Merge pull request #17 from usegalaxy-au/dev

Labs engine fixes

ansible/roles/galaxy_labs_engine/tasks/certbot.yml

@@ -31,12 +31,12 @@
 
     - name: Request SSL certificate with certbot
       shell: >
-        docker compose --profile certbot run --rm certbot certonly \
-          --webroot                                                \
-          --webroot-path /var/www/certbot/                         \
-          --agree-tos                                              \
-          --non-interactive                                        \
-          -d "{{ certbot_domain }}"                                \
+        docker compose --profile certbot run --rm certbot-init certonly \
+          --webroot                                                     \
+          --webroot-path /var/www/certbot/                              \
+          --agree-tos                                                   \
+          --non-interactive                                             \
+          -d "{{ certbot_domain }}"                                     \
           -m "{{ certbot_renew_email }}"
       args:
         chdir: "{{ config_root }}"
@@ -53,7 +53,7 @@
         name: "certbot-renew"
         minute: "0"
         hour: "0"
-        job: "docker compose --profile certbot run --rm certbot renew"
+        job: "cd {{ config_root }} && docker compose --profile certbot run --rm certbot renew"
       tags: certbot
 
   always:

app/labs/lab_export.py

@@ -16,7 +16,7 @@
 from bs4 import BeautifulSoup, MarkupResemblesLocatorWarning
 from django.conf import settings
 from markdown2 import Markdown
-from pydantic import ValidationError
+from pydantic import BaseModel, ValidationError
 
 from types import SimpleNamespace
 from utils.exceptions import LabBuildError
@@ -75,15 +75,19 @@ def validate(self):
 
     def _validate_sections(self):
         """Validate sections against Pydantic schema."""
+        validated_sections = []
         for section in self['sections']:
             try:
-                LabSectionSchema(**section)
+                validated_sections.append(
+                    LabSectionSchema(**section).model_dump()
+                )
             except ValidationError as e:
                 raise LabBuildError(
                     e,
                     section_id=section["id"],
                     source='YAML',
                 )
+        self['sections'] = validated_sections
 
     def _get(
         self,
@@ -167,7 +171,7 @@ def _fetch_yaml_context(self):
         context = self._fetch_yaml_content(self.content_root, extend=False)
 
         if not self.content_root.endswith('base.yml'):
-            # Attempt to extend base.yml with self.content_root
+            # Attempt to extend base.yml with the given content_root
             base_content_url = (self.parent_url + 'base.yml')
             base_context = self._fetch_yaml_content(
                 base_content_url, ignore_404=True, extend=False)
@@ -176,7 +180,7 @@ def _fetch_yaml_context(self):
                 context = base_context
 
         try:
-            LabSchema(**context)
+            context = LabSchema(**context).model_dump()
         except ValidationError as exc:
             raise LabBuildError(exc, url=self.content_root, source='YAML')
 
@@ -216,6 +220,11 @@ def is_excluded_item(item):
                     for item in data
                     if not is_excluded_item(item)
                 ]
+            elif isinstance(data, BaseModel):
+                data = {
+                    k: filter_excluded_items(v)
+                    for k, v in data.model_dump().items()
+                }
             return data
 
         if self.get('root_domain'):

app/labs/lab_schema.py

@@ -98,10 +98,11 @@ def validate_md(cls, value):
 class LabSectionSchema(BaseModel):
     """Validate Galaxy Lab section."""
     id: str
+    title: str
     tabs: list[SectionTab]
 
 
-class LabSchema(BaseModel):
+class LabSchema(BaseModel, extra='allow'):
     """Validate Galaxy Lab content."""
     site_name: str
     lab_name: str

app/labs/static/labs/css/labs.css

@@ -90,4 +90,22 @@ ul.nav-pills li.nav-item {
   color: white;
   background-color: #25537B;
   padding: 0.25rem 0.5rem;
-}
+}
+
+@media screen and (max-width: 850px) {
+  .lab-header {
+    font-size: 3.5rem;
+  }
+}
+
+@media screen and (max-width: 768px) {
+  .lab-header {
+    font-size: 3rem;
+  }
+}
+
+@media screen and (max-width: 650px) {
+  .lab-header {
+    font-size: 2.5rem;
+  }
+}

app/labs/static/labs/js/load-fonts.js

@@ -0,0 +1,20 @@
+// Load material icons and display when page has loaded
+if ('fonts' in document) {
+  document.fonts.ready.then(() => {
+    $('.material-icons').css({
+      'opacity': 1,
+      'max-width': 'unset',
+      'overflow': 'visible'
+    });
+  }).catch((error) => {
+    console.error('Font loading failed:', error);
+  });
+} else {
+  // Fallback for browsers that don't support document.fonts
+  console.warn('Font API not supported in this browser.');
+  $('.material-icons').css({
+    'opacity': 1,
+    'max-width': 'unset',
+    'overflow': 'visible'
+  });
+}

