Refactor deprecation scanning to pre-normalize; allow list-form populated_from on PV

docs/schema/PermissibleValueDerivation.md

@@ -152,7 +152,7 @@ URI: [linkmlmap:PermissibleValueDerivation](https://w3id.org/linkml/transformer/
 | ---  | --- | --- | --- |
 | [name](name.md) | 1 <br/> [String](String.md) | Target permissible value text | direct |
 | [expr](expr.md) | 0..1 <br/> [String](String.md) | An expression evaluated on the source object to derive this permissible value | direct |
-| [populated_from](populated_from.md) | 0..1 <br/> [String](String.md) | Source permissible value that maps to this target permissible value | direct |
+| [populated_from](populated_from.md) | * <br/> [String](String.md) | Source permissible value(s) that map to this target permissible value | direct |
 | [sources](sources.md) | * <br/> [String](String.md) | Deprecated | direct |
 | [hide](hide.md) | 0..1 <br/> [Boolean](Boolean.md) | True if this is suppressed | direct |
 | [copy_directives](copy_directives.md) | * <br/> [CopyDirective](CopyDirective.md) | Directives controlling which sub-elements of the source element are copied in... | [ElementDerivation](ElementDerivation.md) |
@@ -259,19 +259,23 @@ attributes:
     range: string
   populated_from:
     name: populated_from
-    description: Source permissible value that maps to this target permissible value.
+    description: Source permissible value(s) that map to this target permissible value.
+      Accepts a single value or a list; scalar input is normalized to a one-element
+      list at load time.
     from_schema: https://w3id.org/linkml/transformer
     domain_of:
     - ClassDerivation
     - SlotDerivation
     - EnumDerivation
     - PermissibleValueDerivation
     range: string
+    multivalued: true
   sources:
     name: sources
     description: Deprecated. Use populated_from instead.
-    deprecated: Deprecated. Use populated_from instead. See https://github.com/linkml/linkml-map/issues/193
-      for planned list support in populated_from. Will be removed in a future version.
+    deprecated: Deprecated. Use populated_from instead, which now accepts a list.
+      See https://github.com/linkml/linkml-map/issues/193. Will be removed in a future
+      version.
     from_schema: https://w3id.org/linkml/transformer
     domain_of:
     - ClassDerivation
@@ -332,7 +336,9 @@ attributes:
     range: string
   populated_from:
     name: populated_from
-    description: Source permissible value that maps to this target permissible value.
+    description: Source permissible value(s) that map to this target permissible value.
+      Accepts a single value or a list; scalar input is normalized to a one-element
+      list at load time.
     from_schema: https://w3id.org/linkml/transformer
     owner: PermissibleValueDerivation
     domain_of:
@@ -341,11 +347,13 @@ attributes:
     - EnumDerivation
     - PermissibleValueDerivation
     range: string
+    multivalued: true
   sources:
     name: sources
     description: Deprecated. Use populated_from instead.
-    deprecated: Deprecated. Use populated_from instead. See https://github.com/linkml/linkml-map/issues/193
-      for planned list support in populated_from. Will be removed in a future version.
+    deprecated: Deprecated. Use populated_from instead, which now accepts a list.
+      See https://github.com/linkml/linkml-map/issues/193. Will be removed in a future
+      version.
     from_schema: https://w3id.org/linkml/transformer
     owner: PermissibleValueDerivation
     domain_of:

src/linkml_map/cli/cli.py

@@ -254,27 +254,27 @@ def _pre_flight_validate(
 ) -> None:
     """Surface static spec checks before performing a CLI action.
 
-    Runs deprecation checks and reference resolution against the loaded
-    specification, printing all findings to stderr. **Does not gate** —
-    even error-severity findings are informational only; the runtime
-    remains the authoritative arbiter of whether a transformation can
-    actually execute. Users who want fail-fast behavior should run
-    ``validate-spec --strict`` separately.
-
-    Validates the merged ``tr.specification`` (after multi-file loading
-    is complete) so cross-file issues surface where users would see
-    them via ``validate-spec --merge``. Reuses ``tr.source_schemaview``
-    and ``tr.target_schemaview`` when set, avoiding a duplicate load
-    of large or remote schemas.
+    Replays pre-normalize scan messages captured at spec-load time and runs
+    reference resolution, printing all findings to stderr. **Does not gate** —
+    findings are informational only; the runtime remains the authoritative
+    arbiter of whether a transformation can actually execute. Users who want
+    fail-fast behavior should run ``validate-spec --strict`` separately.
+
+    Reading scan messages from ``tr.spec_messages`` rather than re-scanning
+    the post-migration spec means deprecations whose source fields were
+    cleared by normalization (e.g., ``object_derivations``, PV ``sources``)
+    are still surfaced here. Reuses ``tr.source_schemaview`` and
+    ``tr.target_schemaview`` when set, avoiding a duplicate load of large
+    or remote schemas.
     """
-    from linkml_map.validator import check_deprecated_fields, validate_spec_semantics
+    from linkml_map.validator import validate_spec_semantics
 
     if tr.specification is None:
         return
 
     spec_dict = tr.specification.model_dump(exclude_none=True)
 
