.

atlas/migrations/0050_alter_series_description.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.1.4 on 2023-06-12 09:55
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0049_alter_condition_parent_alter_condition_synonym_and_more'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='series',
+            name='description',
+            field=models.TextField(blank=True, help_text='Description of stack, for admin organisation, will not be visible when taking'),
+        ),
+    ]

atlas/models.py

@@ -10,8 +10,6 @@ from django.utils import timezone
 
 
 import pydicom
-import dicognito.anonymizer
-
 
 from django.core.files.storage import FileSystemStorage
 from django.conf import settings
@@ -43,13 +41,11 @@ from generic.models import (
     Plane,
     Contrast,
     QuestionNote,
+    SeriesBase,
 )
 
 # from generic.models import Examination, Site, Condition, Sign
 
-from easy_thumbnails.files import get_thumbnailer
-from easy_thumbnails.exceptions import InvalidImageFormatError
-
 import pydicom.errors
 import datetime
 from django.utils import timezone
@@ -343,7 +339,6 @@ class SeriesImage(models.Model):
 
 
 class SeriesFinding(models.Model):
-
     series = models.ForeignKey(
         "Series", related_name="findings", on_delete=models.SET_NULL, null=True
     )
@@ -364,7 +359,7 @@ class SeriesFinding(models.Model):
 
 
 @reversion.register
-class Series(models.Model):
+class Series(SeriesBase):
     modality = models.ForeignKey(
         Modality,
         related_name="atlas_series_modality",
@@ -394,10 +389,6 @@ class Series(models.Model):
         null=True,
         blank=True,
     )
-    description = models.TextField(
-        blank=True,
-        help_text="Description of stack",
-    )
 
     author = models.ManyToManyField(
         settings.AUTH_USER_MODEL,
@@ -407,13 +398,6 @@ class Series(models.Model):
 
     # findings = models.TextField(null=True, blank=True, help_text="Findings on the series / stack")
 
-    open_access = models.BooleanField(
-        help_text="If a series should be freely available to browse", default=True
-    )
-
-    def __str__(self):
-        return f"{self.pk}:{self.description}"
-
     def get_full_str(self):
         if self.case:
             case_id = ", ".format([case.pk for case in self.case.all()])
@@ -424,167 +408,10 @@ class Series(models.Model):
             self.pk, self.get_examination_full(), self.description, case_id
         )
 
-    def get_absolute_url(self):
-        return reverse("series:question_detail", kwargs={"pk": self.pk})
-
-    #    def get_string(self):
-    #        examination = self.get_examination_full()
-    #        return
-
-    def get_author_objects(self):
-        """Returns a comma seperated text list of authors"""
-        if self.author:
-            return self.author.all()
-        else:
-            return ["None"]
-
-    def get_author_display(self):
-        return ", ".join([i.username for i in self.get_author_objects()])
-
-    def get_examination(self):
-        """Returns a comma seperated text list of regions"""
-        return str(self.examination)
-
-    def get_examination_full(self):
-        examination = ""
-        plane = ""
-        contrast = ""
-
-        if self.examination:
-            examination = self.examination
-        if self.plane:
-            plane = " {}".format(self.plane)
-        if self.contrast:
-            contrast = " {}".format(self.contrast)
-        return "{}{}{}".format(examination, plane, contrast)
 
     def get_absolute_url(self):
         return reverse("atlas:series_detail", kwargs={"pk": self.pk})
 
