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test_ARAX_filter_results.py
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test_ARAX_filter_results.py
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#!/usr/bin/env python3
# Usage:
# run all: pytest -v test_ARAX_filter_results.py
# run just certain tests: pytest -v test_ARAX_filter_results.py -k test_sort
import sys
import os
import pytest
from collections import Counter
import copy
import json
import ast
from typing import List, Union
sys.path.append(os.getcwd()+"/../ARAXQuery")
#sys.path.append(os.getcwd()+"/../ARAXQuery")
from ARAX_filter_results import ARAXFilterResults
from ARAX_query import ARAXQuery
from ARAX_response import ARAXResponse
PACKAGE_PARENT = '../../UI/OpenAPI/python-flask-server'
sys.path.append(os.path.normpath(os.path.join(os.getcwd(), PACKAGE_PARENT)))
from openapi_server.models.edge import Edge
from openapi_server.models.node import Node
from openapi_server.models.q_edge import QEdge
from openapi_server.models.q_node import QNode
from openapi_server.models.query_graph import QueryGraph
from openapi_server.models.knowledge_graph import KnowledgeGraph
from openapi_server.models.node_binding import NodeBinding
from openapi_server.models.edge_binding import EdgeBinding
from openapi_server.models.result import Result
from openapi_server.models.message import Message
def _do_arax_query(query: dict) -> List[Union[ARAXResponse, Message]]:
araxq = ARAXQuery()
response = araxq.query(query)
if response.status != 'OK':
print(response.show(level=response.DEBUG))
#return [response, araxq.message]
return [response, response.envelope.message]
def test_command_definitions():
fr = ARAXFilterResults()
assert fr.allowable_actions == set(fr.command_definitions.keys())
def test_n_results():
query = {"operations": {"actions": [
"create_message",
"add_qnode(name=UMLS:C0040250, key=n00)",
"add_qnode(categories=biolink:ChemicalEntity, key=n01)",
"add_qedge(subject=n00, object=n01, key=e00)",
"expand(edge_key=e00, kp=infores:rtx-kg2)",
"overlay(action=add_node_pmids, max_num=15)",
"resultify(ignore_edge_direction=true)",
"filter_results(action=sort_by_node_attribute, node_attribute=pubmed_ids, direction=a, max_results=8)",
"return(message=true, store=false)"
]}}
[response, message] = _do_arax_query(query)
assert response.status == 'OK'
assert message.n_results == len(message.results) == 8
def test_no_results():
query = {"operations": {"actions": [
"create_message",
"add_qnode(name=DOID:4337, key=n00)",
"add_qnode(categories=biolink:ChemicalEntity, key=n01)",
"add_qedge(subject=n00, object=n01, key=e00)",
"expand(edge_key=e00, kp=infores:rtx-kg2)",
"overlay(action=add_node_pmids, max_num=15)",
"filter_results(action=sort_by_node_attribute, node_attribute=pubmed_ids, direction=a, max_results=20)",
"return(message=true, store=false)"
]}}
[response, message] = _do_arax_query(query)
assert 'WARNING: [] filter_results called with no results.' in response.show(level=ARAXResponse.WARNING)
assert response.status == 'OK'
@pytest.mark.slow
def test_prune():
query = {"operations": {"actions": [
"create_message",
"add_qnode(name=DOID:4337, key=n00)",
"add_qnode(categories=biolink:ChemicalEntity, key=n01)",
"add_qedge(subject=n00, object=n01, key=e00)",
"expand(edge_key=e00, kp=infores:rtx-kg2)",
"overlay(action=add_node_pmids, max_num=15)",
"resultify(ignore_edge_direction=true)",
"filter_results(action=sort_by_node_attribute, node_attribute=pubmed_ids, direction=a, max_results=20, prune_kg=f)",
"return(message=true, store=false)"
]}}
[no_prune_response, no_prune_message] = _do_arax_query(query)
query = {"operations": {"actions": [
"create_message",
"add_qnode(name=DOID:4337, key=n00)",
"add_qnode(categories=biolink:ChemicalEntity, key=n01)",
"add_qedge(subject=n00, object=n01, key=e00)",
"expand(edge_key=e00, kp=infores:rtx-kg2)",
"overlay(action=add_node_pmids, max_num=15)",
"resultify(ignore_edge_direction=true)",
"filter_results(action=sort_by_node_attribute, node_attribute=pubmed_ids, direction=a, max_results=20)",
"return(message=true, store=false)"
]}}
[response, message] = _do_arax_query(query)
assert response.status == 'OK'
result_nodes = set()
result_edges = set()
for result in message.results:
for node_binding_list in result.node_bindings.values():
for node_binding in node_binding_list:
result_nodes.add(node_binding.id)
