def _get_url(self, path):
annex_repo, annex_key = _get_annex_repo_key(path)
if annex_key:
# so we do not have it yet!
repo = AnnexRepo(annex_repo)
whereis = repo.whereis(annex_key, output='full', key=True) # , batch=True)
# TODO: support also regular http remotes etc
urls = list(chain(*(x.get('urls', []) for x in whereis.values())))
# TODO: some kind of analysis/fallback and not just taking the first one
# TODO: Opened connections already might even have already some "equivalent" URL
if urls:
return urls[0]
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.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))
def test_add_archive_content(path_orig, url, repo_path):
with chpwd(repo_path):
# TODO we need to be able to pass path into add_archive_content
# We could mock but I mean for the API
assert_raises(RuntimeError, add_archive_content,
"nonexisting.tar.gz") # no repo yet
repo = AnnexRepo(repo_path, create=True)
assert_raises(ValueError, add_archive_content, "nonexisting.tar.gz")
# we can't add a file from outside the repo ATM
assert_raises(FileNotInRepositoryError, add_archive_content,
opj(path_orig, '1.tar.gz'))
# Let's add first archive to the repo so we could test
with swallow_outputs():
repo.add_urls([opj(url, '1.tar.gz')],
options=["--pathdepth", "-1"])
for s in range(1, 5):
repo.add_urls([opj(url, '%du/1.tar.gz' % s)],
options=["--pathdepth", "-2"])
repo.commit("added 1.tar.gz")
key_1tar = repo.get_file_key(
'1.tar.gz') # will be used in the test later
def d1_basic_checks():
ok_(exists('1'))
ok_file_under_git('1', '1 f.txt', annexed=True)
ok_file_under_git(opj('1', 'd', '1d'), annexed=True)
ok_archives_caches(repo_path, 0)
# and by default it just does it, everything goes to annex
repo_ = add_archive_content('1.tar.gz')
eq_(repo.path, repo_.path)
d1_basic_checks()
# If ran again, should proceed just fine since the content is the same so no changes would be made really
add_archive_content('1.tar.gz')
# But that other one carries updated file, so should fail due to overwrite
with assert_raises(RuntimeError) as cme:
add_archive_content(opj('1u', '1.tar.gz'), use_current_dir=True)
# TODO: somewhat not precise since we have two possible "already exists"
# -- in caching and overwrite check
assert_in("already exists", str(cme.exception))
# but should do fine if overrides are allowed
add_archive_content(opj('1u', '1.tar.gz'),
existing='overwrite',
use_current_dir=True)
add_archive_content(opj('2u', '1.tar.gz'),
existing='archive-suffix',
use_current_dir=True)
add_archive_content(opj('3u', '1.tar.gz'),
existing='archive-suffix',
use_current_dir=True)
add_archive_content(opj('4u', '1.tar.gz'),
existing='archive-suffix',
use_current_dir=True)
# rudimentary test
assert_equal(sorted(map(basename, glob(opj(repo_path, '1', '1*')))),
['1 f-1.1.txt', '1 f-1.2.txt', '1 f-1.txt', '1 f.txt'])
whereis = repo.whereis(glob(opj(repo_path, '1', '1*')))
# they all must be the same
assert (all([x == whereis[0] for x in whereis[1:]]))
# and we should be able to reference it while under subdirectory
subdir = opj(repo_path, 'subdir')
with chpwd(subdir, mkdir=True):
add_archive_content(opj(pardir, '1.tar.gz'), use_current_dir=True)
d1_basic_checks()
# or we could keep relative path and also demand to keep the archive prefix
# while extracting under original (annex root) dir
add_archive_content(opj(pardir, '1.tar.gz'),
add_archive_leading_dir=True)
with chpwd(opj(repo_path, '1')):
d1_basic_checks()
with chpwd(repo_path):
# test with excludes and renames and annex options
add_archive_content('1.tar.gz',
exclude=['d'],
rename=['/ /_', '/^1/2'],
annex_options="-c annex.largefiles=exclude=*.txt",
delete=True)
# no conflicts since new name
ok_file_under_git('2', '1_f.txt', annexed=False)
assert_false(exists(opj('2', 'd')))
assert_false(exists('1.tar.gz')) # delete was in effect
# now test ability to extract within subdir
with chpwd(opj(repo_path, 'd1'), mkdir=True):
# Let's add first archive to the repo so we could test
# named the same way but different content
with swallow_outputs():
repo.add_urls([opj(url, 'd1', '1.tar.gz')],
options=["--pathdepth", "-1"],
cwd=getpwd()) # invoke under current subdir
repo.commit("added 1.tar.gz in d1")
def d2_basic_checks():
ok_(exists('1'))
ok_file_under_git('1', '2 f.txt', annexed=True)
ok_file_under_git(opj('1', 'd2', '2d'), annexed=True)
ok_archives_caches(repo.path, 0)
add_archive_content('1.tar.gz')
d2_basic_checks()
# in manual tests ran into the situation of inability to obtain on a single run
# a file from an archive which was coming from a dropped key. I thought it was
# tested in custom remote tests, but I guess not sufficiently well enough
repo.drop(opj('1', '1 f.txt')) # should be all kosher
repo.get(opj('1', '1 f.txt'))
ok_archives_caches(repo.path, 1, persistent=True)
ok_archives_caches(repo.path, 0, persistent=False)
repo.drop(opj('1', '1 f.txt')) # should be all kosher
repo.drop(key_1tar,
key=True) # is available from the URL -- should be kosher
repo.get(opj('1', '1 f.txt')) # that what managed to not work
# TODO: check if persistent archive is there for the 1.tar.gz
# We should be able to drop everything since available online
with swallow_outputs():
clean(dataset=repo.path)
repo.drop(key_1tar,
key=True) # is available from the URL -- should be kosher
repo.drop(opj('1', '1 f.txt')) # should be all kosher
repo.get(opj('1', '1 f.txt')) # and should be able to get it again
# bug was that dropping didn't work since archive was dropped first
repo.call_annex(["drop", "--all"])
# verify that we can't drop a file if archive key was dropped and online archive was removed or changed size! ;)
repo.get(key_1tar, key=True)
unlink(opj(path_orig, '1.tar.gz'))
with assert_raises(CommandError) as e:
repo.drop(key_1tar, key=True)
assert_equal(e.kwargs['stdout_json'][0]['success'], False)
assert_result_values_cond(
e.kwargs['stdout_json'], 'note', lambda x:
'(Use --force to override this check, or adjust numcopies.)' in x)
assert exists(opj(repo.path, repo.get_contentlocation(key_1tar)))
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(
