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kennethbruskiewiczkennethbruskiewicz
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Revert "test: pin annotator fixtures to production"
This reverts commit 5027bce.
1 parent 5027bce commit 502a636

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Lines changed: 63 additions & 95 deletions

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‎tests/test_node_annotator.py‎

Lines changed: 63 additions & 95 deletions
Original file line numberDiff line numberDiff line change
@@ -1,89 +1,67 @@
11
import TCT
22
import pytest
3-
from TCT.config import reset_config
4-
5-
6-
@pytest.fixture(autouse=True)
7-
def use_node_annotator_prod():
8-
"""Run legacy Node Annotator expectations against production."""
9-
TCT.configure(environment="prod")
10-
yield
11-
reset_config()
12-
133

144
CURIES_with_annotations = [
155
{
16-
"curie": "MONDO:0005148",
17-
"expected": {
18-
"query": "MONDO:0005148",
19-
"disease_ontology.name": "type 2 diabetes mellitus",
20-
"sections": ["disease_ontology", "mondo", "umls"],
6+
'curie': 'MONDO:0005148',
7+
'expected': {
8+
'query': 'MONDO:0005148',
9+
'disease_ontology.name': 'type 2 diabetes mellitus',
10+
'sections': ['disease_ontology', 'mondo', 'umls'],
2111
},
2212
},
2313
{
24-
"curie": "CHEBI:231601",
25-
"expected": {
26-
"query": "CHEBI:231601",
27-
"sections": ["chebi"],
14+
'curie': 'CHEBI:231601',
15+
'expected': {
16+
'query': 'CHEBI:231601',
17+
'sections': ['chebi'],
2818
},
2919
},
3020
{
31-
"curie": "CHEBI:15377",
32-
"expected": {
33-
"query": "CHEBI:15377",
34-
"boxed_warning": True,
35-
"sections": [
36-
"aeolus",
37-
"chebi",
38-
"chembl",
39-
"clinical_approval",
40-
"clinical_trials",
41-
"drugbank",
42-
"ndc",
43-
"pubchem",
44-
"unichem",
45-
"unii",
46-
],
47-
"chembl.availability_type": 2,
21+
'curie': 'CHEBI:15377',
22+
'expected': {
23+
'query': 'CHEBI:15377',
24+
'boxed_warning': True,
25+
'sections': ['aeolus', 'chebi', 'chembl', 'clinical_approval', 'clinical_trials', 'drugbank', 'ndc', 'pubchem', 'unichem', 'unii'],
26+
'chembl.availability_type': 2,
4827
},
4928
},
5029
{
51-
"curie": "NCIT:C34373",
52-
"expected": {},
30+
'curie': 'NCIT:C34373',
31+
'expected': {},
5332
},
5433
{
55-
"curie": "MONDO:0004976",
56-
"expected": {
57-
"query": "MONDO:0004976",
58-
"disease_ontology.name": "amyotrophic lateral sclerosis",
59-
"sections": ["disease_ontology", "mondo", "umls"],
34+
'curie': 'MONDO:0004976',
35+
'expected': {
36+
'query': 'MONDO:0004976',
37+
'disease_ontology.name': 'amyotrophic lateral sclerosis',
38+
'sections': ['disease_ontology', 'mondo', 'umls'],
6039
},
6140
},
6241
{
63-
"curie": "NCBIGene:1756",
64-
"expected": {
65-
"query": "1756",
66-
"taxid": 9606,
67-
"name": "dystrophin",
68-
"symbol": "DMD",
69-
"type_of_gene": "protein-coding",
70-
"sections": ["go", "interpro"],
42+
'curie': 'NCBIGene:1756',
43+
'expected': {
44+
'query': '1756',
45+
'taxid': 9606,
46+
'name': 'dystrophin',
47+
'symbol': 'DMD',
48+
'type_of_gene': 'protein-coding',
49+
'sections': ['go', 'interpro'],
7150
},
7251
},
7352
{
74-
"curie": "UniProtKB:P00395",
75-
"expected": {
76-
"query": "P00395",
77-
"symbol": "MT-CO1",
78-
"taxid": 9606,
79-
"type_of_gene": "protein-coding",
80-
"sections": ["go", "interpro"],
81-
"name": "cytochrome c oxidase subunit I",
53+
'curie': 'UniProtKB:P00395',
54+
'expected': {
55+
'query': 'P00395',
56+
'symbol': 'MT-CO1',
57+
'taxid': 9606,
58+
'type_of_gene': 'protein-coding',
59+
'sections': ['go', 'interpro'],
60+
'name': 'cytochrome c oxidase subunit I',
8261
},
83-
},
62+
}
8463
]
8564

