def __init__(self, endpoint: str = config.get("api", "")) -> None:
""" Initialize Nanopub
Args:
endpoint (str): BEL.bio API endpoint uri, e.g. https://api.bel.bio/v1, default read from config
"""
self.endpoint = endpoint
def get_client(host=None,
port=None,
username=None,
password=None,
enable_logging=True):
"""Get arango client and edgestore db handle"""
host = utils.first_true(
[host, config["bel_api"]["servers"]["arangodb_host"], "localhost"])
port = utils.first_true(
[port, config["bel_api"]["servers"]["arangodb_port"], 8529])
username = utils.first_true(
[username, config["bel_api"]["servers"]["arangodb_username"], ""])
password = utils.first_true([
password,
config.get(
"secrets",
config["secrets"]["bel_api"]["servers"].get("arangodb_password")),
"",
])
client = arango.client.ArangoClient(
protocol=config["bel_api"]["servers"]["arangodb_protocol"],
host=host,
port=port)
return client
def canonicalize(ctx, statement, namespace_targets, version, api, config_fn):
"""Canonicalize statement
Target namespaces can be provided in the following manner:
bel stmt canonicalize "<BELStmt>" --namespace_targets '{"HGNC": ["EG", "SP"], "CHEMBL": ["CHEBI"]}'
the value of target_namespaces must be JSON and embedded in single quotes
reserving double quotes for the dictionary elements
"""
if config_fn:
config = bel.db.Config.merge_config(ctx.config, override_config_fn=config_fn)
else:
config = ctx.config
# Configuration - will return the first truthy result in list else the default option
if namespace_targets:
namespace_targets = json.loads(namespace_targets)
namespace_targets = utils.first_true(
[namespace_targets, config.get("canonical")], None
)
api = utils.first_true([api, config.get("api", None)], None)
version = utils.first_true([version, config.get("bel_version", None)], None)
print("------------------------------")
print("BEL version: {}".format(version))
print("API Endpoint: {}".format(api))
print("------------------------------")
bo = BEL(version=version, endpoint=api)
bo.parse(statement).canonicalize(namespace_targets=namespace_targets)
if bo.ast is None:
print(bo.original_bel_stmt)
print(bo.parse_visualize_error)
print(bo.validation_messages)
else:
print("ORIGINAL ", bo.original_bel_stmt)
print("CANONICAL", bo.ast)
if bo.validation_messages:
print(bo.validation_messages)
else:
print("No problems found")
return
def get_client(host=None, port=None, username=None, password=None, enable_logging=True):
"""Get arango client and edgestore db handle"""
host = utils.first_true([host, config["bel_api"]["servers"]["arangodb_host"], "localhost"])
port = utils.first_true([port, config["bel_api"]["servers"]["arangodb_port"], 8529])
username = utils.first_true([username, config["bel_api"]["servers"]["arangodb_username"], ""])
password = utils.first_true(
[
password,
config.get("secrets", config["secrets"]["bel_api"]["servers"].get("arangodb_password")),
"",
]
)
arango_url = f"http://{host}:{port}"
try:
client = arango.ArangoClient(hosts=arango_url)
client.db(verify=True)
return client
except Exception as e:
log.error(f"Cannot access arangodb at {arango_url}")
return None
if nanopub["nanopub"]["citation"]["database"]["name"].lower(
) == "pubmed":
citation_string = f"PMID:{nanopub['nanopub']['citation']['database']['id']}"
else:
citation_string = f"{nanopub['nanopub']['citation']['database']['name']}:{nanopub['nanopub']['citation']['database']['id']}"
elif nanopub["nanopub"]["citation"].get("reference", False):
citation_string = nanopub["nanopub"]["citation"]["reference"]
elif nanopub["nanopub"]["citation"].get("uri", False):
citation_string = nanopub["nanopub"]["citation"]["uri"]
return citation_string
def main():
pass
if __name__ == "__main__":
# Setup logging
import logging.config
module_fn = os.path.basename(__file__)
module_fn = module_fn.replace(".py", "")
if config.get("logging", False):
logging.config.dictConfig(config.get("logging"))
log = logging.getLogger(f"{module_fn}")
main()
if nanopub['nanopub']['citation']['database']['name'].lower(
) == 'pubmed':
citation_string = f"PMID:{nanopub['nanopub']['citation']['database']['id']}"
else:
citation_string = f"{nanopub['nanopub']['citation']['database']['name']}:{nanopub['nanopub']['citation']['database']['id']}"
elif 'reference' in nanopub['nanopub']['citation'] and isinstance(
nanopub['nanopub']['citation']['reference'], str):
citation_string = nanopub['nanopub']['citation']['reference']
elif 'uri' in nanopub['nanopub']['citation']:
citation_string = nanopub['nanopub']['citation']['uri']
return citation_string
def main():
pass
if __name__ == '__main__':
# Setup logging
import logging.config
module_fn = os.path.basename(__file__)
module_fn = module_fn.replace('.py', '')
if config.get('logging', False):
logging.config.dictConfig(config.get('logging'))
log = logging.getLogger(f'{module_fn}')
main()