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# -*- coding: utf-8 -*-
"""Tests for collections."""
import logging
import unittest
from collections import Counter
import rdflib
from bioregistry import manager
from bioregistry.export.rdf_export import collection_to_rdf_str
from bioregistry.schema import Collection
logger = logging.getLogger(__name__)
class TestCollections(unittest.TestCase):
"""Tests for collections."""
def setUp(self) -> None:
"""Set up the test case."""
self.manager = manager
def test_minimum_metadata(self):
"""Check collections have minimal metadata and correct prefixes."""
registry = self.manager.registry
for key, collection_pydantic in sorted(self.manager.collections.items()):
self.assertIsInstance(collection_pydantic, Collection)
collection = collection_pydantic.dict()
with self.subTest(key=key):
self.assertRegex(key, "^\\d{7}$")
self.assertIn("name", collection)
self.assertIn("authors", collection)
self.assertIsInstance(collection["authors"], list, msg=f"Collection: {collection}")
for author in collection["authors"]:
self.assertIn("name", author)
self.assertIn("orcid", author)
self.assertRegex(author["orcid"], self.manager.get_pattern("orcid"))
self.assertIn("description", collection)
incorrect = {prefix for prefix in collection["resources"] if prefix not in registry}
self.assertEqual(set(), incorrect, msg="Invalid prefixes")
duplicates = {
prefix
for prefix, count in Counter(collection["resources"]).items()
if 1 < count
}
self.assertEqual(set(), duplicates, msg="Duplicates found")
self.assertEqual(
sorted(collection_pydantic.resources), collection_pydantic.resources
)
def test_get_collection(self):
"""Test getting a collection."""
self.assertIsNone(self.manager.collections.get("nope"))
identifier = "0000001"
collection = self.manager.collections.get(identifier)
self.assertIsInstance(collection, Collection)
self.assertEqual(identifier, collection.identifier)
# Check building a prefix map
prefix_map = collection.as_prefix_map()
self.assertIsInstance(prefix_map, dict)
# Check building a JSON-LD context.
context_jsonld = collection.as_context_jsonld()
self.assertIsInstance(context_jsonld, dict)
self.assertIn("@context", context_jsonld)
self.assertEqual(prefix_map, context_jsonld["@context"])
def test_get_rdf(self):
"""Test conversion to RDF."""
collection = manager.collections["0000001"]
s = collection_to_rdf_str(collection, manager=self.manager)
self.assertIsInstance(s, str)
g = rdflib.Graph()
g.parse(data=s)
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