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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
<meta charset="utf-8">
<meta name="generator" content="quarto-1.9.37">
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<title>readme</title>
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<section id="cli-generator" class="level1">
<h1>cli-generator</h1>
<p>Generate a fully-typed Rust CLI and multi-language SDKs from a YAML config for any genomehubs API.</p>
<p><a href="https://github.com/genomehubs/cli-generator/actions/workflows/ci.yml"><img src="https://github.com/genomehubs/cli-generator/actions/workflows/ci.yml/badge.svg" class="img-fluid" alt="CI"></a> <a href="LICENSE"><img src="https://img.shields.io/badge/License-MIT-yellow.svg" class="img-fluid" alt="License: MIT"></a> <a href="tests/python/"><img src="https://img.shields.io/badge/Tests-371%20passed-brightgreen.png" class="img-fluid" alt="Tests"></a> <a href="#testing"><img src="https://img.shields.io/badge/Coverage-65%25%2B-yellowgreen.png" class="img-fluid" alt="Coverage"></a></p>
<section id="what-it-does" class="level2">
<h2 class="anchored" data-anchor-id="what-it-does">What it does</h2>
<p><code>cli-generator</code> reads a YAML config describing an API’s field groups and produces a fully-typed, tested <strong>Rust CLI + Python/R/JavaScript SDKs</strong>.</p>
<section id="rust-cli-features" class="level3">
<h3 class="anchored" data-anchor-id="rust-cli-features">Rust CLI Features</h3>
<ul>
<li><code>--field-groups</code>, <code>--fields</code>, <code>--expand</code>, and <code>--list-field-groups</code> flags backed by compile-time PHF tables — fast and allocation-free</li>
<li><code>--taxon-filter name|tree|lineage</code>, <code>--include-estimates</code>, <code>--format tsv|csv|json</code>, <code>--url</code> (dry-run), and more</li>
<li>Full bash/zsh completion autogeneration</li>
<li>Quarto documentation site generation</li>
</ul>
</section>
<section id="sdk-features-python-r-javascript" class="level3">
<h3 class="anchored" data-anchor-id="sdk-features-python-r-javascript">SDK Features (Python, R, JavaScript)</h3>
<ul>
<li><strong>Cross-language method parity</strong> — all three languages expose identical APIs</li>
<li><strong>QueryBuilder</strong> — chainable, type-hinted query construction
<ul>
<li>Set filters, pagination, sorting, output format</li>
<li>Built-in validation with detailed error messages</li>
<li>Serialize to URL, YAML, or parameter map</li>
</ul></li>
<li><strong>Response parsing</strong> — Rust-backed parsers for performance and correctness
<ul>
<li><code>parse_response_status()</code> — extract hit count and API errors</li>
<li><code>parse_search_json()</code> — flatten fielded results to records</li>
<li><code>parse_search_tsv()</code> — validate and normalize tabular data</li>
</ul></li>
<li><strong>API introspection</strong> — <code>describe()</code> and <code>snippet()</code> methods
<ul>
<li>Query description in human-readable format</li>
<li>Code snippets in CLI, Python, R, or JavaScript</li>
</ul></li>
<li><strong>Multi-page support</strong> — automatic pagination across SDKs</li>
</ul>
<p>Pre-built <code>goat-cli</code> binaries and SDK packages published to PyPI, npm, and CRAN — see <a href="GETTING_STARTED.md#1-try-the-goat-cli-preview">Getting started</a> for instructions.</p>
<pre class="mermaid"><code>graph LR
subgraph repo["cli-generator (repo)"]
direction TB
generator["Generator (Rust)<br/>src/ & codegen"]
core["Core library (Rust)<br/>crates/genomehubs-query<br/>foundation"]
api["API server (Rust)<br/>crates/genomehubs-api"]
templates["Templates (Tera)<br/>templates/"]
docs["Generated Quarto docs (Quarto output)<br/>sites/"]
end
subgraph generated["Generated projects & SDKs"]
gen_src["src/generated/ (generated)"]
gen_py["Python SDK & CLI<br/>python/ (PyO3 wrapper)"]
gen_r["R SDK<br/>extendr wrappers"]
gen_js["JS SDK<br/>WASM glue"]
end
es[(ElasticSearch<br/>Data store)]
generator --> templates
templates -->|Tera render| gen_src
gen_src -->|produces| gen_py
gen_src -->|produces| gen_r
gen_src -->|produces| gen_js
core -->|library / business logic| api
core -->|PyO3 / FFI| gen_py
core -->|WASM / extendr bindings| gen_js
generator -->|invokes codegen & templates| core
api -->|queries / reads| es
gen_py -->|calls REST| api
gen_r -->|calls REST| api
gen_js -->|calls REST| api
gen_src -->|Quarto build| docs
docs -->|documents| gen_py
