Gate gene DE methods in pairwise; centralise DE-method vocabulary#5
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annaquaglieri16 wants to merge 1 commit into
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Gate gene DE methods in pairwise; centralise DE-method vocabulary#5annaquaglieri16 wants to merge 1 commit into
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run_pairwise_comparison accepted any de_method without validating it against entity_type, so an invalid combo (e.g. edgeR for protein) was only caught downstream by the server. run_anova already gated; pairwise did not. - Add de_method gating to run_pairwise_comparison (engine allowed per entity_type + edgeR/DESeq2 companion-param validation). The bulk tool routes through this function, so it inherits the gate. - Centralise the edgeR/DESeq2 allowed-value vocabularies and numeric ranges in _methods.py (_EDGER_NORM_METHODS, _DESEQ2_LFC_SHRINKAGE, _DESEQ2_ALPHA_RANGE, _APEGLM_SEED_RANGE), mirroring process_r.py. anova.py now reads them instead of inline literals. - Each tool keeps its own gating block (no shared validator) so the two can diverge or be updated independently; only the vocabulary is shared. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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What
de_methodgating torun_pairwise_comparison(it had none;run_anovaalready gated). Invalid engine/entity combos — e.g.edgeR/DESeq2for protein/peptide/metabolite/ptm — now fail fast in the MCP with a clear message instead of being rejected downstream by the server._methods.py(single source mirroringMDFlexiComparisons/.../process_r.py).anova.pynow reads them instead of inline literals.Why
pairwise.pyaccepted anyde_methodwithout validating againstentity_type. The allowed values were also hardcoded inline inanova.py, so adding a pairwise gate naively would have created a third copy — centralising removes that drift risk.Design note (intentional)
The two tools keep separate gating blocks and signature defaults on purpose, so
anovaandpairwisecan validate differently or be updated in different orders. Only the vocabulary (the allowed values) is shared, in_methods.py.Keeping in sync
The DE-method vocabulary now lives only in
_methods.py— keep it aligned withprocess_r.py(de_method_gene,edger_norm_method,deseq2_lfc_shrinkageLiterals +deseq2_alpha/apeglm_seedranges). A drift-check script is a possible follow-up.Testing
_methods.pyimports cleanly with the expected values.anova.py/pairwise.pyimport from_methodsexists (no typos).pip install -e ".[mcp]"would allow a runtime check.🤖 Generated with Claude Code