def _copy_for_storage(remote_info, config):
import fabric.api as fabric
import fabric.contrib.files as fabric_files
try:
protocol = config["transfer_protocol"]
except KeyError:
protocol = None
pass
base_dir = config["store_dir"]
fabric.env.host_string = "%s@%s" % \
(config["store_user"], config["store_host"])
remote_copy(remote_info, base_dir, protocol)
def _copy_for_storage(remote_info, config):
import fabric.api as fabric
import fabric.contrib.files as fabric_files
try:
protocol = config["transfer_protocol"]
except KeyError:
protocol = None
pass
base_dir = config["store_dir"]
fabric.env.host_string = "%s@%s" % \
(config["store_user"], config["store_host"])
remote_copy(remote_info, base_dir, protocol)
def _copy_for_storage(remote_info, config):
"""Securely copy files from remote directory to the storage server.
This requires ssh public keys to be setup so that no password entry
is necessary, Fabric is used to manage setting up copies on the remote
storage server.
"""
base_dir = config["store_dir"]
try:
protocol = config["transfer_protocol"]
except KeyError:
protocol = None
pass
fabric.env.host_string = "%s@%s" % \
(config["store_user"], config["store_host"])
remote_copy(remote_info, base_dir, protocol)
def _copy_from_sequencer(remote_info, config):
"""Get local directory of flowcell info, or copy from sequencer.
"""
if "fc_dir" in remote_info:
fc_dir = remote_info["fc_dir"]
assert os.path.exists(fc_dir)
else:
logger.debug("Remote host information: %s" % remote_info)
c_host_str = _config_hosts(config)
c_keyfile = config["analysis"].get("copy_keyfile", None)
with fabric.settings(host_string=c_host_str, key_filename=c_keyfile):
base_dir = config["store_dir"]
protocol = config.get("transfer_protocol", None)
fc_dir = remote_copy(remote_info, base_dir, protocol)
return fc_dir
def _copy_from_sequencer(remote_info, config):
"""Get local directory of flowcell info, or copy from sequencer.
"""
if "fc_dir" in remote_info:
fc_dir = remote_info["fc_dir"]
assert os.path.exists(fc_dir)
else:
logger.debug("Remote host information: %s" % remote_info)
c_host_str = _config_hosts(config)
c_keyfile = config["analysis"].get("copy_keyfile", None)
with fabric.settings(host_string=c_host_str, key_filename=c_keyfile):
base_dir = config["store_dir"]
protocol = config.get("transfer_protocol", None)
fc_dir = remote_copy(remote_info, base_dir, protocol)
return fc_dir
def _copy_from_sequencer(remote_info, config):
"""Get local directory of flowcell info, or copy from sequencer.
"""
if "fc_dir" in remote_info:
fc_dir = remote_info["fc_dir"]
assert os.path.exists(fc_dir)
else:
log.debug("Remote host information: %s" % remote_info)
c_host_str = _config_hosts(config)
with fabric.settings(host_string=c_host_str):
base_dir = config["store_dir"]
try:
protocol = config["transfer_protocol"]
except KeyError:
protocol = None
pass
fc_dir = remote_copy(remote_info, base_dir, protocol)
return fc_dir