docs -->|documents| gen_r
docs -->|documents| gen_js
classDef rust fill:#f3f8ff,stroke:#2b6cb0,stroke-width:1px;
classDef tpl fill:#fff7ed,stroke:#d97706,stroke-width:1px;
classDef gen fill:#f0fff4,stroke:#059669,stroke-width:1px;
class core,generator,api rust;
class templates tpl;
class gen_src,gen_py,gen_r,gen_js gen;</code></pre>
</section>
</section>
<section id="quick-start" class="level2">
<h2 class="anchored" data-anchor-id="quick-start">Quick start</h2>
<section id="try-the-cli" class="level3">
<h3 class="anchored" data-anchor-id="try-the-cli">Try the CLI</h3>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb2"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Install prerequisites (first time only)</span></span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="ex">cargo</span> install cargo-generate</span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="co"># Generate and build the goat-cli</span></span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a><span class="ex">cargo</span> run <span class="at">--</span> new goat <span class="at">--config</span> sites/ <span class="at">--output-dir</span> /tmp</span>
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> /tmp/goat-cli</span>
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a><span class="ex">cargo</span> build <span class="at">--release</span></span>
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a><span class="co"># Try it</span></span>
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a><span class="ex">./target/release/goat-cli</span> taxon search <span class="at">--list-field-groups</span></span>
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a><span class="ex">./target/release/goat-cli</span> taxon search <span class="at">--taxon</span> Mammalia <span class="at">--field-groups</span> busco,genome-size</span>
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a><span class="ex">./target/release/goat-cli</span> taxon search <span class="at">--taxon</span> Mammalia <span class="at">--field-groups</span> G,b <span class="at">--url</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
</section>
<section id="try-the-python-sdk" class="level3">
<h3 class="anchored" data-anchor-id="try-the-python-sdk">Try the Python SDK</h3>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb3"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> goat_sdk <span class="im">import</span> QueryBuilder</span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a>qb <span class="op">=</span> QueryBuilder(index<span class="op">=</span><span class="st">"taxon"</span>, api_base<span class="op">=</span><span class="st">"https://..."</span>)</span>
<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a>qb.set_taxa([<span class="st">"Mammalia"</span>], filter_type<span class="op">=</span><span class="st">"tree"</span>)</span>
<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a>qb.add_field(<span class="st">"genome_size"</span>)</span>
<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a>qb.set_size(<span class="dv">10</span>)</span>
<span id="cb3-7"><a href="#cb3-7" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb3-8"><a href="#cb3-8" aria-hidden="true" tabindex="-1"></a><span class="co"># Validate the query</span></span>
<span id="cb3-9"><a href="#cb3-9" aria-hidden="true" tabindex="-1"></a>errors <span class="op">=</span> qb.validate()</span>
<span id="cb3-10"><a href="#cb3-10" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> errors:</span>
<span id="cb3-11"><a href="#cb3-11" aria-hidden="true" tabindex="-1"></a> <span class="bu">print</span>(<span class="st">"Validation errors:"</span>, errors)</span>
<span id="cb3-12"><a href="#cb3-12" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb3-13"><a href="#cb3-13" aria-hidden="true" tabindex="-1"></a><span class="co"># Build a URL for inspection</span></span>
<span id="cb3-14"><a href="#cb3-14" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(<span class="st">"Query URL:"</span>, qb.to_url())</span>
<span id="cb3-15"><a href="#cb3-15" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb3-16"><a href="#cb3-16" aria-hidden="true" tabindex="-1"></a><span class="co"># Fetch paginated results</span></span>
<span id="cb3-17"><a href="#cb3-17" aria-hidden="true" tabindex="-1"></a>results <span class="op">=</span> qb.search(<span class="bu">format</span><span class="op">=</span><span class="st">"json"</span>)</span>
<span id="cb3-18"><a href="#cb3-18" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(<span class="ss">f"Found </span><span class="sc">{</span><span class="bu">len</span>(results)<span class="sc">}</span><span class="ss"> results"</span>)</span>
<span id="cb3-19"><a href="#cb3-19" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb3-20"><a href="#cb3-20" aria-hidden="true" tabindex="-1"></a><span class="co"># Get a description of what the query does</span></span>
<span id="cb3-21"><a href="#cb3-21" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(qb.describe(mode<span class="op">=</span><span class="st">"short"</span>))</span>
<span id="cb3-22"><a href="#cb3-22" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb3-23"><a href="#cb3-23" aria-hidden="true" tabindex="-1"></a><span class="co"># Generate a code snippet</span></span>
<span id="cb3-24"><a href="#cb3-24" aria-hidden="true" tabindex="-1"></a>snippets <span class="op">=</span> qb.snippet(languages<span class="op">=</span>[<span class="st">"python"</span>, <span class="st">"cli"</span>])</span>
<span id="cb3-25"><a href="#cb3-25" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(<span class="st">"Python snippet:"</span>, snippets[<span class="st">"python"</span>])</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
</section>
<section id="try-the-r-sdk" class="level3">
<h3 class="anchored" data-anchor-id="try-the-r-sdk">Try the R SDK</h3>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb4"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(goat)</span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a>qb <span class="ot"><-</span> QueryBuilder<span class="sc">$</span><span class="fu">new</span>(<span class="at">index =</span> <span class="st">"taxon"</span>, <span class="at">api_base =</span> <span class="st">"https://..."</span>)</span>
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a>qb<span class="sc">$</span><span class="fu">set_taxa</span>(<span class="fu">c</span>(<span class="st">"Mammalia"</span>), <span class="at">filter_type =</span> <span class="st">"tree"</span>)</span>
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a>qb<span class="sc">$</span><span class="fu">add_field</span>(<span class="st">"genome_size"</span>)</span>
<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a>qb<span class="sc">$</span><span class="fu">set_size</span>(<span class="dv">10</span>)</span>
<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-8"><a href="#cb4-8" aria-hidden="true" tabindex="-1"></a><span class="co"># Validate</span></span>
<span id="cb4-9"><a href="#cb4-9" aria-hidden="true" tabindex="-1"></a>errors <span class="ot"><-</span> qb<span class="sc">$</span><span class="fu">validate</span>()</span>
<span id="cb4-10"><a href="#cb4-10" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="fu">length</span>(errors) <span class="sc">></span> <span class="dv">0</span>) <span class="fu">print</span>(errors)</span>
<span id="cb4-11"><a href="#cb4-11" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-12"><a href="#cb4-12" aria-hidden="true" tabindex="-1"></a><span class="co"># Build URL</span></span>
<span id="cb4-13"><a href="#cb4-13" aria-hidden="true" tabindex="-1"></a><span class="fu">print</span>(qb<span class="sc">$</span><span class="fu">to_url</span>())</span>
<span id="cb4-14"><a href="#cb4-14" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-15"><a href="#cb4-15" aria-hidden="true" tabindex="-1"></a><span class="co"># Search</span></span>
<span id="cb4-16"><a href="#cb4-16" aria-hidden="true" tabindex="-1"></a>results <span class="ot"><-</span> qb<span class="sc">$</span><span class="fu">search</span>(<span class="at">format =</span> <span class="st">"json"</span>)</span>
<span id="cb4-17"><a href="#cb4-17" aria-hidden="true" tabindex="-1"></a><span class="fu">print</span>(<span class="fu">paste</span>(<span class="st">"Found"</span>, <span class="fu">nrow</span>(results), <span class="st">"results"</span>))</span>
<span id="cb4-18"><a href="#cb4-18" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-19"><a href="#cb4-19" aria-hidden="true" tabindex="-1"></a><span class="co"># Describe query</span></span>
<span id="cb4-20"><a href="#cb4-20" aria-hidden="true" tabindex="-1"></a><span class="fu">cat</span>(qb<span class="sc">$</span><span class="fu">describe</span>(<span class="at">mode =</span> <span class="st">"short"</span>))</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
