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 _add_answers_to_kg(self, answer_kg, reasoner_std_response, input_qnode_id, output_qnode_id, qedge_id):
kg_to_qg_ids_dict = self._build_kg_to_qg_id_dict(reasoner_std_response['results'])
if reasoner_std_response['knowledge_graph']['edges']:
remapped_node_ids = dict()
self.response.debug(f"Got results back from BTE for this query "
f"({len(reasoner_std_response['knowledge_graph']['edges'])} edges)")
for node in reasoner_std_response['knowledge_graph']['nodes']:
swagger_node = Node()
bte_node_id = node.get('id')
swagger_node.name = node.get('name')
swagger_node.type = eu.convert_string_to_snake_case(node.get('type'))
# Map the returned BTE qg_ids back to the original qnode_ids in our query graph
bte_qg_id = kg_to_qg_ids_dict['nodes'].get(bte_node_id)
if bte_qg_id == "n0":
qnode_id = input_qnode_id
elif bte_qg_id == "n1":
qnode_id = output_qnode_id
else:
self.response.error("Could not map BTE qg_id to ARAX qnode_id", error_code="UnknownQGID")
return answer_kg
# Find and use the preferred equivalent identifier for this node (if it's an 'output' node)
if qnode_id == output_qnode_id:
if bte_node_id in remapped_node_ids:
swagger_node.id = remapped_node_ids.get(bte_node_id)
else:
equivalent_curies = [f"{prefix}:{eu.get_curie_local_id(local_id)}" for prefix, local_ids in
node.get('equivalent_identifiers').items() for local_id in local_ids]
swagger_node.id = eu.get_best_equivalent_curie(equivalent_curies, swagger_node.type)
remapped_node_ids[bte_node_id] = swagger_node.id
else:
swagger_node.id = bte_node_id
eu.add_node_to_kg(answer_kg, swagger_node, qnode_id)
for edge in reasoner_std_response['knowledge_graph']['edges']:
swagger_edge = Edge()
swagger_edge.id = edge.get("id")
swagger_edge.type = edge.get('type')
swagger_edge.source_id = remapped_node_ids.get(edge.get('source_id'), edge.get('source_id'))
swagger_edge.target_id = remapped_node_ids.get(edge.get('target_id'), edge.get('target_id'))
swagger_edge.is_defined_by = "BTE"
swagger_edge.provided_by = edge.get('edge_source')
# Map the returned BTE qg_id back to the original qedge_id in our query graph
bte_qg_id = kg_to_qg_ids_dict['edges'].get(swagger_edge.id)
if bte_qg_id != "e1":
self.response.error("Could not map BTE qg_id to ARAX qedge_id", error_code="UnknownQGID")
return answer_kg
eu.add_edge_to_kg(answer_kg, swagger_edge, qedge_id)
return answer_kg
def _create_ngd_edge(self, ngd_value: float, source_id: str,
target_id: str) -> Edge:
ngd_edge = Edge()
ngd_edge.type = self.ngd_edge_type
ngd_edge.source_id = source_id
ngd_edge.target_id = target_id
ngd_edge.id = f"NGD:{source_id}--{ngd_edge.type}--{target_id}"
ngd_edge.provided_by = "ARAX"
ngd_edge.is_defined_by = "ARAX"
ngd_edge.edge_attributes = [
EdgeAttribute(name=self.ngd_edge_attribute_name,
type=self.ngd_edge_attribute_type,
value=ngd_value,
url=self.ngd_edge_attribute_url)
]
return ngd_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
def add_subgraph(self,
nodes,
edges,
plain_text,
confidence,
return_result=False):
"""
Populate the object model using networkx neo4j subgraph
:param nodes: nodes in the subgraph (g.nodes(data=True))
:param edges: edges in the subgraph (g.edges(data=True))
:return: none
"""
# Get the relevant info from the nodes and edges
node_keys = []
node_descriptions = dict()
node_names = dict()
node_labels = dict()
node_uuids = dict()
node_accessions = dict()
