fix(generators): add --normalize-prefixes flag for well-known prefix names

docs/maintainers/contributing.md

@@ -142,6 +142,11 @@ New tests in any directory should be written using pytest.
   If you make a change that intentionally causes some output to not match the saved snapshot file(s), you should update the snapshots by running `pytest` with the `--generate-snapshots` flag. You should try to run only a single or small group of tests with this flag (as opposed to the entire test suite). An exception to this rule is when preparing a new minor version of linkml after the metamodel changes, changes to the metamodel can have many (inconsequential) changes to multiple snapshots.
   The updated snapshot files should be checked in to Git alongside your other code changes.
 
+  Examples:
+
+  `uv run pytest tests/linkml/test_scripts/test_gen_owl.py --with-slow --generate-snapshots`
+  `uv run pytest tests/linkml/test_scripts/test_gen_shex.py --generate-snapshots --with-network`
+
   Debugging tip: sometimes a snapshot-based test may fail on GitHub actions, but may appear to pass locally. This can happen if the test is marked as a slow test,
   in which case you may need to use `--generate-snapshots` in combination with `--with-slow` (see below).
 

examples/tutorial/tutorial01/personinfo.json

@@ -42,7 +42,7 @@
     "$id": "https://w3id.org/linkml/examples/personinfo",
     "$schema": "https://json-schema.org/draft/2019-09/schema",
     "additionalProperties": true,
-    "metamodel_version": "1.7.0",
+    "metamodel_version": "1.11.0",
     "title": "personinfo",
     "type": "object",
     "version": null

examples/tutorial/tutorial04/personinfo-semantic.shex

@@ -1,4 +1,4 @@
-# metamodel_version: 1.7.0
+# metamodel_version: 1.11.0
 BASE <https://w3id.org/linkml/examples/personinfo/>
 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

examples/tutorial/tutorial05/personinfo.py

@@ -24,7 +24,7 @@
 from linkml_runtime.utils.curienamespace import CurieNamespace
 from linkml_runtime.linkml_model.types import Integer, String
 
-metamodel_version = "1.7.0"
+metamodel_version = "1.11.0"
 
 # Namespaces
 ORCID = CurieNamespace('ORCID', 'https://orcid.org/')

packages/linkml/src/linkml/converter/cli.py

@@ -2,6 +2,7 @@
 import os
 import pathlib
 import sys
+from typing import TYPE_CHECKING
 
 import click
 import yaml
@@ -27,6 +28,9 @@
 from linkml_runtime.utils.inference_utils import infer_all_slot_values
 from linkml_runtime.utils.schemaview import SchemaView
 
+if TYPE_CHECKING:
+    from linkml_runtime.utils.yamlutils import YAMLRoot
+
 logger = logging.getLogger(__name__)
 
 
@@ -197,7 +201,7 @@ def cli(
         target_class = infer_root_class(sv)
     if target_class is None:
         raise Exception("target class not specified and could not be inferred")
-    py_target_class = python_module.__dict__[target_class]
+    py_target_class: YAMLRoot = python_module.__dict__[target_class]
     input_format = _get_format(input, input_format)
     loader = get_loader(input_format)
 
@@ -237,9 +241,7 @@ def cli(
             raise Exception("--schema must be passed in order to validate. Suppress with --no-validate")
         obj_dict = json_dumper.to_dict(obj)
         report = run_validation(obj_dict, schema, target_class)
-        if report.results:
-            errors = "\n".join(r.message for r in report.results)
-            raise Exception(f"Validation failed:\n{errors}")
+        report.raise_for_results()
 
     output_format = _get_format(output, output_format, default="json")
     if output_format == "json-ld":

packages/linkml/src/linkml/generators/common/subproperty.py

@@ -15,6 +15,10 @@
 CURIE_TYPES: frozenset[str] = frozenset({"uriorcurie", "curie"})
 URI_TYPES: frozenset[str] = frozenset({"uri"})
 
+# Types whose XSD mapping is xsd:anyURI (not xsd:string).
+# ``curie`` maps to xsd:string and is deliberately excluded.
+_ANYURI_TYPES: frozenset[str] = frozenset({"uri", "uriorcurie"})
+
 
 def is_uri_range(sv: SchemaView, range_type: str | None) -> bool:
     """
@@ -63,6 +67,35 @@ def is_curie_range(sv: SchemaView, range_type: str | None) -> bool:
     return False
 
 
+def is_xsd_anyuri_range(sv: SchemaView, range_type: str | None) -> bool:
+    """Check if range type resolves to ``xsd:anyURI``.
+
+    Returns True for ``uri``, ``uriorcurie``, and types that inherit from them.
+    Returns False for ``curie`` (which maps to ``xsd:string``).
+
+    This is the correct predicate for the ``--xsd-anyuri-as-iri`` flag: only
+    types whose XSD representation is ``xsd:anyURI`` should be promoted from
+    literal to IRI semantics.  ``curie`` is a compact string representation
+    that resolves to ``xsd:string`` and must not be affected.
+
+    :param sv: SchemaView for type ancestry lookup
+    :param range_type: The range type to check
+    :return: True if range type maps to xsd:anyURI
+    """
+    if range_type is None:
+        return False
+
+    if range_type in _ANYURI_TYPES:
+        return True
+
+    if range_type in sv.all_types():
+        type_ancestors = set(sv.type_ancestors(range_type))
+        if type_ancestors & _ANYURI_TYPES:
+            return True
+
+    return False
+
+
 def format_slot_value_for_range(sv: SchemaView, slot_name: str, range_type: str | None) -> str:
     """
     Format slot value according to the declared range type.

packages/linkml/src/linkml/generators/excelgen.py

@@ -52,18 +52,21 @@ def _create_workbook_and_worksheets(self, output_path: Path, classes: list[str])
         workbook.remove(workbook.active)
         sv = self.schemaview
 
+        # Compute enum lookup before next inner loop
+        enum_set = set(sv.all_enums(imports=self.mergeimports).keys())
+
         for cls_name in classes:
             workbook.create_sheet(cls_name)
 
             # Add columns to the worksheet for the current class
-            slots = [s.name for s in sv.class_induced_slots(cls_name, self.mergeimports)]
-            self.add_columns_to_worksheet(workbook, cls_name, slots)
-            workbook.save(output_path)
+            # (call class_induced_slots, reuse for heading/enum validation)
+            induced_slots = list(sv.class_induced_slots(cls_name, self.mergeimports))
+            slot_names = [s.name for s in induced_slots]
+            self.add_columns_to_worksheet(workbook, cls_name, slot_names)
 
             # Add enum validation for columns with enum types
-            enum_list = list(sv.all_enums(imports=self.mergeimports).keys())
-            for s in sv.class_induced_slots(cls_name, self.mergeimports):
-                if s.range in enum_list:
+            for s in induced_slots:
+                if s.range in enum_set:
                     pv_list = list(sv.get_enum(s.range).permissible_values.keys())
 
                     # Data Validation formula to be applied to the column and
@@ -81,7 +84,6 @@ def _create_workbook_and_worksheets(self, output_path: Path, classes: list[str])
                             "length > 255 characters. Dropdowns may not work properly "
                             f"in {output_path}"
                         )
-                workbook.save(output_path)
 
         workbook.save(output_path)
         if self.split_workbook_by_class: