elixir-toolkit-theme-plugins 0.1.10 → 1.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: bd0a3fc0a5890ba4e7680359f3fa18d06fe7de42a11813e73cf6db604a6205c6
-  data.tar.gz: 965789747727984d24d71b4963ccf58422b0a597450056c0a76a25e8d4d04cf7
+  metadata.gz: 989e78f7e6995bb095549eb94361934f40c944b45c207f24820d91c518006280
+  data.tar.gz: ae7e2b72145732bcdcfc52cabb325eae06c1910a5de7fe2781b958184f93e318
 SHA512:
-  metadata.gz: dffa98f82db6ac590161b0a4e38a60ed70495358f9a4064b144c9e50c642f70738d044c1967692c5a2c2ee6eb37f5f89778e2d436fc67fefb28542bbd2ef5673
-  data.tar.gz: 32b9bbbe4a80b61f70bb2145c910cf50a81a656c5b6053ce989e8cb129898f24cc5d00a2b4db1a800728167285df48df05096c839c50a6e95f2d58b3ee55e921
+  metadata.gz: 2869b8b726d00bb4c58e105c97563e61836f122b449decfa13851d8f7a09d1c489b96121f41af6c0a97c6fbc9f34809b2c64ffb0907943fe2f3041e8a82150f9
+  data.tar.gz: 07eea18abf4bbe4bb3bcca9303bc4a21c121a1d5d6c98309c8d8df3a3383dc468f9fcb2e1be910b6b289e7dc827e7cd939b67b510bd97c72fd5e8cc663a27fb6

data/.github/workflows/release.yml

@@ -11,11 +11,13 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Ruby 3.1
-      uses: actions/setup-ruby@v1
+    - uses: actions/checkout@v5
+    - name: Set up Ruby 3.3
+      uses: ruby/setup-ruby@v1.204.0
       with:
-        ruby-version: 3.1
+        ruby-version: '3.3'
+        bundler-cache: true
+        cache-version: 0
 
     - name: Publish to GPR
       run: |

data/elixir-toolkit-theme-plugins.gemspec

@@ -9,7 +9,7 @@ Gem::Specification.new do |spec|
   spec.name          = "elixir-toolkit-theme-plugins"
   spec.version       =  Jekyll::Ett::VERSION.dup
   spec.authors       = ["bedroesb", "janslifka", "MarekSuchanek"]
-  spec.email         = ["bedro@psb.vib-ugent.be\n"]
+  spec.email         = ["bert.droesbeke@vib.be\n"]
 
   spec.summary       = "Plugins to work together with ELIXIR Toolkit theme"
   spec.homepage      = "https://elixir-belgium.github.io/elixir-toolkit-theme-plugins/"

data/lib/elixir-toolkit-theme-plugins/tool_table_filter.rb

@@ -1,15 +1,25 @@
 require "jekyll"
-
+require "set"
 
 module Jekyll
     class Ett
         module ToolTableFilter
             def add_related_pages(data)
+                return [] if data.nil?
+                return data unless data.is_a?(Array)
+
                 load_page_data
+                instances_index = Jekyll::Ett::ToolTag.instances_index
+
+                data.each do |tool|
+                    next unless tool.is_a?(Hash)
+
+                    if tool["id"] && @related_pages[tool["id"]]
+                        tool["related_pages"] = @related_pages[tool["id"]].to_a
+                    end
 
-                for tool in data
-                    if tool['id'] && @related_pages[tool['id']]
-                        tool['related_pages'] = @related_pages[tool['id']].to_a
+                    if tool["id"] && instances_index[tool["id"]]
+                        tool["instances"] = instances_index[tool["id"]]
                     end
                 end
 
