Merge pull request #1497 from seek4science/cff-citation

Use CFF to generate citation if present

app/assets/javascripts/application_shared.js.erb

@@ -247,9 +247,9 @@ $j(document).ready(function () {
         var style = $j(this).val();
         var url = $j(this).data('url');
         var target = $j('#citation');
-        var currentStyle = $j('#citation').data('citationStyle');
+        var currentStyle = $j('#citation div').data('citationStyle');
 
-        if (style && style !== currentStyle) {
+        if (style && currentStyle && style !== currentStyle) {
             $j.ajax({
                 url: url,
                 data: { style: style },

app/controllers/citations_controller.rb

@@ -4,7 +4,7 @@ class CitationsController < ApplicationController
 
   def fetch
     respond_to do |format|
-      format.js { render partial: 'assets/citation', locals: { doi: params[:doi], style: params[:style] } }
+      format.js { render partial: 'assets/citation_from_doi', locals: { doi: params[:doi], style: params[:style] } }
     end
   end
 

app/controllers/concerns/raw_display.rb

@@ -1,20 +1,24 @@
 module RawDisplay
   extend ActiveSupport::Concern
 
-  RAW_DISPLAY_FORMATS = %w(notebook markdown pdf text image)
+  RAW_DISPLAY_FORMATS = %w(notebook markdown pdf text image citation)
 
   # A method for rendering a given Git/Content Blob in an HTML "Viewer"
   def render_display(blob, url_options: {})
     if params[:display]
-      renderer = Seek::Renderers.const_get("#{params[:display].classify}Renderer").new(blob, url_options: url_options)
-    else
-      renderer = Seek::Renderers::RendererFactory.instance.renderer(blob, url_options: url_options)
+      renderer = Seek::Renderers.const_get("#{params[:display].classify}Renderer").new(blob, url_options: url_options, params: params)
+    else # Render default display
+      renderer = Seek::Renderers::RendererFactory.instance.renderer(blob, url_options: url_options, params: params)
     end
     if renderer.can_render?
       # check if allowed by cookies
       unless renderer.external_embed? && !cookie_consent.allow_embedding?
         response.set_header('Content-Security-Policy', renderer.content_security_policy)
-        render renderer.format => renderer.render_standalone.html_safe, layout: renderer.layout
+        if params[:disposition] == 'inline' # Partial view
+          render renderer.format => renderer.render.html_safe
+        else # Full page view
+          render renderer.format => renderer.render_standalone.html_safe, layout: renderer.layout
+        end
       end
     else
       raise ActionController::UnknownFormat

app/helpers/citations_helper.rb

@@ -2,12 +2,18 @@
 require 'csl/styles'
 
 module CitationsHelper
-  def render_citation(doi, style)
-    Seek::Citations.generate(doi, style)
+  def render_doi_citation(doi, style)
+    Seek::Citations.from_doi(doi, style)
   rescue JSON::ParserError, RestClient::Exception
     'An error occurred whilst fetching the citation'
   end
 
+  def render_cff_citation(blob, style)
+    Seek::Citations.from_cff(blob, style)
+  rescue StandardError
+    'An error occurred whilst fetching the citation'
+  end
+
   def citation_style_options(selected = nil)
     selected ||= selected_citation_style
     options_for_select(Seek::Citations.style_pairs, selected)

app/views/assets/_citation_box.html.erb

@@ -1,4 +1,6 @@
 <% snapshot ||= nil %>
+<% blob ||= nil %>
+<% url = blob ? blob.content_path(display: 'citation', disposition: 'inline') : citation_path(doi) %>
 
 <div class="panel panel-default">
   <div class="panel-heading">
@@ -10,11 +12,15 @@
   </div>
   <div class="panel-body">
     <div id="citation" class="well well-sm citation-box">
-      <%= render partial: 'assets/citation', locals: { doi: doi, style: selected_citation_style } %>
+      <% if blob %>
+        <%= render partial: 'assets/citation_from_cff', locals: { blob: blob, style: selected_citation_style } %>
+      <% else %>
+        <%= render partial: 'assets/citation_from_doi', locals: { doi: doi, style: selected_citation_style } %>
+      <% end %>
     </div>
 
     <%= select_tag(nil, citation_style_options, id: 'citation-style-select', class: 'form-control',
-                   data: { url: citation_path(doi) }) %>
+                   data: { url: url }) %>
 
     <% if snapshot %>
       <span class="subtle">

app/views/assets/_citation_from_cff.html.erb

@@ -0,0 +1,3 @@
+<%= content_tag(:div, data: { 'citation-style' => style }) do %>
+  <%= render_cff_citation(blob, style) %>
+<% end %>

app/views/assets/_citation.html.erb → app/views/assets/_citation_from_doi.html.erb

