def compress_files(files, archive, path=None, overwrite=True):
"""Compress `files` into an `archive` file
Parameters
----------
files : list of str
archive : str
path : str
Alternative directory under which compressor will be invoked, to e.g.
take into account relative paths of files and/or archive
overwrite : bool
Whether to allow overwriting the target archive file if one already exists
"""
runner = Runner(cwd=path)
apath = Path(archive)
if apath.exists():
if overwrite:
apath.unlink()
else:
raise ValueError(
'Target archive {} already exists and overwrite is forbidden'.
format(apath))
if len(apath.suffixes) > 1 and apath.suffixes[-2] == '.tar':
cmd = '7z u .tar -so -- {} | 7z u -si -- {}'.format(
' '.join(quote_cmdlinearg(f) for f in files),
quote_cmdlinearg(str(apath)),
)
else:
cmd = ['7z', 'u', str(apath), '--'] + files
runner.run(cmd)
def test_configs(path=None):
# set up dataset with registered procedure (c&p from test_basics):
ds = Dataset(path).create(force=True)
ds.run_procedure('cfg_yoda')
# configure dataset to look for procedures in its code folder
ds.config.add('datalad.locations.dataset-procedures',
'code',
scope='branch')
# 1. run procedure based on execution guessing by run_procedure:
ds.run_procedure(spec=['datalad_test_proc', 'some_arg'])
# look for traces
ok_file_has_content(op.join(ds.path, 'fromproc.txt'), 'some_arg\n')
# 2. now configure specific call format including usage of substitution config
# for run:
ds.config.add('datalad.procedures.datalad_test_proc.call-format',
u'%s {script} {ds} {{mysub}} {args}' %
quote_cmdlinearg(sys.executable),
scope='branch')
ds.config.add('datalad.run.substitutions.mysub',
'dataset-call-config',
scope='branch')
# TODO: Should we allow for --inputs/--outputs arguments for run_procedure
# (to be passed into run)?
ds.unlock("fromproc.txt")
# run again:
ds.run_procedure(spec=['datalad_test_proc', 'some_arg'])
# look for traces
ok_file_has_content(op.join(ds.path, 'fromproc.txt'),
'dataset-call-config\n')
# 3. have a conflicting config at user-level, which should override the
# config on dataset level:
ds.config.add('datalad.procedures.datalad_test_proc.call-format',
u'%s {script} {ds} local {args}' %
quote_cmdlinearg(sys.executable),
scope='local')
ds.unlock("fromproc.txt")
# run again:
ds.run_procedure(spec=['datalad_test_proc', 'some_arg'])
# look for traces
ok_file_has_content(op.join(ds.path, 'fromproc.txt'), 'local\n')
# 4. get configured help message:
r = ds.run_procedure('datalad_test_proc',
help_proc=True,
on_failure='ignore')
assert_true(len(r) == 1)
assert_in_results(r, status="impossible")
ds.config.add('datalad.procedures.datalad_test_proc.help',
"This is a help message",
scope='branch')
r = ds.run_procedure('datalad_test_proc', help_proc=True)
assert_true(len(r) == 1)
assert_in_results(r, message="This is a help message", status='ok')
def to_str(self, include_output=True):
from datalad.utils import (
ensure_unicode,
ensure_list,
quote_cmdlinearg,
)
to_str = "{}: ".format(self.__class__.__name__)
if self.cmd:
to_str += "'{}'".format(
# go for a compact, normal looking, properly quoted
# command rendering
' '.join(quote_cmdlinearg(c) for c in ensure_list(self.cmd)))
if self.code:
to_str += " failed with exitcode {}".format(self.code)
if self.cwd:
# only if not under standard PWD
to_str += " under {}".format(self.cwd)
if self.msg:
# typically a command error has no specific idea
to_str += " [{}]".format(ensure_unicode(self.msg))
if not include_output:
return to_str
if self.stdout:
to_str += " [out: '{}']".format(
ensure_unicode(self.stdout).strip())
if self.stderr:
to_str += " [err: '{}']".format(
ensure_unicode(self.stderr).strip())
if self.kwargs:
to_str += " [info keys: {}]".format(', '.join(self.kwargs.keys()))
return to_str
def normalize_command(command):
"""Convert `command` to the string representation.
"""
if isinstance(command, list):
command = list(map(assure_unicode, command))
if len(command) == 1 and command[0] != "--":
# This is either a quoted compound shell command or a simple
# one-item command. Pass it as is.
#
# FIXME: This covers the predominant command-line case, but, for
# Python API callers, it means values like ["./script with spaces"]
# requires additional string-like escaping, which is inconsistent
# with the handling of multi-item lists (and subprocess's
# handling). Once we have a way to detect "running from Python API"
# (discussed in gh-2986), update this.
command = command[0]
else:
if command and command[0] == "--":
# Strip disambiguation marker. Note: "running from Python API"
# FIXME from below applies to this too.
command = command[1:]
command = " ".join(quote_cmdlinearg(c) for c in command)
else:
command = assure_unicode(command)
return command
def _guess_exec(script_file):
state = None
try:
is_exec = os.stat(script_file).st_mode & stat.S_IEXEC
except OSError as e:
from errno import ENOENT
if e.errno == ENOENT and op.islink(script_file):
# broken symlink
# does not exist; there's nothing to detect at all
return {'type': None, 'template': None, 'state': 'absent'}
else:
raise e
# TODO check for exec permission and rely on interpreter
if is_exec and not os.path.isdir(script_file):
return {'type': u'executable',
'template': u'{script} {ds} {args}',
'state': 'executable'}
elif script_file.endswith('.sh'):
return {'type': u'bash_script',
'template': u'bash {script} {ds} {args}',
'state': 'executable'}
elif script_file.endswith('.py'):
ex = quote_cmdlinearg(sys.executable)
return {'type': u'python_script',
'template': u'%s {script} {ds} {args}' % ex,
'state': 'executable'}
else:
return {'type': None, 'template': None, 'state': None}
def put(self, source, destination, recursive=False, preserve_attrs=False):
import shutil
copy_fn = shutil.copy2 if preserve_attrs else shutil.copy
if recursive:
args = source, destination
kwargs = {"copy_function": copy_fn}
try:
shutil.copytree(*args, **kwargs)
except FileExistsError:
# SSHConnection.put() is okay with copying a tree if the
# destination directory already exists. With Python 3.8, we can
# make copytree() do the same with dirs_exist_ok=True. But for
# now, just rely on `cp`.
cmd = ["cp", "--recursive"]
if preserve_attrs:
cmd.append("--preserve")
self(cmd + [quote_cmdlinearg(a) for a in args])
else:
copy_fn(source, destination)
def decompress_file(archive, dir_):
"""Decompress `archive` into a directory `dir_`
This is an alternative implementation without patool, but directly calling 7z.
