Merge branch 'master' of gitssh://web.xkjq.uk:30001/ross/rad

anatomy/filters.py

@@ -1,6 +1,22 @@
 import django_filters
 
-from .models import AnatomyQuestion
+from .models import AnatomyQuestion, CidUserAnswer
+
+#from generic.filters import UserAnswerFilter
+
+
+class AnatomyUserAnswerFilter(django_filters.FilterSet):
+    class Meta:
+        model= CidUserAnswer
+        fields = (
+            "cid",
+            "question",
+            "answer",
+            #"answer_compare",
+            "exam",
+            "created",
+            "updated",
+        )
 
 
 class AnatomyQuestionFilter(django_filters.FilterSet):

anatomy/migrations/0029_auto_20210209_2239.py

@@ -0,0 +1,20 @@
+# Generated by Django 3.1.3 on 2021-02-09 22:39
+
+import anatomy.models
+import django.core.files.storage
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('anatomy', '0028_auto_20210206_0905'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='anatomyquestion',
+            name='image',
+            field=models.ImageField(storage=django.core.files.storage.FileSystemStorage(base_url='/media/anatomy/', location='/home/ross/rad/media//anatomy/'), upload_to=anatomy.models.image_directory_path),
+        ),
+    ]

anatomy/models.py

@@ -310,41 +310,6 @@ class Exam(ExamBase):
         return exam_json
 
 
-# class UserAnswer(models.Model):
-#     question = models.ForeignKey(
-#         AnatomyQuestion, related_name="user_answers", on_delete=models.CASCADE
-#     )
-#     answer = models.TextField(max_length=500, blank=True)
-#     user = models.ForeignKey(
-#         settings.AUTH_USER_MODEL, null=True, blank=True, on_delete=models.SET_NULL
-#     )
-
-#     cid = models.BigIntegerField(blank=True, null=True, help_text="Candidate ID (limitied by BigIntegerField size)")
-
-#     # Each user answer is associated with a particular exam
-#     exam = models.ForeignKey(
-#         Exam, related_name="exam", on_delete=models.CASCADE, null=True
-#     )
-
-#     flagged = models.BooleanField(default=False)
-
-#     created = models.DateTimeField(auto_now_add=True)
-#     updated = models.DateTimeField(auto_now=True)
-
-#     def __str__(self):
-#         try:
-#             exam = self.exam
-#         except (Exam.DoesNotExist, KeyError) as e:
-#             exam = "None"
-#         return "{}/{}/{}: {}".format(
-#             exam, self.cid, self.question.GetPrimaryAnswer(), self.answer
-#         )
-
-#     def clean(self):
-#         if self.answer:
-#             self.answer = self.answer.strip()
-
-
 class CidUserAnswer(models.Model):
     """User answers by candidate"""
 

anatomy/tables.py

@@ -1,7 +1,7 @@
 import django_tables2 as tables
 from django_tables2.utils import A
 
-from .models import AnatomyQuestion
+from .models import AnatomyQuestion, CidUserAnswer
 
 from django.utils.html import format_html
 
@@ -9,6 +9,27 @@ from easy_thumbnails.files import get_thumbnailer
 
 from easy_thumbnails.exceptions import InvalidImageFormatError
 
+#from generic.tables import UserAnswerTable
+
+
+class AnatomyUserAnswerTable(tables.Table):
+    select = tables.CheckBoxColumn(accessor=("pk"))
+    delete = tables.LinkColumn(
+        "anatomy:anatomy_user_answer_delete", text="Delete", args=[A("pk")], orderable=False
+    )
+    class Meta:
+        model = CidUserAnswer
+        template_name = "django_tables2/bootstrap4.html"
+        fields = (
+            "cid",
+            "question",
+            "answer",
+            #"answer_compare",
+            "exam",
+            "created",
+            "updated",
+        )
+    
 
 class ImageColumn(tables.Column):
     def render(self, value):

anatomy/templates/anatomy/ciduseranswer_confirm_delete.html

@@ -0,0 +1,4 @@
+<form method="post">{% csrf_token %}
+    <p>Are you sure you want to delete "{{ object }}"?</p>
+    <input type="submit" value="Confirm">
+</form>

