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 _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 predict_drug_treats_disease(self):
"""
Iterate over all the edges in the knowledge graph, add the drug-disease treatment probability for appropriate edges
on the edge_attributes
:return: response
"""
parameters = self.parameters
self.response.debug(f"Computing drug disease treatment probability based on a machine learning model")
self.response.info(f"Computing drug disease treatment probability based on a machine learning model: See [this publication](https://doi.org/10.1101/765305) for more details about how this is accomplished.")
attribute_name = "probability_treats"
attribute_type = "EDAM:data_0951"
value = 0 # this will be the default value. If the model returns 0, or the default is there, don't include that edge
url = "https://doi.org/10.1101/765305"
# if you want to add virtual edges, identify the source/targets, decorate the edges, add them to the KG, and then add one to the QG corresponding to them
if 'virtual_relation_label' in parameters:
source_curies_to_decorate = set()
target_curies_to_decorate = set()
# identify the nodes that we should be adding virtual edges for
for node in self.message.knowledge_graph.nodes:
if hasattr(node, 'qnode_ids'):
if parameters['source_qnode_id'] in node.qnode_ids:
if "drug" in node.type or "chemical_substance" in node.type: # this is now NOT checked by ARAX_overlay
source_curies_to_decorate.add(node.id)
if parameters['target_qnode_id'] in node.qnode_ids:
if "disease" in node.type or "phenotypic_feature" in node.type: # this is now NOT checked by ARAX_overlay
target_curies_to_decorate.add(node.id)
added_flag = False # check to see if any edges where added
# iterate over all pairs of these nodes, add the virtual edge, decorate with the correct attribute
for (source_curie, target_curie) in itertools.product(source_curies_to_decorate, target_curies_to_decorate):
# create the edge attribute if it can be
# loop over all equivalent curies and take the highest probability
max_probability = 0
converted_source_curie = self.convert_to_trained_curies(source_curie)
converted_target_curie = self.convert_to_trained_curies(target_curie)
if converted_source_curie is None or converted_target_curie is None:
continue
res = list(itertools.product(converted_source_curie, converted_target_curie))
if len(res) != 0:
all_probabilities = self.pred.prob_all(res)
if isinstance(all_probabilities, list):
max_probability = max([value for value in all_probabilities if np.isfinite(value)])
value = max_probability
#probability = self.pred.prob_single('ChEMBL:' + source_curie[22:], target_curie) # FIXME: when this was trained, it was ChEMBL:123, not CHEMBL.COMPOUND:CHEMBL123
#if probability and np.isfinite(probability): # finite, that's ok, otherwise, stay with default
# value = probability[0]
edge_attribute = EdgeAttribute(type=attribute_type, name=attribute_name, value=str(value), url=url) # populate the edge attribute
if edge_attribute and value != 0:
added_flag = True
# make the edge, add the attribute
# edge properties
now = datetime.now()
edge_type = "probably_treats"
qedge_ids = [parameters['virtual_relation_label']]
relation = parameters['virtual_relation_label']
is_defined_by = "ARAX"
defined_datetime = now.strftime("%Y-%m-%d %H:%M:%S")
provided_by = "ARAX"
confidence = None
weight = None # TODO: could make the actual value of the attribute
source_id = source_curie
target_id = target_curie
# now actually add the virtual edges in
id = f"{relation}_{self.global_iter}"
self.global_iter += 1
edge = Edge(id=id, type=edge_type, relation=relation, source_id=source_id,
target_id=target_id,
is_defined_by=is_defined_by, defined_datetime=defined_datetime,
provided_by=provided_by,
confidence=confidence, weight=weight, edge_attributes=[edge_attribute], qedge_ids=qedge_ids)
self.message.knowledge_graph.edges.append(edge)
# Now add a q_edge the query_graph since I've added an extra edge to the KG
if added_flag:
edge_type = "probably_treats"
relation = parameters['virtual_relation_label']
qedge_id = parameters['virtual_relation_label']
q_edge = QEdge(id=relation, type=edge_type, relation=relation,
source_id=parameters['source_qnode_id'], target_id=parameters['target_qnode_id']) # TODO: ok to make the id and type the same thing?
self.message.query_graph.edges.append(q_edge)
return self.response
else: # you want to add it for each edge in the KG
# iterate over KG edges, add the information
try:
# map curies to types
curie_to_type = dict()
for node in self.message.knowledge_graph.nodes:
curie_to_type[node.id] = node.type
# then iterate over the edges and decorate if appropriate
for edge in self.message.knowledge_graph.edges:
# Make sure the edge_attributes are not None
if not edge.edge_attributes:
edge.edge_attributes = [] # should be an array, but why not a list?
