def move_files(ctx, source, target, workflow, access_token): # noqa: D301
"""Move files within workspace.
The `mv` command allow to move the files within workspace.
Examples:\n
\t $ reana-client mv data/input.txt input/input.txt
"""
from reana_client.api.client import get_workflow_status, list_files, mv_files
logging.debug("command: {}".format(ctx.command_path.replace(" ", ".")))
for p in ctx.params:
logging.debug("{param}: {value}".format(param=p, value=ctx.params[p]))
if workflow:
try:
current_status = get_workflow_status(workflow,
access_token).get("status")
if current_status == "running":
click.echo(
click.style(
"File(s) could not be moved for running "
"workflow",
fg="red"),
err=True,
)
sys.exit(1)
files = list_files(workflow, access_token)
current_files = [file["name"] for file in files]
if not any(source in item for item in current_files):
click.echo(
click.style(
"Source file(s) {} does not exist in "
"workspace {}".format(source, current_files),
fg="red",
),
err=True,
)
sys.exit(1)
response = mv_files(source, target, workflow, access_token)
click.echo(
click.style(
"{} was successfully moved to {}.".format(source, target),
fg="green",
))
except Exception as e:
logging.debug(traceback.format_exc())
logging.debug(str(e))
click.echo(click.style("Something went wrong. {}".format(e),
fg="red"),
err=True)
def move_files(ctx, source, target, workflow, access_token): # noqa: D301
r"""Move files within workspace.
Examples:\n
\t $ reana-client mv data/input.txt input/input.txt
"""
logging.debug('command: {}'.format(ctx.command_path.replace(" ", ".")))
for p in ctx.params:
logging.debug('{param}: {value}'.format(param=p, value=ctx.params[p]))
if not access_token:
click.echo(click.style(ERROR_MESSAGES['missing_access_token'],
fg='red'),
err=True)
sys.exit(1)
if workflow:
try:
current_status = get_workflow_status(workflow,
access_token).get('status')
if current_status == 'running':
click.echo(click.style(
'File(s) could not be moved for running '
'workflow',
fg='red'),
err=True)
sys.exit(1)
files = list_files(workflow, access_token)
current_files = [file['name'] for file in files]
if not any(source in item for item in current_files):
click.echo(click.style('Source file(s) {} does not exist in '
'workspace {}'.format(
source, current_files),
fg='red'),
err=True)
sys.exit(1)
response = mv_files(source, target, workflow, access_token)
click.echo(
click.style('{} was successfully moved to {}.'.format(
source, target),
fg='green'))
except Exception as e:
logging.debug(traceback.format_exc())
logging.debug(str(e))
click.echo(click.style('Something went wrong. {}'.format(e),
fg='red'),
err=True)
def list_reana_workflow_files(workflow_id, workflow=None):
"""Show the files of a workflow."""
rec_uuid = resolve_uuid(workflow_id)
token = get_reana_token(rec_uuid)
try:
resp = list_files(workflow_id, token)
_files = {
'rec_uuid': rec_uuid,
'workflow_id': workflow_id,
'files': resp
}
return jsonify(_files)
except Exception:
return jsonify({
'message':
'File list from workflow {} could not be '
'retrieved. Aborting listing.'.format(workflow_id)
}), 400
def get_files(ctx, workflow, _filter, output_format, access_token):
"""List workflow workspace files."""
logging.debug('command: {}'.format(ctx.command_path.replace(" ", ".")))
for p in ctx.params:
logging.debug('{param}: {value}'.format(param=p, value=ctx.params[p]))
try:
_url = current_rs_api_client.swagger_spec.api_url
except MissingAPIClientConfiguration as e:
click.secho('REANA client is not connected to any REANA cluster.',
fg='red',
err=True)
sys.exit(1)
if not access_token:
click.echo(click.style(ERROR_MESSAGES['missing_access_token'],
fg='red'),
err=True)
sys.exit(1)
if _filter:
parsed_filters = parse_parameters(_filter)
if workflow:
logging.info('Workflow "{}" selected'.format(workflow))
try:
response = list_files(workflow, access_token)
headers = ['name', 'size', 'last-modified']
data = []
for file_ in response:
data.append(
list(
map(str, [
file_['name'], file_['size'],
file_['last-modified']
])))
tablib_data = tablib.Dataset()
tablib_data.headers = headers
for row in data:
tablib_data.append(row)
if _filter:
tablib_data, filtered_headers = \
filter_data(parsed_filters, headers, tablib_data)
if output_format:
click.echo(json.dumps(tablib_data))
else:
tablib_data = [list(item.values()) for item in tablib_data]
click_table_printer(filtered_headers, filtered_headers,
tablib_data)
else:
if output_format:
click.echo(tablib_data.export(output_format))
else:
click_table_printer(headers, _filter, data)
except Exception as e:
logging.debug(traceback.format_exc())
logging.debug(str(e))
click.echo(click.style(
'Something went wrong while retrieving file list'
' for workflow {0}:\n{1}'.format(workflow, str(e)),
fg='red'),
err=True)
def get_files(ctx, workflow, _filter, output_format,
access_token): # noqa: D301
"""List workspace files.