@@ -1,3 +1,3 @@
 <%= content_tag(:div, data: { 'citation-style' => style }) do %>
-  <%= render_citation(doi, style) %>
+  <%= render_doi_citation(doi, style) %>
 <% end %>

app/views/assets/_resource_main_content_right.html.erb

@@ -32,6 +32,8 @@
 <% elsif versioned_resource.respond_to?(:doi) %>
   <% if versioned_resource.doi.present? %>
     <%= render :partial => "assets/citation_box", locals: { doi: versioned_resource.doi } %>
+  <% elsif versioned_resource.is_git_versioned? && versioned_resource.file_exists?(Seek::WorkflowExtractors::CFF::FILENAME) %>
+    <%= render :partial => "assets/citation_box", locals: { blob: versioned_resource.get_blob(Seek::WorkflowExtractors::CFF::FILENAME) } %>
   <% elsif resource.can_manage? && Seek::Config.doi_minting_enabled && resource.supports_doi? %>
     <%= render :partial => "assets/citation_instructions", locals: { resource: resource, versioned_resource: versioned_resource } %>
   <% end %>

lib/seek/citations.rb

@@ -6,9 +6,17 @@ module Seek
   class Citations
     DEFAULT = 'apa' # This could be a setting one day
 
-    def self.generate(doi, style)
+    def self.from_doi(doi, style)
+      generate(doi_to_csl(doi), style)
+    end
+
+    def self.from_cff(blob, style)
+      generate(cff_to_csl(blob), style)
+    end
+
+    def self.generate(csl, style)
       cp = CiteProc::Processor.new(style: style, format: 'html')
-      cp.register(csl(doi).merge(id: :_))
+      cp.register(csl.merge(id: :_))
       cp.render(:bibliography, id: :_).last.html_safe
     end
 
@@ -18,13 +26,20 @@ def self.style_pairs
       end
     end
 
-    def self.csl(doi)
+    def self.doi_to_csl(doi)
       Rails.cache.fetch("citation-#{doi}") do
         resp = RestClient.get("https://doi.org/#{Addressable::URI.escape(doi)}", accept: 'application/vnd.citationstyles.csl+json')
         JSON.parse(resp)
       end
     end
 
+    def self.cff_to_csl(blob)
+      Rails.cache.fetch("citation-cff-#{blob.cache_key}") do
+        cff = ::CFF::File.read(blob.file)
+        BibTeX.parse(cff.to_bibtex).to_citeproc.first
+      end
+    end
+
     def self.generate_style_pairs
       CSL::Style.list.map { |key| [CSL::Style.load(key).title, key] }.sort_by { |s| s[0] }
     end

lib/seek/content_type_detection.rb

@@ -106,6 +106,10 @@ def is_image?(blob = self)
       blob.content_type.try(:split, '/').try(:first) == 'image'
     end
 
+    def is_cff?(blob = self)
+      blob.content_type_file_extensions.include?('cff')
+    end
+
     def is_image_convertable?(blob = self)
       (IMAGE_CONVERTABLE_FORMAT & blob.content_type_file_extensions).any?
     end

lib/seek/renderers/blob_renderer.rb

@@ -3,11 +3,12 @@ module Renderers
     class BlobRenderer
       include ActionView::Helpers
 
-      attr_reader :blob
+      attr_reader :blob, :params
 
-      def initialize(git_blob_or_blob, url_options: {})
+      def initialize(git_blob_or_blob, url_options: {}, params: {})
         @blob = git_blob_or_blob
         @url_options = url_options
+        @params = params
       end
 
       def render
@@ -66,6 +67,13 @@ def render_template(template_path, variables = {}, layout: 'application')
           layout: layout
         )
       end
+
+      def render_partial(partial_path, variables = {})
+        ApplicationController.renderer.render(
+          partial: partial_path,
+          locals: variables
+        )
+      end
     end
   end
 end

lib/seek/renderers/citation_renderer.rb

@@ -0,0 +1,19 @@
+module Seek
+  module Renderers
+    class CitationRenderer < BlobRenderer
+      def can_render?
+        blob.is_cff?
+      end
+
+      def render_content
+        render_partial('assets/citation_from_cff', blob: blob, style: style)
+      end
+
+      private
+
+      def style
+        params[:style] || Seek::Citations::DEFAULT
+      end
+    end
+  end
+end

lib/seek/renderers/renderer_factory.rb

@@ -3,10 +3,10 @@ module Renderers
     class RendererFactory
       include Singleton
 
