def irods_reg(fs_path, irods_path):
"""Register a file or a directory of files and subdirectory into
iRODS. The file must already exist on the server where the resource is
located. The full path must be supplied for both paths."""
logging.warning('Use of iRODS "ireg" command SHOULD BE AVOIDED!')
out = None
cmdline = ['imkdir', '-p', os.path.dirname(irods_path)]
try:
diag.dbgcmd(cmdline)
out = subprocess.check_output(cmdline)
except subprocess.CalledProcessError as ex:
cmd = ' '.join(cmdline)
logging.error('Execution failed: {}; {} => {}'
.format(ex, cmd, ex.output.decode('utf-8')))
raise
os.chmod(fs_path, 0o664)
cmdline = ['ireg', '-K', fs_path, irods_path]
try:
diag.dbgcmd(cmdline)
out = subprocess.check_output(cmdline)
except subprocess.CalledProcessError as ex:
cmd = ' '.join(cmdline)
logging.error('Execution failed: {}; {} => {}'
.format(ex, cmd, ex.output.decode('utf-8')))
raise
return out
def irods_file_type(irods_fname):
logging.debug('irods_file_type({})'.format(irods_fname))
# lut[file_type.py_key] = irods_data_type (list all using "isysmeta ldt")
lut = dict(FITS = 'FITS image',
JPEG = 'jpeg image',
)
cmdline = ['iexecmd', '-P', irods_fname, 'file_type {}'.format(irods_fname)]
out = 'NONE'
try:
diag.dbgcmd(cmdline)
out = subprocess.check_output(cmdline)
except subprocess.CalledProcessError as ex:
cmd = ' '.join(cmdline)
logging.error('Execution failed: {}; {} => {}'
.format(ex, cmd, ex.output.decode('utf-8')))
raise
typeStr = out.decode('utf-8')[:-1]
# Set datatype in metadata. Not used. Retained for future use.
#! dt = lut.get(typeStr,'generic')
#! cmdline = ['isysmeta', 'mod', irods_fname, 'datatype', dt]
#! try:
#! out = subprocess.check_output(cmdline)
#! except subprocess.CalledProcessError as ex:
#! cmd = ' '.join(cmdline)
#! logging.error('Execution failed: {}; {} => {}'
#! .format(ex, cmd, ex.output.decode('utf-8')))
#! raise
return typeStr
def irods_get_physical(ipath):
#!!! Open access to vault
out = 'NONE'
cmdline = ['iexecmd', 'open_vault.sh']
try:
diag.dbgcmd(cmdline)
out = subprocess.check_output(cmdline)
except subprocess.CalledProcessError as ex:
cmd = ' '.join(cmdline)
logging.error('Execution failed: {}; {} => {}'
.format(ex, cmd, ex.output.decode('utf-8')))
raise
sel = ("select DATA_PATH where COLL_NAME = '{}' and DATA_NAME = '{}'"
.format(os.path.dirname(ipath), os.path.basename(ipath)))
cmdline = ['iquest', '"%s"', sel]
out = 'NONE'
try:
diag.dbgcmd(cmdline)
out = subprocess.check_output(cmdline)
except subprocess.CalledProcessError as ex:
cmd = ' '.join(cmdline)
logging.error('Execution failed: {}; {} => {}'
.format(ex, cmd, ex.output.decode('utf-8')))
raise
physical_fname = out.decode('utf-8').strip('\n \"')
return physical_fname
def get_irods_cksum(irods_path):
cmdline = ['ichksum', irods_path]
try:
diag.dbgcmd(cmdline)
out = subprocess.check_output(cmdline)
except subprocess.CalledProcessError as ex:
cmd = ' '.join(cmdline)
logging.error('Execution failed: {}; {} => {}'
.format(ex, cmd, ex.output.decode('utf-8')))
raise
return(out.split()[1].decode('utf-8'))
def irods_set_meta(ifname, att_name, att_value):
cmdline = ['imeta', 'set', '-d', ifname, 'prep', 'True']
out = 'NONE'
try:
diag.dbgcmd(cmdline)
out = subprocess.check_output(cmdline)
except subprocess.CalledProcessError as ex:
cmd = ' '.join(cmdline)
logging.error('Execution failed: {}; {} => {}'
.format(ex, cmd, ex.output.decode('utf-8')))
raise
def irods_debug():
"""For diagnostics only."""
if logging.getLogger().isEnabledFor(logging.DEBUG):
cmdline = ['ienv']
try:
diag.dbgcmd(cmdline)
out = subprocess.check_output(cmdline)
except subprocess.CalledProcessError as ex:
cmd = ' '.join(cmdline)
logging.error('Execution failed: {}; {} => {}'
.format(ex, cmd, ex.output.decode('utf-8')))
raise
logging.debug('ienv={}'.format(out.decode('utf-8')))
def irods_unreg(irods_path):
"unregister the file or collection"
logging.warning('EXECUTING: "irm -U {}"; Remove need!!!'.format(irods_path))
out = None
cmdline = ['irm', '-U', irods_path]
try:
diag.dbgcmd(cmdline)
out = subprocess.check_output(cmdline)
except subprocess.CalledProcessError as ex:
cmd = ' '.join(cmdline)
logging.error('Execution failed: {}; {} => {}'
.format(ex, cmd, ex.output.decode('utf-8')))
raise
return out
def irods_mv(src_ipath, dst_ipath):
'Move/rename irods file'
logging.debug('irods_mv({}, {})'.format(src_ipath, dst_ipath))
# imv /tempZone/mountain_mirror/vagrant/13/foo.nhs_2014_n14_299403.fits /tempZone/mountain_mirror/vagrant/13/nhs_2014_n14_299403.fits
cmdline = ['imv', src_ipath, dst_ipath]
out = None
try:
diag.dbgcmd(cmdline)
out = subprocess.check_output(cmdline)
except subprocess.CalledProcessError as ex:
cmd = ' '.join(cmdline)
logging.error('Execution failed: {}; {} => {}'
.format(ex, cmd, ex.output.decode('utf-8')))
raise
return out
def irods_get(local_fname, irods_fname, remove_irods=False):
'Get file from irods, creating local parent directories if needed.'
os.makedirs(os.path.dirname(local_fname), exist_ok=True)
cmdargs1 = ['iget', '-f', '-K', irods_fname, local_fname]
try:
diag.dbgcmd(cmdargs1)
subprocess.check_output(cmdargs1)
except subprocess.CalledProcessError as ex:
logging.error('Execution failed: {}; {}'
.format(ex, ex.output.decode('utf-8')))
raise
if remove_irods:
cmdargs2 = ['irm', '-f', '-U', irods_fname]
try:
diag.dbgcmd(cmdargs2)
subprocess.check_output(cmdargs2)
except subprocess.CalledProcessError as ex:
logging.error('Execution failed: {}; {}'
.format(ex, ex.output.decode('utf-8')))
raise
