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start working torwards stack modificaiton

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This commit is contained in:
Ross
2023-12-18 09:17:05 +00:00
parent bdeb2210e1
commit ada3a8906f
4 changed files with 63 additions and 20 deletions
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atlas/models.py
+56 -17
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@@ -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'.")
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'.")
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'.",
)
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="+")
@@ -175,7 +206,7 @@ class ConditionRelationship(models.Model):
def __str__(self):
return f"{self.parent} -> {self.child}"
class Presentation(models.Model):
name = models.CharField(max_length=255)
@@ -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.