def drs_copy(args: argparse.Namespace):
"""
Copy drs:// object to local file or Google Storage bucket
If 'dst' is suffixed with "/", the destination is assumed to be a folder and the file name is
derived from the drs response and appended to 'dst'. Otherwise the destination is assumed
to be absolute.
examples:
tnu drs copy drs://my-drs-id /tmp/doom # copy to /tmp/doom
tnu drs copy drs://my-drs-id /tmp/doom/ # copy to /tmp/doom/{file-name-from-drs-resolution}
tnu drs copy drs://my-drs-id gs://my-cool-bucket/my-cool-bucket-key
tnu drs copy drs://my-drs-id gs://my-cool-bucket/my-cool-bucket-key/
"""
args.workspace, args.workspace_namespace = CLIConfig.resolve(args.workspace, args.workspace_namespace)
kwargs: Dict[str, Any] = dict(workspace_name=args.workspace, workspace_namespace=args.workspace_namespace)
if CLIConfig.progress_indicator_type() is not None:
kwargs['indicator_type'] = CLIConfig.progress_indicator_type()
drs.copy(args.drs_url, args.dst, **kwargs)
def drs_copy_batch(args: argparse.Namespace):
"""
Copy several drs:// objects to local directory or Google Storage bucket
examples:
tnu drs copy-batch drs://my-drs-1 drs://my-drs-2 drs://my-drs-3 --dst /tmp/doom/
tnu drs copy-batch drs://my-drs-1 drs://my-drs-2 drs://my-drs-3 --dst gs://my-cool-bucket/my-cool-folder
tnu drs copy-batch --manifest manifest.json
When not using a manifest, 'dst' is treated as a folder, and file names are derived from the drs response.
Otherwise, in a manifest, 'dst' can either be a folder (if suffixed with "/"), or an absolute path, e.g.
'/home/me/my-file-name.vcf.gz' or 'gs://bucket-name/pfx/my-file.vcf.gz'.
example manifest.json:
[
{
"drs_uri": "drs://my/cool/drs/uri",
"dst": "/path/to/local/dir/"
},
{
"drs_uri": "drs://my/cool/drs/uri",
"dst": "gs://my-cook-bucket/my-cool-prefix"
}
]
"""
args.workspace, args.workspace_namespace = CLIConfig.resolve(args.workspace, args.workspace_namespace)
kwargs: Dict[str, Any] = dict(workspace_name=args.workspace, workspace_namespace=args.workspace_namespace)
if CLIConfig.progress_indicator_type() is not None:
kwargs['indicator_type'] = CLIConfig.progress_indicator_type()
if args.drs_uris:
assert args.manifest is None, "Cannot use 'drs_uris' with '--manifest'"
assert args.dst is not None, "Must specify a destination with '--dst'"
drs.copy_batch_urls(args.drs_uris, args.dst, **kwargs)
elif args.manifest:
with open(args.manifest) as fh:
manifest = json.loads(fh.read())
drs.copy_batch_manifest(manifest, **kwargs)
else:
raise RuntimeError("Must supply either 'drs_uris' or '--manifest'")