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"""Slow test cases."""
import unittest
from collections import defaultdict
import pytest
import bioregistry
class TestDataSlow(unittest.TestCase):
"""Slow tests."""
@pytest.mark.slow
def test_parse_http_vs_https(self):
"""Test parsing both HTTP and HTTPS, even when the provider is only set to one."""
prefix = "neuronames"
ex = bioregistry.get_example(prefix)
with self.subTest(protocol="http"):
a = f"http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID={ex}"
self.assertEqual((prefix, ex), bioregistry.parse_iri(a))
with self.subTest(protocol="https"):
b = f"https://braininfo.rprc.washington.edu/centraldirectory.aspx?ID={ex}"
self.assertEqual((prefix, ex), bioregistry.parse_iri(b))
@pytest.mark.slow
def test_prefix_map_priorities(self):
"""Test that different lead priorities all work for prefix map generation."""
priorities = [
"default",
"miriam",
"ols",
"obofoundry",
"n2t",
"prefixcommons",
# "bioportal",
]
for lead in priorities:
priority = [lead, *(x for x in priorities if x != lead)]
with self.subTest(priority=",".join(priority)):
prefix_map = bioregistry.get_prefix_map(uri_prefix_priority=priority)
self.assertIsNotNone(prefix_map)
@pytest.mark.slow
def test_unique_iris(self):
"""Test that all IRIs are unique, or at least there's a mapping to which one is the preferred prefix."""
# TODO make sure there are also no HTTP vs HTTPS clashes,
# for example if one prefix has http://example.org/foo/$1 and a different one
# has https://example.org/foo/$1
prefix_map = bioregistry.get_prefix_map()
dd = defaultdict(dict)
for prefix, iri in prefix_map.items():
resource = bioregistry.get_resource(prefix)
self.assertIsNotNone(resource)
if resource.provides is not None:
# Don't consider resources that are providing, such as `ctd.gene`
continue
dd[iri][prefix] = resource
x = {}
for iri, resources in dd.items():
if 1 == len(resources):
# This is a unique IRI, so no issues
continue
# Get parts
parts = {prefix: resource.part_of for prefix, resource in resources.items()}
unmapped = [prefix for prefix, part_of in parts.items() if part_of is None]
if len(unmapped) <= 1:
continue
# Get canonical
canonicals = {prefix: resource.has_canonical for prefix, resource in resources.items()}
canonical_target = [prefix for prefix, target in canonicals.items() if target is None]
all_targets = list(
{target for prefix, target in canonicals.items() if target is not None}
)
if (
len(canonical_target) == 1
and len(all_targets) == 1
and canonical_target[0] == all_targets[0]
):
continue
x[iri] = parts, unmapped, canonical_target, all_targets
self.assertEqual({}, x)
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