-    def get_image_urls(self, findings=False):
-        images = [f"{REMOTE_URL}{i.image.url}" for i in self.images.all()]
-
-        return ",".join(images)
-
-    def get_image_url_array_not_json(self):
-        return self.get_image_url_array(json_output=False)
-
-    def get_image_url_array(self, findings=False, json_output=True):
-        images = [f"{REMOTE_URL}{i.image.url}" for i in self.images.all()]
-
-        if json_output:
-            return json.dumps(images)
-        else:
-            # This is a mess...
-            return format_html('", "'.join(images))
-
-    def get_thumbnail(self):
-        images = self.images.all()
-
-        if len(images) < 1:
-            return "No images", 0
-
-        img = findMiddle(images).image
-        try:
-            thumbnailer = get_thumbnailer(img)
-            thumbnail = thumbnailer["exam-list"]
-        except InvalidImageFormatError:
-            return format_html('<span title="{}">Invalid image url<span>', img), len(
-                images
-            )
-        return format_html('<img src="/media/{}" />', thumbnail), len(images)
-
-    def get_thumbnail_link(self):
-        return format_html(
-            "<a href='{}'>{}<a/>", self.get_absolute_url(), self.get_thumbnail()[0]
-        )
-
-    def get_block(self):
-        examination = self.get_examination_full()
-        thumb, image_number = self.get_thumbnail()
-        return format_html(
-            "<div>{}<br/>{}<br/>Images: {}</div>", examination, thumb, image_number
-        )
-
-    def order_by_upload_filename(self):
-        images = self.images.all()
-
-        filenames = []
-        map = {}
-
-        for i in images:
-            filenames.append(i.upload_filename)
-            map[i.upload_filename] = i
-
-        filenames = sorted(filenames)
-
-        n = 1
-        for f in filenames:
-            i = map[f]
-            i.position = n
-            i.save()
-            n = n + 1
-
-    def order_by_dicom(self, field="SliceLocation"):
-        images = self.images.all()
-
-        files = []
-
-        for i in images:
-            files.append((i, pydicom.dcmread(i.image.path)))
-
-        # print("file count: {}".format(len(files)))
-
-        # skip files with no SliceLocation (eg scout views)
-        slices = []
-        map = {}
-        skipcount = 0
-        for i, f in files:
-            if hasattr(f, field):
-                slices.append(f)
-                # map[f.SliceLocation] = i
-                map[f[field].value] = i
-            else:
-                skipcount = skipcount + 1
-
-        print("skipped, no {}: {}".format(field, skipcount))
-
-        # ensure they are in the correct order
-        slices = sorted(slices, key=lambda s: s[field].value)
-
-        # print(slices)
-        n = 1
-        for f in slices:
-            i = map[f[field].value]
-            i.position = n
-            i.save()
-            n = n + 1
-
-    def get_total_image_size(self):
-        images = self.images.all()
-
-        size = 0
-
-        for i in images:
-            size += i.image.size
-
-        return size
-
-    def anonymise_images(self):
-        # NOTE: this will not maintain the correct hashed filename
-        # but that doesn't matter as we will never get the same anonymisation
-        # even with the same dicom...
-        anonymizer = dicognito.anonymizer.Anonymizer()
-
-        for series_image in self.images.all():
-            file_path = os.path.join(settings.MEDIA_ROOT, series_image.image.name)
-
-            try:
-                with pydicom.dcmread(file_path) as dataset:
-                    anonymizer.anonymize(dataset)
-                    dataset.save_as(file_path)
-            except pydicom.errors.InvalidDicomError:
-                pass
 
 
 class CaseCollection(models.Model):
@@ -647,8 +474,11 @@ class CaseCollection(models.Model):
         CidUser, blank=True, related_name="casecollection_exams"
     )
 
-    cid_user_groups = models.ManyToManyField(CidUserGroup, blank=True, help_text="These groups define which candidates are able to be added to the exams/collection.")
-
+    cid_user_groups = models.ManyToManyField(
+        CidUserGroup,
+        blank=True,
+        help_text="These groups define which candidates are able to be added to the exams/collection.",
+    )
 
     archive = models.BooleanField(default=False)
     exam_mode = models.BooleanField(default=False)
@@ -693,7 +523,6 @@ class CaseCollection(models.Model):
             return True
 
         if self.valid_cid_users.exists():
-
             user = self.valid_cid_users.filter(cid=cid).first()
 
             if not user or user.passcode != passcode:
@@ -771,13 +600,13 @@ class BaseReportAnswer(models.Model):
     class Meta:
         abstract = True
 
+
 class CidReportAnswer(BaseReportAnswer):
     cid = models.BigIntegerField(
         blank=False,
         help_text="Candidate ID",
     )
 
+
 class UserReportAnswer(BaseReportAnswer):
-    user = models.ForeignKey(
-        settings.AUTH_USER_MODEL, on_delete=models.CASCADE
-    )
+    user = models.ForeignKey(settings.AUTH_USER_MODEL, on_delete=models.CASCADE)

atlas/tables.py

@@ -25,7 +25,9 @@ class AtlasImageColumn(tables.Column):
         for obj in value.all():
             blocks.append(obj.get_block())
         return format_html(
-            "<span class='multi-image-block'>{}</span>".format("".join(blocks))
+            """<span class='multi-image-block'>
+            {}
+            </span>""".format("".join(blocks))
         )
 
         obj = value.first()

generic/models.py

@@ -1,4 +1,5 @@
 from collections import defaultdict
+import json
 from typing import Tuple
 from django.contrib.auth.mixins import LoginRequiredMixin
 from django.db import models
@@ -23,6 +24,22 @@ from django.contrib.auth.models import User
 
 from django.db.models.signals import post_save
 from django.dispatch import receiver
+from rad.settings import REMOTE_URL
+from django.utils.html import format_html
+
+from easy_thumbnails.files import get_thumbnailer
+from easy_thumbnails.exceptions import InvalidImageFormatError
+
+import pydicom
+import dicognito.anonymizer
+
+
+def findMiddle(input_list):
+    middle = float(len(input_list)) / 2
+    if middle % 2 != 0:
+        return input_list[int(middle - 0.5)]
+    else:
+        return input_list[int(middle)]
 
 
 class Plane(models.Model):
@@ -57,16 +74,19 @@ class Examination(models.Model):
 
 class Site(models.Model):
     """Model to hold site details"""
-    full_name = models.CharField(max_length=255, blank=True, help_text="Name of the site")
-    short_code = models.CharField(max_length=255, blank=True, help_text="Shortcode/name of the site")
 
