Merge pull request #143 from usegalaxy-au/dev

Export embedded snippets

webapp/home/lab_export.py

@@ -1,10 +1,10 @@
 """Exported landing pages to be requested by external Galaxy servers.
 
 Example with local YAML:
-http://127.0.0.1:8000/landing/export?content_root=http://127.0.0.1:8000/static/home/labs/genome/main.yml
+http://127.0.0.1:8000/landing/export?content_root=http://127.0.0.1:8000/static/home/labs/genome/base.yml
 
 Example URL with remote YAML:
-http://127.0.0.1:8000/landing/export?content_root=https://raw.githubusercontent.com/usegalaxy-au/galaxy-media-site/dev/webapp/home/static/home/labs/genome/main.yml
+http://127.0.0.1:8000/landing/export?content_root=https://raw.githubusercontent.com/usegalaxy-au/galaxy-media-site/dev/webapp/home/static/home/labs/genome/base.yml
 
 """
 

webapp/home/labs/docs/base.yml

@@ -1,6 +1,6 @@
 # Default spec for an exported subsite landing page
 
-# You can test with: /lab/export?content_root=https://raw.githubusercontent.com/usegalaxy-au/galaxy-media-site/dev/webapp/home/labs/docs/main.yml
+# You can test with: /lab/export?content_root=https://raw.githubusercontent.com/usegalaxy-au/galaxy-media-site/dev/webapp/home/labs/docs/base.yml
 
 site_name: Antarctica
 lab_name: Galaxy Lab Pages

webapp/home/labs/docs/templates/intro.html

@@ -14,11 +14,11 @@
     </li>
     <li>
       See a full working example of an exported Galaxy Lab page
-      <a href="/lab/export?content_root=http://{{ HOSTNAME }}/static/home/labs/genome/main.yml">here</a>.
+      <a href="/lab/export?content_root=http://{{ HOSTNAME }}/static/home/labs/genome/base.yml">here</a>.
     </li>
     <li>
       See a minimal working example of a lab page
-      <a href="/lab/export?content_root=http://{{ HOSTNAME }}/static/home/labs/simple/main.yml">here</a>.
+      <a href="/lab/export?content_root=http://{{ HOSTNAME }}/static/home/labs/simple/base.yml">here</a>.
     </li>
   </ul>
 
@@ -48,8 +48,8 @@ <h2 class="accordion-header" id="headingOne">
             <ul>
               <li>
                 The root of your site's content should be a YAML file - see
-                <a href="https://github.com/usegalaxy-au/galaxy-media-site/tree/dev/webapp/home/labs/docs/main.yml" target="_blank">
-                  main.yml
+                <a href="https://github.com/usegalaxy-au/galaxy-media-site/tree/dev/webapp/home/labs/docs/base.yml" target="_blank">
+                  base.yml
                 </a>
                 for the content root of this page.
               </li>
@@ -59,16 +59,16 @@ <h2 class="accordion-header" id="headingOne">
                 For example, we can explicitly request this page with:
                 <br>
                 <small>
-                  <a href="/lab/export?content_root=https://raw.githubusercontent.com/usegalaxy-au/galaxy-media-site/dev/webapp/home/labs/docs/main.yml" target="_blank">
-                    http://{{ HOSTNAME }}/lab/export?content_root=https://raw.githubusercontent.com/usegalaxy-au/galaxy-media-site/dev/webapp/home/labs/docs/main.yml
+                  <a href="/lab/export?content_root=https://raw.githubusercontent.com/usegalaxy-au/galaxy-media-site/dev/webapp/home/labs/docs/base.yml" target="_blank">
+                    http://{{ HOSTNAME }}/lab/export?content_root=https://raw.githubusercontent.com/usegalaxy-au/galaxy-media-site/dev/webapp/home/labs/docs/base.yml
                   </a>
                 </small>
               </li>
               <li>
                 The web server will fetch your content from GitHub (or anywhere on the internet) and render it into this page.
               </li>
               <li>
-                Note that <code>main.yml</code> points to other files (YAML, HTML, CSS and images), which are located in the same remote directory (e.g. on GitHub). You can template the entire page with these files!
+                Note that <code>base.yml</code> points to other files (YAML, HTML, CSS and images), which are located in the same remote directory (e.g. on GitHub). You can template the entire page with these files!
               </li>
               <li>
                 The most useful part of this machinery is the <code>sections</code> content, which populates the tool/workflow sections below.
@@ -110,7 +110,7 @@ <h2 class="accordion-header" id="headingTwo">
                 <br>
                 <small>
                   <code>
-                    http://{{ HOSTNAME }}/lab/export?content_root=https://raw.githubusercontent.com/myusername/myrepo/path/to/content/main.yml
+                    http://{{ HOSTNAME }}/lab/export?content_root=https://raw.githubusercontent.com/myusername/myrepo/path/to/content/base.yml
                   </code>
                 </small>
               </li>
@@ -204,7 +204,7 @@ <h5 class="modal-title">Galaxy {{ site_name }}</h5>
     $(`#${id}`).append(exportInfoButton);
   }
   $(document).ready(function() {
-    addHoverInfo('headerSection', 'main.yml');
+    addHoverInfo('headerSection', 'base.yml');
     addHoverInfo('introSection', 'templates/intro.html');
     addHoverInfo('section_1Section', 'section_1.yml');
     addHoverInfo('section_2Section', 'section_2.yml');

