def no_annex(ds):
ds = require_dataset(
ds,
check_installed=True,
purpose='configuration')
if isinstance(ds.repo, AnnexRepo):
repo = ds.repo
# TODO: if procedures can have options -- add --force handling/passing
#
# annex uninit unlocks files for which there is content (nice) but just proceeds
# and leaves broken symlinks for files without content. For the current purpose
# of this procedure we just prevent "uninit" of any annex with some files already
# annexed.
if any(repo.call_annex_items_(['whereis', '--all'])):
raise RuntimeError("Annex has some annexed files, unsafe")
# remove annex
repo.call_annex(['uninit'])
noannex_file = ds.pathobj / ".noannex"
if not noannex_file.exists():
lgr.info("Creating and committing a .noannex file")
noannex_file.touch()
ds.save(noannex_file,
message="Added .noannex to prevent accidental initialization of git-annex")
def _describe_system():
import platform as pl
from datalad import get_encoding_info
if hasattr(pl, 'dist'):
dist = pl.dist()
else:
# Python 3.8 removed .dist but recommended "distro" is slow, so we
# try it only if needed
try:
import distro
dist = distro.linux_distribution(full_distribution_name=False)
except ImportError:
lgr.info(
"Please install 'distro' package to obtain distribution information"
)
dist = tuple()
except Exception as exc:
lgr.warning(
"No distribution information will be provided since 'distro' "
"fails to import/run: %s", exc_str(exc)
)
dist = tuple()
return {
'type': os.name,
'name': pl.system(),
'release': pl.release(),
'version': pl.version(),
'distribution': ' '.join([_t2s(dist),
_t2s(pl.mac_ver()),
_t2s(pl.win32_ver())]).rstrip(),
'max_path_length': get_max_path_length(getpwd()),
'encoding': get_encoding_info(),
}
def _describe_system():
import platform as pl
from datalad import get_encoding_info
if hasattr(pl, 'dist'):
dist = pl.dist()
else:
# Python 3.8 removed .dist but recommended "distro" is slow, so we
# try it only if needed
try:
import distro
dist = distro.linux_distribution(full_distribution_name=False)
except ImportError:
lgr.info(
"Please install 'distro' package to obtain distribution information"
)
dist = tuple()
except Exception as exc:
lgr.warning(
"No distribution information will be provided since 'distro' "
"fails to import/run: %s", exc_str(exc))
dist = tuple()
return {
'type':
os.name,
'name':
pl.system(),
'release':
pl.release(),
'version':
pl.version(),
'distribution':
' '.join([_t2s(dist),
_t2s(pl.mac_ver()),
_t2s(pl.win32_ver())]).rstrip(),
'max_path_length':
get_max_path_length(getpwd()),
'encoding':
get_encoding_info(),
}
for k, v in rec.items():
if v.get('description', '') in [remote, '[%s]' % remote]:
return v.get('urls', [])
return []
if __name__ == '__main__':
annex = AnnexRepo('.', create=False, init=False)
# enable datalad special remote
urls_to_register = defaultdict(list) # key: urls
try:
annex.call_annex(["enableremote", "datalad"])
# go through each and see where urls aren't yet under web
# seems might have also --in=datalad to restrict
w = annex.whereis([], options=['--all'], output='full')
lgr.info("Got %d entries", len(w))
for k, rec in tqdm(w.items()):
datalad_urls = get_remote_urls(rec, 'datalad')
web_urls = set(get_remote_urls(rec, 'web'))
for url in datalad_urls:
if url not in web_urls:
if 'openneuro.s3' in url or 'openfmri.s3' in url:
urls_to_register[k].append(url)
else:
lgr.warning("Found unexpected url %s" % url)
finally:
# disable datalad special remote
annex.remove_remote("datalad") # need to disable it first
lgr.info("Got %d entries which could get new urls", len(urls_to_register))
for k, urls in tqdm(urls_to_register.items()):
def get_remote_urls(rec, remote):
for k, v in rec.items():
if v.get('description', '') in [remote, '[%s]' % remote]:
return v.get('urls', [])
return []
if __name__ == '__main__':
annex = AnnexRepo('.', create=False, init=False)
# enable datalad special remote
urls_to_register = defaultdict(list) # key: urls
try:
annex._annex_custom_command([], ["git", "annex", "enableremote", "datalad"])
# go through each and see where urls aren't yet under web
# seems might have also --in=datalad to restrict
w = annex.whereis([], options=['--all'], output='full')
lgr.info("Got %d entries", len(w))
for k, rec in tqdm(w.items()):
datalad_urls = get_remote_urls(rec, 'datalad')
web_urls = set(get_remote_urls(rec, 'web'))
for url in datalad_urls:
if url not in web_urls:
if 'openneuro.s3' in url or 'openfmri.s3' in url:
urls_to_register[k].append(url)
else:
lgr.warning("Found unexpected url %s" % url)
finally:
# disable datalad special remote
annex.remove_remote("datalad") # need to disable it first
lgr.info(
"Got %d entries which could get new urls",