start atlas app
This commit is contained in:
Ross
Executable
+547
@@ -0,0 +1,547 @@
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import json
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from django.shortcuts import render, get_object_or_404, redirect
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from django import forms
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# from django.contrib.auth.models import User
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from django.contrib.auth.decorators import login_required, user_passes_test
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from django.contrib.auth.models import User
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from django.core.exceptions import (
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ObjectDoesNotExist,
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PermissionDenied,
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ViewDoesNotExist,
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)
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from django.contrib.auth.mixins import LoginRequiredMixin
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from django.views.generic.detail import DetailView
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from generic.mixins import SuperuserRequiredMixin
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from django.views.generic.edit import CreateView, UpdateView, DeleteView
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from django.views.generic import ListView
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from django.views.decorators.csrf import csrf_exempt
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from django.urls import reverse_lazy, reverse
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from django.http import Http404, JsonResponse
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from django.http import HttpResponseRedirect, HttpResponse
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from .forms import (
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AtlasForm,
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SeriesForm,
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SeriesImageFormSet,
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MarkAtlasQuestionDoubleForm,
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MarkAtlasQuestionSingleForm,
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SeriesFormSet,
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ExaminationForm,
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ExamForm,
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)
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from .models import (
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Case,
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Series,
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Examination,
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)
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from .tables import AtlasTable, SeriesTable, UserAnswerTable
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from .filters import AtlasFilter, SeriesFilter, UserAnswerFilter
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from django_tables2 import SingleTableView, SingleTableMixin
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from django_filters.views import FilterView
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from .decorators import (
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user_is_author_or_atlas_checker,
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user_is_author_or_atlas_checker_or_atlas_marker,
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user_is_author_or_atlas_series_checker_or_atlas_marker,
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user_is_atlas_checker,
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user_is_author_or_atlas_series_checker,
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user_is_atlas_marker,
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user_is_author_or_atlas_checker_or_atlas_marker,
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)
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from collections import defaultdict
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import json
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import statistics
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import plotly.express as px
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from django.core.cache import cache
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from django.conf import settings
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from helpers.images import image_as_base64
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import logging
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from copy import deepcopy
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from django.forms.models import model_to_dict
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from atlas.forms import AtlasCreationDefaultForm
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from atlas.models import AtlasCreationDefault
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from generic.views import ExamCloneMixin, ExamViews
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from reversion.views import RevisionMixin
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import reversion
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from rest_framework import viewsets
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from .serializers import ExamSerializer
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from zipview.views import BaseZipView
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import os
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logger = logging.getLogger(__name__)
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class AuthorOrCheckerRequiredMixin(object):
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def get_object(self, *args, **kwargs):
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obj = super().get_object(*args, **kwargs)
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if (
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self.request.user.groups.filter(name="atlas_checker").exists()
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or self.request.user.is_superuser
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):
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return obj
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if self.request.user not in obj.get_author_objects():
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raise PermissionDenied() # or Http404
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return obj
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@login_required
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@user_is_author_or_atlas_checker_or_atlas_marker
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def case_detail(request, pk):
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atlas = get_object_or_404(Case, pk=pk)
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# if request.user not in atlas.author.all():
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# raise PermissionDenied
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# logging.debug(atlas.subspecialty.first().name.all())
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return render(request, "atlas/case_detail.html", {"question": atlas})
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@login_required
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@user_is_author_or_atlas_series_checker_or_atlas_marker
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def atlas_series_detail(request, pk):
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series = get_object_or_404(Series, pk=pk)
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# if request.user not in atlas.author.all():
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# raise PermissionDenied
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# logging.debug(atlas.subspecialty.first().name.all())
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return render(request, "atlas/atlas_series.html", {"series": series})
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@login_required
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@user_is_author_or_atlas_checker
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def author_detail(request, pk):
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# logging.debug(Author.objects.all())
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# author = get_object_or_404(Author, pk=pk)
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author = User.objects.get(pk=pk)
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atlas = Case.objects.filter(author=pk)
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return render(
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request, "atlas/category_detail.html", {"category": author, "atlas": atlas}
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)
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@user_is_author_or_atlas_checker
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def author_list(request):
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authors = User.objects.all()
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return render(request, "atlas/author_list.html", {"authors": authors})
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class AtlasDelete(RevisionMixin, AuthorOrCheckerRequiredMixin, DeleteView):
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model = Case
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success_url = reverse_lazy("atlas:atlas_view")
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class SeriesDelete(RevisionMixin, AuthorOrCheckerRequiredMixin, DeleteView):
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model = Series
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success_url = reverse_lazy("atlas:atlas_series_view")
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@login_required
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@user_is_author_or_atlas_checker
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def case_clone(request, pk):
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new_item = get_object_or_404(Case, pk=pk)
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new_item.pk = None # autogen a new pk (item_id)
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# new_item.name = "Copy of " + new_item.name #need to change uniques
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form = AtlasForm(request.POST or None, instance=new_item)
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series_formset = SeriesFormSet()
