Merge pull request #5080 from galaxyproject/coydog-powan

Moving towards prod workflowhub (not there yet.)

.github/workflows/deploy.yml

@@ -67,6 +67,7 @@ jobs:
           export PATH=/home/runner/.local/bin:$PATH
           make annotate ACTIVATE_ENV=pwd
           curl -L https://docs.google.com/spreadsheets/d/1NfZhi5Jav7kl9zFCkeb7rIC2F8xW1isruv1TeO4WpNI/export\?format\=tsv | ruby bin/prepare_feedback.rb
+          curl -L https://hexylena.github.io/toolshed-version-database/tool-meta.json > metadata/tool-meta.json
           npm install
           make rebuild-search-index ACTIVATE_ENV=pwd
           cat metadata/swagger.yaml | python bin/yaml2json.py > api/swagger.json

.github/workflows/monthly-release-backfill.yml

@@ -66,6 +66,7 @@ jobs:
           sed -i s"|^baseurl: .*|baseurl: '/archive/${SOURCE_TAG}'|g" _config.yml
           sed -i s"|^github_repository_branch: .*|github_repository_branch: '${SOURCE_TAG}'|g" _config.yml
           sed -i s"|^title: .*|title: 'GTN Archive ${SOURCE_TAG}'|g" _config.yml
+          curl -L https://hexylena.github.io/toolshed-version-database/tool-meta.json > metadata/tool-meta.json
           npm install
           make rebuild-search-index ACTIVATE_ENV=pwd
           cat metadata/swagger.yaml | python bin/yaml2json.py > api/swagger.json

.github/workflows/monthly-release.yml

@@ -68,6 +68,7 @@ jobs:
           sed -i s"|^baseurl: .*|baseurl: '/archive/${SOURCE_TAG}'|g" _config.yml
           sed -i s"|^github_repository_branch: .*|github_repository_branch: '${SOURCE_TAG}'|g" _config.yml
           sed -i s"|^title: .*|title: 'GTN Archive ${SOURCE_TAG}'|g" _config.yml
+          curl -L https://hexylena.github.io/toolshed-version-database/tool-meta.json > metadata/tool-meta.json
           npm install
           make rebuild-search-index ACTIVATE_ENV=pwd
           cat metadata/swagger.yaml | ruby bin/yaml2json.rb > api/swagger.json

.github/workflows/workflowhub.yml

@@ -1,10 +1,12 @@
 name: "[Cron] Upload workflows to (DEV)WorkflowHub"
 
+concurrency:
+  group: wfh-${{ github.head_ref }}
+  cancel-in-progress: false # Not sure about this.
+
 on:
   schedule:
-    # * is a special character in YAML so you have to quote this string
-    # We'll run this daily at noon.
-    - cron:  '59 12 * * *'
+    - cron:  '55 12 * * 1'
   workflow_dispatch:
 
 jobs:
@@ -53,7 +55,11 @@ jobs:
         run: |
           python bin/wfh-upload.py
         env:
-          DEV_WFH_TOKEN: ${{ secrets.DEV_WFH_TOKEN }}
+          WFH_TOKEN: ${{ secrets.DEV_WFH_TOKEN }}
+
+      - name: Any changes?
+        run: |
+          git diff
 
       - name: Create Pull Request
         uses: peter-evans/create-pull-request@v3

_layouts/by_tool.html

@@ -2,24 +2,64 @@
 layout: base
 ---
 
-<h1>Tutorials using {{ page.short_tool }}</h1>
+{% assign tool_id_path = page.observed_tool_ids[0][0] %}
+
+<hgroup>
+	<h1>
+		{{ site.data['tool-meta'][tool_id_path].name }}:
+		{{ site.data['tool-meta'][tool_id_path].desc }}
+	</h1>
+	<pre>{{ page.observed_tool_ids[0] }}</pre>
+</hgroup>
+
 <section>
 	<div class="stats">
 		<div class="row">
 			<div class="col-md-3">
-				<h2>Servers Offering this Tool</h2>
+				<h2>Metadata</h2>
+				<h3>Servers Offering this Tool</h3>
 				<a href="https://usegalaxy.eu/?tool_id={{ page.observed_tool_ids[0][0] }}">UseGalaxy.eu ({{ page.observed_tool_ids[0][1] }})</a>
 				<p class="text-muted">This is a guess, we are not currently checking if that is actually present.</p>
 
