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# -*- coding: utf-8 -*-
"""Tests for checking the integrity of the contexts."""
import json
import unittest
import bioregistry
from bioregistry import Resource, manager
from bioregistry.constants import CONTEXTS_PATH
class TestContexts(unittest.TestCase):
"""A test case for checking the integrity of the contexts."""
def setUp(self) -> None:
"""Set up the test case."""
self.contexts = bioregistry.read_contexts()
self.collection_keys = {
collection.context: key
for key, collection in bioregistry.read_collections().items()
if collection.context
}
self.valid_metaprefixes = set(bioregistry.read_metaregistry()) | {"default"}
self.valid_prefixes = set(bioregistry.read_registry())
def test_linted(self):
"""Test the context file is linted."""
text = CONTEXTS_PATH.read_text(encoding="utf-8")
linted_text = json.dumps(
json.loads(text),
indent=2,
sort_keys=True,
ensure_ascii=False,
)
self.assertEqual(linted_text, text)
def test_obo_context(self):
"""Test the OBO context map."""
p = "http://purl.obolibrary.org/obo"
prefix_map, pattern_map = manager.get_context_artifacts("obo", include_synonyms=False)
self.assertIn("KISAO", prefix_map)
self.assertEqual(f"{p}/KISAO_", prefix_map["KISAO"])
self.assertIn("FBcv", prefix_map)
self.assertEqual(f"{p}/FBcv_", prefix_map["FBcv"])
self.assertIn("GEO", prefix_map)
self.assertEqual(f"{p}/GEO_", prefix_map["GEO"])
self.assertEqual("https://www.ncbi.nlm.nih.gov/pubmed/", prefix_map["PMID"])
self.assertNotIn("biomodels.kisao", prefix_map)
prefix_map, pattern_map = manager.get_context_artifacts("obo", include_synonyms=True)
self.assertIn("KISAO", prefix_map)
self.assertIn(
"biomodels.kisao",
prefix_map,
msg="When overriding, this means that bioregistry prefix isn't properly added to the synonyms list",
)
def test_obo_converter(self):
"""Test getting a converter from a context."""
converter = manager.get_converter_from_context("obo")
self.assertEqual("ICD10WHO", converter.standardize_prefix("icd10"))
self.assertEqual("Orphanet", converter.standardize_prefix("ordo"))
self.assertEqual("GO", converter.standardize_prefix("GO"))
self.assertEqual("GO", converter.standardize_prefix("gomf"))
self.assertEqual("https://www.ncbi.nlm.nih.gov/pubmed/", converter.bimap["PMID"])
self.assertEqual("GO", converter.standardize_prefix("go"))
self.assertEqual("oboInOwl", converter.standardize_prefix("oboinowl"))
def test_data(self):
"""Test the data integrity."""
for key, context in self.contexts.items():
self.assertNotIn(
key,
set(self.collection_keys),
msg=f"Context has same key as context assigned by collection {self.collection_keys.get(key)}",
)
for maintainer in context.maintainers:
self.assertIsNotNone(maintainer.name)
# self.assertIsNotNone(maintainer.email, msg=f"{maintainer.name} is missing an email")
self.assertIsNotNone(
maintainer.github, msg=f"{maintainer.name} is missing a GitHub handle"
)
self.assertIsNotNone(maintainer.orcid, msg=f"{maintainer.name} is missing an ORCID")
self.assertRegex(maintainer.orcid, "^\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$")
for metaprefix in context.uri_prefix_priority or []:
self.assertIn(metaprefix, self.valid_metaprefixes.union(Resource.URI_FORMATTERS))
for metaprefix in context.prefix_priority or []:
self.assertIn(
metaprefix,
self.valid_metaprefixes.union({"obofoundry.preferred", "preferred", "default"}),
)
remapping = context.prefix_remapping or {}
_valid_remapping_prefixes = set(
bioregistry.get_prefix_map(
uri_prefix_priority=context.uri_prefix_priority,
)
)
for prefix in remapping:
# Currently this allows overwriting of existing prefixes
self.assertIn(prefix, _valid_remapping_prefixes)
_valid_custom_prefixes = set(
bioregistry.get_prefix_map(
remapping=remapping,
uri_prefix_priority=context.uri_prefix_priority,
)
)
invalid_custom_prefixes = {
prefix
for prefix in (context.custom_prefix_map or {})
if prefix not in _valid_custom_prefixes
}
self.assertEqual(
0,
len(invalid_custom_prefixes),
msg=f"""
All prefixes in the custom prefix mapping should either be canonical prefixes or generated by the prefix remapping
Invalid prefixes: {", ".join(sorted(invalid_custom_prefixes))}
""",
)
for blacklist_prefix in context.blacklist or []:
self.assertIn(blacklist_prefix, self.valid_prefixes)
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