`dynamic_object.py` does not handle key-based (vs identifier-based) classes

[matentzn]

When transforming data using map-data, dynamic_object.py fails to correctly handle classes that use key: true attributes (as opposed to identifier: true).

This affects transformation of LinkML-Map's own datamodel classes like ClassDerivation, SlotDerivation, EnumDerivation, etc., which all use key: true on their name attribute rather than identifier: true.

How to reproduce

The tests/input/examples/fair_mappings_metadata/data/sample-linkmlmap-spec.yaml example has class_derivations and enum_derivations commented out because of this bug — uncommenting them and running the linkml-map-to-fair transformation triggers the issue.

Expected behavior

dynamic_object.py should handle both key-based and identifier-based classes when constructing dynamic objects for transformation.

Context

Discovered during work on PR #81 (enhanced mapping metadata). See comment in sample-linkmlmap-spec.yaml.

Warning

I have not tested this again with the latest version of LinkML-map - this surfaced in a version from 4 months ago.. Sorry if this has been fixed since.

[github-actions]

Issue Summary

Bug: dynamic_object.py crashes when transforming data that uses classes with key: true slots (as opposed to identifier: true).

Root Cause

In src/linkml_map/utils/dynamic_object.py at line 44, when processing multivalued dict-typed slots, the code calls:

id_slot = sv.get_identifier_slot(slot.range)

SchemaView.get_identifier_slot() has a use_key parameter (defaults to False) that controls whether it also searches for key: true slots. Without use_key=True, it returns None for classes whose unique slot is marked key: true rather than identifier: true. The subsequent line:

setattr(v1, id_slot.name, k1)  # AttributeError: 'NoneType' has no attribute 'name'

then fails with an AttributeError.

Affected Classes

LinkML-Map's own datamodel uses key: true on name for several core classes:

• ClassDerivation
• SlotDerivation
• EnumDerivation

This means the linkml-map-to-fair transformation (PR #81 — enhanced mapping metadata) cannot process class_derivations or enum_derivations sections of a spec file.

Fix

One-line fix in dynamic_object.py line 44:

# Before
id_slot = sv.get_identifier_slot(slot.range)

# After
id_slot = sv.get_identifier_slot(slot.range, use_key=True)

The get_identifier_slot method in linkml-runtime already supports this via its use_key parameter — it falls back to get_key_slot() when use_key=True and no identifier slot is found.

Context

• Discovered during work on PR Add first version of enhanced mapping metadata #81 (enhanced mapping metadata / FAIR mappings)
• Workaround in place: class_derivations and enum_derivations are commented out in tests/input/examples/fair_mappings_metadata/data/sample-linkmlmap-spec.yaml
• Fix is minimal and low-risk — just passes use_key=True to an existing API

Suggested test

A regression test should verify that a spec targeting a class with key: true (e.g., using the existing linkml-map datamodel as source schema) successfully transforms without error.

@dragon-ai-agent please implement the one-line fix in src/linkml_map/utils/dynamic_object.py(passuse_key=Truetoget_identifier_slot), uncomment the class_derivations/enum_derivationsintests/input/examples/fair_mappings_metadata/data/sample-linkmlmap-spec.yaml, and add a regression test verifying that key-based classes are handled correctly during transformation.