@@ -21,20 +31,22 @@ module Jekyll
             def load_page_data
                 @related_pages = {}
                 pages_path = File.join(Dir.pwd, "**", "*.md")
+
                 Dir.glob(pages_path).each do |f|
                     file = File.read(f)
                     page_id_matches = file.match(/page_id:\s*(\w+)/)
-                    
-                    if page_id_matches
-                        page_id = page_id_matches[1]
-                        file.scan(/\{%\s*tool\s*"([^"]+)"\s*%}/).flatten.each do |m|
-                            @related_pages[m] = Set[] unless @related_pages[m]
-                            @related_pages[m].add(page_id)
-                        end
+                    next unless page_id_matches
+
+                    page_id = page_id_matches[1]
+
+                    file.scan(/\{%\s*tool\s*"([^"]+)"\s*%}/).flatten.each do |m|
+                        @related_pages[m] ||= Set.new
+                        @related_pages[m].add(page_id)
                     end
                 end
             end
         end
     end
+
     Liquid::Template.register_filter(Jekyll::Ett::ToolTableFilter)
 end

data/lib/elixir-toolkit-theme-plugins/tool_tag.rb

@@ -1,75 +1,188 @@
 require "jekyll"
-
+require "yaml"
 
 module Jekyll
     class Ett
         class ToolTag < Liquid::Tag
+            @@instances_by_tool = nil
+            TOOLS_PATH = File.join(Dir.pwd, "_data", "tool_and_resource_list.yml")
+
             def initialize(tagName, content, tokens)
                 super
                 @content = content
                 load_tools
+                load_instances
             end
 
             def load_tools
-                tools_path = File.join(Dir.pwd, "_data", "tool_and_resource_list.yml")
-                @tools = YAML.load(File.read(tools_path))
+                @tools = YAML.load(File.read(TOOLS_PATH))
+            end
+
+            # --- class-level accessor used by both tag and filters ---
+            def self.instances_index
+                @@instances_by_tool ||= build_instances_index
+            end
+
+            def self.build_instances_index
+                instances_by_tool = Hash.new { |h, k| h[k] = [] }
+
+                tools = YAML.load(File.read(TOOLS_PATH))
+
+                # 1) instances from national_resources in page front matter
+                pages_path = File.join(Dir.pwd, "**", "*.md")
+                files = Dir.glob(pages_path)
+
+                files.each do |f|
+                    raw = File.read(f)
+                    fm  = extract_front_matter(raw)
+                    next unless fm.is_a?(Hash)
+
+                    country_code  = (fm["country_code"] || "").to_s
+                    country_name  = (fm["title"] || "").to_s
+                    resources     = fm["national_resources"] || []
+                    next unless resources.is_a?(Array)
+
+                    resources.each do |res|
+                        next unless res.is_a?(Hash)
+                        inst_of = res["instance_of"]
+                        next if inst_of.nil? || inst_of == "NA"
+
+                        instances_by_tool[inst_of] << {
+                            "name"         => (res["name"] || res["id"] || "Instance"),
+                            "url"          => res["url"],
+                            "id"           => res["id"],
+                            "country_code" => country_code,
+                            "country_name" => country_name,
+                            "page_path"    => f
+                        }
+                    end
+                end
+
+                # 2) instances from tool_and_resource_list.yml itself
+                (tools || []).each do |tool|
+                    parent_id = tool["instance_of"]
+                    next if parent_id.nil? || parent_id == "NA"
+
+                    instances_by_tool[parent_id] << {
+                        "name"         => (tool["name"] || tool["id"] || "Instance"),
+                        "url"          => tool["url"],
+                        "id"           => tool["id"],
+                        "country_code" => "",
+                        "country_name" => "",
+                        "page_path"    => nil
+                    }
+                end
+
+                instances_by_tool
+            end
+
+            # shared front-matter parser (class-level)
+            def self.extract_front_matter(file_string)
+                if file_string =~ /\A---\s*\n(.*?)\n---\s*\n/m
+                    yaml = Regexp.last_match(1)
+                    YAML.safe_load(yaml, permitted_classes: [Date, Time], aliases: true)
+                else
+                    nil
+                end
+            rescue
+                nil
+            end
+
+            # instance-level wrapper uses the shared index
+            def load_instances
+                @instances_by_tool = self.class.instances_index
             end
 