-    messages = list(check_deprecated_fields(spec_dict))
+    messages = list(tr.spec_messages)
     messages.extend(
         validate_spec_semantics(
             spec_dict,

src/linkml_map/compiler/templates/markdown.j2

@@ -20,6 +20,6 @@
 | Target | Source | Info |
 | ------ | ------ | ---- |
     {%- for pvd in ed.permissible_value_derivations.values() %}
-| {{ pvd.name }} | {{ pvd.populated_from }} | . |
+| {{ pvd.name }} | {{ (pvd.populated_from or []) | join(", ") }} | . |
     {%- endfor -%}
 {%  endfor %}

src/linkml_map/datamodel/transformer_model.py

@@ -500,14 +500,13 @@ class PermissibleValueDerivation(ElementDerivation):
     expr: Optional[str] = Field(default=None, description="""An expression evaluated on the source object to derive this permissible value. Should be specified using the LinkML expression language.""", json_schema_extra = { "linkml_meta": {'domain_of': ['SlotDerivation',
                        'EnumDerivation',
                        'PermissibleValueDerivation']} })
-    populated_from: Optional[str] = Field(default=None, description="""Source permissible value that maps to this target permissible value.""", json_schema_extra = { "linkml_meta": {'domain_of': ['ClassDerivation',
+    populated_from: Optional[list[str]] = Field(default_factory=list, description="""Source permissible value(s) that map to this target permissible value. Accepts a single value or a list; scalar input is normalized to a one-element list at load time.""", json_schema_extra = { "linkml_meta": {'domain_of': ['ClassDerivation',
                        'SlotDerivation',
                        'EnumDerivation',
                        'PermissibleValueDerivation']} })
-    sources: Optional[list[str]] = Field(default_factory=list, description="""Deprecated. Use populated_from instead.""", json_schema_extra = { "linkml_meta": {'deprecated': 'Deprecated. Use populated_from instead. See '
-                       'https://github.com/linkml/linkml-map/issues/193 for planned '
-                       'list support in populated_from. Will be removed in a future '
-                       'version.',
+    sources: Optional[list[str]] = Field(default_factory=list, description="""Deprecated. Use populated_from instead.""", json_schema_extra = { "linkml_meta": {'deprecated': 'Deprecated. Use populated_from instead, which now accepts a '
+                       'list. See https://github.com/linkml/linkml-map/issues/193. '
+                       'Will be removed in a future version.',
          'domain_of': ['ClassDerivation',
                        'SlotDerivation',
                        'EnumDerivation',

src/linkml_map/datamodel/transformer_model.yaml

@@ -532,15 +532,18 @@ classes:
         range: string
       populated_from:
         range: string
+        multivalued: true
         description: >-
-          Source permissible value that maps to this target permissible value.
+          Source permissible value(s) that map to this target permissible value.
+          Accepts a single value or a list; scalar input is normalized to a
+          one-element list at load time.
       sources:
         range: string
         multivalued: true
         deprecated: >-
-          Deprecated. Use populated_from instead.
-          See https://github.com/linkml/linkml-map/issues/193 for planned
-          list support in populated_from. Will be removed in a future version.
+          Deprecated. Use populated_from instead, which now accepts a list.
+          See https://github.com/linkml/linkml-map/issues/193. Will be removed
+          in a future version.
         description: >-
           Deprecated. Use populated_from instead.
       hide:

src/linkml_map/inference/inference.py

@@ -1,33 +1,11 @@
 """Infer missing values in a specification."""
 
-import warnings
-
 from linkml_runtime import SchemaView
 
 from linkml_map.datamodel.transformer_model import TransformationSpecification
 from linkml_map.utils.fk_utils import resolve_fk_path
 
