From 81430e17a0fe2349f865ada6625f513e1c816b25 Mon Sep 17 00:00:00 2001
From: Katherine Heal <katherine.heal@pnnl.gov>
Date: Mon, 16 Dec 2024 15:01:43 -0800
Subject: [PATCH] Modify lipid documentation per docu squad's request

---
 docs/README_LCMS_LIPID.md | 14 +++++++++-----
 docs/index_lipid.html     | 18 ++++++++++++------
 docs/index_lipid.rst      | 15 ++++++++++++---
 3 files changed, 33 insertions(+), 14 deletions(-)

diff --git a/docs/README_LCMS_LIPID.md b/docs/README_LCMS_LIPID.md
index 9814c61..04f7922 100644
--- a/docs/README_LCMS_LIPID.md
+++ b/docs/README_LCMS_LIPID.md
@@ -1,6 +1,10 @@
+github_url
+
+:   <https://github.com/microbiomedata/metaMS/blob/master/docs/index_lipid.rst>
+
 # Lipidomics Workflow (v1.0.0)
 
-![](lipid_workflow_v1.png)
+![](lipid_workflow_v1.svg)
 
 ## Workflow Overview
 
@@ -60,7 +64,9 @@ The in-silico lipid spectra in PNNL\'s Metaref database are generated
 from the LipidBlast database (v68), found at
 <https://systemsomicslab.github.io/compms/msdial/main.html>. Note that
 there is no retention time in the PNNL version of the database and the
-workflow does not use retention time scoring.
+workflow does not use retention time scoring. Currently the workflow
+uses a local copy of the database, but the database is available by
+request.
 
 ## Sample datasets
 
@@ -95,9 +101,7 @@ The following inputs are required (declared in the input json file):
 -   Workflow inputs
     -   CoreMS Parameter file (.toml)
     -   Scan Translator Parameter file (.toml)
-    -   MetabRef configuration key (metabref.token). See MetabRef
-        documentation (<https://metabref.emsl.pnnl.gov/api>) for how to
-        generate a token.
+    -   Path to local MetabRef database (.sqlite)
 -   Cores (optional input)
     -   How many cores to use for processing. Default is 1.
 
diff --git a/docs/index_lipid.html b/docs/index_lipid.html
index 952bc1d..de9741d 100644
--- a/docs/index_lipid.html
+++ b/docs/index_lipid.html
@@ -1,6 +1,13 @@
+<dl>
+<dt>github_url</dt>
+<dd>
+<p><a
+href="https://github.com/microbiomedata/metaMS/blob/master/docs/index_lipid.rst">https://github.com/microbiomedata/metaMS/blob/master/docs/index_lipid.rst</a></p>
+</dd>
+</dl>
 <h1 id="lipidomics-workflow-v1.0.0">Lipidomics Workflow (v1.0.0)</h1>
 <figure>
-<img src="lipid_workflow_v1.png" alt="lipid_workflow_v1.png" />
+<img src="lipid_workflow_v1.svg" alt="lipid_workflow_v1.svg" />
 </figure>
 <h2 id="workflow-overview">Workflow Overview</h2>
 <p>The liquid chromatography-mass spectrometry (LC-MS)-based lipidomics
@@ -51,7 +58,9 @@ <h3 id="database">Database</h3>
 from the LipidBlast database (v68), found at <a
 href="https://systemsomicslab.github.io/compms/msdial/main.html">https://systemsomicslab.github.io/compms/msdial/main.html</a>.
 Note that there is no retention time in the PNNL version of the database
-and the workflow does not use retention time scoring.</p>
+and the workflow does not use retention time scoring. Currently the
+workflow uses a local copy of the database, but the database is
+available by request.</p>
 <h2 id="sample-datasets">Sample datasets</h2>
 <ul>
 <li>An example dataset can be downloaded from here: <a
@@ -82,10 +91,7 @@ <h3 id="inputs">Inputs</h3>
 <ul>
 <li>CoreMS Parameter file (.toml)</li>
 <li>Scan Translator Parameter file (.toml)</li>
-<li>MetabRef configuration key (metabref.token). See MetabRef
-documentation (<a
-href="https://metabref.emsl.pnnl.gov/api">https://metabref.emsl.pnnl.gov/api</a>)
-for how to generate a token.</li>
+<li>Path to local MetabRef database (.sqlite)</li>
 </ul></li>
 <li>Cores (optional input)
 <ul>
diff --git a/docs/index_lipid.rst b/docs/index_lipid.rst
index 81ae927..f5ac25f 100644
--- a/docs/index_lipid.rst
+++ b/docs/index_lipid.rst
@@ -1,7 +1,15 @@
+:github_url: https://github.com/microbiomedata/metaMS/blob/master/docs/index_lipid.rst
+
+..
+   Note: The above `github_url` field is used to force the target of the "Edit on GitHub" link
+         to be the specified URL. That makes it so the link will work, regardless of the Sphinx
+         site the file is incorporated into. You can learn more about the `github_url` field at:
+         https://sphinx-rtd-theme.readthedocs.io/en/stable/configuring.html#confval-github_url
+
 Lipidomics Workflow (v1.0.0)
 ============================
 
-.. figure:: lipid_workflow_v1.png
+.. figure:: lipid_workflow_v1.svg
    :alt: diagram of lipid workflow
 
 Workflow Overview
@@ -60,7 +68,8 @@ Database
    (https://metabref.emsl.pnnl.gov/)
 
 The in-silico lipid spectra in PNNL's Metaref database are generated from the LipidBlast database (v68), found at https://systemsomicslab.github.io/compms/msdial/main.html.
-Note that there is no retention time in the PNNL version of the database and the workflow does not use retention time scoring.
+Note that there is no retention time in the PNNL version of the database and the workflow does not use retention time scoring.  
+Currently the workflow uses a local copy of the database, but the database is available by request.
 
 Sample datasets
 ---------------
@@ -95,7 +104,7 @@ The following inputs are required (declared in the input json file):
 -  Workflow inputs
    -  CoreMS Parameter file (.toml)
    -  Scan Translator Parameter file (.toml)
-   -  MetabRef configuration key (metabref.token). See MetabRef documentation (https://metabref.emsl.pnnl.gov/api) for how to generate a token.
+   -  Path to local MetabRef database (.sqlite)
 -  Cores (optional input)
    -  How many cores to use for processing. Default is 1.