             def render(context)
-                tool = find_tool(context[@content.strip])
-                tags = create_tags(tool)
+                site = context.registers[:site]
+                tool_id_from_liquid = context[@content.strip]
+                tool = find_tool(tool_id_from_liquid)
+                tags = create_tags(tool, site)
                 %Q{<a
                     tabindex="0"
                     class="tool"
-                    aria-description="#{tool["description"]}"
+                    aria-description="#{html_escape(tool["description"])}"
                     data-bs-toggle="popover"
                     data-bs-placement="bottom"
                     data-bs-trigger="focus"
-                    data-bs-content="<h5>#{tool["name"]}</h5><div class='mb-2'>#{tool["description"]}</div>#{tags}"
+                    data-bs-content="<h5>#{html_escape(tool["name"])}</h5><div class='mb-2'>#{html_escape(tool["description"])}</div><div class='d-flex flex-wrap gap-1'>#{tags}</div>"
                     data-bs-template="<div class='popover popover-tool' role='tooltip'><div class='popover-arrow'></div><h3 class='popover-header'></h3><div class='popover-body'></div></div>"
                     data-bs-html="true"
-                    ><i class="fa-solid fa-wrench fa-sm me-2"></i>#{ tool["name"] }</a>}
+                    ><i class="fa-solid fa-wrench fa-sm me-2"></i>#{ html_escape(tool["name"]) }</a>}
             end
 
             def find_tool(tool_id)
                 tool = @tools.find { |t| t["id"] == tool_id.strip }
                 return tool if tool
-                
                 raise Exception.new "Undefined tool ID: #{tool_id}"
             end
 
-            def create_tags(tool)
+            def create_tags(tool, site)
                 tags = ""
                 tags << create_tag("#{tool["url"]}", "fa-link", "Website")
                 if tool["registry"]
                     registry = tool["registry"]
+                    tags << create_tag("https://bio.tools/#{registry["biotools"]}", "fa-info", "Tool info") if registry["biotools"] && registry["biotools"] != "NA"
+                    tags << create_tag("https://fairsharing.org/FAIRsharing.#{registry["fairsharing"]}", "fa-database", "Standards/Databases") if registry["fairsharing"] && registry["fairsharing"] != "NA"
+                    tags << create_tag("https://fairsharing.org/#{registry["fairsharing-coll"]}", "fa-database", "Standards/Databases") if registry["fairsharing-coll"] && registry["fairsharing-coll"] != "NA"
+                    tags << create_tag("https://tess.elixir-europe.org/search?q=#{registry["tess"]}", "fa-graduation-cap", "Training") if registry["tess"] && registry["tess"] != "NA"
+                    tags << create_tag("https://europepmc.org/article/MED/#{registry["europmc"]}", "fa-book", "Publication") if registry["europmc"] && registry["europmc"] != "NA"
+                end
 
-                    if registry["biotools"] and registry["biotools"] != "NA"
-                        tags << create_tag("https://bio.tools/#{registry["biotools"]}", "fa-info", "Tool info")
-                    end
+                instances = @instances_by_tool[tool["id"]]
+                tags << instances_dropdown(instances, site, tool["id"]) if instances && !instances.empty?
+                tags
+            end
 
-                    if registry["fairsharing"] and registry["fairsharing"] != "NA"
-                        tags << create_tag("https://fairsharing.org/FAIRsharing.#{registry["fairsharing"]}", "fa-database", "Standards/Databases")
-                    end
+            def create_tag(url, icon, label)
+                "<a href='#{html_attr(url)}' target='_blank' rel='noopener'><span class='badge bg-dark text-white hover-primary'><i class='fa-solid #{icon} me-2'></i>#{html_escape(label)}</span></a>"
+            end
 
