def get_ast_obj(belstr, bel_version, component_type: str = ''):
"""Convert AST partialparse dict to BELAst"""
ast_dict, errors = get_ast_dict(belstr, component_type)
spec = bel_specification.get_specification(bel_version)
subj = ast_dict['subject']
subj_ast = add_ast_fn(subj, spec)
relation = None
obj = None
if 'relation' in ast_dict:
relation = ast_dict['relation']['name']
if 'object' in ast_dict:
obj = ast_dict['object']
obj_ast = add_ast_fn(obj, spec)
return BELAst(subj_ast, relation, obj_ast, spec)
elif 'nested' in ast_dict:
nested_subj = ast_dict['nested']['subject']
nested_subj_ast = add_ast_fn(nested_subj, spec)
nested_relation = ast_dict['nested']['relation']['name']
nested_obj = ast_dict['nested']['object']
nested_obj_ast = add_ast_fn(nested_obj, spec)
return BELAst(subj_ast, relation, BELAst(nested_subj_ast, nested_relation, nested_obj_ast, spec), spec)
return BELAst(subj_ast, None, None, spec)
def get_ast_obj(belstr, bel_version, component_type: str = ""):
"""Convert AST partialparse dict to BELAst"""
ast_dict, errors = get_ast_dict(belstr, component_type)
spec = bel_specification.get_specification(bel_version)
subj = ast_dict["subject"]
subj_ast = add_ast_fn(subj, spec)
relation = None
obj = None
if "relation" in ast_dict:
relation = ast_dict["relation"]["name"]
if "object" in ast_dict:
obj = ast_dict["object"]
obj_ast = add_ast_fn(obj, spec)
return BELAst(subj_ast, relation, obj_ast, spec)
elif "nested" in ast_dict:
nested_subj = ast_dict["nested"]["subject"]
nested_subj_ast = add_ast_fn(nested_subj, spec)
nested_relation = ast_dict["nested"]["relation"]["name"]
nested_obj = ast_dict["nested"]["object"]
nested_obj_ast = add_ast_fn(nested_obj, spec)
return BELAst(
subj_ast, relation,
BELAst(nested_subj_ast, nested_relation, nested_obj_ast, spec),
spec)
return BELAst(subj_ast, None, None, spec)
def __init__(self, version: str = None, api_url: str = None) -> None:
"""Initialize BEL object used for validating/processing/etc BEL statements
Args:
version (str): BEL Version, defaults to config['bel']['lang']['default_bel_version']
api_url (str): BEL API endpoint, defaults to config['bel_api']['servers']['api_url']
"""
bel_versions = bel_specification.get_bel_versions()
# use bel_utils._default_to_version to check if valid version, and if it exists or not
if not version:
self.version = config["bel"]["lang"]["default_bel_version"]
else:
self.version = version
if self.version not in bel_versions:
log.warning(
f"Cannot validate with invalid version: {self.version} in BEL Versions: {bel_versions}"
)
if not api_url:
self.api_url = config["bel_api"]["servers"]["api_url"]
else:
self.api_url = api_url
# Validation error/warning messages
# List[Tuple[str, str]], e.g. [('ERROR', 'this is an error msg'), ('WARNING', 'this is a warning'), ]
self.validation_messages = []
# self.semantics = BELSemantics() # each instance also instantiates a BELSemantics object used in parsing statements
self.spec = bel_specification.get_specification(self.version)
# bel_utils._dump_spec(self.spec)
# Import Tatsu parser
# use importlib to import our parser (a .py file) and set the BELParse object as an instance variable
try:
parser_fn = self.spec["admin"]["parser_fn"]
parser_name = os.path.basename(parser_fn).replace(".py", "")
module_spec = importlib.util.spec_from_file_location(
parser_name, parser_fn)
imported_parser = importlib.util.module_from_spec(module_spec)
module_spec.loader.exec_module(imported_parser)
self.parser = imported_parser.BELParser()
except Exception as e:
# if not found, we raise the NoParserFound exception which can be found in bel.lang.exceptions
raise bel_ex.NoParserFound(f"Version: {self.version} Msg: {e}")
def main():
bel_version = "2.0.0"
bel_spec = bel_specification.get_specification(bel_version)
belstr = "compositeAbundance(proteinAbundance(HGNC:FN1), proteinAbundance(HGNC:VEGFA)) increases translocation(proteinAbundance(HGNC:PRKCA), fromLoc(MESH:Intracellular Space), toLoc(MESH:Cell Membrane))"
belstr = 'proteinAbundance(HGNC:VEGFA) increases (compositeAbundance(proteinAbundance(HGNC:ITGB1), proteinAbundance(HGNC:PRKCA, ma(kin))) increases biologicalProcess(GO:"cell-matrix adhesion"))'
belstr = "complex(p(HGNC:EGFR))"
# belstr = 'p(HGNC:AKT)'
cursor_loc = 18
completions = bel_completion(belstr, cursor_loc, bel_fmt="long")
print("Completions:\n", json.dumps(completions, indent=4))
quit()
ast, errors = pparse.get_ast_dict(belstr)
# print('AST:\n', json.dumps(ast, indent=4))
# quit()
cursor_loc = 8
results = cursor(belstr, ast, cursor_loc)
print(f"Cursor{cursor_loc}:\n", json.dumps(results, indent=4))
quit()
bel_comp = ""
bel_fmt = "long"
species_id = "TAX:9606"
completions = get_completions(belstr, cursor_loc, functions, bel_spec,
bel_comp, bel_fmt, species_id)
print("Completions:\n", json.dumps(completions, indent=4))
quit()
completions = ns_completions("AKT", ["Protein"], "TAX:9606", 10)
print("Completions:\n", json.dumps(completions, indent=4))
quit()
# completions = bel_completion('pa', bel_fmt='long')
# print('DumpVar:\n', json.dumps(completions, indent=4))
completions = bel_completion("path(", cursor_loc=1, bel_fmt="medium")
print("DumpVar:\n", json.dumps(completions, indent=4))
def bel_completion(
belstr: str,
cursor_loc: int = -1,
bel_version: str = default_bel_version,
bel_comp: str = None,
bel_fmt: str = "medium",
species_id: str = None,
size: int = 20,
) -> Mapping[str, Any]:
"""BEL Completion
Args:
belstr (str): BEL String to provide completion for
cursor_loc (int): cursor location - default of -1 means end of string
bel_version (str): BEL Language version to use for completion
bel_comp (str): ['subject', 'object', 'full', None] - a nested statement has to be found in object or full statement
bel_fmt (str): ['short', 'medium', 'long'] BEL function/relation format
species_id (str): optional, species id is used to filter namespace values if applicable (e.g. Gene, RNA, ... entity_types)
size: how many completions to return, defaults to 20
Returns:
Mapping[str, Any]:
{
'completions': completions,
'function_help': function_help,
'entity_spans': spans
}
"""
"""
Completion object: {
completions: [
{
'replacement': <replacement text field string,
'cursor_loc': <new cursor location>
'highlight': <highlighted match>
'label': <label for completion>
},
],
function_help: [{
"function_summary": <template>,
"argument_help": [<argument help>],
"description": <desc>
}],
"entity_spans": {<span info>}
}
"""
bel_spec = bel_specification.get_specification(bel_version)
belstrlen = len(belstr)
if cursor_loc == -1:
cursor_loc = belstrlen - 1
elif cursor_loc >= belstrlen:
cursor_loc = belstrlen - 1
# with timy.Timer() as timer:
# (completion_text, completions, function_help, spans) = get_completions(belstr, cursor_loc, bel_spec, bel_comp, bel_fmt, species_id, size)
(completion_text, completions, function_help,
spans) = get_completions(belstr, cursor_loc, bel_spec, bel_comp, bel_fmt,
species_id, size)
return {
"completion_text": completion_text,
"completions": completions,
"function_help": function_help,
"entity_spans": spans,
}
