def main(argv):
"""
Pokes at a DataONE object's system metadata
Usage:
poke.py pid <pid>
poke.py file <file>
poke.py defaults
Arguments:
pid Pid of object to poke
file File containing pid(s) (one per line) of objects to poke
defaults Print default properties to stdout
"""
args = docopt(str(main.__doc__))
if args['defaults']:
properties.dump()
return 0
pids = []
if args['pid']:
pids.append(args['<pid>'])
elif args['file']:
with open(args['<file>'], 'r') as fn:
pid_list = [_.strip() for _ in fn.readlines()]
for pid in pid_list:
pids.append(pid)
base_url = properties.BASE_URL
cert_pem_path = properties.CERT_PEM
cert_key_path = properties.CERT_KEY
client = MemberNodeClient_2_0(
base_url=base_url,
cert_pem_path=cert_pem_path,
cert_key_path=cert_key_path,
verify_tls=properties.VERIFY_TLS,
)
for pid in pids:
sysmeta = client.getSystemMetadata(pid=pid)
mod_sysmeta = mod_system_metadata(sysmeta=sysmeta)
client.updateSystemMetadata(pid=pid, sysmeta_pyxb=mod_sysmeta)
return 0
def dump(self):
"""
Show the object content
"""
global _createdDirs
print '### Created Dir Objects'
print ' ', '\n '.join(_createdDirs.keys())
for (a, go), d in _createdDirs.items():
print '### Dir: ', a
print ' Rules: ', d.executed_rules
print ' Prev dir: ', d.previous_dir
print ' Given dict: ', go
print ' Options:\n ',
properties.dump(self.options, ' ')
def main(argv):
"""
Peeks at a DataONE Member Node object's system metadata
Usage:
peek.py pid <pid> [--v1] [-n | --node <node>] [-c | --cert <cert>] [-k | --key <key>] [-a | --attr <attr>] [--header] [--to_xml]
peek.py file <file> [--v1] [-n | --node <node>] [-c | --cert <cert>] [-k | --key <key>] [-a | --attr <attr>] [--header] [--to_xml]
peek.py defaults
peek.py -h | --help
Arguments:
pid Pid of object to peek
file File containing pid(s) (one per line) of objects to peek
defaults Print default properties to stdout
Options:
-h --help This page
-n --node Target node (either member or coordinating)
-c --cert Client certificate
-k --key Client certificate key
-a --attr Comma separated list of sysmeta attributes to display (none for all)
--v1 Version 1 client (defaults to version 2)
--header Add header line
--to_xml Export as XML
"""
args = docopt(str(main.__doc__))
if args['defaults']:
properties.dump()
return 0
pids = {}
if args['pid']:
pids[args['<pid>']] = {'pid': args['<pid>']}
elif args['file']:
with open(args['<file>'], 'r') as fn:
pid_list = [_.strip() for _ in fn.readlines()]
for pid in pid_list:
pids[pid] = {'pid': pid}
if args['--node']:
base_url = args['<node>']
else:
base_url = properties.BASE_URL
if args['--cert']:
cert_pem_path = args['<cert>']
if cert_pem_path == 'None':
cert_pem_path = None
else:
cert_pem_path = properties.CERT_PEM
if args['--key']:
cert_key_path = args['<key>']
if cert_key_path == 'None':
cert_key_path = None
else:
cert_key_path = properties.CERT_KEY
add_header_line = False
if args['--header']:
add_header_line = True
attributes = ()
if args['--attr']:
attributes = [ _.strip() for _ in args['<attr>'].split(',')]
else:
attributes = ['checksum', 'size', 'replica', 'archived', 'rights_holder']
to_xml = False
if args['--to_xml']:
to_xml = True
if args['--v1']:
client = MemberNodeClient_1_1(base_url=base_url,
cert_pem_path=cert_pem_path,
cert_key_path=cert_key_path,
verify_tls=properties.VERIFY_TLS,
)
else:
client = MemberNodeClient_2_0(base_url=base_url,
cert_pem_path=cert_pem_path,
cert_key_path=cert_key_path,
verify_tls=properties.VERIFY_TLS,
)
dead_pids = []
for pid in pids:
try:
sm = client.getSystemMetadata(pid=pid)
pids[pid]['xml'] = sm.toxml()
except Exception as e:
logger.error('{pid}: {e}'.format(pid=pid, e=e))
dead_pids.append(pid)
if 'checksum' in attributes:
pids[pid]['checksum'] = sm.checksum.algorithm + ',' + sm.checksum.value()
if 'size' in attributes:
pids[pid]['size'] = sm.size
if 'replica' in attributes:
try:
pids[pid]['replica'] = replicas(sm.replica)
except Exception as e:
pids[pid]['replica'] = ''
if 'archived' in attributes:
try:
pids[pid]['archived'] = sm.archived
except Exception as e:
pids[pid]['archived'] = ''
if 'rights_holder' in attributes:
pids[pid]['rights_holder'] = '\'' + sm.rightsHolder.value() + '\''
clean_pids(pids, dead_pids)
for pid in pids:
if to_xml:
xml = pretty_xml(pids[pid]['xml'])
print('{xml}'.format(xml=xml))
else:
print('{pid}'.format(pid=pid), end=',')
if 'checksum' in attributes:
checksum = pids[pid]['checksum']
print('{checksum}'.format(checksum=checksum), end=',')
if 'size' in attributes:
size = pids[pid]['size']
print('{size}'.format(size=size), end=',')
if 'replica' in attributes:
replica = pids[pid]['replica']
print('{replica}'.format(replica=replica), end=',')
if 'archived' in attributes:
archived = pids[pid]['archived']
print('{archived}'.format(archived=archived), end=',')
if 'rights_holder' in attributes:
rights_holder = pids[pid]['rights_holder']
print('{rights_holder}'.format(rights_holder=rights_holder), end=', ')
print()
return 0
def main(argv):
"""
Lists obsolescence chain of a DataONE object.