anatomy/urls.py

@@ -51,4 +51,6 @@ urlpatterns = [
     path("examination/ajax/get_examination_id",
          views.get_examination_id,
          name="get_examination_id"),
+    path("user_answers/", views.AnatomyUserAnswerView.as_view(), name="anatomy_user_answer_view"),
+    path("user_answers/<int:pk>/delete", views.UserAnswerDelete.as_view(), name="anatomy_user_answer_delete"),
 ]

anatomy/views.py

@@ -46,8 +46,8 @@ from .models import (
 from generic.models import Examination
 from generic.views import ExamViews
 
-from .tables import AnatomyQuestionTable
+from .tables import AnatomyQuestionTable, AnatomyUserAnswerTable
-from .filters import AnatomyQuestionFilter
+from .filters import AnatomyQuestionFilter, AnatomyUserAnswerFilter
 
 from django_tables2 import SingleTableView, SingleTableMixin
 from django_filters.views import FilterView
@@ -62,6 +62,8 @@ from helpers.images import image_as_base64
 
 from django.template.defaulttags import register
 
+from generic.mixins import SuperuserRequiredMixin
+
 
 @register.filter
 def get_item(dictionary, key):
@@ -919,6 +921,13 @@ class AnatomyQuestionView(SingleTableMixin, FilterView):
 
     filterset_class = AnatomyQuestionFilter
 
+class AnatomyUserAnswerView(SingleTableMixin, FilterView):
+    model = CidUserAnswer
+    table_class = AnatomyUserAnswerTable
+    template_name = "anatomy/anatomy_question_view.html"
+
+    filterset_class = AnatomyUserAnswerFilter
+
 
 def question_save_annotation(request, pk):
     if request.is_ajax() and request.method == "POST":
@@ -936,3 +945,7 @@ def question_save_annotation(request, pk):
 
 
 AnatomyExamViews = ExamViews(Exam, "anatomy", "anatomy", loadJsonAnswer)
+
+class UserAnswerDelete(SuperuserRequiredMixin, DeleteView):
+    model = CidUserAnswer
+    success_url = reverse_lazy("anatomy:anatomy_user_answer_view")

generic/filters.py

@@ -0,0 +1,18 @@
+import django_filters
+
+
+
+#class UserAnswerFilter(django_filters.FilterSet):
+#    class Meta:
+#        #model = AnatomyQuestion
+#        abstract = True
+#        fields = (
+#            "cid",
+#            "question",
+#            "answer",
+#            #"answer_compare",
+#            "exam",
+#            "created",
+#            "updateded",
+#            "created_date",
+#        )

generic/mixins.py

@@ -0,0 +1,6 @@
+from django.contrib.auth.mixins import UserPassesTestMixin
+
+
+class SuperuserRequiredMixin(UserPassesTestMixin):
+    def test_func(self):
+        return self.request.user.is_superuser

generic/tables.py

@@ -0,0 +1,47 @@
+import django_tables2 as tables
+from django_tables2.utils import A
+
+from django.utils.html import format_html
+
+from easy_thumbnails.files import get_thumbnailer
+
+from easy_thumbnails.exceptions import InvalidImageFormatError
+
+
+class ImageColumn(tables.Column):
+    def render(self, value):
+        try:
+            thumbnailer = get_thumbnailer(value)
+            return format_html('<img src="/media/{}" />', thumbnailer["exam-list"])
+        except InvalidImageFormatError:
+            return format_html('<span title="{}">Invalid image url<span>', value)
+
+
+#class UserAnswerTable(tables.Table):
+#    #edit = tables.LinkColumn(
+#    #    "anatomy:anatomy_question_update", text="Edit", args=[A("pk")], orderable=False
+#    #)
+#    #view = tables.LinkColumn(
+#    #    "anatomy:question_detail", text="View", args=[A("pk")], orderable=False
+#    #)
+#    #image = ImageColumn("image", orderable=False)
+#    # clone = tables.LinkColumn('anatomy:anatomy_question_clone',
+#    #                          text='Clone',
+#    #                          args=[A('pk')],
+#    #                          orderable=False)
+#    #exams = tables.ManyToManyColumn(verbose_name="Exams")
+#
+#    class Meta:
+#        #model = AnatomyQuestion
+#        abstract = True
+#        template_name = "django_tables2/bootstrap4.html"
+#        fields = (
+#            "cid",
+#            "question",
+#            "answer",
+#            #"answer_compare",
+#            "exam",
+#            "created",
+#            "updated",
+#        )
+#        #sequence = ("view")

