From 5be8e1d38927581e61cbf94b24ca2c154d3d2396 Mon Sep 17 00:00:00 2001
From: Cameron Hyde <chyde@neoformit.com>
Date: Fri, 27 Sep 2024 13:40:22 +1000
Subject: [PATCH] Refactor labs with "communities" as root folder

---
 .../genome => communities/genome/lab}/CONTRIBUTORS  |   0
 .../genome/lab}/annotation.yml                      |   0
 .../genome => communities/genome/lab}/assembly.yml  |   0
 .../genome => communities/genome/lab}/base.yml      |   0
 .../genome => communities/genome/lab}/data.yml      |   0
 .../genome/lab}/static/annotation-overview.png      | Bin
 .../genome/lab}/static/assembly-overview.png        | Bin
 .../genome/lab}/static/custom.css                   |   0
 .../genome/lab}/static/logo.png                     | Bin
 .../genome/lab}/templates/conclusion.html           |   0
 .../genome/lab}/templates/footer.html               |   0
 .../genome/lab}/templates/intro.html                |   2 +-
 .../genome/lab}/usegalaxy.org.au.yml                |   0
 .../lab}/usegalaxy.org.au/templates/conclusion.html |   0
 .../lab}/usegalaxy.org.au/templates/footer.html     |   0
 .../lab}/usegalaxy.org.au/templates/intro.html      |   0
 .../proteomics/lab}/CONTRIBUTORS                    |   0
 .../proteomics/lab}/base.yml                        |   0
 .../lab}/sections/conversion_modification.yml       |   0
 .../proteomics/lab}/sections/data.yml               |   0
 .../proteomics/lab}/sections/database_searching.yml |   0
 .../lab}/sections/dda_standardised_tools.yml        |   0
 .../proteomics/lab}/sections/dda_tmt.yml            |   0
 .../lab}/sections/dia_standardised_tools.yml        |   0
 .../proteomics/lab}/static/custom.css               |   0
 .../proteomics/lab}/static/logo.png                 | Bin
 .../proteomics/lab}/templates/conclusion.html       |   0
 .../proteomics/lab}/templates/footer.html           |   0
 .../proteomics/lab}/templates/intro.html            |   2 +-
 .../proteomics/lab}/usegalaxy.org.au.yml            |   0
 .../lab}/usegalaxy.org.au/templates/conclusion.html |   0
 .../lab}/usegalaxy.org.au/templates/footer.html     |   0
 {subdomains => labs}/assets/site-switcher.png       | Bin
 labs/genome                                         |   1 +
 labs/proteomics                                     |   1 +
 35 files changed, 4 insertions(+), 2 deletions(-)
 rename {subdomains/genome => communities/genome/lab}/CONTRIBUTORS (100%)
 rename {subdomains/genome => communities/genome/lab}/annotation.yml (100%)
 rename {subdomains/genome => communities/genome/lab}/assembly.yml (100%)
 rename {subdomains/genome => communities/genome/lab}/base.yml (100%)
 rename {subdomains/genome => communities/genome/lab}/data.yml (100%)
 rename {subdomains/genome => communities/genome/lab}/static/annotation-overview.png (100%)
 rename {subdomains/genome => communities/genome/lab}/static/assembly-overview.png (100%)
 rename {subdomains/genome => communities/genome/lab}/static/custom.css (100%)
 rename {subdomains/genome => communities/genome/lab}/static/logo.png (100%)
 rename {subdomains/genome => communities/genome/lab}/templates/conclusion.html (100%)
 rename {subdomains/genome => communities/genome/lab}/templates/footer.html (100%)
 rename {subdomains/genome => communities/genome/lab}/templates/intro.html (94%)
 rename {subdomains/genome => communities/genome/lab}/usegalaxy.org.au.yml (100%)
 rename {subdomains/genome => communities/genome/lab}/usegalaxy.org.au/templates/conclusion.html (100%)
 rename {subdomains/genome => communities/genome/lab}/usegalaxy.org.au/templates/footer.html (100%)
 rename {subdomains/genome => communities/genome/lab}/usegalaxy.org.au/templates/intro.html (100%)
 rename {subdomains/proteomics => communities/proteomics/lab}/CONTRIBUTORS (100%)
 rename {subdomains/proteomics => communities/proteomics/lab}/base.yml (100%)