# now go and actually get the NGD
source_curie = edge.source_id
target_curie = edge.target_id
source_types = curie_to_type[source_curie]
target_types = curie_to_type[target_curie]
if (("drug" in source_types) or ("chemical_substance" in source_types)) and (("disease" in target_types) or ("phenotypic_feature" in target_types)):
temp_value = 0
# loop over all pairs of equivalent curies and take the highest probability
max_probability = 0
converted_source_curie = self.convert_to_trained_curies(source_curie)
converted_target_curie = self.convert_to_trained_curies(target_curie)
if converted_source_curie is None or converted_target_curie is None:
continue
res = list(itertools.product(converted_source_curie, converted_target_curie))
if len(res) != 0:
all_probabilities = self.pred.prob_all(res)
if isinstance(all_probabilities, list):
max_probability = max([value for value in all_probabilities if np.isfinite(value)])
value = max_probability
#probability = self.pred.prob_single('ChEMBL:' + source_curie[22:], target_curie) # FIXME: when this was trained, it was ChEMBL:123, not CHEMBL.COMPOUND:CHEMBL123
#if probability and np.isfinite(probability): # finite, that's ok, otherwise, stay with default
# value = probability[0]
elif (("drug" in target_types) or ("chemical_substance" in target_types)) and (("disease" in source_types) or ("phenotypic_feature" in source_types)):
#probability = self.pred.prob_single('ChEMBL:' + target_curie[22:], source_curie) # FIXME: when this was trained, it was ChEMBL:123, not CHEMBL.COMPOUND:CHEMBL123
#if probability and np.isfinite(probability): # finite, that's ok, otherwise, stay with default
# value = probability[0]
max_probability = 0
converted_source_curie = self.convert_to_trained_curies(source_curie)
converted_target_curie = self.convert_to_trained_curies(target_curie)
if converted_source_curie is None or converted_target_curie is None:
continue
res = list(itertools.product(converted_target_curie, converted_source_curie))
if len(res) != 0:
all_probabilities = self.pred.prob_all(res)
if isinstance(all_probabilities, list):
max_probability = max([value for value in all_probabilities if np.isfinite(value)])
value = max_probability
else:
continue
if value != 0:
edge_attribute = EdgeAttribute(type=attribute_type, name=attribute_name, value=str(value), url=url) # populate the attribute
edge.edge_attributes.append(edge_attribute) # append it to the list of attributes
except:
tb = traceback.format_exc()
error_type, error, _ = sys.exc_info()
self.response.error(tb, error_code=error_type.__name__)
self.response.error(f"Something went wrong adding the drug disease treatment probability")
else:
self.response.info(f"Drug disease treatment probability successfully added to edges")
return self.response
def compute_ngd(self):
"""
Iterate over all the edges in the knowledge graph, compute the normalized google distance and stick that info
on the edge_attributes
:default: The default value to set for NGD if it returns a nan
:return: response
"""
if self.response.status != 'OK': # Catches any errors that may have been logged during initialization
self._close_database()
return self.response
parameters = self.parameters
self.response.debug(f"Computing NGD")
self.response.info(
f"Computing the normalized Google distance: weighting edges based on source/target node "
f"co-occurrence frequency in PubMed abstracts")
self.response.info(
"Converting CURIE identifiers to human readable names")
node_curie_to_name = dict()
try:
for node in self.message.knowledge_graph.nodes:
node_curie_to_name[node.id] = node.name
except:
tb = traceback.format_exc()
error_type, error, _ = sys.exc_info()
self.response.error(f"Something went wrong when converting names")
self.response.error(tb, error_code=error_type.__name__)
name = "normalized_google_distance"
type = "EDAM:data_2526"
value = self.parameters['default_value']
url = "https://arax.rtx.ai/api/rtx/v1/ui/#/PubmedMeshNgd"
# if you want to add virtual edges, identify the source/targets, decorate the edges, add them to the KG, and then add one to the QG corresponding to them
if 'virtual_relation_label' in parameters:
source_curies_to_decorate = set()
target_curies_to_decorate = set()
curies_to_names = dict()
# identify the nodes that we should be adding virtual edges for
for node in self.message.knowledge_graph.nodes:
if hasattr(node, 'qnode_ids'):
if parameters['source_qnode_id'] in node.qnode_ids:
source_curies_to_decorate.add(node.id)
curies_to_names[node.id] = node.name
if parameters['target_qnode_id'] in node.qnode_ids:
target_curies_to_decorate.add(node.id)
curies_to_names[node.id] = node.name
# Convert these curies to their canonicalized curies (needed for the local NGD system)
canonicalized_curie_map = self._get_canonical_curies_map(
list(source_curies_to_decorate.union(
target_curies_to_decorate)))
self.load_curie_to_pmids_data(canonicalized_curie_map.values())
added_flag = False # check to see if any edges where added
num_computed_total = 0
num_computed_slow = 0
self.response.debug(
f"Looping through node pairs and calculating NGD values")
# iterate over all pairs of these nodes, add the virtual edge, decorate with the correct attribute
for (source_curie,
target_curie) in itertools.product(source_curies_to_decorate,
target_curies_to_decorate):
# create the edge attribute if it can be
source_name = curies_to_names[source_curie]
target_name = curies_to_names[target_curie]
num_computed_total += 1
canonical_source_curie = canonicalized_curie_map.get(
source_curie, source_curie)
canonical_target_curie = canonicalized_curie_map.get(
target_curie, target_curie)
ngd_value = self.calculate_ngd_fast(canonical_source_curie,
canonical_target_curie)
if ngd_value is None:
ngd_value = self.NGD.get_ngd_for_all(
[source_curie, target_curie],
[source_name, target_name])
self.response.debug(
f"Had to use eUtils to compute NGD between {source_name} "
f"({canonical_source_curie}) and {target_name} ({canonical_target_curie}). "
f"Value is: {ngd_value}")
num_computed_slow += 1
if np.isfinite(
ngd_value
): # if ngd is finite, that's ok, otherwise, stay with default
value = ngd_value
edge_attribute = EdgeAttribute(
type=type, name=name, value=str(value),
url=url) # populate the NGD edge attribute
if edge_attribute:
added_flag = True
# make the edge, add the attribute
# edge properties
now = datetime.now()
edge_type = "has_normalized_google_distance_with"
qedge_ids = [parameters['virtual_relation_label']]
relation = parameters['virtual_relation_label']
is_defined_by = "ARAX"
defined_datetime = now.strftime("%Y-%m-%d %H:%M:%S")
provided_by = "ARAX"
confidence = None
weight = None # TODO: could make the actual value of the attribute
source_id = source_curie
target_id = target_curie
# now actually add the virtual edges in
id = f"{relation}_{self.global_iter}"
self.global_iter += 1
edge = Edge(id=id,
type=edge_type,
relation=relation,
source_id=source_id,
target_id=target_id,
is_defined_by=is_defined_by,
defined_datetime=defined_datetime,
provided_by=provided_by,
confidence=confidence,
weight=weight,
edge_attributes=[edge_attribute],
qedge_ids=qedge_ids)
self.message.knowledge_graph.edges.append(edge)
# Now add a q_edge the query_graph since I've added an extra edge to the KG
if added_flag:
#edge_type = parameters['virtual_edge_type']
edge_type = "has_normalized_google_distance_with"
relation = parameters['virtual_relation_label']
q_edge = QEdge(id=relation,
type=edge_type,
relation=relation,
source_id=parameters['source_qnode_id'],
target_id=parameters['target_qnode_id'])
self.message.query_graph.edges.append(q_edge)
self.response.info(f"NGD values successfully added to edges")
num_computed_fast = num_computed_total - num_computed_slow
percent_computed_fast = round(
(num_computed_fast / num_computed_total) * 100)
self.response.debug(
f"Used fastNGD for {percent_computed_fast}% of edges "
f"({num_computed_fast} of {num_computed_total})")
else: # you want to add it for each edge in the KG
# iterate over KG edges, add the information
try:
# Map all nodes to their canonicalized curies in one batch (need canonical IDs for the local NGD system)
canonicalized_curie_map = self._get_canonical_curies_map(
[node.id for node in self.message.knowledge_graph.nodes])
self.load_curie_to_pmids_data(canonicalized_curie_map.values())
num_computed_total = 0
num_computed_slow = 0
self.response.debug(
f"Looping through edges and calculating NGD values")
for edge in self.message.knowledge_graph.edges:
# Make sure the edge_attributes are not None
if not edge.edge_attributes:
edge.edge_attributes = [
] # should be an array, but why not a list?
