def _drop_files(ds, paths, check, noannex_iserror=False, **kwargs):
"""Helper to drop content in datasets.
Parameters
----------
ds : Dataset
paths : path or list(path)
which content to drop
check : bool
whether to instruct annex to perform minimum copy availability
checks
noannex_iserror : bool
whether calling this function on a pure Git repo results in an
'impossible' or 'notneeded' result.
**kwargs
additional payload for the result dicts
"""
# expensive, access only once
ds_repo = ds.repo
if 'action' not in kwargs:
kwargs['action'] = 'drop'
# always need to make sure that we pass a list
# `normalize_paths` decorator will otherwise screw all logic below
paths = ensure_list(paths)
if not hasattr(ds_repo, 'drop'):
for p in paths:
r = get_status_dict(
status='impossible' if noannex_iserror else 'notneeded',
path=p if isabs(p) else normpath(opj(ds.path, p)),
message="no annex'ed content",
**kwargs)
r['action'] = 'drop'
yield r
return
cmd = ['drop']
if not check:
cmd.append('--force')
respath_by_status = {}
try:
yield from (_postproc_result(res, respath_by_status, ds)
for res in ds_repo._call_annex_records(cmd, files=paths))
except CommandError as e:
# pick up the results captured so far and yield them
# the error will be amongst them
yield from (_postproc_result(res, respath_by_status, ds)
for res in e.kwargs.get('stdout_json', []))
# report on things requested that annex was silent about
for r in results_from_annex_noinfo(
ds,
paths,
respath_by_status,
dir_fail_msg='could not drop some content in %s %s',
noinfo_dir_msg='nothing to drop from %s',
noinfo_file_msg="no annex'ed content",
**kwargs):
r['action'] = 'drop'
yield r
def _drop_files(ds, paths, check, noannex_iserror=False, **kwargs):
"""Helper to drop content in datasets.
Parameters
----------
ds : Dataset
paths : path or list(path)
which content to drop
check : bool
whether to instruct annex to perform minimum copy availability
checks
noannex_iserror : bool
whether calling this function on a pure Git repo results in an
'impossible' or 'notneeded' result.
**kwargs
additional payload for the result dicts
"""
if 'action' not in kwargs:
kwargs['action'] = 'drop'
# always need to make sure that we pass a list
# `normalize_paths` decorator will otherwise screw all logic below
paths = assure_list(paths)
if not hasattr(ds.repo, 'drop'):
for p in paths:
r = get_status_dict(
status='impossible' if noannex_iserror else 'notneeded',
path=p if isabs(p) else normpath(opj(ds.path, p)),
message="no annex'ed content",
**kwargs)
r['action'] = 'drop'
yield r
return
opts = ['--force'] if not check else []
respath_by_status = {}
for res in ds.repo.drop(paths, options=opts):
res = annexjson2result(
# annex reports are always about files
res,
ds,
type='file',
**kwargs)
success = success_status_map[res['status']]
respath_by_status[success] = \
respath_by_status.get(success, []) + [res['path']]
yield res
# report on things requested that annex was silent about
for r in results_from_annex_noinfo(
ds,
paths,
respath_by_status,
dir_fail_msg='could not drop some content in %s %s',
noinfo_dir_msg='nothing to drop from %s',
noinfo_file_msg="no annex'ed content",
**kwargs):
r['action'] = 'drop'
yield r
def _get_targetpaths(ds, content, refds_path, source, jobs):
# not ready for Path instances...
content = [str(c) for c in content]
# hand over to git-annex, get files content,
# report files in git as 'notneeded' to get
ds_repo = ds.repo
# needs to be an annex to get content
if not isinstance(ds_repo, AnnexRepo):
for r in results_from_paths(
content,
status='notneeded',
message="no dataset annex, content already present",
action='get',
type='file',
logger=lgr,
refds=refds_path):
yield r
return
respath_by_status = {}
try:
results = ds_repo.get(content,
options=['--from=%s' % source] if source else [],
jobs=jobs)
except CommandError as exc:
results = exc.kwargs.get("stdout_json")
if not results:
raise
for res in results:
res = annexjson2result(res,
ds,
type='file',
logger=lgr,
refds=refds_path)
success = success_status_map[res['status']]
# TODO: in case of some failed commands (e.g. get) there might
# be no path in the record. yoh has only vague idea of logic
# here so just checks for having 'path', but according to
# results_from_annex_noinfo, then it would be assumed that
# `content` was acquired successfully, which is not the case
if 'path' in res:
respath_by_status[success] = \
respath_by_status.get(success, []) + [res['path']]
yield res
for r in results_from_annex_noinfo(
ds,
content,
respath_by_status,
dir_fail_msg='could not get some content in %s %s',
noinfo_dir_msg='nothing to get from %s',
noinfo_file_msg='already present',
action='get',
logger=lgr,
refds=refds_path):
yield r
def _drop_files(ds, paths, check, noannex_iserror=False, **kwargs):
"""Helper to drop content in datasets.
Parameters
----------
ds : Dataset
paths : path or list(path)
which content to drop
check : bool
whether to instruct annex to perform minimum copy availability
checks
noannex_iserror : bool
whether calling this function on a pure Git repo results in an
'impossible' or 'notneeded' result.