-				<h2>Observed Tool Versions</h2>
+				<hgroup>
+					<h3>Observed Tool Versions</h3>
+					<p>Within GTN tutorials</p>
+				</hgroup>
 				<ul>
 					{% for tool in page.observed_tool_ids %}
 					<li>{{ tool[1] }}</li>
 					{% endfor %}
 				</ul>
+
+				{% if site.data['tool-meta'][tool_id_path].edam_operations %}
+				<h3>EDAM Operations</h3>
+				<ul>
+				{% for topic in site.data['tool-meta'][tool_id_path].edam_operations %}
+					<li>
+						<a href="https://www.ebi.ac.uk/ols4/ontologies/edam/classes/http%253A%252F%252Fedamontology.org%252F{{ topic }}">
+						{{ topic }}
+						</a>
+					</li>
+				{% endfor %}
+				</ul>
+				{% endif %}
+
+				{% if site.data['tool-meta'][tool_id_path].edam_topics%}
+				<h3>EDAM Topics</h3>
+				<ul>
+				{% for topic in site.data['tool-meta'][tool_id_path].edam_topics %}
+					<li>
+						<a href="https://www.ebi.ac.uk/ols4/ontologies/edam/classes/http%253A%252F%252Fedamontology.org%252F{{ topic }}">
+						{{ topic }}
+						</a>
+					</li>
+				{% endfor %}
+				</ul>
+				{% endif %}
 			</div>
 
 			<div class="col-md-9">
+				<h2>Relevant Tutorials</h2>
 				<ul>
 					{% for tutorial in page.tutorial_list %}
 					<li>

_layouts/workflow.html

@@ -116,8 +116,9 @@ <h1 data-toc-skip>{{ workflow.title }}</h1>
 			<br/>
 
 			{% if jekyll.environment == "production" %}
-			<a style="margin-bottom: 0.2rem" href="{{ site.baseurl }}/api/workflows/{{ material.topic_id }}/{{ material.tutorial_id }}/{{ workflow.wfid }}/rocrate.zip" class="btn btn-secondary"><img src="{% link assets/images/ro-crate.png %}" style="height: 32px" alt="RO-Crate logo with flask"/> Download Workflow RO-Crate</a>
+			<a style="margin-bottom: 0.2rem" href="{{ site.baseurl }}/api/workflows/{{ material.topic_name }}/{{ material.tutorial_name }}/{{ workflow.wfname }}/rocrate.zip" class="btn btn-secondary"><img src="{% link assets/images/ro-crate.png %}" style="height: 32px" alt="RO-Crate logo with flask"/> Download Workflow RO-Crate</a>
 			{% endif %}
+
 			{% if workflow.workflowhub_id %}
 			<a style="margin-bottom: 0.2rem" href="https://workflowhub.eu/workflows/{{ workflow.workflowhub_id }}" class="btn btn-secondary"><img src="{% link assets/images/workflowhub-icon.svg %}" style="height: 32px" alt="Workflowhub cloud with gears logo"/> View on WorkflowHub</a>
 			{% endif %}
@@ -148,6 +149,70 @@ <h1 data-toc-skip>{{ workflow.title }}</h1>
 				Download
 			</a>
 			<pre class="mermaid">{{ workflow.mermaid }}</pre>
+			<h2>Inputs</h2>
+			<table class="table table-striped">
+				<thead>
+					<tr>
+						<th>Input</th>
+						<th>Label</th>
+					</tr>
+				</thead>
+				<tbody>
+				{% for input in workflow.inputs %}
+				<tr>
+					<td>{{ input.name }}</td>
+					<td>{{ input.label }}</td>
+				</tr>
+				{% endfor %}
+				</tbody>
+			</table>
+
+			<h2>Outputs</h2>
+			<table class="table table-striped">
+				<thead>
+					<tr>
+						<th>From</th>
+						<th>Output</th>
+						<th>Label</th>
+					</tr>
+				</thead>
+				<tbody>
+				{% for output in workflow.outputs %}
+				<tr>
+					<td>{{ output.tool_id }}</td>
+					<td>{{ output.name }}</td>
+					<td>{{ output.label }}</td>
+				</tr>
+				{% endfor %}
+				</tbody>
+			</table>
+
+
+			<h2>Tools</h2>
+			<table class="table table-striped">
+				<thead>
+					<tr>
+						<th>Tool</th>
+						<th>Links</th>
+					</tr>
+				</thead>
+				<tbody>
+			{% for tool in workflow.workflow_tools %}
+			<tr>
+				<td><a href="https://my.galaxy.training/?path=?tool_id={{ tool }}">{{ tool }}</a></td>
+				<td>
+					{% if site.data['toolshed-revisions'][tool] %}
+					{% assign tsdata = site.data['toolshed-revisions'][tool] %}
+					<a href="https://toolshed.g2.bx.psu.edu/view/{{tsdata[0]}}/{{tsdata[1]}}/{{tsdata[2]}}">
+						View in ToolShed
+					</a>
+					{% endif %}
+				</td>
+			</tr>
+			{% endfor %}
+				</tbody>
+			</table>
+
 