86-
8765
def compare_result_with_expected(result, expected_result):
8866
"""
8967
Compares the actual result with the expected result across multiple fields and
@@ -102,70 +80,60 @@ def compare_result_with_expected(result, expected_result):
10280
assert result == {}
10381

10482
# Check sections.
105-
if "sections" in expected_result:
106-
for section in expected_result["sections"]:
83+
if 'sections' in expected_result:
84+
for section in expected_result['sections']:
10785
assert section in result
10886

10987
# Check some top-level fields.
110-
if "query" in expected_result:
111-
assert result["query"] == expected_result["query"]
88+
if 'query' in expected_result:
89+
assert result['query'] == expected_result['query']
11290

113-
if "name" in expected_result:
114-
assert result["name"] == expected_result["name"]
91+
if 'name' in expected_result:
92+
assert result['name'] == expected_result['name']
11593

116-
if "taxid" in expected_result:
117-
assert result["taxid"] == expected_result["taxid"]
94+
if 'taxid' in expected_result:
95+
assert result['taxid'] == expected_result['taxid']
11896

119-
if "type_of_gene" in expected_result:
120-
assert result["type_of_gene"] == expected_result["type_of_gene"]
97+
if 'type_of_gene' in expected_result:
98+
assert result['type_of_gene'] == expected_result['type_of_gene']
12199

122-
if "boxed_warning" in expected_result:
123-
assert result["boxed_warning"] == expected_result["boxed_warning"]
100+
if 'boxed_warning' in expected_result:
101+
assert result['boxed_warning'] == expected_result['boxed_warning']
124102

125103
# Check some subsection fields.
126-
if "disease_ontology.name" in expected_result:
127-
assert (
128-
result["disease_ontology"]["name"]
129-
== expected_result["disease_ontology.name"]
130-
)
104+
if 'disease_ontology.name' in expected_result:
105+
assert result['disease_ontology']['name'] == expected_result['disease_ontology.name']
131106

132-
if "chembl.availability_type" in expected_result:
133-
assert (
134-
result["chembl"]["availability_type"]
135-
== expected_result["chembl.availability_type"]
136-
)
107+
if 'chembl.availability_type' in expected_result:
108+
assert result['chembl']['availability_type'] == expected_result['chembl.availability_type']
137109

138110

139111
def test_status():
140-
"""Test that the status function returns a success message."""
112+
""" Test that the status function returns a success message. """
141113
result = TCT.node_annotator.status()
142-
assert result["success"]
114+
assert result['success']
143115

144116

145117
def test_lookup_curies():
146-
curies = list(map(lambda x: x["curie"], CURIES_with_annotations))
118+
curies = list(map(lambda x: x['curie'], CURIES_with_annotations))
147119
results = TCT.node_annotator.lookup_curies(curies)
148120
assert len(results) == len(curies)
149121
for curie in curies:
150122
assert curie in results
151123
if isinstance(results[curie], list):
152-
raise RuntimeError(
153-
f"Multiple results found for CURIE '{curie}': {results[curie]}"
154-
)
124+
raise RuntimeError(f"Multiple results found for CURIE '{curie}': {results[curie]}")
155125

156126
actual_result = results[curie]
157-
expected_result = list(
158-
filter(lambda x: x["curie"] == curie, CURIES_with_annotations)
159-
)[0]["expected"]
127+
expected_result = list(filter(lambda x: x['curie'] == curie, CURIES_with_annotations))[0]['expected']
160128

161129
compare_result_with_expected(actual_result, expected_result)
162130

163131

164132
@pytest.mark.parametrize("curie_with_annotations", CURIES_with_annotations)
165133
def test_lookup_curie(curie_with_annotations):
166-
curie = curie_with_annotations["curie"]
134+
curie = curie_with_annotations['curie']
167135
result = TCT.node_annotator.lookup_curie(curie)
168-
if result == {} and curie_with_annotations["expected"] == {}:
136+
if result == {} and curie_with_annotations['expected'] == {}:
169137
# We expected no annotations and got no annotations.
170138
pytest.skip(f"No annotations found for CURIE '{curie}'")
171139

@@ -174,4 +142,4 @@ def test_lookup_curie(curie_with_annotations):
174142
raise RuntimeError(f"Multiple results found for CURIE '{curie}': {result}")
175143

176144
# Compare the result with the expected annotations.
177-
compare_result_with_expected(result, curie_with_annotations["expected"])
145+
compare_result_with_expected(result, curie_with_annotations['expected'])

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