webapp/home/labs/genome/base.yml

@@ -1,8 +1,8 @@
 # Test this locally with:
-# http://127.0.0.1:8000/lab/export?content_root=http://localhost:8000/static/home/labs/genome/main.yml
+# http://127.0.0.1:8000/lab/export?content_root=http://localhost:8000/static/home/labs/genome/base.yml
 
 # Request this on site.usegalaxy.org.au with:
-# https://site.usegalaxy.org.au/lab/export?content_root=https://site.usegalaxy.org.au/static/home/labs/genome/main.yml
+# https://site.usegalaxy.org.au/lab/export?content_root=https://site.usegalaxy.org.au/static/home/labs/genome/base.yml
 
 # Check out the documentation for building exported labs:
 # https://site.usegalaxy.org.au/lab/export

webapp/home/labs/proteomics/base.yml

@@ -1,8 +1,8 @@
 # Test this locally with:
-# http://127.0.0.1:8000/lab/export?content_root=http://localhost:8000/static/home/labs/proteomics/main.yml
+# http://127.0.0.1:8000/lab/export?content_root=http://localhost:8000/static/home/labs/proteomics/base.yml
 
 # Request this on site.usegalaxy.org.au with:
-# https://site.usegalaxy.org.au/lab/export?content_root=https://site.usegalaxy.org.au/static/home/labs/proteomics/main.yml
+# https://site.usegalaxy.org.au/lab/export?content_root=https://site.usegalaxy.org.au/static/home/labs/proteomics/base.yml
 
 # Check out the documentation for building exported labs:
 # https://site.usegalaxy.org.au/lab/export
@@ -30,9 +30,9 @@ footer_md: templates/footer.html
 #   1. Relative to this file URL
 #   2. Full URL to fetch globally centralized content
 sections:
-  - data.yml
-  - conversion_modification.yml
-  - database_searching.yml
-  - dda_standardised_tools.yml
-  - dia_standardised_tools.yml
-  - dda_tmt.yml
+  - sections/data.yml
+  - sections/conversion_modification.yml
+  - sections/database_searching.yml
+  - sections/dda_standardised_tools.yml
+  - sections/dia_standardised_tools.yml
+  - sections/dda_tmt.yml

webapp/home/labs/proteomics/templates/intro.html

@@ -39,29 +39,18 @@
     </div>
 
     <div class="col">
-      <a class="text-danger" href="">
-        <table>
-          <tr>
-            <td>
-              <span class="material-icons px-3" style="font-size: 3rem;">change_circle</span>
-            </td>
-            <td>
-              MS data file format converters
-            </td>
-          </tr>
-        </table>
-      </a>
-    </div>
-
-    <div class="col">
-      <a class="text-danger" href="">
+      <a
+        href="#"
+        data-bs-toggle="modal"
+        data-bs-target="#sharedHistoryModal"
+      >
         <table>
           <tr>
             <td>
               <span class="material-icons px-3" style="font-size: 3rem;">account_tree</span>
             </td>
             <td>
-              MS reference data on Galaxy
+              Shared proteomics histories
             </td>
           </tr>
         </table>
@@ -100,3 +89,50 @@ <h5 class="modal-title">Galaxy {{ site_name }}</h5>
     </div>
   </div>
 </div>
+
+
+<div class="modal fade" id="sharedHistoryModal" tabindex="-1">
+  <div class="modal-dialog modal-lg">
+    <div class="modal-content">
+      <div class="modal-header">
+        <h5 class="modal-title">Galaxy {{ site_name }} Shared Histories</h5>
+        <button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
+      </div>
+      <div class="modal-body">
+        <p>
+          This set of proteomics-specific shared histories contain test or demo data for software available on Proteomics Lab. You can copy these histories directly to your account on Galaxy, making it faster to get started!
+        </p>
+
+        <table class="table table-striped">
+          <tr>
+            <td>
+              Demo data for LFQanalyst and TMTanalyst.
+            </td>
+            <td>
+              <a class="btn btn-primary text-nowrap" href="https://usegalaxy.org.au/u/mike/h/lfq-and-tmt">
+                View history
+              </a>
+            </td>
+          </tr>
+          <tr>
+            <td>
+              Example data provided for the "MaxQuant and MSstats for the analysis of label-free data" Galaxy Training Network (GTN) tutorial, which is available
+              <a href="https://gxy.io/GTN:T00219">here</a>.
+            </td>
+            <td>
+              <a
+                class="btn btn-primary text-nowrap"
+                href="https://usegalaxy.org.au/u/johan/h/maxquant-and-msstats-for-the-analysis-of-label-free-data-1"
+              >
+                View history
+              </a>
+            </td>
+          </tr>
+        </table>
+      </div>
+      <div class="modal-footer">
+        <button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
+      </div>
+    </div>
+  </div>
+</div>

