Merge branch 'main' into issue_1199_add_sharing_permisions_to_sample_…

…types

.github/workflows/ansible-install.yml

@@ -13,7 +13,7 @@ jobs:
     continue-on-error: true
     strategy:
       matrix:
-        os: [ubuntu-20.04,ubuntu-22.04]
+        os: [ubuntu-20.04,ubuntu-22.04,ubuntu-24.04]
 
     services:
       mysql:

Gemfile.lock

@@ -491,7 +491,7 @@ GEM
     net-smtp (0.4.0.1)
       net-protocol
     netrc (0.11.0)
-    nio4r (2.7.0)
+    nio4r (2.7.3)
     nokogiri (1.16.5)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
@@ -563,7 +563,7 @@ GEM
     psych (5.1.0)
       stringio
     public_suffix (5.0.0)
-    puma (5.6.8)
+    puma (5.6.9)
       nio4r (~> 2.0)
     pyu-ruby-sasl (0.0.3.3)
     racc (1.8.0)
@@ -728,8 +728,8 @@ GEM
       netrc (~> 0.8)
     reverse_markdown (2.1.1)
       nokogiri
-    rexml (3.2.8)
-      strscan (>= 3.0.9)
+    rexml (3.3.6)
+      strscan
     rfc-822 (0.4.1)
     rmagick (5.3.0)
       pkg-config (~> 1.4)
@@ -938,7 +938,7 @@ GEM
       addressable (>= 2.3.6)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
-    webrick (1.8.1)
+    webrick (1.8.2)
     webrobots (0.1.2)
     websocket-driver (0.7.6)
       websocket-extensions (>= 0.1.0)

app/assets/javascripts/sample_types.js

@@ -96,6 +96,16 @@ var SampleTypes = {
         else {
             seek_sample_element.hide();
         }
+    },
+
+    expandIRI: function () {
+        var termIRI = $j(this).next('.term-iri');
+        termIRI.toggleClass('visible');
     }
 
 };
+
+
+$j(document).ready(function() {
+    $j('.term-label').on('click', SampleTypes.expandIRI);
+});

app/assets/stylesheets/linked_extended_metadata.css

@@ -1,3 +1,21 @@
+.term-label {
+    font-weight: normal;
+    text-decoration: underline;
+}
+
+.term-iri {
+    display: none;
+    background-color: rgba(177, 183, 187, 0.47);
+    color: black;
+    font-weight: normal;
+}
+
+.term-iri.visible {
+    display: inline;
+    opacity: 1;
+    margin-left: 10px;
+}
+
 .linked_extended_metdata .panel-default .panel-heading {
     font-weight: bold;
     color: #333;

app/assets/stylesheets/styles.scss

@@ -347,6 +347,10 @@ div.renderer {
   color: if(lightness($text-color) > 50, darken($text-color, 20%), lighten($text-color, 30%));
 }
 
+.select2-results__option--highlighted .subtle {
+  color: unset;
+}
+
 span.truncated-name {
   display: inline-block;
   overflow: hidden;

app/controllers/admin_controller.rb

@@ -121,6 +121,7 @@ def update_features_enabled
     Seek::Config.documents_enabled = string_to_boolean params[:documents_enabled]
     Seek::Config.events_enabled = string_to_boolean params[:events_enabled]
     Seek::Config.isa_enabled = string_to_boolean params[:isa_enabled]
+    Seek::Config.observation_units_enabled = string_to_boolean params[:observation_units_enabled]
     Seek::Config.models_enabled = string_to_boolean params[:models_enabled]
     Seek::Config.organisms_enabled = string_to_boolean params[:organisms_enabled]
     Seek::Config.programmes_enabled = string_to_boolean params[:programmes_enabled]

app/controllers/extended_metadata_types_controller.rb

@@ -4,6 +4,8 @@ class ExtendedMetadataTypesController < ApplicationController
   before_action :find_requested_item, only: [:administer_update, :show]
   include Seek::IndexPager
 
+  api_actions :index, :show
+
   # generated for form, to display fields for selected metadata type
   def form_fields
     id = params[:id]

app/controllers/human_diseases_controller.rb

@@ -16,6 +16,8 @@ class HumanDiseasesController < ApplicationController
   include Seek::ExternalServiceWrapper
   include Seek::IndexPager
 
