Merge branch 'main' into new-boxes2

CONTRIBUTORS.yaml

@@ -265,6 +265,10 @@ charitylaw:
     name: Charity Law
     joined: 2018-09
 
+chensy96:
+    name: Siyu Chen
+    joined: 2022-05
+
 Chinonyemildred:
     name: Chinonye Mildred Egenti
     joined: 2021-10
@@ -324,6 +328,10 @@ cstritt:
     name: Christoph Stritt
     joined: 2022-03
 
+davidsalgado:
+    name: David Salgado
+    joined: 2022-10
+
 danielabutano:
     name: Daniela Butano
     joined: 2019-09
@@ -724,6 +732,11 @@ khanteymoori:
     orcid: 0000-0001-6811-9196
     joined: 2019-07
 
+Khaled196:
+    name: Khaled Jum'ah
+    email: [email protected]
+    joined: 2022-09
+
 KlemensFroehlich:
     name: Klemens Fröhlich
     joined: 2021-08
@@ -1059,6 +1072,11 @@ pcm32:
     name: Pablo Moreno
     joined: 2019-06
 
+plushz:
+    name: Polina Polunina
+    gitter: PlushZ
+    joined: 2022-03
+
 polkhe:
     name: Ekaterina Polkh
     joined: 2017-09
@@ -1247,6 +1265,10 @@ tealiie:
     name: tealiie
     joined: 2017-09
 
+teresa-m:
+    name: Teresa Müller
+    joined: 2022-09
+
 themudo:
     name: Gonçalo Themudo
     joined: 2021-10
@@ -1338,7 +1360,7 @@ wee-snufkin:
     name: Julia Jakiela
     email: [email protected]
     joined: 2022-06
-
+    
 willdurand:
     name: William Durand
     joined: 2017-09
@@ -1421,6 +1443,14 @@ elixir-europe:
     funder: true
     #funding_statement: |
 
+
+epsrc-training-grant:
+    name: EPSRC Training Grant DTP 2020-2021 Open University
+    joined: 2022-09
+    funder: true
+    funding_statement: The research internship was supported through EPSRC Training Grant DTP 2020-2021 Open University
+
 elixir-goblet-ttt:
     name: ELIXIR Goblet Train the Trainers
     joined: 2022-09
+

_layouts/topic.html

@@ -55,20 +55,26 @@ <h3 id="st-{{ subtopic.title | slugify }}">{{ subtopic.title}}</h3>
             {% endif %}
           {% endfor %}
 
-          {% assign other_tutorials = topic_material | where: "subtopic",
-nil %}
-          {% unless other_tutorials.size == 0 %}
+          <!--  show the catch-all "other" subtopic if there are (enabled) tutorials not assigned to any subtoppic -->
+          {% assign other_tutorials = topic_material | where: "subtopic", nil %}
+          {% assign other_tutorials_enabled = topic_material | where: "subtopic", nil | where_exp: "tutorial", "tutorial.enable != false" %}
+          {% assign show_other = true %}
+          {% if other_tutorials.size == 0 %} {% assign show_other = false %}{% endif %}
+          {% if jekyll.environment == "production" and other_tutorials_enabled.size == 0 %} {% assign show_other = false %}{% endif %}
+
+          {% if show_other %}
+          </br>
           <div id="tutorial_list">
           <h3> Other </h3>
           <div class="search_box">
             {% icon search %}
             <input data-search-type="tutorial_title" class="search" id="tutorial_search" placeholder="Search" />
             <span id="clear_search" title="Clear filters"> {% icon galaxy-cross %} </span>
           </div></br>
-          Assorted other tutorials </br></br>
+          Assorted tutorials </br></br>
           {% include _includes/tutorial_list.html sub="other" %}
           </div>
-          {% endunless %}
+          {% endif %}
 
         {% else %}
            {% include _includes/tutorial_list.html %}

_plugins/snippet.rb

@@ -70,7 +70,6 @@ def render(context)
             if lang != "en" and lang != "es"
               lang = "en"
             end
-
             if box_type != 'none' and !box_type.nil?
               box_id, box_title = Gtn::Boxify.generate_title(box_type, metadata['title'], lang, context.registers[:page]['path'])
               box_start = '> ' + box_title

bin/schema-faq.yaml

@@ -44,6 +44,7 @@ mapping:
             - question
             - comment
             - warning
+            - details
             - none
         description: |
             The type of box that should be used when rendering this FAQ. Use `none` if it should not be in a box, but just plain text.

bin/workflow_to_tool_yaml.sh

@@ -10,9 +10,10 @@ do
         echo " - Tutorial: $tutorial"
         if [ -d "${tutorial}/workflows" ]
         then
-            wf_files=$(find "${tutorial}/workflows/" -name '*.ga' | wc -l)
-            if (( wf_files > 0 )); then
-                workflow-to-tools -w "${tutorial}/workflows/*.ga" -o "${tutorial}/tools.yaml" -l "$(basename "${tutorial}")"
+            wf_files=$(find "${tutorial}/workflows/" -name '*.ga' | paste -sd " ")
+            num_wf_files=$(find "${tutorial}/workflows/" -name '*.ga' | wc -l)
+            if (( num_wf_files > 0 )); then
+                workflow-to-tools -w ${wf_files} -o "${tutorial}/tools.yaml" -l "$(basename "${tutorial}")"
                 echo "    ..done. Tool list in ${tutorial}/tools.yaml"
             else
                 echo "    No workflows to install (no files found)"

faqs/galaxy/galaxy_creating_an_account.md

@@ -8,12 +8,17 @@ contributors: [jennaj, bernandez, samanthaanjei]
 
 
 1. To create an account at any public Galaxy instance, choose your server from the available [list of Galaxy Platform](https://galaxyproject.org/use/).
-  There are 3 main public Galaxy servers: [UseGalaxy.org](https://usegalaxy.org/), [UseGalaxy.eu](https://usegalaxy.eu/), and [UseGalaxy.org.au](https://usegalaxy.org.au/).
+
+    There are 3 main public Galaxy servers: [UseGalaxy.org](https://usegalaxy.org/), [UseGalaxy.eu](https://usegalaxy.eu/), and [UseGalaxy.org.au](https://usegalaxy.org.au/).
+
 2. Click on **"Login or Register"** in the masthead on the server.
+
+    ![Login or Register on the top panel]({{site.baseurl}}/faqs/galaxy/images/login_register.png)
+
 3. Click on **Register here** and fill in the required information.
 4. Click on the **Create** button, your account is successfully created.
 5. Check for a **Confirmation Email** in the email you used for account creation.
 6. Click on the **Email confirmation link** to fully activate your account.
- 
+
 
 

faqs/galaxy/tutorial_mode.md

@@ -15,3 +15,4 @@ Tools are frequently updated to new versions. Your Galaxy may have multiple vers
   - Tool names in tutorials will be blue buttons that open the correct tool for you
   - **Note:** this does not work for all tutorials (yet)
   ![gif showing how GTN-in-Galaxy works]({% link /topics/contributing/images/88277962-ddda4a80-cce1-11ea-92cd-41b1df063db0.gif %})
+  - You can click anywhere in the grey-ed out area outside of the tutorial box to return back to the Galaxy analytical interface

feedback.md

@@ -143,17 +143,17 @@ layout: base
         {% assign fdbk_over_time_labels = fdbk_over_time_labels | push: f.name %}
     {% endfor %}
     {% assign fdbk_by_note = tn.items | sort:'note' | group_by: 'note' %}
-    <script>
-        var topic_data =
-        {
-            label: "{{ tn.name }}",
-            data: [{% for c in fdbk_over_time %}{x:"{{ fdbk_over_time_labels[forloop.index0] }}", y: {{ c }} } {% unless forloop.last %},{% endunless %}{% endfor %}],
-            fill: false,
-        };
-        fdbk_over_month['topic-{{ topic_name }}'] = [topic_data];
-        fdbk_over_month['all_topics'].push(topic_data);
-        data_notes['topic-{{ topic_name }}'] = [{% for n in (0..5) %}{% assign f_f_n = fdbk_by_note | where: "name",n | first %}{% if f_f_n.size == 0 %}0{% else %}{{ f_f_n.items | size }}{% endif %}{% unless forloop.last %},{% endunless %}{% endfor %}];
-    </script>
+<script>
+    var topic_data =
+    {
+        label: "{{ tn.name }}",
+        data: [{% for c in fdbk_over_time %}{x:"{{ fdbk_over_time_labels[forloop.index0] }}", y: {{ c }} } {% unless forloop.last %},{% endunless %}{% endfor %}],
+        fill: false,
+    };
+    fdbk_over_month['topic-{{ topic_name }}'] = [topic_data];
+    fdbk_over_month['all_topics'].push(topic_data);
+    data_notes['topic-{{ topic_name }}'] = [{% for n in (0..5) %}{% assign f_f_n = fdbk_by_note | where: "name",n | first %}{% if f_f_n.size == 0 %}0{% else %}{{ f_f_n.items | size }}{% endif %}{% unless forloop.last %},{% endunless %}{% endfor %}];
+</script>
 
