def test_create_message_basic():
messenger = ARAXMessenger()
response = messenger.create_message()
assert response.status == 'OK'
message = response.data['message']
assert message.type == 'translator_reasoner_message'
assert message.schema_version == '0.9.3'
def test_add_qnode_bad_parameters():
messenger = ARAXMessenger()
response = messenger.create_message()
assert response.status == 'OK'
message = response.data['message']
bad_parameters_list = [
{
'parameters': ['curie', 'PICKLES:123'],
'error_code': 'ParametersNotDict'
},
{
'parameters': {
'curie': 'UniProtKB:P14136',
'is_set': 'true'
},
'error_code': 'CurieScalarButIsSetTrue'
},
{
'parameters': {
'pickles': 'on the side'
},
'error_code': 'UnknownParameter'
},
]
reference_message = copy.deepcopy(message)
for bad_parameters in bad_parameters_list:
message = copy.deepcopy(reference_message)
print(bad_parameters)
response = messenger.add_qnode(message, bad_parameters['parameters'])
assert response.status == 'ERROR'
assert len(message.query_graph.nodes) == 0
assert response.error_code == bad_parameters['error_code']
def test_create_message_node_edge_types():
messenger = ARAXMessenger()
response = messenger.create_message()
assert response.status == 'OK'
message = response.data['message']
assert isinstance(message.knowledge_graph.nodes, list)
assert isinstance(message.knowledge_graph.edges, list)
assert isinstance(message.query_graph.nodes, list)
assert isinstance(message.query_graph.edges, list)
def test_add_qnode_bad_name():
messenger = ARAXMessenger()
response = messenger.create_message()
assert response.status == 'OK'
message = response.data['message']
response = messenger.add_qnode(message, {'name': 'Big Bird'})
assert response.status == 'ERROR'
assert isinstance(message.query_graph.nodes, list)
assert len(message.query_graph.nodes) == 0
assert response.error_code == 'UnknownCURIE'
def test_add_qnode_basic():
messenger = ARAXMessenger()
response = messenger.create_message()
assert response.status == 'OK'
message = response.data['message']
response = messenger.add_qnode(message, {})
assert response.status == 'OK'
assert isinstance(message.query_graph.nodes, list)
assert len(message.query_graph.nodes) == 1
assert message.query_graph.nodes[0].id == 'n00'
def main():
# Note that most of this is just manually doing what ARAXQuery() would normally do for you
response = Response()
from actions_parser import ActionsParser
actions_parser = ActionsParser()
actions_list = [
"create_message",
"add_qnode(id=n00, curie=CHEMBL.COMPOUND:CHEMBL112)", # acetaminophen
"add_qnode(id=n01, type=protein, is_set=true)",
"add_qedge(id=e00, source_id=n00, target_id=n01)",
"expand(edge_id=e00, kp=BTE)",
"return(message=true, store=false)",
]
# Parse the raw action_list into commands and parameters
result = actions_parser.parse(actions_list)
response.merge(result)
if result.status != 'OK':
print(response.show(level=Response.DEBUG))
return response
actions = result.data['actions']
from ARAX_messenger import ARAXMessenger
messenger = ARAXMessenger()
expander = ARAXExpander()
for action in actions:
if action['command'] == 'create_message':
result = messenger.create_message()
message = result.data['message']
response.data = result.data
elif action['command'] == 'add_qnode':
result = messenger.add_qnode(message, action['parameters'])
elif action['command'] == 'add_qedge':
result = messenger.add_qedge(message, action['parameters'])
elif action['command'] == 'expand':
result = expander.apply(message, action['parameters'])
elif action['command'] == 'return':
break
else:
response.error(f"Unrecognized command {action['command']}",
error_code="UnrecognizedCommand")
print(response.show(level=Response.DEBUG))
return response
# Merge down this result and end if we're in an error state
response.merge(result)
if result.status != 'OK':
print(response.show(level=Response.DEBUG))
return response
# Show the final response
# print(json.dumps(ast.literal_eval(repr(message.knowledge_graph)),sort_keys=True,indent=2))
print(response.show(level=Response.DEBUG))
def test_add_qnode_name():
messenger = ARAXMessenger()
response = messenger.create_message()
assert response.status == 'OK'
message = response.data['message']
response = messenger.add_qnode(message, {'name': 'acetaminophen'})
assert response.status == 'OK'
assert isinstance(message.query_graph.nodes, list)
assert len(message.query_graph.nodes) == 1
assert message.query_graph.nodes[0].id == 'n00'
assert message.query_graph.nodes[0].curie == 'CHEMBL.COMPOUND:CHEMBL112'
def test_add_qnode_curie_scalar():
messenger = ARAXMessenger()
response = messenger.create_message()
assert response.status == 'OK'
message = response.data['message']
response = messenger.add_qnode(message, {'curie': 'UniProtKB:P14136'})
assert response.status == 'OK'
assert isinstance(message.query_graph.nodes, list)
assert len(message.query_graph.nodes) == 1
assert message.query_graph.nodes[0].id == 'n00'
assert message.query_graph.nodes[0].curie == 'UniProtKB:P14136'
def test_add_qedge_multitest():
# Set up a message with two nodes
messenger = ARAXMessenger()
response = messenger.create_message()
assert response.status == 'OK'
message = response.data['message']
