="{% url 'anatomy:question_user_answers_by_compare' question.pk answer.get_answer_url_safe %}">{{ answer }}</span></pre></li>
                             {% else %}
-                                <li><pre><span class="answer not-marked" title="{{answer}}" data-answerurl="{% url 'anatomy:question_user_answers_by_compare' question.pk answer %}">{{ answer }}</span></pre></li>
+                                <li><pre><span class="answer not-marked" title="{{answer}}" data-answerurl="{% url 'anatomy:question_user_answers_by_compare' question.pk answer.get_answer_url_safe %}">{{ answer }}</span></pre></li>
                             {% endif %}
                         {% endfor %}
                     </ul>
                     Marked:
                     <ul id="marked-answer-list" class="answer-list">
                         {% for answer in correct_answers %}
-                            <li><pre><span class="answer correct" title="{{answer}}" data-answerurl="{% url 'anatomy:question_user_answers_by_compare' question.pk answer %}">{{ answer }}</span></pre></li>
+                            <li><pre><span class="answer correct" title="{{answer}}" data-answerurl="{% url 'anatomy:question_user_answers_by_compare' question.pk answer.get_answer_url_safe %}">{{ answer }}</span></pre></li>
                         {% endfor %}
                         {% for answer in half_mark_answers %}
-                            <li><pre><span class="answer half-correct" title="{{answer}}" data-answerurl="{% url 'anatomy:question_user_answers_by_compare' question.pk answer %}">{{ answer }}</span></pre></li>
+                            <li><pre><span class="answer half-correct" title="{{answer}}" data-answerurl="{% url 'anatomy:question_user_answers_by_compare' question.pk answer.get_answer_url_safe %}">{{ answer }}</span></pre></li>
                         {% endfor %}
                         {% for answer in incorrect_answers %}
-                            <li><pre><span class="answer incorrect" title="{{answer}}" data-answerurl="{% url 'anatomy:question_user_answers_by_compare' question.pk answer %}">{{ answer }}</span></pre></li>
+                            <li><pre><span class="answer incorrect" title="{{answer}}" data-answerurl="{% url 'anatomy:question_user_answers_by_compare' question.pk answer.get_answer_url_safe %}">{{ answer }}</span></pre></li>
                         {% endfor %}
                     </ul>
                     <div class="mark-buttons">

atlas/templates/atlas/case_display_block.html

@@ -199,7 +199,13 @@
 
 
     <p class="pre-whitespace"><b>Previous case:</b> {{ case.previous_case.get_link }}</p>
-    <p class="pre-whitespace"><b>Next case:</b> {{ case.next_case.get_link }}</p>
+    <p class="pre-whitespace"><b>Next case:</b> 
+        {% if case.next_case %}
+        {{ case.next_case.get_link }}
+        {% else %}
+        <a href="{% url 'atlas:case_clone_next' case.pk %}">Clone and add next case</a>
+        {% endif %}
+    </p>
     <div>
         {% include 'question_notes.html' %}
 

atlas/urls.py

@@ -306,6 +306,7 @@ urlpatterns = [
         name="structure_update",
     ),
     path("structure/create", views.StructureCreate.as_view(), name="structure_create"),
+    path("series/<int:pk>/thumbnail/fail", views.series_thumbnail_fail, name="series_thumbnail_fail"),
     path("series/<int:pk>/thumbnail", views.series_thumbnail, name="series_thumbnail"),
     # TODO: case context series viewing (so that we can view series in the context of a case)
     path("series/<int:pk>", views.series_detail, name="series_detail"),
@@ -372,6 +373,7 @@ urlpatterns = [
         name="case_collection_form",
     ),
     path("case/<int:pk>/clone", views.AtlasClone.as_view(), name="case_clone"),
+    path("case/<int:pk>/clone/next", views.AtlasCloneNext.as_view(), name="case_clone_next"),
     # path("verified/", views.verified, name="verified"),
     # path("all_questions/", views.all_questions, name="all_questions"),
     path("case/<int:pk>/scrap", views.atlas_scrap, name="case_scrap"),

atlas/views.py

@@ -197,13 +197,17 @@ def case_detail(request, pk):
     # logging.debug(atlas.subspecialty.first().name.all())
     return render(request, "atlas/case_detail.html", {"case": case})
 
