def main(cmdlineargs=None):
# PYTHON_ARGCOMPLETE_OK
parser = setup_parser()
try:
import argcomplete
argcomplete.autocomplete(parser)
except ImportError:
pass
# parse cmd args
cmdlineargs = parser.parse_args(cmdlineargs)
if not cmdlineargs.change_path is None:
for path in cmdlineargs.change_path:
chpwd(path)
# run the function associated with the selected command
if cmdlineargs.common_debug:
# So we could see/stop clearly at the point of failure
setup_exceptionhook()
cmdlineargs.func(cmdlineargs)
else:
# Otherwise - guard and only log the summary. Postmortem is not
# as convenient if being caught in this ultimate except
try:
cmdlineargs.func(cmdlineargs)
except Exception as exc:
lgr.error('%s (%s)' % (exc_str(exc), exc.__class__.__name__))
sys.exit(1)
def get_native_metadata(ds, guess_type=False, ds_identifier=None):
"""Parse a dataset to gather its native metadata
Returns
-------
List
Each item in the list is a metadata dictionary (JSON-LD compliant).
The first items corresponds to the annex-based metadata of the dataset.
The last items contains the native metadata of the dataset content. Any
additional items correspond to subdataset metadata sets.
"""
if ds_identifier is None:
ds_identifier = ds.id
# using a list, because we could get multiple sets of meta data per
# dataset, and we want to quickly collect them without having to do potentially
# complex graph merges
meta = []
# get native metadata
nativetypes = get_metadata_type(ds, guess=guess_type)
if not nativetypes:
return meta
# keep local, who knows what some parsers might pull in
from . import parsers
for nativetype in nativetypes:
if nativetype == 'aggregate':
# this is special and needs to be ignored here, even if it was
# configured. reason: this parser runs anyway in get_metadata()
continue
pmod = import_module('.{}'.format(nativetype),
package=parsers.__package__)
try:
native_meta = pmod.MetadataParser(ds).get_metadata(ds_identifier)
except Exception as e:
lgr.error('failed to get native metadata ({}): {}'.format(
nativetype, exc_str(e)))
continue
if native_meta:
# TODO here we could apply a "patch" to the native metadata, if desired
# try hard to keep things a simple non-nested list
if isinstance(native_meta, list):
meta.extend(native_meta)
else:
meta.append(native_meta)
return meta
def get_native_metadata(ds, guess_type=False, ds_identifier=None):
"""Parse a dataset to gather its native metadata
Returns
-------
List
Each item in the list is a metadata dictionary (JSON-LD compliant).
The first items corresponds to the annex-based metadata of the dataset.
The last items contains the native metadata of the dataset content. Any
additional items correspond to subdataset metadata sets.
"""
if ds_identifier is None:
ds_identifier = ds.id
# using a list, because we could get multiple sets of meta data per
# dataset, and we want to quickly collect them without having to do potentially
# complex graph merges
meta = []
# get native metadata
nativetypes = get_metadata_type(ds, guess=guess_type)
if not nativetypes:
return meta
# keep local, who knows what some parsers might pull in
from . import parsers
for nativetype in nativetypes:
if nativetype == 'aggregate':
# this is special and needs to be ignored here, even if it was
# configured. reason: this parser runs anyway in get_metadata()
continue
pmod = import_module('.{}'.format(nativetype),
package=parsers.__package__)
try:
native_meta = pmod.MetadataParser(ds).get_metadata(ds_identifier)
except Exception as e:
lgr.error('failed to get native metadata ({}): {}'.format(nativetype, exc_str(e)))
continue
if native_meta:
# TODO here we could apply a "patch" to the native metadata, if desired
# try hard to keep things a simple non-nested list
if isinstance(native_meta, list):
meta.extend(native_meta)
else:
meta.append(native_meta)
return meta
def main(args=None):
parser = setup_parser()
# parse cmd args
args = parser.parse_args(args)
# run the function associated with the selected command
if args.common_debug:
# So we could see/stop clearly at the point of failure
setup_exceptionhook()
args.func(args)
else:
# Otherwise - guard and only log the summary. Postmortem is not
# as convenient if being caught in this ultimate except
try:
args.func(args)
except Exception as exc:
lgr.error('%s (%s)' % (str(exc), exc.__class__.__name__))
sys.exit(1)
def main(args=None):
parser = setup_parser()
# parse cmd args
args = parser.parse_args(args)
# run the function associated with the selected command
if args.common_debug:
# So we could see/stop clearly at the point of failure
setup_exceptionhook()
args.func(args)
else:
# Otherwise - guard and only log the summary. Postmortem is not
# as convenient if being caught in this ultimate except
try:
args.func(args)
except Exception as exc:
lgr.error('%s (%s)' % (str(exc), exc.__class__.__name__))
sys.exit(1)
def main(args=None):
# PYTHON_ARGCOMPLETE_OK
parser = setup_parser()
try:
import argcomplete
argcomplete.autocomplete(parser)
except ImportError:
pass
# parse cmd args
cmdlineargs = parser.parse_args(args)
if not cmdlineargs.change_path is None:
for path in cmdlineargs.change_path:
chpwd(path)
ret = None
if cmdlineargs.pbs_runner:
from .helpers import run_via_pbs
from .helpers import strip_arg_from_argv
from .common_args import pbs_runner as pbs_runner_opt
args_ = strip_arg_from_argv(args or sys.argv, cmdlineargs.pbs_runner,
pbs_runner_opt[1])
# run the function associated with the selected command
run_via_pbs(args_, cmdlineargs.pbs_runner)
elif cmdlineargs.common_debug:
# So we could see/stop clearly at the point of failure
setup_exceptionhook()
ret = cmdlineargs.func(cmdlineargs)
else:
# Otherwise - guard and only log the summary. Postmortem is not
# as convenient if being caught in this ultimate except
try:
ret = cmdlineargs.func(cmdlineargs)
except InsufficientArgumentsError as exc:
# if the func reports inappropriate usage, give help output
lgr.error('%s (%s)' % (exc_str(exc), exc.__class__.__name__))
cmdlineargs.subparser.print_usage()
sys.exit(1)
except Exception as exc:
lgr.error('%s (%s)' % (exc_str(exc), exc.__class__.__name__))
sys.exit(1)
if hasattr(cmdlineargs, 'result_renderer'):
cmdlineargs.result_renderer(ret)
def main(args=None):
# PYTHON_ARGCOMPLETE_OK
parser = setup_parser()
try:
import argcomplete
argcomplete.autocomplete(parser)
except ImportError:
pass
# parse cmd args
cmdlineargs = parser.parse_args(args)
if not cmdlineargs.change_path is None:
for path in cmdlineargs.change_path:
chpwd(path)
ret = None
if cmdlineargs.pbs_runner:
from .helpers import run_via_pbs
from .helpers import strip_arg_from_argv
from .common_args import pbs_runner as pbs_runner_opt
args_ = strip_arg_from_argv(args or sys.argv, cmdlineargs.pbs_runner, pbs_runner_opt[1])
# run the function associated with the selected command
run_via_pbs(args_, cmdlineargs.pbs_runner)
elif cmdlineargs.common_debug:
# So we could see/stop clearly at the point of failure
setup_exceptionhook()
ret = cmdlineargs.func(cmdlineargs)
else:
# Otherwise - guard and only log the summary. Postmortem is not
# as convenient if being caught in this ultimate except
try:
ret = cmdlineargs.func(cmdlineargs)
except InsufficientArgumentsError as exc:
# if the func reports inappropriate usage, give help output
lgr.error('%s (%s)' % (exc_str(exc), exc.__class__.__name__))
cmdlineargs.subparser.print_usage()
sys.exit(1)
except Exception as exc:
lgr.error('%s (%s)' % (exc_str(exc), exc.__class__.__name__))
sys.exit(1)
if hasattr(cmdlineargs, 'result_renderer'):
cmdlineargs.result_renderer(ret)
def run(args):
import glob
import os
import os.path
from datalad.api import Dataset
from datalad.log import lgr
lgr.debug("Command line arguments: %r" % args)
# Since GitPython doesn't recognize we ar with in a repo, if we are
# deeper down the tree, walk upwards and look for '.git':
# TODO: May be provide a patch for GitPython to have it cleaner.
cwd_before = cwd = os.getcwd()
while True:
if os.path.exists(os.path.join(cwd, '.git')):
break
else:
if cwd == '/': # TODO: Is this platform-dependend?