**kwargs
additional payload for the result dicts
"""
if 'action' not in kwargs:
kwargs['action'] = 'drop'
# always need to make sure that we pass a list
# `normalize_paths` decorator will otherwise screw all logic below
paths = assure_list(paths)
if not hasattr(ds.repo, 'drop'):
for p in paths:
r = get_status_dict(
status='impossible' if noannex_iserror else 'notneeded',
path=p if isabs(p) else normpath(opj(ds.path, p)),
message="no annex'ed content",
**kwargs)
r['action'] = 'drop'
yield r
return
opts = ['--force'] if not check else []
respath_by_status = {}
for res in ds.repo.drop(paths, options=opts):
res = annexjson2result(
# annex reports are always about files
res, ds, type='file', **kwargs)
success = success_status_map[res['status']]
respath_by_status[success] = \
respath_by_status.get(success, []) + [res['path']]
yield res
# report on things requested that annex was silent about
for r in results_from_annex_noinfo(
ds, paths, respath_by_status,
dir_fail_msg='could not drop some content in %s %s',
noinfo_dir_msg='nothing to drop from %s',
noinfo_file_msg="no annex'ed content",
**kwargs):
r['action'] = 'drop'
yield r
def _drop_files(ds, repo, paths, force=False, jobs=None):
"""Helper to drop content in datasets.
Parameters
----------
repo : AnnexRepo
paths : list
for which files to drop content
check : bool
whether to instruct annex to perform minimum copy availability
checks
Yields
------
dict
"""
cmd = ['drop']
if force:
cmd.append('--force')
if jobs:
cmd.extend(['--jobs', str(jobs)])
respath_by_status = {}
try:
yield from (_postproc_annexdrop_result(
res, respath_by_status,
ds) for res in repo._call_annex_records_items_(cmd, files=paths))
except CommandError as e:
# pick up the results captured so far and yield them
# the error will be amongst them
yield from (_postproc_annexdrop_result(res, respath_by_status, ds)
for res in e.kwargs.get('stdout_json', []))
# report on things requested that annex was silent about
for r in results_from_annex_noinfo(
ds,
paths,
respath_by_status,
dir_fail_msg='could not drop some content in %s %s',
noinfo_dir_msg='nothing to drop from %s',
noinfo_file_msg="no annex'ed content"):
r['action'] = 'drop'
yield r
def __call__(
path=None,
dataset=None,
# support passing this through in a path by path basis
to_git=None,
save=True,
message=None,
message_file=None,
recursive=False,
recursion_limit=None,
ds2super=False,
git_opts=None,
annex_opts=None,
annex_add_opts=None,
jobs=None):
# parameter constraints:
if not path:
raise InsufficientArgumentsError(
"insufficient information for adding: requires at least a path")
refds_path = Interface.get_refds_path(dataset)
common_report = dict(action='add', logger=lgr, refds=refds_path)
if message and message_file:
raise ValueError("Both a message and message file were specified")
if message_file:
with open(message_file, "rb") as mfh:
message = assure_unicode(mfh.read())
to_add = []
subds_to_add = {}
ds_to_annotate_from_recursion = {}
got_nothing = True
for ap in AnnotatePaths.__call__(
path=path,
dataset=dataset,
# never recursion, need to handle manually below to be able to
# discover untracked content
recursive=False,
action='add',
# speed things up by using Git's modification detection, if there
# is a repo with at least one commit
modified='HEAD' \
if dataset and \
GitRepo.is_valid_repo(refds_path) and \
GitRepo(refds_path).get_hexsha() \
else None,
unavailable_path_status='impossible',
unavailable_path_msg="path does not exist: %s",
nondataset_path_status='impossible',
return_type='generator',
on_failure='ignore'):
got_nothing = False
if ap.get('status', None):
# this is done
yield ap
continue
if ap.get('parentds', None) is None and ap.get('type', None) != 'dataset':
yield get_status_dict(
status='impossible',
message='"there is no dataset to add this path to',
**dict(common_report, **ap))
continue
if ap.get('type', None) == 'directory' and \
ap.get('state', None) == 'untracked' and \
GitRepo.is_valid_repo(ap['path']):
# this is an untracked wannabe subdataset in disguise
ap['type'] = 'dataset'
if recursive and \
(ap.get('raw_input', False) or
ap.get('state', None) in ('added', 'modified', 'untracked')) and \
(ap.get('parentds', None) or ap.get('type', None) == 'dataset'):
# this was an actually requested input path, or a path that was found
# modified by path annotation, based on an input argument
# we need to recurse into all subdirs to find potentially
# unregistered subdatasets
# but only if this path has a parent, or is itself a dataset
# otherwise there is nothing to add to
_discover_subdatasets_recursively(
ds_to_annotate_from_recursion,
ap['path'], [ap['parentds'] if 'parentds' in ap else ap['path']],
recursion_limit)
# get the file content of the root dataset of this search added too
# but be careful with extreme recursion_limit settings
if recursion_limit is None or recursion_limit > 0:
ap['process_content'] = True
# record for further processing
if not ap['path'] in ds_to_annotate_from_recursion:
# if it was somehow already discovered
to_add.append(ap)
if got_nothing:
# path annotation yielded nothing, most likely cause is that nothing
# was found modified, we need to say something about the reference
# dataset
yield get_status_dict(
'add',
status='notneeded',
path=refds_path,
type='dataset',
logger=lgr)
return
for subds in ds_to_annotate_from_recursion:
if subds not in subds_to_add:
