def create_message(self, describe=False):
"""
Creates a basic empty Message object with basic boilerplate metadata
:return: Response object with execution information and the new message object inside the data envelope
:rtype: Response
"""
# Internal documentation setup
#allowable_parameters = { 'action': { 'None' } }
allowable_parameters = {
'dsl_command': '`create_message()`'
} # can't get this name at run-time, need to manually put it in per https://www.python.org/dev/peps/pep-3130/
if describe:
allowable_parameters[
'brief_description'] = """The `create_message` method creates a basic empty Message object with basic boilerplate metadata
such as reasoner_id, schema_version, etc. filled in. This DSL command takes no arguments"""
return allowable_parameters
#### Define a default response
response = Response()
self.response = response
#### Create the top-level message
response.info("Creating an empty template ARAX Message")
message = Message()
self.message = message
#### Fill it with default information
message.id = None
message.type = "translator_reasoner_message"
message.reasoner_id = "ARAX"
message.tool_version = RTXConfiguration().version
message.schema_version = "0.9.3"
message.message_code = "OK"
message.code_description = "Created empty template Message"
message.context = "https://raw.githubusercontent.com/biolink/biolink-model/master/context.jsonld"
#### Why is this _datetime ?? FIXME
message._datetime = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
#### Create an empty master knowledge graph
message.knowledge_graph = KnowledgeGraph()
message.knowledge_graph.nodes = []
message.knowledge_graph.edges = []
#### Create an empty query graph
message.query_graph = QueryGraph()
message.query_graph.nodes = []
message.query_graph.edges = []
#### Create empty results
message.results = []
message.n_results = 0
#### Return the response
response.data['message'] = message
return response
def from_dict(self, message):
if str(message.__class__
) != "<class 'swagger_server.models.message.Message'>":
message = Message().from_dict(message)
message.query_graph = QueryGraph().from_dict(message.query_graph)
message.knowledge_graph = KnowledgeGraph().from_dict(
message.knowledge_graph)
#### This is an unfortunate hack that fixes qnode.curie entries
#### Officially a curie can be a str or a list. But Swagger 2.0 only permits one type and we set it to str
#### so when it gets converted from_dict, the list gets converted to a str because that's its type
#### Here we force it back. This should no longer be needed when we are properly on OpenAPI 3.0
if message.query_graph is not None and message.query_graph.nodes is not None:
for qnode in message.query_graph.nodes:
if qnode.curie is not None and isinstance(qnode.curie, str):
if qnode.curie[0:2] == "['":
try:
qnode.curie = ast.literal_eval(qnode.curie)
except:
pass
#new_nodes = []
#for qnode in message.query_graph.nodes:
# print(type(qnode))
# new_nodes.append(QNode().from_dict(qnode))
#message.query_graph.nodes = new_nodes
#for qedge in message.query_graph.edges:
# new_edges.append(QEdge().from_dict(qedge))
#message.query_graph.edges = new_edges
if message.results is not None:
for result in message.results:
if result.result_graph is not None:
#eprint(str(result.result_graph.__class__))
if str(
result.result_graph.__class__
) != "<class 'swagger_server.models.knowledge_graph.KnowledgeGraph'>":
result.result_graph = KnowledgeGraph().from_dict(
result.result_graph)
return message