def __init__(self,
name,
path,
assumed_doc_version=None,
git_ssh=None,
pkey=None,
git_action_class=PhylesystemGitAction,
push_mirror_repo_path=None,
new_doc_prefix=None, # IGNORED in this shard type
infrastructure_commit_author='OpenTree API <*****@*****.**>',
**kwargs):
self.max_file_size = get_config_setting('phylesystem', 'max_file_size')
TypeAwareGitShard.__init__(self,
name,
path,
doc_holder_subpath,
assumed_doc_version,
None, # version detection
refresh_amendment_index, # populates _doc_index
git_ssh,
pkey,
git_action_class,
push_mirror_repo_path,
infrastructure_commit_author,
**kwargs)
self.filepath_for_doc_id_fn = filepath_for_amendment_id
self._doc_counter_lock = Lock()
self._next_ott_id = None
self._id_minting_file = os.path.join(path, 'next_ott_id.json')
# N.B. This is for minting invididual taxon (OTT) ids, not amendment ids!
# We construct each amendment from its unique series of ottids.
self.filepath_for_global_resource_fn = lambda frag: os.path.join(path, frag)
def __init__(
self,
name,
path,
assumed_doc_version=None,
git_ssh=None,
pkey=None,
git_action_class=PhylesystemGitAction,
push_mirror_repo_path=None,
new_doc_prefix=None, # IGNORED in this shard type
infrastructure_commit_author='OpenTree API <*****@*****.**>',
**kwargs):
self.max_file_size = get_config_setting('phylesystem', 'max_file_size')
TypeAwareGitShard.__init__(
self,
name,
path,
doc_holder_subpath,
assumed_doc_version,
None, # version detection
refresh_amendment_index, # populates _doc_index
git_ssh,
pkey,
git_action_class,
push_mirror_repo_path,
infrastructure_commit_author,
**kwargs)
self.filepath_for_doc_id_fn = filepath_for_amendment_id
self._doc_counter_lock = Lock()
self._next_ott_id = None
self._id_minting_file = os.path.join(path, 'next_ott_id.json')
# N.B. This is for minting invididual taxon (OTT) ids, not amendment ids!
# We construct each amendment from its unique series of ottids.
self.filepath_for_global_resource_fn = lambda frag: os.path.join(
path, frag)
def __init__(self,
name,
path,
assumed_doc_version=None,
git_ssh=None,
pkey=None,
git_action_class=PhylesystemGitAction,
push_mirror_repo_path=None,
new_doc_prefix=None, # IGNORED in this shard type
infrastructure_commit_author='OpenTree API <*****@*****.**>',
**kwargs):
self.max_file_size = get_config_setting('phylesystem', 'max_file_size')
TypeAwareGitShard.__init__(self,
name,
path,
doc_holder_subpath,
assumed_doc_version,
None, # version detection
refresh_collection_index, # populates _doc_index
git_ssh,
pkey,
git_action_class,
push_mirror_repo_path,
infrastructure_commit_author,
**kwargs)
self.filepath_for_doc_id_fn = filepath_for_collection_id
self._doc_counter_lock = Lock()
self.filepath_for_global_resource_fn = lambda frag: os.path.join(path, frag)
def Phylesystem(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 <*****@*****.**>'):
"""Factory function for a _Phylesystem object.
A wrapper around the _Phylesystem class instantiation for
the most common use case: a singleton _Phylesystem.
If you need distinct _Phylesystem objects, you'll need to
call that class directly.
