nodecode-caduceus

Caduceus: a private local vault for your DNA, Apple Health numbers and health notes, with four tools and a /caduceus command. A Nodecode rewrite of electricsheephq/caduceus by electricsheephq.

The vault is a folder of plain tab-separated files: what the cell knows is readable with any tool you already have. Nothing is uploaded, nothing dials, and the model sees only the slices a tool answer puts in the conversation. Information with limits, not medical advice.

Get it

Tell the agent "add the caduceus cell", or run nodecode add nc://caduceus.

Set it up

One required setting, the folder the vault lives in; the rest has defaults:

{
  "caduceus": {
    "data_dir": "~/health/caduceus",
    "privacy_level": "open",        // or "standard": sensitive categories stay hidden until unlocked
    "hidden_categories": [],       // never shown at any level
    "unlocked_categories": []      // sensitive categories shown at the standard level
  }
}

standard keeps Alzheimer's risk, cancer predisposition, carrier status, mental health and reproductive findings out of every tool answer until unlocked_categories names them. A category name nothing types is refused at start rather than silently hiding nothing.

Nothing here needs a key or a network: a .zip import uses the unzip command you already have, and everything else is read from disk.

Use it

Tool	What it answers
`caduceus_capture`	`op=import` a file you name by absolute path: 23andMe or AncestryDNA raw data (`.txt`), a Promethease report table (`.tsv`/`.zip`), an unzipped Apple Health `export.xml`, or a FHIR Bundle of Observations (`.json`). `op=medication` (only with `confirm=true` after you agree), `op=journal`, `op=status`, `op=settings`, `op=sources`, `op=brief` (a local HTML brief).
`caduceus_genome`	`op=lookup` a marker, `op=gene` a gene, `op=pgx` a drug (gene-drug evidence with each marker called, absent or off the chip), `op=derived` (APOE and the enzymes a chip can combine), `op=summary`, `op=filter`, `op=report` (a local HTML variant report).
`caduceus_trend`	`op=metrics`, `op=series` by day, week or month, `op=compare` before and after a date or a medication's start, `op=labs`, `op=check` (the latest day against your own 5th to 95th percentile).
`caduceus_search`	Words across DNA annotations, notes, medications and imported reports; `ref` fetches one record whole.

/caduceus answers the vault's status, /caduceus search WORDS and /caduceus pgx DRUG answer the same questions in text. (help :caduceus) carries the same manual to the model.

Consumer chips test common variants: rare ones can be missed or miscalled, a phenotype from a chip is a guess from the common alleles, and a gene-drug answer is a conversation with a prescriber, never a dose.

What is in the folder

File	What it is
`cell.lisp`	The four tools, `/caduceus`, the section and the manual.
`genome.lisp`	Raw data parsing, the evidence pack, APOE and enzyme derivations, the gene-drug entries, both HTML reports.
`health.lisp`	The Apple Health and FHIR imports, and the trend arithmetic.
`store.lisp`	The vault files, the privacy policy and the category rules.
`contracts.lisp`	One declaration per tool that takes arguments.
`test/`	The offline tests and their four fixtures.

Run .github/test-cell.sh tools/nodecode-caduceus from the cells repository.

License

Apache-2.0. The plugin this rewrite comes from is Copyright (c) Electric Sheep: see LICENSE and NOTICE.