perf: skip quadratic curies duplicate check for valid contexts

docs/intro.md

@@ -28,12 +28,10 @@ pip install prefixmaps
 to use in combination with [curies](https://github.com/cthoyt/curies) library:
 
 ```python
-from prefixmaps.io.parser import load_multi_context
-from curies import Converter
+from prefixmaps.io.parser import load_context, load_multi_context
 
 context = load_multi_context(["obo", "bioregistry.upper", "linked_data", "prefixcc"])
-extended_prefix_map = context.as_extended_prefix_map()
-converter = Converter.from_extended_prefix_map(extended_prefix_map)
+converter = context.as_converter()
 
 >>> converter.expand("CHEBI:1")
 'http://purl.obolibrary.org/obo/CHEBI_1'
@@ -55,8 +53,7 @@ If we prioritize prefix.cc the OBO prefix is ignored:
 
 ```python
 >>> ctxt = load_multi_context(["prefixcc", "obo"])
->>> extended_prefix_map = context.as_extended_prefix_map()
->>> converter = Converter.from_extended_prefix_map(extended_prefix_map)
+>>> converter = ctxt.as_converter()
 >>> converter.expand("GEO:1")
 >>> converter.expand("geo:1")
 'http://www.opengis.net/ont/geosparql#1'
@@ -68,8 +65,7 @@ If we push bioregistry at the start of the list then GEOGEO can be used as the p
 
 ```python
 >>> ctxt = load_multi_context(["bioregistry", "prefixcc", "obo"])
->>> extended_prefix_map = context.as_extended_prefix_map()
->>> converter = Converter.from_extended_prefix_map(extended_prefix_map)
+>>> converter = ctxt.as_converter()
 >>> converter.expand("geo:1")
 'http://identifiers.org/geo/1'
 >>> converter.expand("GEO:1")
@@ -83,10 +79,7 @@ We get similar results using the upper-normalized variant of bioregistry:
 
 ```python
 >>> ctxt = load_multi_context(["bioregistry.upper", "prefixcc", "obo"])
->>> extended_prefix_map = context.as_extended_prefix_map()
->>> converter = Converter.from_extended_prefix_map(extended_prefix_map)
->>> converter = Converter.from_extended_prefix_map(extended_prefix_map)
->>> converter = Converter.from_extended_prefix_map(extended_prefix_map)
+>>> converter = ctxt.as_converter()
 >>> converter.expand("GEO:1")
 'http://identifiers.org/geo/1'
 >>> converter.expand("geo:1")
@@ -98,8 +91,7 @@ Users of OBO ontologies will want to place OBO at the start of the list:
 
 ```python
 >>> ctxt = load_multi_context(["obo", "bioregistry.upper", "prefixcc"])
->>> extended_prefix_map = context.as_extended_prefix_map()
->>> converter = Converter.from_extended_prefix_map(extended_prefix_map)
+>>> converter = ctxt.as_converter()
 >>> converter.expand("geo:1")
 >>> converter.expand("GEO:1")
 'http://purl.obolibrary.org/obo/GEO_1'
@@ -114,8 +106,7 @@ You can use the ready-made "merged" prefix set, which prioritizes OBO:
 
 ```python
 >>> ctxt = load_context("merged")
->>> extended_prefix_map = context.as_extended_prefix_map()
->>> converter = Converter.from_extended_prefix_map(extended_prefix_map)
+>>> converter = ctxt.as_converter()
 >>> converter.expand("GEOGEO:1")
 >>> converter.expand("GEO:1")
 'http://purl.obolibrary.org/obo/GEO_1'

src/prefixmaps/datamodel/context.py

@@ -381,7 +381,11 @@ def as_converter(self) -> curies.Converter:
         :return:
         """
         extended_prefix_map = self.as_extended_prefix_map()
-        return curies.Converter.from_extended_prefix_map(extended_prefix_map)
+        # curies' strict check compares every pair of records, which takes 15-25 seconds
+        # per merged context, see https://github.com/linkml/prefixmaps/issues/75.
+        # Only run it when a linear scan finds duplicates, so curies raises its usual error.
+        strict = _has_duplicates(extended_prefix_map)
+        return curies.Converter.from_extended_prefix_map(extended_prefix_map, strict=strict)
 
     def validate(self, canonical_only=True) -> List[str]:
         """
@@ -398,3 +402,26 @@ def validate(self, canonical_only=True) -> List[str]:
         # namespaces = self.namespaces(lower=True)
         # prefixes = self.namespaces(lower=True)
         return messages
+
+
+def _has_duplicates(records: List[curies.Record]) -> bool:
+    """
+    Check whether any two records share a prefix or a URI prefix.
+
+    This finds the same duplicates as curies' strict check, but in linear time.
+
+    :param records: records of an extended prefix map
+    :return: True if a prefix or URI prefix appears in more than one record
+    """
+    prefixes = set()
+    uri_prefixes = set()
+    for record in records:
+        record_prefixes = {record.prefix, *record.prefix_synonyms}
+        record_uri_prefixes = {record.uri_prefix, *record.uri_prefix_synonyms}
+        if not prefixes.isdisjoint(record_prefixes):
+            return True
+        if not uri_prefixes.isdisjoint(record_uri_prefixes):
+            return True
+        prefixes |= record_prefixes
+        uri_prefixes |= record_uri_prefixes
+    return False

