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Merged
merged 9 commits into from
Oct 16, 2025
Merged

Add support for testing NodeNorm ElasticSearch #55

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f6d9cb4
Added ci-es as a test target.
gaurav Oct 6, 2025
a9c3fd8
Added a set-id test.
gaurav Oct 6, 2025
8fd2fb5
Added references and improved documentation.
gaurav Oct 6, 2025
f66046b
Fixed URLs.
gaurav Oct 6, 2025
1392e71
Added exception for NodeNorm ES.
gaurav Oct 6, 2025
cfb6fe2
Added very basic type test.
gaurav Oct 16, 2025
fe98f38
Added additional tests for Biolink types.
gaurav Oct 16, 2025
a000868
Added some GeneProtein conflation tests.
gaurav Oct 16, 2025
1c6e5b0
Added DrugChemical conflation and fully conflated tests.
gaurav Oct 16, 2025
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229 changes: 229 additions & 0 deletions tests/nodenorm/test_nodenorm_setid.py
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Original file line number Diff line number Diff line change
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#
# Tests for the NodeNorm API setid methods.
# These tests are intended to ensure that all the API setid endpoints on NodeNorm are working as intended.
# Copied and modified from https://github.com/NCATSTranslator/NodeNormalization/blob/d697af9f2ff99f16ebfe0c9a8e375b9d440c8f98/tests/test_setid.py
# Note that since this depends on normalization, these examples may need to be updated if any of the CURIEs we
# reference here have different preferred identifiers in a future release.
#

import pytest
import requests

@pytest.fixture
def nodenorm_url(target_info):
return target_info['NodeNormURL']

def test_setid_empty(nodenorm_url):
"""
Make sure we get a sensible response if we call setid without any parameters.
"""
response = requests.get(nodenorm_url + "get_setid")
result = response.json()

# Check for NodeNorm ES:
if response.status_code == 400:
assert result == {
'code': 400,
'error': 'Bad Request',
'success': False,
}
return

assert result == {
"detail":
[
{
"loc": ["query", "curie"],
"msg": "ensure this value has at least 1 items",
"type": "value_error.list.min_items",
"ctx": { "limit_value": 1 }
}
]
}


def test_setid_incorrect_conflation(nodenorm_url):
"""
Make sure we get a sensible response if we call setid without any parameters.
"""
response = requests.get(nodenorm_url + "get_setid", params={
'curie': ['DOID:3812', 'MONDO:0005002', 'MONDO:0005003'],
'conflation': ['GeneProtein', 'DrugChemic']
})
result = response.json()
assert "only 'GeneProtein' and 'DrugChemical' are allowed" in result['error']
assert result['setid'] is None


def test_setid_basic(nodenorm_url):
"""
Some basic tests to make sure normalization works as expected.
"""
expected_setids = [
{
'curie': ['DOID:3812', 'MONDO:0005002', 'MONDO:0005003', 'PUBCHEM.COMPOUND:10129877', ''],
'conflation': ['GeneProtein'],
'curies': ['DOID:3812', 'MONDO:0005002', 'MONDO:0005003', 'PUBCHEM.COMPOUND:10129877', ''],
'normalized_curies': ['', 'DOID:3812', 'MONDO:0005002', 'MONDO:0005003', 'UNII:63M8RYN44N'],
'normalized_string': '||DOID:3812||MONDO:0005002||MONDO:0005003||UNII:63M8RYN44N',
'setid': 'uuid:4a69cea4-e267-5cb5-bf69-66cc19da65ca'
},
{
'curie': ['DOID:3812', 'MONDO:0005002', 'MONDO:0005003', 'PUBCHEM.COMPOUND:10129877', ''],
'conflation': ['GeneProtein', 'DrugChemical'],
'curies': ['DOID:3812', 'MONDO:0005002', 'MONDO:0005003', 'PUBCHEM.COMPOUND:10129877', ''],
'normalized_curies': ['', 'CHEBI:15377', 'DOID:3812', 'MONDO:0005002', 'MONDO:0005003'],
'normalized_string': '||CHEBI:15377||DOID:3812||MONDO:0005002||MONDO:0005003',
'setid': 'uuid:7403b843-5adb-563b-a321-876cb2088f2b'
},
{
'curie': ['!#lk1l4', '09s90ma!:391nasa01AAa', 10.31, 9018, -913],
'conflation': ['GeneProtein', 'DrugChemical'],
'curies': ['!#lk1l4', '09s90ma!:391nasa01AAa', '10.31', '9018', '-913'],
'normalized_curies': ['!#lk1l4', '-913', '09s90ma!:391nasa01AAa', '10.31', '9018'],
'normalized_string': '!#lk1l4||-913||09s90ma!:391nasa01AAa||10.31||9018',
'setid': 'uuid:2fe78021-4a98-53cc-b911-a55962575095'
}
]

for expected_setid in expected_setids:
response = requests.get(nodenorm_url + "get_setid", params={
'curie': expected_setid['curie'],
'conflation': expected_setid['conflation'],
})
result = response.json()
assert result['curies'] == expected_setid['curies']
assert result['error'] is None
assert result['normalized_curies'] == expected_setid['normalized_curies']
assert result['normalized_string'] == expected_setid['normalized_string']
assert result['setid'] == expected_setid['setid']

