193: Output cleanup, help discoverability, and footer rewrite#139
193: Output cleanup, help discoverability, and footer rewrite#139
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Add quickstart block and skills tip to `list` output. Route `list skill`, `list enrich`, `list batch`. Document --biomarker (trial) and --since (article). Expand phenotype/gwas pages with workflow tips. Add conditional Affects column to health output when APIs are unhealthy.
…lean templates - BUG-11: Remove triple-rendered population data; single indented KV list - BUG-12: Convert pipe tables to KV pairs (conservation, AlphaGenome, interactions) and bullet lists (adverse event reactions/outcomes) - BUG-13: Standardize metadata headers to plain Key: Value (no bold) - BUG-09: Sections footer now shows copy-pasteable biomcp get commands - BUG-10: Related footer now shows full biomcp commands under See also: - Update docs with gene helpers and variant trials helper
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src/render/markdown.rs
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| vec![format!("reports {device}"), "recalls class-i".to_string()] | ||
| vec
The new related_device_event footer command uses --classification class-i, but recall classification normalization only accepts Class I/II/III (or 1/2/3), so this copy-paste command now fails with an invalid-argument error instead of running. This directly breaks the new “See also” workflow for every device-event card that includes the recall suggestion.
Useful? React with 👍 / 👎.
src/render/markdown.rs
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| } | ||
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| vec![format!("drugs {id}")] | ||
| vec![format!("biomcp search drug {id}")] |
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This footer now suggests biomcp search drug <pathway-id>, which goes through the generic drug free-text query path (search drug) instead of the pathway-specific traversal (pathway drugs) intended for Reactome IDs. For IDs like R-HSA-..., the suggested command is usually irrelevant or empty, so users lose the expected pathway→drug pivot from the related-command block.
Useful? React with 👍 / 👎.
…lper - related_device_event: use "Class I" (not class-i) for valid normalization - related_pathway: use `pathway drugs` helper (not `search drug` free-text)
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Summary
list skillalias,list enrich/list batchpages,--biomarker/--sincedocs, expanded phenotype/gwas pages, health impact visibilityKey: ValueSections:→More:with copy-pasteablebiomcp getcommands;Related:→See also:with full commandsVerification
cargo test: 349/349cargo clippy -D warnings: 0 warningsdocs/biomcp-cli/: 375/376 (1 pre-existing CI trigger contract)