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Add test for COHD TRAPI set-input query (MCQ)
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‎test_cohd_trapi.py‎

Lines changed: 237 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,7 @@
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# Choose which server to test
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# cr.server = 'https://dev.cohd.io/api'
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cr.server = 'https://cohd-api.ci.transltr.io/api'
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# cr.server = 'https://cohd-api.test.transltr.io/api'
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# cr.server = 'https://cohd-api.test.transltr.io/api'
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# cr.server = 'https://cohd-api.transltr.io/api'
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# Specify what Biolink and TRAPI versions are expected by the server
@@ -927,6 +927,242 @@ def test_translator_query_qnode_empty_constraint():
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assert len(json['message']['results']) >= 1, _print_trapi_log(json)
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def test_translator_set_input_query():
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""" Check the TRAPI endpoint to make sure it returns properly formatted TRAPI for set-input query. """
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print(f'\ntest_cohd_trapi::test_translator_set_input_query: testing TRAPI set-input query on {cr.server}..... ')
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url = f'{cr.server}/query'
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# Query with empty constraints
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query = '''
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{
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"message": {
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"query_graph": {
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"nodes": {
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"input": {
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"categories": [
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"biolink:PhenotypicFeature"
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],
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"ids": [
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"uuid:1"
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],
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"member_ids": [
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"HP:0000739",
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"HP:0001288",
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"HP:0001252",
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"HP:0001250",
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"HP:0000750",
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"HP:0002378",
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"HP:0002019",
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"HP:0007146"
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],
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"set_interpretation": "MANY"
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},
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"output": {
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"categories": [
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"biolink:Disease"
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]
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}
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},
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"edges": {
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"edge_0": {
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"subject": "input",
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"object": "output",
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"predicates": [
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"biolink:correlated_with"
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]
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}
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}
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},
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"knowledge_graph": {
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"nodes": {
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"uuid:1": {
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"categories": [
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"biolink:PhenotypicFeature"
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],
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"is_set": true,
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"name": "set1",
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"attributes": []
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},
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"HP:0000739": {
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"categories": [
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"biolink:PhenotypicFeature"
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],
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"is_set": false,
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"attributes": []
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},
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"HP:0001288": {
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"categories": [
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"biolink:PhenotypicFeature"
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],
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"is_set": false,
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"attributes": []
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},
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"HP:0001252": {
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"categories": [
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"biolink:PhenotypicFeature"
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],
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"is_set": false,
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"attributes": []
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},
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"HP:0001250": {
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"categories": [
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"biolink:PhenotypicFeature"
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],
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"is_set": false,
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"attributes": []
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},
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"HP:0000750": {
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"categories": [
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"biolink:PhenotypicFeature"
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],
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"is_set": false,
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"attributes": []
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},
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"HP:0002378": {
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"categories": [
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"biolink:PhenotypicFeature"
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],
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"is_set": false,
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"attributes": []
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},
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"HP:0002019": {
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"categories": [
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"biolink:PhenotypicFeature"
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],
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"is_set": false,
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"attributes": []
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},
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"HP:0007146": {
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"categories": [
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"biolink:PhenotypicFeature"
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],
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"is_set": false,
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"attributes": []
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}
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},
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"edges": {
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"kgedge_member_of_0001": {
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"attributes": [],
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"object": "uuid:1",
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"predicate": "biolink:member_of",
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"sources": [
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{
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"resource_id": "infores:user-interface",
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"resource_role": "primary_knowledge_source"
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}
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],
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"subject": "HP:0000739"
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},
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"kgedge_member_of_0002": {
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"attributes": [],
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"object": "uuid:1",
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"predicate": "biolink:member_of",
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"sources": [
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{
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"resource_id": "infores:user-interface",
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"resource_role": "primary_knowledge_source"
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}
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],
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"subject": "HP:0001288"
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},
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"kgedge_member_of_0003": {
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"attributes": [],
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"object": "uuid:1",
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"predicate": "biolink:member_of",
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"sources": [
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{
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"resource_id": "infores:user-interface",
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"resource_role": "primary_knowledge_source"
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}
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],
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"subject": "HP:0001252"
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},
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"kgedge_member_of_0004": {
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"attributes": [],
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"object": "uuid:1",
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"predicate": "biolink:member_of",
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"sources": [
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{
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"resource_id": "infores:user-interface",
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"resource_role": "primary_knowledge_source"
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}
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],
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"subject": "HP:0001250"
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},
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"kgedge_member_of_0005": {
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"attributes": [],
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"object": "uuid:1",
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"predicate": "biolink:member_of",
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"sources": [
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{
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"resource_id": "infores:user-interface",
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"resource_role": "primary_knowledge_source"
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}
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],
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"subject": "HP:0000750"
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},
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"kgedge_member_of_0006": {
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"attributes": [],
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"object": "uuid:1",
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"predicate": "biolink:member_of",
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"sources": [
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{
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"resource_id": "infores:user-interface",
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"resource_role": "primary_knowledge_source"
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}
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],
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"subject": "HP:0002378"
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},
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"kgedge_member_of_0007": {
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"attributes": [],
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"object": "uuid:1",
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"predicate": "biolink:member_of",
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"sources": [
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{
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"resource_id": "infores:user-interface",
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"resource_role": "primary_knowledge_source"
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}
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],
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"subject": "HP:0002019"
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},
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"kgedge_member_of_0008": {
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"attributes": [],
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"object": "uuid:1",
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"predicate": "biolink:member_of",
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"sources": [
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{
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"resource_id": "infores:user-interface",
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"resource_role": "primary_knowledge_source"
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}
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],
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"subject": "HP:0007146"
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}
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}
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}
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},
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"query_options": {
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"max_results": 10
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}
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}
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'''
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query = j.loads(query)
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query['query_options']['query_id'] = str(uuid.uuid4())
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print(j.dumps(query))
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resp = requests.post(url, json=query, timeout=300)
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# Expect HTTP 200 status response
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assert resp.status_code == 200, 'Expected an HTTP 200 status response code' \
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f'Received {resp.status_code}: {resp.text}'
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# Use the Reasoner Validator Python package to validate against Reasoner Standard API
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json = resp.json()
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_validate_trapi_response(json)
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# There should be at least 1 result
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assert len(json['message']['results']) >= 1, _print_trapi_log(json)
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def test_translator_workflows():
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""" Check the TRAPI endpoint to make sure COHD only responds when workflow is a single lookup operation. """
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print(f'\ntest_cohd_trapi::test_translator_workflows: testing TRAPI query with workflows on {cr.server}..... ')

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