+    full_name = models.CharField(
+        max_length=255, blank=True, help_text="Name of the site"
+    )
+    short_code = models.CharField(
+        max_length=255, blank=True, help_text="Shortcode/name of the site"
+    )
 
     def __str__(self):
         return self.short_code
 
 
 class QuestionBase(models.Model):
-
     authors_only = models.BooleanField(
         help_text="If true only question authors will be able to view.",
         default=False,
@@ -85,7 +105,7 @@ class QuestionBase(models.Model):
     class Meta:
         abstract = True
 
-    def get_unanswered_mark_and_text(self) -> tuple[ int, str ]:
+    def get_unanswered_mark_and_text(self) -> tuple[int, str]:
         """
         Override in models if needed
         """
@@ -96,6 +116,181 @@ class QuestionBase(models.Model):
         return None
 
 
+class SeriesBase(models.Model):
+    description = models.TextField(
+        blank=True,
+        help_text="Description of stack, for admin organisation, will not be visible when taking",
+    )
+
+    open_access = models.BooleanField(
+        help_text="If a series should be freely available to browse", default=True
+    )
+
+    class Meta:
+        abstract = True
+
+    def __str__(self):
+        return f"{self.pk}:{self.description}"
+
+    def get_author_objects(self):
+        """Returns a comma seperated text list of authors"""
+        if self.author:
+            return self.author.all()
+        else:
+            return ["None"]
+
+    def get_author_display(self):
+        return ", ".join([i.username for i in self.get_author_objects()])
+
+    def get_examination(self):
+        """Returns a comma seperated text list of regions"""
+        return str(self.examination)
+
+    def get_examination_full(self):
+        examination = ""
+        plane = ""
+        contrast = ""
+
+        if self.examination:
+            examination = self.examination
+        if self.plane:
+            plane = " {}".format(self.plane)
+        if self.contrast:
+            contrast = " {}".format(self.contrast)
+        return "{}{}{}".format(examination, plane, contrast)
+
+    def get_image_urls(self):
+        images = [f"{REMOTE_URL}{i.image.url}" for i in self.images.all()]
+
+        return ",".join(images)
+
+    def get_image_url_array_not_json(self):
+        return self.get_image_url_array(json_output=False)
+
+    def get_image_url_array(self, json_output=True):
+        images = [f"{REMOTE_URL}{i.image.url}" for i in self.images.all()]
+
+        if json_output:
+            return json.dumps(images)
+        else:
+            # This is a mess...
+            return format_html('", "'.join(images))
+    def get_thumbnail(self):
+        images = self.images.all()
+
+        if len(images) < 1:
+            return "No images", 0
+
+        img = findMiddle(images).image
+        try:
+            thumbnailer = get_thumbnailer(img)
+            thumbnail = thumbnailer["exam-list"]
+        except InvalidImageFormatError:
+            return format_html('<span title="{}">Invalid image url<span>', img), len(
+                images
+            )
+        return format_html('<img src="/media/{}" />', thumbnail), len(images)
+
+    def get_thumbnail_link(self):
+        return format_html(
+            "<a href='{}'>{}<a/>", self.get_absolute_url(), self.get_thumbnail()[0]
+        )
+
+    def get_block(self):
+        examination = self.get_examination_full()
+        thumb, image_number = self.get_thumbnail()
+        return format_html(
+            """<span>
+            <span class='series-block-examination'>{}</span><br/>
+            <span class='series-block-thumbnail'>{}</span><br/>
+            <span class='series-block-image-number'>Images: <span class='series-block-image-number-count'>{}</span></span>
+            </span>""",
+            examination,
+            thumb,
+            image_number,
+        )
+
+
+    def order_by_upload_filename(self):
+        images = self.images.all()
+
+        filenames = []
+        map = {}
+
+        for i in images:
+            filenames.append(i.upload_filename)
+            map[i.upload_filename] = i
+
+        filenames = sorted(filenames)
+
+        n = 1
+        for f in filenames:
+            i = map[f]
+            i.position = n
+            i.save()
+            n = n + 1
+
+    def order_by_dicom(self, field="SliceLocation"):
+        images = self.images.all()
+
+        files = []
+
+        for i in images:
+            files.append((i, pydicom.dcmread(i.image.path)))
+
+        # print("file count: {}".format(len(files)))
+
+        # skip files with no SliceLocation (eg scout views)
+        slices = []
+        map = {}
+        skipcount = 0
+        for i, f in files:
+            if hasattr(f, field):
+                slices.append(f)
+                # map[f.SliceLocation] = i
+                map[f[field].value] = i
+            else:
+                skipcount = skipcount + 1
+
+        print("skipped, no {}: {}".format(field, skipcount))
+
+        # ensure they are in the correct order
+        slices = sorted(slices, key=lambda s: s[field].value)
+
+        # print(slices)
+        n = 1
+        for f in slices:
+            i = map[f[field].value]
+            i.position = n
+            i.save()
+            n = n + 1
+
+    def get_total_image_size(self):
+        images = self.images.all()
+
+        size = 0
+
+        for i in images:
+            size += i.image.size
+
+        return size
+
+    def anonymise_images(self):
+        # NOTE: this will not maintain the correct hashed filename
+        # but that doesn't matter as we will never get the same anonymisation
+        # even with the same dicom...
+        anonymizer = dicognito.anonymizer.Anonymizer()
+
+        for series_image in self.images.all():
+            file_path = os.path.join(settings.MEDIA_ROOT, series_image.image.name)
+
+            try:
+                with pydicom.dcmread(file_path) as dataset:
+                    anonymizer.anonymize(dataset)
+                    dataset.save_as(file_path)
+            except pydicom.errors.InvalidDicomError:
+                pass
+
 class ExamBase(models.Model):
     name = models.CharField(max_length=200, help_text="Name of the exam")
     # exam_questions = SortedManyToManyField(Long, related_name="exams", blank="true")
@@ -153,7 +348,7 @@ class ExamBase(models.Model):
 