# now go and actually get the NGD
source_curie = edge.source_id
target_curie = edge.target_id
source_name = node_curie_to_name[source_curie]
target_name = node_curie_to_name[target_curie]
num_computed_total += 1
canonical_source_curie = canonicalized_curie_map.get(
source_curie, source_curie)
canonical_target_curie = canonicalized_curie_map.get(
target_curie, target_curie)
ngd_value = self.calculate_ngd_fast(
canonical_source_curie, canonical_target_curie)
if ngd_value is None:
ngd_value = self.NGD.get_ngd_for_all(
[source_curie, target_curie],
[source_name, target_name])
self.response.debug(
f"Had to use eUtils to compute NGD between {source_name} "
f"({canonical_source_curie}) and {target_name} ({canonical_target_curie}). "
f"Value is: {ngd_value}")
num_computed_slow += 1
if np.isfinite(
ngd_value
): # if ngd is finite, that's ok, otherwise, stay with default
value = ngd_value
ngd_edge_attribute = EdgeAttribute(
type=type, name=name, value=str(value),
url=url) # populate the NGD edge attribute
edge.edge_attributes.append(
ngd_edge_attribute
) # append it to the list of attributes
except:
tb = traceback.format_exc()
error_type, error, _ = sys.exc_info()
self.response.error(tb, error_code=error_type.__name__)
self.response.error(
f"Something went wrong adding the NGD edge attributes")
else:
self.response.info(f"NGD values successfully added to edges")
num_computed_fast = num_computed_total - num_computed_slow
percent_computed_fast = round(
(num_computed_fast / num_computed_total) * 100)
self.response.debug(
f"Used fastNGD for {percent_computed_fast}% of edges "
f"({num_computed_fast} of {num_computed_total})")
self._close_database()
return self.response
def compute_ngd(self):
"""
Iterate over all the edges in the knowledge graph, compute the normalized google distance and stick that info
on the edge_attributes
:default: The default value to set for NGD if it returns a nan
:return: response
"""
parameters = self.parameters
self.response.debug(f"Computing NGD")
self.response.info(f"Computing the normalized Google distance: weighting edges based on source/target node "
f"co-occurrence frequency in PubMed abstracts")
self.response.info("Converting CURIE identifiers to human readable names")
node_curie_to_name = dict()
try:
for node in self.message.knowledge_graph.nodes:
node_curie_to_name[node.id] = node.name
except:
tb = traceback.format_exc()
error_type, error, _ = sys.exc_info()
self.response.error(f"Something went wrong when converting names")
self.response.error(tb, error_code=error_type.__name__)
self.response.warning(f"Utilizing API calls to NCBI eUtils, so this may take a while...")
