Fix CopyDirective exclude/exclude_all on slot-list classes

[amc-corey-cox]

The _copy_list path in SchemaMapper (used when a source class declares its slots as a list rather than inline attributes) had two bugs that made exclude and exclude_all non-functional:

• exclude checked the directive's truthiness instead of membership, so it removed every source slot.
• exclude_all mutated the list while iterating, leaving roughly half the elements intact.

Mirrors _copy_dict's behavior (iterate the exclude list, check membership in the target) and uses list.clear() for exclude_all. Adds parametrized tests covering exclude, exclude_all, include, and combinations on the slot-list path — none of this was previously covered.

Closes #67.

Two related items deliberately left out of scope, to be filed as follow-ups:

• CopyDirective.add slot is declared in the YAML schema but has no description and no implementation. Needs design.
• Mechanism for overriding/clearing individual attributes of a copied slot (the use case described in implement the exclude and include slots in the CopyDirective class #67's body) is a different feature, likely belonging on SlotDerivation.target_definition.

[Copilot]

Pull request overview

Fixes SchemaMapper._copy_list so CopyDirective.exclude and exclude_all behave correctly when copying slot-list classes (i.e., classes that declare slots: [...] rather than inline attributes). Adds regression tests to cover these directive behaviors on the slot-list path (closing #67).

Changes:

• Correct exclude logic in _copy_list to remove only specified elements rather than removing everything.
• Fix exclude_all logic in _copy_list by clearing the target list safely.
• Add parametrized tests covering copy_all, exclude, exclude_all, and include for slot-list classes.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
src/linkml_map/inference/schema_mapper.py	Fixes CopyDirective handling for list-based slot copying (exclude / exclude_all).
tests/test_schema_mapper/test_schema_mapper.py	Adds regression tests for CopyDirective behavior on slot-list classes.

Comments suppressed due to low confidence (1)

src/linkml_map/inference/schema_mapper.py:92

• In _copy_list, the include step appends elements unconditionally. If a directive uses copy_all=True (or multiple directives run) and also sets include, this will duplicate slot names in tgt_elements, which can make the derived schema invalid or at least surprising. Consider making list-copy idempotent by only appending when the element is not already present (or by maintaining an order-preserving set) during copy_all/include operations.

            tgt_elements.clear()
        if copy_directive.include:
            for element in copy_directive.include:
                if element in src_elements:
                    tgt_elements.append(element)

[Copilot]

Pull request overview

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.