From e73d8d8111162c9988d86c344bfad747a4a84020 Mon Sep 17 00:00:00 2001
From: Patrick Kalita <pkalita@lbl.gov>
Date: Fri, 19 Apr 2024 16:14:20 -0700
Subject: [PATCH] Update file and folder structure of GO REF generated pages

---
 _config.yml                        | 3 ++-
 _includes/goref_toc_list_item.html | 6 +++++-
 _layouts/goref.html                | 2 +-
 gorefs.html                        | 6 ------
 4 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/_config.yml b/_config.yml
index 423a4966..df692334 100644
--- a/_config.yml
+++ b/_config.yml
@@ -84,4 +84,5 @@ algolia:
 page_gen:
   - data: gorefs
     template: goref
-    name: id
+    dir: GO_REF
+    name_expr: "record['id'].sub('GO_REF:', '')"
diff --git a/_includes/goref_toc_list_item.html b/_includes/goref_toc_list_item.html
index 8f16bf16..4ac86e7f 100644
--- a/_includes/goref_toc_list_item.html
+++ b/_includes/goref_toc_list_item.html
@@ -1,5 +1,9 @@
 <li>
-    <a class="u-margin-bottom-xsmall" href="{{ include.goref.id | datapage_url: 'gorefs' }}">
+    {% comment %} This href must be kept in sync with page_gen settings in _config.yaml {% endcomment %}
+    <a
+        class="u-margin-bottom-xsmall"
+        href="{{ '/GO_REF/' | append: include.goref.id | replace: 'GO_REF:', '' | relative_url }}"
+    >
         [{{ include.goref.id }}] {{ include.goref.title }}
     </a>
 </li>
diff --git a/_layouts/goref.html b/_layouts/goref.html
index f05a3bfc..a5ba5181 100644
--- a/_layouts/goref.html
+++ b/_layouts/goref.html
@@ -4,7 +4,7 @@
 
 <div class="container">
     <div class="u-margin-bottom-medium">
-        <a href="{{ '/gorefs.html' | relative_url }}">
+        <a href="{{ '/gorefs' | relative_url }}">
             <i class="fa fa-chevron-left" aria-hidden="true"></i>
             All GO REFs
         </a>
diff --git a/gorefs.html b/gorefs.html
index 97dff685..0dd5bdf8 100644
--- a/gorefs.html
+++ b/gorefs.html
@@ -1,10 +1,4 @@
 ---
-# Note that when developing locally, this page must be reached by visiting /gorefs.html. Without
-# the .html extension (/gorefs), an index page for the gorefs directory generated by the
-# jekyll-datapage-generator plugin will be displayed instead. This is a quirk of the Jekyll
-# development web server. When deployed on GitHub pages, this page will be available at /gorefs
-# without the .html extension.
-
 layout: default
 ---