Parameters
----------
archive: str
dir_: str
"""
apath = Path(archive)
runner = Runner(cwd=dir_)
suffixes = _normalize_fname_suffixes(apath.suffixes)
if len(suffixes) > 1 and suffixes[-2] == '.tar':
# we have a compressed tar file that needs to be fed through the
# decompressor first
cmd = '7z x {} -so | 7z x -si -ttar'.format(quote_cmdlinearg(archive))
else:
# fire and forget
cmd = ['7z', 'x', archive]
runner.run(cmd, protocol=KillOutput)
def decompress_file(archive, dir_):
"""Decompress `archive` into a directory `dir_`
This is an alternative implementation without patool, but directly calling 7z.
Parameters
----------
archive: str
dir_: str
"""
apath = Path(archive)
runner = Runner(cwd=dir_)
if len(apath.suffixes) > 1 and apath.suffixes[-2] == '.tar':
# we have a compressed tar file that needs to be fed through the
# decompressor first
# hangs somehow, do via single string arg
#cmd = ['7z', 'x', archive, '-so', '|', '7z', 'x', '-si', '-ttar']
cmd = '7z x {} -so | 7z x -si -ttar'.format(quote_cmdlinearg(archive))
else:
# fire and forget
cmd = ['7z', 'x', archive]
runner.run(cmd)
def test_runner(tempfile):
# test non-dry command call
runner = Runner()
content = 'Testing äöü東 real run'
cmd = 'echo %s > %s' % (content, quote_cmdlinearg(tempfile))
ret = runner.run(cmd)
assert_equal(ret, ('', '')) # no out or err
ok_file_has_content(tempfile, content, strip=True)
os.unlink(tempfile)
# Run with shell
ret = runner.run(cmd, shell=True)
assert_equal(ret, ('', '')) # no out or err
ok_file_has_content(tempfile, content, strip=True)
os.unlink(tempfile)
# Pass as a list and with shell - "not exactly what we expect"
# Initial suspicion came from incorrect behavior of Runner as a runner
# for patool. Apparently (docs for 2.7):
# If args is a sequence, the first item specifies the command string,
# and any additional items will be treated as additional arguments to
# the shell itself.
# which is what it ruins it for us! So, for now we are not testing/using
# this form
# ret = runner.run(split_cmdline(cmd), shell=True)
# # ?! for some reason there is an empty line in stdout
# # TODO: figure out. It shouldn't though be of critical effect
# ret = (ret[0].rstrip(), ret[1])
# assert_equal(ret, ('', '')) # no out or err
# # And here we get kaboom ATM!
# ok_file_has_content(tempfile, content, strip=True)
# test non-dry python function call
output = runner.call(os.path.join, 'foo', 'bar')
assert_equal(os.path.join('foo', 'bar'), output,
"Call of: os.path.join, 'foo', 'bar' returned %s" % output)
def _guess_exec(script_file):
try:
is_exec = os.stat(script_file).st_mode & stat.S_IEXEC
except OSError as e:
from errno import ENOENT
if e.errno == ENOENT and op.islink(script_file):
# broken symlink
# does not exist; there's nothing to detect at all
return {'type': None, 'template': None, 'state': 'absent'}
else:
raise e
# on some FS the executable bit might not be all that reliable
# but a procedure might nevertheless be supported.
# go by extension with "known" interpreters first, and only then
# try to execute something that looks executable
if script_file.endswith('.sh'):
return {
'type': u'bash_script',
'template': u'bash {script} {ds} {args}',
'state': 'executable'
}
elif script_file.endswith('.py'):
ex = quote_cmdlinearg(sys.executable)
return {
'type': u'python_script',
'template': u'%s {script} {ds} {args}' % ex,
'state': 'executable'
}
elif is_exec and not os.path.isdir(script_file):
return {
'type': u'executable',
'template': u'{script} {ds} {args}',
'state': 'executable'
}
else:
return {'type': None, 'template': None, 'state': None}
def __call__(keyfile=None,
merge=False,
force_update=False,
bids=False,
non_bids_dir='non-bids',
dataset=None):
ds = require_dataset(dataset, check_installed=True, purpose='update')
repo = ds.repo
if not keyfile:
# will error out, if no config was given
keyfile = repo.config.obtain('datalad.ukbiobank.keyfile')
# prep for yield
res = dict(
action='ukb_update',
path=ds.path,
type='dataset',
logger=lgr,
refds=ds.path,
)
if repo.dirty:
yield dict(
res,
status='error',
message="Refuse to operate on dirty dataset",
)
return
# check if we have 'ukbfetch' before we start fiddling with the dataset
# and leave it in a mess for no reason
try:
subprocess.run(
# pull version info
['ukbfetch', '-i'],
capture_output=True,
)
except Exception as e:
raise RuntimeError(
"Cannot execute 'ukbfetch'. Original error: {}".format(e))
# just to be nice, and to be able to check it out again,
# when we are done
initial_branch = repo.get_active_branch()
initial_incoming = repo.get_hexsha('incoming')
# make sure we are in incoming
repo.call_git(['checkout', 'incoming'])
# first wipe out all prev. downloaded zip files so we can detect
# when some files are no longer available
for fp in repo.pathobj.glob('[0-9]*_[0-9]*_[0-9]_[0-9].*'):
fp.unlink()
# a place to put the download logs
# better be semi-persistent to ease inspection
tmpdir = repo.pathobj / repo.get_git_dir(repo) / 'tmp' / 'ukb'
tmpdir.mkdir(parents=True, exist_ok=True)
# redownload, run with explicit mode, because we just deleted the
# ZIP files and that is OK
ds.run(
cmd='ukbfetch -v -a{} -b.ukbbatch -o{}'.format(
quote_cmdlinearg(keyfile),
quote_cmdlinearg(str(tmpdir)),
),
explicit=True,
outputs=['.'],
message="Update from UKbiobank",
)
# TODO what if something broke before? needs force switch
if not force_update and repo.get_hexsha() == initial_incoming:
yield dict(
res,
status='notneeded',
message='No new content available',
)
repo.call_git(['checkout', initial_branch])
# TODO drop?
return
# onto extraction and transformation of downloaded content
repo.call_git(['checkout', 'incoming-processed'])
# mark the incoming change as merged
# (but we do not actually want any branch content)
repo.call_git(['merge', 'incoming', '--strategy=ours', 'incoming'])
for fp in repo.get_content_info(ref='incoming-processed',
eval_file_type=False):
fp.unlink()
subid = None
if bids:
from datalad_ukbiobank.ukb2bids import restructure_ukb2bids
# get participant ID from batch file
subid = list(
repo.call_git_items_(["cat-file", "-p", "incoming:.ukbbatch"
]))[0].split(maxsplit=1)[0]
# discover all zip files present in the last commit in 'incoming'
for fp, props in repo.get_content_annexinfo(
ref='incoming', eval_availability=False).items():
if fp.name.startswith('.'):
# skip internals
continue
# we have to extract into per-instance directories, otherwise files
# would conflict
ids = fp.stem.split('_')
if not len(ids) >= 3:
raise RuntimeError(
'Unrecognized filename structure: {}'.format(fp))
extract_dir = repo.pathobj / 'instance-{}'.format(ids[2])
extract_dir.mkdir(exist_ok=True)
if fp.suffix == '.zip':
with chpwd(extract_dir):
# extract and add their content
AddArchiveContent.__call__(
props['key'],
key=True,
annex=repo,
# --use-current-dir due to
# https://github.com/datalad/datalad/issues/3995
use_current_dir=True,
allow_dirty=True,
commit=False,
)
else:
# move into instance dir, and strip participant ID, and instance ID
# but keep array index
# e.g. -> 25747_3_0.adv -> instance-3/25747_0
repo.call_git([
'annex', 'fromkey', props['key'],
str(extract_dir /
('_'.join(ids[1::2]) + ''.join(fp.suffixes)))
])
if bids:
yield from restructure_ukb2bids(
ds,
subid=subid,
unrecognized_dir=Path('ses-{}'.format(ids[2])) /
non_bids_dir,
base_path=extract_dir,
session=ids[2],
)