     stats_max_possible = models.FloatField(default=0)
 
-    #stats_graph = models.TextField(default=0)
+    # stats_graph = models.TextField(default=0)
 
     user_scores = models.JSONField(default=dict)
 
@@ -162,7 +357,6 @@ class ExamBase(models.Model):
 
     exam_results_emailed = models.DateTimeField(default=None, null=True)
 
-
     class Meta:
         abstract = True
 
@@ -191,10 +385,14 @@ class ExamBase(models.Model):
         return reverse("{}:exam_overview".format(self.app_name), kwargs={"pk": self.pk})
 
     def get_cid_edit_url(self):
-        return reverse("{}:exam_cids_edit".format(self.app_name), kwargs={"exam_id": self.pk})
+        return reverse(
+            "{}:exam_cids_edit".format(self.app_name), kwargs={"exam_id": self.pk}
+        )
 
     def get_user_edit_url(self):
-        return reverse("{}:exam_users_edit".format(self.app_name), kwargs={"exam_id": self.pk})
+        return reverse(
+            "{}:exam_users_edit".format(self.app_name), kwargs={"exam_id": self.pk}
+        )
 
     def get_take_url(self):
         return f"{settings.REMOTE_URL}/rts"
@@ -206,7 +404,9 @@ class ExamBase(models.Model):
         if cid is None:
             return reverse("{}:exam_json".format(self.app_name), args=(self.pk,))
         else:
-            return reverse("{}:exam_json_cid".format(self.app_name), args=(self.pk,cid, passcode))
+            return reverse(
+                "{}:exam_json_cid".format(self.app_name), args=(self.pk, cid, passcode)
+            )
 
     def get_question_index(self, question):
         return list(self.exam_questions.all()).index(question)
@@ -223,7 +423,14 @@ class ExamBase(models.Model):
         authors = [i for i in self.author.all()]
         return authors
 
-    def check_cid_user(self, cid: int|None, passcode: str|None, request: HttpRequest|None=None, user_id: int|None=None, allow_authors: bool=True):
+    def check_cid_user(
+        self,
+        cid: int | None,
+        passcode: str | None,
+        request: HttpRequest | None = None,
+        user_id: int | None = None,
+        allow_authors: bool = True,
+    ):
         print(f"Check cid user: {cid=}, {passcode=}, exam_id={self.pk}")
         if request is not None and request.user.is_superuser:
             return True
@@ -243,7 +450,6 @@ class ExamBase(models.Model):
 
         # Then test CID data
         if self.valid_cid_users.exists():
-
             cid_user = self.valid_cid_users.filter(cid=cid).first()
 
             if cid_user and cid_user.passcode == passcode:
@@ -253,7 +459,9 @@ class ExamBase(models.Model):
 
         return False
 
-    def get_or_create_cid_user_exam(self, cid_user=None, user_user=None, start_time=None):
+    def get_or_create_cid_user_exam(
+        self, cid_user=None, user_user=None, start_time=None
+    ):
         content_type = ContentType.objects.get_for_model(self)
 
         if cid_user is not None:
@@ -270,11 +478,9 @@ class ExamBase(models.Model):
             if c:
                 return c
 
-
         if start_time is None:
             start_time = timezone.now()
 
-
         if cid_user is not None:
             new = CidUserExam(
                 content_type=content_type,
@@ -312,7 +518,7 @@ class ExamBase(models.Model):
                 )
 
     def get_cid_user_score(self, cid_user):
-        c = "c/"+str(cid_user)
+        c = "c/" + str(cid_user)
         if c in self.user_scores:
             return self.user_scores[c]
         else:
@@ -326,41 +532,35 @@ class ExamBase(models.Model):
         exam_text.append(f"{'='*len(exam_name)}\n{exam_name}\n{'='*len(exam_name)}")
 
         try:
-            user_score = self.user_scores["u/"+str(user.pk)]["score"]
+            user_score = self.user_scores["u/" + str(user.pk)]["score"]
 
             if self.app_name == "rapids":
-                callstate = self.user_scores["u/"+str(user.pk)]["callstates"]
+                callstate = self.user_scores["u/" + str(user.pk)]["callstates"]
         except KeyError:
             user_score = "Score not generated"
 
         try:
-            percentage = (
-                f" ({user_score / int(self.stats_max_possible) * 100:.2f}%)"
-            )
+            percentage = f" ({user_score / int(self.stats_max_possible) * 100:.2f}%)"
         except TypeError:
             percentage = ""
 
