def add_split_results(self, knowledge_graph, result_bindings):
"""
Populate the object model with the resulting raw knowledge_graph and result_bindings (initially from QueryGraphReasoner)
:param nodes: knowledge_graph in native RTX KG dump
:param edges: result_bindings in a native format from QueryGraphReasoner
:return: none
"""
#### Add the knowledge_graph nodes
regular_node_attributes = [
"id", "uri", "name", "description", "symbol"
]
for input_node in knowledge_graph["nodes"]:
node = Node()
for attribute in regular_node_attributes:
if attribute in input_node:
setattr(node, attribute, input_node[attribute])
node.type = [input_node["category"]]
#node.node_attributes = FIXME
self.message.knowledge_graph.nodes.append(node)
#### Add the knowledge_graph edges
regular_edge_attributes = [
"id", "type", "relation", "source_id", "target_id",
"is_defined_by", "defined_datetime", "provided_by", "weight",
"evidence_type", "qualifiers", "negated", "", ""
]
for input_edge in knowledge_graph["edges"]:
edge = Edge()
for attribute in regular_edge_attributes:
if attribute in input_edge:
setattr(edge, attribute, input_edge[attribute])
if "probability" in input_edge:
edge.confidence = input_edge["probability"]
# missing edge properties: defined_datetime, weight, publications, evidence_type, qualifiers, negated
# extra edge properties: predicate,
#edge.edge_attributes = FIXME
#edge.publications = FIXME
self.message.knowledge_graph.edges.append(edge)
#### Add each result
self.message.results = []
for input_result in result_bindings:
result = Result()
result.description = "No description available"
result.essence = "?"
#result.essence_type = "?"
#result.row_data = "?"
#result.score = 0
#result.score_name = "?"
#result.score_direction = "?"
result.confidence = 1.0
result.result_type = "individual query answer"
result.reasoner_id = "RTX"
result.result_graph = None
result.node_bindings = input_result["nodes"]
# #### Convert each binding value to a list because the viewer requires it
# for binding in result.node_bindings:
# result.node_bindings[binding] = [ result.node_bindings[binding] ]
result.edge_bindings = input_result["edges"]
self.message.results.append(result)
#### Set the code_description
n_results = len(result_bindings)
plural = "s"
if n_results == 1: plural = ""
self.message.code_description = f"{n_results} result{plural} found"
#### Complete normally
return ()
def test1(self):
#### Create the response object and fill it with attributes about the response
response = Response()
response.context = "http://translator.ncats.io"
response.id = "http://rtx.ncats.io/api/v1/response/1234"
response.type = "medical_translator_query_response"
response.tool_version = "RTX 0.4"
response.schema_version = "0.5"
response.datetime = datetime.datetime.now().strftime(
"%Y-%m-%d %H:%M:%S")
response.original_question_text = "what proteins are affected by sickle cell anemia"
response.restated_question_text = "Which proteins are affected by sickle cell anemia?"
response.result_code = "OK"
response.message = "1 result found"
#### Create a disease node
node1 = Node()
node1.id = "http://omim.org/entry/603903"
node1.type = "disease"
node1.name = "sickle cell anemia"
node1.accession = "OMIM:603903"
node1.description = "A disease characterized by chronic hemolytic anemia..."
#### Create a protein node
node2 = Node()
node2.id = "https://www.uniprot.org/uniprot/P00738"
node2.type = "protein"
node2.name = "Haptoglobin"
node2.symbol = "HP"
node2.accession = "UNIPROT:P00738"
node2.description = "Haptoglobin captures, and combines with free plasma hemoglobin..."
#### Create a node attribute
node2attribute1 = NodeAttribute()
node2attribute1.type = "comment"
node2attribute1.name = "Complex_description"
node2attribute1.value = "The Hemoglobin/haptoglobin complex is composed of a haptoglobin dimer bound to two hemoglobin alpha-beta dimers"
node2.node_attributes = [node2attribute1]
#### Create an edge between these 2 nodes
edge1 = Edge()
edge1.type = "is_caused_by_a_defect_in"
edge1.source_id = node1.id
edge1.target_id = node2.id
edge1.confidence = 1.0
#### Add an origin and property for the edge
origin1 = Origin()
origin1.id = "https://api.monarchinitiative.org/api/bioentity/disease/OMIM:603903/genes/"
origin1.type = "Monarch_BioLink_API_Relationship"
#### Add an attribute
attribute1 = EdgeAttribute()
attribute1.type = "PubMed_article"
attribute1.name = "Orthopaedic Manifestations of Sickle Cell Disease"
attribute1.value = None
attribute1.url = "https://www.ncbi.nlm.nih.gov/pubmed/29309293"
origin1.attribute_list = [attribute1]
edge1.origin_list = [origin1]
#### Create the first result (potential answer)
result1 = Result()
result1.id = "http://rtx.ncats.io/api/v1/response/1234/result/2345"
result1.text = "A free text description of this result"
result1.confidence = 0.932
#### Create a ResultGraph object and put the list of nodes and edges into it
result_graph = ResultGraph()
result_graph.node_list = [node1, node2]
result_graph.edge_list = [edge1]
#### Put the ResultGraph into the first result (potential answer)
result1.result_graph = result_graph
#### Put the first result (potential answer) into the response
result_list = [result1]
response.result_list = result_list
print(response)