 			<p>To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.</p>
 

_plugins/gtn/ro-crate.rb

@@ -79,9 +79,9 @@ def self.write(site, dir, associated_material, workflow, url, baseurl, time_base
       }
 
       mat_contribs = [
+        ['Workflow Author(s)', workflow['creators'].map { |c| c['name'] }],
         ['Tutorial Author(s)', Gtn::Contributors.get_authors(associated_material).map { |n| name2md(site, n) }],
         ['Tutorial Contributor(s)', Gtn::Contributors.get_non_authors(associated_material).map { |n| name2md(site, n) }],
-        ['Workflow Author(s)', workflow['creators'].map { |c| c['name'] }],
         ['Funder(s)', Gtn::Contributors.get_funders(associated_material).map { |n| name2md(site, n) }],
       ].reject { |_, v| v.empty? }
 
@@ -90,7 +90,7 @@ def self.write(site, dir, associated_material, workflow, url, baseurl, time_base
 
 ## Associated Tutorial
 
-This workflows is part of the tutorial [#{workflow['name']}](#{url}#{baseurl}/topics/#{workflow['topic_id']}/tutorials/#{workflow['tutorial_id']}/tutorial.html), available in the [GTN](https://training.galaxyproject.org)
+This workflows is part of the tutorial [#{associated_material['title']}](#{url}#{baseurl}/topics/#{workflow['topic_id']}/tutorials/#{workflow['tutorial_id']}/tutorial.html), available in the [GTN](https://training.galaxyproject.org)
 
 #{"## Features" if features.values.any?}
 
@@ -100,9 +100,8 @@ def self.write(site, dir, associated_material, workflow, url, baseurl, time_base
 
 #{mat_contribs.map { |k, v| "**#{k}**: #{v.join(', ')}" }.join("\n\n")}
 
-[![gtn star logo followed by the word workflows](http://galaxy-training.s3-website.us-east-1.amazonaws.com/misc/gtn-workflows.png)](https://training.galaxyproject.org/training-material/)
+[![gtn star logo followed by the word workflows](https://training.galaxyproject.org/training-material/assets/branding/gtn-workflows.png)](https://training.galaxyproject.org/training-material/)
       ).strip
-      # ![gtn star logo followed by the word workflows](https://training.galaxyproject.org/training-material/assets/branding/gtn-workflows.png)
 
       crate = {
         '@context' => ['https://w3id.org/ro/crate/1.1/context'],

_plugins/jekyll-topic-filter.rb

@@ -699,7 +699,9 @@ def self.resolve_material(site, material)
           'modified' => File.mtime(wf_path),
           'mermaid' => mermaid(wf_json),
           'graph_dot' => graph_dot(wf_json),
-          'workflow_tools' => extract_workflow_tool_list(wf_json).uniq,
+          'workflow_tools' => extract_workflow_tool_list(wf_json).flatten.uniq.sort,
+          'inputs' => wf_json['steps'].select { |_k, v| ['data_input', 'data_collection_input', 'parameter_input'].include? v['type'] }.map{|_, v| v},
+          'outputs' => wf_json['steps'].select { |_k, v| v['workflow_outputs'] && v['workflow_outputs'].length.positive? }.map{|_, v| v},
         }
       end
     end