node_iris = dict()
node_uuids2iri = dict()
node_curies = dict()
node_uuids2curie = dict()
for u, data in nodes:
node_keys.append(u)
if 'description' in data['properties']:
node_descriptions[u] = data['properties']['description']
else:
node_descriptions[u] = "None"
node_names[u] = data['properties']['name']
node_labels[u] = list(set(data['labels']).difference({'Base'}))[0]
node_uuids[u] = data['properties']['UUID']
node_accessions[u] = data['properties']['accession']
node_iris[u] = data['properties']['uri']
node_uuids2iri[data['properties']
['UUID']] = data['properties']['uri']
curie_id = data['properties']['id']
if curie_id.split(':')[0].upper() == "CHEMBL":
curie_id = "CHEMBL:CHEMBL" + curie_id.split(':')[1]
node_uuids2curie[data['properties']['UUID']] = curie_id
node_curies[
u] = curie_id # These are the actual CURIE IDS eg UBERON:00000941 (uri is the web address)
edge_keys = []
edge_types = dict()
edge_source_db = dict()
edge_source_iri = dict()
edge_target_iri = dict()
edge_source_curie = dict()
edge_target_curie = dict()
for u, v, data in edges:
edge_keys.append((u, v))
edge_types[(u, v)] = data['type']
edge_source_db[(u, v)] = data['properties']['provided_by']
edge_source_iri[(
u, v)] = node_uuids2iri[data['properties']['source_node_uuid']]
edge_target_iri[(
u, v)] = node_uuids2iri[data['properties']['target_node_uuid']]
edge_source_curie[(
u,
v)] = node_uuids2curie[data['properties']['source_node_uuid']]
edge_target_curie[(
u,
v)] = node_uuids2curie[data['properties']['target_node_uuid']]
# For each node, populate the relevant information
node_objects = []
node_iris_to_node_object = dict()
for node_key in node_keys:
node = Node()
node.id = node_curies[node_key]
node.type = node_labels[node_key]
node.name = node_names[node_key]
node.uri = node_iris[node_key]
node.accession = node_accessions[node_key]
node.description = node_descriptions[node_key]
node_objects.append(node)
node_iris_to_node_object[node_iris[node_key]] = node
# for each edge, create an edge between them
edge_objects = []
for u, v in edge_keys:
edge = Edge()
edge.type = edge_types[(u, v)]
edge.source_id = node_iris_to_node_object[edge_source_iri[(u,
v)]].id
edge.target_id = node_iris_to_node_object[edge_target_iri[(u,
v)]].id
#edge.origin_list = []
#edge.origin_list.append(edge_source_db[(u, v)]) # TODO: check with eric if this really should be a list and if it should contain the source DB('s)
edge_objects.append(edge)
#edge.attribute_list
#edge.confidence
#edge.evidence_type
edge.is_defined_by = "RTX"
#edge.provided_by = node_iris_to_node_object[edge_source_iri[(u, v)]].uri
edge.provided_by = edge_source_db[(u, v)]
#edge.publications
#edge.qualifiers
#edge.relation
#edge.source_id
#edge.target_id
#edge.type
# Create the result (potential answer)
result1 = Result()
result1.text = plain_text
result1.confidence = confidence
# Create a ResultGraph object and put the list of nodes and edges into it
result_graph = ResultGraph()
result_graph.node_list = node_objects
result_graph.edge_list = edge_objects
# Put the ResultGraph into the first result (potential answer)
result1.result_graph = result_graph
# Put the first result (potential answer) into the response
self._result_list.append(result1)
self.response.result_list = self._result_list
# Increment the number of results
self._num_results += 1
if self._num_results == 1:
self.response.message = "%s result found" % self._num_results
else:
self.response.message = "%s results found" % self._num_results
if return_result:
return result1
else:
pass
def add_neighborhood_graph(self, nodes, edges, confidence=None):
"""
Populate the object model using networkx neo4j subgraph
:param nodes: nodes in the subgraph (g.nodes(data=True))
:param edges: edges in the subgraph (g.edges(data=True))
:return: none
"""
# Get the relevant info from the nodes and edges
node_keys = []
node_descriptions = dict()
node_names = dict()
node_labels = dict()
node_uuids = dict()
node_accessions = dict()
node_iris = dict()
node_uuids2iri = dict()
node_curies = dict()
node_uuids2curie = dict()
for u, data in nodes:
node_keys.append(u)
if 'description' in data['properties']:
node_descriptions[u] = data['properties']['description']
else:
node_descriptions[u] = "None"
node_names[u] = data['properties']['name']
node_labels[u] = list(set(data['labels']).difference({'Base'}))[0]
node_uuids[u] = data['properties']['UUID']
node_accessions[u] = data['properties']['accession']
node_iris[u] = data['properties']['uri']
node_uuids2iri[data['properties']
['UUID']] = data['properties']['uri']
curie_id = data['properties']['id']
if curie_id.split(':')[0].upper() == "CHEMBL":
curie_id = "CHEMBL:CHEMBL" + curie_id.split(':')[1]
node_uuids2curie[data['properties']['UUID']] = curie_id
node_curies[
u] = curie_id # These are the actual CURIE IDS eg UBERON:00000941 (uri is the web address)
edge_keys = []
edge_types = dict()
edge_source_db = dict()
edge_source_iri = dict()
edge_target_iri = dict()
edge_source_curie = dict()
edge_target_curie = dict()
for u, v, data in edges:
edge_keys.append((u, v))
edge_types[(u, v)] = data['type']
edge_source_db[(u, v)] = data['properties']['provided_by']
edge_source_iri[(
u, v)] = node_uuids2iri[data['properties']['source_node_uuid']]
edge_target_iri[(
u, v)] = node_uuids2iri[data['properties']['target_node_uuid']]
edge_source_curie[(
u,
v)] = node_uuids2curie[data['properties']['source_node_uuid']]
edge_target_curie[(
u,
v)] = node_uuids2curie[data['properties']['target_node_uuid']]
# For each node, populate the relevant information
node_objects = []
node_iris_to_node_object = dict()
for node_key in node_keys:
node = Node()
node.id = node_curies[node_key]
node.type = node_labels[node_key]
node.name = node_names[node_key]
node.uri = node_iris[node_key]
node.accession = node_accessions[node_key]
node.description = node_descriptions[node_key]
node_objects.append(node)
node_iris_to_node_object[node_iris[node_key]] = node
# for each edge, create an edge between them
edge_objects = []
for u, v in edge_keys:
edge = Edge()
edge.type = edge_types[(u, v)]
edge.source_id = node_iris_to_node_object[edge_source_iri[(u,
v)]].id
edge.target_id = node_iris_to_node_object[edge_target_iri[(u,
v)]].id
#edge.origin_list = []
#edge.origin_list.append(edge_source_db[(u, v)]) # TODO: check with eric if this really should be a list and if it should contain the source DB('s)
edge.provided_by = edge_source_db[(u, v)]
edge.is_defined_by = "RTX"
edge_objects.append(edge)
# Create the result (potential answer)
result1 = Result()
text = "This is a subgraph extracted from the full RTX knowledge graph, including nodes and edges relevant to the query." \
" This is not an answer to the query per se, but rather an opportunity to examine a small region of the RTX knowledge graph for further study. " \
"Formal answers to the query are below."
