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 handle(self, *args, **options):
samples = (IgvSample.objects.filter(
individual__family__project__name__in=args
) if args else IgvSample.objects.all()).filter(
file_path__startswith='gs://'
).prefetch_related('individual', 'individual__family__project')
missing_counter = collections.defaultdict(int)
guids_of_samples_with_missing_file = set()
for sample in tqdm.tqdm(samples, unit=" samples"):
if not hl.hadoop_is_file(sample.file_path):
individual_id = sample.individual.individual_id
project = sample.individual.family.project.name
missing_counter[project] += 1
logger.info('Individual: {} file not found: {}'.format(individual_id, sample.file_path))
if not options.get('dry_run'):
guids_of_samples_with_missing_file.add(sample.guid)
if len(guids_of_samples_with_missing_file) > 0:
IgvSample.bulk_update(user=None, update_json={'file_path': ''}, guid__in=guids_of_samples_with_missing_file)
logger.info('---- DONE ----')
logger.info('Checked {} samples'.format(len(samples)))
if missing_counter:
logger.info('{} files not found:'.format(sum(missing_counter.values())))
for project_name, c in sorted(missing_counter.items(), key=lambda t: -t[1]):
logger.info(' {} in {}'.format(c, project_name))
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 handle(self, *args, **options):
samples = (IgvSample.objects.filter(
individual__family__project__name__in=args
) if args else IgvSample.objects.all()).filter(
file_path__startswith='gs://'
).prefetch_related('individual', 'individual__family__project')
missing_counter = collections.defaultdict(int)
guids_of_samples_with_missing_file = set()
project_name_to_missing_paths = collections.defaultdict(list)
for sample in tqdm.tqdm(samples, unit=" samples"):
if not hl.hadoop_is_file(sample.file_path):
individual_id = sample.individual.individual_id
project_name = sample.individual.family.project.name
missing_counter[project_name] += 1
project_name_to_missing_paths[project_name].append((individual_id, sample.file_path))
logger.info('Individual: {} file not found: {}'.format(individual_id, sample.file_path))
if not options.get('dry_run'):
guids_of_samples_with_missing_file.add(sample.guid)
if len(guids_of_samples_with_missing_file) > 0:
IgvSample.bulk_update(user=None, update_json={'file_path': ''}, guid__in=guids_of_samples_with_missing_file)
logger.info('---- DONE ----')
logger.info('Checked {} samples'.format(len(samples)))
if missing_counter:
logger.info('{} files not found:'.format(sum(missing_counter.values())))
for project_name, c in sorted(missing_counter.items(), key=lambda t: -t[1]):
logger.info(' {} in {}'.format(c, project_name))
# post to slack
if not options.get('dry_run'):
slack_message = 'Found {} broken bam/cram path(s)\n'.format(sum(missing_counter.values()))
for project_name, missing_paths_list in project_name_to_missing_paths.items():
slack_message += "\nIn project {}:\n".format(project_name)
slack_message += "\n".join([
" {} {}".format(individual_id, path) for individual_id, path in missing_paths_list
])
communication_utils.safe_post_to_slack(SEQR_SLACK_DATA_ALERTS_NOTIFICATION_CHANNEL, slack_message)