 rename {subdomains/proteomics => communities/proteomics/lab}/sections/conversion_modification.yml (100%)
 rename {subdomains/proteomics => communities/proteomics/lab}/sections/data.yml (100%)
 rename {subdomains/proteomics => communities/proteomics/lab}/sections/database_searching.yml (100%)
 rename {subdomains/proteomics => communities/proteomics/lab}/sections/dda_standardised_tools.yml (100%)
 rename {subdomains/proteomics => communities/proteomics/lab}/sections/dda_tmt.yml (100%)
 rename {subdomains/proteomics => communities/proteomics/lab}/sections/dia_standardised_tools.yml (100%)
 rename {subdomains/proteomics => communities/proteomics/lab}/static/custom.css (100%)
 rename {subdomains/proteomics => communities/proteomics/lab}/static/logo.png (100%)
 rename {subdomains/proteomics => communities/proteomics/lab}/templates/conclusion.html (100%)
 rename {subdomains/proteomics => communities/proteomics/lab}/templates/footer.html (100%)
 rename {subdomains/proteomics => communities/proteomics/lab}/templates/intro.html (97%)
 rename {subdomains/proteomics => communities/proteomics/lab}/usegalaxy.org.au.yml (100%)
 rename {subdomains/proteomics => communities/proteomics/lab}/usegalaxy.org.au/templates/conclusion.html (100%)
 rename {subdomains/proteomics => communities/proteomics/lab}/usegalaxy.org.au/templates/footer.html (100%)
 rename {subdomains => labs}/assets/site-switcher.png (100%)
 create mode 120000 labs/genome
 create mode 120000 labs/proteomics

diff --git a/subdomains/genome/CONTRIBUTORS b/communities/genome/lab/CONTRIBUTORS
similarity index 100%
rename from subdomains/genome/CONTRIBUTORS
rename to communities/genome/lab/CONTRIBUTORS
diff --git a/subdomains/genome/annotation.yml b/communities/genome/lab/annotation.yml
similarity index 100%
rename from subdomains/genome/annotation.yml
rename to communities/genome/lab/annotation.yml
diff --git a/subdomains/genome/assembly.yml b/communities/genome/lab/assembly.yml
similarity index 100%
rename from subdomains/genome/assembly.yml
rename to communities/genome/lab/assembly.yml
diff --git a/subdomains/genome/base.yml b/communities/genome/lab/base.yml
similarity index 100%
rename from subdomains/genome/base.yml
rename to communities/genome/lab/base.yml
diff --git a/subdomains/genome/data.yml b/communities/genome/lab/data.yml
similarity index 100%
rename from subdomains/genome/data.yml
rename to communities/genome/lab/data.yml
diff --git a/subdomains/genome/static/annotation-overview.png b/communities/genome/lab/static/annotation-overview.png
similarity index 100%
rename from subdomains/genome/static/annotation-overview.png
rename to communities/genome/lab/static/annotation-overview.png
diff --git a/subdomains/genome/static/assembly-overview.png b/communities/genome/lab/static/assembly-overview.png
similarity index 100%
rename from subdomains/genome/static/assembly-overview.png
rename to communities/genome/lab/static/assembly-overview.png
diff --git a/subdomains/genome/static/custom.css b/communities/genome/lab/static/custom.css
similarity index 100%
rename from subdomains/genome/static/custom.css
rename to communities/genome/lab/static/custom.css
diff --git a/subdomains/genome/static/logo.png b/communities/genome/lab/static/logo.png
similarity index 100%
rename from subdomains/genome/static/logo.png
rename to communities/genome/lab/static/logo.png
diff --git a/subdomains/genome/templates/conclusion.html b/communities/genome/lab/templates/conclusion.html
similarity index 100%
rename from subdomains/genome/templates/conclusion.html
rename to communities/genome/lab/templates/conclusion.html
diff --git a/subdomains/genome/templates/footer.html b/communities/genome/lab/templates/footer.html
similarity index 100%
rename from subdomains/genome/templates/footer.html
rename to communities/genome/lab/templates/footer.html
diff --git a/subdomains/genome/templates/intro.html b/communities/genome/lab/templates/intro.html
