Pin linkml-map to main and fix runtime 1.11 fallout

pyproject.toml

@@ -48,12 +48,16 @@ dependencies = [
     "tomlkit >= 0.11.4",
     "inflect >= 6.0.0",
     "linkml-runtime >= 1.10.0, < 2",
-    # NB: the *reverse* Frictionless adapter trans-spec needs the
-    # is_str / is_bool / is_list type predicates, which land in
-    # linkml-map 0.5.3. Forward adapter and codes utility work on
-    # 0.5.2. Bump this and remove the xfail in
-    # tests/test_adapters/test_frictionless.py once 0.5.3 ships.
-    "linkml-map >= 0.5.2, < 1",
+    # Pinned to linkml-map main (see [tool.uv.sources]) — recent work
+    # adds dot-path populated_from, safe-builtin functions, dictionary_key,
+    # strict expression mode, and the SchemaReference shape for
+    # source/target_schema. The EML importer and the next batch of
+    # adapters need these. This pin also satisfies the is_str /
+    # is_bool / is_list predicate need that the *reverse* Frictionless
+    # adapter has — the xfail in tests/test_adapters/test_frictionless.py
+    # can come off once we're on a real release tag. Restore a version
+    # constraint and drop the source override here when 0.5.3+ releases.
+    "linkml-map",
     "click >= 8.1.7, < 9",
     "deprecated >= 1.2.15, < 2",
     "sqlalchemy >= 2.0.36, < 3",
@@ -94,6 +98,9 @@ extract-schema = "schema_automator.utils.schema_extractor:cli"
 repository = "https://github.com/linkml/schema-automator/"
 documentation = "https://linkml.io/schema-automator/"
 
+[tool.uv.sources]
+linkml-map = { git = "https://github.com/linkml/linkml-map.git", branch = "main" }
+
 [tool.uv-dynamic-versioning]
 vcs = "git"
 style = "pep440"

schema_automator/adapters/dbgap/dbgap_to_dd.transform.yaml

@@ -26,8 +26,10 @@ description: >-
     ``example_values`` but it would mix "examples" with "exhaustive
     observed values" and confuse the slot's purpose.
 
-source_schema: https://w3id.org/linkml/schema-automator/dbgap
-target_schema: https://w3id.org/linkml/schema-automator/data-dictionary
+source_schema:
+  name: https://w3id.org/linkml/schema-automator/dbgap
+target_schema:
+  name: https://w3id.org/linkml/schema-automator/data-dictionary
 
 class_derivations:
 

schema_automator/adapters/frictionless/dd_to_frictionless.transform.yaml

@@ -24,8 +24,10 @@ description: >-
   constraint slot has a known semantic type, so the predicates
   double as both sentinel-filter and type-correctness check.
 
-source_schema: https://w3id.org/linkml/schema-automator/data-dictionary
-target_schema: https://specs.frictionlessdata.io/table-schema
+source_schema:
+  name: https://w3id.org/linkml/schema-automator/data-dictionary
+target_schema:
+  name: https://specs.frictionlessdata.io/table-schema
 
 class_derivations:
 

schema_automator/adapters/frictionless/frictionless_to_dd.transform.yaml

@@ -13,8 +13,10 @@ description: >-
   - `unique`, `minLength`, `maxLength` constraints (no DD equivalent).
   - Foreign keys, `missingValues`, `primaryKey` (drop; out of DD scope).
 
-source_schema: https://specs.frictionlessdata.io/table-schema
-target_schema: https://w3id.org/linkml/schema-automator/data-dictionary
+source_schema:
+  name: https://specs.frictionlessdata.io/table-schema
+target_schema:
+  name: https://w3id.org/linkml/schema-automator/data-dictionary
 
 class_derivations:
 

schema_automator/importers/xsd_import_engine.py

@@ -228,9 +228,13 @@ def visit_element(self, el: etree._Element) -> SlotDefinition:
                     name=cls_name,
                     class_uri=urljoin(self.target_ns, cls_name) if self.target_ns else None
                 )
-                self.sb.add_class(cls)
                 slot.range = cls_name
                 self.visit_complex_type(child, cls)
+                # In linkml-runtime >=1.11 add_class() pydantic-validates
+                # its input, so the registered class is a copy; later
+                # mutations to the local `cls` don't reach it. Register
+                # after populating attributes.
+                self.sb.add_class(cls)
             elif child.tag == SIMPLE_TYPE:
                 # If we find a simple type, the range is a restriction of a primitive type
                 self.visit_simple_type(child, slot)

schema_automator/utils/instance_extractor.py

@@ -52,7 +52,10 @@ def create_index(self, obj: Union[YAMLRoot, Dict, List] = None,
         elif isinstance(obj, YAMLRoot):
             cn = type(obj).class_name
             for slot in sv.class_induced_slots(cn):
-                v = getattr(obj, slot.alias, None)
+                # slot.alias is None unless explicitly set in the schema;
+                # linkml-runtime <1.11 used to fall back to slot.name on
+                # access, 1.11 returns None. Mirror the old behavior.
+                v = getattr(obj, slot.alias or slot.name, None)
                 if v is not None:
                     if slot.identifier:
                         self.references.append((parent, v))
@@ -69,7 +72,7 @@ def create_index(self, obj: Union[YAMLRoot, Dict, List] = None,
                         if slot.range in sv.all_classes():
                             if isinstance(v, str):
                                 self.references.append((parent, v))
-                        self.create_index(v, path=path+[slot.alias], parent=obj)
+                        self.create_index(v, path=path+[slot.alias or slot.name], parent=obj)
         logging.debug(f'Created index')
 
     def fetch_object(self, id_ref: ID_REF, default_val = None) -> Optional[YAMLRoot]:
@@ -133,7 +136,7 @@ def extract(self, seeds: List[ID_REF], preserve_slots: List[SlotDefinitionName]
         root_cls = type(self.root)
         for slot in self.schemaview.class_induced_slots(root_cls.class_name):
             if slot.required:
-                preserve_slots.append(slot.alias)
+                preserve_slots.append(slot.alias or slot.name)
         for slot in preserve_slots:
             xdict[slot] = getattr(self.root, slot)
         #print(f'VISITED={visited}')
@@ -156,7 +159,7 @@ def get_object_references(self, start_obj: Optional[Union[YAMLRoot, Dict, List]]
             obj = seeds.pop()
             if isinstance(obj, YAMLRoot):
                 for slot in sv.class_induced_slots(type(obj).class_name):
-                    v = getattr(obj, slot.alias, None)
+                    v = getattr(obj, slot.alias or slot.name, None)
                     if v is not None:
                         if slot.identifier:
                             refs.append(v)

tests/test_importers/test_rdfs_importer.py

@@ -61,7 +61,7 @@ def test_infer_prefix():
     """
     rdf = StringIO("""
     @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-    @prefix foo: <https://foo.com> .
+    @prefix foo: <https://foo.com/> .
 
     foo:Class a rdfs:Class ;
         rdfs:comment "A class." .
@@ -73,7 +73,7 @@ def test_infer_prefix():
     schema = engine.convert(rdf)
     # Although not explicitly provided, the importer should realise that the prefix is "foo"
     assert schema.default_prefix == "foo"
-    assert schema.id == "https://foo.com"
+    assert schema.id == "https://foo.com/"
     assert schema.name == "foo"
 
 def test_from_rdfs():