def delete_individuals(project, individual_guids, user):
"""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)
Sample.bulk_delete(user, individual__family__project=project, individual__guid__in=individual_guids)
IgvSample.bulk_delete(user, individual__family__project=project, individual__guid__in=individual_guids)
families = {individual.family for individual in individuals_to_delete}
Individual.bulk_delete(user, queryset=individuals_to_delete)
update_pedigree_images(families, user)
families_with_deleted_individuals = list(families)
return families_with_deleted_individuals
def _update_variant_samples(matched_sample_id_to_sample_record, user, elasticsearch_index, loaded_date=None,
dataset_type=Sample.DATASET_TYPE_VARIANT_CALLS, sample_type=Sample.SAMPLE_TYPE_WES):
if not loaded_date:
loaded_date = timezone.now()
updated_samples = [sample.id for sample in matched_sample_id_to_sample_record.values()]
activated_sample_guids = Sample.bulk_update(user, {
'elasticsearch_index': elasticsearch_index,
'is_active': True,
'loaded_date': loaded_date,
}, id__in=updated_samples, is_active=False)
matched_sample_id_to_sample_record.update({
sample.sample_id: sample for sample in Sample.objects.filter(guid__in=activated_sample_guids)
})
inactivate_samples = Sample.objects.filter(
individual_id__in={sample.individual_id for sample in matched_sample_id_to_sample_record.values()},
is_active=True,
dataset_type=dataset_type,
sample_type=sample_type,
).exclude(id__in=updated_samples)
inactivate_sample_guids = Sample.bulk_update(user, {'is_active': False}, queryset=inactivate_samples)
return inactivate_sample_guids
def _delete_project(project_guid, user):
"""Delete project.
Args:
project_guid (string): GUID of the project to delete
user (object): Django ORM model for the user
"""
project = Project.objects.get(guid=project_guid)
check_user_created_object_permissions(project, user)
IgvSample.bulk_delete(user, individual__family__project=project)
Sample.bulk_delete(user, individual__family__project=project)
Individual.bulk_delete(user, family__project=project)
Family.bulk_delete(user, project=project)
project.delete_model(user, user_can_delete=True)
def match_sample_ids_to_sample_records(
project,
user,
sample_ids,
sample_type,
dataset_type=Sample.DATASET_TYPE_VARIANT_CALLS,
elasticsearch_index=None,
create_sample_records=True,
sample_id_to_individual_id_mapping=None,
loaded_date=None,
):
"""Goes through the given list of sample_ids and finds existing Sample records of the given
sample_type and dataset_type with ids from the list. For sample_ids that aren't found to have existing Sample
records, it looks for Individual records that have an individual_id that either exactly or
approximately equals one of the sample_ids in the list or is contained in the optional
sample_id_to_individual_id_mapping and optionally creates new Sample records for these.
Args:
project (object): Django ORM project model
user (object): Django ORM User model
sample_ids (list): a list of sample ids for which to find matching Sample records
sample_type (string): one of the Sample.SAMPLE_TYPE_* constants
dataset_type (string): one of the Sample.DATASET_TYPE_* constants
elasticsearch_index (string): an optional string specifying the index where the dataset is loaded
max_edit_distance (int): max permitted edit distance for approximate matches
create_sample_records (bool): whether to create new Sample records for sample_ids that
don't match existing Sample records, but do match individual_id's of existing
Individual records.
sample_id_to_individual_id_mapping (object): Mapping between sample ids and their corresponding individual ids
Returns:
tuple:
[0] dict: sample_id_to_sample_record containing the matching Sample records (including any
newly-created ones)
[1] array: array of the sample_ids of any samples that were created
"""
sample_id_to_sample_record = find_matching_sample_records(
project, sample_ids, sample_type, dataset_type, elasticsearch_index)
logger.debug(
str(len(sample_id_to_sample_record)) + " exact sample record matches",
user)
remaining_sample_ids = set(sample_ids) - set(
sample_id_to_sample_record.keys())
if len(remaining_sample_ids) > 0:
already_matched_individual_ids = {
sample.individual.individual_id
for sample in sample_id_to_sample_record.values()
}
remaining_individuals_dict = {
i.individual_id: i
for i in Individual.objects.filter(
family__project=project).exclude(
individual_id__in=already_matched_individual_ids)
}
# find Individual records with exactly-matching individual_ids
sample_id_to_individual_record = {}
for sample_id in remaining_sample_ids:
individual_id = sample_id
if sample_id_to_individual_id_mapping and sample_id in sample_id_to_individual_id_mapping:
individual_id = sample_id_to_individual_id_mapping[sample_id]
if individual_id not in remaining_individuals_dict:
continue
sample_id_to_individual_record[
sample_id] = remaining_individuals_dict[individual_id]
del remaining_individuals_dict[individual_id]
logger.debug(
str(len(sample_id_to_individual_record)) +
" matched individual ids", user)
# create new Sample records for Individual records that matches
if create_sample_records:
new_samples = [
Sample(
guid='S{}_{}'.format(random.randint(10**9, 10**10),
sample_id)[:Sample.MAX_GUID_SIZE],
sample_id=sample_id,
sample_type=sample_type,
dataset_type=dataset_type,
elasticsearch_index=elasticsearch_index,
individual=individual,
created_date=timezone.now(),
loaded_date=loaded_date or timezone.now(),
) for sample_id, individual in
sample_id_to_individual_record.items()
]
sample_id_to_sample_record.update({
sample.sample_id: sample
for sample in Sample.bulk_create(user, new_samples)
})
log_model_bulk_update(logger, new_samples, user, 'create')
return sample_id_to_sample_record