correct_lane = tantalus_api.get(
'sequencing_lane',
flowcell_id=row['correct_flowcell_id'],
lane_number=str(row['correct_lane_number']),
dna_library=incorrect_lane['dna_library'],
)
except NotFoundError:
correct_lane = None
if correct_lane is None:
correct_lane = tantalus_api.create(
'sequencing_lane',
flowcell_id=row['correct_flowcell_id'],
lane_number=str(row['correct_lane_number']),
dna_library=incorrect_lane['dna_library'],
sequencing_centre="GSC",
sequencing_instrument=incorrect_lane['sequencing_instrument'],
sequencing_library_id=incorrect_lane['sequencing_library_id'],
read_type=incorrect_lane['read_type'],
)
pass
else:
for field in ('sequencing_centre', 'sequencing_instrument',
'sequencing_library_id'):
if correct_lane[field] != incorrect_lane[field]:
logging.warning('updating {} from {} to {}'.format(
field, correct_lane[field], incorrect_lane[field]))
correct_lane = tantalus_api.update(
'sequencing_lane',
id=correct_lane['id'],
def fix():
tantalus_api = TantalusApi()
datasets = list(
tantalus_api.list(
'sequence_dataset',
dataset_type='BAM',
library__library_type__name='WGS',
))
for dataset in datasets:
bams = {}
bais = {}
specs = {}
for file_resource_id in dataset['file_resources']:
file_resource = tantalus_api.get('file_resource',
id=file_resource_id)
if file_resource['filename'].endswith('.bam'):
bams[file_resource_id] = file_resource['filename']
elif file_resource['filename'].endswith('.spec'):
specs[file_resource_id] = file_resource['filename']
elif file_resource['filename'].endswith('.bam.bai'):
bais[file_resource_id] = file_resource['filename']
if len(bams) == 0 and len(specs) == 0:
print(dataset['id'])
elif len(bams) > 1:
logging.info(f"fixing {dataset['name']}, {bams}")
to_remove_bam_id = max(bams.keys())
to_remove_bai_id = None
for id_, bai in bais.items():
if bai.startswith(bams[to_remove_bam_id]):
assert to_remove_bai_id is None
to_remove_bai_id = id_
break
assert to_remove_bai_id is not None
logging.info((to_remove_bam_id, bams[to_remove_bam_id],
to_remove_bai_id, bais[to_remove_bai_id]))
new_file_resources = dataset['file_resources']
new_file_resources.remove(to_remove_bam_id)
new_file_resources.remove(to_remove_bai_id)
logging.info(
f"updating {dataset['id']} to have files {new_file_resources}")
tantalus_api.update('sequencedataset',
id=dataset['id'],
file_resources=new_file_resources)
assert dataset["name"].endswith(str(dataset["version_number"]))
similar_datasets = list(
tantalus_api.list(
"sequence_dataset",
name=dataset["name"],
))
new_version_number = max(d['version_number']
for d in similar_datasets) + 1
new_dataset_params = dict(
sample=dataset['sample']['id'],
library=dataset['library']['id'],
sequence_lanes=[l['id'] for l in dataset['sequence_lanes']],
aligner=dataset['aligner'],
reference_genome=dataset['reference_genome'],
name=dataset['name'][:-1] + str(new_version_number),
dataset_type=dataset['dataset_type'],
version_number=new_version_number,
file_resources=[to_remove_bam_id, to_remove_bai_id],
)
logging.info(new_dataset_params)
new_dataset = tantalus_api.create('sequencedataset',
**new_dataset_params)
logging.info(new_dataset)