def main():
#### Create a response object
response = Response()
ranker = ARAXRanker()
#### Get a Message to work on
messenger = ARAXMessenger()
print("INFO: Fetching message to work on from arax.rtx.ai", flush=True)
message = messenger.fetch_message(
'https://arax.rtx.ai/api/rtx/v1/message/2614')
if message is None:
print("ERROR: Unable to fetch message")
return
ranker.aggregate_scores(message, response=response)
#### Show the final result
print(response.show(level=Response.DEBUG))
print("Results:")
for result in message.results:
confidence = result.confidence
if confidence is None:
confidence = 0.0
print(" -" + '{:6.3f}'.format(confidence) + f"\t{result.essence}")
def main():
# For faster testing, cache the testing messages locally
import requests_cache
requests_cache.install_cache('ARAX_ranker_testing_cache')
import argparse
argparser = argparse.ArgumentParser(description='Ranker system')
argparser.add_argument('--local', action='store_true', help='If set, use local RTXFeedback database to fetch messages')
params = argparser.parse_args()
# --- Create a response object
response = ARAXResponse()
ranker = ARAXRanker()
# --- Get a Message to work on
from ARAX_messenger import ARAXMessenger
messenger = ARAXMessenger()
if not params.local:
print("INFO: Fetching message to work on from arax.ncats.io", flush=True)
message = messenger.fetch_message('https://arax.ncats.io/api/rtx/v1/message/2614') # acetaminophen - > protein, just NGD as virtual edge
# message = messenger.fetch_message('https://arax.ncats.io/api/rtx/v1/message/2687') # neutropenia -> drug, predict_drug_treats_disease and ngd
# message = messenger.fetch_message('https://arax.ncats.io/api/rtx/v1/message/2701') # observed_expected_ratio and ngd
# message = messenger.fetch_message('https://arax.ncats.io/api/rtx/v1/message/2703') # a huge one with jaccard
# message = messenger.fetch_message('https://arax.ncats.io/api/rtx/v1/message/2706') # small one with paired concept frequency
# message = messenger.fetch_message('https://arax.ncats.io/api/rtx/v1/message/2709') # bigger one with paired concept frequency
# For local messages due to local changes in code not rolled out to production:
if params.local:
sys.path.append(os.path.dirname(os.path.abspath(__file__)) + "/../../UI/Feedback")
from RTXFeedback import RTXFeedback
araxdb = RTXFeedback()
message_dict = araxdb.getMessage(294) # local version of 2709 but with updates to COHD
# message_dict = araxdb.getMessage(297)
# message_dict = araxdb.getMessage(298)
# message_dict = araxdb.getMessage(299) # observed_expected_ratio different disease
# message_dict = araxdb.getMessage(300) # chi_square
# message_dict = araxdb.getMessage(302) # chi_square, different disease
# message_dict = araxdb.getMessage(304) # all clinical info, osteoarthritis
# message_dict = araxdb.getMessage(305) # all clinical info, neurtropenia
# message_dict = araxdb.getMessage(306) # all clinical info, neurtropenia, but with virtual edges
# message_dict = araxdb.getMessage(307) # all clinical info, osteoarthritis, but with virtual edges
# message_dict = araxdb.getMessage(322) # Parkinsons Jaccard, top 50
# message_dict = araxdb.getMessage(324) # chi_square, KG2
# message_dict = araxdb.getMessage(325) # chi_square, ngd, KG2
# message_dict = araxdb.getMessage(326) # prob drug treats disease as attribute to all edge thrombocytopenia
# message_dict = araxdb.getMessage(327)
# add_qnode(name=DOID:1227, id=n00)
# add_qnode(type=protein, is_set=true, id=n01)
# add_qnode(type=chemical_substance, id=n02)
# add_qedge(subject=n00, object=n01, id=e00)
# add_qedge(subject=n01, object=n02, id=e01, type=physically_interacts_with)
# expand(edge_id=[e00,e01], kp=ARAX/KG1)
# overlay(action=compute_jaccard, start_node_id=n00, intermediate_node_id=n01, end_node_id=n02, virtual_relation_label=J1)
# overlay(action=predict_drug_treats_disease, source_qnode_id=n02, target_qnode_id=n00, virtual_relation_label=P1)
# overlay(action=overlay_clinical_info, chi_square=true, virtual_relation_label=C1, source_qnode_id=n00, target_qnode_id=n02)
# overlay(action=compute_ngd, virtual_relation_label=N1, source_qnode_id=n00, target_qnode_id=n01)
# overlay(action=compute_ngd, virtual_relation_label=N2, source_qnode_id=n00, target_qnode_id=n02)
# overlay(action=compute_ngd, virtual_relation_label=N3, source_qnode_id=n01, target_qnode_id=n02)
# resultify(ignore_edge_direction=true)
# filter_results(action=limit_number_of_results, max_results=100)
from ARAX_messenger import ARAXMessenger
message = ARAXMessenger().from_dict(message_dict)
if message is None:
print("ERROR: Unable to fetch message")
return
# ranker.aggregate_scores(message,response=response)
ranker.aggregate_scores_dmk(message, response=response)
# Show the final result
print(response.show(level=ARAXResponse.DEBUG))
print("Results:")
for result in message.results:
confidence = result.confidence
if confidence is None:
confidence = 0.0
print(" -" + '{:6.3f}'.format(confidence) + f"\t{result.essence}")
# print(json.dumps(message.to_dict(),sort_keys=True,indent=2))
# Show the message number
print(json.dumps(ast.literal_eval(repr(message.id)), sort_keys=True, indent=2))