Merge branch 'main' into full-test-suite

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)
@@ -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

@@ -351,6 +351,8 @@ def update_settings
     Seek::Config.metadata_license = params[:metadata_license]
     Seek::Config.recommended_data_licenses = params[:recommended_data_licenses]&.compact_blank
     Seek::Config.recommended_software_licenses = params[:recommended_software_licenses]&.compact_blank
+    Seek::Config.sandbox_instance_url = params[:sandbox_instance_url]
+    Seek::Config.sandbox_instance_name = params[:sandbox_instance_name]
     update_flag = (pubmed_email == '' || pubmed_email_valid) && (crossref_email == '' || crossref_email_valid)
     update_redirect_to update_flag, 'settings'
   end

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/isa_assays_controller.rb

@@ -44,6 +44,8 @@ def new
   end
 
   def create
+    update_sharing_policies @isa_assay.assay
+    @isa_assay.sample_type.policy = @isa_assay.assay.policy
     if @isa_assay.save
       flash[:notice] = "The #{t('isa_assay')} was successfully created.<br/>".html_safe
       respond_to do |format|
@@ -66,8 +68,9 @@ def edit
   end
 
   def update
+    update_sharing_policies @isa_assay.assay
     @isa_assay.assay.attributes = isa_assay_params[:assay]
-
+    @isa_assay.sample_type.policy = @isa_assay.assay.policy
     # update the sample_type
     unless @isa_assay&.assay&.is_assay_stream?
       if requested_item_authorized?(@isa_assay.sample_type)

app/controllers/isa_studies_controller.rb

@@ -12,6 +12,8 @@ def new
   def create
     @isa_study = IsaStudy.new(isa_study_params)
     update_sharing_policies @isa_study.study
+    @isa_study.source.policy = @isa_study.study.policy
+    @isa_study.sample_collection.policy = @isa_study.study.policy
     @isa_study.source.contributor = User.current_user.person
     @isa_study.sample_collection.contributor = User.current_user.person
     @isa_study.study.sample_types = [@isa_study.source, @isa_study.sample_collection]
@@ -43,6 +45,8 @@ def update
     # update the study
     @isa_study.study.attributes = isa_study_params[:study]
     update_sharing_policies @isa_study.study
+    @isa_study.source.policy = @isa_study.study.policy
+    @isa_study.sample_collection.policy = @isa_study.study.policy
     update_relationships(@isa_study.study, isa_study_params[:study])
 
     # update the source

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

@@ -2,24 +2,26 @@ class SampleTypesController < ApplicationController
   respond_to :html, :json
   include Seek::UploadHandling::DataUpload
   include Seek::IndexPager
+  include Seek::AssetsCommon
 
   before_action :samples_enabled?
-  before_action :find_sample_type, only: [:show, :edit, :update, :destroy, :template_details, :batch_upload]
   before_action :check_no_created_samples, only: [:destroy]
+  before_action :find_and_authorize_requested_item, except: %i[create batch_upload index new template_details]
+  before_action :find_sample_type, only: %i[batch_upload template_details]
+  before_action :check_isa_json_compliance, only: %i[edit update manage manage_update]
   before_action :find_assets, only: [:index]
-  before_action :auth_to_create, only: [:new, :create]
-  before_action :project_membership_required, only: [:create, :new, :select, :filter_for_select]
+  before_action :auth_to_create, only: %i[new create]
+  before_action :project_membership_required, only: %i[create new select filter_for_select]
 
-  before_action :authorize_requested_sample_type, except: [: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
   def show
     respond_to do |format|
       format.html
-      format.json {render json: @sample_type, include: [params[:include]]}
+      format.json { render json: @sample_type, include: [params[:include]] }
     end
   end
 
@@ -28,7 +30,7 @@ def show
   def new
     @tab = 'manual'
 
-    attr = params["sample_type"] ? sample_type_params : {}
+    attr = params['sample_type'] ? sample_type_params : {}
     @sample_type = SampleType.new(attr)
     @sample_type.sample_attributes.build(is_title: true, required: true) # Initial attribute
 
@@ -62,17 +64,24 @@ def create
     @sample_type = SampleType.new(sample_type_params)
     @sample_type.contributor = User.current_user.person
 
+    # Update sharing policies
+    update_sharing_policies(@sample_type)
+    # Update relationships
+    update_relationships(@sample_type, params)
+    # Update tags
+    update_annotations(params[:tag_list], @sample_type)
+
     # removes controlled vocabularies or linked seek samples where the type may differ
     @sample_type.resolve_inconsistencies
     @tab = 'manual'
 
     respond_to do |format|
       if @sample_type.save
         format.html { redirect_to @sample_type, notice: 'Sample type was successfully created.' }
-        format.json { render json: @sample_type, status: :created, location: @sample_type, include: [params[:include]]}
+        format.json { render json: @sample_type, status: :created, location: @sample_type, include: [params[:include]] }
       else
         format.html { render action: 'new' }
-        format.json { render json: @sample_type.errors, status: :unprocessable_entity}
+        format.json { render json: @sample_type.errors, status: :unprocessable_entity }
       end
     end
   end
@@ -83,31 +92,25 @@ def update
 