# always prefer the already annotated path
subds_to_add[subds] = ds_to_annotate_from_recursion[subds]
if dataset:
# we have a base dataset, discover any intermediate datasets between
# the base and any already discovered dataset
discovered = {}
discover_dataset_trace_to_targets(
# from here
dataset.path,
# to any dataset we are aware of
subds_to_add.keys(),
[],
discovered)
for parentds in discovered:
for subds in discovered[parentds]:
subds_to_add[subds] = subds_to_add.get(
subds,
dict(path=subds, parentds=parentds, type='dataset'))
# merge custom paths and discovered dataset records, paths needs to go first,
# because we know most about then, and subsequent annotation call we skip the
# later duplicate ones
to_add.extend(subds_to_add.values())
# and compact, this should be OK as all the info is in each ap dict
to_add = unique(to_add, lambda x: x['path'])
if not to_add:
# nothing left to do, potentially all errored before
return
# now re-annotate all paths, this will be fast for already annotated ones
# and will amend the annotation for others, it will also deduplicate
annotated_paths = AnnotatePaths.__call__(
path=to_add,
dataset=dataset,
# never recursion, done already
recursive=False,
action='add',
unavailable_path_status='impossible',
unavailable_path_msg="path does not exist: %s",
nondataset_path_status='impossible',
return_type='generator',
# if there is an error now, we made this mistake in here
on_failure='stop')
content_by_ds, ds_props, completed, nondataset_paths = \
annotated2content_by_ds(
annotated_paths,
refds_path=refds_path)
assert(not completed)
if not content_by_ds:
# we should have complained about any inappropriate path argument
# above, so if nothing is left, we can simply exit
return
# simple loop over datasets -- save happens later
# start deep down
to_save = []
for ds_path in sorted(content_by_ds, reverse=True):
ds = Dataset(ds_path)
torepoadd = {}
respath_by_status = {}
for ap in content_by_ds[ds_path]:
# we have a new story
ap.pop('status', None)
torepoadd[ap['path']] = ap
# skip anything that doesn't look like a wannabe subdataset
if not ap.get('type', None) == 'dataset' or \
ap['path'] == ds_path:
continue
if ap.get('registered_subds', False):
# subdataset that might be in this list because of the
# need to save all the way up to a super dataset
respath_by_status['success'] = \
respath_by_status.get('success', []) + [ap['path']]
yield get_status_dict(
status='notneeded',
message="already known subdataset",
**dict(common_report, **ap))
continue
subds = Dataset(ap['path'])
subds_relpath = relpath(ap['path'], ds_path)
# Register the repository in the repo tree as a submodule
try:
ds.repo.add_submodule(subds_relpath, url=None, name=None)
except (CommandError, InvalidGitRepositoryError) as e:
yield get_status_dict(
ds=subds, status='error', message=e.stderr,
**dict(common_report, **ap))
continue
# queue for saving using the updated annotated path
ap['registered_subds'] = True
# I hope this is true in direct mode too
# TODO this is disabled, because in some circumstances
# staging just doesn't happen, and it is unclear when
# exactly -- the case that prompted disabling was a submodule
# that had no content except for other submodules was not staged,
# whereas another submodule on the same level in the same
# superdataset which also has one file in it was staged
# disable to work correctly, while paying a little bit of
# slow down
#ap['staged'] = True
to_save.append(ap)
# report added subdatasets -- `annex add` below won't do it
yield get_status_dict(
ds=subds,
status='ok',
message='added new subdataset',
**dict(common_report, **ap))
# make sure that .gitmodules is added to the list of files
gitmodules_path = opj(ds.path, '.gitmodules')
# for git
torepoadd[gitmodules_path] = dict(path=gitmodules_path)
# and for save
to_save.append(dict(
path=gitmodules_path,
parentds=ds_path,
type='file'))
# make sure any last minute additions make it to the saving stage
# XXX? should content_by_ds become OrderedDict so that possible
# super here gets processed last?
lgr.debug('Adding content to repo %s: %s', ds.repo, torepoadd)
is_annex = isinstance(ds.repo, AnnexRepo)
add_kw = {'jobs': jobs} if is_annex and jobs else {}
added = ds.repo.add_(
list(torepoadd.keys()),
git=to_git if is_annex else True,
**add_kw
)
for a in added:
res = annexjson2result(a, ds, type='file', **common_report)
success = success_status_map[res['status']]
respath_by_status[success] = \
respath_by_status.get(success, []) + [res['path']]
# produce best possible path/result annotation
if res['path'] in torepoadd:
# pull out correct ap for any path that comes out here
# (that we know things about), and use the original annotation
# instead of just the annex report
res = dict(torepoadd[res['path']], **res)
# override this in all cases to be safe
res['parentds'] = ds.path
if success:
# this was successfully added, queue for saving this very path
# in the dataset
ap = {k: v for k, v in res.items() if k != 'status'}
ap['staged'] = True
# strip any status and state info (e.g. save will refuse to save
# stuff that is marked state='untracked'
to_save.append({k: v for k, v in res.items()
if k not in ('status', 'state')})
if a['file'] == '.gitmodules':
# filter out .gitmodules, because this is only included for
# technical reasons and has nothing to do with the actual content
continue
if GitRepo.is_valid_repo(res['path']):