</section>
<section id="try-the-javascript-sdk" class="level3">
<h3 class="anchored" data-anchor-id="try-the-javascript-sdk">Try the JavaScript SDK</h3>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb5"><pre class="sourceCode javascript code-with-copy"><code class="sourceCode javascript"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="kw">const</span> { QueryBuilder } <span class="op">=</span> <span class="pp">require</span>(<span class="st">"goat-sdk"</span>)<span class="op">;</span></span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a><span class="kw">const</span> qb <span class="op">=</span> <span class="kw">new</span> <span class="fu">QueryBuilder</span>(<span class="st">"taxon"</span><span class="op">,</span> <span class="st">"https://..."</span>)<span class="op">;</span></span>
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a>qb<span class="op">.</span><span class="fu">setTaxa</span>([<span class="st">"Mammalia"</span>]<span class="op">,</span> <span class="st">"tree"</span>)<span class="op">;</span></span>
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a>qb<span class="op">.</span><span class="fu">addField</span>(<span class="st">"genome_size"</span>)<span class="op">;</span></span>
<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a>qb<span class="op">.</span><span class="fu">setSize</span>(<span class="dv">10</span>)<span class="op">;</span></span>
<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-8"><a href="#cb5-8" aria-hidden="true" tabindex="-1"></a><span class="co">// Validate</span></span>
<span id="cb5-9"><a href="#cb5-9" aria-hidden="true" tabindex="-1"></a><span class="kw">const</span> errors <span class="op">=</span> qb<span class="op">.</span><span class="fu">validate</span>()<span class="op">;</span></span>
<span id="cb5-10"><a href="#cb5-10" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (errors<span class="op">.</span><span class="at">length</span> <span class="op">></span> <span class="dv">0</span>) <span class="bu">console</span><span class="op">.</span><span class="fu">log</span>(<span class="st">"Errors:"</span><span class="op">,</span> errors)<span class="op">;</span></span>
<span id="cb5-11"><a href="#cb5-11" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-12"><a href="#cb5-12" aria-hidden="true" tabindex="-1"></a><span class="co">// Build URL</span></span>
<span id="cb5-13"><a href="#cb5-13" aria-hidden="true" tabindex="-1"></a><span class="bu">console</span><span class="op">.</span><span class="fu">log</span>(<span class="st">"Query URL:"</span><span class="op">,</span> qb<span class="op">.</span><span class="fu">toUrl</span>())<span class="op">;</span></span>
<span id="cb5-14"><a href="#cb5-14" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-15"><a href="#cb5-15" aria-hidden="true" tabindex="-1"></a><span class="co">// Search</span></span>
<span id="cb5-16"><a href="#cb5-16" aria-hidden="true" tabindex="-1"></a><span class="kw">const</span> results <span class="op">=</span> <span class="cf">await</span> qb<span class="op">.</span><span class="fu">search</span>(<span class="st">"json"</span>)<span class="op">;</span></span>
<span id="cb5-17"><a href="#cb5-17" aria-hidden="true" tabindex="-1"></a><span class="bu">console</span><span class="op">.</span><span class="fu">log</span>(<span class="vs">`Found </span><span class="sc">${</span>results<span class="op">.</span><span class="at">length</span><span class="sc">}</span><span class="vs"> results`</span>)<span class="op">;</span></span>
<span id="cb5-18"><a href="#cb5-18" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-19"><a href="#cb5-19" aria-hidden="true" tabindex="-1"></a><span class="co">// Describe query</span></span>
<span id="cb5-20"><a href="#cb5-20" aria-hidden="true" tabindex="-1"></a><span class="bu">console</span><span class="op">.</span><span class="fu">log</span>(qb<span class="op">.</span><span class="fu">describe</span>({ <span class="dt">mode</span><span class="op">:</span> <span class="st">"short"</span> }))<span class="op">;</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
</section>
<section id="generate-a-new-cli-from-your-own-config" class="level3">
<h3 class="anchored" data-anchor-id="generate-a-new-cli-from-your-own-config">Generate a new CLI from your own config</h3>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb6"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="fu">cp</span> sites/goat.yaml sites/my-site.yaml</span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a><span class="fu">cp</span> sites/goat-cli-options.yaml sites/my-site-options.yaml</span>
<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a><span class="co"># edit the two files to point at your API and define your field groups</span></span>
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a><span class="ex">cargo</span> run <span class="at">--</span> new my-site <span class="at">--config</span> sites/ <span class="at">--output-dir</span> /tmp</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
</section>
</section>
<section id="update-an-existing-generated-cli" class="level2">
<h2 class="anchored" data-anchor-id="update-an-existing-generated-cli">Update an existing generated CLI</h2>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb7"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="co"># From inside the generated repo (after editing config/):</span></span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a><span class="ex">cargo</span> run <span class="at">--manifest-path</span> /path/to/cli-generator/Cargo.toml <span class="at">--</span> update</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
</section>
<section id="status-documentation" class="level2">
<h2 class="anchored" data-anchor-id="status-documentation">Status & Documentation</h2>
<p><strong>MVP Status</strong>: Feature-complete multi-language CLI + SDK generation. Phase 0–3 implemented:</p>
<ul>
<li>✅ Rust CLI with full feature set</li>
<li>✅ Python SDK via PyO3 (PyPI)</li>
<li>✅ R SDK via extendr (CRAN)</li>
<li>✅ JavaScript SDK via WASM (npm)</li>
<li>✅ Method parity across all three SDKs</li>
<li>✅ Response parsing with Rust correctness</li>
<li>✅ Validation, introspection, and code generation</li>
<li>✅ Multi-page result fetching</li>
<li>✅ CI integration and 371+ test coverage</li>
</ul>
<section id="for-users-and-integrators" class="level3">
<h3 class="anchored" data-anchor-id="for-users-and-integrators">For users and integrators</h3>
<p>Start with <a href="GETTING_STARTED.md">GETTING_STARTED.md</a> — choose your role to navigate to the right section:</p>
<ul>
<li>📦 <strong>SDK users</strong> — use the generated QueryBuilder in Python, R, or JavaScript</li>
<li>🔌 <strong>Integration teams</strong> — add your API to cli-generator; see <a href="docs/planning/integration-runbook.md">Integration Runbook</a></li>
<li>📊 <strong>Release managers</strong> — publish new SDKs; see <a href="docs/planning/release-strategy.md">Release Strategy</a></li>
</ul>
</section>
<section id="for-developers-contributors" class="level3">
<h3 class="anchored" data-anchor-id="for-developers-contributors">For developers & contributors</h3>
<p>See <a href="docs/MAIN.md">MAIN.md</a> for documentation index by topic.</p>
<p>Key references:</p>
<ul>
<li><a href="CONTRIBUTING.md">CONTRIBUTING.md</a> — code style, testing, PR process</li>
<li><a href="AGENTS.md">AGENTS.md</a> — AI agent guidelines and multi-language extension patterns</li>
<li><a href=".github/copilot-instructions.md">Copilot Instructions</a> — workspace conventions for GitHub Copilot</li>
<li><a href="docs/planning/extension-guide.md">Extension Guide</a> — add parameters, validators, or new languages (Rust → Python → R/JS pattern)</li>
<li><a href="docs/testing/test-strategy.md">Test Strategy</a> — coverage targets, fixture generation, parity testing</li>
</ul>
</section>
</section>
<section id="development" class="level2">
<h2 class="anchored" data-anchor-id="development">Development</h2>
<p>See <a href="GETTING_STARTED.md#development">GETTING_STARTED.md</a> for full setup and contributor workflow.</p>
<p>Run verification:</p>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb8"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="fu">bash</span> scripts/verify_code.sh <span class="co"># Rust + Python lint, format, test, coverage</span></span>
<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a><span class="fu">bash</span> scripts/test_sdk_fixtures.sh <span class="at">--help</span> <span class="co"># SDK fixture generation and validation</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
</section>
<section id="project-structure" class="level2">
<h2 class="anchored" data-anchor-id="project-structure">Project structure</h2>
<pre><code>src/
core/ Pure Rust library logic — no PyO3 or clap dependencies.