tests/test_core/test_curies.py

@@ -2,9 +2,11 @@
 
 import unittest
 
-from curies import Converter
+from curies import Converter, DuplicatePrefixes, DuplicateURIPrefixes
 
 import prefixmaps
+from prefixmaps.data import context_paths
+from prefixmaps.datamodel.context import Context, PrefixExpansion, StatusType
 
 
 class TestCuries(unittest.TestCase):
@@ -37,3 +39,65 @@ def test_load(self):
         self.assertIn(uri_prefix_2, converter.reverse_prefix_map)
         self.assertEqual(prefix, converter.reverse_prefix_map[uri_prefix_1])
         self.assertEqual(prefix, converter.reverse_prefix_map[uri_prefix_2])
+
+    def test_load_all(self):
+        """Test that every bundled context can be loaded into a converter."""
+        for key in context_paths:
+            with self.subTest(key=key):
+                self.assertIsInstance(prefixmaps.load_converter(key), Converter)
+
+    def test_duplicate_uri_prefixes(self):
+        """Test that two records sharing a URI prefix are still rejected."""
+        context = Context("test")
+        context.prefix_expansions = [
+            PrefixExpansion("test", "a", "https://example.org/a/", StatusType.canonical),
+            PrefixExpansion("test", "b", "https://example.org/a/", StatusType.canonical),
+        ]
+        with self.assertRaises(DuplicateURIPrefixes):
+            context.as_converter()
+
+    def test_duplicate_prefixes(self):
+        """Test that two records sharing a prefix synonym are still rejected."""
+        context = Context("test")
+        context.prefix_expansions = [
+            PrefixExpansion("test", "a", "https://example.org/a/", StatusType.canonical),
+            PrefixExpansion("test", "b", "https://example.org/b/", StatusType.canonical),
+            PrefixExpansion("test", "c", "https://example.org/a/", StatusType.namespace_alias),
+            PrefixExpansion("test", "c", "https://example.org/b/", StatusType.namespace_alias),
+        ]
+        with self.assertRaises(DuplicatePrefixes):
+            context.as_converter()
+
+    def test_duplicate_uri_prefix_synonyms(self):
+        """Test that a URI prefix synonym shared with another record is still rejected."""
+        context = Context("test")
+        context.prefix_expansions = [
+            PrefixExpansion("test", "a", "https://example.org/a/", StatusType.canonical),
+            PrefixExpansion("test", "b", "https://example.org/b/", StatusType.canonical),
+            PrefixExpansion("test", "b", "https://example.org/a/", StatusType.prefix_alias),
+        ]
+        with self.assertRaises(DuplicateURIPrefixes):
+            context.as_converter()
+
+    def test_duplicate_canonical_prefix_synonym(self):
+        """Test that a prefix synonym equal to another record's prefix is still rejected."""
+        context = Context("test")
+        context.prefix_expansions = [
+            PrefixExpansion("test", "a", "https://example.org/a/", StatusType.canonical),
+            PrefixExpansion("test", "b", "https://example.org/b/", StatusType.canonical),
+            PrefixExpansion("test", "a", "https://example.org/b/", StatusType.namespace_alias),
+        ]
+        with self.assertRaises(DuplicatePrefixes):
+            context.as_converter()
+
+    def test_duplicate_shared_uri_prefix_synonym(self):
+        """Test that two records sharing a URI prefix synonym are still rejected."""
+        context = Context("test")
+        context.prefix_expansions = [
+            PrefixExpansion("test", "a", "https://example.org/a/", StatusType.canonical),
+            PrefixExpansion("test", "b", "https://example.org/b/", StatusType.canonical),
+            PrefixExpansion("test", "a", "https://example.org/z/", StatusType.prefix_alias),
+            PrefixExpansion("test", "b", "https://example.org/z/", StatusType.prefix_alias),
+        ]
+        with self.assertRaises(DuplicateURIPrefixes):
+            context.as_converter()

tests/test_core/test_integrity.py

@@ -14,11 +14,12 @@ class TestIntegrity(unittest.TestCase):
 
     def setUp(self) -> None:
         """Set up the test case with all contexts."""
-        # We don't expect some merged contexts to pass all tests, see:
-        # See: https://github.com/linkml/prefixmaps/issues/26
+        self.contexts: Mapping[str, Context] = {key: load_context(key) for key in context_paths}
+        # We don't expect merged contexts to pass the alias tests, see:
+        # https://github.com/linkml/prefixmaps/issues/26
         skip = {"merged", "merged.oak", "merged.monarch"}
-        self.contexts: Mapping[str, Context] = {
-            key: load_context(key) for key, path in context_paths.items() if key not in skip
+        self.alias_contexts: Mapping[str, Context] = {
+            key: context for key, context in self.contexts.items() if key not in skip
         }
 
     def test_unique_canonical_prefix(self):
@@ -56,7 +57,7 @@ def test_unique_canonical_namespace(self):
 
     def test_prefix_aliases(self):
         """Test that namespace aliases have a valid prefix."""
-        for key, context in self.contexts.items():
+        for key, context in self.alias_contexts.items():
             with self.subTest(key=key):
                 canonical_prefixes = {
                     expansion.prefix
@@ -78,7 +79,7 @@ def test_prefix_aliases(self):
 
     def test_namespace_aliases(self):
         """Test that prefix aliases have a valid namespace."""
-        for key, context in self.contexts.items():
+        for key, context in self.alias_contexts.items():
             with self.subTest(key=key):
                 canonical_namespaces = {
                     expansion.namespace: expansion.prefix