Merge pull request #4881 from nomadscientist/header_example_history

GTN Header - Adding a Answer Key Histories drop-down menu
galaxyproject · May 13, 2024 · 48d0f4f · 48d0f4f
2 parents 2534da7 + 740a40e
commit 48d0f4f
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Showing 10 changed files with 149 additions and 3 deletions.
diff --git a/_config.yml b/_config.yml
@@ -128,6 +128,8 @@ icon-tag:
   galaxy-gear: fas fa-cog
   galaxy-history: fas fa-columns
   galaxy-history-archive: fas fa-archive
+  galaxy-history-input: fas fa-sign-in-alt
+  galaxy-history-answer: fas fa-sign-out-alt
   galaxy-home: fas fa-home
   galaxy-info: fas fa-info-circle
   galaxy-lab: fa fa-tv

diff --git a/_includes/resource-answer-histories.html b/_includes/resource-answer-histories.html
@@ -0,0 +1,21 @@
+{% if include.material.answer_histories %}
+    <a href="#" class="btn btn-default dropdown-toggle topic-icon" data-toggle="dropdown" aria-expanded="false" title="Answer Histories">
+        {% icon galaxy-history-answer %}{% if include.label %}&nbsp;Answer Histories{% endif %}
+    </a>
+    <ul class="dropdown-menu">
+      {% for key in include.material.answer_histories %}
+        <li>
+            <a class="dropdown-item" href="{{ key.history }}">
+              {{ key.label }}
+              {% if key.date %}
+              <br/><span class="text-muted">{{ key.date }}</span>
+              {% endif %}
+            </a>
+        </li>
+      {% endfor %}
+      <li class="dropdown-divider"></li>
+      <li>
+        <a class="dropdown-item" href="{{ site.baseurl }}/faqs/gtn/gtn_example_histories.html">{% icon help %} How to Use This</a>
+      </li>
+    </ul>
+{% endif %}
diff --git a/_includes/resource-input-histories.html b/_includes/resource-input-histories.html
@@ -0,0 +1,21 @@
+{% if include.material.input_histories %}
+    <a href="#" class="btn btn-default dropdown-toggle topic-icon" data-toggle="dropdown" aria-expanded="false" title="Input Histories">
+        {% icon galaxy-history-input %}{% if include.label %}&nbsp;Input Histories{% endif %}
+    </a>
+    <ul class="dropdown-menu">
+      {% for key in include.material.input_histories %}
+        <li>
+            <a class="dropdown-item" href="{{ key.history }}">
+              {{ key.label }}
+              {% if key.date %}
+              <br/><span class="text-muted">{{ key.date }}</span>
+              {% endif %}
+            </a>
+        </li>
+      {% endfor %}
+      <li class="dropdown-divider"></li>
+      <li>
+        <a class="dropdown-item" href="{{ site.baseurl }}/faqs/gtn/gtn_example_histories.html">{% icon help %} How to Use This</a>
+      </li>
+    </ul>
+{% endif %}
diff --git a/_layouts/tutorial_hands_on.html b/_layouts/tutorial_hands_on.html
@@ -128,6 +128,14 @@ <h4 class="alert-heading">Under Development!</h4>
                 <li class="btn btn-default supporting_material">{% include _includes/resource-tours.html material=own_material topic=topic.name label=true %}</li>
             {% endif %}
 
+            {% if own_material.input_histories %}
+                <li class="btn btn-default supporting_material">{% include _includes/resource-input-histories.html material=own_material topic=topic.name label=true %}</li>
+            {% endif %}
+
+            {% if own_material.answer_histories %}
+                <li class="btn btn-default supporting_material">{% include _includes/resource-answer-histories.html material=own_material topic=topic.name label=true %}</li>
+            {% endif %}
+
             {% if own_material.notebook %}
                 <li class="btn btn-default supporting_material">{% include _includes/resource-notebooks.html material=own_material topic=topic.name label=true %}</li>
             {% endif %}

diff --git a/bin/schema-tutorial.yaml b/bin/schema-tutorial.yaml
@@ -465,4 +465,31 @@ mapping:
             link to the external tutorial
         examples:
             - "https://docs.qiime2.org/jupyterbooks/cancer-microbiome-intervention-tutorial/index.html#"
-
+    answer_histories:
+        type: seq
+        examples: |
+          - label: "UseGalaxy.eu"
+            history: https://humancellatlas.usegalaxy.eu/u/j.jakiela/h/generating-a-single-cell-matrix-using-alevin-3
+          - label: "Older Alevin version"
+            history: https://humancellatlas.usegalaxy.eu/u/wendi.bacon.training/h/cs1pre-processing-with-alevin---answer-key
+        sequence:
+          - type: map
+            mapping: &answer_histories
+              label:
+                type: str
+                required: true
+              history:
+                type: str
+                required: true
+              date:
+                type: date
+                pattern: /[0-9]{4,}-[0-9]{2}-[0-9]{2}/
+    input_histories:
+        type: seq
+        examples: |
+          input_histories:
+            - label: "UseGalaxy.eu"
+              history: https://humancellatlas.usegalaxy.eu/u/wendi.bacon.training/h/cs1pre-processing-with-alevin---input-1
+        sequence:
+          - type: map
+            mapping: *answer_histories
diff --git a/bin/validate-frontmatter.rb b/bin/validate-frontmatter.rb
@@ -1,6 +1,7 @@
 #!/usr/bin/env ruby
 # frozen_string_literal: true
 
