def handle(self, *args, **options):
project_id = options.get('project_id')
print("Deleting phenotips records in project: %s" % project_id)
try:
proj = Project.objects.get(deprecated_project_id=project_id)
except ObjectDoesNotExist:
raise CommandError("Project %s not found." % project_id)
for family in Family.objects.filter(project=proj):
for individual in Individual.objects.filter(family=family):
print("Deleting records for %s - %s" %
(family.family_id, individual.individual_id))
delete_patient(proj, individual)
print("Deleted all phenotips records for %s!" % project_id)
def delete_individuals(project, individual_guids):
"""Delete one or more individuals
Args:
project (object): Django ORM model for project
individual_guids (list): GUIDs of individuals to delete
Returns:
list: Family objects for families with deleted individuals
"""
individuals_to_delete = Individual.objects.filter(
family__project=project, guid__in=individual_guids)
samples_to_delete = Sample.objects.filter(
individual__family__project=project,
individual__guid__in=individual_guids)
for sample in samples_to_delete:
logger.info("Deleting sample: %s" % sample)
sample.delete()
families = {}
for individual in individuals_to_delete:
families[individual.family.family_id] = individual.family
# delete phenotips records
try:
delete_patient(project,
individual.phenotips_eid,
is_external_id=True)
except (PhenotipsException, ValueError) as e:
logger.error(
"Error: couldn't delete patient from phenotips: %s %s",
individual.phenotips_eid, individual)
# delete Individual
individual.delete()
_deprecated_delete_individual(project, individual)
update_pedigree_images(families.values())
families_with_deleted_individuals = list(families.values())
return families_with_deleted_individuals
def delete_individuals(project, individual_guids):
"""Delete one or more individuals
Args:
project (object): Django ORM model for project
individual_guids (list): GUIDs of individuals to delete
Returns:
list: Family objects for families with deleted individuals
"""
individuals_to_delete = Individual.objects.filter(
family__project=project, guid__in=individual_guids)
samples_to_delete = Sample.objects.filter(
individual__family__project=project, individual__guid__in=individual_guids)
for sample in samples_to_delete:
logger.info("Deleting sample: %s" % sample)
sample.delete()
families = {}
for individual in individuals_to_delete:
families[individual.family.family_id] = individual.family
# delete phenotips records
try:
delete_patient(project, individual)
except (PhenotipsException, ValueError) as e:
logger.error("Error: couldn't delete patient from phenotips: %s %s",
individual.phenotips_eid,
individual)
# delete Individual
delete_seqr_model(individual)
update_pedigree_images(families.values())
families_with_deleted_individuals = list(families.values())
return families_with_deleted_individuals