-                    if registry["fairsharing-coll"] and registry["fairsharing-coll"] != "NA"
-                        tags << create_tag("https://fairsharing.org/#{registry["fairsharing-coll"]}", "fa-database", "Standards/Databases")
-                    end
+            def instances_dropdown(instances, site, tool_id)
+                dd_id = "instances-dd-#{tool_id}-#{object_id}"
 
-                    if registry["tess"] and registry["tess"] != "NA"
-                        tags << create_tag("https://tess.elixir-europe.org/search?q=#{registry["tess"]}", "fa-graduation-cap", "Training")
-                    end
+                items = instances.map do |inst|
+                    href = inst["url"] || resolve_page_url(inst["page_path"], site) || "#"
+                    flag = inst["country_code"].to_s.strip.empty? ? "" : "<span class='flag-icon ms-2 shadow-sm flag-icon-#{inst["country_code"].downcase}'></span>"
+                    name = html_escape(inst["name"])
+                    url  = html_attr(href)
+                    "<li><a class='dropdown-item' href='#{url}' target='_blank' rel='noopener'>#{name} #{flag}</a></li>"
+                end.join
 
-                    if registry["europmc"] and registry["europmc"] != "NA"
-                        tags << create_tag("https://europepmc.org/article/MED/#{registry["europmc"]}", "fa-book", "Publication")
-                    end
+                %Q{
+                <div class='dropdown d-inline-block'>
+                    <button class='btn btn-badge btn-outline-primary dropdown-toggle'
+                            type='button'
+                            id='#{dd_id}'
+                            data-bs-toggle='dropdown'
+                            aria-expanded='false'>
+                    <i class='fa-solid fa-globe me-2'></i>Instances
+                    </button>
+                    <ul class='dropdown-menu' aria-labelledby='#{dd_id}'>
+                    #{items}
+                    </ul>
+                </div>
+                }
+            end
 
-                end
-                tags
+            # Resolve a site-relative URL from an absolute file path stored in page_path
+            def resolve_page_url(abs_path, site)
+                return nil unless abs_path && site
+                rel = abs_path.sub(%r{\A#{Regexp.escape(Dir.pwd)}/?}, "")
+                doc = (site.pages + site.collections.values.flat_map(&:docs)).find { |p| p.path == rel }
+                doc&.url
+            rescue
+                nil
             end
 
-            def create_tag(url, icon, label)
-                "<a href='#{url}' target='_blank' rel='noopener' class='mt-2 me-2'><span class='badge bg-dark text-white hover-primary'><i class='fa-solid #{icon} me-2'></i>#{label}</span></a>"
+            # --- escaping helpers ---
+
+            def html_escape(s)
+                (s || "").to_s.gsub("&","&amp;").gsub("<","&lt;").gsub(">","&gt;").gsub('"',"&quot;")
+            end
+
+            def html_attr(s)
+                html_escape(s).gsub("'","&#39;")
             end
         end
     end

data/lib/elixir-toolkit-theme-plugins/version.rb

@@ -1,5 +1,5 @@
 module Jekyll
     class Ett
-      VERSION = '0.1.10'
+      VERSION = '1.1.0'
     end
   end

metadata

@@ -1,16 +1,16 @@
 --- !ruby/object:Gem::Specification
 name: elixir-toolkit-theme-plugins
 version: !ruby/object:Gem::Version
-  version: 0.1.10
+  version: 1.1.0
 platform: ruby
 authors:
 - bedroesb
 - janslifka
 - MarekSuchanek
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-03-20 00:00:00.000000000 Z
+date: 2025-12-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: jekyll
@@ -46,9 +46,9 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '12.0'
-description: 
+description:
 email:
-- 'bedro@psb.vib-ugent.be
+- 'bert.droesbeke@vib.be
 
   '
 executables: []
@@ -69,7 +69,7 @@ homepage: https://elixir-belgium.github.io/elixir-toolkit-theme-plugins/
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -84,8 +84,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.3.26
-signing_key: 
+rubygems_version: 3.5.22
+signing_key:
 specification_version: 4
 summary: Plugins to work together with ELIXIR Toolkit theme
 test_files: []