i should break these commits up

atlas/views.py

@@ -31,6 +31,7 @@ from django.http import Http404, JsonResponse
 from django.http import HttpResponseRedirect, HttpResponse
 
 from generic.models import CidUser, CidUserExam
+from atlas.helpers import get_cases_available_to_user
 
 from .forms import (
     AddCollectionToCaseForm,
@@ -45,6 +46,7 @@ from .forms import (
     ConditionAutocompleteForm,
     ConditionForm,
     FindingForm,
+    ResourceForm,
     SelfReviewForm,
     SeriesForm,
     SeriesImageFormSet,
@@ -63,6 +65,7 @@ from .models import (
     Differential,
     PathologicalProcess,
     Presentation,
+    Resource,
     SelfReview,
     Series,
     Examination,
@@ -127,7 +130,12 @@ import logging
 from copy import deepcopy
 from django.forms.models import model_to_dict
 
-from generic.views import AuthorRequiredMixin, ExamCloneMixin, ExamViews, SeriesImagesZipViewBase
+from generic.views import (
+    AuthorRequiredMixin,
+    ExamCloneMixin,
+    ExamViews,
+    SeriesImagesZipViewBase,
+)
 from reversion.views import RevisionMixin
 import reversion
 
@@ -139,14 +147,6 @@ import difflib
 
 logger = logging.getLogger(__name__)
 
-def get_cases_available_to_user(user):
-    """Returns a queryset of cases available to the user"""
-    return Case.objects.filter(author=user) | Case.objects.filter(open_access=True)
-    if user.is_superuser:
-        return Case.objects.all()
-    else:
-        return Case.objects.filter(author=user) | Case.objects.filter(open_access=True)
-
 
 class AuthorOrCheckerRequiredMixin(object):
     def get_object(self, *args, **kwargs):
@@ -160,6 +160,7 @@ class AuthorOrCheckerRequiredMixin(object):
             raise PermissionDenied()  # or Http404
         return obj
 
+
 class AtlasEditorRequiredMixin(object):
     def get_object(self, *args, **kwargs):
         obj = super().get_object(*args, **kwargs)
@@ -170,6 +171,7 @@ class AtlasEditorRequiredMixin(object):
             return obj
         raise PermissionDenied("You must be an atlas editor to do this.")  # or Http404
 
+
 @login_required
 @user_has_case_view_access
 def case_detail(request, pk):
@@ -208,7 +210,7 @@ def series_detail(request, pk, finding_pk=None):
 
 
 @login_required
-#@user_is_atlas_editor
+# @user_is_atlas_editor
 def condition_detail(request, pk):
     condition = get_object_or_404(Condition, pk=pk)
 
@@ -216,7 +218,10 @@ def condition_detail(request, pk):
 
     can_merge = False
 
-    if request.user.is_superuser or request.user.groups.filter(name="atlas_editor").exists():
+    if (
+        request.user.is_superuser
+        or request.user.groups.filter(name="atlas_editor").exists()
+    ):
         can_merge = True
 
     # logging.debug(atlas.subspecialty.first().name.all())
@@ -275,7 +280,7 @@ def condition_merge(request, pk_to_merge):
 
 
 @login_required
-#@user_is_atlas_editor
+# @user_is_atlas_editor
 def subspecialty_detail(request, pk):
     subspecialty = get_object_or_404(Subspecialty, pk=pk)
 
@@ -290,7 +295,7 @@ def subspecialty_detail(request, pk):
 
 
 @login_required
-#@user_is_atlas_editor
+# @user_is_atlas_editor
 def presentation_detail(request, pk):
     presentation = get_object_or_404(Presentation, pk=pk)
 
@@ -305,7 +310,7 @@ def presentation_detail(request, pk):
 
 
 @login_required
-#@user_is_atlas_editor
+# @user_is_atlas_editor
 def pathological_process_detail(request, pk):
     pathological_process = get_object_or_404(PathologicalProcess, pk=pk)
 
@@ -320,7 +325,7 @@ def pathological_process_detail(request, pk):
 
 
 @login_required
-#@user_is_atlas_editor
+# @user_is_atlas_editor
 def structure_detail(request, pk):
     structure = get_object_or_404(Structure, pk=pk)
 
@@ -335,7 +340,7 @@ def structure_detail(request, pk):
 