# Test all of them at once using the 'POST' interface.
setid_query = [{'curies': e['curie'], 'conflations': e['conflation']} for e in expected_setids]
response = requests.post(nodenorm_url + "get_setid", json=setid_query)
results = response.json()
for index, result in enumerate(results):
expected_setid = expected_setids[index]

assert result['error'] is None
assert result['normalized_curies'] == expected_setid['normalized_curies']
assert result['normalized_string'] == expected_setid['normalized_string']
assert result['setid'] == expected_setid['setid']


def test_setid_long(nodenorm_url):
"""
Some basic tests to make sure normalization of long lists of setid.
"""
# Generate up to a hundred rubbish IDs (between RUBBISH:10000 and RUBBISH:99999).
# rubbish_ids = [f'RUBBISH:{random.randint(10000, 99999)}' for _ in range(100)]
rubbish_ids = ["RUBBISH:47029", "RUBBISH:11782", "RUBBISH:19841", "RUBBISH:74772", "RUBBISH:50159", "RUBBISH:72510", "RUBBISH:71390", "RUBBISH:93274", "RUBBISH:54177", "RUBBISH:11018", "RUBBISH:75654", "RUBBISH:82342", "RUBBISH:58851", "RUBBISH:37847", "RUBBISH:39315", "RUBBISH:95403", "RUBBISH:87724", "RUBBISH:76080", "RUBBISH:62554", "RUBBISH:11207", "RUBBISH:24788", "RUBBISH:97930", "RUBBISH:98994", "RUBBISH:10111", "RUBBISH:46486", "RUBBISH:42114", "RUBBISH:97410", "RUBBISH:71911", "RUBBISH:10444", "RUBBISH:71057", "RUBBISH:16589", "RUBBISH:79128", "RUBBISH:32169", "RUBBISH:76813", "RUBBISH:13051", "RUBBISH:75665", "RUBBISH:33554", "RUBBISH:73285", "RUBBISH:79791", "RUBBISH:99397", "RUBBISH:36508", "RUBBISH:81324", "RUBBISH:27651", "RUBBISH:60525", "RUBBISH:13237", "RUBBISH:21080", "RUBBISH:21874", "RUBBISH:94750", "RUBBISH:95994", "RUBBISH:35060", "RUBBISH:15816", "RUBBISH:65196", "RUBBISH:74530", "RUBBISH:61006", "RUBBISH:97287", "RUBBISH:29972", "RUBBISH:36823", "RUBBISH:31799", "RUBBISH:68589", "RUBBISH:68594", "RUBBISH:63257", "RUBBISH:81351", "RUBBISH:38292", "RUBBISH:84666", "RUBBISH:50607", "RUBBISH:52926", "RUBBISH:48712", "RUBBISH:14093", "RUBBISH:88546", "RUBBISH:29904", "RUBBISH:75316", "RUBBISH:68679", "RUBBISH:99691", "RUBBISH:59711", "RUBBISH:57302", "RUBBISH:18425", "RUBBISH:71720", "RUBBISH:37939", "RUBBISH:23971", "RUBBISH:64822", "RUBBISH:69092", "RUBBISH:73348", "RUBBISH:56239", "RUBBISH:17439", "RUBBISH:80884", "RUBBISH:36822", "RUBBISH:11304", "RUBBISH:18228", "RUBBISH:59644", "RUBBISH:15815", "RUBBISH:93668", "RUBBISH:84725", "RUBBISH:40687", "RUBBISH:95196", "RUBBISH:12572", "RUBBISH:98753", "RUBBISH:52910", "RUBBISH:27338", "RUBBISH:28744", "RUBBISH:70919"]
response = requests.get(nodenorm_url + "get_setid", params={
'curie': rubbish_ids
})
result = response.json()
assert result['curies'] == rubbish_ids
assert result['normalized_curies'] == [
'RUBBISH:10111',
'RUBBISH:10444',
'RUBBISH:11018',
'RUBBISH:11207',
'RUBBISH:11304',
'RUBBISH:11782',
'RUBBISH:12572',
'RUBBISH:13051',
'RUBBISH:13237',
'RUBBISH:14093',
'RUBBISH:15815',
'RUBBISH:15816',
'RUBBISH:16589',
'RUBBISH:17439',
'RUBBISH:18228',
'RUBBISH:18425',
'RUBBISH:19841',
'RUBBISH:21080',
