def __init__(self,
repos_dict=None,
repos_par=None,
with_caching=True,
repo_nexml2json=None,
git_ssh=None,
pkey=None,
git_action_class=PhylesystemGitAction,
mirror_info=None,
new_study_prefix=None,
infrastructure_commit_author='OpenTree API <*****@*****.**>',
**kwargs):
"""
Repos can be found by passing in a `repos_par` (a directory that is the parent of the repos)
or by trusting the `repos_dict` mapping of name to repo filepath.
`with_caching` should be True for non-debugging uses.
`repo_nexml2json` is optional. If specified all PhylesystemShard repos are assumed to store
files of this version of nexson syntax.
`git_ssh` is the path of an executable for git-ssh operations.
`pkey` is the PKEY that has to be in the env for remote, authenticated operations to work
`git_action_class` is a subclass of GitActionBase to use. the __init__ syntax must be compatible
with PhylesystemGitAction
If you want to use a mirrors of the repo for pushes or pulls, send in a `mirror_info` dict:
mirror_info['push'] and mirror_info['pull'] should be dicts with the following keys:
'parent_dir' - the parent directory of the mirrored repos
'remote_map' - a dictionary of remote name to prefix (the repo name + '.git' will be
appended to create the URL for pushing).
"""
self._new_study_prefix = None
TypeAwareDocStore.__init__(self,
prefix_from_doc_id=prefix_from_study_id,
repos_dict=repos_dict,
repos_par=repos_par,
with_caching=with_caching,
assumed_doc_version=repo_nexml2json,
git_ssh=git_ssh,
pkey=pkey,
git_action_class=PhylesystemGitAction,
git_shard_class=PhylesystemShard,
mirror_info=mirror_info,
new_doc_prefix=new_study_prefix,
infrastructure_commit_author='OpenTree API <*****@*****.**>',
**kwargs)
self._new_study_prefix = self._growing_shard._new_study_prefix # TODO:shard-edits?
self._growing_shard._determine_next_study_id()
if with_caching:
self._cache_region = _make_phylesystem_cache_region()
else:
self._cache_region = None
self._cache_hits = 0
def __init__(self,
repos_dict=None,
repos_par=None,
with_caching=True,
repo_nexml2json=None,
git_ssh=None,
pkey=None,
git_action_class=GitAction,
mirror_info=None,
new_study_prefix=None,
infrastructure_commit_author='OpenTree API <*****@*****.**>',
**kwargs):
'''
Repos can be found by passing in a `repos_par` (a directory that is the parent of the repos)
or by trusting the `repos_dict` mapping of name to repo filepath.
`with_caching` should be True for non-debugging uses.
`repo_nexml2json` is optional. If specified all PhylesystemShard repos are assumed to store
files of this version of nexson syntax.
`git_ssh` is the path of an executable for git-ssh operations.
`pkey` is the PKEY that has to be in the env for remote, authenticated operations to work
`git_action_class` is a subclass of GitAction to use. the __init__ syntax must be compatible
with GitAction
If you want to use a mirrors of the repo for pushes or pulls, send in a `mirror_info` dict:
mirror_info['push'] and mirror_info['pull'] should be dicts with the following keys:
'parent_dir' - the parent directory of the mirrored repos
'remote_map' - a dictionary of remote name to prefix (the repo name + '.git' will be
appended to create the URL for pushing).
