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# -*- coding: utf-8 -*-
"""Tests for managers."""
import unittest
import bioregistry
from bioregistry import Manager, parse_curie
from bioregistry.export.rdf_export import get_full_rdf
from bioregistry.resource_manager import MappingsDiff
class TestResourceManager(unittest.TestCase):
"""Test the registry manager."""
def setUp(self) -> None:
"""Set up the test case with a resource manager."""
self.manager = Manager()
def test_get_records(self):
"""Test getting records."""
resource = self.manager.registry["uniprot.isoform"]
self.assertEqual("uniprot.isoform", resource.get_priority_prefix())
prefixes = {
resource.prefix
for resource in self.manager.registry.values()
if resource.get_uri_prefix()
}
self.assertIn(
"uniprot.isoform",
prefixes,
msg="uniprot.isoform isn't registered with a URI prefix properly",
)
converter = self.manager.get_converter()
prefixes = {record.prefix for record in converter.records}
self.assertIn("uniprot.isoform", prefixes)
def test_prefix_map(self):
"""Test getting a prefix map."""
prefix_map = self.manager.get_prefix_map()
# Non-obo, but need to check it works right
self.assertIn("uniprot.isoform", prefix_map)
self.assertEqual("http://purl.uniprot.org/isoforms/", prefix_map["uniprot.isoform"])
def test_prefix_map_preferred(self):
"""Test using preferred prefixes in the prefix map."""
prefix_map = self.manager.get_prefix_map(
prefix_priority=["preferred", "default"],
uri_prefix_priority=["obofoundry", "default"],
)
self.assertNotIn("fbbt", prefix_map)
self.assertIn("FBbt", prefix_map)
prefix_map = bioregistry.get_prefix_map(
uri_prefix_priority=["obofoundry", "default"],
prefix_priority=["preferred", "default"],
)
self.assertNotIn("fbbt", prefix_map)
self.assertIn("FBbt", prefix_map)
def test_rasterized_manager(self):
"""Test that generating a rasterized manager works the same for all functions."""
rasterized_registry = self.manager._rasterized_registry()
self.assertEqual(set(self.manager.registry), set(rasterized_registry))
rast_manager = Manager(rasterized_registry)
self.assertEqual(set(self.manager.registry), set(rast_manager.registry))
self.assertEqual(self.manager.synonyms, rast_manager.synonyms)
for prefix in self.manager.registry:
with self.subTest(prefix=prefix):
self.assertEqual(
self.manager.is_deprecated(prefix),
rast_manager.is_deprecated(prefix),
)
self.assertEqual(
self.manager.get_example(prefix),
rast_manager.get_example(prefix),
)
self.assertEqual(
self.manager.get_uri_format(prefix),
rast_manager.get_uri_format(prefix),
)
self.assertEqual(
self.manager.get_name(prefix),
rast_manager.get_name(prefix),
)
self.assertEqual(
self.manager.get_pattern(prefix),
rast_manager.get_pattern(prefix),
)
self.assertEqual(
self.manager.get_preferred_prefix(prefix) or prefix,
rast_manager.get_preferred_prefix(prefix),
)
self.assertEqual(
self.manager.get_synonyms(prefix),
rast_manager.get_synonyms(prefix),
)
self.assertEqual(
self.manager.get_depends_on(prefix),
rast_manager.get_depends_on(prefix),
)
self.assertEqual(
self.manager.get_appears_in(prefix),
rast_manager.get_appears_in(prefix),
)
self.assertEqual(
self.manager.get_provides_for(prefix),
rast_manager.get_provides_for(prefix),
)
self.assertEqual(
self.manager.get_provided_by(prefix),
rast_manager.get_provided_by(prefix),
)
self.assertEqual(
self.manager.get_has_canonical(prefix),
rast_manager.get_has_canonical(prefix),
)
self.assertEqual(
self.manager.get_canonical_for(prefix),
rast_manager.get_canonical_for(prefix),
)
self.assertEqual(
self.manager.get_part_of(prefix),
rast_manager.get_part_of(prefix),
)
self.assertEqual(
self.manager.get_has_parts(prefix),
rast_manager.get_has_parts(prefix),
)
def test_formatted_iri(self):
"""Test formatted IRI."""