webapp/home/labs/simple/main.yml → webapp/home/labs/simple/base.yml

@@ -1,6 +1,6 @@
 # Default spec for an exported subsite landing page
 
-# You can test with: /lab/export?content_root=https://raw.githubusercontent.com/usegalaxy-au/galaxy-media-site/dev/webapp/home/labs/docs/main.yml
+# You can test with: /lab/export?content_root=https://raw.githubusercontent.com/usegalaxy-au/galaxy-media-site/dev/webapp/home/labs/docs/base.yml
 
 site_name: Archaeology
 lab_name: Archaeology Lab

webapp/home/static/home/css/embedded.css

@@ -0,0 +1,6 @@
+body {
+  padding: 1rem;
+}
+footer {
+  margin-top: 100px;
+}

webapp/home/templates/embed-snippet.html

@@ -0,0 +1,12 @@
+{% extends 'home/header-export.html' %}
+
+{% load static %}
+
+{% block head %}
+<link rel="stylesheet" href="{% static 'home/css/embedded.css' %}">
+{% endblock %}
+
+
+{% block content %}
+{% include snippet_path %}
+{% endblock %}

webapp/home/tests.py

@@ -30,7 +30,7 @@
     'Report statistics from sequencing reads',
     'Assemble Nanopore long reads.',
 )
-TEST_LAB_CONTENT_URL = f'{MOCK_LAB_BASE_URL}/static/home/labs/docs/main.yml'
+TEST_LAB_CONTENT_URL = f'{MOCK_LAB_BASE_URL}/static/home/labs/docs/base.yml'
 TEST_LAB_URL = f'/lab/export?content_root={TEST_LAB_CONTENT_URL}'
 
 

webapp/home/urls.py

@@ -29,6 +29,10 @@
          api.validate_institutional_email,
          name="validate_institutional_email"),
 
+    # Arbitrary HTML snippets
+    re_path(r'^embed\/([\S\/]+\.html)', views.embed_snippet,
+            name='embed_snippet'),
+
     # Arbitrary *.html / *.md pages
     re_path(r'^[\w\d\_-]+\.(?:html|md)$', views.page, name='html_pages'),
 

webapp/home/views.py

@@ -309,3 +309,16 @@ def custom_400(request, exception, template_name="400.html"):
     return render(request, template_name, {
         'exc': exception,
     }, status=400)
+
+
+def embed_snippet(request, snippet_path):
+    """Serve an embeddable snippet."""
+    try:
+        if 'snippets' not in snippet_path:
+            raise Http404
+        return render(request, 'embed-snippet.html', {
+            'title': 'Galaxy Media - embedded snippet',
+            'snippet_path': snippet_path,
+        })
+    except TemplateDoesNotExist:
+        raise Http404

webapp/webapp/settings/base.py

@@ -38,7 +38,7 @@
 LOG_ROOT = ensure_dir(BASE_DIR / 'webapp/logs')
 RECIPIENT_MASTER_CSV = BASE_DIR / '../scripts/mail/recipient_records.csv'
 DEFAULT_EXPORTED_LAB_CONTENT_ROOT = (
-    f'http://{HOSTNAME}/static/home/labs/docs/main.yml'
+    f'http://{HOSTNAME}/static/home/labs/docs/base.yml'
 )
 
 # Hostnames