     @sample_type.update(sample_type_params)
     @sample_type.resolve_inconsistencies
+
+    # Update sharing policies
+    update_sharing_policies(@sample_type)
+    # Update relationships
+    update_relationships(@sample_type, params)
+    # Update tags
+    update_annotations(params[:tag_list], @sample_type)
+
     respond_to do |format|
       if @sample_type.save
         format.html { redirect_to @sample_type, notice: 'Sample type was successfully updated.' }
-        format.json {render json: @sample_type, include: [params[:include]]}
+        format.json { render json: @sample_type, include: [params[:include]] }
       else
         format.html { render action: 'edit', status: :unprocessable_entity }
-        format.json { render json: @sample_type.errors, status: :unprocessable_entity}
+        format.json { render json: @sample_type.errors, status: :unprocessable_entity }
       end
     end
   end
 
-  # DELETE /sample_types/1
-  # DELETE /sample_types/1.json
-  def destroy
-    respond_to do |format|
-    if @sample_type.can_delete? && @sample_type.destroy
-      format.html { redirect_to @sample_type,location: sample_types_path, notice: 'Sample type was successfully deleted.' }
-      format.json {render json: @sample_type, include: [params[:include]]}
-    else
-      format.html { redirect_to @sample_type, location: sample_types_path, notice: 'It was not possible to delete the sample type.' }
-      format.json { render json: @sample_type.errors, status: :unprocessable_entity}
-    end
-    end
-  end
-
   def template_details
     render partial: 'template'
   end
@@ -133,40 +136,39 @@ def filter_for_select
     render partial: 'sample_types/select/filtered_sample_types'
   end
 
-  def batch_upload
-
-  end
+  def batch_upload; end
 
   private
 
   def sample_type_params
     attributes = params[:sample_type][:sample_attributes]
-    if (attributes)
+    if attributes
       params[:sample_type][:sample_attributes_attributes] = []
       attributes.each do |attribute|
         if attribute[:sample_attribute_type]
           if attribute[:sample_attribute_type][:id]
             attribute[:sample_attribute_type_id] = attribute[:sample_attribute_type][:id].to_i
           elsif attribute[:sample_attribute_type][:title]
-            attribute[:sample_attribute_type_id] = SampleAttributeType.where(title: attribute[:sample_attribute_type][:title]).first.id
+            attribute[:sample_attribute_type_id] =
+              SampleAttributeType.where(title: attribute[:sample_attribute_type][:title]).first.id
           end
         end
         attribute[:unit_id] = Unit.where(symbol: attribute[:unit_symbol]).first.id unless attribute[:unit_symbol].nil?
         params[:sample_type][:sample_attributes_attributes] << attribute
       end
     end
 
-    if (params[:sample_type][:assay_assets_attributes])
+    if params[:sample_type][:assay_assets_attributes]
       params[:sample_type][:assay_ids] = params[:sample_type][:assay_assets_attributes].map { |x| x[:assay_id] }
     end
 
-    params.require(:sample_type).permit(:title, :description, {tags: []}, :template_id, *creator_related_params,
+    params.require(:sample_type).permit(:title, :description, { tags: [] }, :template_id, *creator_related_params,
                                         { project_ids: [],
-                                          sample_attributes_attributes: [:id, :title, :pos, :required, :is_title,
-                                                                         :description, :pid, :sample_attribute_type_id,
-                                                                         :sample_controlled_vocab_id, :isa_tag_id,
-                                                                         :allow_cv_free_text, :linked_sample_type_id,
-                                                                         :unit_id, :_destroy] }, :assay_ids => [])
+                                          sample_attributes_attributes: %i[id title pos required is_title
+                                                                           description pid sample_attribute_type_id
+                                                                           sample_controlled_vocab_id isa_tag_id
+                                                                           allow_cv_free_text linked_sample_type_id
+                                                                           unit_id _destroy] }, assay_ids: [])
   end
 
 
@@ -179,28 +181,22 @@ def build_sample_type_from_template
     @sample_type.build_attributes_from_template
   end
 
-  private
+  def check_isa_json_compliance
+    @sample_type ||= SampleType.find(params[:id])
+    return unless Seek::Config.isa_json_compliance_enabled && @sample_type.is_isa_json_compliant?
+
+    flash[:error] = 'This sample type is ISA JSON compliant and cannot be managed.'
+    redirect_to sample_types_path
+  end
 
   def find_sample_type
     scope = Seek::Config.isa_json_compliance_enabled ? SampleType.without_template : SampleType
     @sample_type = scope.find(params[:id])
   end
 
-  #intercepts the standard 'find_and_authorize_requested_item' for additional special check for a referring_sample_id
-  def authorize_requested_sample_type
-    privilege = Seek::Permissions::Translator.translate(action_name)
-    return if privilege.nil?
-
-    if privilege == :view && params[:referring_sample_id].present?
-      @sample_type.can_view?(User.current_user,Sample.find_by_id(params[:referring_sample_id])) || find_and_authorize_requested_item
-    else
-      find_and_authorize_requested_item
-    end
-
-  end
-
   def check_no_created_samples
-    if (count = @sample_type.samples.count) > 0
+    @sample_type ||= SampleType.find(params[:id])
+    if (count = @sample_type.samples.count).positive?
       flash[:error] = "Cannot #{action_name} this sample type - There are #{count} samples using it."
       redirect_to @sample_type
     end