for edge_binding_list in result.edge_bindings.values():
for edge_binding in edge_binding_list:
result_edges.add(edge_binding.id)
for key, node in message.knowledge_graph.nodes.items():
assert key in result_nodes
for key, edge in message.knowledge_graph.edges.items():
assert key in result_edges
assert len(message.knowledge_graph.nodes) < len(no_prune_message.knowledge_graph.nodes)
assert len(message.knowledge_graph.edges) < len(no_prune_message.knowledge_graph.edges)
def test_warning():
query = {"operations": {"actions": [
"create_message",
"add_qnode(name=UMLS:C0040250, key=n00)",
"add_qnode(categories=biolink:ChemicalEntity, key=n01)",
"add_qedge(subject=n00, object=n01, key=e00)",
"expand(edge_key=e00, kp=infores:rtx-kg2)",
"overlay(action=add_node_pmids, max_num=15)",
"resultify(ignore_edge_direction=true)",
"filter_results(action=sort_by_node_attribute, node_attribute=pubmed_ids, direction=a, max_results=8)",
"filter_results(action=sort_by_node_attribute, node_attribute=asdfghjkl, direction=a, max_results=8)",
"return(message=true, store=false)"
]}}
[response, message] = _do_arax_query(query)
assert response.status == 'OK'
assert len(message.results) == 8
@pytest.mark.slow
def test_sort_by_edge_attribute():
query = {"operations": {"actions": [
"create_message",
"add_qnode(name=DOID:0060680, key=n00)",
"add_qnode(categories=biolink:Protein, is_set=true, key=n01)",
"add_qnode(categories=biolink:ChemicalEntity, key=n02)",
"add_qedge(subject=n00, object=n01, key=e00)",
"add_qedge(subject=n01, object=n02, key=e01)",
"expand(edge_key=[e00,e01], kp=infores:rtx-kg2)",
"overlay(action=compute_jaccard, start_node_key=n00, intermediate_node_key=n01, end_node_key=n02, virtual_relation_label=J1)",
"overlay(action=compute_jaccard, start_node_key=n00, intermediate_node_key=n01, end_node_key=n02, virtual_relation_label=J2)",
"resultify(ignore_edge_direction=true)",
"filter_results(action=sort_by_edge_attribute, edge_attribute=jaccard_index, direction=d, max_results=20, qedge_keys=[J2])",
"return(message=true, store=false)"
]}}
[response, message] = _do_arax_query(query)
#return response, message
assert response.status == 'OK'
assert len(message.results) == 20
def test_sort_by_node_attribute():
query = {"operations": {"actions": [
"create_message",
"add_qnode(name=UMLS:C0040250, key=n00)",
"add_qnode(categories=biolink:ChemicalEntity, key=n01)",
"add_qedge(subject=n00, object=n01, key=e00)",
"expand(edge_key=e00, kp=infores:rtx-kg2)",
"overlay(action=add_node_pmids, max_num=15)",
"resultify(ignore_edge_direction=true)",
"filter_results(action=sort_by_node_attribute, node_attribute=pubmed_ids, direction=a, max_results=8, qnode_keys=[n01])",
"return(message=true, store=false)"
]}}
[response, message] = _do_arax_query(query)
assert response.status == 'OK'
assert len(message.results) == 8
# add something to test if the results are assending and the correct numbers
def test_sort_by_score():
query = {"operations": {"actions": [
"create_message",
"add_qnode(name=UMLS:C0040250, key=n00)",
"add_qnode(categories=biolink:ChemicalEntity, key=n01)",
"add_qedge(subject=n00, object=n01, key=e00)",
"expand(edge_key=e00, kp=infores:rtx-kg2)",
"resultify(ignore_edge_direction=true)",
"filter_results(action=sort_by_score, direction=a, max_results=8)",
"return(message=true, store=false)"
]}}
[response, message] = _do_arax_query(query)
assert response.status == 'OK'
assert len(message.results) == 8
result_scores = [x.analyses[0].score for x in message.results]
assert result_scores == sorted(result_scores)
assert max(result_scores) <= 1
@pytest.mark.external
def test_issue1506():
query = {"operations": {"actions": [
"create_message",
"add_qnode(ids=MONDO:0005301, key=n00)",
"add_qnode(categories=biolink:ChemicalEntity, key=n01)",
"add_qedge(subject=n01, object=n00, key=e00, predicates=biolink:related_to)",
"expand(kp=infores:biothings-multiomics-clinical-risk, edge_key=e00)",
"overlay(action=compute_ngd, virtual_relation_label=N1, subject_qnode_key=n01, object_qnode_key=n00)",
"resultify()",
"filter_results(action=sort_by_edge_attribute, edge_attribute=feature_coefficient, direction=descending, max_results=30, prune_kg=true)",
"return(message=true, store=false)"
]}}
[response, message] = _do_arax_query(query)
assert response.status == 'OK'
assert len(message.results) == 30
if __name__ == "__main__":
pytest.main(['-v'])