+@login_required
+@user_is_author_or_atlas_series_checker_or_atlas_marker_or_open_access
+def series_thumbnail_fail(request, pk):
+    return series_thumbnail(request, pk=pk, fail_loudly=True)
 
 @login_required
 @user_is_author_or_atlas_series_checker_or_atlas_marker_or_open_access
-def series_thumbnail(request, pk, finding_pk=None):
+def series_thumbnail(request, pk, fail_loudly=False):
     series = get_object_or_404(Series, pk=pk)
 
-    thumbnail, _ = series.get_thumbnail(recreate=True)
+    thumbnail, _ = series.get_thumbnail(recreate=True, fail_loudly=fail_loudly)
 
     return HttpResponse(thumbnail)
 
@@ -1115,7 +1119,6 @@ def add_collection_to_case_form(request, case_id):
 #        pk = self.kwargs["pk"]
 #        return reverse("atlas:case_detail", kwargs={"pk": pk})
 
-
 class AtlasClone(AtlasCreateBase, AuthorOrCheckerRequiredMixin, CreateView):
     """Clones a existing atlas"""
 
@@ -1138,7 +1141,14 @@ class AtlasClone(AtlasCreateBase, AuthorOrCheckerRequiredMixin, CreateView):
             else:
                 pass
 
-        initial_data = model_to_dict(old_object, exclude=["id"])
+        initial_data = model_to_dict(old_object, exclude=["id", "previous_case"])
+        return initial_data
+
+class AtlasCloneNext(AtlasClone):
+    """Extends AtlasClone to set the previous_case field to the case being cloned"""
+    def get_initial(self):
+        initial_data = super().get_initial()
+        initial_data["previous_case"] = self.kwargs["pk"]
         return initial_data
 
 

docker/docker-compose.yml

@@ -1,5 +1,3 @@
-version: '3.8'
-
 services:
   web:
     build: ./rad

generic/models.py

@@ -42,6 +42,8 @@ from django.contrib.auth.models import User
 from django.forms.models import model_to_dict
 from django.forms.utils import from_current_timezone, to_current_timezone
 
+from loguru import logger
+
 
 def findMiddle(input_list):
     """Returns the middle element of a list"""
@@ -419,7 +421,7 @@ class SeriesBase(models.Model):
             else:
                 return format_html('", "'.join(images))
 
-    def get_thumbnail(self, recreate=False):
+    def get_thumbnail(self, recreate=False, fail_loudly=False):
         images = self.images.filter(removed=False)
 
         if len(images) < 1:
@@ -431,7 +433,9 @@ class SeriesBase(models.Model):
             if recreate:
                 thumbnailer.delete_thumbnails()
             thumbnail = thumbnailer["exam-list"]
-        except InvalidImageFormatError:
+        except InvalidImageFormatError as e:
+            if fail_loudly:
+                raise e
             return format_html(
                 '<img title="{}" src="/static/not-found-image.jpg" />', img
             ), len(images)

generic/views.py

@@ -33,8 +33,10 @@ from django.utils.decorators import method_decorator
 
 from django.core.cache import cache
 
+
 import json
 import urllib
+import urllib.parse
 
 from django.views import View
 from django.views.generic.edit import CreateView, UpdateView, DeleteView
@@ -2652,6 +2654,7 @@ class GenericViewBase:
     @method_decorator(login_required)
     def question_user_answers_by_compare(self, request, pk, answer_compare):
         print(answer_compare)
+        answer_compare = urllib.parse.unquote(answer_compare)
         return self.question_user_answers(request, pk, answer_compare)
 
     @method_decorator(login_required)

helpers/images.py

@@ -62,7 +62,7 @@ def pil_dicom_image(source, exif_orientation=True, **options):
     #source = BytesIO(source.read())
 
     # open file with pydicom
-    ds = pydicom.read_file(source)
+    ds = pydicom.dcmread(source)
 
     # return the image file
     return get_PIL_image(ds)

requirements.txt

@@ -1,5 +1,5 @@
 #Django==3.2.13
-Django==5.0.2
+Django==5.1.4
 django_debug_toolbar
 django_jquery
 django_reversion
@@ -53,3 +53,4 @@ django_svelte_jsoneditor
 psutil
 django-psutil-dash
 django-template-partials
+easy_thumbnails