Merge pull request #188 from mshadbolt/main

Add EuroPMC as a tool registry

Gemfile

@@ -1,6 +1,6 @@
 source "https://rubygems.org"
 
-gem "elixir-toolkit-theme-plugins", "~> 0.1.6"
+gem "elixir-toolkit-theme-plugins", "~> 0.1.7"
 gem "webrick", "~> 1.7"
 gem "jekyll", "~> 4.3.1"
 gem "jemoji", "~> 0.13.0"

Gemfile.lock

@@ -1,7 +1,7 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (7.0.5)
+    activesupport (7.0.6)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -10,20 +10,20 @@ GEM
       public_suffix (>= 2.0.2, < 6.0)
     colorator (1.1.0)
     concurrent-ruby (1.2.2)
-    elixir-toolkit-theme-plugins (0.1.6)
+    elixir-toolkit-theme-plugins (0.1.7)
       jekyll (~> 4.3, >= 4.3.1)
     em-websocket (0.5.3)
       eventmachine (>= 0.12.9)
       http_parser.rb (~> 0)
     eventmachine (1.2.7)
-    faraday (2.7.6)
+    faraday (2.7.10)
       faraday-net_http (>= 2.0, < 3.1)
       ruby2_keywords (>= 0.0.4)
     faraday-net_http (3.0.2)
     ffi (1.15.5)
     forwardable-extended (2.6.0)
     gemoji (4.1.0)
-    google-protobuf (3.23.3-x86_64-linux)
+    google-protobuf (3.23.4-x86_64-linux)
     html-pipeline (2.14.3)
       activesupport (>= 2)
       nokogiri (>= 1.4)
@@ -80,14 +80,14 @@ GEM
       rb-inotify (~> 0.9, >= 0.9.10)
     mercenary (0.4.0)
     minitest (5.18.1)
-    nokogiri (1.15.2-x86_64-linux)
+    nokogiri (1.15.3-x86_64-linux)
       racc (~> 1.4)
     octokit (6.1.1)
       faraday (>= 1, < 3)
       sawyer (~> 0.9)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
-    public_suffix (5.0.1)
+    public_suffix (5.0.3)
     racc (1.7.1)
     rake (13.0.6)
     rb-fsevent (0.11.2)
@@ -98,7 +98,7 @@ GEM
     ruby2_keywords (0.0.5)
     rubyzip (2.3.2)
     safe_yaml (1.0.5)
-    sass-embedded (1.63.4)
+    sass-embedded (1.63.6)
       google-protobuf (~> 3.23)
       rake (>= 13.0.0)
     sawyer (0.9.2)
@@ -115,7 +115,7 @@ PLATFORMS
   x86_64-linux
 
 DEPENDENCIES
-  elixir-toolkit-theme-plugins (~> 0.1.6)
+  elixir-toolkit-theme-plugins (~> 0.1.7)
   jekyll (~> 4.3.1)
   jekyll-github-metadata (~> 2.15)
   jekyll-redirect-from (~> 0.16.0)

README.md

@@ -174,7 +174,6 @@ If you like our work, you can add following badge to the readme of your project:
 
 
 
-
 ## License
 
 The theme is available as open source under the terms of the [MIT License](http://opensource.org/licenses/MIT).

_data/tool_and_resource_list.yml

@@ -44,3 +44,11 @@
   registry:
     fairsharing: wy4egf
     tess: Zenodo
+- description:
+    API framework and data model for cross-cohort searching.
+  url: https://github.com/ga4gh-beacon/beacon-v2
+  id: beacon
+  name: Beacon v2
+  registry:
+    fairsharing: 6fba91
+    europmc: 35297548

_includes/resource-table-all.html

@@ -88,6 +88,9 @@ <h2>Relevant tools and resources</h2>
                     {%- if tool.registry.tess %}
                     <a data-bs-toggle="tooltip" data-bs-original-title="TeSS" href="https://tess.elixir-europe.org/search?q={{tool.registry.tess}}"><span class="badge bg-dark text-white hover-primary"><i class="fa-solid fa-graduation-cap me-2"></i>Training</span></a>
                     {%- endif %}
+                    {%- if tool.registry.europmc %}
+                    <a data-bs-toggle="tooltip" data-bs-original-title="EuroPMC" href="https://europepmc.org/article/MED/{{tool.registry.europmc}}"><span class="badge bg-dark text-white hover-primary"><i class="fa-solid fa-book me-2"></i>Publication</span></a>
+                    {%- endif %}
                 </td>
             </tr>
             {%- endfor %}
@@ -155,6 +158,9 @@ <h2>Relevant tools and resources</h2>
                     {%- if tool.registry.tess %}
                     <a data-bs-toggle="tooltip" data-bs-original-title="TeSS" href="https://tess.elixir-europe.org/search?q={{tool.registry.tess}}"><span class="badge bg-dark text-white hover-primary"><i class="fa-solid fa-graduation-cap me-2"></i>Training</span></a>
                     {%- endif %}
+                    {%- if tool.registry.europmc %}
+                    <a data-bs-toggle="tooltip" data-bs-original-title="EuroPMC" href="https://europepmc.org/article/MED/{{tool.registry.europmc}}"><span class="badge bg-dark text-white hover-primary"><i class="fa-solid fa-book me-2"></i>Publication</span></a>
+                    {%- endif %}
                 </td>
             </tr>
             {%- endfor %}

