def get_edge(self, plan, source_name, source_type, target_name,
target_type, predicate, edge_direction):
""" Determine if a transition between two types is supported by
any of the registered sub-schemas.
"""
edge = None
schema = None
for schema_name, sub_schema_package in self.schema.items():
sub_schema = sub_schema_package['schema']
sub_schema_url = sub_schema_package['url']
#print (sub_schema)
if source_type in sub_schema:
print(f" --{schema_name} - {source_type} => {target_type}")
if target_type in sub_schema[source_type]:
top_schema = None
if len(plan) > 0:
top = plan[-1]
top_schema = top[0]
if top_schema == schema_name:
# this is the next edge in an ongoing segment.
top[2].append([
source_name, source_type, predicate,
edge_direction, target_name, target_type
])
else:
plan.append([
schema_name, sub_schema_url,
[[
source_name, source_type, predicate,
edge_direction, target_name, target_type
]]
])
else:
implicit_conversion = BiolinkModelWalker()
for conv_type in implicit_conversion.get_transitions(
source_type):
implicit_conversion_schema = "implicit_conversion"
implicit_conversion_url = self.schema[
implicit_conversion_schema]['url']
if conv_type in sub_schema:
print(
f" --impconv: {schema_name} - {conv_type} => {target_type}"
)
if target_type in sub_schema[conv_type]:
plan.append([
implicit_conversion_schema,
implicit_conversion_url,
[[
source_name, source_type, predicate,
edge_direction, conv_type, conv_type
]]
])
plan.append([
schema_name, sub_schema_url,
[[
conv_type, conv_type, predicate,
edge_direction, target_name, target_type
]]
])
def post(self):
"""
biolink-model conversions.
---
tag: validation
description: Convert biolink model types.
requestBody:
description: Input message
required: true
content:
application/json:
schema:
$ref: '#/definitions/Message'
responses:
'200':
description: Success
content:
text/plain:
schema:
type: string
example: "Successfully validated"
'400':
description: Malformed message
content:
text/plain:
schema:
type: string
"""
self.validate(request)
question = request.json['question_graph']
question_nodes = question['nodes']
source_node = question_nodes[0]
target_node = question_nodes[1]
target_type = target_node['type']
response = copy.deepcopy(request.json)
if len(question_nodes) == 2:
biolink_model_walker = BiolinkModelWalker()
conversion = biolink_model_walker.translate(
node=source_node, target_type=target_type)
if conversion is not None:
response['knowledge_graph'] = {
"nodes": [conversion],
"edges": []
}
response['answers'] = [{
'node_bindings': {
target_type: conversion['id']
}
}]
else:
raise ValueError(
f"Unable to convert {source_node} to {target_type}")
print(json.dumps(response, indent=2))
if not 'answers' in response:
response['answers'] = []
return self.normalize_message(response)
def plan_edge(self, plan, source, target, predicate):
""" Determine if a transition between two types is supported by
any of the registered sub-schemas.
"""
edge = None
schema = None
for schema_name, sub_schema_package in self.schema.schema.items():
""" Look for a path satisfying this edge in each schema. """
sub_schema = sub_schema_package['schema']
sub_schema_url = sub_schema_package['url']
if source.type_name in sub_schema:
logger.debug(
f" --{schema_name} - {source.type_name} => {target.type_name}"
)
if target.type_name in sub_schema[source.type_name]:
""" Matching path. Write it to the plan. """
top_schema = None
if len(plan) > 0:
top = plan[-1]
top_schema = top[0]
if top_schema == schema_name:
# this is the next edge in an ongoing segment.
top[2].append([source, predicate, target])
else:
plan.append([
schema_name, sub_schema_url,
[[source, predicate, target]]
])
else:
""" No explicit matching plan for this edge. Do implicit conversions make it work? """
implicit_conversion = BiolinkModelWalker()
for conv_type in implicit_conversion.get_transitions(
source.type_name):
implicit_conversion_schema = "implicit_conversion"
implicit_conversion_url = self.schema.schema[
implicit_conversion_schema]['url']
if conv_type in sub_schema:
logger.debug(
f" --impconv: {schema_name} - {conv_type} => {target.type_name}"
)
if target.type_name in sub_schema[conv_type]:
plan.append([
implicit_conversion_schema,
implicit_conversion_url,
[[
source, predicate,
Concept(name=conv_type,
type_name=conv_type,
include_patterns=target.
include_patterns,
exclude_patterns=target.
exclude_patterns)
]]
])
plan.append([
schema_name, sub_schema_url,
[[
Concept(name=conv_type,
type_name=conv_type,
include_patterns=source.
include_patterns,
exclude_patterns=source.
exclude_patterns), predicate,
target
]]
])