 
 @login_required
-#@user_is_atlas_editor
+# @user_is_atlas_editor
 def finding_detail(request, pk):
     finding = get_object_or_404(Finding, pk=pk)
 
@@ -349,6 +354,13 @@ def finding_detail(request, pk):
     )
 
 
+@login_required
+def resource_detail(request, pk):
+    resource = get_object_or_404(Resource, pk=pk)
+
+    return render(request, "atlas/resource_detail.html", {"resource": resource})
+
+
 @login_required
 def author_detail(request, pk):
     # logging.debug(Author.objects.all())
@@ -381,11 +393,11 @@ def user_collections(request):
 
     return render(request, "atlas/user_collections.html", {"collections": collections})
 
+
 def add_case_to_collection(request, collection_id):
     if not request.htmx:
         return Http404
 
-
     collection = get_object_or_404(CaseCollection, pk=collection_id)
 
     if request.method == "POST":
@@ -395,14 +407,18 @@ def add_case_to_collection(request, collection_id):
             return HttpResponse("Case already in collection")
         print(case)
         collection.add_case(case)
-        return HttpResponse("Case added to collection")
+        return HttpResponse("Case added to collection (refresh to see)")
 
-
-    #if request.method == "POST":
+    # if request.method == "POST":
 
     cases = get_cases_available_to_user(request.user)
 
-    return render(request, "atlas/add_case_to_collection.html", {"cases": cases, "collection": collection})
+    return render(
+        request,
+        "atlas/add_case_to_collection.html",
+        {"cases": cases, "collection": collection},
+    )
+
 
 @login_required
 def user_uploads_series(request, series_instance_uid: str):
@@ -418,17 +434,25 @@ def user_uploads_series(request, series_instance_uid: str):
         {"dicoms": dicoms, "series_id": series_instance_uid},
     )
 
+
 @login_required
 @user_passes_test(lambda u: u.is_superuser)
 def all_uploads(request, case_id: int | None = None):
     return user_uploads(request, case_id, user_only=False)
 
+
 @user_passes_test(lambda u: u.is_superuser)
 def other_user_uploads(request, user_pk: int, case_id: int | None = None):
     return user_uploads(request, case_id, user_only=False, user_pk=user_pk)
 
+
 @login_required
-def user_uploads(request, case_id: int | None = None, user_only: bool = True, user_pk: int | None = None):
+def user_uploads(
+    request,
+    case_id: int | None = None,
+    user_only: bool = True,
+    user_pk: int | None = None,
+):
     user = request.user
     if user_only:
         dicoms = UncategorisedDicom.objects.filter(user=request.user)
@@ -446,7 +470,6 @@ def user_uploads(request, case_id: int | None = None, user_only: bool = True, us
             d.save()
             tags = d.basic_dicom_tags
 
-
         data[tags["SeriesInstanceUID"]].append((tags, d.created_date))
 
     series_list = []
@@ -461,7 +484,9 @@ def user_uploads(request, case_id: int | None = None, user_only: bool = True, us
         case = get_object_or_404(Case, pk=case_id)
 
     return render(
-        request, "atlas/user_uploads.html", {"series_list": series_list, "case": case, "user": user}
+        request,
+        "atlas/user_uploads.html",
+        {"series_list": series_list, "case": case, "user": user},
     )
 
 
@@ -513,9 +538,34 @@ class StructureDelete(RevisionMixin, AtlasEditorRequiredMixin, DeleteView):
     success_url = reverse_lazy("atlas:structure_view")
 
 
+class ResourceDelete(LoginRequiredMixin, DeleteView):
+    model = Resource
+    template_name = "confirm_delete.html"
+
+    success_url = reverse_lazy("atlas:resource_view")
+
+
+class ResourceCreate(LoginRequiredMixin, CreateView):
+    model = Resource
+    form_class = ResourceForm
+
+    def form_valid(self, form):
+        self.object = form.save(commit=False)
+        self.object.save()
+        form.instance.author.add(self.request.user.id)
+
+        return super().form_valid(form)
+
+
+class ResourceView(LoginRequiredMixin, ListView):
+    model = Resource
+    # form_class = ResourceForm
+
+
 class CaseCollectionCreate(RevisionMixin, LoginRequiredMixin, CreateView):
     model = CaseCollection
     form_class = CaseCollectionForm
+    template_name = "atlas/casecollection_form.html"
 
     def get_initial(self):
         # print(self.request)
@@ -553,7 +603,6 @@ class CaseCollectionCreate(RevisionMixin, LoginRequiredMixin, CreateView):
         self.object.save()
         form.instance.author.add(self.request.user.id)
 