     {% assign fdbk_by_tutorial = tn.items | group_by: 'tutorial' | sort: 'name' %}
     {% for tun in fdbk_by_tutorial %}
@@ -175,17 +175,17 @@ layout: base
                 {% assign fdbk_over_time_labels = fdbk_over_time_labels | push: f.name %}
             {% endfor %}
             {% assign fdbk_by_note = tun.items | sort:'note' | group_by: 'note' %}
-            <script>
-                var tuto_data =
-                {
-                    label: "{{ tun.name }}",
-                    data: [{% for c in fdbk_over_time %}{x:"{{ fdbk_over_time_labels[forloop.index0] }}", y: {{ c }} } {% unless forloop.last %},{% endunless %}{% endfor %}],
-                    fill: false,
-                };
-                fdbk_over_month['tuto-{{ tuto_name }}'] = [tuto_data];
-                fdbk_over_month['topic-{{ topic_name }}'].push(tuto_data);
-                data_notes['tuto-{{ tuto_name }}'] = [{% for n in (0..5) %}{% assign f_f_n = fdbk_by_note | where: "name",n | first %}{% if f_f_n.size == 0 %}0{% else %}{{ f_f_n.items | size }}{% endif %}{% unless forloop.last %},{% endunless %}{% endfor %}];
-            </script>
+<script>
+    var tuto_data =
+    {
+        label: "{{ tun.name }}",
+        data: [{% for c in fdbk_over_time %}{x:"{{ fdbk_over_time_labels[forloop.index0] }}", y: {{ c }} } {% unless forloop.last %},{% endunless %}{% endfor %}],
+        fill: false,
+    };
+    fdbk_over_month['tuto-{{ tuto_name }}'] = [tuto_data];
+    fdbk_over_month['topic-{{ topic_name }}'].push(tuto_data);
+    data_notes['tuto-{{ tuto_name }}'] = [{% for n in (0..5) %}{% assign f_f_n = fdbk_by_note | where: "name",n | first %}{% if f_f_n.size == 0 %}0{% else %}{{ f_f_n.items | size }}{% endif %}{% unless forloop.last %},{% endunless %}{% endfor %}];
+</script>
         {% endif %}
     {% endfor %}
 {% endfor %}
@@ -209,9 +209,9 @@ layout: base
                             <h5 class="card-title">{{ fdbk | size }} responses</h5>
                             {% assign chart_id = 'allFdbkOverMonthGraph' %}
                             <canvas id="{{ chart_id }}" width="400" height="400">
-                                <script>
-                                    drawFdbkOverMonthGraph("{{ chart_id }}", fdbk_over_month.all_topics);
-                                </script>
+<script>
+    drawFdbkOverMonthGraph("{{ chart_id }}", fdbk_over_month.all_topics);
+</script>
                             </canvas>
                         </div>
                     </div>
@@ -223,10 +223,10 @@ layout: base
                             <h5 class="card-title">Rating Distribution</h5>
                             {% assign chart_id = 'allFdbkNoteGraph' %}
                             <canvas id="{{ chart_id }}" width="400" height="400">
-                                <script>
-                                    drawFdbkNoteGraph("{{ chart_id }}", data_notes.all_topics, labels_notes);
-                                    var counter = 0;
-                                </script>
+<script>
+    drawFdbkNoteGraph("{{ chart_id }}", data_notes.all_topics, labels_notes);
+    var counter = 0;
+</script>
                             </canvas>
                         </div>
                     </div>
@@ -246,15 +246,15 @@ layout: base
                                 <h5 class="card-title">{{ tn.items | size }} responses</h5>
                                 {% assign chart_id = topic_name | append: '-topic-fdbkOverMonthGraph' %}
                                 <canvas id="{{ chart_id }}" width="400" height="400">
-                                    <script>
-                                        if ( counter > 4) {
-                                            window.addEventListener('DOMContentLoaded', (event) => {
-                                                drawFdbkOverMonthGraph("{{ chart_id }}", fdbk_over_month['topic-{{ topic_name }}']);
-                                            });
-                                        } else {
-                                            drawFdbkOverMonthGraph("{{ chart_id }}", fdbk_over_month['topic-{{ topic_name }}']);
-                                        }
-                                    </script>
+<script>
+    if ( counter > 4) {
+        window.addEventListener('DOMContentLoaded', (event) => {
+            drawFdbkOverMonthGraph("{{ chart_id }}", fdbk_over_month['topic-{{ topic_name }}']);
+        });
+    } else {
+        drawFdbkOverMonthGraph("{{ chart_id }}", fdbk_over_month['topic-{{ topic_name }}']);
+    }
+</script>
                                 </canvas>
                             </div>
                         </div>
@@ -266,16 +266,16 @@ layout: base
                                 <h5 class="card-title">Rating Distribution</h5>
                                 {% assign chart_id = topic_name | append: '-topic-fdbkNoteGraph' %}
                                 <canvas id="{{ chart_id }}" width="400" height="400">
-                                    <script>
-                                        if ( counter > 4) {
-                                            window.addEventListener('DOMContentLoaded', (event) => {
-                                                drawFdbkNoteGraph("{{ chart_id }}", data_notes['topic-{{ topic_name }}'], labels_notes);
-                                            });
-                                        } else {
-                                            drawFdbkNoteGraph("{{ chart_id }}", data_notes['topic-{{ topic_name }}'], labels_notes);
-                                        }
-                                        counter = counter + 1;
-                                    </script>
+<script>
+    if ( counter > 4) {
+        window.addEventListener('DOMContentLoaded', (event) => {
+            drawFdbkNoteGraph("{{ chart_id }}", data_notes['topic-{{ topic_name }}'], labels_notes);
+        });
+    } else {
+        drawFdbkNoteGraph("{{ chart_id }}", data_notes['topic-{{ topic_name }}'], labels_notes);
+    }
+    counter = counter + 1;
+</script>
                                 </canvas>
                             </div>
                         </div>
@@ -320,11 +320,11 @@ layout: base
                                                     <h5 class="card-title">{{ tun.items | size }} responses</h5>
                                                     {% assign chart_id = tuto_name | append: '-tutorial-fdbkOverMonthGraph' %}
                                                     <canvas id="{{ chart_id }}" width="400" height="400">
-                                                        <script>
-                                                            window.addEventListener('DOMContentLoaded', (event) => {
-                                                                drawFdbkOverMonthGraph("{{ chart_id }}", fdbk_over_month['tuto-{{ tuto_name }}']);
-                                                            });
-                                                        </script>
+<script>
+    window.addEventListener('DOMContentLoaded', (event) => {
+        drawFdbkOverMonthGraph("{{ chart_id }}", fdbk_over_month['tuto-{{ tuto_name }}']);
+    });
+</script>
                                                     </canvas>
                                                 </div>
                                             </div>
@@ -336,11 +336,11 @@ layout: base
                                                     <h5 class="card-title">Rating Distribution</h5>
                                                     {% assign chart_id = tuto_name | append: '-tutorial-fdbkNoteGraph' %}
                                                     <canvas id="{{ chart_id }}" width="400" height="400">
-                                                        <script>
-                                                            window.addEventListener('DOMContentLoaded', (event) => {
-                                                                drawFdbkNoteGraph("{{ chart_id }}", data_notes['tuto-{{ tuto_name }}'], labels_notes);
-                                                            });
-                                                        </script>
+<script>
+    window.addEventListener('DOMContentLoaded', (event) => {
+        drawFdbkNoteGraph("{{ chart_id }}", data_notes['tuto-{{ tuto_name }}'], labels_notes);
+    });
+</script>
                                                     </canvas>
                                                 </div>
                                             </div>
@@ -367,8 +367,8 @@ layout: base
                                                                     {% if f.pro != null or f.con != null %}
                                                                     <tr>
                                                                         <td>{{ f.date | date: "%b %-d, %Y"  }}</td>
-                                                                        <td>{{ f.pro }}</td>
-                                                                        <td>{{ f.con }}</td>
+                                                                        <td>{{ f.pro | xml_escape }}</td>
+                                                                        <td>{{ f.con | xml_escape }}</td>
                                                                     </tr>
                                                                     {% endif %}
                                                                 {% endif %}