The `ls` command lists workspace files of a workflow specified by the
environment variable REANA_WORKON or provided as a command-line flag
`--workflow` or `-w`.
Examples: \n
\t $ reana-client ls --workflow myanalysis.42
"""
import tablib
from reana_client.api.client import current_rs_api_client, list_files
logging.debug('command: {}'.format(ctx.command_path.replace(" ", ".")))
for p in ctx.params:
logging.debug('{param}: {value}'.format(param=p, value=ctx.params[p]))
if _filter:
parsed_filters = parse_parameters(_filter)
if workflow:
logging.info('Workflow "{}" selected'.format(workflow))
try:
response = list_files(workflow, access_token)
headers = ['name', 'size', 'last-modified']
data = []
file_path = get_path_from_operation_id(
current_rs_api_client.swagger_spec.spec_dict['paths'],
'download_file')
urls = []
for file_ in response:
if not file_['name'].startswith(FILES_BLACKLIST):
data.append(
list(
map(str, [
file_['name'], file_['size'],
file_['last-modified']
])))
urls.append(ctx.obj.reana_server_url + file_path.format(
workflow_id_or_name=workflow, file_name=file_['name']))
tablib_data = tablib.Dataset()
tablib_data.headers = headers
for row in data:
tablib_data.append(row)
if output_format == URL:
click.echo('\n'.join(urls))
elif _filter:
tablib_data, filtered_headers = \
filter_data(parsed_filters, headers, tablib_data)
if output_format == JSON:
click.echo(json.dumps(tablib_data))
else:
tablib_data = [list(item.values()) for item in tablib_data]
click_table_printer(filtered_headers, filtered_headers,
tablib_data)
else:
if output_format == JSON:
click.echo(tablib_data.export(output_format))
else:
click_table_printer(headers, _filter, data)
except Exception as e:
logging.debug(traceback.format_exc())
logging.debug(str(e))
click.echo(click.style(
'Something went wrong while retrieving file list'
' for workflow {0}:\n{1}'.format(workflow, str(e)),
fg='red'),
err=True)
def get_files(
ctx,
workflow,
_format,
filters,
output_format,
filename,
access_token,
page,
size,
human_readable_or_raw,
): # noqa: D301
"""List workspace files.
The ``ls`` command lists workspace files of a workflow specified by the
environment variable REANA_WORKON or provided as a command-line flag
``--workflow`` or ``-w``. The SOURCE argument is optional and specifies a
pattern matching files and directories.
Examples: \n
\t $ reana-client ls --workflow myanalysis.42 \n
\t $ reana-client ls --workflow myanalysis.42 --human-readable \n
\t $ reana-client ls --workflow myanalysis.42 'data/*root*' \n
\t $ reana-client ls --workflow myanalysis.42 --filter name=hello
""" # noqa: W605
import tablib
from reana_client.api.client import current_rs_api_client, list_files
logging.debug("command: {}".format(ctx.command_path.replace(" ", ".")))
for p in ctx.params:
logging.debug("{param}: {value}".format(param=p, value=ctx.params[p]))
search_filter = None
headers = ["name", "size", "last-modified"]
if filters:
_, search_filter = parse_filter_parameters(filters, headers)
if _format:
parsed_format_filters = parse_format_parameters(_format)
if workflow:
logging.info('Workflow "{}" selected'.format(workflow))
try:
response = list_files(workflow, access_token, filename, page, size,
search_filter)
data = []
file_path = get_path_from_operation_id(
current_rs_api_client.swagger_spec.spec_dict["paths"],
"download_file")
urls = []
for file_ in response:
if not file_["name"].startswith(FILES_BLACKLIST):
data.append(
list(
map(
str,
[
file_["name"],
file_["size"][human_readable_or_raw],
file_["last-modified"],
],
)))
urls.append(ctx.obj.reana_server_url + file_path.format(
workflow_id_or_name=workflow, file_name=file_["name"]))
tablib_data = tablib.Dataset()
tablib_data.headers = headers
for row in data:
tablib_data.append(row)
if output_format == URL:
display_message("\n".join(urls))
elif _format:
tablib_data, filtered_headers = format_data(
parsed_format_filters, headers, tablib_data)
if output_format == JSON:
display_message(json.dumps(tablib_data))
else:
tablib_data = [list(item.values()) for item in tablib_data]
click_table_printer(filtered_headers, filtered_headers,
tablib_data)
else:
if output_format == JSON:
display_message(tablib_data.export(output_format))
else:
click_table_printer(headers, _format, data)
except Exception as e:
logging.debug(traceback.format_exc())
logging.debug(str(e))
display_message(
"Something went wrong while retrieving file list"
" for workflow {0}:\n{1}".format(workflow, str(e)),
msg_type="error",
)