+  api_actions :index, :show, :create, :update, :destroy
+
   def show
     respond_to do |format|
       format.html

app/controllers/observation_units_controller.rb

@@ -10,6 +10,9 @@ class ObservationUnitsController < ApplicationController
   before_action :login_required,:except=>[:show,:index]
   before_action :find_assets, only: [:index]
 
+  include Seek::Publishing::PublishingCommon
+  include Seek::IsaGraphExtensions
+
   api_actions :index, :show, :create, :update, :destroy
 
   def show

app/controllers/projects_controller.rb

@@ -203,8 +203,8 @@ def submit_fairdata_station
     path = params[:datastation_data].path
     policy = Policy.new
     policy.set_attributes_with_sharing(policy_params)
-    datadata_inv = Seek::FairDataStation::Reader.instance.parse_graph(path)
-    @investigation = Seek::FairDataStation::Writer.instance.construct_isa(datadata_inv.first, current_person, [@project], policy)
+    datadata_inv = Seek::FairDataStation::Reader.new.parse_graph(path)
+    @investigation = Seek::FairDataStation::Writer.new.construct_isa(datadata_inv.first, current_person, [@project], policy)
     @investigation.save!
 
     respond_to do |format|

app/controllers/sample_types_controller.rb

@@ -14,7 +14,7 @@ class SampleTypesController < ApplicationController
 
   before_action :find_and_authorize_requested_item, except: %i[index new create]
 
-  api_actions :index
+  api_actions :index, :show, :create, :update, :destroy
 
   # GET /sample_types/1  ,'sample_attributes','linked_sample_attributes'
   # GET /sample_types/1.json

app/controllers/samples_controller.rb

@@ -15,6 +15,8 @@ class SamplesController < ApplicationController
   include Seek::IsaGraphExtensions
   include Seek::Publishing::PublishingCommon
 
+  api_actions :index, :show, :create, :update, :destroy, :batch_create
+
   def index
     # There must be better ways of coding this
     if @data_file || @sample_type
@@ -221,31 +223,45 @@ def typeahead
 
   def query
     project_ids = params[:project_ids]&.map(&:to_i)
-
+    attribute_filter_value = params[:template_attribute_value]&.downcase
     @result = params[:template_id].present? ?
       Template.find(params[:template_id]).sample_types.map(&:samples).flatten : []
 
-    if params[:template_attribute_id].present? && params[:template_attribute_value].present?
-      attribute_title = TemplateAttribute.find(params[:template_attribute_id]).title
-      @result = @result.select { |s| s.get_attribute_value(attribute_title)&.include?(params[:template_attribute_value]) }
+    if params[:template_attribute_id].present? && attribute_filter_value.present?
+      template_attribute = TemplateAttribute.find(params[:template_attribute_id])
+      @result = @result.select do |s|
+        sample_attribute = s.sample_type.sample_attributes.detect { |sa| template_attribute.sample_attributes.include? sa }
+        sample_attribute_title = sample_attribute&.title
+        if sample_attribute&.sample_attribute_type&.seek_sample_multi?
+          attr_value = s.get_attribute_value(sample_attribute_title)
+          attr_value&.any? { |v| v[:title].downcase.include?(attribute_filter_value) }
+        elsif sample_attribute&.sample_attribute_type&.seek_sample?
+          s.get_attribute_value(sample_attribute_title)[:title]&.downcase&.include?(attribute_filter_value)
+        elsif sample_attribute&.sample_attribute_type&.seek_cv_list?
+          attr_value = s.get_attribute_value(sample_attribute_title)
+          attr_value&.any? { |v| v.downcase.include?(attribute_filter_value) }
+        else
+          s.get_attribute_value(sample_attribute_title)&.downcase&.include?(attribute_filter_value)
+        end
+      end
     end
 