# save whatever the state is now, `save` will discover deletions
# automatically and also commit them -- wonderful!
ds.save(message="Track ZIP file content")
yield dict(
res,
status='ok',
)
if not merge:
return
# and update active branch
repo.call_git(['checkout', initial_branch])
if initial_branch in ('incoming', 'incoming-processed'):
yield dict(
res,
action='ukb_merge_update',
status='impossible',
message='Refuse to merge into incoming* branch',
)
return
repo.call_git([
'merge', '-m', "Merge update from UKbiobank", 'incoming-processed'
])
yield dict(
res,
action='ukb_merge_update',
status='ok',
)
return
def __str__(self):
s = self._str
if s is None:
s = self._str = \
'%s(%s)' % (self.__class__.__name__, ut.quote_cmdlinearg(self.path))
return s
def __call__(subjects='list', dataset=None, ifexists=None, force=False):
from pyxnat import Interface as XNATInterface
ds = require_dataset(dataset, check_installed=True, purpose='update')
subjects = ensure_list(subjects)
# require a clean dataset
if ds.repo.dirty:
yield get_status_dict(
'update',
ds=ds,
status='impossible',
message=(
'Clean dataset required; use `datalad status` to inspect '
'unsaved changes'))
return
# prep for yield
res = dict(
action='xnat_update',
path=ds.path,
type='dataset',
logger=lgr,
refds=ds.path,
)
# obtain configured XNAT url and project name
xnat_cfg_name = ds.config.get('datalad.xnat.default-name', 'default')
cfg_section = 'datalad.xnat.{}'.format(xnat_cfg_name)
xnat_url = ds.config.get('{}.url'.format(cfg_section))
xnat_project = ds.config.get('{}.project'.format(cfg_section))
file_path = ds.config.get('{}.path'.format(cfg_section))
# obtain user credentials
parsed_url = urlparse(xnat_url)
no_proto_url = '{}{}'.format(parsed_url.netloc,
parsed_url.path).replace(' ', '')
cred = UserPassword(name=no_proto_url, url=None)()
xn = XNATInterface(server=xnat_url, **cred)
# provide subject list
if 'list' in subjects:
from datalad.ui import ui
subs = xn.select.project(xnat_project).subjects().get()
ui.message('The following subjects are available for XNAT '
'project {}:'.format(xnat_project))
for s in sorted(subs):
ui.message(" {}".format(quote_cmdlinearg(s)))
ui.message(
'Specify a specific subject(s) or "all" to download associated '
'files for.')
return
# query the specified subject(s) to make sure it exists and is accessible
if 'all' not in subjects:
from datalad.ui import ui
subs = []
for s in subjects:
sub = xn.select.project(xnat_project).subject(s)
nexp = len(sub.experiments().get())
if nexp > 0:
subs.append(s)
else:
ui.message(
'Failed to obtain information on subject {} from XNAT '
'project {}:'.format(s, xnat_project))
return
else:
# if all, get list of all subjects
subs = xn.select.project(xnat_project).subjects().get()
# parse and download one subject at a time
from datalad_xnat.parser import parse_xnat
addurl_dir = ds.pathobj / 'code' / 'addurl_files'
for sub in subs:
yield from parse_xnat(
ds,
sub=sub,
force=force,
xn=xn,
xnat_url=xnat_url,
xnat_project=xnat_project,
)
# add file urls for subject
lgr.info('Downloading files for subject %s', sub)
table = f"{addurl_dir}/{sub}_table.csv"
# this corresponds to the header field 'filename' in the csv table
filename = '{filename}'
filenameformat = f"{file_path}{filename}"
ds.addurls(
table,
'{url}',
filenameformat,
ifexists=ifexists,
save=False,
cfg_proc='xnat_dataset',
result_renderer='default',
)
ds.save(message=f"Update files for subject {sub}", recursive=True)
lgr.info(
'Files were updated for the following subjects in XNAT project %s:',
xnat_project)
for s in sorted(subs):
lgr.info(" {}".format(quote_cmdlinearg(s)))
yield dict(res, status='ok')
return
def __call__(
spec=None,
dataset=None,
discover=False,
help_proc=False):
if not spec and not discover:
raise InsufficientArgumentsError('requires at least a procedure name')
if help_proc and not spec:
raise InsufficientArgumentsError('requires a procedure name')
try:
ds = require_dataset(
dataset, check_installed=False,
purpose='run a procedure')
except NoDatasetFound:
ds = None
if discover:
# specific path of procedures that were already reported
reported = set()
# specific names of procedure for which an active one has been
# found
active = set()
for m, cmd_name, cmd_tmpl, cmd_help in \
_get_procedure_implementation('*', ds=ds):
if m in reported:
continue
ex = _guess_exec(m)
# configured template (call-format string) takes precedence:
if cmd_tmpl:
ex['template'] = cmd_tmpl
if ex['state'] is None:
# doesn't seem like a match
lgr.debug("%s does not look like a procedure, ignored.", m)
continue
state = 'overridden' if cmd_name in active else ex['state']
message = ex['type'] if ex['type'] else 'unknown type'
message += ' ({})'.format(state) if state != 'executable' else ''
res = get_status_dict(
action='discover_procedure',
path=m,
type='file',
logger=lgr,
refds=ds.path if ds else None,
status='ok',
state=state,
procedure_name=cmd_name,
procedure_type=ex['type'],
procedure_callfmt=ex['template'],
procedure_help=cmd_help,
message=message)
reported.add(m)
if state == 'executable':
active.add(cmd_name)
yield res
return
if not isinstance(spec, (tuple, list)):
# maybe coming from config
spec = split_cmdline(spec)
name = spec[0]
args = spec[1:]
try:
# get the first match an run with it
procedure_file, cmd_name, cmd_tmpl, cmd_help = \
next(_get_procedure_implementation(name, ds=ds))
except StopIteration:
