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"""Tests for reconciliation."""
import unittest
from curies import Converter, Record, remap_curie_prefixes, remap_uri_prefixes, rewire
from curies.reconciliation import (
CycleDetected,
DuplicateKeys,
DuplicateValues,
InconsistentMapping,
_order_curie_remapping,
)
#: The beginning of URIs used throughout examples
P = "https://example.org"
class TestUtils(unittest.TestCase):
"""Test utilities."""
def test_ordering(self):
"""Test ordering."""
converter = Converter(
[
Record(prefix="a", uri_prefix=f"{P}/a/"),
Record(prefix="b", uri_prefix=f"{P}/b/"),
Record(prefix="c", uri_prefix=f"{P}/c/"),
]
)
self.assertEqual(
[("a", "a1"), ("b", "b1")], _order_curie_remapping(converter, {"a": "a1", "b": "b1"})
)
# we want to be as low down the chain first. Test both constructions of the dictionary
self.assertEqual(
[("c", "a"), ("b", "c")], _order_curie_remapping(converter, {"c": "a", "b": "c"})
)
self.assertEqual(
[("c", "a"), ("b", "c")], _order_curie_remapping(converter, {"b": "c", "c": "a"})
)
def test_duplicate_values(self):
"""Test detecting bad mapping with duplicate."""
converter = Converter(
[
Record(prefix="a", uri_prefix=f"{P}/a/"),
Record(prefix="b", uri_prefix=f"{P}/b/"),
Record(prefix="c", uri_prefix=f"{P}/c/"),
]
)
curie_remapping = {"b": "c", "a": "c"}
with self.assertRaises(DuplicateValues):
_order_curie_remapping(converter, curie_remapping)
def test_duplicate_keys(self):
"""Test detecting a bad mapping that contains multiple references to the same record in the keys."""
converter = Converter(
[
Record(prefix="a", prefix_synonyms=["a1"], uri_prefix=f"{P}/a/"),
Record(prefix="b", uri_prefix=f"{P}/b/"),
Record(prefix="c", uri_prefix=f"{P}/c/"),
]
)
curie_remapping = {"a": "c", "a1": "b"}
with self.assertRaises(DuplicateKeys):
_order_curie_remapping(converter, curie_remapping)
def test_duplicate_correspondence(self):
"""Test detecting a bad mapping containing inconsistent references to the same record in the keys and values."""
converter = Converter(
[
Record(prefix="a", prefix_synonyms=["a1"], uri_prefix=f"{P}/a/"),
Record(prefix="b", uri_prefix=f"{P}/b/"),
Record(prefix="c", uri_prefix=f"{P}/c/"),
]
)
curie_remapping = {"a": "c", "b": "a1"}
with self.assertRaises(InconsistentMapping):
_order_curie_remapping(converter, curie_remapping)
def test_cycles(self):
"""Test detecting bad mapping with cycles."""
converter = Converter(
[
Record(prefix="a", uri_prefix=f"{P}/a/"),
Record(prefix="b", uri_prefix=f"{P}/b/"),
Record(prefix="c", uri_prefix=f"{P}/c/"),
]
)
curie_remapping = {"b": "c", "c": "b"}
with self.assertRaises(CycleDetected):
remap_curie_prefixes(converter, curie_remapping)
curie_remapping = {"a": "b", "b": "c", "c": "a"}
with self.assertRaises(CycleDetected):
_order_curie_remapping(converter, curie_remapping)
class TestCURIERemapping(unittest.TestCase):
"""A test case for CURIE prefix remapping."""
def test_missing(self):
"""Test simple upgrade."""
records = [
Record(prefix="a", prefix_synonyms=["x"], uri_prefix=f"{P}/a/"),
]
converter = Converter(records)
curie_remapping = {"b": "c"}
converter = remap_curie_prefixes(converter, curie_remapping)
self.assertEqual(records, converter.records)
def test_simple(self):
"""Test simple upgrade."""
records = [
Record(prefix="a", prefix_synonyms=["x"], uri_prefix=f"{P}/a/"),
]
converter = Converter(records)
curie_remapping = {"a": "a1"}
converter = remap_curie_prefixes(converter, curie_remapping)
self.assertEqual(1, len(converter.records))
self.assertEqual(
Record(prefix="a1", prefix_synonyms=["a", "x"], uri_prefix=f"{P}/a/"),
converter.records[0],
)
def test_synonym(self):
"""Test that an upgrade configuration that would cause a clash does nothing."""