 
-def _warn_deprecated_fields(specification: TransformationSpecification) -> None:
-    """Emit ``DeprecationWarning`` for any deprecated field usage.
-
-    Thin shim over ``validator._check_deprecated_fields`` that re-emits
-    deprecation-category messages as ``DeprecationWarning`` so runtime
-    callers (and any code with Python ``warnings`` filters configured)
-    keep getting the same signal they always did.
-
-    The same underlying check is consumed by static validation paths
-    (``validate-spec`` and pre-flight from other CLI commands) via
-    ``ValidationMessage`` records — see ``validator._check_deprecated_fields``.
-    """
-    from linkml_map.validator import check_deprecated_fields
-
-    spec_dict = specification.model_dump(exclude_none=True)
-    for msg in check_deprecated_fields(spec_dict):
-        if msg.category == "deprecated":
-            warnings.warn(msg.message, DeprecationWarning, stacklevel=3)
-
-
 def induce_missing_values(specification: TransformationSpecification, source_schemaview: SchemaView) -> None:
     """
     Infer missing values in a specification.
@@ -41,7 +19,6 @@ def induce_missing_values(specification: TransformationSpecification, source_sch
     for cd in specification.class_derivations:
         if not cd.populated_from:
             cd.populated_from = cd.name
-    _warn_deprecated_fields(specification)
 
     for cd in specification.class_derivations:
         for sd in cd.slot_derivations.values():

src/linkml_map/inference/inverter.py

@@ -93,9 +93,18 @@ def invert_enum_derivation(self, ed: EnumDerivation, spec: TransformationSpecifi
             msg = "TODO: invert enum derivation with expression"
             raise NonInvertibleSpecificationError(msg)
         for pv_deriv in ed.permissible_value_derivations.values():
+            sources = pv_deriv.populated_from or [pv_deriv.name]
+            if len(sources) > 1:
+                msg = (
+                    f"Cannot invert PermissibleValueDerivation '{pv_deriv.name}': "
+                    f"populated_from has multiple source values {sources}, "
+                    f"which is not a one-to-one mapping."
+                )
+                raise NonInvertibleSpecificationError(msg)
+            inverted_name = sources[0]
             inverted_pv_deriv = PermissibleValueDerivation(
-                name=pv_deriv.populated_from if pv_deriv.populated_from else pv_deriv.name,
-                populated_from=pv_deriv.name,
+                name=inverted_name,
+                populated_from=[pv_deriv.name],
             )
             inverted_ed.permissible_value_derivations[inverted_pv_deriv.name] = inverted_pv_deriv
         return inverted_ed

src/linkml_map/inference/schema_mapper.py

@@ -311,16 +311,13 @@ def _derive_enum(self, enum_derivation: EnumDerivation) -> EnumDefinition:
             target_enum.attributes = {}
             target_enum.slot_usage = {}
         for pv_derivation in enum_derivation.permissible_value_derivations.values():
-            if pv_derivation.populated_from:
-                pv = PermissibleValue(text=pv_derivation.populated_from)
-                target_enum.permissible_values[pv.text] = pv
-            elif pv_derivation.sources:
-                for source in pv_derivation.sources:
-                    pv = PermissibleValue(text=source)
-                    target_enum.permissible_values[pv.text] = pv
-            else:
+            sources = pv_derivation.populated_from or pv_derivation.sources
+            if not sources:
                 msg = f"Missing populated_from or sources for {pv_derivation}"
                 raise ValueError(msg)
+            for source in sources:
+                pv = PermissibleValue(text=source)
+                target_enum.permissible_values[pv.text] = pv
         if enum_derivation.mirror_source:
             for pv in source_enum.permissible_values.values():
                 if pv.text not in target_enum.permissible_values:

src/linkml_map/transformer/errors.py

@@ -6,6 +6,18 @@
 from typing import Any
 
 
+class SpecificationError(ValueError):
+    """The transformation specification is malformed or internally inconsistent.
+
+    Raised during spec loading when the pre-normalize scan detects a
+    user-intent error that the runtime cannot disambiguate (e.g., setting
+    both ``populated_from`` and ``sources`` on the same derivation, or
+    setting both ``object_derivations`` and ``class_derivations`` on a
+    slot). Subclasses ``ValueError`` for backward compatibility with
+    callers that already catch ``ValueError`` from ``_normalize_spec_dict``.
+    """
+
+
 @dataclass
 class TransformationError(Exception):
     """A row-level error during data transformation.

src/linkml_map/transformer/object_transformer.py

@@ -1174,9 +1174,16 @@ def transform_enum(self, source_value: str, enum_names: list[str], source_obj: A
                 if v is not None:
                     return v
             for pv_deriv in enum_deriv.permissible_value_derivations.values():
-                if source_value == pv_deriv.populated_from:
-                    return pv_deriv.name
-                if source_value in pv_deriv.sources:
+                if pv_deriv.sources:
+                    from linkml_map.transformer.errors import SpecificationError
+
+                    msg = (
+                        f"PermissibleValueDerivation '{pv_deriv.name}' has 'sources' set; "
+                        "this should have been migrated to 'populated_from' during spec load. "
+                        "Did the spec bypass Transformer._normalize_spec_dict?"
+                    )
+                    raise SpecificationError(msg)
+                if pv_deriv.populated_from and source_value in pv_deriv.populated_from:
                     return pv_deriv.name
             if enum_deriv.mirror_source:
                 return str(source_value)