def test_scidb_afl_module():
"""Testing all public methods in scidblib.scidb_afl."""
print '*** testing scidblib.scidb_afl...'
class TmpArgs:
def __init__(self):
self.host = ''
self.port = ''
args = TmpArgs()
iquery_cmd = scidb_afl.get_iquery_cmd(args)
scidb_afl.execute_it_return_out_err('ls')
scidb_afl.afl(iquery_cmd, 'list()')
print 'time_afl(..., \'list()\') =', scidb_afl.time_afl(
iquery_cmd, 'list()')
print 'single_cell_afl(..., \'build(<v:int64>[i=0:0,1,0], 5)\', 1) =', \
scidb_afl.single_cell_afl(iquery_cmd, 'build(<v:int64>[i=0:0,1,0], 5)', 1)
print 'single_cell_afl(..., \'apply(build(<v:int64>[i=0:0,1,0], 5), v2, 6)\', 2) =', \
scidb_afl.single_cell_afl(iquery_cmd, 'apply(build(<v:int64>[i=0:0,1,0], 5), v2, 6)', 2)
print 'get_num_instances(...) =', scidb_afl.get_num_instances(iquery_cmd)
print 'get_array_names(...) =', scidb_afl.get_array_names(iquery_cmd)
print
def remove_arrays_by_prefix(self, prefix):
names=scidb_afl.get_array_names(self._iquery_cmd)
names_to_remove = []
for name in names:
if name.startswith(prefix):
names_to_remove.append(name)
for name in names_to_remove:
self.query('remove('+name+')')
def remove_arrays_by_prefix(self, prefix):
names = scidb_afl.get_array_names(self._iquery_cmd)
names_to_remove = []
for name in names:
if name.startswith(prefix):
names_to_remove.append(name)
for name in names_to_remove:
self.query('remove(' + name + ')')
def test_scidb_afl_module():
"""Testing all public methods in scidblib.scidb_afl."""
print '*** testing scidblib.scidb_afl...'
class TmpArgs:
def __init__(self):
self.host = ''
self.port = ''
args = TmpArgs()
iquery_cmd = scidb_afl.get_iquery_cmd(args)
scidb_afl.execute_it_return_out_err('ls')
scidb_afl.afl(iquery_cmd, 'list()')
print 'time_afl(..., \'list()\') =', scidb_afl.time_afl(iquery_cmd, 'list()')
print 'single_cell_afl(..., \'build(<v:int64>[i=0:0,1,0], 5)\', 1) =', \
scidb_afl.single_cell_afl(iquery_cmd, 'build(<v:int64>[i=0:0,1,0], 5)', 1)
print 'single_cell_afl(..., \'apply(build(<v:int64>[i=0:0,1,0], 5), v2, 6)\', 2) =', \
scidb_afl.single_cell_afl(iquery_cmd, 'apply(build(<v:int64>[i=0:0,1,0], 5), v2, 6)', 2)
print 'get_num_instances(...) =', scidb_afl.get_num_instances(iquery_cmd)
print 'get_array_names(...) =', scidb_afl.get_array_names(iquery_cmd)
print
def main():
"""The main function lists all arrays
"""
parser = argparse.ArgumentParser(
description='List all scidb arrays.',
epilog='Assumptions:\n' + ' - SciDB is running.\n'
' - The environment is setup to support namespaces.\n'
' - The iquery application is in your path.',
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-c',
'--host',
help='Host name to be passed to iquery.')
parser.add_argument('-p',
'--port',
help='Port number to be passed to iquery.')
parser.add_argument('-t',
'--temp-only',
action='store_true',
help='Limiting the candidates to temp arrays.')
parser.add_argument('-v',
'--versions',
help='Include all versions in the list.')
parser.add_argument('-A',
'--auth-file',
help='Authentication file to be passed to iquery.')
parser.add_argument('-s',
'--sort-by',
default='array',
choices=['array', 'namespace'],
help='Either array or namespace.')
parser.add_argument('-f',
'--find-array',
help='find a particular array name.')
