.github/workflows/run_tests.yaml

@@ -22,8 +22,14 @@ jobs:
 
       - name: run tests
         run: |
-          hatch run tests:run --ignore=dump_things_service/tests/test_generators.py
+          hatch run tests:run \
+            --ignore=dump_things_service/tests/test_generators.py \
+            --ignore=dump_things_service/tests/test_ifabsent_patch.py
 
       - name: run generator tests
         run: |
           hatch run tests:run dump_things_service/tests/test_generators.py
+
+      - name: run ifabsent-patch tests
+        run: |
+          hatch run tests:run dump_things_service/tests/test_ifabsent_patch.py

CHANGELOG.md

@@ -1,3 +1,10 @@
+# 5.3.2 (2025-12-15)
+
+## Bugfixes
+
+- add a patch for faulty `ifabsent`-code generation in LinkML's Pydantic-code generator.
+
+
 # 5.3.1 (2025-12-11)
 
 ## Bugfixes

dump_things_service/__about__.py

@@ -1 +1 @@
-__version__ = '5.3.1'
+__version__ = '5.3.2'

dump_things_service/patches/enabled.py

@@ -1,5 +1,6 @@
 
 import dump_things_service.patches.compile
 import dump_things_service.patches.enumerations
+import dump_things_service.patches.ifabsent_processing
 import dump_things_service.patches.rdflib_loader
 import dump_things_service.patches.yamlutils

dump_things_service/patches/ifabsent_processing.py

@@ -0,0 +1,22 @@
+""" Monkeypatch for linkml.generators.common.ifabsent_processor.IfAbsentProcessor
+
+Patches the ifabsent-processor to not use namespace objects. Those are not
+generated in the pydantic code generator.
+"""
+import logging
+from importlib import import_module
+
+
+logger = logging.getLogger('dump_things_service')
+
+
+def patched_uri_for(self, s: str) -> str:
+    uri = str(self.schema_view.namespaces().uri_for(s))
+    curie = self.schema_view.namespaces().curie_for(uri, True)
+    return f"'{curie}'" if curie else self._strval(uri)
+
+
+logger.info('patching linkml.generators.common.ifabsent_processor.IfAbsentProcessor._uri_for')
+
+cls = import_module('linkml.generators.common.ifabsent_processor')
+cls.IfAbsentProcessor._uri_for = patched_uri_for

dump_things_service/tests/assets/schema-ifabsent-error.yaml

@@ -0,0 +1,31 @@
+id: https://example.org/ifabsent-error-trigger
+name: if-absent-error-trigger
+version: UNRELEASED
+title: ifabsent error trigger
+
+
+prefixes:
+  xsd: http://www.w3.org/2001/XMLSchema#
+  xyzrse: https://concepts.datalad.org/s/demo-rse-group/unreleased/
+
+
+types:
+  uriorcurie:
+    name: uriorcurie
+    uri: xsd:anyURI
+    repr: str
+
+
+slots:
+  creator:
+    slot_uri: xyzrse:creator
+    range: uriorcurie
+
+
+classes:
+  ORCID:
+    slots:
+    - creator
+    slot_usage:
+      creator:
+        ifabsent: uriorcurie(xsd:04fa4r544)

dump_things_service/tests/test_ifabsent_patch.py

@@ -0,0 +1,33 @@
+from importlib import reload
+from pathlib import Path
+
+import linkml
+import linkml.generators.common.ifabsent_processor as if_abs_proc
+
+import dump_things_service.patches.ifabsent_processing
+
+
+# Path to a local simple test schema
+schema_dir = Path(__file__).parent / 'assets'
+
+
+def _original_uri_for(self, s: str) -> str:
+    uri = str(self.schema_view.namespaces().uri_for(s))
+    return self.schema_view.namespaces().curie_for(uri, True, True) or self._strval(uri)
+
+
+def test_ifabsent_patch():
+
+    # Patch in the faulty, original code and check for its result
+    if_abs_proc.IfAbsentProcessor._uri_for = _original_uri_for
+    gen1 = linkml.generators.PydanticGenerator(str(schema_dir / 'schema-ifabsent-error.yaml'))
+    x = gen1.serialize()
+    assert 'default=XSD["04fa4r544"]' in x
+
+    # Apply the patch
+    reload(dump_things_service.patches.ifabsent_processing)
+
+    # Check for proper code generation
+    gen2 = linkml.generators.PydanticGenerator(str(schema_dir / 'schema-ifabsent-error.yaml'))
+    y = gen2.serialize()
+    assert 'XSD' not in y