     if params[:input_template_id].present? # linked
-      title =
-        TemplateAttribute.find(params[:input_attribute_id]).title if params[:input_attribute_id].present?
-      @result = find_samples(@result, :linked_samples,
-        { attribute_id: params[:input_attribute_id],
+      input_template_attribute =
+        TemplateAttribute.find(params[:input_attribute_id])
+      @result = filter_linked_samples(@result, :linked_samples,
+                                      { attribute_id: params[:input_attribute_id],
           attribute_value: params[:input_attribute_value],
-          template_id: params[:input_template_id] }, title)
+          template_id: params[:input_template_id] }, input_template_attribute)
     end
 
     if params[:output_template_id].present? # linking
-      title =
-        TemplateAttribute.find(params[:output_attribute_id]).title if params[:output_attribute_id].present?
-      @result = find_samples(@result, :linking_samples,
-        { attribute_id: params[:output_attribute_id],
+      output_template_attribute =
+        TemplateAttribute.find(params[:output_attribute_id])
+      @result = filter_linked_samples(@result, :linking_samples,
+                                      { attribute_id: params[:output_attribute_id],
           attribute_value: params[:output_attribute_value],
-          template_id: params[:output_template_id] }, title)
+          template_id: params[:output_template_id] }, output_template_attribute)
     end
 
     @result = @result.select { |s| (project_ids & s.project_ids).any? } if project_ids.present?
@@ -319,16 +335,36 @@ def find_index_assets
     end
   end
 
-  def find_samples(samples, link, options, title)
+  # Filters linked samples based on the provided options and template attribute title.
+  #
+  # @param samples [Array<Sample>] the list of samples to filter
+  # @param link [Symbol] the method to call on each sample to get the linked samples (:linked_samples or :linking_samples)
+  # @param options [Hash] the options for filtering
+  # @option options [Integer] :template_id the ID of the template to filter by
+  # @option options [String] :attribute_value the value of the attribute to filter by
+  # @option options [Integer] :attribute_id the ID of the attribute to filter by
+  # @param template_attribute_title [String] the title of the template attribute to filter by
+  # @return [Array<Sample>] the filtered list of samples
+  def filter_linked_samples(samples, link, options, template_attribute)
+    raise ArgumentError, "Invalid linking method provided. '#{link.to_s}' is not allowed!" unless %i[linked_samples linking_samples].include? link
+
+    template_attribute_title = template_attribute&.title
     samples.select do |s|
       s.send(link).any? do |x|
         selected = x.sample_type.template_id == options[:template_id].to_i
-        selected = x.get_attribute_value(title)&.include?(options[:attribute_value]) if title.present? && selected
-        selected || find_samples([x], link, options, title).present?
+        if template_attribute.sample_attribute_type.seek_sample_multi?
+          selected = x.get_attribute_value(template_attribute_title)&.any? { |v| v[:title].downcase.include?(options[:attribute_value]) } if template_attribute.present? && selected
+        elsif  template_attribute.sample_attribute_type.seek_sample?
+          selected = x.get_attribute_value(template_attribute_title)&[:title].downcase&.include?(options[:attribute_value]) if template_attribute.present? && selected
+        elsif template_attribute.sample_attribute_type.seek_cv_list?
+          selected = x.get_attribute_value(template_attribute_title)&.any? { |v| v.downcase.include?(options[:attribute_value]) } if template_attribute.present? && selected
+        else
+          selected = x.get_attribute_value(template_attribute_title)&.downcase&.include?(options[:attribute_value]&.downcase) if template_attribute.present? && selected
+        end
+        selected || filter_linked_samples([x], link, options, template_attribute).present?
       end
     end
   end
-
   def templates_enabled?
     unless Seek::Config.isa_json_compliance_enabled
       flash[:error] = 'Not available'

app/controllers/sessions_controller.rb

@@ -66,16 +66,7 @@ def omniauth_failure
   def destroy
     logout_user
     flash[:notice] = 'You have been logged out.'
-
-    begin
-      if request.env['HTTP_REFERER'].try(:normalize_trailing_slash) == search_url.normalize_trailing_slash
-        redirect_to :root
-      else
-        redirect_back(fallback_location: root_path)
-      end
-    rescue RedirectBackError
-      redirect controller: :homes, action: :index
-    end
+    redirect_to :root
   end
 
   protected

app/controllers/templates_controller.rb

@@ -116,7 +116,7 @@ def populate_template
   # post
   def template_attributes
     template = Template.find(params[:id])
-    items = template.template_attributes.map { |a| { id: a.id, title: a.title } }
+    items = template.template_attributes.map { |a| { id: a.id, title: a.title.sanitize } }
     respond_to do |format|
       format.json { render json: items.to_json }
     end

app/controllers/workflows_controller.rb

@@ -21,7 +21,7 @@ class WorkflowsController < ApplicationController
   include RoCrateHandling
   include Legacy::WorkflowSupport
 