args = parser.parse_args()
try:
arrays = []
iquery_cmd = scidb_afl.get_iquery_cmd(args)
namespaces = scidb_afl.get_namespace_names(iquery_cmd)
for namespace in namespaces:
new_arrays = scidb_afl.get_array_names(iquery_cmd=iquery_cmd,
temp_only=args.temp_only,
versions=args.versions,
namespace=namespace)
for array in new_arrays:
t = (array, namespace)
arrays.append(t)
if arrays:
if args.find_array:
result = [tup for tup in arrays if tup[0] == args.find_array]
if not result:
raise ValueError, 'array {0} not found'.format(
args.find_array)
array, namespace = result[0]
print scidb_make_qualified_array_name('namespace', 'array')
print scidb_make_qualified_array_name(namespace, array)
else:
print scidb_make_qualified_array_name('namespace', 'array')
item = 0
if args.sort_by == 'namespace':
item = 1
for (array, namespace) in sorted(arrays, key=itemgetter(item)):
print scidb_make_qualified_array_name(namespace, array)
else:
print >> sys.stderr, 'No arrays found'
except Exception, e:
print >> sys.stderr, '------ Exception -----------------------------'
print >> sys.stderr, e
if _print_traceback_upon_exception:
print >> sys.stderr, '------ Traceback (for debug purpose) ---------'
traceback.print_exc()
print >> sys.stderr, '----------------------------------------------'
sys.exit(-1) # upon an exception, throw -1
def main():
"""The main function gets command-line argument as a pattern, and removes all arrays with that pattern.
"""
parser = argparse.ArgumentParser(
description='Remove all SciDB arrays whose names match a given pattern.',
epilog=
'assumptions:\n' +
' - iquery is in your path.',
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-f', '--force', action='store_true',
help='Forced removal of the arrays without asking for confirmation.')
parser.add_argument('-c', '--host',
help='Host name to be passed to iquery.')
parser.add_argument('-p', '--port',
help='Port number to be passed to iquery.')
parser.add_argument('-t', '--temp-only', action='store_true',
help='Limiting the candidates to temp arrays.')
parser.add_argument('-U', '--user-name',
help='User name to be passed to iquery.')
parser.add_argument('-P', '--user-password',
help='User password to be passed to iquery.')
parser.add_argument('-v', '--verbose ', default=True,
help='display verbose output.')
parser.add_argument('regex', metavar='REGEX', type=str, nargs='?', default='.*',
help='''Regular expression to match against array names.
The utility will remove arrays whose names match the regular expression.
Default is '.+', meaning to remove all arrays, because the pattern matches all names.
The regular expression must match the full array name.
For instance, '.*s' will match array 'dogs' because it ends with 's',
but will not match array 'moose' because it does not end with 's'.'''
)
args = parser.parse_args()
try:
iquery_cmd = scidb_afl.get_iquery_cmd(args)
namespaces = scidb_afl.get_namespace_names(iquery_cmd)
for namespace in namespaces:
print "\nSearching namespace: ", namespace
names = scidb_afl.get_array_names(
iquery_cmd = iquery_cmd,
temp_only=args.temp_only,
namespace=namespace)
names_to_remove = []
for name in names:
match_name = re.match('^'+args.regex+'$', name)
if match_name:
names_to_remove.append(name)
if not names_to_remove:
print "There are no arrays to remove in namespace", namespace
continue
if not args.force:
print 'The following arrays are about to be removed from namespace ' + namespace + ':'
print names_to_remove
proceed = scidb_psf.confirm(prompt='Are you sure you want to remove?', resp=False)
if not proceed:
return
for name in names_to_remove:
scidb_afl.remove_array(name, namespace, iquery_cmd)
if namespace != 'public':
names = scidb_afl.get_array_names(
iquery_cmd=iquery_cmd,
temp_only=args.temp_only,
namespace=namespace)
if not names:
scidb_afl.afl(
iquery_cmd,
'drop_namespace(\'' + namespace + '\');')
print "namespace " + namespace + " removed"
print 'Number of arrays removed =', len(names_to_remove)
except Exception, e:
print >> sys.stderr, '------ Exception -----------------------------'
print >> sys.stderr, e
if args.verbose:
print >> sys.stderr, '------ Traceback (for debug purpose) ---------'
traceback.print_exc()
print >> sys.stderr, '----------------------------------------------'
sys.exit(-1) # upon an exception, throw -1
def main():
"""The main function lists all arrays
"""
parser = argparse.ArgumentParser(
description='List all scidb arrays.',
epilog=
'Assumptions:\n' +
' - SciDB is running.\n'
' - The environment is setup to support namespaces.\n'
' - The iquery application is in your path.',
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-c', '--host',
help='Host name to be passed to iquery.')
parser.add_argument('-p', '--port',
help='Port number to be passed to iquery.')
parser.add_argument('-t', '--temp-only', action='store_true',
help='Limiting the candidates to temp arrays.')
parser.add_argument('-v', '--versions',
help='Include all versions in the list.')
parser.add_argument('-A', '--auth-file',
help='Authentication file to be passed to iquery.')
parser.add_argument('-s', '--sort-by', default='array', choices=['array', 'namespace'],
help='Either array or namespace.')