-
         context = self.get_context_data(form=form)
         case_formset = context["case_formset"]
         if case_formset.is_valid():
@@ -618,7 +667,7 @@ class SeriesCreate(RevisionMixin, LoginRequiredMixin, CreateView):
 class CaseCollectionUpdate(RevisionMixin, AuthorOrCheckerRequiredMixin, UpdateView):
     model = CaseCollection
     form_class = CaseCollectionForm
-    template_name = "atlas/collection_update_form.html"
+    template_name = "atlas/casecollection_form.html"
 
     #    fields = '__all__'
     #    #fields = [ 'condition' ]
@@ -724,6 +773,18 @@ class SeriesUpdate(
             return super().form_invalid(form)
 
 
+class ResourceUpdate(LoginRequiredMixin, UpdateView):
+    model = Resource
+    form_class = ResourceForm
+
+    def form_valid(self, form):
+        self.object = form.save(commit=False)
+        self.object.save()
+        form.instance.author.add(self.request.user.id)
+
+        return super().form_valid(form)
+
+
 class ConditionUpdate(RevisionMixin, LoginRequiredMixin, UpdateView):
     model = Condition
     form_class = ConditionForm
@@ -775,7 +836,8 @@ class AtlasCreateBase(RevisionMixin, LoginRequiredMixin):
                 self.request.POST, self.request.FILES
             )
             context["caseresource_formset"] = CaseResourceFormSet(
-                self.request.POST, self.request.FILES,
+                self.request.POST,
+                self.request.FILES,
                 form_kwargs={"user": self.request.user},
             )
             context["series_formset"].full_clean()
@@ -805,7 +867,11 @@ class AtlasCreateBase(RevisionMixin, LoginRequiredMixin):
         series_formset = context["series_formset"]
         casedifferential_formset = context["casedifferential_formset"]
         caseresource_formset = context["caseresource_formset"]
-        if series_formset.is_valid() and casedifferential_formset.is_valid() and caseresource_formset.is_valid():
+        if (
+            series_formset.is_valid()
+            and casedifferential_formset.is_valid()
+            and caseresource_formset.is_valid()
+        ):
             response = super().form_valid(form)
             series_formset.instance = self.object
             series_formset.save()
@@ -871,8 +937,15 @@ class AtlasUpdate(
             context["casedifferential_formset"] = CaseDifferentialFormSet(
                 self.request.POST, self.request.FILES, instance=self.object
             )
+            context["caseresource_formset"] = CaseResourceFormSet(
+                self.request.POST,
+                self.request.FILES,
+                instance=self.object,
+                form_kwargs={"user": self.request.user},
+            )
             context["series_formset"].full_clean()
             context["casedifferential_formset"].full_clean()
+            context["caseresource_formset"].full_clean()
         else:
             context["series_formset"] = SeriesFormSet(
                 instance=self.object, form_kwargs={"user": self.request.user}
@@ -880,6 +953,10 @@ class AtlasUpdate(
             context["casedifferential_formset"] = CaseDifferentialFormSet(
                 instance=self.object
             )
+            context["caseresource_formset"] = CaseResourceFormSet(
+                instance=self.object,
+                form_kwargs={"user": self.request.user},
+            )
         return context
 
     def form_valid(self, form):
@@ -891,13 +968,20 @@ class AtlasUpdate(
         context = self.get_context_data(form=form)
         series_formset = context["series_formset"]
         casedifferential_formset = context["casedifferential_formset"]
+        caseresource_formset = context["caseresource_formset"]
         # logger.debug(formset.is_valid())
-        if series_formset.is_valid() and casedifferential_formset.is_valid():
+        if (
+            series_formset.is_valid()
+            and casedifferential_formset.is_valid()
+            and caseresource_formset.is_valid()
+        ):
             response = super().form_valid(form)
             series_formset.instance = self.object
             series_formset.save()
             casedifferential_formset.instance = self.object
             casedifferential_formset.save()
+            caseresource_formset.instance = self.object
+            caseresource_formset.save()
 
             return response
         else:
@@ -970,7 +1054,6 @@ class AtlasClone(AtlasCreateBase, AuthorOrCheckerRequiredMixin, CreateView):
         return initial_data
 