res = get_status_dict(
action='run_procedure',
# TODO: Default renderer requires a key "path" to exist.
# Doesn't make a lot of sense in this case
path=name,
logger=lgr,
refds=ds.path if ds else None,
status='impossible',
message="Cannot find procedure with name '%s'" % name)
yield res
return
ex = _guess_exec(procedure_file)
# configured template (call-format string) takes precedence:
if cmd_tmpl:
ex['template'] = cmd_tmpl
if help_proc:
if cmd_help:
res = get_status_dict(
action='procedure_help',
path=procedure_file,
type='file',
logger=lgr,
refds=ds.path if ds else None,
status='ok',
state=ex['state'],
procedure_name=cmd_name,
procedure_type=ex['type'],
procedure_callfmt=ex['template'],
message=cmd_help)
else:
res = get_status_dict(
action='procedure_help',
path=procedure_file,
type='file',
logger=lgr,
refds=ds.path if ds else None,
status='impossible',
state=ex['state'],
procedure_name=cmd_name,
procedure_type=ex['type'],
procedure_callfmt=ex['template'],
message="No help available for '%s'" % name)
yield res
return
if not ex['template']:
raise ValueError("No idea how to execute procedure %s. "
"Missing 'execute' permissions?" % procedure_file)
cmd = ex['template'].format(
script=quote_cmdlinearg(procedure_file),
ds=quote_cmdlinearg(ds.path) if ds else '',
args=(u' '.join(quote_cmdlinearg(a) for a in args) if args else ''))
lgr.info(u"Running procedure %s", name)
lgr.debug(u'Full procedure command: %r', cmd)
for r in Run.__call__(
cmd=cmd,
dataset=ds,
explicit=True,
inputs=None,
outputs=None,
# pass through here
on_failure='ignore',
return_type='generator'
):
yield r
def __call__(url,
path="{subject}/{session}/{scan}/",
project=None,
force=False,
dataset=None):
from pyxnat import Interface as XNATInterface
ds = require_dataset(dataset,
check_installed=True,
purpose='initialization')
config = ds.config
path = with_pathsep(path)
# prep for yield
res = dict(
action='xnat_init',
path=ds.path,
type='dataset',
logger=lgr,
refds=ds.path,
)
# obtain user credentials, use simplified/stripped URL as identifier
# given we don't have more knowledge than the user, do not
# give a `url` to provide hints on how to obtain credentials
parsed_url = urlparse(url)
no_proto_url = '{}{}'.format(parsed_url.netloc,
parsed_url.path).replace(' ', '')
cred = UserPassword(name=no_proto_url, url=None)()
xn = XNATInterface(server=url, **cred)
# now we make a simple request to obtain the server version
# we don't care much, but if the URL or the credentials are wrong
# we will not get to see one
try:
xnat_version = xn.version()
lgr.debug("XNAT server version is %s", xnat_version)
except Exception as e:
yield dict(
res,
status='error',
message=('Failed to access the XNAT server. Full error:\n%s',
e),
)
return
if project is None:
from datalad.ui import ui
projects = xn.select.projects().get()
ui.message('No project name specified. The following projects are '
'available on {} for user {}:'.format(
url, cred['user']))
for p in sorted(projects):
# list and prep for C&P
# TODO multi-column formatting?
ui.message(" {}".format(quote_cmdlinearg(p)))
return
# query the specified project to make sure it exists and is accessible
proj = xn.select.project(project)
try:
nsubj = len(proj.subjects().get())
except Exception as e:
yield dict(
res,
status='error',
message=(
'Failed to obtain information on project %s from XNAT. '
'Full error:\n%s', project, e),
)
return
lgr.info('XNAT reports %i subjects currently on-record for project %s',
nsubj, project)
# check if dataset already initialized
auth_dir = ds.pathobj / '.datalad' / 'providers'
if auth_dir.exists() and not force:
yield dict(
res,
status='error',
message='Dataset found already initialized, '
'use `force` to reinitialize',
)
return
# put essential configuration into the dataset
config.set('datalad.xnat.default.url',
url,
where='dataset',
reload=False)
config.set('datalad.xnat.default.project', project, where='dataset')
config.set('datalad.xnat.default.path', path, where='dataset')
ds.save(
path=ds.pathobj / '.datalad' / 'config',
to_git=True,
message="Configure default XNAT url and project",
)
# Configure XNAT access authentication
ds.run_procedure(spec='cfg_xnat_dataset')
yield dict(
res,
status='ok',
)
return
def _create_sibling_ria(
ds,
url,
name,
storage_sibling,
storage_name,
existing,
shared,
group,
post_update_hook,
trust_level,
res_kwargs):
# be safe across datasets
res_kwargs = res_kwargs.copy()
# update dataset
res_kwargs['ds'] = ds
if not isinstance(ds.repo, AnnexRepo):
# No point in dealing with a special remote when there's no annex.
# Note, that in recursive invocations this might only apply to some of
# the datasets. Therefore dealing with it here rather than one level up.
lgr.debug("No annex at %s. Ignoring special remote options.", ds.path)
storage_sibling = False
storage_name = None
# parse target URL
try:
ssh_host, base_path, rewritten_url = verify_ria_url(url, ds.config)
except ValueError as e:
yield get_status_dict(
status='error',
message=str(e),
**res_kwargs
)
return
base_path = Path(base_path)
git_url = decode_source_spec(
# append dataset id to url and use magic from clone-helper:
url + '#{}'.format(ds.id),
cfg=ds.config
)['giturl']
# determine layout locations; go for a v1 layout
repo_path, _, _ = get_layout_locations(1, base_path, ds.id)
ds_siblings = [r['name'] for r in ds.siblings(result_renderer=None)]
# Figure whether we are supposed to skip this very dataset
if existing == 'skip' and (
name in ds_siblings or (
storage_name and storage_name in ds_siblings)):
yield get_status_dict(
status='notneeded',
message="Skipped on existing sibling",
**res_kwargs
)
# if we skip here, nothing else can change that decision further
# down
return
# figure whether we need to skip or error due an existing target repo before
# we try to init a special remote.
if ssh_host:
from datalad import ssh_manager
ssh = ssh_manager.get_connection(
ssh_host,
use_remote_annex_bundle=False)
ssh.open()
if existing in ['skip', 'error']:
config_path = repo_path / 'config'
