diff --git a/pkgdown.yml b/pkgdown.yml
index a595da8..f18396f 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.7
pkgdown_sha: ~
articles:
proofr: proofr.html
-last_built: 2024-01-08T19:45Z
+last_built: 2024-01-10T19:29Z
urls:
reference: http://getwilds.org/proofr/reference
article: http://getwilds.org/proofr/articles
diff --git a/reference/index.html b/reference/index.html
index d982b4d..fddf8b2 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -63,7 +63,12 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
<code><a href="proof_cancel.html">proof_cancel()</a></code>
</dt>
- <dd>Delete PROOF Cromwell server</dd>
+ <dd>Cancel/stop PROOF Cromwell server</dd>
+ </dl><dl><dt>
+
+ <code><a href="proof_header.html">proof_header()</a></code>
+ </dt>
+ <dd>Get header for PROOF API calls</dd>
</dl><dl><dt>
<code><a href="proof_start.html">proof_start()</a></code>
diff --git a/reference/proof_authenticate.html b/reference/proof_authenticate.html
index c0c945c..32d2fbc 100644
--- a/reference/proof_authenticate.html
+++ b/reference/proof_authenticate.html
@@ -1,5 +1,5 @@
<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Authenticates with HutchNet credentials, returns PROOF API token"><title>Authenticate with PROOF API — proof_authenticate • proofr</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Authenticate with PROOF API — proof_authenticate"><meta property="og:description" content="Authenticates with HutchNet credentials, returns PROOF API token"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Authenticate with PROOF API"><title>Authenticate with PROOF API — proof_authenticate • proofr</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Authenticate with PROOF API — proof_authenticate"><meta property="og:description" content="Authenticate with PROOF API"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]--></head><body>
@@ -46,7 +46,7 @@
</div>
<div class="ref-description section level2">
- <p>Authenticates with HutchNet credentials, returns PROOF API token</p>
+ <p>Authenticate with PROOF API</p>
</div>
<div class="section level2">
diff --git a/reference/proof_cancel.html b/reference/proof_cancel.html
index ea1cee1..bc767cb 100644
--- a/reference/proof_cancel.html
+++ b/reference/proof_cancel.html
@@ -1,5 +1,5 @@
<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Delete PROOF Cromwell server"><title>Delete PROOF Cromwell server — proof_cancel • proofr</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Delete PROOF Cromwell server — proof_cancel"><meta property="og:description" content="Delete PROOF Cromwell server"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Cancel/stop PROOF Cromwell server"><title>Cancel/stop PROOF Cromwell server — proof_cancel • proofr</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Cancel/stop PROOF Cromwell server — proof_cancel"><meta property="og:description" content="Cancel/stop PROOF Cromwell server"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]--></head><body>
@@ -40,13 +40,13 @@
</nav><div class="container template-reference-topic">
<div class="row">
<main id="main" class="col-md-9"><div class="page-header">
- <img src="" class="logo" alt=""><h1>Delete PROOF Cromwell server</h1>
+ <img src="" class="logo" alt=""><h1>Cancel/stop PROOF Cromwell server</h1>
<small class="dont-index">Source: <a href="https://github.com/getwilds/proofr/blob/HEAD/R/cancel.R" class="external-link"><code>R/cancel.R</code></a></small>
<div class="d-none name"><code>proof_cancel.Rd</code></div>
</div>
<div class="ref-description section level2">
- <p>Delete PROOF Cromwell server</p>
+ <p>Cancel/stop PROOF Cromwell server</p>
</div>
<div class="section level2">
