start working torwards stack modificaiton

atlas/api.py

@@ -183,7 +183,6 @@ def series_remove_duplicate_images(request, series_id: int):
 
 @router.get("/get_cases_user", auth=django_auth, response=List[CaseSchema])
 def get_cases_user(request):
-    print("HELLO")
     return Case.objects.filter(author=request.user)
 
 
@@ -250,8 +249,6 @@ def series_split_by_tag(request, series_id: int, dicom_tag:str):
     if dicom_tag.startswith("(") and dicom_tag.endswith(")"):
         dicom_tag = tuple([hex(int(i.strip(),16)) for i in dicom_tag[1:-1].split(",")])
 
-    print("1", dicom_tag)
-
     image_map = defaultdict(list)
 
     # Split teh associated images

atlas/models.py

@@ -32,7 +32,12 @@ from sortedm2m.fields import SortedManyToManyField
 
 import string
 from collections import defaultdict
-from helpers.images import get_image_dicom_hash, get_image_hash, image_as_base64, pretty_print_dicom
+from helpers.images import (
+    get_image_dicom_hash,
+    get_image_hash,
+    image_as_base64,
+    pretty_print_dicom,
+)
 
 
 from generic.models import (
@@ -143,16 +148,42 @@ class Finding(SynMixin, models.Model):
 class Condition(SynMixin, models.Model):
     name = models.CharField(max_length=255, unique=True)
 
-    synonym = models.ManyToManyField("self", blank=True, help_text="Use if a direct synonym for the condition exists, e.g. 'Wegener granulomatosis' and 'Granulomatosis with Polyangitis'.")
+    synonym = models.ManyToManyField(
-    parent = models.ManyToManyField("self", blank=True, related_name="child", symmetrical=False, through="ConditionRelationship", help_text="Use if the condition could be considered a subset of another, e.g. 'Alzheimer disease' and 'Dementia'.")
+        "self",
+        blank=True,
+        help_text="Use if a direct synonym for the condition exists, e.g. 'Wegener granulomatosis' and 'Granulomatosis with Polyangitis'.",
+    )
+    parent = models.ManyToManyField(
+        "self",
+        blank=True,
+        related_name="child",
+        symmetrical=False,
+        through="ConditionRelationship",
+        help_text="Use if the condition could be considered a subset of another, e.g. 'Alzheimer disease' and 'Dementia'.",
+    )
 
-    primary = models.BooleanField(default="True", help_text="Sets if this should be the canonical item, all other synonyms will then redirect to this by default.")
+    primary = models.BooleanField(
+        default="True",
+        help_text="Sets if this should be the canonical item, all other synonyms will then redirect to this by default.",
+    )
 
-    subspecialty = models.ManyToManyField("subspecialty", blank=True, help_text="Sets the subspecialty(/ies) that this condition falls under.")
+    subspecialty = models.ManyToManyField(
+        "subspecialty",
+        blank=True,
+        help_text="Sets the subspecialty(/ies) that this condition falls under.",
+    )
 
-    rcr_curriculum_map = models.ManyToManyField("self", blank=True, limit_choices_to={"rcr_curriculum": True}, help_text="Specifies the related RCR curriculum condition (if it exists).")
+    rcr_curriculum_map = models.ManyToManyField(
+        "self",
+        blank=True,
+        limit_choices_to={"rcr_curriculum": True},
+        help_text="Specifies the related RCR curriculum condition (if it exists).",
+    )
 
-    rcr_curriculum = models.BooleanField(default=False, help_text="The condition is from the (non exhaustive) RCR curriculum")
+    rcr_curriculum = models.BooleanField(
+        default=False,
+        help_text="The condition is from the (non exhaustive) RCR curriculum",
+    )
 
     def get_absolute_url(self):
         return reverse("atlas:condition_detail", kwargs={"pk": self.pk})
@@ -163,10 +194,10 @@ class Condition(SynMixin, models.Model):
     def get_descendents(self):
         """TODO"""
 