generic/views.py

@@ -210,7 +210,7 @@ class ExamViews(View, LoginRequiredMixin):
         return JsonResponse(active_exams)
 
     @method_decorator(csrf_exempt)
-    def postExamAnswers(request):
+    def postExamAnswers(self, request):
         if request.is_ajax and request.method == "POST":
 
             n = 0

helpers/images.py

@@ -21,6 +21,8 @@ def image_as_base64(image_file):
     #    encoded_string = base64.b64encode(img_f.read())
     encoded_string = base64.b64encode(image_file.file.read())
     mimetype, enc = mimetypes.guess_type(image_file.path)
+    if "dicom" in mimetype:
+        return "data:{};base64,{}".format(mimetype, encoded_string.decode("utf-8"))
     return "data:image/{};base64,{}".format(mimetype, encoded_string.decode("utf-8"))
 
 

longs/migrations/0014_auto_20210211_1827.py

@@ -0,0 +1,20 @@
+# Generated by Django 3.1.3 on 2021-02-11 18:27
+
+import django.core.files.storage
+from django.db import migrations, models
+import longs.models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('longs', '0013_auto_20210206_2147'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='longseriesimage',
+            name='image',
+            field=models.FileField(storage=django.core.files.storage.FileSystemStorage(base_url='/media/longs/', location='/home/ross/rad/media/longs/'), upload_to=longs.models.image_directory_path),
+        ),
+    ]

longs/models.py

@@ -15,9 +15,13 @@ from django.urls import reverse
 from django.utils.translation import ugettext_lazy as _
 from django.utils.html import mark_safe
 
+from django.core.exceptions import ValidationError
+
 from sortedm2m.fields import SortedManyToManyField
 
 import string
+from collections import defaultdict
+from helpers.images import image_as_base64
 
 from anatomy.models import Modality
 
@@ -30,7 +34,7 @@ from easy_thumbnails.exceptions import InvalidImageFormatError
 
 image_storage = FileSystemStorage(
     # Physical file location ROOT
-    location=u"{0}/longs/".format(settings.MEDIA_ROOT),
+    location=u"{0}longs/".format(settings.MEDIA_ROOT),
     # Url for file
     base_url=u"{0}longs/".format(settings.MEDIA_URL),
 )
@@ -139,8 +143,11 @@ class Long(models.Model):
     # return self.GetImages()
 
 
+def test_image_validator(file):
+    pass
+
 class LongSeriesImage(models.Model):
-    image = models.ImageField(upload_to=image_directory_path, storage=image_storage)
+    image = models.FileField(upload_to=image_directory_path, storage=image_storage)
     position = models.IntegerField(default=0)
     series = models.ForeignKey(
         "LongSeries", related_name="images", on_delete=models.SET_NULL, null=True
@@ -200,7 +207,7 @@ class LongSeries(models.Model):
         return authors
 
     def get_author_display(self):
-        return ", ".join(self.get_author_objects())
+        return ", ".join([i.username for i in self.get_author_objects()])
 
     def get_examination(self):
         """Returns a comma seperated text list of regions"""
@@ -303,6 +310,57 @@ class Exam(ExamBase):
         default=4500,
     )
 