-        
         exam_text.append(
-                f"""Results\n{'-'*len('Results')}
+            f"""Results\n{'-'*len('Results')}
 # Score: {user_score} / {int(self.stats_max_possible)}{percentage}
 """
-            )
+        )
         stats = self.get_exam_stats(name=False)
         exam_text.append(f"Stats\n{'-'*len('Stats')}\n{stats}")
 
-
         if self.app_name == "rapids":
-            exam_text.append(
-                f"Answers breakdown: {callstate}"
-            )
+            exam_text.append(f"Answers breakdown: {callstate}")
 
         msg = "\n\n".join(exam_text)
 
         return msg
 
     def email_user_results(self, user, resend=False, additional_emails=None):
-        #if self.results_email_sent and not resend:
+        # if self.results_email_sent and not resend:
         #    return False, "Already sent."
 
         # Get a list of taken exams
@@ -376,7 +576,6 @@ class ExamBase(models.Model):
         if supervisor_email:
             emails.append(supervisor_email)
 
-
         if additional_emails is not None:
             emails.extend(additional_emails)
 
@@ -392,14 +591,19 @@ class ExamBase(models.Model):
         except SMTPException as e:
             return [False, e]
 
-        #self.results_email_sent = True
-        #self.save()
+        # self.results_email_sent = True
+        # self.save()
         return [True, ""]
 
+
 class ExamUserStatus(models.Model):
     datetime = models.DateTimeField(auto_now_add=True)
-    cid_user = models.ForeignKey("CidUser", blank=True, null=True, on_delete=models.SET_NULL)
-    user_user = models.ForeignKey(settings.AUTH_USER_MODEL, blank=True, null=True, on_delete=models.SET_NULL)
+    cid_user = models.ForeignKey(
+        "CidUser", blank=True, null=True, on_delete=models.SET_NULL
+    )
+    user_user = models.ForeignKey(
+        settings.AUTH_USER_MODEL, blank=True, null=True, on_delete=models.SET_NULL
+    )
     status = models.CharField(max_length=255)
     extra = models.CharField(max_length=255)
 
@@ -413,10 +617,9 @@ class ExamUserStatus(models.Model):
         else:
             user = self.user_user.username
         return f"{self.datetime}: {user} - {self.status} ({self.extra})"
-    
+
 
 class UserAnswerBase(models.Model):
-
     cid = models.BigIntegerField(
         blank=True,
         null=True,
@@ -426,16 +629,13 @@ class UserAnswerBase(models.Model):
     created = models.DateTimeField(auto_now_add=True)
     updated = models.DateTimeField(auto_now=True)
 
-
     class Meta:
         abstract = True
         ordering = ["cid"]
 
-
     def __str__(self) -> str:
         return "{}/{}/{}".format(self.get_candidate_name(), self.exam, self.question.pk)
 
-
     def get_candidate_name(self) -> str:
         if self.cid is not None:
             return str(self.cid)
@@ -454,7 +654,7 @@ class UserAnswerBase(models.Model):
     def get_answer(self):
         """might need overriding"""
         return self.answer
-        
+
 
 class NoteType(models.Model):
     note_type = models.CharField(max_length=200)
@@ -512,6 +712,7 @@ class QuestionNote(models.Model):
     def get_short_str(self):
         return f"{self.note_type} - {self.note}"
 
+
 EXAM_TYPES = (
     ("physics", "physics_exams"),
     ("rapids", "rapid_exams"),
@@ -521,25 +722,31 @@ EXAM_TYPES = (
     ("casecollection", "casecollection_exams"),
 )
 
-class CidUser(models.Model):
 
+class CidUser(models.Model):
     cid = models.IntegerField(blank=True, null=True, unique=True)
     passcode = models.CharField(blank=True, max_length=50)
     active = models.BooleanField(default=True)
     internal_candidate = models.BooleanField(default=False)
     name = models.CharField(blank=True, max_length=255)
     email = models.EmailField(blank=True)
-    supervisor = models.ForeignKey("Supervisor", on_delete=models.SET_NULL, blank=True, null=True, related_name="cid_user")
+    supervisor = models.ForeignKey(
+        "Supervisor",
+        on_delete=models.SET_NULL,
+        blank=True,
+        null=True,
+        related_name="cid_user",
+    )
 
     login_email_sent = models.BooleanField(default=False)
     results_email_sent = models.BooleanField(default=False)
 
-    group = models.ForeignKey("CidUserGroup", on_delete=models.SET_NULL, null=True, blank=True)
+    group = models.ForeignKey(
+        "CidUserGroup", on_delete=models.SET_NULL, null=True, blank=True
+    )
 
     class Meta:
-        indexes = [ 
-            models.Index(fields=["cid"])
-        ]
+        indexes = [models.Index(fields=["cid"])]
 
     def __str__(self) -> str:
         return str(self.cid)
@@ -575,7 +782,7 @@ class CidUser(models.Model):
 
             for exam in exams:
                 try:
-                    user_score = exam.user_scores["c/"+str(self.cid)]
+                    user_score = exam.user_scores["c/" + str(self.cid)]
                 except KeyError:
                     user_score = "Score not generated"
                 t = exam.get_exam_stats()
@@ -634,7 +841,7 @@ class CidUser(models.Model):
         self.save()
         return True, ""
 