lgr.error("No repository found.")
raise ValueError # TODO: Proper Exception or clean exit?
else:
os.chdir(os.pardir)
cwd = os.getcwd()
ds = Dataset(cwd)
os.chdir(cwd_before)
# args.path comes as a list
# Expansions (like globs) provided by the shell itself are already done.
# But: We don't know exactly what shells we are running on and what it may provide or not.
# Therefore, make any expansion we want to guarantee, per item of the list:
expanded_list = []
for item in args.path:
expanded_list.extend(glob.glob(item))
# TODO: regexp + may be ext. glob zsh-style
# TODO: what about spaces in filenames and similar things?
# TODO: os.path.expandvars, os.path.expanduser? Is not needed here, isn't it? Always?
ds.get(expanded_list)
def main(args=None, cls=None, remote_name=None, description=None):
import sys
parser = setup_parser(remote_name, description)
# parse cmd args
args = parser.parse_args(args)
# stdin/stdout will be used for interactions with annex
ui.set_backend('annex')
if args.common_debug:
# So we could see/stop clearly at the point of failure
setup_exceptionhook()
_main(args, cls)
else:
# Otherwise - guard and only log the summary. Postmortem is not
# as convenient if being caught in this ultimate except
try:
_main(args, cls)
except Exception as exc:
lgr.error('%s (%s)', str(exc), exc.__class__.__name__)
sys.exit(1)
def main(args=None, backend=None):
import sys
# TODO: redirect lgr output to stderr if it is stdout and not "forced"
# by env variable...
#
parser = setup_parser()
# parse cmd args
args = parser.parse_args(args)
if args.common_debug:
# So we could see/stop clearly at the point of failure
setup_exceptionhook()
_main(args, backend)
else:
# Otherwise - guard and only log the summary. Postmortem is not
# as convenient if being caught in this ultimate except
try:
_main(args, backend)
except Exception as exc:
lgr.error('%s (%s)' % (str(exc), exc.__class__.__name__))
sys.exit(1)
def __call__(self, url, name=None):
# TODO: After publishing new demo collection, adapt doctest
"""
Examples
--------
>>> from datalad.api import register_collection, list_collections
>>> def test_register_collection_simple():
... assert(col.name not in [c.name for c in list_collections()])
... col =register_collection("http://collections.datalad.org/demo/DATALAD_COL_demo_collection")
... assert(col.name in [c.name for c in list_collections()])
... assert(col.url == "http://collections.datalad.org/demo/DATALAD_COL_demo_collection/.git")
... assert(col.name == "DATALAD_COL_demo_collection")
Returns
-------
Collection
"""
local_master = get_datalad_master()
# check whether url is a local path:
if isdir(abspath(expandvars(expanduser(url)))):
url = abspath(expandvars(expanduser(url)))
# raise exception, if it's not a valid collection:
repo = CollectionRepo(url, create=False)
if name is None:
name = repo.name
else:
# Try to auto complete collection's url:
url += '/' if not url.endswith('/') else ''
url_completions = [url,
url + '.git',
url + url.rstrip('/').split('/')[-1] +
'.datalad-collection/.git']
url_ok = False
for address in url_completions:
try:
# use ls-remote to verify git can talk to that repository:
local_master.git_ls_remote(address, "-h")
url = address
url_ok = True
break
except CommandError as e:
if re.match("fatal.+?%s.+?not found" % url, e.stderr):
continue
else:
lgr.error("Registering collection failed.\n%s" % e)
return
if not url_ok:
lgr.error("Registering collection failed. "
"Couldn't find remote repository.")
return
if name is None:
# derive name from url:
parts = url.rstrip('/').split('/')
if parts[-1] == '.git':
name = parts[-2]
elif parts[-1].endswith('.git'):
name = parts[-1][0:-4]
elif parts[-1].endswith('.datalad-collection'):
name = parts[-1][0:-19]
else:
name = parts[-1]
local_master.git_remote_add(name, url)
local_master.git_fetch(name)
return Collection(CollectionRepoBackend(local_master,
name + "/master"))