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if form.is_valid():
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form.instance.author.add(request.user.id)
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# logger.debug(formset.is_valid())
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if series_formset.is_valid():
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response = super().form_valid(form)
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series_formset.instance = obj
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series_formset.save()
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return response
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else:
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return super().form_invalid(form)
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context = {
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"form": form,
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"series_formset": series_formset,
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# other context
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}
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return render(request, "atlas/atlas_form.html", context)
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class SeriesCreate(RevisionMixin, LoginRequiredMixin, CreateView):
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model = Series
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form_class = SeriesForm
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def get_initial(self):
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# print(self.request)
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if "pk" in self.kwargs:
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initial = super().get_initial()
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case = get_object_or_404(Case, pk=self.kwargs["pk"])
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initial["case"] = case.id
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return initial
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def get_context_data(self, **kwargs):
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context = super(SeriesCreate, self).get_context_data(**kwargs)
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if self.request.POST:
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context["image_formset"] = SeriesImageFormSet(
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self.request.POST, self.request.FILES
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)
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context["image_formset"].full_clean()
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else:
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context["image_formset"] = SeriesImageFormSet()
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return context
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def form_valid(self, form):
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self.object = form.save(commit=False)
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self.object.save()
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form.instance.author.add(self.request.user.id)
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context = self.get_context_data(form=form)
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series_formset = context["image_formset"]
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if series_formset.is_valid():
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response = super().form_valid(form)
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series_formset.instance = self.object
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series_formset.save()
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return response
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else:
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return super().form_invalid(form)
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class SeriesUpdate(
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RevisionMixin, LoginRequiredMixin, AuthorOrCheckerRequiredMixin, UpdateView
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):
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model = Series
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form_class = SeriesForm
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# fields = '__all__'
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# #fields = [ 'condition' ]
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# #initial = {'date_of_death': '05/01/2018'}
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# exclude = [ 'created_date', 'published_date' ]
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def get_context_data(self, **kwargs):
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context = super(SeriesUpdate, self).get_context_data(**kwargs)
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if self.request.POST:
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context["image_formset"] = SeriesImageFormSet(
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self.request.POST, self.request.FILES, instance=self.object
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)
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context["image_formset"].full_clean()
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else:
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context["image_formset"] = SeriesImageFormSet(instance=self.object)
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return context
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def form_valid(self, form):
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self.object = form.save(commit=False)
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self.object.save()
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# Do this in the form.save()
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# new_exams = list(form.cleaned_data['exams'].values_list("pk", flat=True))
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# self.object.exams.clear()
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# self.object.exams.add(*new_exams)
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form.instance.author.add(self.request.user.id)
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context = self.get_context_data(form=form)
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image_formset = context["image_formset"]
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# logger.debug(formset.is_valid())
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if image_formset.is_valid():
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response = super().form_valid(form)
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image_formset.instance = self.object
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image_formset.save()
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return response
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else:
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return super().form_invalid(form)
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class AtlasCreateBase(RevisionMixin, LoginRequiredMixin, CreateView):
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model = Case
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form_class = AtlasForm
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def get_form_kwargs(self):
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kwargs = super(AtlasCreateBase, self).get_form_kwargs()
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kwargs.update({"user": self.request.user})
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return kwargs
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def get_context_data(self, **kwargs):
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context = super(AtlasCreateBase, self).get_context_data(**kwargs)
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if self.request.POST:
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context["series_formset"] = SeriesFormSet(
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self.request.POST, self.request.FILES
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)
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context["series_formset"].full_clean()
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else:
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context["series_formset"] = SeriesFormSet()
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return context
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def form_valid(self, form):
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self.object = form.save(commit=False)
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# Add exam objects
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self.object.save()
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# Do this in the form.save()
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# new_exams = list(form.cleaned_data['exams'].values_list("pk", flat=True))
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# self.object.exams.clear()
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# self.object.exams.add(*new_exams)
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form.instance.author.add(self.request.user.id)
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context = self.get_context_data(form=form)
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series_formset = context["series_formset"]
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if series_formset.is_valid():
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response = super().form_valid(form)
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series_formset.instance = self.object
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series_formset.save()
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# If the normal submit button is pressed we save as normal
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if "submit" in self.request.POST:
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return response
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# else we redirect to the clone url
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else:
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return redirect("atlas:case_clone", pk=self.object.pk)
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else:
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return super().form_invalid(form)
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# @login_required
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class AtlasCreate(AtlasCreateBase):
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def get_initial(self):
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# There has to be a better way...
