def __init__(self, domain, **kwargs):
self._config = kwargs.get('config')
if self._config is None:
self._config = get_config_object()
self._api_vers = self._config.get_from_config_setting_cascade([('apis', 'taxomachine_api_version'),
('apis', 'api_version')],
"2")
self.use_v1 = (self._api_vers == "1")
r = self._config.get_from_config_setting_cascade([('apis', 'taxomachine_raw_urls'),
('apis', 'raw_urls')],
"FALSE")
self._raw_urls = (r.lower() == 'true')
if 'cache_taxa' in kwargs:
cache_taxa = kwargs.get('cache_taxa', False)
else:
cache_taxa = self._config.get_config_setting('apis', 'cache_taxa', 'false').lower() in ['true', '1']
if cache_taxa:
self._ott_id2taxon = {}
else:
self._ott_id2taxon = None
self._contexts = None
self._valid_contexts = None
self.prefix = None
_WSWrapper.__init__(self, domain, **kwargs)
self.domain = domain
self._wr = weakref.proxy(self)
def __init__(self, **kwargs):
self._config = get_config_object(None, **kwargs)
self._oti = kwargs.get('oti')
self._phylografter = 'http://www.reelab.net/phylografter'
self._phylesystem_api = kwargs.get('phylesystem')
self._taxomachine = kwargs.get('taxomachine')
self._treemachine = kwargs.get('treemachine')
def __init__(self, ott_dir=None, **kwargs):
self._config = kwargs.get('config')
if self._config is None:
self._config = get_config_object()
if ott_dir is None:
ott_dir = self._config.get_config_setting('ott', 'parent')
if ott_dir is None:
raise ValueError(
'Either the ott_dir arg must be used or "parent" must '
'exist in the "[ott]" section of your config (~/.peyotl/config by default)'
)
self.ott_dir = ott_dir
if not os.path.isdir(self.ott_dir):
raise ValueError('"{}" is not a directory'.format(self.ott_dir))
# self.skip_prefixes = ('environmental samples (', 'uncultured (', 'Incertae Sedis (')
self.skip_prefixes = ('environmental samples (', )
self._ott_id_to_names = None
self._ott_id2par_ott_id = None
self._version = None
self._root_name = None
self._root_ott_id = None
self._name2ott_ids = None
self._ott_id_to_flags = None
self._ott_id_to_sources = None
self._ott_id_to_ranks = None
self._flag_set_id2flag_set = None
self._taxonomic_sources = None
self._ncbi_2_ott_id = None
self._forward_table = None
def __init__(self, **kwargs):
self._config = get_config_object(None, **kwargs)
self._oti = kwargs.get('oti')
self._phylografter = 'http://www.reelab.net/phylografter'
self._phylesystem_api = kwargs.get('phylesystem')
self._taxomachine = kwargs.get('taxomachine')
self._treemachine = kwargs.get('treemachine')
def __init__(self, ott_dir=None, **kwargs):
self._config = kwargs.get('config')
if self._config is None:
self._config = get_config_object()
if ott_dir is None:
ott_dir = self._config.get_config_setting('ott', 'parent')
if ott_dir is None:
raise ValueError('Either the ott_dir arg must be used or "parent" must '
'exist in the "[ott]" section of your config (~/.peyotl/config by default)')
self.ott_dir = ott_dir
if not os.path.isdir(self.ott_dir):
raise ValueError('"{}" is not a directory'.format(self.ott_dir))
# self.skip_prefixes = ('environmental samples (', 'uncultured (', 'Incertae Sedis (')
self.skip_prefixes = ('environmental samples (',)
self._ott_id_to_names = None
self._ott_id2par_ott_id = None
self._preorder2ott_id = None
self._version = None
self._root_name = None
self._root_ott_id = None
self._name2ott_ids = None
self._ott_id_to_flags = None
self._ott_id_to_sources = None
self._ott_id_to_ranks = None
self._flag_set_id2flag_set = None
self._taxonomic_sources = None
self._ncbi_2_ott_id = None
self._forward_table = None
def __init__(self, domains=None, phylesystem_api_kwargs=None, collections_api_kwargs=None,
amendments_api_kwargs=None, **kwargs):
if domains is None:
domains = get_domains_obj(**kwargs)
self.domains = domains
self._phylografter = None
self._phylesystem_api = None
self._collections_api = None
self._amendments_api = None
self._amendments = None
self._taxomachine = None
self._treemachine = None
self._oti = None
self._tree_of_life_wrapper = None
self._graph_wrapper = None
self._taxonomy_wrapper = None
self._tnrs_wrapper = None
self._studies_wrapper = None
self._study_wrapper = None
self._config = kwargs.get('config')
if self._config is None:
self._config = get_config_object()
if phylesystem_api_kwargs is None:
self._phylesystem_api_kwargs = {}
else:
self._phylesystem_api_kwargs = dict(phylesystem_api_kwargs)
if collections_api_kwargs is None:
self._collections_api_kwargs = {}
else:
self._collections_api_kwargs = dict(collections_api_kwargs)
if amendments_api_kwargs is None:
self._amendments_api_kwargs = {}
else:
self._amendments_api_kwargs = dict(amendments_api_kwargs)
def __init__(self, domain, **kwargs):
self._config = kwargs.get('config')
if self._config is None:
self._config = get_config_object()
self._api_vers = self._config.get_from_config_setting_cascade(
[('apis', 'taxomachine_api_version'),
('apis', 'api_version')], "2")
self.use_v1 = (self._api_vers == "1")
r = self._config.get_from_config_setting_cascade(
[('apis', 'taxomachine_raw_urls'), ('apis', 'raw_urls')], "FALSE")