+require 'date'
 require 'yaml'
 require 'find'
 require 'pathname'
@@ -11,7 +12,11 @@
 module SchemaValidator
   # Schemas
   @TOPIC_SCHEMA_UNSAFE = YAML.load_file('bin/schema-topic.yaml')
-  @TUTORIAL_SCHEMA_UNSAFE = YAML.load_file('bin/schema-tutorial.yaml')
+  begin
+    @TUTORIAL_SCHEMA_UNSAFE = YAML.load_file('bin/schema-tutorial.yaml', aliases: true)
+  rescue
+    @TUTORIAL_SCHEMA_UNSAFE = YAML.load_file('bin/schema-tutorial.yaml')
+  end
   @SLIDES_SCHEMA_UNSAFE = YAML.load_file('bin/schema-slides.yaml')
   @FAQ_SCHEMA_UNSAFE = YAML.load_file('bin/schema-faq.yaml')
   @QUIZ_SCHEMA_UNSAFE = YAML.load_file('bin/schema-quiz.yaml')
@@ -104,7 +109,11 @@ def self.validate_requirements(requirements)
 
   def self.lintable?(fn)
     begin
-      data = YAML.load_file(fn)
+      begin
+        data = YAML.load_file(fn, permitted_classes:[Date])
+      rescue
+        data = YAML.load_file(fn)
+      end
     rescue StandardError => e
       return ["YAML error, failed to parse #{fn}, #{e}"]
     end

diff --git a/faqs/gtn/gtn_example_histories.md b/faqs/gtn/gtn_example_histories.md
@@ -0,0 +1,25 @@
+---
+title: Using Answer Key Histories
+area: introduction
+layout: faq
+box_type: tip
+contributors: [nomadscientist]
+---
+
+If you get stuck, you can first check your history against an exemplar history, from your tutorial.
+
+First, import the target history.
+
+{% snippet faqs/galaxy/histories_import.md %}
+
+Next, compare the answer key history with your own history.
+
+{% snippet faqs/galaxy/histories_side_by_side_view.md %}
+
+You can compare there, or if you're really stuck, you can also click and drag a given dataset to your history to continue the tutorial from there.
+
+{% snippet faqs/galaxy/histories_copy_dataset.md %}
+
+You can also use our handy troubleshooting guide.
+
+{% snippet faqs/galaxy/analysis_troubleshooting.md %}
diff --git a/...contributing/tutorials/create-new-tutorial-content/images/example-histories.png b/...contributing/tutorials/create-new-tutorial-content/images/example-histories.png
diff --git a/topics/contributing/tutorials/create-new-tutorial-content/tutorial.md b/topics/contributing/tutorials/create-new-tutorial-content/tutorial.md
@@ -921,6 +921,27 @@ The alternative is to figure out the ID for the tool you want to use:
 
 ![Finding the tool ID](../../images/tool-id.png)
 
+## Example Histories
+
+If you have example input histories for your tutorial, perhaps for specific servers where trainees will often follow a tutorial but want to skip a slow input step, then you can provide example histories as part of your tutorial.
+
+> <code-in-title>Tutorial Frontmatter</code-in-title>
+> ```yaml
+> answer_histories:
+>   - label: "UseGalaxy.eu"
+>     history: https://humancellatlas.usegalaxy.eu/u/j.jakiela/h/generating-a-single-cell-matrix-using-alevin-3
+>   - label: "Older Alevin version"
+>     history: https://humancellatlas.usegalaxy.eu/u/wendi.bacon.training/h/cs1pre-processing-with-alevin---answer-key
+>     date: 2024-01-01
+> input_histories:
+>   - label: "UseGalaxy.eu"
+>     history: https://humancellatlas.usegalaxy.eu/u/wendi.bacon.training/h/cs1pre-processing-with-alevin---input-1
+> ```
+{: .code-in}
+
+> <code-out-title>Rendered Tutorial</code-out-title>
+> ![a screenshot of the GTN metadata box showing a dropdown for input histories and answer histories. The answer histories features two examples one on UseGalaxy.eu and an older alevin one, each with a date. In the dropdown is also a link to an FAQ titled how to use this](images/example-histories.png)
+{: .code-out}
 
 ## Workflows
 

diff --git a/topics/single-cell/tutorials/scrna-case_alevin/tutorial.md b/topics/single-cell/tutorials/scrna-case_alevin/tutorial.md
@@ -14,6 +14,18 @@ redirect_from:
 questions:
   - I have some single cell FASTQ files I want to analyse. Where do I start?
 
+answer_histories:
+  - label: "UseGalaxy.eu"
+    history: https://humancellatlas.usegalaxy.eu/u/j.jakiela/h/generating-a-single-cell-matrix-using-alevin-3
+    date: 2024-05-01
+  - label: "Older Alevin version"
+    history: https://humancellatlas.usegalaxy.eu/u/wendi.bacon.training/h/cs1pre-processing-with-alevin---answer-key
+    date: 2024-01-01
+
+input_histories:
+  - label: "UseGalaxy.eu"
+    history: https://humancellatlas.usegalaxy.eu/u/wendi.bacon.training/h/cs1pre-processing-with-alevin---input-1
+
 objectives:
   - Generate a cellxgene matrix for droplet-based single cell sequencing data
   - Interpret quality control (QC) plots to make informed decisions on cell thresholds