def biosamples_list(
basespace_project_id,
host,
email,
password,
api_key,
):
"""List all Biosamples from BaseSpace project.
Examples:
List Biosamples of a BaseSpace project:
gencove basespace biosamples list 12345678
List Biosamples of a BaseSpace projects:
gencove basespace biosamples list 12345678,87654321
"""
BiosamplesList(
basespace_project_id,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def list_project_batch_types(project_id, host, email, password, api_key):
"""List batch types that are available for a project."""
ListBatchTypes(
project_id,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def create_project_batch( # pylint: disable=too-many-arguments
project_id,
batch_type,
batch_name,
sample_ids,
host,
email,
password,
api_key,
):
"""Create a batch in a project."""
if sample_ids:
sample_ids = [s_id.strip() for s_id in sample_ids.split(",")]
echo_debug("Sample ids translation: {}".format(sample_ids))
else:
sample_ids = []
CreateBatch(
project_id,
batch_type,
batch_name,
sample_ids,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def get_batch(batch_id, output_filename, host, email, password, api_key,
no_progress):
"""Get batch that is available for a project."""
GetBatch(
batch_id,
output_filename,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
no_progress,
).run()
def create_merged_vcf(
project_id,
host,
email,
password,
api_key,
):
"""Merge VCF files in a project."""
CreateMergedVCF(
project_id,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def status_merged_vcf(
project_id,
host,
email,
password,
api_key,
):
"""Get status of merge VCF files job in a project."""
StatusMergedVCF(
project_id,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def get_metadata(
sample_id,
output_filename,
host,
email,
password,
api_key,
):
"""Get sample metadata."""
GetMetadata(
sample_id,
output_filename,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def set_metadata(
sample_id,
json,
host,
email,
password,
api_key,
):
"""Set sample metadata."""
SetMetadata(
sample_id,
json,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def get_merged_vcf(
project_id,
output_filename,
host,
email,
password,
api_key,
no_progress,
):
"""Download merged VCF file in a project."""
GetMergedVCF(
project_id,
output_filename,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
no_progress,
).run()
def delete_project_samples( # pylint: disable=too-many-arguments
project_id,
sample_ids,
host,
email,
password,
api_key,
):
"""Delete samples in a project."""
sample_ids = ([s_id.strip()
for s_id in sample_ids.split(",")] if sample_ids else [])
echo_debug("Sample ids translation: {}".format(sample_ids))
DeleteSamples(
project_id,
sample_ids,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def basespace_list(
host,
email,
password,
api_key,
):
"""List all BaseSpace projects.
Examples:
Import Biosamples to a project:
gencove basespace projects list
"""
BaseSpaceList(
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def autoimport_list(
host,
email,
password,
api_key,
):
"""Lists S3 automatic import jobs.
Examples:
List S3 automatic import jobs:
gencove s3 autoimports list
""" # noqa: E501
S3AutoImportList(
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def list_projects(host, email, password, api_key):
"""List your projects."""
List(
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
).run()
def download_file(
sample_id,
file_type,
destination,
host,
email,
password,
api_key,
no_progress,
): # noqa: D413,D301,D412 # pylint: disable=C0301
"""Download sample file metadata.
SAMPLE_ID specific sample for which to download the results
FILE_TYPE specific deliverable to download results for
DESTINATION path/to/file
Examples:
Download sample:
gencove samples download-file e6b45af7-07c5-4a6d-9f97-6e1efbf3e215 ancestry-json ancestry.json
Download and print to stdout then compress using gzip:
gencove samples download-file e6b45af7-07c5-4a6d-9f97-6e1efbf3e215 ancestry-json - | gzip > ancestry.json.gz
\f
Args:
sample_id (str): specific sample for which
to download the results.
file_type (str): specific deliverable to download
results for.
destination (str): path/to/file.
no_progress (bool, optional, default False): do not show progress
bar.
""" # noqa: E501
if destination in ("-", "/dev/stdout"):
DownloadFile(
sample_id,
file_type,
sys.stdout.buffer,
Credentials(email=email, password=password, api_key=api_key),
Optionals(host=host),
no_progress,
).run()
else:
try:
with open(destination, "wb") as destination_file:
DownloadFile(
sample_id,
file_type,
destination_file,
Credentials(email=email,
password=password,
api_key=api_key),
Optionals(host=host),
no_progress,
).run()
except IsADirectoryError:
echo_error("Please specify a file path (not directory path)"
" for DESTINATION")
raise click.Abort() # pylint: disable=raise-missing-from