def _convert_kg2_node_to_swagger_node(self, neo4j_node):
swagger_node = Node()
swagger_node.id = neo4j_node.get('id')
swagger_node.name = neo4j_node.get('name')
swagger_node.description = neo4j_node.get('description')
swagger_node.uri = neo4j_node.get('iri')
swagger_node.node_attributes = []
node_category = neo4j_node.get('category_label')
swagger_node.type = eu.convert_string_or_list_to_list(node_category)
# Fill out the 'symbol' property (only really relevant for nodes from UniProtKB)
if swagger_node.symbol is None and swagger_node.id.lower().startswith(
"uniprot"):
swagger_node.symbol = neo4j_node.get('name')
swagger_node.name = neo4j_node.get('full_name')
# Add all additional properties on KG2 nodes as swagger NodeAttribute objects
additional_kg2_node_properties = [
'publications', 'synonym', 'category', 'provided_by', 'deprecated',
'update_date'
]
node_attributes = self._create_swagger_attributes(
"node", additional_kg2_node_properties, neo4j_node)
swagger_node.node_attributes += node_attributes
return swagger_node
def _convert_kg1_node_to_swagger_node(neo4j_node: Dict[str, any]) -> Node:
swagger_node = Node()
swagger_node.id = neo4j_node.get('id')
swagger_node.name = neo4j_node.get('name')
swagger_node.symbol = neo4j_node.get('symbol')
swagger_node.description = neo4j_node.get('description')
swagger_node.uri = neo4j_node.get('uri')
swagger_node.node_attributes = []
node_category = neo4j_node.get('category')
swagger_node.type = eu.convert_string_or_list_to_list(node_category)
return swagger_node
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)