parser.add_argument('-f', '--find-array',
help='find a particular array name.')
args = parser.parse_args()
try:
arrays = []
iquery_cmd = scidb_afl.get_iquery_cmd(args)
namespaces = scidb_afl.get_namespace_names(iquery_cmd)
for namespace in namespaces:
new_arrays = scidb_afl.get_array_names(
iquery_cmd=iquery_cmd,
temp_only=args.temp_only,
versions=args.versions,
namespace=namespace)
for array in new_arrays:
t=(array, namespace)
arrays.append(t)
if arrays:
if args.find_array:
result=[tup for tup in arrays if tup[0] == args.find_array]
if not result:
raise ValueError, 'array {0} not found'.format(args.find_array)
array, namespace = result[0]
print scidb_make_qualified_array_name('namespace', 'array')
print scidb_make_qualified_array_name(namespace, array)
else:
print scidb_make_qualified_array_name('namespace', 'array')
item=0
if args.sort_by == 'namespace':
item=1
for (array, namespace) in sorted(arrays, key=itemgetter(item)):
print scidb_make_qualified_array_name(namespace, array)
else:
print >> sys.stderr, 'No arrays found'
except Exception, e:
print >> sys.stderr, '------ Exception -----------------------------'
print >> sys.stderr, e
if _print_traceback_upon_exception:
print >> sys.stderr, '------ Traceback (for debug purpose) ---------'
traceback.print_exc()
print >> sys.stderr, '----------------------------------------------'
sys.exit(-1) # upon an exception, throw -1
def main():
"""The main function gets command-line argument as a pattern, and removes all arrays with that pattern.
"""
parser = argparse.ArgumentParser(
description=
'Remove all SciDB arrays whose names match a given pattern.',
epilog='assumptions:\n' + ' - iquery is in your path.',
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
'-f',
'--force',
action='store_true',
help='Forced removal of the arrays without asking for confirmation.')
parser.add_argument('-c',
'--host',
help='Host name to be passed to iquery.')
parser.add_argument('-p',
'--port',
help='Port number to be passed to iquery.')
parser.add_argument('-t',
'--temp-only',
action='store_true',
help='Limiting the candidates to temp arrays.')
parser.add_argument('-U',
'--user-name',
help='User name to be passed to iquery.')
parser.add_argument('-P',
'--user-password',
help='User password to be passed to iquery.')
parser.add_argument('-v',
'--verbose ',
default=True,
help='display verbose output.')
parser.add_argument(
'regex',
metavar='REGEX',
type=str,
nargs='?',
default='.*',
help='''Regular expression to match against array names.
The utility will remove arrays whose names match the regular expression.
Default is '.+', meaning to remove all arrays, because the pattern matches all names.
The regular expression must match the full array name.
For instance, '.*s' will match array 'dogs' because it ends with 's',
but will not match array 'moose' because it does not end with 's'.'''
)
args = parser.parse_args()
try:
iquery_cmd = scidb_afl.get_iquery_cmd(args)
namespaces = scidb_afl.get_namespace_names(iquery_cmd)
for namespace in namespaces:
print "\nSearching namespace: ", namespace
names = scidb_afl.get_array_names(iquery_cmd=iquery_cmd,
temp_only=args.temp_only,
namespace=namespace)
names_to_remove = []
for name in names:
match_name = re.match('^' + args.regex + '$', name)
if match_name:
names_to_remove.append(name)
if not names_to_remove:
print "There are no arrays to remove in namespace", namespace
continue
if not args.force:
print 'The following arrays are about to be removed from namespace ' + namespace + ':'
print names_to_remove
proceed = scidb_psf.confirm(
prompt='Are you sure you want to remove?', resp=False)
if not proceed:
return
for name in names_to_remove:
scidb_afl.remove_array(name, namespace, iquery_cmd)
if namespace != 'public':
names = scidb_afl.get_array_names(iquery_cmd=iquery_cmd,
temp_only=args.temp_only,
namespace=namespace)
if not names:
scidb_afl.afl(iquery_cmd,
'drop_namespace(\'' + namespace + '\');')
print "namespace " + namespace + " removed"
print 'Number of arrays removed =', len(names_to_remove)
except Exception, e:
print >> sys.stderr, '------ Exception -----------------------------'
print >> sys.stderr, e
if args.verbose:
print >> sys.stderr, '------ Traceback (for debug purpose) ---------'
traceback.print_exc()
print >> sys.stderr, '----------------------------------------------'
sys.exit(-1) # upon an exception, throw -1
def main():
"""The main function gets command-line argument as a pattern, and removes all arrays with that pattern.
