biostudies-cli

biostudies

A command line for biostudies.

biostudies is a single pure-Go binary. It reads public biostudies data over plain HTTPS, shapes it into clean records, and prints output that pipes into the rest of your tools. No API key, nothing to run alongside it.

The same package is also a resource-URI driver, so a host program like ant can address biostudies as biostudies:// URIs.

Install

go install github.com/tamnd/biostudies-cli/cmd/biostudies@latest

Or grab a prebuilt binary from the releases, or run the container image:

docker run --rm ghcr.io/tamnd/biostudies:latest --help

Usage

biostudies page <path>                      # fetch one page as a record
biostudies page <path> -o json              # as JSON, ready for jq
biostudies page <path> --template '{{.Body}}'  # just the readable body text
biostudies links <path>                     # the pages it links to, one per line
biostudies --help                           # the whole command tree

Every command shares one output contract: -o table|json|jsonl|csv|tsv|url|raw, --fields to pick columns, --template for a custom line, and -n to limit. The default adapts to where output goes (a table on a terminal, JSONL in a pipe), so the same command reads well by hand and parses cleanly downstream.

This is a fresh scaffold. It ships one example resource type, page, wired end to end. Model the real biostudies records in biostudies/ and declare their operations in biostudies/domain.go; each one becomes a command, an HTTP route, and an MCP tool at once.

Serve it

The same operations are available over HTTP and as an MCP tool set for agents, with no extra code:

biostudies serve --addr :7777    # GET /v1/page/<path>  returns NDJSON
biostudies mcp                   # speak MCP over stdio

Use it as a resource-URI driver

biostudies registers a biostudies domain the way a program registers a database driver with database/sql. A host enables it with one blank import:

import _ "github.com/tamnd/biostudies-cli/biostudies"

Then ant (or any program that links the package) dereferences biostudies:// URIs without knowing anything about biostudies:

ant get biostudies://page/<path>   # fetch the record
ant cat biostudies://page/<path>   # just the body text
ant ls  biostudies://page/<path>   # the pages it links to, each addressable
ant url biostudies://page/<path>   # the live https URL

Development

cmd/biostudies/   thin main: hands cli.NewApp to kit.Run
cli/                 assembles the kit App from the biostudies domain
biostudies/                the library: HTTP client, data models, and domain.go (the driver)
docs/                tago documentation site

make build      # ./bin/biostudies
make test       # go test ./...
make vet        # go vet ./...

Releasing

Push a version tag and GitHub Actions runs GoReleaser, which builds the archives, Linux packages, the multi-arch GHCR image, checksums, SBOMs, and a cosign signature:

git tag v0.1.0
git push --tags

The Homebrew and Scoop steps self-disable until their tokens exist, so the first release works with no extra secrets.

License

Apache-2.0. See LICENSE.