def _get_phylesystem_parent_with_source(**kwargs):
src = "environment"
if "PHYLESYSTEM_PARENT" in os.environ:
phylesystem_parent = os.environ.get("PHYLESYSTEM_PARENT")
else:
try:
phylesystem_parent = expand_path(get_config_setting_kwargs(None, "phylesystem", "parent", **kwargs))
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 _get_phylesystem_parent_with_source(**kwargs):
src = 'environment'
if 'PHYLESYSTEM_PARENT' in os.environ:
phylesystem_parent = os.environ.get('PHYLESYSTEM_PARENT')
else:
try:
phylesystem_parent = expand_path(
get_config_setting_kwargs(None, 'phylesystem', 'parent',
**kwargs))
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,
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
#! /usr/bin/env python
from peyotl.evaluate_tree import evaluate_tree_rooting
from peyotl.ott import OTT
from peyotl.utility import get_config_setting_kwargs, get_logger
from peyotl.nexson_proxy import NexsonProxy
from peyotl.test.support import pathmap
import unittest
_LOG = get_logger(__name__)
do_test = False
try:
ott_dir = get_config_setting_kwargs(None,
section='ott',
param='parent',
default=False)
if ott_dir is False or not ott_dir.endswith('/aster'):
_LOG.debug(
'ott_dir setting is "{}" this does not look like it is the Asterales system'
.format(ott_dir))
else:
do_test = True
except:
_LOG.debug('[ott]/parent setting could not be read correctly.')
@unittest.skipIf(not do_test, 'the test_evaluate_tree.py is only run if you have your OTT/parent configuration set' \
' to point to a directory called "aster" (which should hold the taxonomy of Asterales) ' \
'See http://opentreeoflife.github.io/peyotl/configuration/ ' \
' and open tree of life reference taxonomy documentation about the Asterales test system')
class TestProxy(unittest.TestCase):
def setUp(self):
self.nexson = pathmap.nexson_obj('pg_329/pg_329.json')
self.np = NexsonProxy(nexson=self.nexson)
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
#! /usr/bin/env python
from peyotl.evaluate_tree import evaluate_tree_rooting
from peyotl.ott import OTT
from peyotl.utility import get_config_setting_kwargs, get_logger
from peyotl.nexson_proxy import NexsonProxy
from peyotl.test.support import pathmap
import unittest
_LOG = get_logger(__name__)
do_test = False
try:
ott_dir = get_config_setting_kwargs(None, section='ott', param='parent', default=False)
if ott_dir is False or not ott_dir.endswith('/aster'):
_LOG.debug('ott_dir setting is "{}" this does not look like it is the Asterales system'.format(ott_dir))
else:
do_test = True
except:
_LOG.debug('[ott]/parent setting could not be read correctly.')
@unittest.skipIf(not do_test, 'the test_evaluate_tree.py is only run if you have your OTT/parent configuration set' \
' to point to a directory called "aster" (which should hold the taxonomy of Asterales) ' \
'See http://opentreeoflife.github.io/peyotl/configuration/ ' \
' and open tree of life reference taxonomy documentation about the Asterales test system')
class TestProxy(unittest.TestCase):
def setUp(self):
self.nexson = pathmap.nexson_obj('pg_329/pg_329.json')
self.np = NexsonProxy(nexson=self.nexson)
def testTaxoRooting(self):
ott = OTT()
phylo = self.np.get_tree(tree_id='tree324')
evaluate_tree_rooting(self.nexson, ott, phylo)
if __name__ == "__main__":