@@ -58,16 +58,8 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-<p>A list with fields <code>job_id</code> and <code>info</code></p>
-
-
- </div>
- <div class="section level2">
- <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
- <p>Does not return PROOF/Cromwell server URL, for that you have to
-periodically call <code><a href="proof_status.html">proof_status()</a></code>, or wait for the email from the
-PROOF API</p>
- </div>
+<p>A list with a single field:</p><ul><li><p><code>message</code> (character)</p></li>
+</ul></div>
<div class="section level2">
<h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
<p><a href="https://github.com/FredHutch/proof-api#delete-cromwell-server" class="external-link">https://github.com/FredHutch/proof-api#delete-cromwell-server</a></p>
diff --git a/reference/proof_header.html b/reference/proof_header.html
index d545175..8dc9494 100644
--- a/reference/proof_header.html
+++ b/reference/proof_header.html
@@ -1,5 +1,5 @@
<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Utility method to get header for PROOF API calls"><title>Get header for PROOF API calls — proof_header • proofr</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get header for PROOF API calls — proof_header"><meta property="og:description" content="Utility method to get header for PROOF API calls"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Get header for PROOF API calls"><title>Get header for PROOF API calls — proof_header • proofr</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get header for PROOF API calls — proof_header"><meta property="og:description" content="Get header for PROOF API calls"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]--></head><body>
@@ -46,7 +46,7 @@
</div>
<div class="ref-description section level2">
- <p>Utility method to get header for PROOF API calls</p>
+ <p>Get header for PROOF API calls</p>
</div>
<div class="section level2">
@@ -57,7 +57,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>token</dt>
-<dd><p>PROOF API token</p></dd>
+<dd><p>(character) PROOF API token. optional</p></dd>
</dl></div>
<div class="section level2">
diff --git a/reference/proof_start.html b/reference/proof_start.html
index 5d37cf3..e6683a5 100644
--- a/reference/proof_start.html
+++ b/reference/proof_start.html
@@ -65,10 +65,9 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-<p>A list with fields <code>job_id</code> and <code>info</code></p>
-
-
- </div>
+<p>A list with fields:</p><ul><li><p><code>job_id</code> (character)</p></li>
+<li><p><code>info</code> (character)</p></li>
+</ul></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>Does not return PROOF/Cromwell server URL, for that you have to
diff --git a/reference/proof_status.html b/reference/proof_status.html
index b5c2cf3..71c80e8 100644
--- a/reference/proof_status.html
+++ b/reference/proof_status.html
@@ -41,7 +41,7 @@
<div class="row">
<main id="main" class="col-md-9"><div class="page-header">
<img src="" class="logo" alt=""><h1>Get PROOF API job status - is job running, what's its URL...</h1>
- <small class="dont-index">Source: <a href="https://github.com/getwilds/proofr/blob/HEAD/R/job_status.R" class="external-link"><code>R/job_status.R</code></a></small>
+ <small class="dont-index">Source: <a href="https://github.com/getwilds/proofr/blob/HEAD/R/status.R" class="external-link"><code>R/status.R</code></a></small>
<div class="d-none name"><code>proof_status.Rd</code></div>
</div>
@@ -58,9 +58,14 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-<p>A list with slots:</p><ul><li><p><code>canJobStart</code></p></li>
-<li><p><code>jobStatus</code></p></li>
-<li><p><code>cromwellUrl</code></p></li>
+<p>A list with fields:</p><ul><li><p><code>canJobStart</code> (logical): can a job to make a Cromwell server be started?
