reasoner-validator 4.2.1__tar.gz → 4.2.2__tar.gz

{reasoner_validator-4.2.1 → reasoner_validator-4.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: reasoner-validator
-Version: 4.2.1
+Version: 4.2.2
 Summary: Validation tools for Reasoner API
 Home-page: https://github.com/NCATSTranslator
 License: MIT

{reasoner_validator-4.2.1 → reasoner_validator-4.2.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "reasoner-validator"
-version = "4.2.1"
+version = "4.2.2"
 description = "Validation tools for Reasoner API"
 authors = [
     "Richard Bruskiewich <richard.bruskiewich@delphinai.com>",

{reasoner_validator-4.2.1 → reasoner_validator-4.2.2}/reasoner_validator/utils/__init__.py

@@ -79,13 +79,9 @@ def get_aliases(identifier: str) -> List[str]:
                         # preferred_curie = preferred_id["identifier"]
                         # preferred_name = preferred_id["label"]
                         if "equivalent_identifiers" in clique.keys():
+                            # Sanity check: returned aliases
+                            # are all converted to upper case
                             aliases = [entry["identifier"] for entry in clique["equivalent_identifiers"]]
-                            #
-                            # Decided that it was a bad idea to remove
-                            # the original identifier from the aliases...
-                            # aliases.remove(identifier)
-                            #
-                            # print(dumps(aliases, indent=2))
                         else:
                             logging.warning(
                                 f"get_aliases(): missing the 'equivalent identifiers' for the '{identifier}' clique?"
@@ -103,6 +99,10 @@ def get_aliases(identifier: str) -> List[str]:
         # Logging various errors but always
         # return the identifier as its own alias
         aliases = [identifier]
+    elif identifier not in aliases:
+        # If the identifier itself is missing in the aliases, then
+        # could just be a letter case mismatch? See if you can correct for this...
+        aliases = [identifier if str(i).upper() == identifier.upper() else i for i in aliases]
 
     return aliases
 

{reasoner_validator-4.2.1 → reasoner_validator-4.2.2}/reasoner_validator/validator.py

@@ -1,4 +1,4 @@
-from typing import Optional, Tuple, List, Dict, Set
+from typing import Optional, List, Dict, Set
 
 from reasoner_validator.biolink import (
     BiolinkValidator,
@@ -777,7 +777,7 @@ class TRAPIResponseValidator(BiolinkValidator):
         # Check for testcase 'subject_id' and 'object_id',
         # with expected categories, in nodes catalog
         nodes: Dict = knowledge_graph["nodes"]
-        subject_id = testcase["subject_id"] if "subject_id" in testcase else testcase["subject"]
+        subject_id: str = testcase["subject_id"] if "subject_id" in testcase else testcase["subject"]
         subject_aliases = get_aliases(subject_id)
         if not self.testcase_node_found("subject", subject_aliases, testcase, nodes):
             self.report(
@@ -787,7 +787,7 @@ class TRAPIResponseValidator(BiolinkValidator):
             )
             return False
 
-        object_id = testcase["object_id"] if "object_id" in testcase else testcase["object"]
+        object_id: str = testcase["object_id"] if "object_id" in testcase else testcase["object"]
         object_aliases = get_aliases(object_id)
         if not self.testcase_node_found("object", object_aliases, testcase, nodes):
             self.report(

reasoner_validator-4.2.2/tests/test_utils.py

@@ -0,0 +1,77 @@
+"""
+Unit tests against reasoner-validator utils
+"""
+from typing import List, Optional
+import pytest
+
+from reasoner_validator.utils import is_curie, get_aliases, get_reference
+
+
+@pytest.mark.parametrize(
+    "identifier,outcome",
+    [
+        (None, False),
+        ("foo:bar", True),
+        ("not-a-curie", False),
+    ]
+)
+def test_is_curie(identifier: str, outcome: bool):
+    assert is_curie(identifier) is outcome
+
+
+@pytest.mark.parametrize(
+    "identifier",
+    [
+        None,
+        ""
+    ]
+)
+def test_get_aliases_of_empty_identifier(identifier):
+    with pytest.raises(RuntimeError):
+        get_aliases(identifier)
+
+
+@pytest.mark.parametrize(
+    "identifier,one_alias",
+    [
+        (   # Special test for a CURIE for which
+            # NodeNormalization is known to
+            # return a lower case namespace
+            "ORPHANET:33110",
+            "MONDO:0011096"
+        ),
+        (   # Test that the alias search is also
+            # input namespace case-insensitive:
+            # A modification of case of the input
+            # identifier is still properly returned.
+            "Orphanet:33110",
+            "MONDO:0011096"
+        ),
+        (   # only CURIEs can be resolved to aliases
+            # but just logs a warning but returns the identifier
+            "not-a-curie",
+            ""
+        ),
+    ]
+)
+def test_get_aliases(identifier: str, one_alias: str):
+    aliases: List[str] = get_aliases(identifier)
+    assert identifier in aliases
+    assert one_alias in aliases if one_alias in aliases else True
+
+
+@pytest.mark.parametrize(
+    "identifier,reference",
+    [
+        (   # Valid CURIE has a reference
+            "ORPHANET:33110",
+            "33110"
+        ),
+        (   # Only CURIEs can be resolved to references
+            "not-a-curie",
+            None
+        ),
+    ]
+)
+def test_get_reference(identifier: str, reference: str):
+    assert get_reference(identifier) == reference