lib.rs PyO3 module: wires core functions to Python.
main.rs clap CLI: wires core functions to subcommands.
cli_meta.rs CLI name/description constants (generator-controlled).
generated/ Auto-generated code only. Never edited by hand.
commands/ new, update, preview, validate subcommand handlers.
crates/
genomehubs-query/ WASM + extendr subcrate: query parsing, validation, introspection.
python/
cli_generator/ Python package re-exporting the Rust extension + QueryBuilder.
templates/
rust/, python/, r/, js/ Language-specific templates rendered into each generated project.
snippets/ Code snippet templates (python, r, javascript, cli).
docs/ Generated project documentation (HTML, quarto).
sites/ YAML config for known sites (goat, boat, …).
tests/
python/ pytest + Hypothesis tests for all modules + parity tests.
generated_goat_cli.rs Integration tests — generate goat-cli and validate.
docs/
MAIN.md Documentation index and navigation guide.
HISTORY.md Archive of completed phase documentation.
planning/ Strategic docs: release strategy, integration runbook, extension guide.
testing/ Test fixtures, parameter coverage, test strategies.
reference/ API schema caching, coverage measurements.
api-schemas/ Cached API responses for fixture generation.
agent-logs/ Committed LLM session summaries for transparency and reproducibility.
scripts/
verify_code.sh Run all linting, formatting, and tests.
test_sdk_fixtures.sh Generate SDKs and validate fixture round-trips.
dev_site.sh Full end-to-end test: generate, build, smoke-test all languages.</code></pre>
</section>
<section id="package-distribution" class="level2">
<h2 class="anchored" data-anchor-id="package-distribution">Package distribution</h2>
<p>Generated SDKs are published to all major package registries:</p>
<table class="caption-top table">
<colgroup>
<col style="width: 14%">
<col style="width: 22%">
<col style="width: 62%">
</colgroup>
<thead>
<tr class="header">
<th>Language</th>
<th>Registry</th>
<th>Example</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>Python</td>
<td>PyPI</td>
<td><code>pip install goat-sdk</code></td>
</tr>
<tr class="even">
<td>R</td>
<td>CRAN</td>
<td><code>install.packages("goat")</code></td>
</tr>
<tr class="odd">
<td>JavaScript</td>
<td>npm</td>
<td><code>npm install goat-sdk</code></td>
</tr>
<tr class="even">
<td>Rust CLI</td>
<td>GitHub Releases</td>
<td>Pre-built binaries (<code>goat-cli-*-*.tar.gz</code>)</td>
</tr>
</tbody>
</table>
<p>Each site has independent semantic versioning (e.g., <code>goat-sdk</code> v1.2.3 ≠ <code>boat-sdk</code> v2.1.0). Release strategy, API polling for drift detection, and publishing checklists are documented in <a href="docs/planning/release-strategy.md">Release Strategy</a>.</p>
</section>
<section id="license" class="level2">
<h2 class="anchored" data-anchor-id="license">License</h2>
<p>MIT — see <a href="LICENSE">LICENSE</a>.</p>
</section>
</section>
</main>
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instance.setContent(html);
}
}).finally(() => {
instance.enable();
instance.show();
});
}
}, function(instance) {
});
}
let selectedAnnoteEl;
const selectorForAnnotation = ( cell, annotation) => {
let cellAttr = 'data-code-cell="' + cell + '"';
let lineAttr = 'data-code-annotation="' + annotation + '"';
const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
return selector;
}
const selectCodeLines = (annoteEl) => {
const doc = window.document;
const targetCell = annoteEl.getAttribute("data-target-cell");
const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
const lines = annoteSpan.getAttribute("data-code-lines").split(",");
const lineIds = lines.map((line) => {
return targetCell + "-" + line;