records = [
Record(prefix="a", prefix_synonyms=["x"], uri_prefix=f"{P}/a/"),
]
converter = Converter(records)
curie_remapping = {"a": "x"}
converter = remap_curie_prefixes(converter, curie_remapping)
self.assertEqual(1, len(converter.records))
self.assertEqual(
Record(prefix="x", prefix_synonyms=["a"], uri_prefix=f"{P}/a/"),
converter.records[0],
)
def test_clash(self):
"""Test that an upgrade configuration that would cause a clash does nothing."""
records = [
Record(prefix="a", prefix_synonyms=["x"], uri_prefix=f"{P}/a/"),
Record(prefix="b", prefix_synonyms=["y"], uri_prefix=f"{P}/b/"),
]
converter = Converter(records)
curie_remapping = {"a": "b"}
converter = remap_curie_prefixes(converter, curie_remapping)
self.assertEqual(2, len(converter.records))
self.assertEqual(records, converter.records)
def test_clash_synonym(self):
"""Test a clash on a synonym."""
records = [
Record(prefix="a", prefix_synonyms=["x"], uri_prefix=f"{P}/a/"),
Record(prefix="b", prefix_synonyms=["y"], uri_prefix=f"{P}/b/"),
]
converter = Converter(records)
curie_remapping = {"a": "y"}
converter = remap_curie_prefixes(converter, curie_remapping)
self.assertEqual(2, len(converter.records))
self.assertEqual(records, converter.records)
def test_simultaneous(self):
"""Test simultaneous remapping."""
records = [
Record(prefix="geo", uri_prefix="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc="),
Record(prefix="geogeo", uri_prefix="http://purl.obolibrary.org/obo/GEO_"),
]
converter = Converter(records)
curie_remapping = {"geo": "ncbi.geo", "geogeo": "geo"}
converter = remap_curie_prefixes(converter, curie_remapping)
self.assertEqual(
[
Record(
prefix="geo",
prefix_synonyms=["geogeo"],
uri_prefix="http://purl.obolibrary.org/obo/GEO_",
),
Record(
prefix="ncbi.geo",
uri_prefix="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=",
),
],
converter.records,
)
def test_simultaneous_synonym(self):
"""Test simultaneous remapping with synonyms raises an error."""
records = [
Record(
prefix="geo",
prefix_synonyms=["ggg"],
uri_prefix="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=",
),
Record(prefix="geogeo", uri_prefix="http://purl.obolibrary.org/obo/GEO_"),
]
converter = Converter(records)
curie_remapping = {"ggg": "ncbi.geo", "geogeo": "geo"}
with self.assertRaises(InconsistentMapping):
remap_curie_prefixes(converter, curie_remapping)
class TestURIRemapping(unittest.TestCase):
"""A test case for URI prefix remapping."""
def test_transitive_error(self):
"""Test error on transitive remapping."""
converter = Converter([])
uri_remapping = {f"{P}/nope/": f"{P}/more-nope/", f"{P}/more-nope/": f"{P}/more-more-nope/"}
with self.assertRaises(NotImplementedError) as e:
remap_uri_prefixes(converter, uri_remapping)
# check that stringification works
self.assertIn("75", str(e.exception))
def test_missing(self):
"""Test simple upgrade."""
records = [
Record(prefix="a", uri_prefix=f"{P}/a/"),
]
converter = Converter(records)
uri_remapping = {f"{P}/nope/": f"{P}/more-nope/"}
converter = remap_uri_prefixes(converter, uri_remapping)
self.assertEqual(records, converter.records)
def test_simple(self):
"""Test simple upgrade."""
records = [
Record(prefix="a", uri_prefix=f"{P}/a/", uri_prefix_synonyms=[f"{P}/a1/"]),
]
converter = Converter(records)
uri_remapping = {f"{P}/a/": f"{P}/a2/"}
converter = remap_uri_prefixes(converter, uri_remapping)
self.assertEqual(1, len(converter.records))
self.assertEqual(
Record(
prefix="a",
uri_prefix=f"{P}/a2/",
uri_prefix_synonyms=[f"{P}/a/", f"{P}/a1/"],
),
converter.records[0],
)
def test_synonym(self):
"""Test that an upgrade configuration that would cause a clash does nothing."""
records = [
Record(prefix="a", uri_prefix=f"{P}/a/", uri_prefix_synonyms=[f"{P}/a1/"]),
]
converter = Converter(records)
uri_remapping = {f"{P}/a1/": f"{P}/a2/"}
converter = remap_uri_prefixes(converter, uri_remapping)
self.assertEqual(1, len(converter.records))
self.assertEqual(
Record(prefix="a", uri_prefix=f"{P}/a2/", uri_prefix_synonyms=[f"{P}/a/", f"{P}/a1/"]),
converter.records[0],
)
def test_clash_preferred(self):
"""Test that an upgrade configuration that would cause a clash does nothing."""