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try:
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s = (i.pk for i in self.request.user.atlas_default.site.all())
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self.initial.update({"site": s})
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except AttributeError:
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pass
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return self.initial
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class AtlasUpdate(
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RevisionMixin, LoginRequiredMixin, AuthorOrCheckerRequiredMixin, UpdateView
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):
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model = Case
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form_class = AtlasForm
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# fields = '__all__'
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# #fields = [ 'condition' ]
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# #initial = {'date_of_death': '05/01/2018'}
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# exclude = [ 'created_date', 'published_date' ]
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def get_form_kwargs(self):
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kwargs = super(AtlasUpdate, self).get_form_kwargs()
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kwargs.update({"user": self.request.user})
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return kwargs
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def get_context_data(self, **kwargs):
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context = super(AtlasUpdate, self).get_context_data(**kwargs)
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if self.request.POST:
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context["series_formset"] = SeriesFormSet(
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self.request.POST, self.request.FILES, instance=self.object
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)
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context["series_formset"].full_clean()
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else:
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context["series_formset"] = SeriesFormSet(instance=self.object)
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return context
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def form_valid(self, form):
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# save exam orders (there must be a better way to do this)
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exam_orders = {}
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for exam in self.object.exams.all():
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exam_orders[exam] = list(exam.exam_questions.all())
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self.object = form.save(commit=False)
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self.object.save()
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# Do this in the form.save()
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# new_exams = list(form.cleaned_data['exams'].values_list("pk", flat=True))
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# self.object.exams.clear()
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# self.object.exams.add(*new_exams)
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form.instance.author.add(self.request.user.id)
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context = self.get_context_data(form=form)
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series_formset = context["series_formset"]
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# logger.debug(formset.is_valid())
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if series_formset.is_valid():
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response = super().form_valid(form)
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series_formset.instance = self.object
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series_formset.save()
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# restore exam orders
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for exam in self.object.exams.all():
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if exam in exam_orders and self.object in exam_orders[exam]:
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print(exam_orders[exam])
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exam.exam_questions.set(exam_orders[exam])
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exam.save()
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return response
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else:
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return super().form_invalid(form)
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class AtlasClone(AtlasCreateBase):
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"""Clones a existing atlas"""
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# fields = '__all__'
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# #fields = [ 'condition' ]
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# #initial = {'date_of_death': '05/01/2018'}
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# exclude = [ 'created_date', 'published_date' ]
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def get_initial(self):
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# print(self.request)
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old_object = get_object_or_404(Case, pk=self.kwargs["pk"])
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initial_data = model_to_dict(old_object, exclude=["id"])
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return initial_data
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@login_required
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@user_is_author_or_atlas_checker
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def atlas_scrap(request, pk):
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try:
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atlas = Case.objects.get(pk=pk)
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except Case.DoesNotExist:
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raise Http404("Case does not exist")
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atlas.scrapped = not atlas.scrapped
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atlas.save()