-  api_actions :index, :show, :create, :update, :destroy, :ro_crate, :ro_crate_metadata, :create_version
+  api_actions :index, :show, :create, :update, :destroy, :ro_crate, :ro_crate_metadata, :create_version, :submit
 
   rescue_from ROCrate::ReadException do |e|
     logger.error("Error whilst attempting to read RO-Crate metadata for Workflow #{@workflow&.id}: #{e.exception.class.name} #{e.message}")

app/helpers/assays_helper.rb

@@ -57,16 +57,6 @@ def list_assay_human_diseases(attribute, assay_human_diseases, html_options = {}
     result.html_safe
   end
 
-  # the selection dropdown box for selecting the study for an assay
-  def assay_study_selection(element_name, current_study)
-    grouped_options = grouped_options_for_study_selection(current_study)
-    blank = current_study.blank? ? 'Not specified' : nil
-    disabled = current_study && !current_study.can_edit?
-    options = grouped_options_for_select(grouped_options, current_study.try(:id))
-    select_tag(element_name, options,
-               class: 'form-control', include_blank: blank, disabled: disabled).html_safe
-  end
-
   # a lightway way to select a SOP - specifically for the assay creation during data file creation
   def assay_sop_selection(element_name, current_sop)
     sops = authorised_sops(User.current_user.person.projects)

app/helpers/samples_helper.rb

@@ -145,7 +145,9 @@ def display_attribute_value(value, attribute, options = {})
       when Seek::Samples::BaseType::CV
         seek_cv_attribute_display(value, attribute)
       when Seek::Samples::BaseType::CV_LIST
-        value.each{|v| seek_cv_attribute_display(v, attribute) }.join(', ')
+        value.map do |v|
+          seek_cv_attribute_display(v, attribute)
+        end.join(', ').html_safe
       when Seek::Samples::BaseType::LINKED_EXTENDED_METADATA
         linked_extended_metadata_attribute_display(value, attribute)
       when Seek::Samples::BaseType::LINKED_EXTENDED_METADATA_MULTI
@@ -173,12 +175,15 @@ def select_cv_source_ontology(sample_controlled_vocab)
   end
 
   def seek_cv_attribute_display(value, attribute)
-    term = attribute.sample_controlled_vocab.sample_controlled_vocab_terms.where(label:value).last
-    content = value
+    term = attribute.sample_controlled_vocab.sample_controlled_vocab_terms.where(label: value).last
     if term && term.iri.present?
-      content << " (#{term.iri}) "
+      iri_content = term.iri.match?(/^https?:\/\//) ? link_to(term.iri, term.iri, target: '_blank') : term.iri
+      label_tag = content_tag(:label, term.label, class: 'term-label')
+      iri_tag = content_tag(:label, iri_content, class: 'term-iri badge')
+      "#{label_tag}#{iri_tag}".html_safe
+    else
+      term.label
     end
-    content
   end
 
   def linked_extended_metadata_attribute_display(value, attribute)

app/helpers/studies_helper.rb

@@ -26,4 +26,14 @@ def authorised_studies(projects = nil)
   def show_batch_miappe_button?
     ExtendedMetadataType.where(supported_type: 'Study', title: ExtendedMetadataType::MIAPPE_TITLE, enabled: true).any?
   end
+
+  # the selection dropdown box for selecting the study for a resource, such as assay or observation unit
+  def resource_study_selection(element_name, current_study)
+    grouped_options = grouped_options_for_study_selection(current_study)
+    blank = current_study.blank? ? 'Not specified' : nil
+    disabled = current_study && !current_study.can_edit?
+    options = grouped_options_for_select(grouped_options, current_study.try(:id))
+    select_tag(element_name, options,
+               class: 'form-control', include_blank: blank, disabled: disabled).html_safe
+  end
 end