-    def email_details(self, resend: bool=False) -> Tuple[bool, str]:
+    def email_details(self, resend: bool = False) -> Tuple[bool, str]:
         """Email candidate details to the CID user
 
         Args:
@@ -648,7 +855,6 @@ class CidUser(models.Model):
 
         login_url = reverse("cid_selector")
 
-
         msg = f"""
         See below for your details for: {self.group}
 
@@ -682,7 +888,7 @@ class CidUser(models.Model):
                 msg,
                 "no-reply@penracourses.org.uk",
                 [self.email],
-                #["ross.kruger@nhs.net"],
+                # ["ross.kruger@nhs.net"],
             )
             email.send(fail_silently=False)
         except SMTPException as e:
@@ -699,14 +905,16 @@ class CidUser(models.Model):
         return reverse("generic:candidate_email_results", kwargs={"cid": self.cid})
 
     def get_email_results_resend_url(self):
-        return reverse("generic:candidate_email_results_resend", kwargs={"cid": self.cid})
+        return reverse(
+            "generic:candidate_email_results_resend", kwargs={"cid": self.cid}
+        )
+
 
 def get_next_cid():
     """Returns the next available CID"""
     return CidUser.objects.order_by("-cid").first().cid + 1
 
 
-
 class CidUserExam(models.Model):
     content_type = models.ForeignKey(ContentType, on_delete=models.CASCADE)
     object_id = models.PositiveIntegerField()
@@ -715,8 +923,20 @@ class CidUserExam(models.Model):
     start_time = models.DateTimeField(blank=True, null=True)
     end_time = models.DateTimeField(blank=True, null=True)
 
-    cid_user = models.ForeignKey(CidUser, on_delete=models.CASCADE, blank=True, null=True, related_name="cid_userexam")
-    user_user = models.ForeignKey(settings.AUTH_USER_MODEL, on_delete=models.CASCADE, blank=True, null=True, related_name="user_userexam")
+    cid_user = models.ForeignKey(
+        CidUser,
+        on_delete=models.CASCADE,
+        blank=True,
+        null=True,
+        related_name="cid_userexam",
+    )
+    user_user = models.ForeignKey(
+        settings.AUTH_USER_MODEL,
+        on_delete=models.CASCADE,
+        blank=True,
+        null=True,
+        related_name="user_userexam",
+    )
 
     manual_submission = models.BooleanField(default=False)
 
@@ -728,7 +948,10 @@ class CidUserExam(models.Model):
             user = self.user_user.username
         else:
             user = self.cid_user.cid
-        return f"{user}: {self.start_time:%Y-%m-%d %H:%M} {self.end_time:%Y-%m-%d %H:%M}"
+        return (
+            f"{user}: {self.start_time:%Y-%m-%d %H:%M} {self.end_time:%Y-%m-%d %H:%M}"
+        )
+
 
 CID_GROUP_EXAMS = (
     ("SBAs", "sba_cid_user_groups"),
@@ -738,6 +961,7 @@ CID_GROUP_EXAMS = (
     ("Longs", "longs_cid_user_groups"),
 )
 
+
 class CidUserGroup(models.Model):
     name = models.CharField(blank=True, max_length=50)
     archive = models.BooleanField(default=False)
@@ -760,11 +984,10 @@ class CidUserGroup(models.Model):
 
         return dict(exams)
 
-
     def get_absolute_url(self):
         return reverse("generic:cid_group_update", kwargs={"pk": self.pk})
 
-    
+
 USER_GROUP_EXAMS = (
     ("SBAs", "sba_user_user_groups"),
     ("Physics", "physics_user_user_groups"),
@@ -773,9 +996,15 @@ USER_GROUP_EXAMS = (
     ("Longs", "longs_user_user_groups"),
 )
 
+
 class UserUserGroup(models.Model):
-    name = models.CharField(blank=True, max_length=50, help_text="Name of the User Group")
-    archive = models.BooleanField(default=False, help_text="Archived groups remain on the test system but are not displayed by default")
+    name = models.CharField(
+        blank=True, max_length=50, help_text="Name of the User Group"
+    )
+    archive = models.BooleanField(
+        default=False,
+        help_text="Archived groups remain on the test system but are not displayed by default",
+    )
 
     users = models.ManyToManyField(
         settings.AUTH_USER_MODEL,
@@ -803,30 +1032,44 @@ class UserUserGroup(models.Model):
 
     def get_absolute_url(self):
         return reverse("generic:user_group_update", kwargs={"pk": self.pk})
-    
+
+
 class UserGrades(models.Model):
     name = models.CharField(max_length=100)
 
     def __str__(self):
         return self.name
 
+
 USER_EXAM_TYPES = (
     ("Physics", "user_physics_exams"),
     ("Rapids", "user_rapid_exams"),
     ("SBAs", "user_sba_exams"),
     ("Anatomy", "user_anatomy_exams"),
     ("Longs", "user_longs_exams"),
-    #("CaseCollection", "user_casecollection_exams"),
+    # ("CaseCollection", "user_casecollection_exams"),
 )
 
