From 56a52c708e3d6a74d9cc59b5ec4898fb86a37cc0 Mon Sep 17 00:00:00 2001
From: Cameron Hyde <chyde@neoformit.com>
Date: Tue, 15 Oct 2024 07:49:18 +1000
Subject: [PATCH 1/6] Refactor header-cards component to use embedded snippet

---
 .../lab/usegalaxy.org.au/templates/conclusion.html       | 9 ++++++++-
 .../lab/usegalaxy.org.au/templates/footer.html           | 1 -
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html b/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html
index c097223b..97e27194 100644
--- a/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html
+++ b/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html
@@ -1 +1,8 @@
-{% include 'home/snippets/header-cards.html' %}
+<iframe id="headerCardsIframe" style="width: 100%; height" src="https://site.usegalaxy.org.au/embed/home/snippets/header-cards.html"></iframe>
+<script>
+  window.addEventListener("message", function(event) {
+    const iframe = document.getElementById('headerCardsIframe');
+    const height = event.data.height + 'px';
+    iframe.style.height = height;
+  }, false);
+</script>
diff --git a/communities/proteomics/lab/usegalaxy.org.au/templates/footer.html b/communities/proteomics/lab/usegalaxy.org.au/templates/footer.html
index 259d18e6..579c69a3 100644
--- a/communities/proteomics/lab/usegalaxy.org.au/templates/footer.html
+++ b/communities/proteomics/lab/usegalaxy.org.au/templates/footer.html
@@ -3,7 +3,6 @@
   window.addEventListener("message", function(event) {
     const iframe = document.getElementById('footerIframe');
     const height = event.data.height + 'px';
-    console.log('Set footer height:', height);
     iframe.style.height = height;
   }, false);
 </script>

From d68b58d88917388e1c0668a32d45f2c547ba5fe9 Mon Sep 17 00:00:00 2001
From: Cameron Hyde <chyde@neoformit.com>
Date: Tue, 15 Oct 2024 07:56:11 +1000
Subject: [PATCH 2/6] Remove hard-coded "Australia"

---
 .../genome/lab/usegalaxy.org.au/templates/conclusion.html     | 2 +-
 communities/proteomics/lab/templates/intro.html               | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/communities/genome/lab/usegalaxy.org.au/templates/conclusion.html b/communities/genome/lab/usegalaxy.org.au/templates/conclusion.html
index 13e7d771..54382373 100644
--- a/communities/genome/lab/usegalaxy.org.au/templates/conclusion.html
+++ b/communities/genome/lab/usegalaxy.org.au/templates/conclusion.html
@@ -35,7 +35,7 @@ <h5 class="modal-title">Feedback</h5>
         <div class="modal-body">
           <div class="default-content">
             <p>
-              We'd love to hear your feedback on the Galaxy Australia {{ site_name }}. Please let us know what
+              We'd love to hear your feedback on the Galaxy {{ site_name }} {{ lab_name }}. Please let us know what
               you think!
             </p>
             <div class="mb-3">
diff --git a/communities/proteomics/lab/templates/intro.html b/communities/proteomics/lab/templates/intro.html
index 253193b1..9f38fa35 100644
--- a/communities/proteomics/lab/templates/intro.html
+++ b/communities/proteomics/lab/templates/intro.html
@@ -8,7 +8,7 @@
     What is this page?
   </a>
   <p>
-    Welcome to the {{ site_name }} {{ lab_name }}. Get quick access to the
+    Welcome to the Galaxy {{ site_name }} {{ lab_name }}. Get quick access to the
     tools, workflows and tutorials you need to get started with proteomics on
     Galaxy.
   </p>
@@ -17,7 +17,7 @@
     This page is currently under development in consultation with the
     <a href="https://www.biocommons.org.au/proteomics-community" target="_blank">
       Australian Proteomics Bioinformatics community</a>.
-    </p>
+  </p>
 </section>
 
 <hr>

From 796b783929cdc6ea3a3bdaa4fcf194af50d5add1 Mon Sep 17 00:00:00 2001
From: Cameron Hyde <chyde@neoformit.com>
Date: Tue, 15 Oct 2024 08:01:03 +1000
Subject: [PATCH 3/6] Hide overflow

---
 .../lab/usegalaxy.org.au/templates/conclusion.html          | 6 ++----
 .../proteomics/lab/usegalaxy.org.au/templates/footer.html   | 6 ++----
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html b/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html
index 97e27194..5cff8f40 100644
--- a/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html
+++ b/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html
@@ -1,8 +1,6 @@
-<iframe id="headerCardsIframe" style="width: 100%; height" src="https://site.usegalaxy.org.au/embed/home/snippets/header-cards.html"></iframe>
+<iframe id="headerCardsIframe" style="width: 100%; overflow: hidden;" src="https://site.usegalaxy.org.au/embed/home/snippets/header-cards.html"></iframe>
 <script>
   window.addEventListener("message", function(event) {
-    const iframe = document.getElementById('headerCardsIframe');
-    const height = event.data.height + 'px';
-    iframe.style.height = height;
+    document.getElementById('footerIframe').style.height = event.data.height + 'px';
   }, false);
 </script>
diff --git a/communities/proteomics/lab/usegalaxy.org.au/templates/footer.html b/communities/proteomics/lab/usegalaxy.org.au/templates/footer.html
index 579c69a3..b6244fdd 100644
--- a/communities/proteomics/lab/usegalaxy.org.au/templates/footer.html
+++ b/communities/proteomics/lab/usegalaxy.org.au/templates/footer.html
@@ -1,8 +1,6 @@
-<iframe id="footerIframe" style="width: 100%;" src="https://site.usegalaxy.org.au/embed/home/snippets/footer.html"></iframe>
+<iframe id="footerIframe" style="width: 100%; overflow: hidden;" src="https://site.usegalaxy.org.au/embed/home/snippets/footer.html"></iframe>
 <script>
   window.addEventListener("message", function(event) {
-    const iframe = document.getElementById('footerIframe');
-    const height = event.data.height + 'px';
-    iframe.style.height = height;
+    document.getElementById('footerIframe').style.height = event.data.height + 'px';
   }, false);
 </script>