similarity index 94%
rename from subdomains/genome/templates/intro.html
rename to communities/genome/lab/templates/intro.html
index 67c8467a..9460cb1b 100644
--- a/subdomains/genome/templates/intro.html
+++ b/communities/genome/lab/templates/intro.html
@@ -24,7 +24,7 @@ <h5 class="modal-title">Galaxy {{ site_name }}</h5>
 
           <div class="my-3">
             Switch between sites quickly using the dropdown in Galaxy {{ site_name }}'s main navigation bar (note, if your Galaxy server does not have this, please request that they install the "Site Switcher" plugin from Galaxy Australia):
-            <img class="w-100 my-3 mx-auto" src="https://github.com/galaxyproject/galaxy-codex/blob/main/subdomains/assets/site-switcher.png?raw=true" alt="Switch site button">
+            <img class="w-100 my-3 mx-auto" src="https://github.com/galaxyproject/galaxy-codex/blob/main/labs/assets/site-switcher.png?raw=true" alt="Switch site button">
           </div>
 
           <p><a class="ga-btn" href="{{ galaxy_base_url }}" target="_blank">Take me back to Galaxy {{ site_name }}</a></p>
diff --git a/subdomains/genome/usegalaxy.org.au.yml b/communities/genome/lab/usegalaxy.org.au.yml
similarity index 100%
rename from subdomains/genome/usegalaxy.org.au.yml
rename to communities/genome/lab/usegalaxy.org.au.yml
diff --git a/subdomains/genome/usegalaxy.org.au/templates/conclusion.html b/communities/genome/lab/usegalaxy.org.au/templates/conclusion.html
similarity index 100%
rename from subdomains/genome/usegalaxy.org.au/templates/conclusion.html
rename to communities/genome/lab/usegalaxy.org.au/templates/conclusion.html
diff --git a/subdomains/genome/usegalaxy.org.au/templates/footer.html b/communities/genome/lab/usegalaxy.org.au/templates/footer.html
similarity index 100%
rename from subdomains/genome/usegalaxy.org.au/templates/footer.html
rename to communities/genome/lab/usegalaxy.org.au/templates/footer.html
diff --git a/subdomains/genome/usegalaxy.org.au/templates/intro.html b/communities/genome/lab/usegalaxy.org.au/templates/intro.html
similarity index 100%
rename from subdomains/genome/usegalaxy.org.au/templates/intro.html
rename to communities/genome/lab/usegalaxy.org.au/templates/intro.html
diff --git a/subdomains/proteomics/CONTRIBUTORS b/communities/proteomics/lab/CONTRIBUTORS
similarity index 100%
rename from subdomains/proteomics/CONTRIBUTORS
rename to communities/proteomics/lab/CONTRIBUTORS
diff --git a/subdomains/proteomics/base.yml b/communities/proteomics/lab/base.yml
similarity index 100%
rename from subdomains/proteomics/base.yml
rename to communities/proteomics/lab/base.yml
diff --git a/subdomains/proteomics/sections/conversion_modification.yml b/communities/proteomics/lab/sections/conversion_modification.yml
similarity index 100%
rename from subdomains/proteomics/sections/conversion_modification.yml
rename to communities/proteomics/lab/sections/conversion_modification.yml
diff --git a/subdomains/proteomics/sections/data.yml b/communities/proteomics/lab/sections/data.yml
similarity index 100%
rename from subdomains/proteomics/sections/data.yml
rename to communities/proteomics/lab/sections/data.yml
diff --git a/subdomains/proteomics/sections/database_searching.yml b/communities/proteomics/lab/sections/database_searching.yml
similarity index 100%
rename from subdomains/proteomics/sections/database_searching.yml
rename to communities/proteomics/lab/sections/database_searching.yml
diff --git a/subdomains/proteomics/sections/dda_standardised_tools.yml b/communities/proteomics/lab/sections/dda_standardised_tools.yml
similarity index 100%
rename from subdomains/proteomics/sections/dda_standardised_tools.yml
rename to communities/proteomics/lab/sections/dda_standardised_tools.yml
diff --git a/subdomains/proteomics/sections/dda_tmt.yml b/communities/proteomics/lab/sections/dda_tmt.yml
similarity index 100%
