From 65208226f5fbc0a37512977cb6ecc0f63be6cea5 Mon Sep 17 00:00:00 2001
From: Henry Luetcke <hluetcke@ethz.ch>
Date: Mon, 5 Aug 2024 13:58:48 +0200
Subject: [PATCH] change code formatting style
---
RRP-User-Documentation.html | 12 ++++++------
rrp-docs.md | 8 +++++---
2 files changed, 11 insertions(+), 9 deletions(-)
diff --git a/RRP-User-Documentation.html b/RRP-User-Documentation.html
index 165acf1..4928466 100644
--- a/RRP-User-Documentation.html
+++ b/RRP-User-Documentation.html
@@ -278,10 +278,10 @@ Selected datasets are mounted directly on the RRP server for read-only
access. To specify which datasets should be mounted, add a folder called
<code>.rrp</code> to your Git repository. In this folder, add a file
called <code>datasets.yaml</code> with following content:</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">server-url</span><span class="kw">:</span><span class="at"> </span><span class="st">"https://openbis-xyz.ethz.ch/"</span></span>
-<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">destinations</span><span class="kw">:</span></span>
-<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="at"> </span><span class="fu">"input"</span><span class="kw">:</span></span>
-<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="at"> </span><span class="kw">-</span><span class="at"> </span><span class="st">"20220425184271099-1234"</span></span></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode numberSource yaml number-lines"><code class="sourceCode yaml"><span id="cb1-1"><a href="#cb1-1"></a><span class="fu">server-url</span><span class="kw">:</span><span class="at"> </span><span class="st">"https://openbis-xyz.ethz.ch/"</span></span>
+<span id="cb1-2"><a href="#cb1-2"></a><span class="fu">destinations</span><span class="kw">:</span></span>
+<span id="cb1-3"><a href="#cb1-3"></a><span class="at"> </span><span class="fu">"input"</span><span class="kw">:</span></span>
+<span id="cb1-4"><a href="#cb1-4"></a><span class="at"> </span><span class="kw">-</span><span class="at"> </span><span class="st">"20220425184271099-1234"</span></span></code></pre></div>
<ul>
<li>server-url is the adress of the openBIS server</li>
<li>under destinations, provide a list of openBIS permIDs for datasets
@@ -309,10 +309,10 @@ with JupyterLab</h2>
Your project, with Status: not running.</li>
<li>Select the “Play†button to start the project. Status will switch to
“processing†and then to “runningâ€.</li>
-<li>Select the “Launch†button to start JupyterLab / RStudio in a new
+<li>Select the “Launch†button to start the JupyterLab UI in a new
browser tab / window.</li>
<li>You can now work as usual with your project either in the JupyterLab
-or RStudio UI.</li>
+UI.</li>
<li>The repository content is available in the folder
<code>project</code>.</li>
<li>Mounted openBIS datasets are available in the folder
diff --git a/rrp-docs.md b/rrp-docs.md
index d274486..38d99e9 100644
--- a/rrp-docs.md
+++ b/rrp-docs.md
@@ -7,12 +7,14 @@
## Mounting openBIS datasets
RRP projects can access datasets stored in the openBIS server. Selected datasets are mounted directly on the RRP server for read-only access. To specify which datasets should be mounted, add a folder called `.rrp` to your Git repository. In this folder, add a file called `datasets.yaml` with following content:
-```yaml
+
+```{.yaml .number-lines}
server-url: "https://openbis-xyz.ethz.ch/"
destinations:
"input":
- "20220425184271099-1234"
```
+
- server-url is the adress of the openBIS server
- under destinations, provide a list of openBIS permIDs for datasets to be mounted by RRP
@@ -27,8 +29,8 @@ It is also possible to add datasets to be mounted in the RRP UI once a project h
## Starting a project and working with JupyterLab
1. Once the build of the project is complete, it will be listed under Your project, with Status: not running.
2. Select the "Play" button to start the project. Status will switch to "processing" and then to "running".
-3. Select the "Launch" button to start JupyterLab / RStudio in a new browser tab / window.
-4. You can now work as usual with your project either in the JupyterLab or RStudio UI.
+3. Select the "Launch" button to start the JupyterLab UI in a new browser tab / window.
+4. You can now work as usual with your project either in the JupyterLab UI.
5. The repository content is available in the folder `project`.
6. Mounted openBIS datasets are available in the folder `openbis`.
7. Results to be uploaded back to openBIS can be stored in the folder `results` (see below).
--
GitLab