+<code>FALSE</code> if server already running; <code>TRUE</code> if server not running</p></li>
+<li><p><code>jobStatus</code> (character): status of the job that controls the Cromwell
+server. e.g., "RUNNING". <code>NULL</code> if server not running</p></li>
+<li><p><code>cromwellUrl</code> (character): the URL for the Cromwell server. <code>NULL</code> if
+server not running</p></li>
+<li><p><code>jobInfo</code> (list): metadata on the Cromwell server. All slots <code>NULL</code>
+if server not running</p></li>
</ul></div>
<div class="section level2">
<h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
diff --git a/search.json b/search.json
index a973cd5..89a504c 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"http://getwilds.org/proofr/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 proofr authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"authenticate-with-the-proof-api","dir":"Articles","previous_headings":"","what":"Authenticate with the PROOF API","title":"Getting Started","text":"Run function proof_authenticate(), calls PROOF API username password, returns API token (alphanumeric string). (note: token real token) token returned set environment variable within R session. important ’s good security practice pass secrets API tokens parameters functions. say, please save API token environment variable somewhere computer, shouldn’t need running proof_authenticate() ’ll look environment variable.","code":"proof_authenticate(\"username\", \"password\") #> xyGKibGctQ92rmMKKb39q43XgPxGCmrWoX7NZtamTjDP"},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"start-a-cromwell-server","dir":"Articles","previous_headings":"","what":"Start a Cromwell Server","title":"Getting Started","text":"Start server Get URL","code":"proof_start() metadata <- proof_status() cromwell_url <- metadata$cromwellUrl cromwell_url"},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"rcromwell-setup","dir":"Articles","previous_headings":"","what":"rcromwell setup","title":"Getting Started","text":"Load rcromwell Set Cromwell server URL recognized rcromwell Set Authorization HTTP header used rcromwell HTTP requests now able interact Cromwell server authentication details retrieved via proofr package!","code":"library(rcromwell) library(httr) cromwell_config(cromwell_url) httr::set_config(proof_header())"},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"interact-with-the-cromwell-server","dir":"Articles","previous_headings":"","what":"Interact with the Cromwell server","title":"Getting Started","text":"Now, check version Cromwell server","code":"cromwell_version()"},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"done","dir":"Articles","previous_headings":"","what":"Done!","title":"Getting Started","text":"’re now setup interact Cromwell server. See rcromwell package docs get started.","code":""},{"path":"http://getwilds.org/proofr/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Scott Chamberlain. Author, maintainer.","code":""},{"path":"http://getwilds.org/proofr/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Chamberlain S (2024). proofr: Client PROOF API. R package version 0.0.0.91http://getwilds.org/proofr/ (website) https://github.com/getwilds/proofr (devel), http://getwilds.org/proofr/ (website)https://github.com/getwilds/proofr (devel).","code":"@Manual{, title = {proofr: Client for the PROOF API}, author = {Scott Chamberlain}, year = {2024}, note = {R package version 0.0.0.91http://getwilds.org/proofr/ (website) https://github.com/getwilds/proofr (devel)}, url = {http://getwilds.org/proofr/ (website) https://github.com/getwilds/proofr (devel)}, }"},{"path":"http://getwilds.org/proofr/index.html","id":"proofr","dir":"","previous_headings":"","what":"Client for the PROOF API","title":"Client for the PROOF API","text":"R client PROOF API PROOF API https://github.com/FredHutch/proof-api","code":""},{"path":"http://getwilds.org/proofr/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Client for the PROOF API","text":"can install development version proofr GitHub :","code":"# install.packages(\"pak\") pak::pak(\"getwilds/proofr\")"},{"path":"http://getwilds.org/proofr/index.html","id":"get-started","dir":"","previous_headings":"","what":"Get started","title":"Client for the PROOF API","text":"get started proofr, see Getting Started vignette.","code":""},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":null,"dir":"Reference","previous_headings":"","what":"Authenticate with PROOF API — proof_authenticate","title":"Authenticate with PROOF API — proof_authenticate","text":"Authenticates HutchNet credentials, returns PROOF API token","code":""},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Authenticate with PROOF API — proof_authenticate","text":"","code":"proof_authenticate(username, password)"},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Authenticate with PROOF API — proof_authenticate","text":"username (character) HutchNet username password (character) HutchNet password","code":""},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Authenticate with PROOF API — proof_authenticate","text":"single token (character) bearer authentication PROOF API","code":""},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Authenticate with PROOF API — proof_authenticate","text":"","code":"# Sys.getenv(\"PROOF_TOKEN\") # x <- proof_authenticate() # Sys.getenv(\"PROOF_TOKEN\")"},{"path":"http://getwilds.org/proofr/reference/proof_cancel.html","id":null,"dir":"Reference","previous_headings":"","what":"Delete PROOF Cromwell server — proof_cancel","title":"Delete PROOF Cromwell server — proof_cancel","text":"Delete PROOF Cromwell server","code":""},{"path":"http://getwilds.org/proofr/reference/proof_cancel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Delete PROOF Cromwell server — proof_cancel","text":"","code":"proof_cancel()"},{"path":"http://getwilds.org/proofr/reference/proof_cancel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Delete PROOF Cromwell server — proof_cancel","text":"list fields job_id info","code":""},{"path":"http://getwilds.org/proofr/reference/proof_cancel.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Delete PROOF Cromwell server — proof_cancel","text":"return PROOF/Cromwell server URL, periodically call proof_status(), wait email PROOF API","code":""},{"path":"http://getwilds.org/proofr/reference/proof_cancel.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Delete PROOF Cromwell server — proof_cancel","text":"https://github.com/FredHutch/proof-api#delete-cromwell-server","code":""},{"path":"http://getwilds.org/proofr/reference/proof_header.html","id":null,"dir":"Reference","previous_headings":"","what":"Get header for PROOF API calls — proof_header","title":"Get header for PROOF API calls — proof_header","text":"Utility method get header PROOF API calls","code":""},{"path":"http://getwilds.org/proofr/reference/proof_header.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get header for PROOF API calls — proof_header","text":"","code":"proof_header(token = NULL)"},{"path":"http://getwilds.org/proofr/reference/proof_header.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get header for PROOF API calls — proof_header","text":"token PROOF API token","code":""},{"path":"http://getwilds.org/proofr/reference/proof_header.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get header for PROOF API calls — proof_header","text":"request S3 class HTTP header can passed httr::GET(), httr::POST(), etc.","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":null,"dir":"Reference","previous_headings":"","what":"Start PROOF Cromwell server — proof_start","title":"Start PROOF Cromwell server — proof_start","text":"Start PROOF Cromwell server","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Start PROOF Cromwell server — proof_start","text":"","code":"proof_start(pi_name = NULL)"},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Start PROOF Cromwell server — proof_start","text":"pi_name (character) PI name form last_f; needed user one SLURM account","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Start PROOF Cromwell server — proof_start","text":"list fields job_id info","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Start PROOF Cromwell server — proof_start","text":"return PROOF/Cromwell server URL, periodically call proof_status(), wait email PROOF API","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Start PROOF Cromwell server — proof_start","text":"https://github.com/FredHutch/proof-api#post-cromwell-server","code":""},{"path":"http://getwilds.org/proofr/reference/proof_status.html","id":null,"dir":"Reference","previous_headings":"","what":"Get PROOF API job status - is job running, what's its URL... — proof_status","title":"Get PROOF API job status - is job running, what's its URL... — proof_status","text":"Get PROOF API job status - job running, URL...","code":""},{"path":"http://getwilds.org/proofr/reference/proof_status.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get PROOF API job status - is job running, what's its URL... — proof_status","text":"","code":"proof_status()"},{"path":"http://getwilds.org/proofr/reference/proof_status.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get PROOF API job status - is job running, what's its URL... — proof_status","text":"list slots: canJobStart jobStatus cromwellUrl","code":""},{"path":"http://getwilds.org/proofr/reference/proof_status.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Get PROOF API job status - is job running, what's its URL... — proof_status","text":"https://github.com/FredHutch/proof-api#get-cromwell-server","code":""},{"path":"http://getwilds.org/proofr/reference/proofr-package.html","id":null,"dir":"Reference","previous_headings":"","what":"proofr: Client for the PROOF API — proofr-package","title":"proofr: Client for the PROOF API — proofr-package","text":"Client PROOF API.","code":""},{"path":[]},{"path":"http://getwilds.org/proofr/reference/proofr-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"proofr: Client for the PROOF API — proofr-package","text":"Maintainer: Scott Chamberlain sachamber@fredhutch.org (ORCID)","code":""}]