rename from subdomains/proteomics/sections/dda_tmt.yml
rename to communities/proteomics/lab/sections/dda_tmt.yml
diff --git a/subdomains/proteomics/sections/dia_standardised_tools.yml b/communities/proteomics/lab/sections/dia_standardised_tools.yml
similarity index 100%
rename from subdomains/proteomics/sections/dia_standardised_tools.yml
rename to communities/proteomics/lab/sections/dia_standardised_tools.yml
diff --git a/subdomains/proteomics/static/custom.css b/communities/proteomics/lab/static/custom.css
similarity index 100%
rename from subdomains/proteomics/static/custom.css
rename to communities/proteomics/lab/static/custom.css
diff --git a/subdomains/proteomics/static/logo.png b/communities/proteomics/lab/static/logo.png
similarity index 100%
rename from subdomains/proteomics/static/logo.png
rename to communities/proteomics/lab/static/logo.png
diff --git a/subdomains/proteomics/templates/conclusion.html b/communities/proteomics/lab/templates/conclusion.html
similarity index 100%
rename from subdomains/proteomics/templates/conclusion.html
rename to communities/proteomics/lab/templates/conclusion.html
diff --git a/subdomains/proteomics/templates/footer.html b/communities/proteomics/lab/templates/footer.html
similarity index 100%
rename from subdomains/proteomics/templates/footer.html
rename to communities/proteomics/lab/templates/footer.html
diff --git a/subdomains/proteomics/templates/intro.html b/communities/proteomics/lab/templates/intro.html
similarity index 97%
rename from subdomains/proteomics/templates/intro.html
rename to communities/proteomics/lab/templates/intro.html
index 89e30a5d..253193b1 100644
--- a/subdomains/proteomics/templates/intro.html
+++ b/communities/proteomics/lab/templates/intro.html
@@ -93,7 +93,7 @@ <h5 class="modal-title">Galaxy {{ site_name }} {{ lab_name }}</h5>
           and {{ lab_name }}
           (<a href="galaxy_base_url">{{ subdomain }}.{{ root_domain }}</a>)
           is easy - look for the icon in the top navigation bar to switch between sites:
-          <img class="w-100 my-3 mx-auto" src="https://github.com/galaxyproject/galaxy-codex/blob/main/subdomains/assets/site-switcher.png?raw=true" alt="Switch site button">
+          <img class="w-100 my-3 mx-auto" src="https://github.com/galaxyproject/galaxy-codex/blob/main/labs/assets/site-switcher.png?raw=true" alt="Switch site button">
         </p>
 
         {% if site_name == 'Australia' %}
diff --git a/subdomains/proteomics/usegalaxy.org.au.yml b/communities/proteomics/lab/usegalaxy.org.au.yml
similarity index 100%
rename from subdomains/proteomics/usegalaxy.org.au.yml
rename to communities/proteomics/lab/usegalaxy.org.au.yml
diff --git a/subdomains/proteomics/usegalaxy.org.au/templates/conclusion.html b/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html
similarity index 100%
rename from subdomains/proteomics/usegalaxy.org.au/templates/conclusion.html
rename to communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html
diff --git a/subdomains/proteomics/usegalaxy.org.au/templates/footer.html b/communities/proteomics/lab/usegalaxy.org.au/templates/footer.html
similarity index 100%
rename from subdomains/proteomics/usegalaxy.org.au/templates/footer.html
rename to communities/proteomics/lab/usegalaxy.org.au/templates/footer.html
diff --git a/subdomains/assets/site-switcher.png b/labs/assets/site-switcher.png
similarity index 100%
rename from subdomains/assets/site-switcher.png
rename to labs/assets/site-switcher.png
diff --git a/labs/genome b/labs/genome
new file mode 120000
index 00000000..257b6474
--- /dev/null
+++ b/labs/genome
@@ -0,0 +1 @@
+../communities/genome/lab
\ No newline at end of file
diff --git a/labs/proteomics b/labs/proteomics
new file mode 120000
index 00000000..c05c4e68
--- /dev/null
+++ b/labs/proteomics
@@ -0,0 +1 @@
+../communities/proteomics/lab
\ No newline at end of file