result1.text = text
result1.confidence = confidence
result1.result_type = "neighborhood graph"
# Create a ResultGraph object and put the list of nodes and edges into it
result_graph = ResultGraph()
result_graph.node_list = node_objects
result_graph.edge_list = edge_objects
# Put the ResultGraph into the first result (potential answer)
result1.result_graph = result_graph
# Put the first result (potential answer) into the response
self._result_list.append(result1)
self.response.result_list = self._result_list
def add_subgraph(self,
nodes,
edges,
description,
confidence,
return_result=False,
suppress_bindings=False):
"""
Populate the object model using networkx neo4j subgraph
:param nodes: nodes in the subgraph (g.nodes(data=True))
:param edges: edges in the subgraph (g.edges(data=True))
:return: none
"""
# Get the relevant info from the nodes and edges
node_keys = []
node_descriptions = dict()
node_names = dict()
node_labels = dict()
node_uuids = dict()
node_accessions = dict()
node_iris = dict()
node_uuids2iri = dict()
node_curies = dict()
node_uuids2curie = dict()
for u, data in nodes:
node_keys.append(u)
if 'description' in data['properties']:
node_descriptions[u] = data['properties']['description']
else:
node_descriptions[u] = "None"
node_names[u] = data['properties']['name']
node_labels[u] = list(set(data['labels']).difference({'Base'}))[0]
node_uuids[u] = data['properties']['UUID']
node_accessions[u] = data['properties']['accession']
node_iris[u] = data['properties']['uri']
node_uuids2iri[data['properties']
['UUID']] = data['properties']['uri']
curie_id = data['properties']['id']
if curie_id.split(':')[0].upper() == "CHEMBL":
curie_id = "CHEMBL:CHEMBL" + curie_id.split(':')[1]
node_uuids2curie[data['properties']['UUID']] = curie_id
node_curies[
u] = curie_id # These are the actual CURIE IDS eg UBERON:00000941 (uri is the web address)
edge_keys = []
edge_types = dict()
edge_source_db = dict()
edge_source_iri = dict()
edge_target_iri = dict()
edge_source_curie = dict()
edge_target_curie = dict()
edge_ids = dict()
for u, v, data in edges:
edge_keys.append((u, v))
edge_types[(u, v)] = data['type']
edge_source_db[(u, v)] = data['properties']['provided_by']
edge_source_iri[(
u, v)] = node_uuids2iri[data['properties']['source_node_uuid']]
edge_target_iri[(
u, v)] = node_uuids2iri[data['properties']['target_node_uuid']]
edge_source_curie[(
u,
v)] = node_uuids2curie[data['properties']['source_node_uuid']]
edge_target_curie[(
u,
v)] = node_uuids2curie[data['properties']['target_node_uuid']]
edge_ids[(u, v)] = data['properties']['provided_by'] # FIXME
# For each node, populate the relevant information
node_objects = []
node_iris_to_node_object = dict()
for node_key in node_keys:
node = Node()
node.id = node_curies[node_key]
node.type = [node_labels[node_key]]
node.name = node_names[node_key]
node.uri = node_iris[node_key]
node.accession = node_accessions[node_key]
node.description = node_descriptions[node_key]
node_objects.append(node)
node_iris_to_node_object[node_iris[node_key]] = node
#### Add this node to the master knowledge graph
if node.id not in self._node_ids:
self.message.knowledge_graph.nodes.append(node)
self._node_ids[node.id] = node.type[
0] # Just take the first of potentially several FIXME
#### Create the bindings lists
node_bindings = list()
edge_bindings = list()
# for each edge, create an edge between them
edge_objects = []
for u, v in edge_keys:
edge = Edge()
#edge.id is set below when building the bindings
edge.type = edge_types[(u, v)]
edge.source_id = node_iris_to_node_object[edge_source_iri[(u,
v)]].id
edge.target_id = node_iris_to_node_object[edge_target_iri[(u,
v)]].id
edge_objects.append(edge)
#edge.attribute_list
#edge.confidence
#edge.evidence_type
edge.is_defined_by = "RTX"
edge.provided_by = edge_source_db[(u, v)]
#edge.publications
#edge.qualifiers
#edge.relation
#edge.source_id
#edge.target_id
#edge.type
#### Add this edge to the master knowledge graph
edge_str = "%s -%s- %s" % (edge.source_id, edge.type,
edge.target_id)
if edge_str not in self._edge_ids:
self.message.knowledge_graph.edges.append(edge)
edge.id = "%d" % self._edge_counter