-      def renderer(blob, url_options: {})
+      def renderer(blob, url_options: {}, params: {})
         renderer_class = cache.fetch(blob.cache_key) { detect_renderer(blob).name }.constantize
 
-        renderer_class.new(blob, url_options: url_options)
+        renderer_class.new(blob, url_options: url_options, params: params)
       end
 
       private

test/functional/git_controller_test.rb

@@ -659,6 +659,20 @@ def setup
     assert_select '.markdown-body h1', text: 'FAIRDOM-SEEK'
   end
 
+  test 'should display blob as markdown inline' do
+    @git_version.add_file('file.md', FactoryBot.create(:markdown_content_blob))
+    disable_authorization_checks { @git_version.save! }
+
+    get :raw, xhr: true, params: { workflow_id: @workflow.id, version: @git_version.version, path: 'file.md',
+                                   display: 'markdown', disposition: 'inline' }
+
+    assert_response :success
+    assert @response.header['Content-Type'].start_with?('text/html')
+    assert_equal ApplicationController::USER_CONTENT_CSP, @response.header['Content-Security-Policy']
+    assert_select 'body', count: 0
+    assert_select 'iframe'
+  end
+
   test 'should display blob as jupyter' do
     @git_version.add_file('file.ipynb', FactoryBot.create(:jupyter_notebook_content_blob))
     disable_authorization_checks { @git_version.save! }
@@ -784,4 +798,48 @@ def setup
     assert_equal 'file.md', log.data[:path]
     assert_equal 'markdown', log.data[:display]
   end
+
+  test 'should display CFF blob as citation' do
+    @git_version.add_file('CITATION.cff', open_fixture_file('CITATION.cff'))
+    disable_authorization_checks { @git_version.save! }
+
+    get :raw, params: { workflow_id: @workflow.id, version: @git_version.version, path: 'CITATION.cff',
+                        display: 'citation' }
+
+    assert_response :success
+    assert @response.header['Content-Type'].start_with?('text/html')
+    assert_equal ApplicationController::USER_CONTENT_CSP, @response.header['Content-Security-Policy']
+    assert_select 'body'
+    assert_select '#navbar', count: 0
+    assert_select 'div[data-citation-style=?]', 'apa', text: /van der Real Person, O\. T\./
+  end
+
+  test 'should display CFF blob as citation with selected style' do
+    @git_version.add_file('CITATION.cff', open_fixture_file('CITATION.cff'))
+    disable_authorization_checks { @git_version.save! }
+
+    get :raw, params: { workflow_id: @workflow.id, version: @git_version.version, path: 'CITATION.cff',
+                        display: 'citation', style: 'bibtex' }
+
+    assert_response :success
+    assert @response.header['Content-Type'].start_with?('text/html')
+    assert_equal ApplicationController::USER_CONTENT_CSP, @response.header['Content-Security-Policy']
+    assert_select 'body'
+    assert_select '#navbar', count: 0
+    assert_select 'div[data-citation-style=?]', 'bibtex', text: /author=\{Real Person, One Truly van der, IV and/
+  end
+
+  test 'should display CFF blob as citation inline' do
+    @git_version.add_file('CITATION.cff', open_fixture_file('CITATION.cff'))
+    disable_authorization_checks { @git_version.save! }
+
+    get :raw, xhr: true, params: { workflow_id: @workflow.id, version: @git_version.version, path: 'CITATION.cff',
+                                   display: 'citation', disposition: 'inline', style: 'the-lancet' }
+
+    assert_response :success
+    assert @response.header['Content-Type'].start_with?('text/html')
+    assert_equal ApplicationController::USER_CONTENT_CSP, @response.header['Content-Security-Policy']
+    assert_select 'body', count: 0
+    assert_select 'div[data-citation-style=?]', 'the-lancet', text: /Real Person OT van der IV/
+  end
 end

test/functional/workflows_controller_test.rb

@@ -1737,4 +1737,22 @@ def bad_generator.write_graph(struct)
     # Reset the view parameter
     session.delete(:view)
   end
+
+  test 'can get citation for workflow with CFF' do
+    workflow = FactoryBot.create(:local_git_workflow, policy: FactoryBot.create(:public_policy))
+
+    get :show, params: { id: workflow }
+    assert_response :success
+    assert_select '#citation', text: /van der Real Person, O\. T\./, count: 0
+
+    gv = workflow.latest_git_version
+    disable_authorization_checks do
+      gv.add_file('CITATION.cff', open_fixture_file('CITATION.cff'))
+      disable_authorization_checks { gv.save! }
+    end
+
+    get :show, params: { id: workflow }
+    assert_response :success
+    assert_select '#citation', text: /van der Real Person, O\. T\./, count: 1
+  end
 end