app/labs/templates/labs/components/accordion.html

@@ -26,7 +26,7 @@ <h2 class="accordion-header" id="{{ section.id }}-{{ tab_id }}-{{ forloop.counte
           <div class="col">
             {{ item.description_md|markdown }}
             {% if item.inputs %}
-            {% include 'labs//components/inputs.html' with inputs=item.inputs %}
+            {% include 'labs/components/inputs.html' with inputs=item.inputs %}
             {% endif %}
           </div>
 

app/labs/templates/labs/components/section.html

@@ -41,10 +41,10 @@ <h4 class="mb-3">{{ section.title }}</h4>
           {% if tab.content.subsections %}
             {% for subsection in tab.content.subsections %}
             <p class="fw-bold my-3 mt-4 mx-3">{{ subsection.title }}</p>
-            {% include 'labs//components/accordion.html' with content=subsection.content tab_id=tab.id accordion_id=subsection.id %}
+            {% include 'labs/components/accordion.html' with content=subsection.content tab_id=tab.id accordion_id=subsection.id %}
             {% endfor %}
           {% else %}
-            {% include 'labs//components/accordion.html' with content=tab.content tab_id=tab.id %}
+            {% include 'labs/components/accordion.html' with content=tab.content tab_id=tab.id %}
           {% endif %}
         </div>
       </div>

app/labs/templates/labs/exported.html

@@ -27,7 +27,7 @@
 
 <main>
 
-  {% include 'labs//components/gtn-modal.html' %}
+  {% include 'labs/components/gtn-modal.html' %}
 
   <section id="headerSection" class="lab-header d-flex align-items-center h-100">
     {% if snippets.header_logo %}
@@ -41,22 +41,22 @@
   {% endif %}
 
   {% for section in sections %}
-    {% include 'labs//components/section.html' with section=section %}
+    {% include 'labs/components/section.html' with section=section %}
   {% endfor %}
 
   {% if snippets.conclusion_md %}
   {{ snippets.conclusion_md|markdown }}
   {% endif %}
 
   {% if contributors %}
-  {% include 'labs//components/contributors.html' %}
+  {% include 'labs/components/contributors.html' %}
   {% endif %}
 
 </main>
 
 
 {% if feedback_email %}
-{% include 'labs//components/feedback-modal.html' %}
+{% include 'labs/components/feedback-modal.html' %}
 {% endif %}
 
 

app/labs/templates/labs/header.html

@@ -7,7 +7,6 @@
     {% include 'labs/snippets/head.html' %}
     <title> {% if title %}{{ title }}{% else %}Galaxy - data analysis for everyone{% endif %} </title>
     {% include 'labs/snippets/imports.html' %}
-    {% include 'labs/snippets/posthog.html' %}
 
     {% block head %}
     {% endblock %}
@@ -30,17 +29,8 @@
     {% block script %}
     {% endblock %}
 
+    <script src="{% static 'labs/js/load-fonts.js' %}"></script>
     <script type="text/javascript">
-
-      // Load material icons and display when page has loaded
-      document.fonts.onloadingdone = () => {
-        $('.material-icons').css({
-          'opacity': 1,
-          'max-width': 'unset',
-          'overflow': 'visible'
-        });
-      }
-
       $(document).ready( () => {
         // Enable bootstrap tooltips
         var tooltipTriggerList = [].slice.call(document.querySelectorAll('[data-bs-toggle="tooltip"]'))

docker-compose.yml

@@ -92,7 +92,7 @@ services:
       - /etc/letsencrypt:/etc/letsencrypt:ro
     restart: always
 
-  certbot:
+  certbot-init:
     profiles:
       - certbot
     depends_on:
@@ -103,6 +103,17 @@ services:
       - /var/www/certbot:/var/www/certbot:rw
       - /etc/letsencrypt:/etc/letsencrypt:rw
 
+  certbot:
+    profiles:
+      - certbot
+    # depends_on:  # N.B. certbot depends on nginx but it's usually running and
+    #   - nginx    # causes a container name collision
+    image: certbot/certbot:latest
+    container_name: certbot
+    volumes:
+      - /var/www/certbot:/var/www/certbot:rw
+      - /etc/letsencrypt:/etc/letsencrypt:rw
+
 networks:
   labs-engine-network:
     driver: bridge