+    def get_exam_json(self):
+        questions = self.exam_questions.all()
+
+        exam_questions = defaultdict(dict)
+
+        exam_order = []
+
+        for q in questions:
+            exam_order.append(q.id)
+
+            # Loop through longimage associations
+            images = []
+            image_titles = []
+            for series in q.series.all():
+                image_array = []
+                for i in series.images.all():
+                    image_array.append(image_as_base64(i.image))
+                    #image_array.append(i.image.url)
+                images.append(image_array)
+                image_titles.append(series.get_examination())
+
+
+
+            exam_questions[q.id] = {
+                "title": q.history,
+                "images": images,
+                "image_titles": image_titles,
+                #"feedback_image": [],
+                #"annotations": [str(q.image_annotations)],
+                "type": "long",
+            }
+
+            #if feedback_images:
+            #    exam_questions[q.id]["feedback_image"] = feedback_images
+
+
+        exam_json = {
+            "eid": "long/{}".format(self.id),
+            "cached": False,
+            "exam_type": "long",
+            "exam_name": self.name,
+            "exam_mode": True,
+            "exam_order": exam_order,
+            "questions": exam_questions,
+        }
+
+
+        if self.time_limit:
+            exam_json["exam_time"] = self.time_limit
+
+        return exam_json
 
 class CidUserAnswer(models.Model):
     """User answers by candidate"""

longs/tables.py

@@ -31,6 +31,9 @@ class LongSeriesImageColumn(tables.Column):
     def render(self, value):
         obj = value.first()
 
+        if obj is None:
+            return "None"
+
         image_object = obj.image
         try:
             thumbnailer = get_thumbnailer(image_object)

longs/urls.py

@@ -48,7 +48,7 @@ urlpatterns = [
     path("exam/submit", views.LongExamViews.postExamAnswers, name="exam_answers_submit"),
     path("exam/", views.LongExamViews.exam_list, name="exam_list"),
     path("exam/json/", views.LongExamViews.active_exams, name="active_exams"),
-    path("exam/json/<int:pk>", views.exam_json, name="exam_json"),
+    path("exam/json/<int:pk>", views.LongExamViews.exam_json, name="exam_json"),
     path(
         "exam/json/<int:pk>/recreate",
         views.LongExamViews.exam_json_recreate,

longs/views.py

@@ -796,75 +796,6 @@ def mark(request, pk, sk):
     )
 
 
-
-def exam_json(request, pk):
-
-    exam = get_object_or_404(Exam, pk=pk)
-
-    if not exam.active:
-        raise Http404("No available exam")
-
-    exam_json_cache = cache.get("longs_exam_json_{}".format(pk))
-
-    if exam_json_cache is not None and not exam.recreate_json:
-        exam_json_cache["cached"] = True
-        return JsonResponse(exam_json_cache)
-
-    questions = exam.exam_questions.all()
-
-    exam_questions = defaultdict(dict)
-
-    exam_order = []
-
-    for q in questions:
-        exam_order.append(q.id)
-
-        # Loop through longimage associations
-        images = []
-        feedback_images = []
-        for i in q.images.all():
-            if i.feedback_image == True:
-                feedback_images.append(image_as_base64(i.image))
-                # feedback_images.append(i.image.url)
-            else:
-                images.append(image_as_base64(i.image))
-                #images.append(i.image.url)
-
-
-
-        exam_questions[q.id] = {
-            "images": images,
-            #"feedback_image": [],
-            #"annotations": [str(q.image_annotations)],
-            "type": "long",
-        }
-
-        #if feedback_images:
-        #    exam_questions[q.id]["feedback_image"] = feedback_images
-
-
-    exam_json = {
-        "eid": "long/{}".format(exam.id),
-        "cached": False,
-        "exam_type": "long",
-        "exam_name": exam.name,
-        "exam_mode": True,
-        "exam_order": exam_order,
-        "questions": exam_questions,
-    }
-
-
-    if exam.time_limit:
-        exam_json["exam_time"] = exam.time_limit
-
-    exam.recreate_json = False
-    exam.save()
-
-    cache.set("longs_exam_json_{}".format(pk), exam_json, 3600)
-
-    return JsonResponse(exam_json)
-
-
 @login_required
 def exam_scores_cid(request, pk):
     exam = get_object_or_404(Exam, pk=pk)

rad/settings.py

@@ -50,6 +50,7 @@ INSTALLED_APPS = [
     'django.contrib.staticfiles',
     'debug_toolbar',
     "tagulous",
+    "dbbackup",
 ]
 
