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parser.py
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parser.py
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"""KGCL parser."""
import logging
import sys
from pathlib import Path
from typing import List
import click
from kgcl_schema.utils import to_json, to_rdf, to_yaml
from lark import Lark, Token
from kgcl_schema.datamodel.kgcl import (ClassCreation, EdgeCreation, EdgeDeletion,
NewSynonym, NodeAnnotationChange, NodeCreation,
NodeDeepening, NodeDeletion, NodeMove,
NodeObsoletion, NodeRename, NodeShallowing,
NodeUnobsoletion, PlaceUnder, PredicateChange,
RemovedNodeFromSubset, RemoveUnder, Change, Session)
from kgcl_schema.datamodel.ontology_model import Edge
def id_generator():
"""Return a new ID for KGCL change operations."""
id = 0
while True:
yield id
id += 1
# initialise ID generator
id_gen = id_generator()
# initialise parser
path = Path(__file__).parent
kgcl_parser = Lark.open(str(path) + "/kgcl.lark", start="expression")
def parse(input: str) -> List[Change]:
"""
Parse a set of KGCL command separated by next-line operator.
Returns instantiated dataclass objects from model.kgcl_schema.
"""
statements = input.splitlines()
parsed = []
for s in statements:
parsed.append(parse_statement(s))
return parsed
def parse_statement(input: str) -> Change:
"""
Parse a KGCL command.
Return an instantiated dataclass object from model.kgcl_schema.
"""
tree = kgcl_parser.parse(input)
id = "kgcl_change_id_" + str(next(id_gen))
command = tree.data
if command == "rename":
return parse_rename(tree, id)
elif command == "obsolete":
return parse_obsolete(tree, id)
elif command == "unobsolete":
return parse_unobsolete(tree, id)
elif command == "delete":
return parse_delete(tree, id)
elif command == "move":
return parse_move(tree, id)
elif command == "deepen":
return parse_deepen(tree, id)
elif command == "shallow":
return parse_shallow(tree, id)
elif command == "create_edge":
return parse_create_edge(tree, id)
elif command == "delete_edge":
return parse_delete_edge(tree, id)
elif command == "change_relationship":
return parse_change_relationship(tree, id)
elif command == "change_annotation":
return parse_change_annotation(tree, id)
elif command == "create":
return parse_create(tree, id)
elif command == "create_class":
return parse_create_class(tree, id)
elif command == "create_synonym":
return parse_create_synonym(tree, id)
elif command == "remove_from_subset":
return parse_remove_from_subset(tree, id)
else:
raise NotImplementedError("No implementation for KGCL command: " + command)
# TODO: does not have a field for subsets
# if(command == "add_to_subset"):
# term_id = next(tree.find_data('id'))
# term_id_token = next(get_tokens(term_id))
# subset_id = next(tree.find_data('subset'))
# subset_id_token = next(get_tokens(subset_id))
# return AddNodeToSubset(
# id=id, in_subset=subset_id_token, about_node=term_id_token
# )
# TODO: more commands
# if(command == "merge"):
# if(command == "add"):
# if(command == "add_parent"):
# if(command == "add_annotation"):
# if(command == "add_axiom"): (in Manchester Syntax?)
# if(command == "add_class"):
# if(command == "add_text_definition"):
# if(command == "merge"):
def parse_remove_from_subset(tree, id):
"""Remove node from subset."""
term_id_token = extract(tree, "id")
subset_id_token = extract(tree, "subset")
return RemovedNodeFromSubset(
id=id, subset=subset_id_token, about_node=term_id_token
)
def parse_create_synonym(tree, id):
"""Create new synonym."""
entity_token = extract(tree, "entity")
entity, representation = get_entity_representation(entity_token)
synonym_string_token = extract(tree, "synonym")
synonym, representation2 = get_entity_representation(synonym_string_token)
language_token = extract(tree, "language")
qualifier_token = extract(tree, "synonym_qualifier")
return NewSynonym(
id=id,
about_node=entity,
about_node_representation=representation,
new_value=synonym,
qualifier=qualifier_token,
language=language_token,
)
def parse_create_class(tree, id):
"""Create new class."""
term_id_token = extract(tree, "id")
entity, representation = get_entity_representation(term_id_token)
return ClassCreation(
id=id, node_id=entity, about_node_representation=representation
)
# the KGCL model suggests the command
# 'create node {id} {label} with {annotation set}'
# TODO: handling of {annotation set}
def parse_create(tree, id):
"""Create a node."""
term_id_token = extract(tree, "id")
label_token = extract(tree, "label")
language_token = extract(tree, "language")
entity, representation = get_entity_representation(term_id_token)
return NodeCreation(
id=id,
about_node=entity,
about_node_representation=representation,
node_id=term_id_token,
name=label_token,
language=language_token,
)
def parse_change_annotation(tree, id):
"""Change node annotation."""