quiz/poll.yaml

@@ -0,0 +1,17 @@
+title: Simple poll
+contributors:
+- hexylena
+
+questions:
+- title: What do you think?
+  answers:
+    - Amazing! I love it
+    - Neat!
+    - Meh
+    - Please remove this
+  correct:
+    - count(name)
+    - count(*)
+  timeout: 30
+  type: poll
+  live: true

topics/admin/tutorials/pulsar/tutorial.md

@@ -272,7 +272,7 @@ More information about the rabbitmq ansible role can be found [in the repository
 >       SelectTypeParameters: CR_CPU_Memory  # Allocate individual cores/memory instead of entire node
 >     
 >    +# RabbitMQ
->    +rabbitmq_version: 3.8.16-1
+>    +rabbitmq_version: 3.8.35-1
 >    +rabbitmq_plugins: rabbitmq_management
 >    +
 >    +rabbitmq_config:
@@ -306,6 +306,10 @@ More information about the rabbitmq ansible role can be found [in the repository
 >    ```
 >    {: data-commit="Configure RabbitMQ"}
 >
+>    > ### {% icon tip %} RabbitMQ installation errors?
+>    > RabbitMQ depends on specific Erlang versions. If the Erlang version has been updated, you may need to change the value of `rabbitmq_version:` in the configuration above. [Information on the RabbitMQ Erlag version requirements.](https://www.rabbitmq.com/which-erlang.html)
+>    {: .tip}
+>
 > 3. Update the Galaxy playbook to include the *usegalaxy_eu.rabbitmq* role.
 >
 >    {% raw %}