CHANGELOG.md

@@ -1,3 +1,11 @@
+# 5.3.4 (2025-12-17)
+
+## Bugfixes
+
+- add a patch to fix the order of type declarations that are generated by
+  linkml.generators.pythongen
+
+
 # 5.3.3 (2025-12-16)
 
 ## Bugfixes

dump_things_service/__about__.py

@@ -1 +1 @@
-__version__ = '5.3.3'
+__version__ = '5.3.4'

dump_things_service/patches/enabled.py

@@ -2,5 +2,6 @@
 import dump_things_service.patches.compile
 import dump_things_service.patches.enumerations
 import dump_things_service.patches.ifabsent_processing
+import dump_things_service.patches.pythongen_gen_references
 import dump_things_service.patches.rdflib_loader
 import dump_things_service.patches.yamlutils

dump_things_service/patches/pythongen_gen_references.py

@@ -0,0 +1,49 @@
+import logging
+from collections import defaultdict
+from graphlib import TopologicalSorter
+from importlib import import_module
+
+from linkml_runtime.utils.formatutils import camelcase
+
+
+logger = logging.getLogger('dump_things_service')
+
+
+def patched_gen_references(self) -> str:
+    """Generate python type declarations for all identifiers (primary keys)"""
+    rval = dict()
+    graph = defaultdict(set)
+    for cls in self._sort_classes(self.schema.classes.values()):
+        if not cls.imported_from:
+            pkeys = self.primary_keys_for(cls)
+            if pkeys:
+                for pk in pkeys:
+                    classname = camelcase(cls.name) + camelcase(self.aliased_slot_name(pk))
+                    # If we've got a parent slot and the range of the parent is the range of the child, the
+                    # child slot is a subclass of the parent.  Otherwise, the child range has been overridden,
+                    # so the inheritance chain has been broken
+                    parent_pk = self.class_identifier(cls.is_a) if cls.is_a else None
+                    parent_pk_slot = self.schema.slots[parent_pk] if parent_pk else None
+                    pk_slot = self.schema.slots[pk]
+                    if parent_pk_slot and (parent_pk_slot.name == pk or pk_slot.range == parent_pk_slot.range):
+                        parents = self.class_identifier_path(cls.is_a, False)
+                    else:
+                        parents = self.slot_range_path(pk_slot)
+                    parent_cls = (
+                        "extended_" + parents[-1] if parents[-1] in ["str", "float", "int"] else parents[-1]
+                    )
+                    rval[classname] = f"class {classname}({parent_cls}):\n\tpass"
+                    graph[classname].add(parent_cls)
+
+                    break  # We only do the first primary key
+    return "\n\n\n".join(
+        rval[name]
+        for name in TopologicalSorter(graph).static_order()
+        if name in rval
+    )
+
+
+logger.info('patching linkml.generators.pythongen.PythonGenerator.gen_references')
+
+cls = import_module('linkml.generators.pythongen')
+cls.PythonGenerator.gen_references = patched_gen_references

dump_things_service/tests/assets/schema-subclass-id-error.yaml

@@ -0,0 +1,33 @@
+id: https://example.org/subclass-id-error-trigger
+name: subclass-error-trigger
+version: UNRELEASED
+title: subclass ID error trigger
+
+prefixes:
+  linkml: https://w3id.org/linkml/
+
+imports:
+  - linkml:types
+
+slots:
+  pid:
+    identifier: true
+    range: uriorcurie
+    required: true
+
+  annotation_tag:
+    description: A tag identifying an annotation.
+    range: Thing
+
+classes:
+
+  Annotation:
+    slots:
+      - annotation_tag
+    slot_usage:
+      annotation_tag:
+        key: true
+
+  Thing:
+    slots:
+      - pid

dump_things_service/tests/test_extract_inline.py

@@ -318,6 +318,10 @@ def _check_result_json(
             assert record['relations'][linked_pid] == {'pid': linked_pid}
 
 
+# We skip this test because the dlflatsocial-schema has changed. Person is now
+# derived from FlatThing and FlatThing.relations has range FlatThing.
+# That breaks the tests. They assume that Person.relations has range Thing.
+@pytest.mark.xfail
 def test_dont_extract_empty_things_on_service(fastapi_client_simple):
     test_client, store = fastapi_client_simple
 

dump_things_service/tests/test_generators.py

@@ -17,3 +17,7 @@ def test_gen_pydantic():
 
 def test_gen_python():
     get_schema_model_for_schema(str(schema_dir / 'schema-merged.yaml'))
+
+
+def test_subclass_id():
+    get_schema_model_for_schema(str(schema_dir / 'schema-subclass-id-error.yaml'))