@exception AppError if something goes wrong.
@note If print_traceback_upon_exception (defined at the top of the script) is True,
stack trace will be printed. This is helpful during debugging.
"""
parser = argparse.ArgumentParser(
description=
'Remove all SciDB arrays whose names match a given pattern.',
epilog='assumptions:\n' + ' - iquery is in your path.',
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
'-f',
'--force',
action='store_true',
help='Forced removal of the arrays without asking for confirmation.')
parser.add_argument('-c',
'--host',
help='Host name to be passed to iquery.')
parser.add_argument('-p',
'--port',
help='Port number to be passed to iquery.')
parser.add_argument('-t',
'--temp-only',
action='store_true',
help='Limiting the candidates to temp arrays.')
parser.add_argument(
'regex',
metavar='REGEX',
type=str,
nargs='?',
default='.*',
help='''Regular expression to match against array names.
The utility will remove arrays whose names match the regular expression.
Default is '.+', meaning to remove all arrays, because the pattern matches all names.
The regular expression must match the full array name.
For instance, '.*s' will match array 'dogs' because it ends with 's',
but will not match array 'moose' because it does not end with 's'.'''
)
args = parser.parse_args()
try:
names = scidb_afl.get_array_names(temp_only=args.temp_only)
iquery_cmd = scidb_afl.get_iquery_cmd(args)
names_to_remove = []
for name in names:
match_name = re.match('^' + args.regex + '$', name)
if match_name:
names_to_remove.append(name)
if not names_to_remove:
print 'There is no array to remove.'
sys.exit(0)
if not args.force:
print 'The following arrays are about to be removed:'
print names_to_remove
proceed = scidb_psf.confirm(
prompt='Are you sure you want to remove?', resp=False)
if not proceed:
sys.exit(0)
for name in names_to_remove:
scidb_afl.afl(iquery_cmd, 'remove(' + name + ')')
print 'Number of arrays removed =', len(names_to_remove)
except Exception, e:
print >> sys.stderr, '------ Exception -----------------------------'
print >> sys.stderr, e
if _print_traceback_upon_exception:
print >> sys.stderr, '------ Traceback (for debug purpose) ---------'
traceback.print_exc()
print >> sys.stderr, '----------------------------------------------'
sys.exit(-1) # upon an exception, throw -1
def main():
"""The main function gets command-line argument as a pattern, and removes all arrays with that pattern.
@exception AppError if something goes wrong.
@note If print_traceback_upon_exception (defined at the top of the script) is True,
stack trace will be printed. This is helpful during debugging.
"""
parser = argparse.ArgumentParser(
description='Remove all SciDB arrays whose names match a given pattern.',
epilog=
'assumptions:\n' +
' - iquery is in your path.',
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-f', '--force', action='store_true',
help='Forced removal of the arrays without asking for confirmation.')
parser.add_argument('-c', '--host',
help='Host name to be passed to iquery.')
parser.add_argument('-p', '--port',
help='Port number to be passed to iquery.')
parser.add_argument('-t', '--temp-only', action='store_true',
help='Limiting the candidates to temp arrays.')
parser.add_argument('regex', metavar='REGEX', type=str, nargs='?', default='.*',
help='''Regular expression to match against array names.
The utility will remove arrays whose names match the regular expression.
Default is '.+', meaning to remove all arrays, because the pattern matches all names.
The regular expression must match the full array name.
For instance, '.*s' will match array 'dogs' because it ends with 's',
but will not match array 'moose' because it does not end with 's'.'''
)
args = parser.parse_args()
try:
names = scidb_afl.get_array_names(temp_only=args.temp_only)
iquery_cmd = scidb_afl.get_iquery_cmd(args)
names_to_remove = []
for name in names:
match_name = re.match('^'+args.regex+'$', name)
if match_name:
names_to_remove.append(name)
if not names_to_remove:
print 'There is no array to remove.'
sys.exit(0)
if not args.force:
print 'The following arrays are about to be removed:'
print names_to_remove
proceed = scidb_psf.confirm(prompt='Are you sure you want to remove?', resp=False)
if not proceed:
sys.exit(0)
for name in names_to_remove:
scidb_afl.afl(iquery_cmd, 'remove('+name+')')
print 'Number of arrays removed =', len(names_to_remove)
except Exception, e:
print >> sys.stderr, '------ Exception -----------------------------'
print >> sys.stderr, e
if _print_traceback_upon_exception:
print >> sys.stderr, '------ Traceback (for debug purpose) ---------'
traceback.print_exc()
print >> sys.stderr, '----------------------------------------------'
sys.exit(-1) # upon an exception, throw -1
def main():
"""The main function gets command-line argument as a pattern, and removes all arrays with that
pattern.