# more accurate report in case of an added submodule
# mountpoint.
# XXX Actually not sure if this can really happen
# (depends on what our low-level code would do)
# but worst case is that we loose a little bit of
# coverage...
res['type'] = 'dataset'
res['message'] = 'added new state as submodule'
yield res
for r in results_from_annex_noinfo(
ds, torepoadd, respath_by_status,
dir_fail_msg='could not add some content in %s %s',
noinfo_dir_msg='nothing to add from %s',
noinfo_file_msg='already included in the dataset',
action='add',
logger=lgr,
refds=refds_path):
if r['path'] in torepoadd:
# pull out correct ap for any path that comes out here
# (that we know things about), and use the original annotation
# instead of just the annex report
r = dict(r, **torepoadd[r['path']])
if r['status'] == 'notneeded':
# this could be a file that was staged already, it doesn't need
# to be added, but it should be saved/commited if so desired
to_save.append({k: v for k, v in r.items()
if k not in ('status', 'state')})
# XXX something is fishy with the next one, rethink when sober....
if r['path'] == ds_path and r['status'] == 'ok':
# this is for the entire dataset itself which was explicitly requested
# make sure to save all
r['type'] = 'dataset'
r['process_content'] = True
to_save.append({k: v for k, v in r.items() if k != 'status'})
yield r
if refds_path and ds_path != refds_path and len(respath_by_status.get('success', [])):
# TODO XXX we have an issue here when with `add('.')` and annex ignores any
# dotfiles. In this case we end up not saving a dataset completely, because
# we rely on accurate reporting. there is an issue about this already
# TODO look up the issue ID
# if there is a base dataset, but we are below it, and we have anything done to this
# dataset -> queue dataset itself for saving its state in the parent
ds_ap = dict(
path=ds.path,
# we have to look for the parent here, as we must save the
# subdataset in the parent and not the whole subdataset itself
type='dataset')
parentds = get_dataset_root(normpath(opj(ds.path, pardir)))
if parentds:
ds_ap['parentds'] = parentds
if dataset:
ds_ap['refds'] = refds_path
to_save.append(ds_ap)
if not save:
lgr.debug('Not calling `save` as instructed')
return
# TODO tell save what was staged already! Set 'staged=True' for
# respective annotated paths that are fed into `save`
# do not reuse any of the sorting done in here for saving, but instead
# pass on all the annotated paths to have `save` figure out what to do with
# them -- this is costs something, but should be safer, and frankly is
# more comprehensible
for res in Save.__call__(
# hand-selected annotated paths
path=to_save,
dataset=refds_path,
message=message if message else '[DATALAD] added content',
return_type='generator',
result_xfm=None,
result_filter=None,
on_failure='ignore'):
yield res
def __call__(
path=None,
dataset=None,
# support passing this through in a path by path basis
to_git=None,
save=True,
message=None,
recursive=False,
recursion_limit=None,
ds2super=False,
git_opts=None,
annex_opts=None,
annex_add_opts=None,
jobs=None):
# parameter constraints:
if not path:
raise InsufficientArgumentsError(
"insufficient information for adding: requires at least a path"
)
refds_path = Interface.get_refds_path(dataset)
common_report = dict(action='add', logger=lgr, refds=refds_path)
to_add = []
subds_to_add = {}
ds_to_annotate_from_recursion = {}
got_nothing = True
for ap in AnnotatePaths.__call__(
path=path,
dataset=dataset,
# never recursion, need to handle manually below to be able to
# discover untracked content
recursive=False,
action='add',
# speed things up by using Git's modification detection, if there
# is a repo with at least one commit
modified='HEAD' \
if dataset and \
GitRepo.is_valid_repo(refds_path) and \
GitRepo(refds_path).get_hexsha() \
else None,
unavailable_path_status='impossible',
unavailable_path_msg="path does not exist: %s",
nondataset_path_status='impossible',
return_type='generator',
on_failure='ignore'):
got_nothing = False
if ap.get('status', None):
# this is done
yield ap
continue
if ap.get('parentds', None) is None and ap.get('type',
None) != 'dataset':
yield get_status_dict(
status='impossible',
message='"there is no dataset to add this path to',
**dict(common_report, **ap))
continue
if ap.get('type', None) == 'directory' and \
ap.get('state', None) == 'untracked' and \
GitRepo.is_valid_repo(ap['path']):
# this is an untracked wannabe subdataset in disguise
ap['type'] = 'dataset'
if recursive and \
(ap.get('raw_input', False) or
ap.get('state', None) in ('added', 'modified', 'untracked')) and \
(ap.get('parentds', None) or ap.get('type', None) == 'dataset'):
# this was an actually requested input path, or a path that was found
# modified by path annotation, based on an input argument
# we need to recurse into all subdirs to find potentially
# unregistered subdatasets
# but only if this path has a parent, or is itself a dataset
# otherwise there is nothing to add to
_discover_subdatasets_recursively(
ds_to_annotate_from_recursion, ap['path'],
[ap['parentds'] if 'parentds' in ap else ap['path']],
recursion_limit)
# get the file content of the root dataset of this search added too
# but be careful with extreme recursion_limit settings
if recursion_limit is None or recursion_limit > 0:
ap['process_content'] = True
# record for further processing
if not ap['path'] in ds_to_annotate_from_recursion:
# if it was somehow already discovered
to_add.append(ap)