subject_token = extract(tree, "entity_subject")
predicate_token = extract(tree, "entity_predicate")
subject, s_representation = get_entity_representation(subject_token)
predicate, p_representation = get_entity_representation(predicate_token)
old_token = extract(tree, "old_entity_object")
new_token = extract(tree, "new_entity_object")
old, old_representation = get_entity_representation(old_token)
new, new_representation = get_entity_representation(new_token)
old_language_token = extract(tree, "old_language")
new_language_token = extract(tree, "new_language")
old_datatype_token = extract(tree, "old_datatype")
new_datatype_token = extract(tree, "new_datatype")
return NodeAnnotationChange(
id=id,
about_node=subject,
about_node_representation=s_representation,
annotation_property=predicate,
annotation_property_type=p_representation,
old_value=old,
new_value=new,
old_value_type=old_representation,
new_value_type=new_representation,
old_language=old_language_token,
new_language=new_language_token,
old_datatype=old_datatype_token,
new_datatype=new_datatype_token,
)
def parse_change_relationship(tree, id):
"""Change predicate."""
subject_token = extract(tree, "entity_subject")
object_token = extract(tree, "entity_object")
subject, s_representation = get_entity_representation(subject_token)
object, o_representation = get_entity_representation(object_token)
old_token = extract(tree, "old_entity")
new_token = extract(tree, "new_entity")
old, old_representation = get_entity_representation(old_token)
new, new_representation = get_entity_representation(new_token)
edge = Edge(
subject=subject,
predicate=old,
object=object,
subject_representation=s_representation,
predicate_representation=old_representation,
object_representation=o_representation,
)
language_token = extract(tree, "language")
datatype_token = extract(tree, "datatype")
return PredicateChange(
id=id,
about_edge=edge,
old_value=old,
new_value=new,
old_value_type=old_representation,
new_value_type=new_representation,
language=language_token,
datatype=datatype_token,
)
def parse_delete_edge(tree, id):
"""Delete edge."""
subject_token = extract(tree, "entity_subject")
predicate_token = extract(tree, "entity_predicate")
object_token = extract(tree, "entity_object_id")
subject, s_representation = get_entity_representation(subject_token)
predicate, p_representation = get_entity_representation(predicate_token)
object, o_representation = get_entity_representation(object_token)
if (
predicate == "rdfs:subClassOf"
or predicate == "<http://www.w3.org/2000/01/rdf-schema#subClassOf>"
):
return RemoveUnder(
id=id,
subject=subject,
predicate=predicate,
object=object,
subject_type=s_representation,
predicate_type=p_representation,
object_type=o_representation,
)
else:
return EdgeDeletion(
id=id,
subject=subject,
predicate=predicate,
object=object,
subject_type=s_representation,
predicate_type=p_representation,
object_type=o_representation,
)
def parse_create_edge(tree, id):
"""Create new edge."""
subject_token = extract(tree, "entity_subject")
predicate_token = extract(tree, "entity_predicate")
object_token = extract(tree, "entity_object_id")
subject, s_representation = get_entity_representation(subject_token)
predicate, p_representation = get_entity_representation(predicate_token)
object, o_representation = get_entity_representation(object_token)
if (
predicate == "rdfs:subClassOf"
or predicate == "<http://www.w3.org/2000/01/rdf-schema#subClassOf>"
):
return PlaceUnder(
id=id,
subject=subject,
predicate=predicate,
object=object,
subject_type=s_representation,
predicate_type=p_representation,
object_type=o_representation,
)
else:
return EdgeCreation(
id=id,
subject=subject,
predicate=predicate,
object=object,
subject_type=s_representation,
predicate_type=p_representation,
object_type=o_representation,
)
def parse_shallow(tree, id):
"""Perform node shallowing."""
entity_token = extract(tree, "entity")
old_token = extract(tree, "old_entity")
new_token = extract(tree, "new_entity")
entity, e_representation = get_entity_representation(entity_token)
old_entity, o_representation = get_entity_representation(old_token)
new_entity, n_representation = get_entity_representation(new_token)
edge = Edge(
subject=entity,
object=old_entity,
subject_representation=e_representation,
object_representation=o_representation,
)
return NodeShallowing(
id=id,
about_edge=edge,
old_value=old_entity,
new_value=new_entity,
old_object_type=o_representation,
new_object_type=n_representation,
)
def parse_deepen(tree, id):
"""Perform node deepening."""