})
let top = null;
let height = null;
let parent = null;
if (lineIds.length > 0) {
//compute the position of the single el (top and bottom and make a div)
const el = window.document.getElementById(lineIds[0]);
top = el.offsetTop;
height = el.offsetHeight;
parent = el.parentElement.parentElement;
if (lineIds.length > 1) {
const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
const bottom = lastEl.offsetTop + lastEl.offsetHeight;
height = bottom - top;
}
if (top !== null && height !== null && parent !== null) {
// cook up a div (if necessary) and position it
let div = window.document.getElementById("code-annotation-line-highlight");
if (div === null) {
div = window.document.createElement("div");
div.setAttribute("id", "code-annotation-line-highlight");
div.style.position = 'absolute';
parent.appendChild(div);
}
div.style.top = top - 2 + "px";
div.style.height = height + 4 + "px";
div.style.left = 0;
let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
if (gutterDiv === null) {
gutterDiv = window.document.createElement("div");
gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
gutterDiv.style.position = 'absolute';
const codeCell = window.document.getElementById(targetCell);
const gutter = codeCell.querySelector('.code-annotation-gutter');
gutter.appendChild(gutterDiv);
}
gutterDiv.style.top = top - 2 + "px";
gutterDiv.style.height = height + 4 + "px";
}
selectedAnnoteEl = annoteEl;
}
};
const unselectCodeLines = () => {
const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
elementsIds.forEach((elId) => {
const div = window.document.getElementById(elId);
if (div) {
div.remove();
}
});
selectedAnnoteEl = undefined;
};
// Handle positioning of the toggle
window.addEventListener(
"resize",
throttle(() => {
elRect = undefined;
if (selectedAnnoteEl) {
selectCodeLines(selectedAnnoteEl);
}
}, 10)
);
function throttle(fn, ms) {
let throttle = false;
let timer;
return (...args) => {
if(!throttle) { // first call gets through
fn.apply(this, args);
throttle = true;
} else { // all the others get throttled
if(timer) clearTimeout(timer); // cancel #2
timer = setTimeout(() => {
fn.apply(this, args);
timer = throttle = false;
}, ms);
}
};
}
// Attach click handler to the DT
const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
for (const annoteDlNode of annoteDls) {
annoteDlNode.addEventListener('click', (event) => {
const clickedEl = event.target;
if (clickedEl !== selectedAnnoteEl) {
unselectCodeLines();
const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
if (activeEl) {
activeEl.classList.remove('code-annotation-active');
}
selectCodeLines(clickedEl);
clickedEl.classList.add('code-annotation-active');
} else {
// Unselect the line
unselectCodeLines();
clickedEl.classList.remove('code-annotation-active');
}
});
}
const findCites = (el) => {
const parentEl = el.parentElement;
if (parentEl) {
const cites = parentEl.dataset.cites;
if (cites) {
return {
el,
cites: cites.split(' ')
};
} else {
return findCites(el.parentElement)
}
} else {
return undefined;
}
};
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
for (var i=0; i<bibliorefs.length; i++) {
const ref = bibliorefs[i];
const citeInfo = findCites(ref);
if (citeInfo) {
tippyHover(citeInfo.el, function() {
var popup = window.document.createElement('div');
citeInfo.cites.forEach(function(cite) {
var citeDiv = window.document.createElement('div');
citeDiv.classList.add('hanging-indent');
citeDiv.classList.add('csl-entry');
var biblioDiv = window.document.getElementById('ref-' + cite);
if (biblioDiv) {
citeDiv.innerHTML = biblioDiv.innerHTML;
}
popup.appendChild(citeDiv);
});
return popup.innerHTML;
});
}
}
});
</script>
</div> <!-- /content -->
</body></html>