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# -*- coding: utf-8 -*-
"""Tests for the bioregistry client."""
import unittest
from typing import Iterable, Tuple
import bioregistry
from bioregistry import manager
from bioregistry.resolve import get_external
class TestResolve(unittest.TestCase):
"""Tests for getting Bioregistry content."""
def test_resolve(self):
"""Test prefixes can be resolved properly."""
for expected, query in [
("ncbitaxon", "ncbitaxon"),
("ncbitaxon", "NCBITaxon"),
("ncbitaxon", "taxonomy"),
("scomp", "SCOMP"),
("sfam", "SFAM"),
("eccode", "ec-code"),
("eccode", "EC_CODE"),
("chembl.compound", "chembl.compound"),
("chembl.compound", "chemblcompound"),
("chembl", "chembl"),
]:
with self.subTest(query=query):
self.assertEqual(expected, bioregistry.normalize_prefix(query))
def test_get(self):
"""Test getting content from the bioregistry."""
ncbitaxon_entry = bioregistry.get_resource("ncbitaxon")
self.assertIn("NCBI_Taxon_ID", ncbitaxon_entry.synonyms)
self.assertIsNotNone(get_external("ncbitaxon", "miriam"))
self.assertIsNotNone(get_external("ncbitaxon", "obofoundry"))
self.assertIsNotNone(get_external("ncbitaxon", "ols"))
self.assertIsNotNone(get_external("ncbitaxon", "wikidata"))
def test_validate_true(self):
"""Test that validation returns true."""
tests = [
("eccode", "1"),
("eccode", "1.1"),
("eccode", "1.1.1"),
("eccode", "1.1.1.1"),
("eccode", "1.1.123.1"),
("eccode", "1.1.1.123"),
# Namespace in LUI: Standard rule for upper-casing
("chebi", "24867"),
("chebi", "CHEBI:1234"),
# BANANA (explicit)
(
"vario",
"0376",
), # this showcases the banana problem where the namespace in LUI is weird
("VariO", "0376"),
("did", "sov:WRfXPg8dantKVubE3HX8pw"),
("did", "did:sov:WRfXPg8dantKVubE3HX8pw"),
("go.ref", "0000041"),
("go.ref", "GO_REF:0000041"),
# bananas from OBO
("go", "0000001"),
("go", "GO:0000001"),
("go", "go:0000001"),
# banana are strange
("omim.ps", "PS214100"),
("omim.ps", "214100"),
("OMIMPS", "214100"),
("PS", "214100"),
("PS", "PS214100"),
("agrovoc", "1234"),
("agrovoc", "c_1234"),
]
for prefix, resource in bioregistry.read_registry().items():
if bioregistry.is_deprecated(prefix):
continue
banana = bioregistry.get_banana(prefix)
if banana is None or bioregistry.has_no_terms(prefix):
continue
peel = resource.get_banana_peel()
example = bioregistry.get_example(prefix)
with self.subTest(prefix=prefix):
if example is None:
self.fail(msg=f"{prefix} has a banana {banana} but is missing an example")
else:
tests.append((prefix, example))
tests.append((prefix, f"{banana}{peel}{example}"))
self.assert_known_identifiers(tests)
def assert_known_identifiers(self, examples: Iterable[Tuple[str, str]]) -> None:
"""Validate the examples."""
for prefix, identifier in examples:
with self.subTest(prefix=prefix, identifier=identifier):
self.assertTrue(
bioregistry.is_standardizable_identifier(prefix, identifier),
msg=f"CURIE {prefix}:{identifier} does not loosely match {bioregistry.get_pattern(prefix)}",
)
def test_validate_false(self):
"""Test that validation returns false."""
for prefix, identifier in [
("chebi", "A1234"),
("chebi", "GO:A1234"),
]:
with self.subTest(prefix=prefix, identifier=identifier):
self.assertFalse(bioregistry.is_standardizable_identifier(prefix, identifier))
def test_lui(self):
"""Test the LUI makes sense (spoilers, they don't).
Discussion is ongoing at:
- https://github.com/identifiers-org/identifiers-org.github.io/issues/151
"""
for prefix in bioregistry.read_registry():
if not bioregistry.get_namespace_in_lui(prefix):
continue
if bioregistry.get_banana(prefix):
continue # rewrite rules are applied to prefixes with bananas
if prefix in {"ark", "obi"}:
continue # these patterns on identifiers.org are garb
with self.subTest(prefix=prefix):
re_pattern = bioregistry.get_pattern(prefix)
miriam_prefix = bioregistry.get_identifiers_org_prefix(prefix)
self.assertTrue(
re_pattern.startswith(f"^{miriam_prefix.upper()}")
or re_pattern.startswith(miriam_prefix.upper()),
msg=f"{prefix} pattern: {re_pattern}",
)
def test_curie_pattern(self):
"""Test CURIE pattern.
.. seealso:: https://github.com/biopragmatics/bioregistry/issues/245
"""
self.assertEqual("^chebi:\\d+$", bioregistry.get_curie_pattern("chebi"))
self.assertEqual("^CHEBI:\\d+$", bioregistry.get_curie_pattern("chebi", use_preferred=True))
self.assertEqual(
"^chembl\\.compound:CHEMBL\\d+$", bioregistry.get_curie_pattern("chembl.compound")
)
pattern = bioregistry.get_curie_pattern("panther.pthcmp")
self.assertRegex("panther.pthcmp:P00266", pattern)
self.assertNotRegex("pantherXpthcmp:P00266", pattern)
def test_depends_on(self):
"""Test getting dependencies."""
test_prefix = "foodon"
test_target = "bfo"
resource = bioregistry.get_resource(test_prefix)
self.assertIsNotNone(resource)
obofoundry = resource.get_external("obofoundry")
self.assertIsNotNone(obofoundry)
self.assertIn("depends_on", obofoundry)
fobi_dependencies = manager.get_depends_on(test_prefix)
self.assertIsNotNone(fobi_dependencies)
self.assertIn(test_target, fobi_dependencies)
fobi_dependencies = bioregistry.get_depends_on(test_prefix)
self.assertIsNotNone(fobi_dependencies)
self.assertIn(test_target, fobi_dependencies)
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