def _locked_refresh_study_ids(self):
d = create_id2study_info(self.study_dir, self.name)
rc_dict = diagnose_repo_study_id_convention(self.path)
self.filepath_for_study_id_fn = rc_dict['fp_fn']
self.id_alias_list_fn = rc_dict['id2alias_list']
if rc_dict['convention'] != 'simple':
a = {}
for k, v in d.items():
alias_list = self.id_alias_list_fn(k)
for alias in alias_list:
a[alias] = v
d = a
self.has_aliases = True
else:
self.has_aliases = False
self._study_index = d
def _locked_refresh_study_ids(self):
d = create_id2study_info(self.study_dir, self.name)
rc_dict = diagnose_repo_study_id_convention(self.path)
self.filepath_for_study_id_fn = rc_dict['fp_fn']
self.id_alias_list_fn = rc_dict['id2alias_list']
if rc_dict['convention'] != 'simple':
a = {}
for k, v in d.items():
alias_list = self.id_alias_list_fn(k)
for alias in alias_list:
a[alias] = v
d = a
self.has_aliases = True
else:
self.has_aliases = False
self._study_index = d
def refresh_study_index(shard, initializing=False):
from peyotl.phylesystem.helper import create_id2study_info, \
diagnose_repo_study_id_convention
d = create_id2study_info(shard.doc_dir, shard.name)
rc_dict = diagnose_repo_study_id_convention(shard.path)
shard.filepath_for_doc_id_fn = rc_dict['fp_fn']
shard.id_alias_list_fn = rc_dict['id2alias_list']
if rc_dict['convention'] != 'simple':
a = {}
for k, v in d.items():
alias_list = shard.id_alias_list_fn(k)
for alias in alias_list:
a[alias] = v
d = a
shard.has_aliases = True
if initializing:
shard.infer_study_prefix()
else:
shard.has_aliases = False
shard.study_index = d
def refresh_study_index(shard, initializing=False):
from peyotl.phylesystem.helper import create_id2study_info, \
diagnose_repo_study_id_convention
d = create_id2study_info(shard.doc_dir, shard.name)
rc_dict = diagnose_repo_study_id_convention(shard.path)
shard.filepath_for_doc_id_fn = rc_dict['fp_fn']
shard.id_alias_list_fn = rc_dict['id2alias_list']
if rc_dict['convention'] != 'simple':
a = {}
for k, v in d.items():
alias_list = shard.id_alias_list_fn(k)
for alias in alias_list:
a[alias] = v
d = a
shard.has_aliases = True
if initializing:
shard.infer_study_prefix()
else:
shard.has_aliases = False
shard.study_index = d
def __init__(self,
name,
path,
repo_nexml2json=None,
git_ssh=None,
pkey=None,
git_action_class=GitAction,
push_mirror_repo_path=None,
new_study_prefix=None,
infrastructure_commit_author='OpenTree API <*****@*****.**>',
**kwargs):
self._index_lock = Lock()
PhylesystemShardBase.__init__(self, name)
self._infrastructure_commit_author = infrastructure_commit_author
self._study_counter_lock = Lock()
self._master_branch_repo_lock = Lock()
self._new_study_prefix = new_study_prefix
self._ga_class = git_action_class
self.git_ssh = git_ssh
self.pkey = pkey
path = os.path.abspath(path)
dot_git = os.path.join(path, '.git')
study_dir = os.path.join(path, 'study')
if not os.path.isdir(path):
raise ValueError('"{p}" is not a directory'.format(p=path))
if not os.path.isdir(dot_git):
raise ValueError('"{p}" is not a directory'.format(p=dot_git))
if not os.path.isdir(study_dir):
raise ValueError('"{p}" is not a directory'.format(p=study_dir))
self.path = path
self._id_minting_file = os.path.join(path, 'next_study_id.json')
if self._new_study_prefix is None:
prefix_file = os.path.join(path, 'new_study_prefix')
if os.path.exists(prefix_file):
pre_content = open(prefix_file, 'r').read().strip()
valid_pat = re.compile('^[a-zA-Z0-9]+_$')
if len(pre_content) != 3 or not valid_pat.match(pre_content):
raise ValueError('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
d = create_id2study_info(study_dir, name)
rc_dict = diagnose_repo_study_id_convention(path)
self.filepath_for_study_id_fn = rc_dict['fp_fn']
self.filepath_for_global_resource_fn = lambda frag: os.path.join(path, frag)