'''
_PhylesystemBase.__init__(self)
if repos_dict is not None:
self._filepath_args = 'repos_dict = {}'.format(repr(repos_dict))
elif repos_par is not None:
self._filepath_args = 'repos_par = {}'.format(repr(repos_par))
else:
fmt = '<No arg> default phylesystem_parent from {}'
a = _get_phylesystem_parent_with_source(**kwargs)[1]
self._filepath_args = fmt.format(a)
push_mirror_repos_par = None
push_mirror_remote_map = {}
if mirror_info:
push_mirror_info = mirror_info.get('push', {})
if push_mirror_info:
push_mirror_repos_par = push_mirror_info['parent_dir']
push_mirror_remote_map = push_mirror_info.get('remote_map', {})
if push_mirror_repos_par:
if not os.path.exists(push_mirror_repos_par):
os.makedirs(push_mirror_repos_par)
if not os.path.isdir(push_mirror_repos_par):
e_fmt = 'Specified push_mirror_repos_par, "{}", is not a directory'
e = e_fmt.format(push_mirror_repos_par)
raise ValueError(e)
if repos_dict is None:
repos_dict = get_repos(repos_par, **kwargs)
shards = []
repo_name_list = list(repos_dict.keys())
repo_name_list.sort()
for repo_name in repo_name_list:
repo_filepath = repos_dict[repo_name]
push_mirror_repo_path = None
if push_mirror_repos_par:
expected_push_mirror_repo_path = os.path.join(push_mirror_repos_par, repo_name)
if os.path.isdir(expected_push_mirror_repo_path):
push_mirror_repo_path = expected_push_mirror_repo_path
try:
shard = PhylesystemShard(repo_name,
repo_filepath,
git_ssh=git_ssh,
pkey=pkey,
repo_nexml2json=repo_nexml2json,
git_action_class=git_action_class,
push_mirror_repo_path=push_mirror_repo_path,
new_study_prefix=new_study_prefix,
infrastructure_commit_author=infrastructure_commit_author)
except NotAPhylesystemShardError as x:
f = 'Git repo "{d}" found in your phylesystem parent, but it does not appear to be a phylesystem ' \
'shard. Please report this as a bug if this directory is supposed to be phylesystem shard. '\
'The triggering error message was:\n{e}'
f = f.format(d=repo_filepath, e=str(x))
_LOG.warn(f)
continue
# if the mirror does not exist, clone it...
if push_mirror_repos_par and (push_mirror_repo_path is None):
GitAction.clone_repo(push_mirror_repos_par,
repo_name,
repo_filepath)
if not os.path.isdir(expected_push_mirror_repo_path):
e_msg = 'git clone in mirror bootstrapping did not produce a directory at {}'
e = e_msg.format(expected_push_mirror_repo_path)
raise ValueError(e)
for remote_name, remote_url_prefix in push_mirror_remote_map.items():
if remote_name in ['origin', 'originssh']:
f = '"{}" is a protected remote name in the mirrored repo setup'
m = f.format(remote_name)
raise ValueError(m)
remote_url = remote_url_prefix + '/' + repo_name + '.git'
GitAction.add_remote(expected_push_mirror_repo_path, remote_name, remote_url)
shard.push_mirror_repo_path = expected_push_mirror_repo_path
for remote_name in push_mirror_remote_map.keys():
mga = shard._create_git_action_for_mirror() #pylint: disable=W0212
mga.fetch(remote_name)
shards.append(shard)
self._shards = shards
self._growing_shard = shards[-1] # generalize with config...
self._prefix2shard = {}
for shard in shards:
for prefix in shard.known_prefixes:
assert prefix not in self._prefix2shard # we don't currently support multiple shards with the same ID prefix scheme
self._prefix2shard[prefix] = shard
with self._index_lock:
self._locked_refresh_study_ids()
self.repo_nexml2json = shards[-1].repo_nexml2json
if with_caching:
self._cache_region = _make_phylesystem_cache_region()
else:
self._cache_region = None
self.git_action_class = git_action_class
self._cache_hits = 0
def __init__(
self,
repos_dict=None,
repos_par=None,
with_caching=True,
repo_nexml2json=None,
git_ssh=None,
pkey=None,
git_action_class=GitAction,
mirror_info=None,
new_study_prefix=None,
infrastructure_commit_author='OpenTree API <*****@*****.**>',
**kwargs):
'''
Repos can be found by passing in a `repos_par` (a directory that is the parent of the repos)
or by trusting the `repos_dict` mapping of name to repo filepath.
`with_caching` should be True for non-debugging uses.
`repo_nexml2json` is optional. If specified all PhylesystemShard repos are assumed to store
files of this version of nexson syntax.
`git_ssh` is the path of an executable for git-ssh operations.