# No .git -- if it's an existing repo in a RIA store it should be a
# bare repo.
# Theoretically we could have additional checks for whether we have
# an empty repo dir or a non-bare repo or whatever else.
if ssh_host:
try:
ssh('[ -e {p} ]'.format(p=quote_cmdlinearg(str(config_path))))
exists = True
except CommandError:
exists = False
else:
exists = config_path.exists()
if exists:
if existing == 'skip':
# 1. not rendered by default
# 2. message doesn't show up in ultimate result
# record as shown by -f json_pp
yield get_status_dict(
status='notneeded',
message="Skipped on existing remote "
"directory {}".format(repo_path),
**res_kwargs
)
return
else: # existing == 'error'
yield get_status_dict(
status='error',
message="remote directory {} already "
"exists.".format(repo_path),
**res_kwargs
)
return
if storage_sibling == 'only':
lgr.info("create storage sibling '{}' ...".format(name))
else:
lgr.info("create sibling{} '{}'{} ...".format(
's' if storage_name else '',
name,
" and '{}'".format(storage_name) if storage_name else '',
))
create_ds_in_store(SSHRemoteIO(ssh_host) if ssh_host else LocalIO(),
base_path, ds.id, '2', '1')
if storage_sibling:
# we are using the main `name`, if the only thing we are creating
# is the storage sibling
srname = name if storage_sibling == 'only' else storage_name
lgr.debug('init special remote {}'.format(srname))
special_remote_options = [
'type=external',
'externaltype=ora',
'encryption=none',
'autoenable=true',
'url={}'.format(url)]
try:
ds.repo.init_remote(
srname,
options=special_remote_options)
except CommandError as e:
if existing == 'reconfigure' \
and 'git-annex: There is already a special remote' \
in e.stderr:
# run enableremote instead
lgr.debug(
"special remote '%s' already exists. "
"Run enableremote instead.",
srname)
# TODO: Use AnnexRepo.enable_remote (which needs to get
# `options` first)
ds.repo.call_annex([
'enableremote',
srname] + special_remote_options)
else:
yield get_status_dict(
status='error',
message="initremote failed.\nstdout: %s\nstderr: %s"
% (e.stdout, e.stderr),
**res_kwargs
)
return
if trust_level:
ds.repo.call_annex([trust_level, srname])
# get uuid for use in bare repo's config
uuid = ds.config.get("remote.{}.annex-uuid".format(srname))
if storage_sibling == 'only':
# we can stop here, the rest of the function is about setting up
# the git remote part of the sibling
yield get_status_dict(
status='ok',
**res_kwargs,
)
return
# 2. create a bare repository in-store:
lgr.debug("init bare repository")
# TODO: we should prob. check whether it's there already. How?
# Note: like the special remote itself, we assume local FS if no
# SSH host is specified
disabled_hook = repo_path / 'hooks' / 'post-update.sample'
enabled_hook = repo_path / 'hooks' / 'post-update'
if group:
chgrp_cmd = "chgrp -R {} {}".format(
quote_cmdlinearg(str(group)),
quote_cmdlinearg(str(repo_path)))
if ssh_host:
ssh('cd {rootdir} && git init --bare{shared}'.format(
rootdir=quote_cmdlinearg(str(repo_path)),
shared=" --shared='{}'".format(
quote_cmdlinearg(shared)) if shared else ''
))
if storage_sibling:
# write special remote's uuid into git-config, so clone can
# which one it is supposed to be and enable it even with
# fallback URL
ssh("cd {rootdir} && git config datalad.ora-remote.uuid {uuid}"
"".format(rootdir=quote_cmdlinearg(str(repo_path)),
uuid=uuid))
if post_update_hook:
ssh('mv {} {}'.format(quote_cmdlinearg(str(disabled_hook)),
quote_cmdlinearg(str(enabled_hook))))
if group:
# Either repository existed before or a new directory was
# created for it, set its group to a desired one if was
# provided with the same chgrp
ssh(chgrp_cmd)
else:
gr = GitRepo(repo_path, create=True, bare=True,
shared=shared if shared else None)
if storage_sibling:
# write special remote's uuid into git-config, so clone can
# which one it is supposed to be and enable it even with
# fallback URL
gr.config.add("datalad.ora-remote.uuid", uuid, where='local')
if post_update_hook:
disabled_hook.rename(enabled_hook)
if group:
# TODO; do we need a cwd here?
subprocess.run(chgrp_cmd, cwd=quote_cmdlinearg(ds.path))
# add a git remote to the bare repository
# Note: needs annex-ignore! Otherwise we might push into dirhash
# lower annex/object tree instead of mixed, since it's a bare
# repo. This in turn would be an issue, if we want to pack the
# entire thing into an archive. Special remote will then not be
# able to access content in the "wrong" place within the archive
lgr.debug("set up git remote")
if name in ds_siblings:
# otherwise we should have skipped or failed before
assert existing == 'reconfigure'
ds.config.set(
"remote.{}.annex-ignore".format(name),
value="true",
where="local")
ds.siblings(
'configure',
name=name,
url=git_url
if ssh_host
else str(repo_path),
recursive=False,
# Note, that this should be None if storage_sibling was not set
publish_depends=storage_name,
result_renderer=None,
# Note, that otherwise a subsequent publish will report
# "notneeded".
fetch=True
)
yield get_status_dict(
status='ok',
**res_kwargs,
)
def _create_sibling_ria(ds, url, name, ria_remote, ria_remote_name, existing,
shared, group, post_update_hook, res_kwargs):
# be safe across datasets
res_kwargs = res_kwargs.copy()
# parse target URL
try:
ssh_host, base_path = verify_ria_url(url, ds.config)
except ValueError as e:
yield get_status_dict(status='error', message=str(e), **res_kwargs)
return
base_path = Path(base_path)
git_url = decode_source_spec(
# append dataset id to url and use magic from clone-helper:
url + '#{}'.format(ds.id),
cfg=ds.config)['giturl']
# go for a v1 layout
repo_path, _, _ = get_layout_locations(1, base_path, ds.id)
ds_siblings = [r['name'] for r in ds.siblings(result_renderer=None)]
# Figure whether we are supposed to skip this very dataset
if existing == 'skip' and (name in ds_siblings or
(ria_remote_name
and ria_remote_name in ds_siblings)):
yield get_status_dict(status='notneeded',
message="Skipped on existing sibling",
**res_kwargs)
# if we skip here, nothing else can change that decision further
# down
return
# we might learn that some processing (remote repo creation is
# not desired)
skip = False
lgr.info("create sibling{} '{}'{} ...".format(
's' if ria_remote_name else '',
name,
" and '{}'".format(ria_remote_name) if ria_remote_name else '',
))
if ssh_host:
from datalad import ssh_manager
ssh = ssh_manager.get_connection(ssh_host,
use_remote_annex_bundle=False)
ssh.open()
# determine layout locations
if ria_remote:
lgr.debug('init special remote {}'.format(ria_remote_name))
ria_remote_options = [
'type=external', 'externaltype=ria', 'encryption=none',
'autoenable=true', 'url={}'.format(url)
]
try:
ds.repo.init_remote(ria_remote_name, options=ria_remote_options)
except CommandError as e:
if existing in ['replace', 'reconfigure'] \
and 'git-annex: There is already a special remote' \
in e.stderr:
# run enableremote instead
lgr.debug(
"special remote '%s' already exists. "
"Run enableremote instead.", ria_remote_name)
# TODO: Use AnnexRepo.enable_remote (which needs to get
# `options` first)
cmd = ['git', 'annex', 'enableremote', ria_remote_name
] + ria_remote_options
subprocess.run(cmd, cwd=quote_cmdlinearg(ds.repo.path))
else:
yield get_status_dict(
status='error',
message="initremote failed.\nstdout: %s\nstderr: %s" %
(e.stdout, e.stderr),
**res_kwargs)
return
# 1. create remote object store:
# Note: All it actually takes is to trigger the special
# remote's `prepare` method once.
# ATM trying to achieve that by invoking a minimal fsck.
# TODO: - It's probably faster to actually talk to the special
# remote (i.e. pretending to be annex and use
# the protocol to send PREPARE)
# - Alternatively we can create the remote directory and
# ria version file directly, but this means
# code duplication that then needs to be kept in sync
# with ria-remote implementation.
# - this leads to the third option: Have that creation
# routine importable and callable from
# ria-remote package without the need to actually
# instantiate a RIARemote object
lgr.debug("initializing object store")
ds.repo.fsck(remote=ria_remote_name,
fast=True,
annex_options=['--exclude=*/*'])
else:
# with no special remote we currently need to create the
# required directories
# TODO: This should be cleaner once we have access to the
# special remote's RemoteIO classes without
# talking via annex
if ssh_host:
try:
stdout, stderr = ssh('test -e {repo}'.format(
repo=quote_cmdlinearg(str(repo_path))))
exists = True
except CommandError as e:
exists = False
if exists:
if existing == 'skip':
# 1. not rendered by default
# 2. message doesn't show up in ultimate result
# record as shown by -f json_pp
yield get_status_dict(status='notneeded',
message="Skipped on existing remote "
"directory {}".format(repo_path),
**res_kwargs)
skip = True
elif existing in ['error', 'reconfigure']:
yield get_status_dict(
status='error',
message="remote directory {} already "
"exists.".format(repo_path),
**res_kwargs)
return
elif existing == 'replace':
ssh('chmod u+w -R {}'.format(
quote_cmdlinearg(str(repo_path))))
ssh('rm -rf {}'.format(quote_cmdlinearg(str(repo_path))))
if not skip:
ssh('mkdir -p {}'.format(quote_cmdlinearg(str(repo_path))))
else:
if repo_path.exists():
if existing == 'skip':
skip = True
elif existing in ['error', 'reconfigure']:
yield get_status_dict(
status='error',
message="remote directory {} already "
"exists.".format(repo_path),
**res_kwargs)
return
elif existing == 'replace':
rmtree(repo_path)
if not skip:
repo_path.mkdir(parents=True)
# Note, that this could have changed since last tested due to existing
# remote dir
if skip:
return
# 2. create a bare repository in-store:
lgr.debug("init bare repository")
# TODO: we should prob. check whether it's there already. How?
# Note: like the special remote itself, we assume local FS if no
# SSH host is specified
disabled_hook = repo_path / 'hooks' / 'post-update.sample'
enabled_hook = repo_path / 'hooks' / 'post-update'
if group:
chgrp_cmd = "chgrp -R {} {}".format(quote_cmdlinearg(str(group)),
quote_cmdlinearg(str(repo_path)))
if ssh_host:
ssh('cd {rootdir} && git init --bare{shared}'.format(
rootdir=quote_cmdlinearg(str(repo_path)),
shared=" --shared='{}'".format(quote_cmdlinearg(shared))
if shared else ''))
if post_update_hook:
ssh('mv {} {}'.format(quote_cmdlinearg(str(disabled_hook)),
quote_cmdlinearg(str(enabled_hook))))
if group:
# Either repository existed before or a new directory was
# created for it, set its group to a desired one if was
# provided with the same chgrp
ssh(chgrp_cmd)
else:
GitRepo(repo_path,
create=True,
bare=True,
shared=" --shared='{}'".format(quote_cmdlinearg(shared))
if shared else None)
if post_update_hook:
disabled_hook.rename(enabled_hook)
if group:
# TODO; do we need a cwd here?
subprocess.run(chgrp_cmd, cwd=quote_cmdlinearg(ds.path))
# add a git remote to the bare repository
# Note: needs annex-ignore! Otherwise we might push into default
# annex/object tree instead of directory type tree with dirhash
# lower. This in turn would be an issue, if we want to pack the
# entire thing into an archive. Special remote will then not be
# able to access content in the "wrong" place within the archive
lgr.debug("set up git remote")
# TODO:
# - This sibings call results in "[WARNING] Failed to determine
# if datastore carries annex."
# (see https://github.com/datalad/datalad/issues/4028)
# => for now have annex-ignore configured before. Evtl. Allow
# configure/add to include that option
# - additionally there's
# https://github.com/datalad/datalad/issues/3989,
# where datalad-siblings might hang forever
if name in ds_siblings:
# otherwise we should have skipped or failed before
assert existing in ['replace', 'reconfigure']
ds.config.set("remote.{}.annex-ignore".format(name),
value="true",
where="local")
ds.siblings(
'configure',
name=name,
url=git_url if ssh_host else str(repo_path),
recursive=False,
# Note, that this should be None if ria_remote was not set
publish_depends=ria_remote_name,
result_renderer=None,
# Note, that otherwise a subsequent publish will report
# "notneeded".
fetch=True)
yield get_status_dict(
status='ok',
**res_kwargs,
)
def __call__(keyfile=None,
merge=False,
force=False,
drop=None,
dataset=None):
ds = require_dataset(dataset, check_installed=True, purpose='update')
if drop and drop not in ('extracted', 'archives'):
raise ValueError(
"Unrecognized value for 'drop' option: {}".format(drop))
repo = ds.repo
if not keyfile:
# will error out, if no config was given
keyfile = repo.config.obtain(
'datalad.ukbiobank.keyfile',
dialog_type='question',
title='Key file location',
text=
'Where is the location of the file with the UKB access key?',
)
# prep for yield
res = dict(
action='ukb_update',
path=ds.path,
type='dataset',
logger=lgr,
refds=ds.path,
)
if repo.dirty:
yield dict(
res,
status='error',
message="Refuse to operate on dirty dataset",
)
return
# check if we have 'ukbfetch' before we start fiddling with the dataset
# and leave it in a mess for no reason
try:
subprocess.run(
# pull version info
['ukbfetch', '-i'],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
)
except Exception as e:
raise RuntimeError(
"Cannot execute 'ukbfetch'. Original error: {}".format(e))
# just to be nice, and to be able to check it out again,
# when we are done
initial_branch = repo.get_active_branch()
initial_incoming = repo.get_hexsha('incoming')
# make sure we are in incoming
repo.call_git(['checkout', 'incoming'])
# first wipe out all prev. downloaded zip files so we can detect
# when some files are no longer available
for fp in repo.pathobj.glob('[0-9]*_[0-9]*_[0-9]_[0-9].*'):
fp.unlink()
# a place to put the download logs
# better be semi-persistent to ease inspection
tmpdir = repo.pathobj / repo.get_git_dir(repo) / 'tmp' / 'ukb'
tmpdir.mkdir(parents=True, exist_ok=True)
# redownload, run with explicit mode, because we just deleted the
# ZIP files and that is OK
ds.run(
cmd='ukbfetch -v -a{} -b.ukbbatch -o{}'.format(
quote_cmdlinearg(keyfile),
# use relative path to tmpdir to avoid leakage
# of system-specific information into the run record
quote_cmdlinearg(str(tmpdir.relative_to(repo.pathobj))),
),
explicit=True,
outputs=['.'],
message="Update from UKBiobank",
)
# TODO what if something broke before? needs force switch
if not force and repo.get_hexsha() == initial_incoming:
yield dict(
res,
status='notneeded',
message='No new content available',
)
repo.call_git(['checkout', initial_branch])