Note: Empty namespaces will NOT be removed.
"""
parser = argparse.ArgumentParser(
description=
'Remove all SciDB arrays whose names match a given pattern.',
epilog='assumptions:\n' + ' - iquery is in your path.',
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
'-f',
'--force',
action='store_true',
help='Forced removal of the arrays without asking for confirmation.')
parser.add_argument('-c',
'--host',
help='Host name to be passed to iquery.')
parser.add_argument('-p',
'--port',
help='Port number to be passed to iquery.')
parser.add_argument('-t',
'--temp-only',
action='store_true',
help='Limiting the candidates to temp arrays.')
parser.add_argument('-A',
'--auth-file',
help='Authentication file to be passed to iquery.')
parser.add_argument(
'-U',
'--user-name',
help=
'Deprecated: Use --auth-file instead. User name to be passed to iquery.'
)
parser.add_argument(
'-P',
'--user-password',
help=
'Deprecated: Use --auth-file instead. User password to be passed to iquery.'
)
parser.add_argument('-v',
'--verbose',
default=True,
help='display verbose output.')
parser.add_argument(
'regex',
metavar='REGEX',
type=str,
nargs='?',
default='.*',
help='''Regular expression to match against array names.
The utility will remove arrays whose names match the regular expression.
Default is '.+', meaning to remove all arrays, because the pattern matches all names.
The regular expression must match the full array name.
For instance, '.*s' will match array 'dogs' because it ends with 's',
but will not match array 'moose' because it does not end with 's'.'''
)
_temp_auth_file = None
_arrays_removed = 0
args = parser.parse_args()
try:
if args.verbose == True:
print >> sys.stderr, "args={0}".format(args)
if args.user_name and args.user_password and (args.auth_file == None):
print >> sys.stderr, '\nWARNING: --user-name and --user-password are deprecated. Use --auth-file instead.\n'
_temp_auth_file = create_auth_file(args.user_name,
args.user_password)
args.auth_file = _temp_auth_file.name
args.user_name = None
args.user_password = None
iquery_cmd = scidb_afl.get_iquery_cmd(args)
namespaces = scidb_afl.get_namespace_names(iquery_cmd)
if args.verbose == True:
print >> sys.stderr, "namespaces={0}".format(namespaces)
_arrays_removed = 0
for namespace in namespaces:
if args.verbose == True:
print >> sys.stderr, "\nSearching namespace: ", namespace
names = scidb_afl.get_array_names(iquery_cmd=iquery_cmd,
temp_only=args.temp_only,
namespace=namespace)
if args.verbose == True:
print >> sys.stderr, "names={0}".format(names)
names_to_remove = []
for name in names:
match_name = re.match('^' + args.regex + '$', name)
if match_name:
if args.verbose == True:
print >> sys.stderr, "Schedule {0}.{1} to be removed".format(
namespace, name)
names_to_remove.append(name)
if not names_to_remove:
if args.verbose == True:
print "There are no arrays to remove in namespace", namespace
continue
if not args.force:
print 'The following arrays are about to be removed from namespace {0}:'.format(
namespace)
print names_to_remove
proceed = scidb_psf.confirm(
prompt='Are you sure you want to remove?', resp=False)
if not proceed:
return
for name in names_to_remove:
scidb_afl.remove_array(name, namespace, iquery_cmd)
if args.verbose == True:
print >> sys.stderr, "array {0}.{1} removed".format(
namespace, name)
_arrays_removed += 1
if namespace != 'public':
names = scidb_afl.get_array_names(iquery_cmd=iquery_cmd,
temp_only=args.temp_only,
namespace=namespace)
if not names:
scidb_afl.afl(iquery_cmd,
"drop_namespace('{0}');".format(namespace))
if args.verbose == True:
print >> sys.stderr, "namespace {0} removed".format(
namespace)
if args.verbose == True:
print >> sys.stderr, 'Number of arrays removed =', _arrays_removed
if _temp_auth_file:
_temp_auth_file.close()
_temp_auth_file = None
except Exception, e:
print >> sys.stderr, '------ Exception -----------------------------'
print >> sys.stderr, e
if args.verbose == True:
print >> sys.stderr, 'Number of arrays removed =', _arrays_removed
if args.verbose == True:
print >> sys.stderr, '------ Traceback (for debug purpose) ---------'
traceback.print_exc()
if _temp_auth_file:
_temp_auth_file.close()
_temp_auth_file = None
print >> sys.stderr, '----------------------------------------------'
sys.exit(-1) # upon an exception, throw -1