response = messenger.add_qnode(message, {'name': 'acetaminophen'})
assert response.status == 'OK'
response = messenger.add_qnode(message, {'type': 'protein'})
assert response.status == 'OK'
# Set up a list of parameters to feed to add_qedge() and what the result should be
parameters_list = [
{
'status': 'ERROR',
'parameters': ['source_id', 'n00'],
'error_code': 'ParametersNotDict'
},
{
'status': 'OK',
'parameters': {
'source_id': 'n00',
'target_id': 'n01'
},
'error_code': 'OK'
},
{
'status': 'OK',
'parameters': {
'source_id': 'n00',
'target_id': 'n01',
'id': 'e99'
},
'error_code': 'OK'
},
{
'status': 'OK',
'parameters': {
'source_id': 'n00',
'target_id': 'n01',
'id': 'e99',
'type': 'physically_interacts_with'
},
'error_code': 'OK'
},
{
'status': 'ERROR',
'parameters': {
'source_id': 'n00'
},
'error_code': 'MissingTargetId'
},
{
'status': 'ERROR',
'parameters': {
'target_id': 'n00'
},
'error_code': 'MissingSourceId'
},
{
'status': 'ERROR',
'parameters': {
'source_id': 'n99',
'target_id': 'n01'
},
'error_code': 'UnknownSourceId'
},
{
'status': 'ERROR',
'parameters': {
'source_id': 'n00',
'target_id': 'n99'
},
'error_code': 'UnknownTargetId'
},
{
'status': 'ERROR',
'parameters': {
'pickles': 'on the side'
},
'error_code': 'UnknownParameter'
},
]
# Loop over all the parameter sets and try to run it
reference_message = copy.deepcopy(message)
for parameters in parameters_list:
message = copy.deepcopy(reference_message)
print(parameters)
response = messenger.add_qedge(message, parameters['parameters'])
assert response.status == parameters['status']
if parameters['status'] == 'OK':
assert len(message.query_graph.edges) == 1
continue
assert len(message.query_graph.edges) == 0
assert response.error_code == parameters['error_code']
def main():
#### Some qnode examples
test_query_graphs = [
[{
'id': 'n10',
'curie': 'DOID:9281'
}, {
'id': 'n11',
'type': 'protein'
}, {
'id': 'e10',
'source_id': 'n10',
'target_id': 'n11'
}],
[{
'id': 'n10',
'curie': 'DOID:9281'
}, {
'id': 'n11',
'type': 'protein'
}, {
'id': 'n12',
'type': 'chemical_substance'
}, {
'id': 'e10',
'source_id': 'n10',
'target_id': 'n11'
}, {
'id': 'e11',
'source_id': 'n11',
'target_id': 'n12'
}],
[{
'id': 'n10',
'curie': 'DOID:9281'
}, {
'id': 'n11',
'type': 'chemical_substance'
}, {
'id': 'e10',
'source_id': 'n10',
'target_id': 'n11'
}],
[{
'id': 'n10',
'curie': 'DOID:9281',
'type': 'disease'
}, {
'id': 'n11',
'type': 'chemical_substance'
}, {
'id': 'e10',
'source_id': 'n10',
'target_id': 'n11'
}],
]
#interpreter = ARAXQueryGraphInterpreter()
#print(json.dumps(interpreter.query_graph_tree,sort_keys=True,indent=2))
#return
for test_query_graph in test_query_graphs:
#### Create a response object for each test
response = Response()
#### Create a template Message
messenger = ARAXMessenger()
result = messenger.create_message()
response.merge(result)
message = messenger.message
for parameters in test_query_graph:
if 'n' in parameters['id']:
result = messenger.add_qnode(message, parameters)
response.merge(result)
if result.status != 'OK':
print(response.show(level=Response.DEBUG))
return response
elif 'e' in parameters['id']:
result = messenger.add_qedge(message, parameters)
response.merge(result)
if result.status != 'OK':
print(response.show(level=Response.DEBUG))
return response
else:
response.error(f"Unrecognized type {parameters['id']}")
return response
interpreter = ARAXQueryGraphInterpreter()
result = interpreter.translate_to_araxi(message)
response.merge(result)
if result.status != 'OK':
print(response.show(level=Response.DEBUG))
return response
araxi_commands = result.data['araxi_commands']
print(araxi_commands)
def main():
#### Create a response object
response = Response()
#### Some qnode examples
test_query_graphs = [
[{
'id': 'n10',
'curie': 'DOID:9281'
}, {
'id': 'n11',
'type': 'protein'
}, {
'id': 'e10',
'source_id': 'n10',
'target_id': 'n11'
}],
[{
'id': 'n10',
'curie': 'DOID:9281'
}, {
'id': 'n11',
'type': 'protein'
}, {
'id': 'n12',
'type': 'drug'
}, {
'id': 'e10',
'source_id': 'n10',
'target_id': 'n11'
}, {
'id': 'e11',
'source_id': 'n11',
'target_id': 'n12'
}],
]
for test_query_graph in test_query_graphs:
#### Create a template Message
messenger = ARAXMessenger()
result = messenger.create_message()
response.merge(result)
message = messenger.message
for parameters in test_query_graph:
if 'n' in parameters['id']:
result = messenger.add_qnode(message, parameters)
response.merge(result)
if result.status != 'OK':
print(response.show(level=Response.DEBUG))
return response
elif 'e' in parameters['id']:
result = messenger.add_qedge(message, parameters)
response.merge(result)
if result.status != 'OK':
print(response.show(level=Response.DEBUG))
return response
else:
response.error(f"Unrecognized type {parameters['id']}")
return response
interpreter = ARAXQueryGraphInterpreter()
result = interpreter.translate_to_araxi(message)
response.merge(result)
if result.status != 'OK':
print(response.show(level=Response.DEBUG))
return response
araxi_commands = result.data['araxi_commands']
print(araxi_commands)
#### Show the final result
print('-------------------------')
print(response.show(level=Response.DEBUG))