def _assign_disease_by_morpho_topo(instance, icdo_morpho, icdo_topo_list, disease_field='disease'):
"""
Given an instance with a disease:models.ForeignKey(Disease) field (specified by 'disease_field'),
an icdo_morpho id, and an optional set of icdo_topo IDs in icdo_topo_list,
creates a new disease matching the morpho, topo spec, or retrieves it if it already exists.
Assigns the new or retrieved disease to the instance's disease field if successful.
"""
# approach: now that Disease is mutable, we can't simply point
# multiple curation entries at the same Disease; instead, we need
# to either look up a Disease that matches the morpho code + topo set
# in this entry, or create it if it doesn't exist.
# note that this produces a trail of Diseases that are *potentially*
# no longer in use if we ever change the morpho code or topo codes.
# we can either clean up these unused entries after updating, or
# 'vacuum' them on a schedule with a script. this will require
# identifying every model that refers to a Disease
with transaction.atomic():
if not icdo_morpho:
# we can't assign a disease if they didn't specify a morpho field
setattr(instance, disease_field, None)
instance.save()
return None
instance_disease = getattr(instance, disease_field)
if instance_disease:
# if there was previously a disease, check if it's in use and delete it if not
collector = NestedObjects(using='default') # or specific database
collector.collect([instance_disease])
if collector.can_fast_delete():
print("Fast-deleting old disease")
instance_disease.delete()
else:
print("Can't fast-delete old disease: %s" % collector.nested())
# build a Q-object that's all the topo entries related to the target Disease ANDed together
q_objects = Q(icd_o_morpho=icdo_morpho['id'])
if icdo_topo_list:
for x in icdo_topo_list:
q_objects &= Q(icdotopoapidisease__icd_o_topo__id=x['id'])
else:
# we need to search for a morpho that has no associated topo codes
q_objects &= Q(icdotopoapidisease=None)
# either retrieve an existing disease that matches the description, or create it
candidate = Disease.objects.filter(q_objects).first()
if not candidate:
candidate = Disease.objects.create(
icd_o_morpho=IcdOMorpho.objects.get(id=icdo_morpho['id']))
IcdOTopoApiDisease.objects.bulk_create([
IcdOTopoApiDisease(api_disease=candidate,
icd_o_topo=IcdOTopo.objects.get(id=x['id']))
for x in (icdo_topo_list if icdo_topo_list else [])
])
candidate.save()
setattr(instance, disease_field, candidate)
instance.save()