name = "normalized_google_distance"
type = "data:2526"
value = self.parameters['default_value']
url = "https://arax.rtx.ai/api/rtx/v1/ui/#/PubmedMeshNgd"
ngd_method_counts = {"fast": 0, "slow": 0}
# if you want to add virtual edges, identify the source/targets, decorate the edges, add them to the KG, and then add one to the QG corresponding to them
if 'virtual_relation_label' in parameters:
source_curies_to_decorate = set()
target_curies_to_decorate = set()
curies_to_names = dict()
# identify the nodes that we should be adding virtual edges for
for node in self.message.knowledge_graph.nodes:
if hasattr(node, 'qnode_ids'):
if parameters['source_qnode_id'] in node.qnode_ids:
source_curies_to_decorate.add(node.id)
curies_to_names[node.id] = node.name
if parameters['target_qnode_id'] in node.qnode_ids:
target_curies_to_decorate.add(node.id)
curies_to_names[node.id] = node.name
added_flag = False # check to see if any edges where added
# iterate over all pairs of these nodes, add the virtual edge, decorate with the correct attribute
for (source_curie, target_curie) in itertools.product(source_curies_to_decorate, target_curies_to_decorate):
# create the edge attribute if it can be
source_name = curies_to_names[source_curie]
target_name = curies_to_names[target_curie]
self.response.debug(f"Computing NGD between {source_name} and {target_name}")
ngd_value, method_used = self.NGD.get_ngd_for_all_fast([source_curie, target_curie], [source_name, target_name])
ngd_method_counts[method_used] += 1
if np.isfinite(ngd_value): # if ngd is finite, that's ok, otherwise, stay with default
value = ngd_value
edge_attribute = EdgeAttribute(type=type, name=name, value=str(value), url=url) # populate the NGD edge attribute
if edge_attribute:
added_flag = True
# make the edge, add the attribute
# edge properties
now = datetime.now()
edge_type = "has_normalized_google_distance_with"
qedge_ids = [parameters['virtual_relation_label']]
relation = parameters['virtual_relation_label']
is_defined_by = "ARAX"
defined_datetime = now.strftime("%Y-%m-%d %H:%M:%S")
provided_by = "ARAX"
confidence = None
weight = None # TODO: could make the actual value of the attribute
source_id = source_curie
target_id = target_curie
# now actually add the virtual edges in
id = f"{relation}_{self.global_iter}"
self.global_iter += 1
edge = Edge(id=id, type=edge_type, relation=relation, source_id=source_id,
target_id=target_id,
is_defined_by=is_defined_by, defined_datetime=defined_datetime,
provided_by=provided_by,
confidence=confidence, weight=weight, edge_attributes=[edge_attribute], qedge_ids=qedge_ids)
self.message.knowledge_graph.edges.append(edge)
# Now add a q_edge the query_graph since I've added an extra edge to the KG
if added_flag:
#edge_type = parameters['virtual_edge_type']
edge_type = "has_normalized_google_distance_with"
relation = parameters['virtual_relation_label']
q_edge = QEdge(id=relation, type=edge_type, relation=relation,
source_id=parameters['source_qnode_id'], target_id=parameters[
'target_qnode_id'])
self.message.query_graph.edges.append(q_edge)
else: # you want to add it for each edge in the KG
# iterate over KG edges, add the information
try:
for edge in self.message.knowledge_graph.edges:
# Make sure the edge_attributes are not None
if not edge.edge_attributes:
edge.edge_attributes = [] # should be an array, but why not a list?
# now go and actually get the NGD
source_curie = edge.source_id
target_curie = edge.target_id
source_name = node_curie_to_name[source_curie]
target_name = node_curie_to_name[target_curie]
ngd_value, method_used = self.NGD.get_ngd_for_all_fast([source_curie, target_curie], [source_name, target_name])
ngd_method_counts[method_used] += 1
if np.isfinite(ngd_value): # if ngd is finite, that's ok, otherwise, stay with default
value = ngd_value
ngd_edge_attribute = EdgeAttribute(type=type, name=name, value=str(value), url=url) # populate the NGD edge attribute
edge.edge_attributes.append(ngd_edge_attribute) # append it to the list of attributes
except:
tb = traceback.format_exc()
error_type, error, _ = sys.exc_info()
self.response.error(tb, error_code=error_type.__name__)
self.response.error(f"Something went wrong adding the NGD edge attributes")
else:
self.response.info(f"NGD values successfully added to edges")
self.response.debug(f"Used fast NGD for {ngd_method_counts['fast']} edges, back-up NGD method for {ngd_method_counts['slow']}")
return self.response