+
 class UserProfile(models.Model):
     user = models.OneToOneField(settings.AUTH_USER_MODEL, on_delete=models.CASCADE)
-    supervisor = models.ForeignKey("Supervisor", on_delete=models.SET_NULL, blank=True, null=True, related_name="trainee")
+    supervisor = models.ForeignKey(
+        "Supervisor",
+        on_delete=models.SET_NULL,
+        blank=True,
+        null=True,
+        related_name="trainee",
+    )
     registration_number = models.CharField(max_length=25, blank=True)
-    grade = models.ForeignKey(UserGrades, null=True, blank=True, help_text="User grade", on_delete=models.CASCADE)
+    grade = models.ForeignKey(
+        UserGrades,
+        null=True,
+        blank=True,
+        help_text="User grade",
+        on_delete=models.CASCADE,
+    )
     peninsula_trainee = models.BooleanField(default=False)
 
-
     def getusername(self):
         return self.user.username
 
@@ -846,34 +1089,50 @@ class UserProfile(models.Model):
 
         return dict(available_exams)
 
+
 class Supervisor(models.Model):
     """Model to hold individual supervisor details (email and name)
-    
+
     This can be linked with a user account.
     """
-    email = models.EmailField(unique=True, help_text="The (nhs.net) email address of the supervisor")
+
+    email = models.EmailField(
+        unique=True, help_text="The (nhs.net) email address of the supervisor"
+    )
     name = models.CharField(max_length=255, help_text="Name of the supervisor")
-    user = models.OneToOneField(settings.AUTH_USER_MODEL, on_delete=models.CASCADE, null=True, blank=True, help_text="If the supervisor has an account on the test system that can be associated here")
-    site = models.ForeignKey("Site", on_delete=models.SET_NULL, null=True, blank=True, help_text="Hospital site at which the supervisor is based")
+    user = models.OneToOneField(
+        settings.AUTH_USER_MODEL,
+        on_delete=models.CASCADE,
+        null=True,
+        blank=True,
+        help_text="If the supervisor has an account on the test system that can be associated here",
+    )
+    site = models.ForeignKey(
+        "Site",
+        on_delete=models.SET_NULL,
+        null=True,
+        blank=True,
+        help_text="Hospital site at which the supervisor is based",
+    )
     active = models.BooleanField(default=True)
 
     def __str__(self) -> str:
         return f"{self.name} ({self.email})"
 
     def get_absolute_url(self):
-        return reverse('generic:supervisor_detail', kwargs={'pk': self.pk})
+        return reverse("generic:supervisor_detail", kwargs={"pk": self.pk})
 
     def clean(self):
         self.email = self.email.strip()
         self.name = self.name.strip()
-    
+
 
 @receiver(post_save, sender=User)
 def create_user_profile(sender, instance, created, **kwargs):
     if created:
         UserProfile.objects.create(user=instance)
 
+
 @receiver(post_save, sender=User)
 def save_user_profile(sender, instance, **kwargs):
     instance.userprofile.save()
-

longs/migrations/0070_remove_long_condition_remove_long_sign_and_more.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.1.4 on 2023-06-12 09:55
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('longs', '0069_alter_long_feedback'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='longseries',
+            name='open_access',
+            field=models.BooleanField(default=True, help_text='If a series should be freely available to browse'),
+        ),
+    ]

longs/models.py

@@ -32,13 +32,12 @@ from generic.models import (
     CidUserGroup,
     ExamUserStatus,
     Examination,
-    # Condition,
-    # Sign,
     ExamBase,
     Plane,
     Contrast,
     QuestionBase,
     QuestionNote,
+    SeriesBase,
     UserAnswerBase,
     UserUserGroup,
 )
@@ -70,14 +69,6 @@ def image_directory_path(instance, filename):
     return "longs/picture/{0}".format(filename)
 
 
-def findMiddle(input_list):
-    middle = float(len(input_list)) / 2
-    if middle % 2 != 0:
-        return input_list[int(middle - 0.5)]
-    else:
-        return input_list[int(middle)]
-        return (input_list[int(middle)], input_list[int(middle - 1)])
-
 
 @reversion.register
 class Long(QuestionBase):
@@ -380,7 +371,7 @@ class LongSeriesImage(models.Model):
 
 
 @reversion.register
-class LongSeries(models.Model):
+class LongSeries(SeriesBase):
     modality = models.ForeignKey(
         Modality, related_name="series_modality", on_delete=models.SET_NULL, null=True
     )
@@ -407,16 +398,6 @@ class LongSeries(models.Model):
         null=True,
         blank=True,
     )
-    # long = models.ManyToManyField(
-    #    "Long",
-    #    help_text="The question(s) this series should be associated with",
-    #    related_name="series",
-    #    blank=True,
-    # )
-    description = models.TextField(
-        blank=True,
-        help_text="Description of stack, for admin organisation, will not be visible when taking",
-    )
 
     author = models.ManyToManyField(
         settings.AUTH_USER_MODEL,
@@ -424,169 +405,11 @@ class LongSeries(models.Model):
         related_name="long_series",
     )
 