'RUBBISH:21874',
'RUBBISH:23971',
'RUBBISH:24788',
'RUBBISH:27338',
'RUBBISH:27651',
'RUBBISH:28744',
'RUBBISH:29904',
'RUBBISH:29972',
'RUBBISH:31799',
'RUBBISH:32169',
'RUBBISH:33554',
'RUBBISH:35060',
'RUBBISH:36508',
'RUBBISH:36822',
'RUBBISH:36823',
'RUBBISH:37847',
'RUBBISH:37939',
'RUBBISH:38292',
'RUBBISH:39315',
'RUBBISH:40687',
'RUBBISH:42114',
'RUBBISH:46486',
'RUBBISH:47029',
'RUBBISH:48712',
'RUBBISH:50159',
'RUBBISH:50607',
'RUBBISH:52910',
'RUBBISH:52926',
'RUBBISH:54177',
'RUBBISH:56239',
'RUBBISH:57302',
'RUBBISH:58851',
'RUBBISH:59644',
'RUBBISH:59711',
'RUBBISH:60525',
'RUBBISH:61006',
'RUBBISH:62554',
'RUBBISH:63257',
'RUBBISH:64822',
'RUBBISH:65196',
'RUBBISH:68589',
'RUBBISH:68594',
'RUBBISH:68679',
'RUBBISH:69092',
'RUBBISH:70919',
'RUBBISH:71057',
'RUBBISH:71390',
'RUBBISH:71720',
'RUBBISH:71911',
'RUBBISH:72510',
'RUBBISH:73285',
'RUBBISH:73348',
'RUBBISH:74530',
'RUBBISH:74772',
'RUBBISH:75316',
'RUBBISH:75654',
'RUBBISH:75665',
'RUBBISH:76080',
'RUBBISH:76813',
'RUBBISH:79128',
'RUBBISH:79791',
'RUBBISH:80884',
'RUBBISH:81324',
'RUBBISH:81351',
'RUBBISH:82342',
'RUBBISH:84666',
'RUBBISH:84725',
'RUBBISH:87724',
'RUBBISH:88546',
'RUBBISH:93274',
'RUBBISH:93668',
'RUBBISH:94750',
'RUBBISH:95196',
'RUBBISH:95403',
'RUBBISH:95994',
'RUBBISH:97287',
'RUBBISH:97410',
'RUBBISH:97930',
'RUBBISH:98753',
'RUBBISH:98994',
'RUBBISH:99397',
'RUBBISH:99691'
]
assert result['normalized_string'] == 'RUBBISH:10111||RUBBISH:10444||RUBBISH:11018||RUBBISH:11207||RUBBISH:11304||RUBBISH:11782||RUBBISH:12572||RUBBISH:13051||RUBBISH:13237||RUBBISH:14093||RUBBISH:15815||RUBBISH:15816||RUBBISH:16589||RUBBISH:17439||RUBBISH:18228||RUBBISH:18425||RUBBISH:19841||RUBBISH:21080||RUBBISH:21874||RUBBISH:23971||RUBBISH:24788||RUBBISH:27338||RUBBISH:27651||RUBBISH:28744||RUBBISH:29904||RUBBISH:29972||RUBBISH:31799||RUBBISH:32169||RUBBISH:33554||RUBBISH:35060||RUBBISH:36508||RUBBISH:36822||RUBBISH:36823||RUBBISH:37847||RUBBISH:37939||RUBBISH:38292||RUBBISH:39315||RUBBISH:40687||RUBBISH:42114||RUBBISH:46486||RUBBISH:47029||RUBBISH:48712||RUBBISH:50159||RUBBISH:50607||RUBBISH:52910||RUBBISH:52926||RUBBISH:54177||RUBBISH:56239||RUBBISH:57302||RUBBISH:58851||RUBBISH:59644||RUBBISH:59711||RUBBISH:60525||RUBBISH:61006||RUBBISH:62554||RUBBISH:63257||RUBBISH:64822||RUBBISH:65196||RUBBISH:68589||RUBBISH:68594||RUBBISH:68679||RUBBISH:69092||RUBBISH:70919||RUBBISH:71057||RUBBISH:71390||RUBBISH:71720||RUBBISH:71911||RUBBISH:72510||RUBBISH:73285||RUBBISH:73348||RUBBISH:74530||RUBBISH:74772||RUBBISH:75316||RUBBISH:75654||RUBBISH:75665||RUBBISH:76080||RUBBISH:76813||RUBBISH:79128||RUBBISH:79791||RUBBISH:80884||RUBBISH:81324||RUBBISH:81351||RUBBISH:82342||RUBBISH:84666||RUBBISH:84725||RUBBISH:87724||RUBBISH:88546||RUBBISH:93274||RUBBISH:93668||RUBBISH:94750||RUBBISH:95196||RUBBISH:95403||RUBBISH:95994||RUBBISH:97287||RUBBISH:97410||RUBBISH:97930||RUBBISH:98753||RUBBISH:98994||RUBBISH:99397||RUBBISH:99691'
assert result['setid'] == 'uuid:c81cd168-996a-5ca7-8107-2c82c36232fe'
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