"""
if not repo_nexml2json:
repo_nexml2json = get_config_setting('phylesystem', 'repo_nexml2json')
global _THE_PHYLESYSTEM
if _THE_PHYLESYSTEM is None:
_THE_PHYLESYSTEM = _Phylesystem(repos_dict=repos_dict,
repos_par=repos_par,
with_caching=with_caching,
repo_nexml2json=repo_nexml2json,
git_ssh=git_ssh,
pkey=pkey,
git_action_class=git_action_class,
mirror_info=mirror_info,
new_study_prefix=new_study_prefix,
infrastructure_commit_author=infrastructure_commit_author)
return _THE_PHYLESYSTEM
def __init__(
self,
name,
path,
assumed_doc_version=None,
git_ssh=None,
pkey=None,
git_action_class=PhylesystemGitAction,
push_mirror_repo_path=None,
new_doc_prefix=None, # IGNORED in this shard type
infrastructure_commit_author='OpenTree API <*****@*****.**>',
**kwargs):
self.max_file_size = get_config_setting('phylesystem', 'max_file_size')
TypeAwareGitShard.__init__(
self,
name,
path,
doc_holder_subpath,
assumed_doc_version,
None, # version detection
refresh_collection_index, # populates _doc_index
git_ssh,
pkey,
git_action_class,
push_mirror_repo_path,
infrastructure_commit_author,
**kwargs)
self.filepath_for_doc_id_fn = filepath_for_collection_id
self._doc_counter_lock = Lock()
self.filepath_for_global_resource_fn = lambda frag: os.path.join(
path, frag)
def _get_phylesystem_parent_with_source(**kwargs):
src = 'environment'
try:
phylesystem_parent = expand_path(get_config_setting('phylesystem', 'parent'))
src = 'configfile'
except:
raise ValueError('No [phylesystem] "parent" specified in config or environmental variables')
x = phylesystem_parent.split(':') # TEMP hardcoded assumption that : does not occur in a path name
return x, src
def __init__(
self,
name,
path,
assumed_doc_version=None,
git_ssh=None,
pkey=None,
git_action_class=PhylesystemGitAction,
push_mirror_repo_path=None,
new_study_prefix=None,
infrastructure_commit_author='OpenTree API <*****@*****.**>',
**kwargs):
self.max_file_size = get_config_setting('phylesystem', 'max_file_size')
TypeAwareGitShard.__init__(
self,
name,
path,
doc_holder_subpath,
assumed_doc_version,
diagnose_repo_nexml2json, # version detection
refresh_study_index, # populates 'study_index'
git_ssh,
pkey,
git_action_class,
push_mirror_repo_path,
infrastructure_commit_author,
**kwargs)
self._doc_counter_lock = Lock()
self._next_study_id = None
self._new_study_prefix = new_study_prefix
if self._new_study_prefix is None:
prefix_file = os.path.join(path, 'new_study_prefix')
if os.path.exists(prefix_file):
with open(prefix_file, 'r') as f:
pre_content = f.read().strip()
valid_pat = re.compile('^[a-zA-Z0-9]+_$')
if len(pre_content) != 3 or not valid_pat.match(pre_content):
raise FailedShardCreationError(
'Expecting prefix in new_study_prefix file to be two '
'letters followed by an underscore')
self._new_study_prefix = pre_content
else:
self._new_study_prefix = 'ot_' # ot_ is the default if there is no file
self._id_minting_file = os.path.join(path, 'next_study_id.json')
self.filepath_for_global_resource_fn = lambda frag: os.path.join(
path, frag)
def __init__(self,
name,
path,
assumed_doc_version=None,
git_ssh=None,
pkey=None,
git_action_class=PhylesystemGitAction,
push_mirror_repo_path=None,
new_study_prefix=None,
infrastructure_commit_author='OpenTree API <*****@*****.**>',
**kwargs):
self.max_file_size = get_config_setting('phylesystem', 'max_file_size')
TypeAwareGitShard.__init__(self,
name,
path,
doc_holder_subpath,
assumed_doc_version,
diagnose_repo_nexml2json, # version detection
refresh_study_index, # populates 'study_index'
git_ssh,
pkey,
git_action_class,
push_mirror_repo_path,
infrastructure_commit_author,
**kwargs)
self._doc_counter_lock = Lock()
self._next_study_id = None
self._new_study_prefix = new_study_prefix
if self._new_study_prefix is None:
prefix_file = os.path.join(path, 'new_study_prefix')
if os.path.exists(prefix_file):
with open(prefix_file, 'r') as f:
pre_content = f.read().strip()
valid_pat = re.compile('^[a-zA-Z0-9]+_$')
if len(pre_content) != 3 or not valid_pat.match(pre_content):
raise FailedShardCreationError('Expecting prefix in new_study_prefix file to be two '
'letters followed by an underscore')
self._new_study_prefix = pre_content
else:
self._new_study_prefix = 'ot_' # ot_ is the default if there is no file
self._id_minting_file = os.path.join(path, 'next_study_id.json')
self.filepath_for_global_resource_fn = lambda frag: os.path.join(path, frag)
