1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
|
# -*- coding: utf-8 -*-
"""Test the ability of the bioregistry to cover INDRA identifiers."""
import unittest
import bioregistry
try:
import indra
import indra.databases.identifiers
except ImportError:
indra = None
NON_BIOLOGY = {
"UN",
"WDI",
"HUME", # hume is a reading system
"SOFIA", # sofia is a reading system
"CWMS", # world modelers
}
@unittest.skipIf(indra is None, "INDRA not installed")
class TestIndra(unittest.TestCase):
"""Test the Bioregistry is a superset of INDRA identifier utilities."""
def test_identifiers_mapping(self):
"""Test the identifier mappings are all contained in the Bioregistry."""
for prefix, target in indra.databases.identifiers.identifiers_mappings.items():
if prefix in {"CTD", "NONCODE", "NCBI"}: # these aren't specific enough
continue
with self.subTest(prefix=prefix):
self.assertIsNotNone(
bioregistry.normalize_prefix(prefix), msg=f"should be {target}"
)
def test_non_registry(self):
"""Test the Bioregistry has entries for all non-registry entries in INDRA."""
for prefix in indra.databases.identifiers.non_registry:
if prefix == "SPINE":
continue # Special case due to a collaboration
with self.subTest(prefix=prefix):
self.assertIsNotNone(bioregistry.normalize_prefix(prefix))
def test_url_prefixes(self):
"""Test that all of the INDRA custom URL prefixes are mapped in the Bioregistry."""
for prefix in indra.databases.identifiers.url_prefixes:
if prefix in NON_BIOLOGY:
continue
with self.subTest(prefix=prefix):
self.assertIsNotNone(bioregistry.normalize_prefix(prefix))
|