-    open_access = models.BooleanField(
-        help_text="If a question should be freely available to browse", default=True
-    )
-
     def __str__(self):
-        # if self.long:
-        #    long_id = ", ".format([long.pk for long in self.long.all()])
-        #    # long_id = self.long.pk
-        # else:
-        #    long_id = "None"
         return "{}/{} : {}".format(self.pk, self.get_examination(), self.description)
 
-    def get_author_objects(self):
-        """Returns a comma seperated text list of authors"""
-        if self.author:
-            return self.author.all()
-        else:
-            return ["None"]
-        if self.long:
-            authors = [i for i in self.long.author.all()]
-        else:
-            authors = []
-
-        return authors
-
-    def get_author_display(self):
-        return ", ".join([i.username for i in self.get_author_objects()])
-
-    def get_examination(self):
-        """Returns a comma seperated text list of regions"""
-        return str(self.examination)
-
-    def get_examination_full(self):
-        examination = ""
-        plane = ""
-        contrast = ""
-
-        if self.examination:
-            examination = self.examination
-        if self.plane:
-            plane = " {}".format(self.plane)
-        if self.contrast:
-            contrast = " {}".format(self.contrast)
-        return "{}{}{}".format(examination, plane, contrast)
-
     def get_absolute_url(self):
-        return reverse("longs:long_series_detail", kwargs={"pk": self.pk})
-
-    def get_image_urls(self, feedback=False):
-        images = [f"{REMOTE_URL}{i.image.url}" for i in self.images.all()]
-
-        return ",".join(images)
-
-    def get_image_url_array(self, feedback=False):
-        images = [f"{REMOTE_URL}{i.image.url}" for i in self.images.all()]
-
-        return json.dumps(images)
-
-    def get_thumbnail(self):
-        images = self.images.all()
-
-        if len(images) < 1:
-            return "No images", 0
-
-        img = findMiddle(images).image
-        try:
-            thumbnailer = get_thumbnailer(img)
-            thumbnail = thumbnailer["exam-list"]
-        except InvalidImageFormatError:
-            return format_html('<span title="{}">Invalid image url<span>', img), len(
-                images
-            )
-        return format_html('<img src="/media/{}" />', thumbnail), len(images)
-
-    def get_block(self):
-        examination = self.get_examination_full()
-        thumb, image_number = self.get_thumbnail()
-        return format_html(
-            "<div>{}<br/>{}<br/>Images: {}</div>", examination, thumb, image_number
-        )
-
-    def order_by_upload_filename(self):
-        images = self.images.all()
-
-        filenames = []
-        map = {}
-
-        for i in images:
-            filenames.append(i.upload_filename)
-            map[i.upload_filename] = i
-
-        filenames = sorted(filenames)
-
-        n = 1
-        for f in filenames:
-            i = map[f]
-            i.position = n
-            i.save()
-            n = n + 1
-
-    def order_by_dicom(self, field="SliceLocation"):
-        images = self.images.all()
-
-        files = []
-
-        for i in images:
-            files.append((i, pydicom.dcmread(i.image.path)))
-
-        # print("file count: {}".format(len(files)))
-
-        # skip files with no SliceLocation (eg scout views)
-        slices = []
-        map = {}
-        skipcount = 0
-        for i, f in files:
-            if hasattr(f, field):
-                slices.append(f)
-                # map[f.SliceLocation] = i
-                map[f[field].value] = i
-            else:
-                skipcount = skipcount + 1
-
-        print("skipped, no {}: {}".format(field, skipcount))
-
-        # ensure they are in the correct order
-        slices = sorted(slices, key=lambda s: s[field].value)
-
-        # print(slices)
-        n = 1
-        for f in slices:
-            i = map[f[field].value]
-            i.position = n
-            i.save()
-            n = n + 1
-
-    def get_total_image_size(self):
-        images = self.images.all()
-
-        size = 0
-
-        for i in images:
-            size += i.image.size
-
-        return size
-
-
-# class LongImage(models.Model):
-#    long = models.ForeignKey(Long,
-#                              related_name="images",
-#                              on_delete=models.CASCADE)
-#    image = models.ImageField(upload_to=image_directory_path, storage=image_storage)
-#
-#    feedback_image = models.BooleanField(default=False)
-#
-#    def image_tag(self):
-#        if self.image:
-#            return mark_safe(
-#                '<img src="{}" class="admin-long-image" /><span class="admin-long-image-info">Click and hold to zoom<span>'
-#                .format(self.image.url))
-#        else:
-#            return ""
-#
-#    image_tag.short_description = 'Image'
+        return reverse("longs:series_detail", kwargs={"pk": self.pk})
 
 
 class LongCreationDefault(models.Model):