entity_token = extract(tree, "entity")
old_token = extract(tree, "old_entity")
new_token = extract(tree, "new_entity")
entity, e_representation = get_entity_representation(entity_token)
old_entity, o_representation = get_entity_representation(old_token)
new_entity, n_representation = get_entity_representation(new_token)
edge = Edge(
subject=entity,
object=old_entity,
subject_representation=e_representation,
object_representation=o_representation,
)
return NodeDeepening(
id=id,
about_edge=edge,
old_value=old_entity,
new_value=new_entity,
old_object_type=o_representation,
new_object_type=n_representation,
)
def parse_move(tree, id):
"""Move a node."""
subject_token = extract(tree, "entity_subject")
predicate_token = extract(tree, "entity_predicate")
object_token = extract(tree, "entity_object")
subject, s_representation = get_entity_representation(subject_token)
predicate, p_representation = get_entity_representation(predicate_token)
object, o_representation = get_entity_representation(object_token)
old_token = extract(tree, "old_entity")
new_token = extract(tree, "new_entity")
old, old_representation = get_entity_representation(old_token)
new, new_representation = get_entity_representation(new_token)
edge = Edge(
subject=subject,
predicate=predicate,
object=object,
subject_representation=s_representation,
predicate_representation=p_representation,
object_representation=o_representation,
)
return NodeMove(
id=id,
about_edge=edge,
old_value=old,
new_value=new,
old_object_type=old_representation,
new_object_type=new_representation,
)
def parse_delete(tree, id):
"""Delete a node."""
entity_token = extract(tree, "entity")
entity, representation = get_entity_representation(entity_token)
return NodeDeletion(
id=id, about_node=entity, about_node_representation=representation
)
def parse_unobsolete(tree, id):
"""Unobsolete a node."""
entity_token = extract(tree, "entity")
entity, representation = get_entity_representation(entity_token)
return NodeUnobsoletion(
id=id, about_node=entity, about_node_representation=representation
)
def parse_obsolete(tree, id):
"""Obsolete a node."""
entity_token = extract(tree, "entity")
entity, representation = get_entity_representation(entity_token)
replacement_token = extract(tree, "replacement")
return NodeObsoletion(
id=id,
about_node=entity,
about_node_representation=representation,
has_direct_replacement=replacement_token,
)
def parse_rename(tree, id):
"""Rename a node."""
old_token = extract(tree, "old_label")
new_token = extract(tree, "new_label")
old_language = extract(tree, "old_language")
new_language = extract(tree, "new_language")
# TODO old_token and new_token are enclosed in ''
term_id_token = extract(tree, "id")
if term_id_token is not None:
entity, representation = get_entity_representation(term_id_token)
else:
entity = None
representation = None
return NodeRename(
id=id,
about_node=entity,
about_node_representation=representation,
old_value=old_token,
new_value=new_token,
old_language=old_language,
new_language=new_language,
)
def extract(tree, data):
"""Extract node."""
node = get_next(tree.find_data(data))
if node is not None:
node_token = next(get_tokens(node))
return node_token
else:
return None
def get_tokens(tree):
"""Get tokens."""
return tree.scan_values(lambda v: isinstance(v, Token))
def get_next(generator):
"""Next generator."""
try:
res = next(generator)
return res
except StopIteration:
return None
def get_entity_representation(entity):
"""Get entity representation."""
first_character = entity[0]
last_character = entity[-1:]
if first_character == "<" and last_character == ">":
return entity, "uri" # not removing brackets (TODO why?)
if first_character == "'" and last_character == "'" and entity[1] != "'":
return entity[1:-1], "label"
if first_character == '"' and last_character == '"':
return entity[1:-1], "literal"
if entity[0:3] == '"""' and entity[-3:] == '"""':
return entity[3:-3], "literal"
if entity[0:3] == "'''" and entity[-3:] == "'''":
return entity[3:-3], "literal"
# TODO: use predefined set of prefixes to identify CURIEs
return entity, "curie"
# return entity, "error"
@click.command()
@click.option("--output",
"-o",
type=click.File(mode='w'),
default=sys.stdout)
@click.option("--output-type",
"-O",
help="format for output")
@click.option("-v", "--verbose", count=True)
@click.argument('patches', nargs=-1)
def cli(patches, verbose: int, output, output_type):
"""
Parse a patch or patches specified in KGCL DSL
"""
if verbose >= 2:
logging.basicConfig(level=logging.DEBUG)
elif verbose == 1:
logging.basicConfig(level=logging.INFO)
else:
logging.basicConfig(level=logging.WARNING)
# parser kgcl_schema commands
changes = []
for patch in patches:
logging.info(f"Patch: {patch}")
changes += parse(patch)
session = Session(change_set=changes)
if output_type is None or output_type == 'yaml':
output.write(to_yaml(session))
elif output_type == 'json':
output.write(to_json(session))
elif output_type == 'rdf':
output.write(to_rdf(session))
else:
raise NotImplementedError(output_type)
if __name__ == "__main__":
cli()