# TODO drop?
return
# onto extraction and transformation of downloaded content
repo.call_git(['checkout', 'incoming-native'])
# mark the incoming change as merged
# (but we do not actually want any branch content)
repo.call_git(['merge', 'incoming', '--strategy=ours'])
for fp in repo.get_content_info(ref='incoming-native',
eval_file_type=False):
fp.unlink()
# discover all files present in the last commit in 'incoming'
for fp, props in repo.get_content_annexinfo(
ref='incoming', eval_availability=False).items():
if fp.name.startswith('.'):
# skip internals
continue
# we have to extract into per-instance directories, otherwise files
# would conflict
ids = fp.stem.split('_')
if not len(ids) >= 3:
raise RuntimeError(
'Unrecognized filename structure: {}'.format(fp))
# build an ID from the data record and the array index
rec_id = '_'.join(ids[1:])
if fp.suffix == '.zip':
extract_dir = repo.pathobj / rec_id
extract_dir.mkdir(exist_ok=True)
with chpwd(extract_dir):
# extract and add their content
AddArchiveContent.__call__(
props['key'],
key=True,
annex=repo,
# --use-current-dir due to
# https://github.com/datalad/datalad/issues/3995
use_current_dir=True,
allow_dirty=True,
commit=False,
)
else:
# move into instance dir, and strip participant ID, and instance ID
# but keep array index
# e.g. -> 25747_3_0.adv -> instance-3/25747_0
repo.call_git([
'annex', 'fromkey', props['key'],
str(repo.pathobj / (rec_id + ''.join(fp.suffixes)))
])
# save whatever the state is now, `save` will discover deletions
# automatically and also commit them -- wonderful!
ds.save(message="Update native layout")
yield dict(
res,
status='ok',
)
want_bids = 'incoming-bids' in repo.get_branches()
if want_bids:
repo.call_git(['checkout', 'incoming-bids'])
# mark the incoming change as merged
# (but we do not actually want any branch content)
repo.call_git(['merge', 'incoming', '--strategy=ours'])
# prepare the worktree to match the latest state
# of incoming-native but keep histories separate
# (ie. no merge), because we cannot handle partial
# changes
repo.call_git(['read-tree', '-u', '--reset', 'incoming-native'])
# unstage change to present a later `datalad save` a single
# changeset to be saved (otherwise it might try to keep staged
# content staged und only save additional modifications)
#repo.call_git(['restore', '--staged', '.'])
repo.call_git(['reset', 'HEAD', '.'])
# and now do the BIDSification
from datalad_ukbiobank.ukb2bids import restructure_ukb2bids
# get participant ID from batch file
subid = list(
repo.call_git_items_(["cat-file", "-p", "incoming:.ukbbatch"
]))[0].split(maxsplit=1)[0]
yield from restructure_ukb2bids(
ds,
subid=subid,
unrecognized_dir='non-bids',
base_path=repo.pathobj,
)
ds.save(message="Update BIDS layout")
if drop:
if drop == 'archives':
# we need to force the drop, because the download is the
# only copy we have in general
drop_opts = ['--force', '--branch', 'incoming', '-I', '*.zip']
else: # drop == 'extracted':
drop_opts = [
'--in', 'datalad-archives', '--branch', 'incoming-native'
]
for rec in repo.call_annex_records(['drop'] + drop_opts):
if not rec.get('success', False):
yield dict(
action='drop',
status='error',
message=rec.get('note', 'could not drop key'),
key=rec.get('key', None),
type='key',
path=ds.path,
)
if not merge:
return
# and update active branch
repo.call_git(['checkout', initial_branch])
if initial_branch in ('incoming', 'incoming-native', 'incoming-bids'):
yield dict(
res,
action='ukb_merge_update',
status='impossible',
message='Refuse to merge into incoming* branch',
)
return
repo.call_git([
'merge', '-m', "Merge update from UKbiobank",
'incoming-bids' if want_bids else 'incoming-native'
])
yield dict(
res,
action='ukb_merge_update',
status='ok',
)
return
def _test_bare_git_version_2(host, dspath, store):
# Similarly to test_bare_git_version_1, this should ensure a bare git repo
# at the store location for a dataset doesn't conflict with the ORA remote.
# Note: Usability of git remote by annex depends on dataset layout version
# (dirhashlower vs. -mixed).
# For version 2 (mixed) upload via ORA and consumption via git should
# work. But not the other way around, since git-annex uses
# dirhashlower with bare repos.
ds_path = Path(dspath)
store = Path(store)
ds = Dataset(ds_path).create()
populate_dataset(ds)
ds.save()
bare_repo_path, _, _ = get_layout_locations(1, store, ds.id)
# Use git to make sure the remote end is what git thinks a bare clone of it
# should look like
subprocess.run([
'git', 'clone', '--bare',
quote_cmdlinearg(str(dspath)),
quote_cmdlinearg(str(bare_repo_path))
])
if host:
url = "ria+ssh://{host}{path}".format(host=host, path=store)
else:
url = "ria+{}".format(store.as_uri())
init_opts = common_init_opts + ['url={}'.format(url)]
# set up store:
io = SSHRemoteIO(host) if host else LocalIO()
create_store(io, store, '1')
# set up the dataset location, too.
# Note: Dataset layout version 2 (dirhash mixed):
create_ds_in_store(io, store, ds.id, '2', '1')
# Now, let's have the bare repo as a git remote
git_url = "ssh://{host}{path}".format(host=host, path=bare_repo_path) \
if host else bare_repo_path.as_uri()
ds.repo.add_remote('bare-git', git_url)
ds.repo.enable_remote('bare-git')
# and the ORA remote in addition:
ds.repo.init_remote('ora-remote', options=init_opts)
# upload keys via ORA:
ds.repo.copy_to('.', 'ora-remote')
# bare-git doesn't know yet:
eq_(len(ds.repo.whereis('one.txt')), 2)
# fsck to make availability known
assert_status('ok', [
annexjson2result(r, ds)
for r in ds.repo.fsck(remote='bare-git', fast=True)
])
eq_(len(ds.repo.whereis('one.txt')), 3)
ds.drop('.')
eq_(len(ds.repo.whereis('one.txt')), 2)
# actually consumable via git remote:
ds.repo.call_annex(['move', 'one.txt', '--from', 'bare-git'])
eq_(len(ds.repo.whereis('one.txt')), 2)
# now, move back via git - shouldn't be consumable via ORA
ds.repo.call_annex(['move', 'one.txt', '--to', 'bare-git'])
# fsck to make availability known, but there's nothing from POV of ORA:
fsck_res = [
annexjson2result(r, ds)
for r in ds.repo.fsck(remote='ora-remote', fast=True)
]
assert_result_count(fsck_res,
1,
status='error',
message='** Based on the location log, one.txt\n'
'** was expected to be present, '
'but its content is missing.')