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return HttpResponseRedirect(reverse("atlas:case_detail", args=(pk,)))
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# @login_required
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# def edit_abnormality_popup(request):
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# instance = get_object_or_404(Abnormality, pk = pk)
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# form = AbnormalityForm(request.POST or None)
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# if form.is_valid():
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# instance = form.save()
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# return HttpResponse('<script>opener.closePopup(window, "%s", "%s", "#id_abnormality");</script>' % (instance.pk, instance))
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# return render(request, "atlas/create_simple.html", {'form': form})
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@login_required
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def create_examination(request):
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form = ExaminationForm(request.POST or None)
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if form.is_valid():
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instance = form.save()
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return HttpResponse(
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'<script>opener.closePopup(window, "%s", "%s", "#id_examination");</script>'
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% (instance.pk, instance)
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)
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return render(
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request, "atlas/create_simple.html", {"form": form, "name": "Examination"}
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)
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@csrf_exempt
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def get_examination_id(request):
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if request.is_ajax():
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examination_name = request.GET["examination_name"]
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examination_id = Examination.objects.get(name=examination_name).id
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data = {
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"examination_id": examination_id,
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}
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return HttpResponse(json.dumps(data), content_type="application/json")
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return HttpResponse("/")
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class AtlasView(LoginRequiredMixin, SingleTableMixin, FilterView):
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model = Case
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table_class = AtlasTable
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template_name = "atlas/view.html"
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||||
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filterset_class = AtlasFilter
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class SeriesView(LoginRequiredMixin, SingleTableMixin, FilterView):
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model = Series
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table_class = SeriesTable
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template_name = "atlas/view.html"
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||||
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||||
filterset_class = SeriesFilter
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||||
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||||
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||||
@login_required
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||||
@user_is_author_or_atlas_series_checker
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||||
def atlas_series_order_dicom(request, pk):
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series = get_object_or_404(Series, pk=pk)
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||||
try:
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series.order_by_dicom()
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||||
except:
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||||
return HttpResponse("<h1>Series does not appear to contain dicoms</h1>")
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||||
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||||
return redirect("atlas:atlas_series_detail", pk=pk)
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||||
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||||
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||||
@login_required
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||||
@user_is_author_or_atlas_series_checker
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||||
def atlas_series_order_dicom_instance(request, pk):
|
||||
series = get_object_or_404(Series, pk=pk)
|
||||
try:
|
||||
series.order_by_dicom("InstanceNumber")
|
||||
except:
|
||||
return HttpResponse(
|
||||
"<h1>Series does not appear to contain dicoms (or field InstanceNumber)</h1>"
|
||||
)
|
||||
|
||||
return redirect("atlas:atlas_series_detail", pk=pk)
|
||||
|
||||
|
||||
@login_required
|
||||
@user_is_author_or_atlas_series_checker
|
||||
def atlas_series_order_dicom_SeriesInstanceUID(request, pk):
|
||||
series = get_object_or_404(Series, pk=pk)
|
||||
try:
|
||||
series.order_by_dicom("SeriesInstanceUID")
|
||||
except:
|
||||
return HttpResponse(
|
||||
"<h1>Series does not appear to contain dicoms (or field SeriesInstanceUID)</h1>"
|
||||
)
|
||||
|
||||
return redirect("atlas:atlas_series_detail", pk=pk)
|
||||
|
||||
|
||||
@login_required
|
||||
@user_is_author_or_atlas_series_checker
|
||||
def atlas_series_order_upload_filename(request, pk):
|
||||
series = get_object_or_404(Series, pk=pk)
|
||||
series.order_by_upload_filename()
|
||||
|
||||
return redirect("atlas:atlas_series_detail", pk=pk)
|
||||
|
||||
|
||||
|
||||
class SeriesImagesZipView(SuperuserRequiredMixin, BaseZipView):
|
||||
"""Download all images from an image series"""
|
||||
|
||||
def get_files(self):
|
||||
series = Series.objects.get(pk=self.kwargs["pk"])
|
||||
|
||||
return [i.image.file for i in series.images.all()]
|
||||
|
||||
Reference in New Issue
Block a user