self._edge_ids[edge_str] = edge.id
self._edge_counter += 1
else:
edge.id = self._edge_ids[edge_str]
#### Try to figure out how the source fits into the query_graph for the bindings
source_type = self._node_ids[edge.source_id]
if edge.source_id in self._type_map:
source_knowledge_map_key = self._type_map[edge.source_id]
else:
source_knowledge_map_key = self._type_map[source_type]
if not source_knowledge_map_key:
eprint(
"Expected to find '%s' in the response._type_map, but did not"
% source_type)
raise Exception(
"Expected to find '%s' in the response._type_map, but did not"
% source_type)
node_bindings.append(
NodeBinding(qg_id=source_knowledge_map_key,
kg_id=edge.source_id))
# if source_knowledge_map_key not in node_bindings:
# node_bindings[source_knowledge_map_key] = list()
# node_bindings_dict[source_knowledge_map_key] = dict()
# if edge.source_id not in node_bindings_dict[source_knowledge_map_key]:
# node_bindings[source_knowledge_map_key].append(edge.source_id)
# node_bindings_dict[source_knowledge_map_key][edge.source_id] = 1
#### Try to figure out how the target fits into the query_graph for the knowledge map
target_type = self._node_ids[edge.target_id]
if edge.target_id in self._type_map:
target_knowledge_map_key = self._type_map[edge.target_id]
else:
target_knowledge_map_key = self._type_map[target_type]
if not target_knowledge_map_key:
eprint(
"ERROR: Expected to find '%s' in the response._type_map, but did not"
% target_type)
raise Exception(
"Expected to find '%s' in the response._type_map, but did not"
% target_type)
node_bindings.append(
NodeBinding(qg_id=target_knowledge_map_key,
kg_id=edge.target_id))
# if target_knowledge_map_key not in node_bindings:
# node_bindings[target_knowledge_map_key] = list()
# node_bindings_dict[target_knowledge_map_key] = dict()
# if edge.target_id not in node_bindings_dict[target_knowledge_map_key]:
# node_bindings[target_knowledge_map_key].append(edge.target_id)
# node_bindings_dict[target_knowledge_map_key][edge.target_id] = 1
#### Try to figure out how the edge fits into the query_graph for the knowledge map
source_target_key = "e" + source_knowledge_map_key + "-" + target_knowledge_map_key
target_source_key = "e" + target_knowledge_map_key + "-" + source_knowledge_map_key
if edge.type in self._type_map:
knowledge_map_key = self._type_map[edge.type]
elif source_target_key in self._type_map:
knowledge_map_key = source_target_key
elif target_source_key in self._type_map:
knowledge_map_key = target_source_key
else:
eprint(
"ERROR: Expected to find '%s' or '%s' or '%s' in the response._type_map, but did not"
% (edge.type, source_target_key, target_source_key))
knowledge_map_key = "ERROR"
edge_bindings.append(
EdgeBinding(qg_id=knowledge_map_key, kg_id=edge.id))
# if knowledge_map_key not in edge_bindings:
# edge_bindings[knowledge_map_key] = list()
# edge_bindings_dict[knowledge_map_key] = dict()
# if edge.id not in edge_bindings_dict[knowledge_map_key]:
# edge_bindings[knowledge_map_key].append(edge.id)
# edge_bindings_dict[knowledge_map_key][edge.id] = 1
# Create the result (potential answer)
result1 = Result()
result1.reasoner_id = "RTX"
result1.description = description
result1.confidence = confidence
if suppress_bindings is False:
result1.node_bindings = node_bindings
result1.edge_bindings = edge_bindings
# Create a KnowledgeGraph object and put the list of nodes and edges into it
#### This is still legal, then is redundant with the knowledge map, so leave it out maybe
knowledge_graph = KnowledgeGraph()
knowledge_graph.nodes = node_objects
knowledge_graph.edges = edge_objects
if suppress_bindings is True:
result1.result_graph = knowledge_graph
# Put the first result (potential answer) into the message
self._results.append(result1)
self.message.results = self._results
# Increment the number of results
self._num_results += 1
if self._num_results == 1:
self.message.code_description = "%s result found" % self._num_results
else:
self.message.code_description = "%s results found" % self._num_results
#### Finish and return the result if requested
if return_result:
return result1
else:
pass