 
-
 @login_required
 @user_is_author_or_atlas_editor
 def atlas_scrap(request, pk):
@@ -1069,6 +1152,7 @@ class FindingView(LoginRequiredMixin, SingleTableMixin, FilterView):
 
     filterset_class = FindingFilter
 
+
 @login_required
 def case_order_dicom(request, pk):
     if request.htmx:
@@ -1086,11 +1170,12 @@ def case_order_dicom(request, pk):
                 fail.append(series.pk)
 
         if fail:
-            return HttpResponse(f"Unable to order series {','.join([str(i) for i in fail])}")
+            return HttpResponse(
+                f"Unable to order series {','.join([str(i) for i in fail])}"
+            )
         else:
             return HttpResponse("Series reordered")
 
-
     raise Http404
 
 
@@ -1105,6 +1190,7 @@ def series_order_dicom(request, pk):
 
     return redirect("atlas:series_detail", pk=pk)
 
+
 @login_required
 def image_diff(request):
     if request.htmx:
@@ -1116,23 +1202,23 @@ def image_diff(request):
             second: SeriesImage = get_object_or_404(SeriesImage, pk=image_ids[1])
 
             first_ds = pydicom.read_file(first.image.file)
-            #del first_ds.PixelData
-            #j1 = first_ds.to_json_dict()
+            # del first_ds.PixelData
+            # j1 = first_ds.to_json_dict()
             f = print_dicom(first_ds, join=False)
 
             second_ds = pydicom.read_file(second.image.file)
-            #del second_ds.PixelData
-            #j2 = second_ds.to_json_dict()
+            # del second_ds.PixelData
+            # j2 = second_ds.to_json_dict()
             s = print_dicom(second_ds, join=False)
 
             diff = difflib.HtmlDiff().make_table(f, s)
-            
+
             dict_diff = pprint.pformat(compare_dicom_datasets(first_ds, second_ds))
 
-            #return HttpResponse(diff)
+            # return HttpResponse(diff)
 
             return HttpResponse(f"<pre>{dict_diff}</pre><br/>{diff}")
-        
+
         else:
             ds_set = []
             for pk in image_ids:
@@ -1142,7 +1228,6 @@ def image_diff(request):
             dict_diff = pprint.pformat(compare_dicom_datasets(*ds_set))
             return HttpResponse(f"<pre>{dict_diff}</pre>")
 
-
     return HttpResponse("Fail")
 
 
@@ -1366,6 +1451,7 @@ class CollectionView(LoginRequiredMixin, SingleTableMixin, FilterView):
 
     filterset_class = CaseCollectionFilter
 
+
 @user_is_collection_author_or_atlas_editor
 def collection_viva(request, pk):
     collection = get_object_or_404(CaseCollection, pk=pk)
@@ -1378,11 +1464,12 @@ def collection_viva(request, pk):
         {"collection": collection, "cases": cases, "can_edit": True},
     )
 
+
 @user_is_collection_author_or_atlas_editor
 def collection_viva_case(request, pk, case_number):
     collection = get_object_or_404(CaseCollection, pk=pk)
 
-    #cases = collection.cases.all().order_by("casedetail__sort_order")
+    # cases = collection.cases.all().order_by("casedetail__sort_order")
     current_case = collection.get_case_by_index(case_number)
 
     return render(
@@ -1391,6 +1478,7 @@ def collection_viva_case(request, pk, case_number):
         {"collection": collection, "current_case": current_case},
     )
 
+
 @user_is_collection_author_or_atlas_editor
 def collection_viva_series(request, pk, series_id):
     collection = get_object_or_404(CaseCollection, pk=pk)
@@ -1408,8 +1496,10 @@ def collection_viva_series(request, pk, series_id):
 def collection_detail(request, pk):
     collection = get_object_or_404(CaseCollection, pk=pk)
 
-    #cases = collection.cases.all().order_by("casedetail__sort_order")
-    casedetails =  CaseDetail.objects.filter(collection=collection).order_by("sort_order")
+    # cases = collection.cases.all().order_by("casedetail__sort_order")
+    casedetails = CaseDetail.objects.filter(collection=collection).order_by(
+        "sort_order"
+    )
 
     return render(
         request,
@@ -1725,12 +1815,20 @@ def collection_case_view_take(
                 else:
                     form = ReportAnswerForm(request.POST)
 