assert_result_count(fsck_res, 1, status='ok')
eq_(len(fsck_res), 2)
eq_(len(ds.repo.whereis('one.txt')), 1)
def _test_bare_git_version_1(host, dspath, store):
# This test should take a dataset and create a bare repository at the remote
# end from it.
# Given, that it is placed correctly within a tree of dataset, that remote
# thing should then be usable as an ora-remote as well as as a git-type
# remote.
# Note: Usability of git remote by annex depends on dataset layout version
# (dirhashlower vs. -mixed).
# For version 1 (lower) upload and consumption should be
# interchangeable. It doesn't matter which remote is used for what
# direction.
ds_path = Path(dspath)
store = Path(store)
ds = Dataset(ds_path).create()
populate_dataset(ds)
ds.save()
bare_repo_path, _, _ = get_layout_locations(1, store, ds.id)
# Use git to make sure the remote end is what git thinks a bare clone of it
# should look like
subprocess.run([
'git', 'clone', '--bare',
quote_cmdlinearg(str(dspath)),
quote_cmdlinearg(str(bare_repo_path))
])
if host:
url = "ria+ssh://{host}{path}".format(host=host, path=store)
else:
url = "ria+{}".format(store.as_uri())
init_opts = common_init_opts + ['url={}'.format(url)]
# set up store:
io = SSHRemoteIO(host) if host else LocalIO()
create_store(io, store, '1')
# set up the dataset location, too.
# Note: Dataset layout version 1 (dirhash lower):
create_ds_in_store(io, store, ds.id, '1', '1')
# Now, let's have the bare repo as a git remote and use it with annex
git_url = "ssh://{host}{path}".format(host=host, path=bare_repo_path) \
if host else bare_repo_path.as_uri()
ds.repo.add_remote('bare-git', git_url)
ds.repo.enable_remote('bare-git')
# copy files to the remote
ds.repo.copy_to('.', 'bare-git')
eq_(len(ds.repo.whereis('one.txt')), 2)
# now we can drop all content locally, reobtain it, and survive an
# fsck
ds.drop('.')
ds.get('.')
assert_status('ok', [annexjson2result(r, ds) for r in ds.repo.fsck()])
# Now, add the ora remote:
ds.repo.init_remote('ora-remote', options=init_opts)
# fsck to make availability known
assert_status('ok', [
annexjson2result(r, ds)
for r in ds.repo.fsck(remote='ora-remote', fast=True)
])
eq_(len(ds.repo.whereis('one.txt')), 3)
# Now move content from git-remote to local and see it not being available
# via bare-git anymore.
ds.repo.call_annex(['move', '--all', '--from=bare-git'])
# ora-remote doesn't know yet:
eq_(len(ds.repo.whereis('one.txt')), 2)
# But after fsck it does:
fsck_res = [
annexjson2result(r, ds)
for r in ds.repo.fsck(remote='ora-remote', fast=True)
]
assert_result_count(fsck_res,
1,
status='error',
message='** Based on the location log, one.txt\n'
'** was expected to be present, '
'but its content is missing.')
assert_result_count(fsck_res,
1,
status='error',
message='** Based on the location log, subdir/two\n'
'** was expected to be present, '
'but its content is missing.')
eq_(len(ds.repo.whereis('one.txt')), 1)
# and the other way around: upload via ora-remote and have it available via
# git-remote:
ds.repo.copy_to('.', 'ora-remote')
# fsck to make availability known
assert_status('ok', [
annexjson2result(r, ds)
for r in ds.repo.fsck(remote='bare-git', fast=True)
])
eq_(len(ds.repo.whereis('one.txt')), 3)
def __call__(spec=None, *, dataset=None, discover=False, help_proc=False):
if not spec and not discover:
raise InsufficientArgumentsError(
'requires at least a procedure name')
if help_proc and not spec:
raise InsufficientArgumentsError('requires a procedure name')
try:
ds = require_dataset(dataset,
check_installed=False,
purpose='run a procedure')
except NoDatasetFound:
ds = None
if discover:
# specific path of procedures that were already reported
reported = set()
# specific names of procedure for which an active one has been
# found
active = set()
for m, cmd_name, cmd_tmpl, cmd_help in \
_get_procedure_implementation('*', ds=ds):
if m in reported:
continue
ex = _guess_exec(m)
# configured template (call-format string) takes precedence:
if cmd_tmpl:
ex['template'] = cmd_tmpl
if ex['state'] is None:
# doesn't seem like a match
lgr.debug("%s does not look like a procedure, ignored.", m)
continue
state = 'overridden' if cmd_name in active else ex['state']
message = ex['type'] if ex['type'] else 'unknown type'
message += ' ({})'.format(
state) if state != 'executable' else ''
res = get_status_dict(action='discover_procedure',
path=m,
type='file',
logger=lgr,
refds=ds.path if ds else None,
status='ok',
state=state,
procedure_name=cmd_name,
procedure_type=ex['type'],
procedure_callfmt=ex['template'],
procedure_help=cmd_help,
message=message)
reported.add(m)
if state == 'executable':
active.add(cmd_name)
yield res
return
if isinstance(spec, dict):
# Skip getting procedure implementation if called with a
# dictionary (presumably coming from --discover)
procedure_file = spec['path']
cmd_name = spec['procedure_name']
cmd_tmpl = spec['procedure_callfmt']
cmd_help = spec['procedure_help']
name = cmd_name
args = []
else:
if not isinstance(spec, (tuple, list)):
# maybe coming from config
spec = split_cmdline(spec)
name = spec[0]
args = spec[1:]
try:
# get the first match an run with it
procedure_file, cmd_name, cmd_tmpl, cmd_help = \
next(_get_procedure_implementation(name, ds=ds))
except StopIteration:
raise ValueError("Cannot find procedure with name '%s'" % name)
ex = _guess_exec(procedure_file)
# configured template (call-format string) takes precedence:
if cmd_tmpl:
ex['template'] = cmd_tmpl
if help_proc:
if cmd_help:
res = get_status_dict(action='procedure_help',
path=procedure_file,
type='file',
logger=lgr,
refds=ds.path if ds else None,
status='ok',
state=ex['state'],
procedure_name=cmd_name,
procedure_type=ex['type'],
procedure_callfmt=ex['template'],
message=cmd_help)
else:
res = get_status_dict(action='procedure_help',
path=procedure_file,
type='file',
logger=lgr,
refds=ds.path if ds else None,
status='impossible',
state=ex['state'],
procedure_name=cmd_name,
procedure_type=ex['type'],
procedure_callfmt=ex['template'],
message="No help available for '%s'" %
name)
yield res
return
if not ex['template']:
raise ValueError("No idea how to execute procedure %s. "
"Missing 'execute' permissions?" % procedure_file)
cmd = ex['template'].format(
script=guard_for_format(quote_cmdlinearg(procedure_file)),
ds=guard_for_format(quote_cmdlinearg(ds.path)) if ds else '',
args=join_cmdline(args) if args else '')
lgr.info(u"Running procedure %s", name)
lgr.debug(u'Full procedure command: %r', cmd)
for r in Run.__call__(
cmd=cmd,
dataset=ds,
explicit=True,
inputs=None,
outputs=None,
# pass through here
on_failure='ignore',
return_type='generator',
result_renderer='disabled'):
yield r
if ds:
# the procedure ran and we have to anticipate that it might have
# changed the dataset config, so we need to trigger an unforced
# reload.
# we have to do this despite "being done here", because
# run_procedure() runs in the same process and reuses dataset (config
# manager) instances, and the next interaction with a dataset should
# be able to count on an up-to-date config
ds.config.reload()