 MIDDLEWARE = [
@@ -199,8 +200,14 @@ THUMBNAIL_ALIASES = {
 }
 
 THUMBNAIL_SOURCE_GENERATORS = ('easy_thumbnails.source_generators.pil_image', 'helpers.images.pil_dicom_image')
+DBBACKUP_STORAGE = 'django.core.files.storage.FileSystemStorage'
+DBBACKUP_STORAGE_OPTIONS = {'location': os.path.join(BASE_DIR, '../backups')}
 
 try:
     from .settings_local import *
 except ImportError:
     pass
+<<<<<<< HEAD
+=======
+
+>>>>>>> 5763aae287cbceee318f975495f7d9429517c88f

rapids/migrations/0013_auto_20210209_2239.py

@@ -0,0 +1,20 @@
+# Generated by Django 3.1.3 on 2021-02-09 22:39
+
+import django.core.files.storage
+from django.db import migrations, models
+import rapids.models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('rapids', '0012_auto_20210206_0905'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='rapidimage',
+            name='image',
+            field=models.ImageField(storage=django.core.files.storage.FileSystemStorage(base_url='/media/rapids/', location='/home/ross/rad/media//rapids/'), upload_to=rapids.models.image_directory_path),
+        ),
+    ]

rapids/migrations/0014_auto_20210211_2034.py

@@ -0,0 +1,20 @@
+# Generated by Django 3.1.3 on 2021-02-11 20:34
+
+import django.core.files.storage
+from django.db import migrations, models
+import rapids.models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('rapids', '0013_auto_20210209_2239'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='rapidimage',
+            name='image',
+            field=models.FileField(storage=django.core.files.storage.FileSystemStorage(base_url='/media/rapids/', location='/home/ross/rad/media//rapids/'), upload_to=rapids.models.image_directory_path),
+        ),
+    ]

rapids/migrations/0015_auto_20210211_2035.py

@@ -0,0 +1,20 @@
+# Generated by Django 3.1.3 on 2021-02-11 20:35
+
+import django.core.files.storage
+from django.db import migrations, models
+import rapids.models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('rapids', '0014_auto_20210211_2034'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='rapidimage',
+            name='image',
+            field=models.FileField(storage=django.core.files.storage.FileSystemStorage(base_url='/media/rapids/', location='/home/ross/rad/media/rapids/'), upload_to=rapids.models.image_directory_path),
+        ),
+    ]

rapids/models.py

@@ -16,13 +16,15 @@ from django.utils.html import mark_safe
 from sortedm2m.fields import SortedManyToManyField
 
 import string
+from collections import defaultdict
+from helpers.images import image_as_base64
 
 
 from generic.models import Site, Condition, Sign, ExamBase
 
 image_storage = FileSystemStorage(
     # Physical file location ROOT
-    location=u"{0}/rapids/".format(settings.MEDIA_ROOT),
+    location=u"{0}rapids/".format(settings.MEDIA_ROOT),
     # Url for file
     base_url=u"{0}rapids/".format(settings.MEDIA_URL),
 )
@@ -286,7 +288,7 @@ class RapidImage(models.Model):
     rapid = models.ForeignKey(Rapid,
                               related_name="images",
                               on_delete=models.CASCADE)
-    image = models.ImageField(upload_to=image_directory_path, storage=image_storage)
+    image = models.FileField(upload_to=image_directory_path, storage=image_storage)
 
     feedback_image = models.BooleanField(default=False)
 
@@ -350,6 +352,55 @@ class Exam(ExamBase):
         help_text="Exam time limit (in seconds). Default is 2100 secondse (35 minutes)", default=2100
     )
 