From f3f39c22e416ff3c0275a8af8e4d313f2af2f59f Mon Sep 17 00:00:00 2001
From: Cameron Hyde <chyde@neoformit.com>
Date: Tue, 15 Oct 2024 08:04:33 +1000
Subject: [PATCH 4/6] Fix header-cards ID

---
 .../proteomics/lab/usegalaxy.org.au/templates/conclusion.html   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html b/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html
index 5cff8f40..d9388170 100644
--- a/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html
+++ b/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html
@@ -1,6 +1,6 @@
 <iframe id="headerCardsIframe" style="width: 100%; overflow: hidden;" src="https://site.usegalaxy.org.au/embed/home/snippets/header-cards.html"></iframe>
 <script>
   window.addEventListener("message", function(event) {
-    document.getElementById('footerIframe').style.height = event.data.height + 'px';
+    document.getElementById('headerCardsIframe').style.height = event.data.height + 'px';
   }, false);
 </script>

From 41db5902fb3dec2011efd60174e40374921e89f4 Mon Sep 17 00:00:00 2001
From: Cameron Hyde <chyde@neoformit.com>
Date: Tue, 15 Oct 2024 08:43:32 +1000
Subject: [PATCH 5/6] Set overflow hidden in iframe URL

---
 .../proteomics/lab/usegalaxy.org.au/templates/conclusion.html   | 2 +-
 .../proteomics/lab/usegalaxy.org.au/templates/footer.html       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html b/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html
index d9388170..d11a7fc9 100644
--- a/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html
+++ b/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html
@@ -1,4 +1,4 @@
-<iframe id="headerCardsIframe" style="width: 100%; overflow: hidden;" src="https://site.usegalaxy.org.au/embed/home/snippets/header-cards.html"></iframe>
+<iframe id="headerCardsIframe" style="width: 100%;" src="https://site.usegalaxy.org.au/embed/home/snippets/header-cards.html?overflow=hidden"></iframe>
 <script>
   window.addEventListener("message", function(event) {
     document.getElementById('headerCardsIframe').style.height = event.data.height + 'px';
diff --git a/communities/proteomics/lab/usegalaxy.org.au/templates/footer.html b/communities/proteomics/lab/usegalaxy.org.au/templates/footer.html
index b6244fdd..be87c78e 100644
--- a/communities/proteomics/lab/usegalaxy.org.au/templates/footer.html
+++ b/communities/proteomics/lab/usegalaxy.org.au/templates/footer.html
@@ -1,4 +1,4 @@
-<iframe id="footerIframe" style="width: 100%; overflow: hidden;" src="https://site.usegalaxy.org.au/embed/home/snippets/footer.html"></iframe>
+<iframe id="footerIframe" style="width: 100%;" src="https://site.usegalaxy.org.au/embed/home/snippets/footer.html?overflow=hidden"></iframe>
 <script>
   window.addEventListener("message", function(event) {
     document.getElementById('footerIframe').style.height = event.data.height + 'px';

From 82aa52e3a6bae61b03d9fb72972d1847c8fde260 Mon Sep 17 00:00:00 2001
From: Cameron Hyde <chyde@neoformit.com>
Date: Tue, 15 Oct 2024 09:13:36 +1000
Subject: [PATCH 6/6] Fix genome lab image src URLs

---
 communities/genome/lab/annotation.yml | 2 +-
 communities/genome/lab/assembly.yml   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/communities/genome/lab/annotation.yml b/communities/genome/lab/annotation.yml
index e693290a..e6086761 100644
--- a/communities/genome/lab/annotation.yml
+++ b/communities/genome/lab/annotation.yml
@@ -312,7 +312,7 @@ tabs:
           <p>
             The flowchart below shows how you might use your input data (in green) with different Galaxy tools (in blue) to annotate a genome assembly. For example, one pathway would be taking an assembled genome, plus information about repeats, and data from RNA-seq, to run in the Maker pipeline. The annotatations can then be viewed in JBrowse.
           </p>
-          <img class="img-fluid" src="/static/home/labs/genome/static/annotation-overview.png" alt="Genome annotation flowchart">
+          <img class="img-fluid" src="./static/annotation-overview.png" alt="Genome annotation flowchart">
           <p class="text-center">
             A graphical representation of genome annotation
           </p>
diff --git a/communities/genome/lab/assembly.yml b/communities/genome/lab/assembly.yml
index fcd13631..19ffd1b3 100644
--- a/communities/genome/lab/assembly.yml
+++ b/communities/genome/lab/assembly.yml
@@ -331,7 +331,7 @@ tabs:
             <li>Assessment - at any stage, the assembly can be assessed for number of contigs, number of base pairs, whether expected genes are present, and many other metrics.</li>
             <li>Annotation - identify features on the genome assembly such as gene names and locations.</li>
           </ul>
-          <img class="img-fluid" src="/static/home/labs/genome/static/assembly-overview.png" alt="Genome assembly flowchart">
+          <img class="img-fluid" src="./static/assembly-overview.png" alt="Genome assembly flowchart">
           <p class="text-center">
             A graphical representation of genome assembly
           </p>