self.id_alias_list_fn = rc_dict['id2alias_list']
if rc_dict['convention'] != 'simple':
a = {}
for k, v in d.items():
alias_list = self.id_alias_list_fn(k)
for alias in alias_list:
a[alias] = v
d = a
self.has_aliases = True
self.inferred_study_prefix = True
self.infer_study_prefix()
else:
self.inferred_study_prefix = False
self.study_dir = study_dir
with self._index_lock:
self._locked_refresh_study_ids()
self.parent_path = os.path.split(path)[0] + '/'
self.git_dir = dot_git
self.push_mirror_repo_path = push_mirror_repo_path
if repo_nexml2json is None:
try:
repo_nexml2json = get_config_setting_kwargs(None, 'phylesystem', 'repo_nexml2json', **kwargs)
except:
pass
if repo_nexml2json == None:
repo_nexml2json = self.diagnose_repo_nexml2json()
self.repo_nexml2json = repo_nexml2json
self._next_study_id = None
self._study_counter_lock = None
self._known_prefixes = None
def __init__(self,
name,
path,
repo_nexml2json=None,
git_ssh=None,
pkey=None,
git_action_class=GitAction,
push_mirror_repo_path=None,
new_study_prefix=None,
infrastructure_commit_author='OpenTree API <*****@*****.**>',
**kwargs):
self._index_lock = Lock()
PhylesystemShardBase.__init__(self, name)
self._infrastructure_commit_author = infrastructure_commit_author
self._study_counter_lock = Lock()
self._master_branch_repo_lock = Lock()
self._new_study_prefix = new_study_prefix
self._ga_class = git_action_class
self.git_ssh = git_ssh
self.pkey = pkey
path = os.path.abspath(path)
dot_git = os.path.join(path, '.git')
study_dir = os.path.join(path, 'study')
if not os.path.isdir(path):
raise NotAPhylesystemShardError('"{p}" is not a directory'.format(p=path))
if not os.path.isdir(dot_git):
raise NotAPhylesystemShardError('"{p}" is not a directory'.format(p=dot_git))
if not os.path.isdir(study_dir):
raise NotAPhylesystemShardError('"{p}" is not a directory'.format(p=study_dir))
self.path = path
self._id_minting_file = os.path.join(path, 'next_study_id.json')
if self._new_study_prefix is None:
prefix_file = os.path.join(path, 'new_study_prefix')
if os.path.exists(prefix_file):
pre_content = open(prefix_file, 'r').read().strip()
valid_pat = re.compile('^[a-zA-Z0-9]+_$')
if len(pre_content) != 3 or not valid_pat.match(pre_content):
raise NotAPhylesystemShardError('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
d = create_id2study_info(study_dir, name)
rc_dict = diagnose_repo_study_id_convention(path)
self.filepath_for_study_id_fn = rc_dict['fp_fn']
self.filepath_for_global_resource_fn = lambda frag: os.path.join(path, frag)
self.id_alias_list_fn = rc_dict['id2alias_list']
if rc_dict['convention'] != 'simple':
a = {}
for k, v in d.items():
alias_list = self.id_alias_list_fn(k)
for alias in alias_list:
a[alias] = v
d = a
self.has_aliases = True
self.inferred_study_prefix = True
self.infer_study_prefix()
else:
self.inferred_study_prefix = False
self.study_dir = study_dir
with self._index_lock:
self._locked_refresh_study_ids()
self.parent_path = os.path.split(path)[0] + '/'
self.git_dir = dot_git
self.push_mirror_repo_path = push_mirror_repo_path
if repo_nexml2json is None:
try:
repo_nexml2json = get_config_setting_kwargs(None, 'phylesystem', 'repo_nexml2json', **kwargs)
except:
pass
if repo_nexml2json == None:
repo_nexml2json = self.diagnose_repo_nexml2json()
max_file_size = kwargs.get('max_file_size')
if max_file_size is None:
max_file_size = get_config_setting_kwargs(None, 'phylesystem', 'max_file_size', default=None, **kwargs)
if max_file_size is not None:
try:
max_file_size = int(max_file_size)
except:
m = 'Configuration-base value of max_file_size was "{}". Expecting and integer.'
m = m.format(max_file_size)
raise RuntimeError(m)
self.max_file_size = max_file_size
self.repo_nexml2json = repo_nexml2json
self._next_study_id = None
self._study_counter_lock = None
self._known_prefixes = None