`pkey` is the PKEY that has to be in the env for remote, authenticated operations to work
`git_action_class` is a subclass of GitAction to use. the __init__ syntax must be compatible
with GitAction
If you want to use a mirrors of the repo for pushes or pulls, send in a `mirror_info` dict:
mirror_info['push'] and mirror_info['pull'] should be dicts with the following keys:
'parent_dir' - the parent directory of the mirrored repos
'remote_map' - a dictionary of remote name to prefix (the repo name + '.git' will be
appended to create the URL for pushing).
'''
_PhylesystemBase.__init__(self)
if repos_dict is not None:
self._filepath_args = 'repos_dict = {}'.format(repr(repos_dict))
elif repos_par is not None:
self._filepath_args = 'repos_par = {}'.format(repr(repos_par))
else:
fmt = '<No arg> default phylesystem_parent from {}'
a = _get_phylesystem_parent_with_source(**kwargs)[1]
self._filepath_args = fmt.format(a)
push_mirror_repos_par = None
push_mirror_remote_map = {}
if mirror_info:
push_mirror_info = mirror_info.get('push', {})
if push_mirror_info:
push_mirror_repos_par = push_mirror_info['parent_dir']
push_mirror_remote_map = push_mirror_info.get('remote_map', {})
if push_mirror_repos_par:
if not os.path.exists(push_mirror_repos_par):
os.makedirs(push_mirror_repos_par)
if not os.path.isdir(push_mirror_repos_par):
e_fmt = 'Specified push_mirror_repos_par, "{}", is not a directory'
e = e_fmt.format(push_mirror_repos_par)
raise ValueError(e)
if repos_dict is None:
repos_dict = get_repos(repos_par, **kwargs)
shards = []
repo_name_list = list(repos_dict.keys())
repo_name_list.sort()
for repo_name in repo_name_list:
repo_filepath = repos_dict[repo_name]
push_mirror_repo_path = None
if push_mirror_repos_par:
expected_push_mirror_repo_path = os.path.join(
push_mirror_repos_par, repo_name)
if os.path.isdir(expected_push_mirror_repo_path):
push_mirror_repo_path = expected_push_mirror_repo_path
shard = PhylesystemShard(
repo_name,
repo_filepath,
git_ssh=git_ssh,
pkey=pkey,
repo_nexml2json=repo_nexml2json,
git_action_class=git_action_class,
push_mirror_repo_path=push_mirror_repo_path,
new_study_prefix=new_study_prefix,
infrastructure_commit_author=infrastructure_commit_author)
# if the mirror does not exist, clone it...
if push_mirror_repos_par and (push_mirror_repo_path is None):
GitAction.clone_repo(push_mirror_repos_par, repo_name,
repo_filepath)
if not os.path.isdir(expected_push_mirror_repo_path):
e_msg = 'git clone in mirror bootstrapping did not produce a directory at {}'
e = e_msg.format(expected_push_mirror_repo_path)
raise ValueError(e)
for remote_name, remote_url_prefix in push_mirror_remote_map.items(
):
if remote_name in ['origin', 'originssh']:
f = '"{}" is a protected remote name in the mirrored repo setup'
m = f.format(remote_name)
raise ValueError(m)
remote_url = remote_url_prefix + '/' + repo_name + '.git'
GitAction.add_remote(expected_push_mirror_repo_path,
remote_name, remote_url)
shard.push_mirror_repo_path = expected_push_mirror_repo_path
for remote_name in push_mirror_remote_map.keys():
mga = shard._create_git_action_for_mirror() #pylint: disable=W0212
mga.fetch(remote_name)
shards.append(shard)
self._shards = shards
self._growing_shard = shards[-1] # generalize with config...
self._prefix2shard = {}
for shard in shards:
for prefix in shard.known_prefixes:
assert prefix not in self._prefix2shard # we don't currently support multiple shards with the same ID prefix scheme
self._prefix2shard[prefix] = shard
with self._index_lock:
self._locked_refresh_study_ids()
self.repo_nexml2json = shards[-1].repo_nexml2json
if with_caching:
self._cache_region = _make_phylesystem_cache_region()
else:
self._cache_region = None
self.git_action_class = git_action_class
self._cache_hits = 0