def orthologize(ctx, assertion_str, species, version):
"""Orthologize statement
species ID needs to be the NCBI Taxonomy ID in this format: TAX:<tax_id_number>
You can use the following common names for species id: human, mouse, rat
(basically whatever is supported at the api orthologs endpoint)
"""
print("------------------------------")
print(f"BEL version: {version}")
print("------------------------------")
bo = BEL(assertion_str, version=version)
bo.orthologize(species)
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("ORTHOLOGIZED ", bo.ast)
if bo.validation_messages:
print(bo.validation_messages)
else:
print("No problems found")
def stmt_validate(ctx, statement, version, api, config_fn):
"""Parse statement and validate """
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
api = utils.first_true([api, config["bel_api"]["servers"].get("api_url", None)], None)
version = utils.first_true(
[version, config["bel"]["lang"].get("default_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)
if bo.ast is None:
print(bo.original_bel_stmt)
print(bo.parse_visualize_error)
print(bo.validation_messages)
else:
print(bo.ast.to_triple())
if bo.validation_messages:
print(bo.validation_messages)
else:
print("No problems found")
return
def canonicalize(ctx, assertion_str, namespace_targets, version):
"""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
"""
version = bel.belspec.crud.check_version(version)
print("------------------------------")
print(f"BEL version: {version}")
print("------------------------------")
bo = BEL(assertion_str, version=version)
namespace_targets = [a for a in namespace_targets.split(",") if a]
bo.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")
def on_get(self, req, resp, version, belstr=''):
api_url = config['bel_api']['servers']['api_url']
bel_obj = BEL(version=version, api_url=api_url)
decanon_belstr = bel_obj.parse(belstr).decanonicalize().to_string()
resp.media = {'decanonicalized': decanon_belstr, 'original': belstr}
resp.status = falcon.HTTP_200
def on_get(self, req, resp, version, belstr=""):
api_url = config["bel_api"]["servers"]["api_url"]
bel_obj = BEL(version=version, api_url=api_url)
decanon_belstr = bel_obj.parse(belstr).decanonicalize().to_string()
resp.media = {"decanonicalized": decanon_belstr, "original": belstr}
resp.status = falcon.HTTP_200
def edges(ctx, statement, rules, species, namespace_targets, version, api, config_fn):
"""Create BEL Edges from BEL Statement"""
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)
if rules:
rules = rules.replace(" ", "").split(",")
namespace_targets = utils.first_true(
[namespace_targets, config["bel"]["lang"].get("canonical")], None
)
api_url = utils.first_true(
[api, config["bel_api"]["servers"].get("api_url", None)], None
)
version = utils.first_true(
[version, config["bel"]["lang"].get("default_bel_version", None)], None
)
print("------------------------------")
print("BEL version: {}".format(version))
print("API Endpoint: {}".format(api))
print("------------------------------")
bo = BEL(version=version, endpoint=api_url)
if species:
edges = (
bo.parse(statement)
.orthologize(species)
.canonicalize(namespace_targets=namespace_targets)
.compute_edges(rules=rules)
)
else:
edges = (
bo.parse(statement)
.canonicalize(namespace_targets=namespace_targets)
.compute_edges(rules=rules)
)
if edges is None:
print(bo.original_bel_stmt)
print(bo.parse_visualize_error)
print(bo.validation_messages)
else:
print(json.dumps(edges, indent=4))
if bo.validation_messages:
print(bo.validation_messages)
else:
print("No problems found")
return
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 on_get(self, req, resp, version, belstr=""):
namespace_targets = req.get_param("namespace_targets", default=None)
api_url = config["bel_api"]["servers"]["api_url"]
log.info(f"Api_url {api_url}")
bel_obj = BEL(version=version, api_url=api_url)
canon_belstr = (bel_obj.parse(belstr).canonicalize(
namespace_targets=namespace_targets).to_string())
# TODO figure out how to handle naked namespace:val better
if not canon_belstr:
canon_belstr = terms.canonicalize(belstr)
resp.media = {"canonicalized": canon_belstr, "original": belstr}
resp.status = falcon.HTTP_200
def on_get(self, req, resp, version, belstr=''):
namespace_targets = req.get_param('namespace_targets', default=None)
api_url = config['bel_api']['servers']['api_url']
log.info(f'Api_url {api_url}')
bel_obj = BEL(version=version, api_url=api_url)
canon_belstr = bel_obj.parse(belstr).canonicalize(
namespace_targets=namespace_targets).to_string()
# TODO figure out how to handle naked namespace:val better
log.info(f'Canonicalize BEL string {canon_belstr}')
if not canon_belstr:
canon_belstr = terms.canonicalize(belstr)
resp.media = {'canonicalized': canon_belstr, 'original': belstr}
resp.status = falcon.HTTP_200
def orthologize(ctx, statement, species, version, api, config_fn):
"""Orthologize statement
species ID needs to be the NCBI Taxonomy ID in this format: TAX:<tax_id_number>
You can use the following common names for species id: human, mouse, rat
(basically whatever is supported at the api orthologs endpoint)
"""
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
api_url = utils.first_true(
[api, config["bel_api"]["servers"].get("api_url", None)], None
)
version = utils.first_true(
[version, config["bel"]["lang"].get("default_bel_version", None)], None
)
print("------------------------------")
print("BEL version: {}".format(version))
print("API Endpoint: {}".format(api))
print("------------------------------")
bo = BEL(version=version, endpoint=api_url)
bo.parse(statement).orthologize(species)
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("ORTHOLOGIZED ", bo.ast)
if bo.validation_messages:
print(bo.validation_messages)
else:
print("No problems found")
return
def stmt_validate(ctx, assertion_str, version):
"""Parse statement and validate """
version = bel.belspec.crud.check_version(version)
print("------------------------------")
print(f"BEL version: {version}")
print("------------------------------")
bo = BEL(assertion_str, version=version)
if bo.ast is None:
print(bo.original_bel_stmt)
print(bo.parse_visualize_error)
print(bo.validation_messages)
else:
print(bo.ast.to_triple())
if bo.validation_messages:
print(bo.validation_messages)
else:
print("No problems found")
# Standard Library
import json
# Third Party
from loguru import logger
# Local
import bel.belspec.crud
import bel.core.settings as settings
from bel.belspec.crud import get_enhanced_belspec
from bel.lang.ast import BELAst, Function, NSArg, StrArg
from bel.lang.belobj import BEL
version = bel.belspec.crud.get_latest_version()
bo = BEL("", version=version)
belspec = get_enhanced_belspec(bo.version)
def migrate(belstr: str) -> str:
"""Migrate BEL 1 to 2.0.0
Args:
bel: BEL 1
Returns:
bel: BEL 2
"""
bo.parse(belstr)