def convert_fus(ast):
"""Convert BEL1 fus() to BEL2 fus()"""
parent_fn_name = ast.name_short
prefix_list = {'p': 'p.', 'r': 'r.', 'g': 'c.'}
prefix = prefix_list[parent_fn_name]
fus1_ns = ast.args[0].namespace
fus1_val = ast.args[0].value
arg_fus = ast.args[1]
fus_args = [None, '?', '?']
for idx, arg in enumerate(arg_fus.args):
fus_args[idx] = arg
fus2_ns = fus_args[0].namespace
fus2_val = fus_args[0].value
if fus_args[1] == '?':
fus1_range = fus_args[1]
else:
fus1_range = f'"{prefix}1_{fus_args[1].value}"'
if fus_args[2] == '?':
fus2_range = fus_args[2]
else:
fus2_range = f'"{prefix}{fus_args[2].value}_?"'
fus = Function('fus', spec, parent_function=ast)
fus.args = [
NSArg(fus1_ns, fus1_val, fus),
StrArg(fus1_range, fus),
NSArg(fus2_ns, fus2_val, fus),
StrArg(fus2_range, fus),
]
# Remove BEL
ast_args = ast.args
ast_args.pop(0)
ast_args.pop(0)
if ast_args == [None]:
ast_args = []
ast.args = []
ast.add_argument(fus)
if len(ast_args) > 0:
ast.args.extend(ast_args)
return ast
def convert_fus(ast):
"""Convert BEL1 fus() to BEL2 fus()"""
parent_fn_name = ast.name_short
prefix_list = {"p": "p.", "r": "r.", "g": "c."}
prefix = prefix_list[parent_fn_name]
fus1_ns = ast.args[0].namespace
fus1_val = ast.args[0].value
arg_fus = ast.args[1]
fus_args = [None, "?", "?"]
for idx, arg in enumerate(arg_fus.args):
fus_args[idx] = arg
fus2_ns = fus_args[0].namespace
fus2_val = fus_args[0].value
if fus_args[1] == "?":
fus1_range = fus_args[1]
else:
fus1_range = f'"{prefix}1_{fus_args[1].value}"'
if fus_args[2] == "?":
fus2_range = fus_args[2]
else:
fus2_range = f'"{prefix}{fus_args[2].value}_?"'
fus = Function("fus", version=version, parent=ast)
fus.args = [
NSArg(fus1_ns, fus1_val, fus),
StrArg(fus1_range, fus),
NSArg(fus2_ns, fus2_val, fus),
StrArg(fus2_range, fus),
]
# Remove BEL
ast_args = ast.args
ast_args.pop(0)
ast_args.pop(0)
if ast_args == [None]:
ast_args = []
ast.args = []
ast.add_argument(fus)
if len(ast_args) > 0:
ast.args.extend(ast_args)
return ast
def convert_tloc(ast):
"""Convert BEL1 tloc() to BEL2"""
from_loc_arg = ast.args[1]
to_loc_arg = ast.args[2]
from_loc = Function("fromLoc", version=version, parent=ast)
from_loc.add_argument(
NSArg(from_loc_arg.namespace, from_loc_arg.value, parent=from_loc))
to_loc = Function("toLoc", version=version, parent=ast)
to_loc.add_argument(
NSArg(to_loc_arg.namespace, to_loc_arg.value, parent=to_loc))
ast.args[1] = from_loc
ast.args[2] = to_loc
return ast
def add_ast_fn(d, spec, parent_function=None):
"""Convert dict AST to object AST Function
Args:
ast_fn: AST object Function
d: AST as dictionary
spec: BEL Specification
Return:
ast_fn
"""
if d["type"] == "Function":
ast_fn = Function(d["function"]["name"],
spec,
parent_function=parent_function)
for arg in d["args"]:
if arg["type"] == "Function":
ast_fn.add_argument(
add_ast_fn(arg, spec, parent_function=ast_fn))
elif arg["type"] == "NSArg":
ast_fn.add_argument(
NSArg(arg["nsarg"]["ns"], arg["nsarg"]["ns_val"], ast_fn))
elif arg["type"] == "StrArg":
ast_fn.add_argument(StrArg(arg["arg"], ast_fn))
return ast_fn
def add_ast_fn(d, spec, parent_function=None):
"""Convert dict AST to object AST Function
Args:
ast_fn: AST object Function
d: AST as dictionary
spec: BEL Specification
Return:
ast_fn
"""
if d['type'] == 'Function':
ast_fn = Function(d['function']['name'], spec, parent_function=parent_function)
for arg in d['args']:
if arg['type'] == 'Function':
ast_fn.add_argument(add_ast_fn(arg, spec, parent_function=ast_fn))
elif arg['type'] == 'NSArg':
ast_fn.add_argument(NSArg(arg['nsarg']['ns'], arg['nsarg']['ns_val'], ast_fn))
elif arg['type'] == 'StrArg':
ast_fn.add_argument(StrArg(arg['arg'], ast_fn))
return ast_fn
import copy
from typing import List, Any, Mapping, MutableSequence
from bel.lang.ast import BELAst, Function, NSArg
from structlog import get_logger
log = get_logger()
# Typings
Edges = MutableSequence[Mapping[str, Any]]
BELSpec = Mapping[str, Any]
ComputeRules = List[str]
locations = {
"extracellular": NSArg("GO", "extracellular space"),
"cellsurface": NSArg("GO", "cell surface"),
}
def compute_edges(ast: BELAst, spec: BELSpec) -> Edges:
"""Compute edges"""
edges = []
if ast.bel_object.__class__.__name__ == "BELAst":
edges.append(ast.bel_object)
process_ast(edges, ast, spec)
return edges