Add basic_search and fix node() for external refs in FunOwlImplementation#878
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cmungall wants to merge 1 commit into
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Add basic_search and fix node() for external refs in FunOwlImplementation#878cmungall wants to merge 1 commit into
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… FunOwlImplementation Implements basic_search() supporting exact, partial, starts-with, and regex matching across labels, identifiers, aliases, and mapped identifiers. Fixes node() to return a stub Node for entities referenced but not defined in the ontology (e.g. external CURIEs), instead of returning None which broke graph visualization output. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Summary
basic_search()onFunOwlImplementation, supporting exact, partial, starts-with, and regex matching across labels, identifiers, aliases, and mapped identifiersnode()to return a stubNodefor entities referenced but not defined in the ontology (e.g. external CURIEs likeGO:0008150in a CL ontology file), instead of returningNonewhich broke graph/viz outputinfo, search, andvizwith OFN inputTest plan
poetry run pytest tests/test_implementations/test_funowl.py::TestFunOwlImplementation::test_basic_searchpoetry run pytest tests/test_implementations/test_funowl.py::TestFunOwlImplementation::test_stub_nodes_for_unresolved_external_referencespoetry run pytest tests/test_cli.py::TestCommandLineInterface::test_funowl_info_search_and_graph_outputs🤖 Generated with Claude Code