# TODO check if next isn't covered by discover_dataset_trace_to_targets already??
if dataset and ap.get('type', None) == 'dataset':
# duplicates not possible, annotated_paths returns unique paths
subds_to_add[ap['path']] = ap
if got_nothing:
# path annotation yielded nothing, most likely cause is that nothing
# was found modified, we need to say something about the reference
# dataset
yield get_status_dict('add',
status='notneeded',
path=refds_path,
type='dataset',
logger=lgr)
return
for subds in ds_to_annotate_from_recursion:
if subds not in subds_to_add:
# always prefer the already annotated path
subds_to_add[subds] = ds_to_annotate_from_recursion[subds]
if dataset:
# we have a base dataset, discover any intermediate datasets between
# the base and any already discovered dataset
discovered = {}
discover_dataset_trace_to_targets(
# from here
dataset.path,
# to any dataset we are aware of
subds_to_add.keys(),
[],
discovered)
for parentds in discovered:
for subds in discovered[parentds]:
subds_to_add[subds] = subds_to_add.get(
subds,
dict(path=subds, parentds=parentds, type='dataset'))
# merge custom paths and discovered dataset records, paths needs to go first,
# because we know most about then, and subsequent annotation call we skip the
# later duplicate ones
to_add.extend(subds_to_add.values())
# and compact, this should be OK as all the info is in each ap dict
to_add = unique(to_add, lambda x: x['path'])
if not to_add:
# nothing left to do, potentially all errored before
return
# now re-annotate all paths, this will be fast for already annotated ones
# and will amend the annotation for others, it will also deduplicate
annotated_paths = AnnotatePaths.__call__(
path=to_add,
dataset=dataset,
# never recursion, done already
recursive=False,
action='add',
unavailable_path_status='impossible',
unavailable_path_msg="path does not exist: %s",
nondataset_path_status='impossible',
return_type='generator',
# if there is an error now, we made this mistake in here
on_failure='stop')
content_by_ds, ds_props, completed, nondataset_paths = \
annotated2content_by_ds(
annotated_paths,
refds_path=refds_path)
assert (not completed)
if not content_by_ds:
# we should have complained about any inappropriate path argument
# above, so if nothing is left, we can simply exit
return
# simple loop over datasets -- save happens later
# start deep down
to_save = []
for ds_path in sorted(content_by_ds, reverse=True):
ds = Dataset(ds_path)
torepoadd = {}
respath_by_status = {}
for ap in content_by_ds[ds_path]:
# we have a new story
ap.pop('status', None)
torepoadd[ap['path']] = ap
# skip anything that doesn't look like a wannabe subdataset
if not ap.get('type', None) == 'dataset' or \
ap['path'] == ds_path:
continue
if ap.get('registered_subds', False):
# subdataset that might be in this list because of the
# need to save all the way up to a super dataset
respath_by_status['success'] = \
respath_by_status.get('success', []) + [ap['path']]
yield get_status_dict(status='notneeded',
message="already known subdataset",
**dict(common_report, **ap))
continue
subds = Dataset(ap['path'])
# check that the subds has a commit, and refuse
# to operate on it otherwise, or we would get a bastard
# submodule that cripples git operations
if not subds.repo.get_hexsha():
yield get_status_dict(
ds=subds,
status='impossible',
message='cannot add subdataset with no commits',
**dict(common_report, **ap))
continue
subds_relpath = relpath(ap['path'], ds_path)
# make an attempt to configure a submodule source URL based on the
# discovered remote configuration
remote, branch = subds.repo.get_tracking_branch()
subds_url = subds.repo.get_remote_url(
remote) if remote else None
# Register the repository in the repo tree as a submodule
try:
ds.repo.add_submodule(subds_relpath,
url=subds_url,
name=None)
except CommandError as e:
yield get_status_dict(ds=subds,
status='error',
message=e.stderr,
**dict(common_report, **ap))
continue
# queue for saving using the updated annotated path
ap['registered_subds'] = True
# I hope this is true in direct mode too
# TODO this is disabled, because in some circumstances
# staging just doesn't happen, and it is unclear when
# exactly -- the case that prompted disabling was a submodule
# that had no content except for other submodules was not staged,
# whereas another submodule on the same level in the same
# superdataset which also has one file in it was staged
# disable to work correctly, while paying a little bit of
# slow down
#ap['staged'] = True
to_save.append(ap)
_fixup_submodule_dotgit_setup(ds, subds_relpath)
# report added subdatasets -- `annex add` below won't do it
yield get_status_dict(ds=subds,
status='ok',
message='added new subdataset',
**dict(common_report, **ap))
# make sure that .gitmodules is added to the list of files
gitmodules_path = opj(ds.path, '.gitmodules')
# for git
torepoadd[gitmodules_path] = dict(path=gitmodules_path)
# and for save
to_save.append(
dict(path=gitmodules_path, parentds=ds_path, type='file'))
# make sure any last minute additions make it to the saving stage
# XXX? should content_by_ds become OrderedDict so that possible
# super here gets processed last?
lgr.debug('Adding content to repo %s: %s', ds.repo, torepoadd)
is_annex = isinstance(ds.repo, AnnexRepo)
add_kw = {'jobs': jobs} if is_annex and jobs else {}
added = ds.repo.add(list(torepoadd.keys()),
git=to_git if is_annex else True,
**add_kw)
for a in added:
res = annexjson2result(a, ds, type='file', **common_report)
success = success_status_map[res['status']]
respath_by_status[success] = \
respath_by_status.get(success, []) + [res['path']]
# produce best possible path/result annotation
if res['path'] in torepoadd:
# pull out correct ap for any path that comes out here
# (that we know things about), and use the original annotation
# instead of just the annex report
res = dict(torepoadd[res['path']], **res)
# override this in all cases to be safe
res['parentds'] = ds.path
if success:
# this was successfully added, queue for saving this very path
# in the dataset
ap = {k: v for k, v in res.items() if k != 'status'}
ap['staged'] = True
# strip any status and state info (e.g. save will refuse to save
# stuff that is marked state='untracked'
to_save.append({
k: v
for k, v in res.items() if k not in ('status', 'state')
})
if a['file'] == '.gitmodules':
# filter out .gitmodules, because this is only included for
# technical reasons and has nothing to do with the actual content
continue
if GitRepo.is_valid_repo(res['path']):