+    def get_exam_json(self):
+        questions = self.exam_questions.all()
+
+        exam_questions = defaultdict(dict)
+
+        exam_order = []
+
+        for q in questions:
+            exam_order.append(q.id)
+
+            # Loop through rapidimage associations
+            images = []
+            feedback_images = []
+            for i in q.images.all():
+                if i.feedback_image == True:
+                    feedback_images.append(image_as_base64(i.image))
+                    # feedback_images.append(i.image.url)
+                else:
+                    images.append(image_as_base64(i.image))
+                    #images.append(i.image.url)
+
+
+
+            exam_questions[q.id] = {
+                "images": images,
+                #"feedback_image": [],
+                #"annotations": [str(q.image_annotations)],
+                "type": "rapid",
+            }
+
+            #if feedback_images:
+            #    exam_questions[q.id]["feedback_image"] = feedback_images
+
+
+        exam_json = {
+            "eid": "rapid/{}".format(self.id),
+            "cached": False,
+            "exam_type": "rapid",
+            "exam_name": self.name,
+            "exam_mode": True,
+            "exam_order": exam_order,
+            "questions": exam_questions,
+        }
+
+        if self.time_limit:
+            exam_json["exam_time"] = self.time_limit
+
+        return exam_json
+
 
 class CidUserAnswer(models.Model):
     """User answers by candidate"""

rapids/urls.py

@@ -32,7 +32,7 @@ urlpatterns = [
     path("exam/submit", views.RapidExamViews.postExamAnswers, name="exam_answers_submit"),
     path("exam/", views.RapidExamViews.exam_list, name="exam_list"),
     path("exam/json/", views.RapidExamViews.active_exams, name="active_exams"),
-    path("exam/json/<int:pk>", views.exam_json, name="exam_json"),
+    path("exam/json/<int:pk>", views.RapidExamViews.exam_json, name="exam_json"),
     path("exam/json/<int:pk>/recreate", views.RapidExamViews.exam_json_recreate, name="exam_json_recreate"),
     path("create/", views.RapidCreate.as_view(), name="rapid_create"),
     path("create/defaults",

rapids/views.py

@@ -699,73 +699,6 @@ def mark(request, pk, sk):
     )
 
 
-def exam_json(request, pk):
-
-    exam = get_object_or_404(Exam, pk=pk)
-
-    if not exam.active:
-        raise Http404("No available exam")
-
-    exam_json_cache = cache.get("rapids_exam_json_{}".format(pk))
-
-    if exam_json_cache is not None and not exam.recreate_json:
-        exam_json_cache["cached"] = True
-        return JsonResponse(exam_json_cache)
-
-    questions = exam.exam_questions.all()
-
-    exam_questions = defaultdict(dict)
-
-    exam_order = []
-
-    for q in questions:
-        exam_order.append(q.id)
-
-        # Loop through rapidimage associations
-        images = []
-        feedback_images = []
-        for i in q.images.all():
-            if i.feedback_image == True:
-                feedback_images.append(image_as_base64(i.image))
-                # feedback_images.append(i.image.url)
-            else:
-                images.append(image_as_base64(i.image))
-                #images.append(i.image.url)
-
-
-
-        exam_questions[q.id] = {
-            "images": images,
-            #"feedback_image": [],
-            #"annotations": [str(q.image_annotations)],
-            "type": "rapid",
-        }
-
-        #if feedback_images:
-        #    exam_questions[q.id]["feedback_image"] = feedback_images
-
-
-    exam_json = {
-        "eid": "rapid/{}".format(exam.id),
-        "cached": False,
-        "exam_type": "rapid",
-        "exam_name": exam.name,
-        "exam_mode": True,
-        "exam_order": exam_order,
-        "questions": exam_questions,
-    }
-
-    if exam.time_limit:
-        exam_json["exam_time"] = exam.time_limit
-
-    exam.recreate_json = False
-    exam.save()
-
-    cache.set("rapids_exam_json_{}".format(pk), exam_json, 3600)
-
-    return JsonResponse(exam_json)
-
-
 @login_required
 def exam_scores_cid(request, pk):
     exam = get_object_or_404(Exam, pk=pk)

requirements.txt

@@ -15,3 +15,4 @@ django-sortedm2m
 pytesseract
 opencv-python
 pydicom
+django-dbbackup