def _ontology_local_repo(self):
try:
stated_repo = Path(self.config['ontology_local_repo'])
except (KeyError, TypeError, FileNotFoundError) as e:
stated_repo = Path('/dev/null/does-not-exist')
maybe_repo = self._maybe_repo
if stated_repo.exists():
return stated_repo
elif maybe_repo.exists():
return maybe_repo
else:
maybe_start = Path(__file__).parent.parent.parent.absolute()
maybe_base = maybe_start
fsroot = Path('/')
while maybe_base != fsroot:
maybe_repo = maybe_base / self.ontology_repo
if maybe_repo.exists():
log.info(
tc.blue('INFO:') +
f'Ontology repository found at {maybe_repo}')
return maybe_repo
else:
maybe_base = maybe_base.parent
else:
log.warning(
tc.red('WARNING:') +
f'No repository found in any parent directory of {maybe_start}'
)
return Path('/dev/null/does-not-exist') # seems reaonsable ...
def secrets(self):
try:
return oa.stores.Secrets(self.secrets_file)
except FileNotFoundError:
log.warning(
f'secrets file {self.secrets_file} does not exist. '
'You can set an alternate path under the secrets_file: '
f'variable in {self.config_file}')
def exists(self):
e = Path(self.filename).exists()
if not e:
log.warning(
f'secrets file {self.filename} does not exist. '
'You can set an alternate path under the secrets_file: '
f'variable in {self.devconfig.config_file}')
return e
from pathlib import Path
from tempfile import gettempdir
from functools import wraps
import orthauth as oa
from pyontutils.utils import TermColors as tc, log
from pyontutils.utils import get_working_dir
oa.utils.log.removeHandler(oa.utils.log.handlers[0])
oa.utils.log.addHandler(log.handlers[0])
auth = oa.configure_here('auth-config.py', __name__)
pyontutils_config_path = auth.dynamic_config._path.parent
if not pyontutils_config_path.parent.exists():
log.warning(
f'config path does not exist! Errors incoming! {pyontutils_config_path.parent}'
)
default_config = pyontutils_config_path / 'devconfig.yaml'
working_dir = get_working_dir(__file__)
_data_curies_string = 'share/idlib/local-conventions/nifstd/curie_map.yaml' # XXX
system_curies_path = Path(sys.prefix) / _data_curies_string
if working_dir is None:
# we are not in git, we are probably testing or installed by a user
default_curies = pyontutils_config_path / 'curie_map.yaml'
# hardcoding the default api here to avoid importing the scigraph client
default_scigraph_api = 'https://scicrunch.org/api/1/scigraph'
else:
default_curies = working_dir / 'nifstd' / 'scigraph' / 'curie_map.yaml'
default_scigraph_api = 'http://localhost:9000/scigraph'