-
     def get_parents(self):
         return self.parent.all()
 
+
 class ConditionRelationship(models.Model):
     child = models.ForeignKey(Condition, on_delete=models.CASCADE)
     parent = models.ForeignKey(Condition, on_delete=models.CASCADE, related_name="+")
@@ -263,7 +294,6 @@ class Case(models.Model):
         ALMOST_CERTAIN = 3
         CERTAIN = 4
 
-
     title = models.CharField(max_length=255, help_text="Title of the case", default="")
     description = models.TextField(
         blank=True,
@@ -293,7 +323,9 @@ class Case(models.Model):
         Condition, through=Differential, related_name="casedifferential"
     )
 
-    diagnostic_certainty = models.IntegerField(choices=CertaintyChoices.choices, default=CertaintyChoices.NONE)
+    diagnostic_certainty = models.IntegerField(
+        choices=CertaintyChoices.choices, default=CertaintyChoices.NONE
+    )
 
     verified = models.BooleanField(default=False)
     created_date = models.DateTimeField(default=timezone.now)
@@ -348,7 +380,7 @@ class Case(models.Model):
         return authors
 
     def get_link(self):
-        #return f"{self.pk}: {self.title}"
+        # return f"{self.pk}: {self.title}"
         return format_html("<a href='{}'>{}</a>", self.get_absolute_url(), str(self))
 
     def __str__(self):
@@ -439,8 +471,14 @@ class SeriesImage(SeriesImageBase):
         "Series", related_name="images", on_delete=models.CASCADE, null=True
     )
 
+    replaced = models.ForeignKey(
+        "self",
+        null=True,
+        blank=True,
+        help_text="Reference to the object that has replaced this one.",
+    )
+
     def get_dicom_data(self):
-        print(self.image)
         try:
             with pydicom.dcmread(self.image) as d:
                 return d
@@ -844,7 +882,11 @@ class UncategorisedDicom(models.Model):
     )
 
     series = models.ForeignKey(
-        "Series", related_name="imported_dicoms", on_delete=models.SET_NULL, null=True, blank=True
+        "Series",
+        related_name="imported_dicoms",
+        on_delete=models.SET_NULL,
+        null=True,
+        blank=True,
     )
 
     series_instance_uid = models.CharField(max_length=255, blank=True, null=True)
@@ -864,13 +906,11 @@ class UncategorisedDicom(models.Model):
         if obj := SeriesImage.objects.filter(image_md5_hash=image_hash).first():
             duplicate = obj
 
-
         return duplicate
 
     def save(self, *args, **kwargs):
         """Override save method to add image hash"""
         if self.image:
-
             ds = self.get_dicom_info()
 
             self.series_instance_uid = ds["SeriesInstanceUID"].value
@@ -886,7 +926,6 @@ class UncategorisedDicom(models.Model):
             if duplicate is not None:
                 raise DuplicateDicom
 
-
         # Hack for tests
         if image_hash != "1234":
             super().save(*args, **kwargs)  # Call the "real" save() method.

atlas/views.py

@@ -398,6 +398,8 @@ def user_uploads(request, case_id: int | None = None):
         series_list.append((series, len(data[series]), tags, date))
     print(series_list)
 
+    series_list.sort(key=lambda l: l[-1])
+
     case = False
     if case_id is not None:
         case = get_object_or_404(Case, pk=case_id)

generic/models.py

@@ -183,6 +183,11 @@ class QuestionBase(models.Model):
 
 
 class SeriesImageBase(models.Model):
+    """
+    Series Images may be modified (usually downsampled to save space), in this case the
+    (larger) original file will be deleted but the model object will be persisted so that
+    the duplicate check continues to function.
+    """
     position = models.IntegerField(default=0)
     upload_filename = models.CharField(max_length=255, blank=True)
     series = models.ForeignKey(