# more accurate report in case of an added submodule
# mountpoint.
# XXX Actually not sure if this can really happen
# (depends on what our low-level code would do)
# but worst case is that we loose a little bit of
# coverage...
res['type'] = 'dataset'
res['message'] = 'added new state as submodule'
yield res
for r in results_from_annex_noinfo(
ds,
torepoadd,
respath_by_status,
dir_fail_msg='could not add some content in %s %s',
noinfo_dir_msg='nothing to add from %s',
noinfo_file_msg='already included in the dataset',
action='add',
logger=lgr,
refds=refds_path):
if r['path'] in torepoadd:
# pull out correct ap for any path that comes out here
# (that we know things about), and use the original annotation
# instead of just the annex report
r = dict(r, **torepoadd[r['path']])
if r['status'] == 'notneeded':
# this could be a file that was staged already, it doesn't need
# to be added, but it should be saved/commited if so desired
to_save.append({
k: v
for k, v in r.items() if k not in ('status', 'state')
})
# XXX something is fishy with the next one, rethink when sober....
if r['path'] == ds_path and r['status'] == 'ok':
# this is for the entire dataset itself which was explicitly requested
# make sure to save all
r['type'] = 'dataset'
r['process_content'] = True
to_save.append(
{k: v
for k, v in r.items() if k != 'status'})
yield r
if refds_path and ds_path != refds_path and len(
respath_by_status.get('success', [])):
# TODO XXX we have an issue here when with `add('.')` and annex ignores any
# dotfiles. In this case we end up not saving a dataset completely, because
# we rely on accurate reporting. there is an issue about this already
# TODO look up the issue ID
# if there is a base dataset, but we are below it, and we have anything done to this
# dataset -> queue dataset itself for saving its state in the parent
ds_ap = dict(
path=ds.path,
# we have to look for the parent here, as we must save the
# subdataset in the parent and not the whole subdataset itself
type='dataset')
parentds = get_dataset_root(normpath(opj(ds.path, pardir)))
if parentds:
ds_ap['parentds'] = parentds
if dataset:
ds_ap['refds'] = refds_path
to_save.append(ds_ap)
if not save:
lgr.debug('Not calling `save` as instructed')
return
# TODO tell save what was staged already! Set 'staged=True' for
# respective annotated paths that are fed into `save`
# do not reuse any of the sorting done in here for saving, but instead
# pass on all the annotated paths to have `save` figure out what to do with
# them -- this is costs something, but should be safer, and frankly is
# more comprehensible
for res in Save.__call__(
# hand-selected annotated paths
path=to_save,
dataset=refds_path,
message=message if message else '[DATALAD] added content',
return_type='generator',
result_xfm=None,
result_filter=None,
on_failure='ignore'):
yield res
def __call__(
path=None,
source=None,
dataset=None,
recursive=False,
recursion_limit=None,
get_data=True,
description=None,
reckless=False,
#git_opts=None,
#annex_opts=None,
#annex_get_opts=None,
jobs='auto',
verbose=False,
):
# IMPLEMENTATION CONCEPT:
#
# 1. Sort the world into existing handles and the rest
# 2. Try locate missing handles (obtain subdatasets along the way)
# 3. Expand into subdatasets with recursion enables (potentially
# obtain even more subdatasets
# 4. Shoot info of which handles to get in each subdataset to,
# git-annex, once at the very end
refds_path = Interface.get_refds_path(dataset)
if not (dataset or path):
raise InsufficientArgumentsError(
"Neither dataset nor target path(s) provided")
if dataset and not path:
# act on the whole dataset if nothing else was specified
path = refds_path
# remember which results we already reported, to avoid duplicates
yielded_ds = []
to_get = []
unavailable_paths = []
for ap in AnnotatePaths.__call__(
path=path,
dataset=refds_path,
recursive=recursive,
recursion_limit=recursion_limit,
action='get',
# NOTE: Do not act upon unavailable paths yet! Done below after
# testing which ones could be obtained
unavailable_path_status='',
nondataset_path_status='impossible',
return_type='generator',
on_failure='ignore'):
if ap.get('status', None):
# we know what to report already
yield ap
continue
if ap.get('state', None) == 'absent' and ap.get(
'raw_input', False):
# if this wasn't found, but directly requested, queue for further
# exploration
unavailable_paths.append(ap)
continue
if ap.get('type', None) == 'dataset' and \
GitRepo.is_valid_repo(ap['path']) and \
not ap['path'] == refds_path:
# do not report what hasn't arived yet
# also do not report the base dataset that is already
# present -- no surprise
yield dict(ap,
status='notneeded',
logger=lgr,
message='already installed')
yielded_ds.append(ap['path'])
ap['process_content'] = get_data
to_get.append(ap)
# explore the unknown
for ap in sorted(unavailable_paths, key=lambda x: x['path']):
lgr.debug("Investigate yet unavailable path %s", ap)
# how close can we get?
dspath = ap.get('parentds', get_dataset_root(ap['path']))
if dspath is None:
# nothing we can do for this path
continue
lgr.debug("Found containing dataset %s for path %s", dspath,
ap['path'])
ds = Dataset(dspath)
# now actually obtain whatever is necessary to get to this path
containing_ds = [dspath]
for res in _install_necessary_subdatasets(ds,
ap['path'],
reckless,
refds_path,
description=description):
# yield immediately so errors could be acted upon outside, before
# we continue
if not (res['type'] == 'dataset'
and res['path'] in yielded_ds):
# unless we reported on this dataset before
if res['type'] == 'dataset':
# make a record, recursive below might now want to report
# a 'notneeded'
yielded_ds.append(res['path'])
yield res
# update to the current innermost dataset
containing_ds.append(res['path'])
if len(containing_ds) < 2:
# no subdataset was installed, hence if the path was unavailable
# before it still is, no need to bother git annex
ap.update(status='impossible', message='path does not exist')