self._raw_urls = (r.lower() == 'true')
if 'cache_taxa' in kwargs:
cache_taxa = kwargs.get('cache_taxa', False)
else:
cache_taxa = self._config.get_config_setting(
'apis', 'cache_taxa', 'false').lower() in ['true', '1']
if cache_taxa:
self._ott_id2taxon = {}
else:
self._ott_id2taxon = None
self._contexts = None
self._valid_contexts = None
self.prefix = None
_WSWrapper.__init__(self, domain, **kwargs)
self.domain = domain
self._wr = weakref.proxy(self)
def __init__(self, **kwargs):
self._config = kwargs.get('config')
if self._config is None:
self._config = get_config_object()
self._oti = kwargs.get('oti')
self._phylesystem_api = kwargs.get('phylesystem')
self._collections_api = kwargs.get('collections')
self._amendments_api = kwargs.get('amendments')
self._taxomachine = kwargs.get('taxomachine')
self._treemachine = kwargs.get('treemachine')
def __init__(self, domain, **kwargs):
self._config = get_config_object(None, **kwargs)
self._api_vers = self._config.get_from_config_setting_cascade(
[('apis', 'taxomachine_api_version'),
('apis', 'api_version')], "2")
self.use_v1 = (self._api_vers == "1")
r = self._config.get_from_config_setting_cascade(
[('apis', 'taxomachine_raw_urls'), ('apis', 'raw_urls')], "FALSE")
self._raw_urls = (r.lower() == 'true')
self._contexts = None
self._valid_contexts = None
self.prefix = None
_WSWrapper.__init__(self, domain, **kwargs)
self.domain = domain
def __init__(self, domain, **kwargs):
self._config = get_config_object(None, **kwargs)
self._current_synth_info = None
self._current_synth_id = None
self.prefix = None
r = self._config.get_from_config_setting_cascade([('apis', 'treemachine_raw_urls'),
('apis', 'raw_urls')],
"FALSE")
self._raw_urls = (r.lower() == 'true')
self._api_vers = self._config.get_from_config_setting_cascade([('apis', 'treemachine_api_version'),
('apis', 'api_version')],
"2")
self.use_v1 = (self._api_vers == "1")
_WSWrapper.__init__(self, domain, **kwargs)
self.domain = domain
def __init__(self, domain, **kwargs):
self._config = get_config_object(None, **kwargs)
self._api_vers = self._config.get_from_config_setting_cascade(
[('apis', 'oti_api_version'), ('apis', 'api_version')], "2")
self.use_v1 = (self._api_vers == "1")
self._node_search_prop = None
self._search_terms = None
self._tree_search_prop = None
self._study_search_prop = None
self.indexing_prefix = None
self.query_prefix = None
r = self._config.get_from_config_setting_cascade(
[('apis', 'oti_raw_urls'), ('apis', 'raw_urls')], "FALSE")
self._raw_urls = (r.lower() == 'true')
_WSWrapper.__init__(self, domain, **kwargs)
self.domain = domain
def __init__(self, domain, **kwargs):
self._config = kwargs.get('config')
if self._config is None:
self._config = get_config_object()
self._current_synth_info = None
self._current_synth_id = None
self.prefix = None
r = self._config.get_from_config_setting_cascade([('apis', 'treemachine_raw_urls'),
('apis', 'raw_urls')],
"FALSE")
self._raw_urls = (r.lower() == 'true')
self._api_vers = self._config.get_from_config_setting_cascade([('apis', 'treemachine_api_version'),
('apis', 'api_version')],
"2")
self.use_v1 = (self._api_vers == "1")
_WSWrapper.__init__(self, domain, **kwargs)
self.domain = domain
def __init__(self, domain, **kwargs):
self._config = get_config_object(None, **kwargs)
self._api_vers = self._config.get_from_config_setting_cascade([('apis', 'oti_api_version'),
('apis', 'api_version')],
"2")
self.use_v1 = (self._api_vers == "1")
self._node_search_prop = None
self._search_terms = None
self._tree_search_prop = None
self._study_search_prop = None
self.indexing_prefix = None
self.query_prefix = None
r = self._config.get_from_config_setting_cascade([('apis', 'oti_raw_urls'),
('apis', 'raw_urls')],
"FALSE")
self._raw_urls = (r.lower() == 'true')
_WSWrapper.__init__(self, domain, **kwargs)
self.domain = domain
def __init__(self, domains=None, phylesystem_api_kwargs=None, **kwargs):
if domains is None:
domains = get_domains_obj(**kwargs)
self.domains = domains
self._phylografter = None
self._phylesystem_api = None
self._taxomachine = None
self._treemachine = None
self._oti = None
self._tree_of_life_wrapper = None
self._graph_wrapper = None
self._taxonomy_wrapper = None
self._tnrs_wrapper = None
self._studies_wrapper = None
self._study_wrapper = None
self._config = get_config_object(None, **kwargs)
if phylesystem_api_kwargs is None:
self._phylesystem_api_kwargs = {}
else:
self._phylesystem_api_kwargs = dict(phylesystem_api_kwargs)
def __init__(self, domains=None, phylesystem_api_kwargs=None, **kwargs):
if domains is None:
domains = get_domains_obj(**kwargs)
self.domains = domains
self._phylografter = None
self._phylesystem_api = None
self._taxomachine = None
self._treemachine = None
self._oti = None
self._tree_of_life_wrapper = None
self._graph_wrapper = None
self._taxonomy_wrapper = None
self._tnrs_wrapper = None
self._studies_wrapper = None
self._study_wrapper = None
self._config = get_config_object(None, **kwargs)
if phylesystem_api_kwargs is None:
self._phylesystem_api_kwargs = {}
else:
self._phylesystem_api_kwargs = dict(phylesystem_api_kwargs)