records = [
Record(prefix="a", prefix_synonyms=["x"], uri_prefix=f"{P}/a/"),
Record(prefix="b", prefix_synonyms=["y"], uri_prefix=f"{P}/b/"),
]
converter = Converter(records)
upgrades = {f"{P}/a/": f"{P}/b/"}
converter = remap_uri_prefixes(converter, upgrades)
self.assertEqual(2, len(converter.records))
self.assertEqual(records, converter.records)
def test_clash_synonym(self):
"""Test clashing with a synonym."""
records = [
Record(prefix="a", uri_prefix=f"{P}/a/"),
Record(prefix="b", uri_prefix=f"{P}/b/", uri_prefix_synonyms=[f"{P}/b1/"]),
]
converter = Converter(records)
upgrades = {f"{P}/a/": f"{P}/b1/"}
converter = remap_uri_prefixes(converter, upgrades)
self.assertEqual(2, len(converter.records))
self.assertEqual(records, converter.records)
class TestRewire(unittest.TestCase):
"""A test case for rewiring."""
def test_idempotent(self):
"""Test that a redundant rewiring doesn't do anything."""
records = [
Record(prefix="a", uri_prefix=f"{P}/a/", uri_prefix_synonyms=["https://a.org/"]),
]
converter = Converter(records)
rewiring = {"a": f"{P}/a/"}
converter = rewire(converter, rewiring)
self.assertEqual(records, converter.records)
def test_upgrade_uri_prefixes_simple(self):
"""Test simple upgrade."""
records = [
Record(prefix="a", uri_prefix=f"{P}/a/", uri_prefix_synonyms=["https://a.org/"]),
]
converter = Converter(records)
rewiring = {"a": f"{P}/a1/"}
converter = rewire(converter, rewiring)
self.assertEqual(1, len(converter.records))
self.assertEqual(
Record(
prefix="a", uri_prefix=f"{P}/a1/", uri_prefix_synonyms=["https://a.org/", f"{P}/a/"]
),
converter.records[0],
)
# def test_upgrade_uri_prefixes_add(self):
# """Test an upgrade that adds an extra prefix."""
# records = [
# Record(prefix="a", uri_prefix=f"{P}/a/"),
# ]
# converter = Converter(records)
# rewiring = {"b": f"{P}/b/"}
# converter = rewire(converter, rewiring)
# self.assertEqual(2, len(converter.records))
# self.assertEqual(
# [
# Record(prefix="a", uri_prefix=f"{P}/a/"),
# Record(prefix="b", uri_prefix=f"{P}/b/"),
# ],
# converter.records,
# )
def test_upgrade_uri_prefixes_clash(self):
"""Test an upgrade that does nothing since it would create a clash."""
records = [
Record(prefix="a", uri_prefix=f"{P}/a/"),
Record(prefix="b", uri_prefix=f"{P}/b/"),
]
converter = Converter(records)
rewiring = {"b": f"{P}/a/"}
converter = rewire(converter, rewiring)
self.assertEqual(2, len(converter.records))
self.assertEqual(
[
Record(prefix="a", uri_prefix=f"{P}/a/"),
Record(prefix="b", uri_prefix=f"{P}/b/"),
],
converter.records,
)
def test_upgrade_uri_upgrade(self):
"""Test an upgrade of an existing URI prefix synonym."""
records = [
Record(prefix="a", uri_prefix=f"{P}/a/", uri_prefix_synonyms=[f"{P}/a1/"]),
]
converter = Converter(records)
rewiring = {"a": f"{P}/a1/"}
converter = rewire(converter, rewiring)
self.assertEqual(1, len(converter.records))
self.assertEqual(
[
Record(
prefix="a",
uri_prefix=f"{P}/a1/",
uri_prefix_synonyms=[f"{P}/a/"],
),
],
converter.records,
)
def test_upgrade_uri_upgrade_with_curie_prefix(self):
"""Test an upgrade of an existing URI prefix synonym via a CURIE prefix synonym."""
records = [
Record(
prefix="a",
prefix_synonyms=["a1"],
uri_prefix=f"{P}/a/",
uri_prefix_synonyms=[f"{P}/a1/"],
),
]
converter = Converter(records)
rewiring = {"a1": f"{P}/a1/"}
converter = rewire(converter, rewiring)
self.assertEqual(1, len(converter.records))
self.assertEqual(
[
Record(
prefix="a",
prefix_synonyms=["a1"],
uri_prefix=f"{P}/a1/",
uri_prefix_synonyms=[f"{P}/a/"],
),
],
converter.records,
)
|