Usage:
chains.py pid <pid> [-n | --node <node>] [-c | --cert <cert>] [-k | --key <key>]
chains.py defaults
chains.py (-h | --help)
Arguments:
pid Persistent identifier of object
defaults Print default properties to stdout
Options:
-h --help This page
-n --node Target node (either member or coordinating)
-c --cert Client certificate
-k --key Client certificate key
"""
args = docopt(str(main.__doc__))
if args['defaults']:
properties.dump()
return 0
pid = args['<pid>']
if args['--node']:
base_url = args['<node>']
else:
base_url = properties.BASE_URL
if args['--cert']:
cert_pem_path = args['<cert>']
if cert_pem_path == 'None':
cert_pem_path = None
else:
cert_pem_path = properties.CERT_PEM
if args['--key']:
cert_key_path = args['<key>']
if cert_key_path == 'None':
cert_key_path = None
else:
cert_key_path = properties.CERT_KEY
mn_client = MemberNodeClient_2_0(
base_url=base_url,
cert_pem_path=cert_pem_path,
cert_key_path=cert_key_path,
verify_tls=properties.VERIFY_TLS,
)
# Find oldest pid
current_pid = None
while pid is not None:
current_pid = pid
pid = predecessor(pid, mn_client)
pid = current_pid
# Walk obsolescence chain from oldest pid to newest pid
pids = []
while pid is not None:
pids.append(pid)
pid = successor(pid, mn_client)
for pid in pids:
print(pid)
return 0
def main(argv):
"""A DataONE tool to manually replicate content from one node to another
Replicates objects, including system metadata, from one DataONE member
node to another member node, with the option of modifying system metadata
attributes. It is assumed that the destination member node base URL,
certificate, and private key are specified in the properties.
Usage:
replicator.py pid <pid> <src_mn> [-c | --cert <cert>]
[-k | --key <key>]
replicator.py file <file> <src_mn> [-c | --cert <cert>]
[-k | --key <key>]
replicator.py defaults
replicator.py -h | --help
Arguments:
pid Pid of object to replicate
file File of pids of objects to replicate one per line
src_mn Base URL of the source member node (or path on local
file system from / where objects reside)
defaults Prints default properties to stdout
Options:
-h --help This page
-c --cert Client certificate of source member node (if needed to
access private content)
-k --key Client private key of source member node (if needed to
access private content)
"""
args = docopt(str(main.__doc__))
if args['defaults']:
properties.dump()
return 0
pids = []
if args['pid']:
pids.append(args['<pid>'])
else:
try:
with open(args['<file>'], 'rt') as f:
for pid in f:
pids.append(pid.strip())
except IOError as e:
logger.error(e)
return 1
src_mn = args['<src_mn>']
if args['--cert'] and args['--key']:
src_cert = args['<cert>']
src_key = args['<key>']
else:
src_cert = None
src_key = None
src = {'src_mn': src_mn, 'src_cert': src_cert, 'src_key': src_key}
logger.info(len(pids))
cnt = 0
for pid in pids:
cnt += 1
information = '{cnt}: {pid}'.format(cnt=cnt, pid=pid)
logger.info(information)
obj = get_object(pid=pid, src=src)
sys_meta = get_sys_meta(pid=pid, src=src)
modify_sys_meta(sys_meta=sys_meta)
try:
replicate_object(pid=pid, obj=obj, sys_meta=sys_meta)
except d1_common.types.exceptions.DataONEException as e:
logger.error(e)
return 0
def main():
"""
List objects at a DataONE Member Node
Usage:
list_objects.py [--v1] [-n | --node <node>] [-c | --cert <cert>] [-k | --key <key>]
list_objects.py defaults
list_objects.py -h | --help
Arguments:
defaults Print default properties to stdout
Options:
-h --help This page
-n --node Target node (either member or coordinating)
-c --cert Client certificate
-k --key Client certificate key
"""
args = docopt(str(main.__doc__))
if args['defaults']:
properties.dump()
return 0
if args['--node']:
base_url = args['<node>']
else:
base_url = properties.BASE_URL
if args['--cert']:
cert_pem_path = args['<cert>']
if cert_pem_path == 'None':
cert_pem_path = None
else:
cert_pem_path = properties.CERT_PEM
if args['--key']:
cert_key_path = args['<key>']
if cert_key_path == 'None':
cert_key_path = None
else:
cert_key_path = properties.CERT_KEY
if args['--v1']:
client = MemberNodeClient_1_1(
base_url=base_url,
cert_pem_path=cert_pem_path,
cert_key_path=cert_key_path,
verify_tls=properties.VERIFY_TLS,
)
else:
client = MemberNodeClient_2_0(
base_url=base_url,
cert_pem_path=cert_pem_path,
cert_key_path=cert_key_path,
verify_tls=properties.VERIFY_TLS,
)
objects = ObjectListIterator(client=client)
for obj in objects:
print('{pid}'.format(pid=obj.identifier.value()))
return 0