yield ap
continue
# important to only do the next for the innermost subdataset
# as the `recursive` logic below relies on that!
# set the correct parent, for a dataset this would be the second-last
# reported subdataset
ap.update(parentds=containing_ds[-1])
if containing_ds[-1] == ap['path']:
# the path actually refers to the last installed dataset
ap.update(parentds=containing_ds[-2],
process_content=get_data,
type='dataset')
to_get.append(ap)
# results of recursive installation of yet undiscovered datasets
rec_get = []
if recursive and not recursion_limit == 'existing':
# obtain any subdatasets underneath the paths given inside the
# subdatasets that we know already exist
# unless we do not want recursion into not-yet-installed datasets
for ap in sorted(to_get, key=lambda x: x['path']):
if ap['type'] not in ('dataset', 'directory') or not ap.get(
'raw_input', False):
# a non-directory cannot have content underneath
# also we do NOT want to recurse into anything that was specifically
# requested, to avoid duplication
continue
subds = Dataset(ap['path'] if ap['type'] ==
'dataset' else ap['parentds'])
lgr.info("Installing %s%s recursively", subds,
(" underneath %s" %
ap['path'] if subds.path != ap['path'] else ""))
for res in _recursive_install_subds_underneath(
subds,
# `ap['path']` was explicitly given as input
# we count recursions from the input, hence we
# can start with the full number
recursion_limit,
reckless,
start=ap['path'],
refds_path=refds_path,
description=description):
# yield immediately so errors could be acted upon
# outside, before we continue
if not (res['type'] == 'dataset'
and res['path'] in yielded_ds):
# unless we reported on this dataset before
if res['type'] == 'dataset':
# make a record
yielded_ds.append(res['path'])
yield res
if not (res['status'] == 'ok'
and res['type'] == 'dataset'):
# not a dataset that was just installed, we just reported it
# upstairs, and can ignore it from now on
continue
# paranoia, so popular these days...
assert GitRepo.is_valid_repo(res['path'])
# keep a copy of the install record for `get` later on
get_ap = {
k: v
for k, v in res.items() if not k == 'status'
}
get_ap['process_content'] = get_data
rec_get.append(get_ap)
if not get_data:
# done already
return
# merge the two AP lists
to_get.extend(rec_get)
# sort into datasets
content_by_ds, ds_props, completed, nondataset_paths = \
annotated2content_by_ds(
to_get,
refds_path=refds_path)
assert (not completed)
# hand over to git-annex, get files content,
# report files in git as 'notneeded' to get
for ds_path in sorted(content_by_ds.keys()):
ds = Dataset(ds_path)
# grab content, ignore subdataset entries
content = [
ap['path'] for ap in content_by_ds[ds_path]
if ap.get('type', None) != 'dataset' or ap['path'] == ds.path
]
if not content:
# cut this short should there be nothing
continue
# needs to be an annex to get content
if not isinstance(ds.repo, AnnexRepo):
for r in results_from_paths(
content,
status='notneeded',
message="no dataset annex, content already present",
action='get',
logger=lgr,
refds=refds_path):
yield r
continue
respath_by_status = {}
for res in ds.repo.get(content,
options=['--from=%s' %
source] if source else [],
jobs=jobs):
res = annexjson2result(res,
ds,
type='file',
logger=lgr,
refds=refds_path)
success = success_status_map[res['status']]
# TODO: in case of some failed commands (e.g. get) there might
# be no path in the record. yoh has only vague idea of logic
# here so just checks for having 'path', but according to
# results_from_annex_noinfo, then it would be assumed that
# `content` was acquired successfully, which is not the case
if 'path' in res:
respath_by_status[success] = \
respath_by_status.get(success, []) + [res['path']]
yield res
for r in results_from_annex_noinfo(
ds,
content,
respath_by_status,
dir_fail_msg='could not get some content in %s %s',
noinfo_dir_msg='nothing to get from %s',
noinfo_file_msg='already present',
action='get',
logger=lgr,
refds=refds_path):
yield r
def __call__(
path=None,
source=None,
dataset=None,
recursive=False,
recursion_limit=None,
get_data=True,
description=None,
reckless=False,
#git_opts=None,
#annex_opts=None,
#annex_get_opts=None,
jobs='auto',
verbose=False,
):
# IMPLEMENTATION CONCEPT:
#
# 1. Sort the world into existing handles and the rest
# 2. Try locate missing handles (obtain subdatasets along the way)
# 3. Expand into subdatasets with recursion enables (potentially
# obtain even more subdatasets
# 4. Shoot info of which handles to get in each subdataset to,
# git-annex, once at the very end
refds_path = Interface.get_refds_path(dataset)
if not (dataset or path):
raise InsufficientArgumentsError(
"Neither dataset nor target path(s) provided")
if dataset and not path:
# act on the whole dataset if nothing else was specified
path = refds_path
# remember which results we already reported, to avoid duplicates
yielded_ds = []
to_get = []
unavailable_paths = []
for ap in AnnotatePaths.__call__(
path=path,
dataset=refds_path,
recursive=recursive,
recursion_limit=recursion_limit,
action='get',
# NOTE: Do not act upon unavailable paths yet! Done below after
# testing which ones could be obtained
unavailable_path_status='',
nondataset_path_status='impossible',
return_type='generator',
on_failure='ignore'):
if ap.get('status', None):
# we know what to report already
yield ap
continue
if ap.get('state', None) == 'absent' and ap.get('raw_input', False):
# if this wasn't found, but directly requested, queue for further
# exploration
unavailable_paths.append(ap)
continue
if ap.get('type', None) == 'dataset' and \
GitRepo.is_valid_repo(ap['path']) and \
not ap['path'] == refds_path:
# do not report what hasn't arived yet
# also do not report the base dataset that is already
# present -- no surprise
yield dict(ap, status='notneeded', logger=lgr,
message='already installed')
yielded_ds.append(ap['path'])
ap['process_content'] = get_data
to_get.append(ap)
# explore the unknown
for ap in sorted(unavailable_paths, key=lambda x: x['path']):
lgr.debug("Investigate yet unavailable path %s", ap)