-                if not cid_user_exam.completed:
+                if not cid_user_exam.completed and not (
+                    answer is not None and answer.completed
+                ):
                     if form.is_valid():
                         answer = form.save(commit=False)
                         answer.set_cid_or_user(cid=cid, user=request.user)
                         answer.question = case_detail
                         # answer.published_date = timezone.now()
+
+                        if "complete_case" in request.POST:
+                            if not collection.self_review:
+                                raise Http404("Self review not enabled")
+                            answer.completed = True
+
                         answer.save()
 
                         cid_user_exam.end_time = timezone.now()
@@ -1769,7 +1867,11 @@ def collection_case_view_take(
 
     # Set what details a user is / is not able to view when taking the case
     # this can be configured via the collection edit menu
-    if collection.publish_results or cid_user_exam.completed:
+    if (
+        collection.publish_results
+        or cid_user_exam.completed
+        or (answer is not None and answer.completed)
+    ):
         completed = True
         show_title = collection.show_title_post
         show_history = collection.show_history_post
@@ -1778,6 +1880,8 @@ def collection_case_view_take(
         show_report = collection.show_report_post
 
         self_review = cid_user_exam.selfreview_set.filter(case=case)
+
+        resources = case.caseresource_set.all()
     else:
         completed = False
         show_title = collection.show_title_pre
@@ -1787,6 +1891,8 @@ def collection_case_view_take(
         show_report = collection.show_report_pre
         self_review = []
 
+        resources = case.caseresource_set.filter(pre_review=True)
+
     return render(
         request,
         "atlas/collection_case_view_take.html",
@@ -1806,6 +1912,7 @@ def collection_case_view_take(
             "show_description": show_description,
             "show_discussion": show_discussion,
             "show_report": show_report,
+            "resources": resources,
             "cid_user_exam": cid_user_exam,
             "completed": completed,
             "self_review": self_review,
@@ -1856,11 +1963,13 @@ def collection_case_view(request, pk, case_number):
         },
     )
 
+
 def collection_dicom_json(request, pk):
     collection = get_object_or_404(CaseCollection, pk=pk)
 
     return JsonResponse(collection.get_ohif_dicom_json())
 
+
 @user_is_author_or_atlas_editor
 def use_dates_as_descriptions(request, pk):
     case = get_object_or_404(Case, pk=pk)
@@ -1871,16 +1980,19 @@ def use_dates_as_descriptions(request, pk):
 
     return HttpResponse("Done")
 
+
 def case_dicom_json(request, pk):
     case = get_object_or_404(Case, pk=pk)
 
     return JsonResponse(case.get_case_dicom_json())
 
+
 def series_dicom_json(request, pk):
     series = get_object_or_404(Series, pk=pk)
 
     return JsonResponse(series.get_ohif_dicom_json())
 
+
 @user_is_collection_author_or_atlas_editor
 def delete_collection_cid_answers(request, exam_id, cid):
     collection = get_object_or_404(CaseCollection, pk=exam_id)
@@ -2227,7 +2339,7 @@ def combine_series(request):
     it will not migrate other models such as SeriesFinding or other details
     """
     series_ids = request.POST.getlist("series-ids")
-    #series = get_object_or_404(Series, pk=series_id)
+    # series = get_object_or_404(Series, pk=series_id)
     if len(series_ids) < 2:
         return HttpResponse("Not enough series to combine")
 
@@ -2252,7 +2364,8 @@ def combine_series(request):
         series.delete()
 
     return HttpResponse(f"Series {series_ids} combines")
-    #return HttpResponse("Fail")
+    # return HttpResponse("Fail")
+
 
 class CaseCollectionAuthorUpdate(RevisionMixin, AuthorRequiredMixin, UpdateView):
     model = CaseCollection
@@ -2264,6 +2377,7 @@ class CaseCollectionAuthorUpdate(RevisionMixin, AuthorRequiredMixin, UpdateView)
         context["collection"] = context["object"]
         return context
 
+
 class CaseAuthorUpdate(RevisionMixin, AuthorRequiredMixin, UpdateView):
     model = Case
     form_class = CaseAuthorForm
@@ -2272,4 +2386,4 @@ class CaseAuthorUpdate(RevisionMixin, AuthorRequiredMixin, UpdateView):
     def get_context_data(self, **kwargs):
         context = super(CaseAuthorUpdate, self).get_context_data(**kwargs)
         context["collection"] = context["object"]
-        return context
+        return context