_includes/resource-table-page.html

@@ -70,6 +70,9 @@ <h3>Tailored to users in {{page.title}}</h3>
                     {%- if tool.registry.tess %}
                     <a data-bs-toggle="tooltip" data-bs-original-title="TeSS" href="https://tess.elixir-europe.org/search?q={{tool.registry.tess}}"><span class="badge bg-dark text-white hover-primary"><i class="fa-solid fa-graduation-cap me-2"></i>Training</span></a>
                     {%- endif %}
+                    {%- if tool.registry.europmc %}
+                    <a data-bs-toggle="tooltip" data-bs-original-title="EuroPMC" href="https://europepmc.org/article/MED/{{tool.registry.europmc}}"><span class="badge bg-dark text-white hover-primary"><i class="fa-solid fa-book me-2"></i>Publication</span></a>
+                    {%- endif %}
                 </td>
             </tr>
             {%- endfor %}
@@ -141,11 +144,14 @@ <h3>{{page.title}} contributes to</h3>
                     {%- if tool.registry.tess %}
                     <a data-bs-toggle="tooltip" data-bs-original-title="TeSS" href="https://tess.elixir-europe.org/search?q={{tool.registry.tess}}"><span class="badge bg-dark text-white hover-primary"><i class="fa-solid fa-graduation-cap me-2"></i>Training</span></a>
                     {%- endif %}
+                    {%- if tool.registry.europmc %}
+                    <a data-bs-toggle="tooltip" data-bs-original-title="EuroPMC" href="https://europepmc.org/article/MED/{{tool.registry.europmc}}"><span class="badge bg-dark text-white hover-primary"><i class="fa-solid fa-book me-2"></i>Publication</span></a>
+                    {%- endif %}
                 </td>
             </tr>
             {%- endfor %}
         </tbody>
     </table>
 </div>
 <div id="skip-tool-table-2"></div>
-{%- endif %}
+{%- endif %}

pages/documentation/resource_table.md

@@ -1,13 +1,14 @@
 ---
 title: Tools and resources table
+page_id: tools_and_resources_table
 ---
 
 One of the themes key features is the support for a central tool and resource table. This means that tools that are mentioned at multiple places on the website, can be described centrally, and these descriptions/metadata fields can be used to automatically populate a tools and resources table at the bottom of the page.
 
 
 ## Way of working
 
-The [all_tools_and_resources](all_tools_and_resources) list is based on the [yaml file](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/blob/main/_data/tool_and_resource_list.yml) in the `_data` directory. Tools and resources can be manually linked to [FAIRsharing.org](https://fairsharing.org/), [Bio.tools](https://bio.tools) and [TeSS](https://tess.elixir-europe.org/).
+The [all_tools_and_resources](all_tools_and_resources) list is based on the [yaml file](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/blob/main/_data/tool_and_resource_list.yml) in the `_data` directory. Tools and resources can be manually linked to [FAIRsharing.org](https://fairsharing.org/), [Bio.tools](https://bio.tools) and [TeSS](https://tess.elixir-europe.org/) and [EuroPMC](https://europepmc.org/).
 
 
 ## Prerequisites
@@ -19,14 +20,15 @@ The [all_tools_and_resources](all_tools_and_resources) list is based on the [yam
   * `- elixir-toolkit-theme-plugins` is added to the plugins block in the `_config.yml` file
 * GitHub Actions is used to deploy the website. See [instructions](/#deployment).
 
+
 ## The main yaml file
 
 Each tool or resource mentioned in the text has metadata stored in the [main yaml file](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/blob/main/_data/tool_and_resource_list.yml). The metadata block for each tool consists of 5 attributes:
 - **id**: The ID of a tool, in kebab-case, lowercase with hyphens.
 - **name**: The name of the tool or resource
 - **url**: URL to the main page of the tool or resource, make sure to let the URL start with `https://`
 - **description**: A short description of the tool or resource. Try to not use the characters `"` or `'` 
-- **registry**: 3 registries are supported: [Bio.tools](https://bio.tools), [FAIRsharing.org](https://fairsharing.org/) and [TeSS](https://tess.elixir-europe.org/). The keywords you can use respectively are: `biotools`, `fairsharing`, `fairsharing-coll` and `tess`, specifying the id or query with a colon. FAIRsharing collections have an ID that follows the pattern `bsg-s000XXX`. List registries under the `registry` attribute as `key: value pairs`.
+- **registry**: 3 registries are supported: [Bio.tools](https://bio.tools), [FAIRsharing.org](https://fairsharing.org/), [TeSS](https://tess.elixir-europe.org/) and [EuroPMC](https://europepmc.org/). The keywords you can use respectively are: `biotools`, `fairsharing`, `fairsharing-coll`, `tess` and `europmc`, specifying the id or query with a colon. FAIRsharing collections have an ID that follows the pattern `bsg-s000XXX`. List registries under the `registry` attribute as `key: value pairs`.
 - **related_pages**: List of page_ids (Deprecated, This is replaced by the `{% raw %}{% tool "tool_id" %}{% endraw %}` snippet in the text)
 - **how_to_access**: This is free text feels that describes the accessibility of the tool or resource.
 
@@ -63,7 +65,7 @@ Tools and resources specifically mentioned in the text of the pages should be pr
     {% endraw %}
     ```
 
-    Example:
+    **Examples:**
 
     ```
     {% raw %}
@@ -74,6 +76,15 @@ Tools and resources specifically mentioned in the text of the pages should be pr
 
     {% tool "zenodo" %} is a powerful data publication service, which is supported by the European commission and focused on research data, including supplemental material like software, tables, figures or slides.
 
+    ```
+    {% raw %}
+    {% tool "beacon" %} is a GA4GH standard which enables standardised querying across multiple sources.
+    {% endraw %}
+    ```
+    Will give: 
 
+    {% tool "beacon" %} is a GA4GH standard which enables standardised querying across multiple sources.
+
+
 {% include callout.html type="important" content="Don't forget to add the `\"` double quotes around the tool_id and make sure to use the exact tool_id as described in the yaml file." %}