# how close can we get?
dspath = ap.get('parentds', get_dataset_root(ap['path']))
if dspath is None:
# nothing we can do for this path
continue
lgr.debug("Found containing dataset %s for path %s", dspath, ap['path'])
ds = Dataset(dspath)
# now actually obtain whatever is necessary to get to this path
containing_ds = [dspath]
for res in _install_necessary_subdatasets(
ds, ap['path'], reckless, refds_path, description=description):
# yield immediately so errors could be acted upon outside, before
# we continue
if not (res['type'] == 'dataset' and res['path'] in yielded_ds):
# unless we reported on this dataset before
if res['type'] == 'dataset':
# make a record, recursive below might now want to report
# a 'notneeded'
yielded_ds.append(res['path'])
yield res
# update to the current innermost dataset
containing_ds.append(res['path'])
if len(containing_ds) < 2:
# no subdataset was installed, hence if the path was unavailable
# before it still is, no need to bother git annex
ap.update(status='impossible',
message='path does not exist')
yield ap
continue
# important to only do the next for the innermost subdataset
# as the `recursive` logic below relies on that!
# set the correct parent, for a dataset this would be the second-last
# reported subdataset
ap.update(parentds=containing_ds[-1])
if containing_ds[-1] == ap['path']:
# the path actually refers to the last installed dataset
ap.update(parentds=containing_ds[-2],
process_content=get_data,
type='dataset')
to_get.append(ap)
# results of recursive installation of yet undiscovered datasets
rec_get = []
if recursive and not recursion_limit == 'existing':
# obtain any subdatasets underneath the paths given inside the
# subdatasets that we know already exist
# unless we do not want recursion into not-yet-installed datasets
for ap in sorted(to_get, key=lambda x: x['path']):
if ap['type'] not in ('dataset', 'directory') or not ap.get('raw_input', False):
# a non-directory cannot have content underneath
# also we do NOT want to recurse into anything that was specifically
# requested, to avoid duplication
continue
subds = Dataset(ap['path'] if ap['type'] == 'dataset' else ap['parentds'])
lgr.info(
"Installing %s%s recursively",
subds,
(" underneath %s" % ap['path']
if subds.path != ap['path']
else ""))
for res in _recursive_install_subds_underneath(
subds,
# `ap['path']` was explicitly given as input
# we count recursions from the input, hence we
# can start with the full number
recursion_limit,
reckless,
start=ap['path'],
refds_path=refds_path,
description=description):
# yield immediately so errors could be acted upon
# outside, before we continue
if not (res['type'] == 'dataset' and res['path'] in yielded_ds):
# unless we reported on this dataset before
if res['type'] == 'dataset':
# make a record
yielded_ds.append(res['path'])
yield res
if not (res['status'] == 'ok' and res['type'] == 'dataset'):
# not a dataset that was just installed, we just reported it
# upstairs, and can ignore it from now on
continue
# paranoia, so popular these days...
assert GitRepo.is_valid_repo(res['path'])
# keep a copy of the install record for `get` later on
get_ap = {k: v for k, v in res.items()
if not k == 'status'}
get_ap['process_content'] = get_data
rec_get.append(get_ap)
if not get_data:
# done already
return
# merge the two AP lists
to_get.extend(rec_get)
# sort into datasets
content_by_ds, ds_props, completed, nondataset_paths = \
annotated2content_by_ds(
to_get,
refds_path=refds_path)
assert(not completed)
# hand over to git-annex, get files content,
# report files in git as 'notneeded' to get
for ds_path in sorted(content_by_ds.keys()):
ds = Dataset(ds_path)
# grab content, ignore subdataset entries
content = [ap['path'] for ap in content_by_ds[ds_path]
if ap.get('type', None) != 'dataset' or ap['path'] == ds.path]
if not content:
# cut this short should there be nothing
continue
# needs to be an annex to get content
if not isinstance(ds.repo, AnnexRepo):
for r in results_from_paths(
content, status='notneeded',
message="no dataset annex, content already present",
action='get', logger=lgr,
refds=refds_path):
yield r
continue
respath_by_status = {}
for res in ds.repo.get(
content,
options=['--from=%s' % source] if source else [],
jobs=jobs):
res = annexjson2result(res, ds, type='file', logger=lgr,
refds=refds_path)
success = success_status_map[res['status']]
# TODO: in case of some failed commands (e.g. get) there might
# be no path in the record. yoh has only vague idea of logic
# here so just checks for having 'path', but according to
# results_from_annex_noinfo, then it would be assumed that
# `content` was acquired successfully, which is not the case
if 'path' in res:
respath_by_status[success] = \
respath_by_status.get(success, []) + [res['path']]
yield res
for r in results_from_annex_noinfo(
ds,
content,
respath_by_status,
dir_fail_msg='could not get some content in %s %s',
noinfo_dir_msg='nothing to get from %s',
noinfo_file_msg='already present',
action='get',
logger=lgr,
refds=refds_path):
yield r