+[{"path":"http://getwilds.org/proofr/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 proofr authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"authenticate-with-the-proof-api","dir":"Articles","previous_headings":"","what":"Authenticate with the PROOF API","title":"Getting Started","text":"Run function proof_authenticate(), calls PROOF API username password, returns API token (alphanumeric string). (note: token real token) token returned set environment variable within R session. important ’s good security practice pass secrets API tokens parameters functions. say, please save API token environment variable somewhere computer, shouldn’t need running proof_authenticate() ’ll look environment variable.","code":"proof_authenticate(\"username\", \"password\") #> xyGKibGctQ92rmMKKb39q43XgPxGCmrWoX7NZtamTjDP"},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"start-a-cromwell-server","dir":"Articles","previous_headings":"","what":"Start a Cromwell Server","title":"Getting Started","text":"Start server Get URL","code":"proof_start() metadata <- proof_status() cromwell_url <- metadata$cromwellUrl cromwell_url"},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"rcromwell-setup","dir":"Articles","previous_headings":"","what":"rcromwell setup","title":"Getting Started","text":"Load rcromwell Set Cromwell server URL recognized rcromwell Set Authorization HTTP header used rcromwell HTTP requests now able interact Cromwell server authentication details retrieved via proofr package!","code":"library(rcromwell) library(httr) cromwell_config(cromwell_url) httr::set_config(proof_header())"},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"interact-with-the-cromwell-server","dir":"Articles","previous_headings":"","what":"Interact with the Cromwell server","title":"Getting Started","text":"Now, check version Cromwell server","code":"cromwell_version()"},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"done","dir":"Articles","previous_headings":"","what":"Done!","title":"Getting Started","text":"’re now setup interact Cromwell server. See rcromwell package docs get started.","code":""},{"path":"http://getwilds.org/proofr/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Scott Chamberlain. Author, maintainer.","code":""},{"path":"http://getwilds.org/proofr/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Chamberlain S (2024). proofr: Client PROOF API. R package version 0.0.0.91http://getwilds.org/proofr/ (website) https://github.com/getwilds/proofr (devel), http://getwilds.org/proofr/ (website)https://github.com/getwilds/proofr (devel).","code":"@Manual{, title = {proofr: Client for the PROOF API}, author = {Scott Chamberlain}, year = {2024}, note = {R package version 0.0.0.91http://getwilds.org/proofr/ (website) https://github.com/getwilds/proofr (devel)}, url = {http://getwilds.org/proofr/ (website) https://github.com/getwilds/proofr (devel)}, }"},{"path":"http://getwilds.org/proofr/index.html","id":"proofr","dir":"","previous_headings":"","what":"Client for the PROOF API","title":"Client for the PROOF API","text":"R client PROOF API PROOF API https://github.com/FredHutch/proof-api","code":""},{"path":"http://getwilds.org/proofr/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Client for the PROOF API","text":"can install development version proofr GitHub :","code":"# install.packages(\"pak\") pak::pak(\"getwilds/proofr\")"},{"path":"http://getwilds.org/proofr/index.html","id":"get-started","dir":"","previous_headings":"","what":"Get started","title":"Client for the PROOF API","text":"get started proofr, see Getting Started vignette.","code":""},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":null,"dir":"Reference","previous_headings":"","what":"Authenticate with PROOF API — proof_authenticate","title":"Authenticate with PROOF API — proof_authenticate","text":"Authenticate PROOF API","code":""},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Authenticate with PROOF API — proof_authenticate","text":"","code":"proof_authenticate(username, password)"},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Authenticate with PROOF API — proof_authenticate","text":"username (character) HutchNet username password (character) HutchNet password","code":""},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Authenticate with PROOF API — proof_authenticate","text":"single token (character) bearer authentication PROOF API","code":""},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Authenticate with PROOF API — proof_authenticate","text":"","code":"# Sys.getenv(\"PROOF_TOKEN\") # x <- proof_authenticate() # Sys.getenv(\"PROOF_TOKEN\")"},{"path":"http://getwilds.org/proofr/reference/proof_cancel.html","id":null,"dir":"Reference","previous_headings":"","what":"Cancel/stop PROOF Cromwell server — proof_cancel","title":"Cancel/stop PROOF Cromwell server — proof_cancel","text":"Cancel/stop PROOF Cromwell server","code":""},{"path":"http://getwilds.org/proofr/reference/proof_cancel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cancel/stop PROOF Cromwell server — proof_cancel","text":"","code":"proof_cancel()"},{"path":"http://getwilds.org/proofr/reference/proof_cancel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cancel/stop PROOF Cromwell server — proof_cancel","text":"list single field: message (character)","code":""},{"path":"http://getwilds.org/proofr/reference/proof_cancel.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Cancel/stop PROOF Cromwell server — proof_cancel","text":"https://github.com/FredHutch/proof-api#delete-cromwell-server","code":""},{"path":"http://getwilds.org/proofr/reference/proof_header.html","id":null,"dir":"Reference","previous_headings":"","what":"Get header for PROOF API calls — proof_header","title":"Get header for PROOF API calls — proof_header","text":"Get header PROOF API calls","code":""},{"path":"http://getwilds.org/proofr/reference/proof_header.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get header for PROOF API calls — proof_header","text":"","code":"proof_header(token = NULL)"},{"path":"http://getwilds.org/proofr/reference/proof_header.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get header for PROOF API calls — proof_header","text":"token (character) PROOF API token. optional","code":""},{"path":"http://getwilds.org/proofr/reference/proof_header.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get header for PROOF API calls — proof_header","text":"request S3 class HTTP header can passed httr::GET(), httr::POST(), etc.","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":null,"dir":"Reference","previous_headings":"","what":"Start PROOF Cromwell server — proof_start","title":"Start PROOF Cromwell server — proof_start","text":"Start PROOF Cromwell server","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Start PROOF Cromwell server — proof_start","text":"","code":"proof_start(pi_name = NULL)"},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Start PROOF Cromwell server — proof_start","text":"pi_name (character) PI name form last_f; needed user one SLURM account","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Start PROOF Cromwell server — proof_start","text":"list fields: job_id (character) info (character)","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Start PROOF Cromwell server — proof_start","text":"return PROOF/Cromwell server URL, periodically call proof_status(), wait email PROOF API","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Start PROOF Cromwell server — proof_start","text":"https://github.com/FredHutch/proof-api#post-cromwell-server","code":""},{"path":"http://getwilds.org/proofr/reference/proof_status.html","id":null,"dir":"Reference","previous_headings":"","what":"Get PROOF API job status - is job running, what's its URL... — proof_status","title":"Get PROOF API job status - is job running, what's its URL... — proof_status","text":"Get PROOF API job status - job running, URL...","code":""},{"path":"http://getwilds.org/proofr/reference/proof_status.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get PROOF API job status - is job running, what's its URL... — proof_status","text":"","code":"proof_status()"},{"path":"http://getwilds.org/proofr/reference/proof_status.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get PROOF API job status - is job running, what's its URL... — proof_status","text":"list fields: canJobStart (logical): can job make Cromwell server started? FALSE server already running; TRUE server running jobStatus (character): status job controls Cromwell server. e.g., \"RUNNING\". NULL server running cromwellUrl (character): URL Cromwell server. NULL server running jobInfo (list): metadata Cromwell server. slots NULL server running","code":""},{"path":"http://getwilds.org/proofr/reference/proof_status.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Get PROOF API job status - is job running, what's its URL... — proof_status","text":"https://github.com/FredHutch/proof-api#get-cromwell-server","code":""},{"path":"http://getwilds.org/proofr/reference/proofr-package.html","id":null,"dir":"Reference","previous_headings":"","what":"proofr: Client for the PROOF API — proofr-package","title":"proofr: Client for the PROOF API — proofr-package","text":"Client PROOF API.","code":""},{"path":[]},{"path":"http://getwilds.org/proofr/reference/proofr-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"proofr: Client for the PROOF API — proofr-package","text":"Maintainer: Scott Chamberlain sachamber@fredhutch.org (ORCID)","code":""}]