def _convert_kg2_edge_to_swagger_edge(self, neo4j_edge):
swagger_edge = Edge()
swagger_edge.type = neo4j_edge.get('simplified_edge_label')
swagger_edge.source_id = neo4j_edge.get('subject')
swagger_edge.target_id = neo4j_edge.get('object')
swagger_edge.id = self._create_edge_id(swagger_edge)
swagger_edge.relation = neo4j_edge.get('relation')
swagger_edge.publications = ast.literal_eval(
neo4j_edge.get('publications'))
swagger_edge.provided_by = self._convert_strange_provided_by_field_to_list(
neo4j_edge.get('provided_by')
) # Temporary hack until provided_by is fixed in KG2
swagger_edge.negated = ast.literal_eval(neo4j_edge.get('negated'))
swagger_edge.is_defined_by = "ARAX/KG2"
swagger_edge.edge_attributes = []
# Add additional properties on KG2 edges as swagger EdgeAttribute objects
# TODO: fix issues coming from strange characters in 'publications_info'! (EOF error)
additional_kg2_edge_properties = [
'relation_curie', 'simplified_relation_curie',
'simplified_relation', 'edge_label'
]
edge_attributes = self._create_swagger_attributes(
"edge", additional_kg2_edge_properties, neo4j_edge)
swagger_edge.edge_attributes += edge_attributes
return swagger_edge
def _convert_kg1_edge_to_swagger_edge(self, neo4j_edge: Dict[str, any], node_uuid_to_curie_dict: Dict[str, str]) -> Edge:
swagger_edge = Edge()
swagger_edge.type = neo4j_edge.get("predicate")
swagger_edge.source_id = node_uuid_to_curie_dict[neo4j_edge.get("source_node_uuid")]
swagger_edge.target_id = node_uuid_to_curie_dict[neo4j_edge.get("target_node_uuid")]
swagger_edge.id = f"KG1:{neo4j_edge.get('id')}"
swagger_edge.relation = neo4j_edge.get("relation")
swagger_edge.provided_by = neo4j_edge.get("provided_by")
swagger_edge.is_defined_by = "ARAX/KG1"
if neo4j_edge.get("probability"):
swagger_edge.edge_attributes = self._create_swagger_attributes("edge", ["probability"], neo4j_edge)
return swagger_edge
def _convert_kg1_edge_to_swagger_edge(self, neo4j_edge,
node_uuid_to_curie_dict):
swagger_edge = Edge()
swagger_edge.type = neo4j_edge.get('predicate')
swagger_edge.source_id = node_uuid_to_curie_dict[neo4j_edge.get(
'source_node_uuid')]
swagger_edge.target_id = node_uuid_to_curie_dict[neo4j_edge.get(
'target_node_uuid')]
swagger_edge.id = self._create_edge_id(swagger_edge)
swagger_edge.relation = neo4j_edge.get('relation')
swagger_edge.provided_by = neo4j_edge.get('provided_by')
swagger_edge.is_defined_by = "ARAX/KG1"
if neo4j_edge.get('probability'):
swagger_edge.edge_attributes = self._create_swagger_attributes(
"edge", ['probability'], neo4j_edge)
return swagger_edge
def _convert_kg2_edge_to_swagger_edge(self, neo4j_edge: Dict[str, any]) -> Edge:
swagger_edge = Edge()
swagger_edge.id = f"KG2:{neo4j_edge.get('id')}"
swagger_edge.type = neo4j_edge.get("simplified_edge_label")
swagger_edge.source_id = neo4j_edge.get("subject")
swagger_edge.target_id = neo4j_edge.get("object")
swagger_edge.relation = neo4j_edge.get("relation")
swagger_edge.publications = ast.literal_eval(neo4j_edge.get("publications"))
swagger_edge.provided_by = self._convert_strange_provided_by_field_to_list(neo4j_edge.get("provided_by")) # Temporary hack until provided_by is fixed in KG2
swagger_edge.negated = ast.literal_eval(neo4j_edge.get("negated"))
swagger_edge.is_defined_by = "ARAX/KG2"
swagger_edge.edge_attributes = []
# Add additional properties on KG2 edges as swagger EdgeAttribute objects
# TODO: fix issues coming from strange characters in 'publications_info'! (EOF error)
additional_kg2_edge_properties = ["relation_curie", "simplified_relation_curie", "simplified_relation",
"edge_label"]
edge_attributes = self._create_swagger_attributes("edge", additional_kg2_edge_properties, neo4j_edge)
swagger_edge.edge_attributes += edge_attributes
return swagger_edge