for metaprefix, prefix, identifier, uri in [
("miriam", "hgnc", "16793", "https://identifiers.org/hgnc:16793"),
("n2t", "hgnc", "16793", "https://n2t.net/hgnc:16793"),
("obofoundry", "fbbt", "00007294", "http://purl.obolibrary.org/obo/FBbt_00007294"),
]:
with self.subTest(metaprefix=metaprefix, prefix=prefix, identifier=identifier):
self.assertEqual(
uri, self.manager.get_formatted_iri(metaprefix, prefix, identifier)
)
def test_lookup_from(self):
"""Test the lookup_from method."""
for metaprefix, key, normalize, expected in [
("obofoundry", "GO", False, "go"),
("obofoundry", "go", False, None),
("obofoundry", "go", True, "go"),
]:
with self.subTest(meteprefix=metaprefix, key=key, norm=normalize):
self.assertEqual(
expected, self.manager.lookup_from(metaprefix, key, normalize=normalize)
)
def test_curie_validation(self):
"""Test validation functions."""
valid = [
"go:0000001",
]
for curie in valid:
with self.subTest(curie=curie):
self.assertTrue(self.manager.is_valid_curie(curie))
invalid = [
"0000001",
"go:000001", # too short
"GO:0000001",
# Wrong syntax
"GO-0000001",
"GO_0000001",
# banana variations
"go:GO:0000001",
"GO:GO:0000001",
"go:go:0000001",
"go:go:000001",
# invalid prefix
"xxx:yyy",
# TODO add one with no pattern validation
]
for curie in invalid:
with self.subTest(curie=curie):
self.assertFalse(self.manager.is_valid_curie(curie))
def test_curie_standardizable(self):
"""Test CURIEs that can be standardized."""
valid = [
"go:0000001",
"GO:0000001",
# banana variations
"go:GO:0000001",
"GO:GO:0000001",
"go:go:0000001",
]
for curie in valid:
with self.subTest(curie=curie):
self.assertTrue(self.manager.is_standardizable_curie(curie))
invalid = [
"0000001",
# Too short
"go:000001",
"go:GO:000001",
"GO:GO:000001",
# Wrong syntax
"GO-0000001",
"GO_0000001",
# Invalid banana (needs to be capitalized)
"go:go:000001",
# invalid prefix
"xxx:yyy",
# TODO add one with no pattern validation
]
for curie in invalid:
with self.subTest(curie=curie):
self.assertFalse(self.manager.is_standardizable_curie(curie))
def test_full_rdf(self):
"""Test the full dump."""
full = get_full_rdf(self.manager)
prefixes = {
prefix[len("https://bioregistry.io/registry/") :]
for prefix, in full.query(
"SELECT ?s WHERE { ?s a <https://bioregistry.io/schema/#0000001> }"
)
}
self.assertEqual(set(self.manager.registry), prefixes)
def test_parse_curie(self):
"""Test parsing CURIEs."""
for curie, pref, sep, p, i in [
("pdb:1234", False, ":", "pdb", "1234"),
("go:GO:1234", False, ":", "go", "1234"),
("go:go:1234", False, ":", "go", "1234"),
("go:1234", False, ":", "go", "1234"),
("fbbt:FBbt:1234", False, ":", "fbbt", "1234"),
("fbbt:fbbt:1234", False, ":", "fbbt", "1234"),
("fbbt:1234", False, ":", "fbbt", "1234"),
("go.ref:GO_REF:1234", False, ":", "go.ref", "1234"),
("go.ref:1234", False, ":", "go.ref", "1234"),
("GO_1234", False, "_", "go", "1234"),
("omim.ps:PS12345", False, ":", "omim.ps", "12345"),
("GO_1234", True, "_", "GO", "1234"),
("pdb:1234", True, ":", "pdb", "1234"),
]:
with self.subTest(curie=curie, use_preferred=pref, sep=sep):
actual_prefix, actual_i = parse_curie(curie, sep=sep, use_preferred=pref)
self.assertEqual(p, actual_prefix)
self.assertEqual(i, actual_i)
def test_external_registry_mappings(self):
"""Test external registry mappings."""
res = self.manager.get_external_mappings("obofoundry", "bioportal")
self.assertIsInstance(res, MappingsDiff)
self.assertEqual("obofoundry", res.source_metaprefix)
self.assertEqual("bioportal", res.target_metaprefix)
self.assertIn("gaz", res.mappings)
self.assertEqual("GAZ", res.mappings["gaz"])
# This is an obsolete OBO Foundry ontology so it won't get uploaded to BioPortal
self.assertIn("loggerhead", res.source_only)
# This is a non-ontology so it won't get in OBO Foundry
self.assertIn("DCTERMS", res.target_only)
|
