Merge pull request #3 from seek4science/master

Update to latest master version

.gitignore

@@ -47,6 +47,7 @@ tmp/testing-seek-cache
 tmp/rubycritic
 tmp/fleximage
 tmp/performance
+tmp/user_uuid_studies_upload
 *.tmp*
 *~
 

Gemfile

@@ -131,7 +131,6 @@ gem "doorkeeper", ">= 5.2.5"
 
 gem 'request_store'
 
-# javascript assets from https://rails-assets.org
 gem 'bundler', '>= 1.8.4'
 
 gem 'ro-crate-ruby', git: 'https://github.com/ResearchObject/ro-crate-ruby.git', ref: '70804d34264481e70d0fe83ecc6ad76eda164e74'
@@ -141,18 +140,6 @@ gem 'redcarpet'
 gem 'i18n-js'
 gem 'whenever', '~> 1.0.0', require: false
 
-source 'https://rails-assets.org' do
-  gem 'rails-assets-bootstrap-multiselect', '~> 0.9.13'
-  gem 'rails-assets-bootstrap-tagsinput', '~> 0.8.0'
-  gem 'rails-assets-typeahead.js', '~> 0.10.5'
-  gem 'rails-assets-clipboard', '~> 1.5.12'
-  gem 'rails-assets-vue', '~> 2.1.8'
-  gem 'rails-assets-eonasdan-bootstrap-datetimepicker', '~> 4.17.42'
-  gem 'rails-assets-x-editable', '~> 1.5.1'
-  gem 'rails-assets-chartjs', '~> 2.7.2'
-  gem 'rails-assets-lightbox2', '~> 2.10.0'
-end
-
 group :production do
   gem 'passenger'
 end

Gemfile.lock

@@ -49,7 +49,6 @@ GIT
 
 GEM
   remote: https://rubygems.org/
-  remote: https://rails-assets.org/
   specs:
     RedCloth (4.3.2)
     actioncable (5.2.4.5)
@@ -377,8 +376,9 @@ GEM
     mime-types (3.3.1)
       mime-types-data (~> 3.2015)
     mime-types-data (3.2021.0225)
-    mimemagic (0.3.7)
-      nokogiri (~> 1.11.2)
+    mimemagic (0.3.10)
+      nokogiri (~> 1)
+      rake
     mini_mime (1.0.2)
     mini_portile2 (2.5.0)
     minitest (5.14.4)
@@ -402,7 +402,7 @@ GEM
     net-ldap (0.16.0)
     netrc (0.11.0)
     nio4r (2.5.5)
-    nokogiri (1.11.2)
+    nokogiri (1.11.3)
       mini_portile2 (~> 2.5.0)
       racc (~> 1.4)
     nokogumbo (1.5.0)
@@ -502,27 +502,6 @@ GEM
       bundler (>= 1.3.0)
       railties (= 5.2.4.5)
       sprockets-rails (>= 2.0.0)
-    rails-assets-bootstrap (3.3.7)
-      rails-assets-jquery (>= 1.9.1, < 4)
-    rails-assets-bootstrap-multiselect (0.9.13)
-      rails-assets-bootstrap (>= 2.3.2)
-      rails-assets-jquery (>= 1.11.0)
-    rails-assets-bootstrap-tagsinput (0.8.0)
-      rails-assets-jquery (~> 2.1.1)
-    rails-assets-chartjs (2.7.2)
-    rails-assets-clipboard (1.5.16)
-    rails-assets-eonasdan-bootstrap-datetimepicker (4.17.47)
-      rails-assets-jquery (>= 1.8.3)
-      rails-assets-moment (>= 2.10.5)
-    rails-assets-jquery (2.1.4)
-    rails-assets-lightbox2 (2.10.0)
-      rails-assets-jquery (> 2)
-    rails-assets-moment (2.18.1)
-    rails-assets-typeahead.js (0.10.5)
-      rails-assets-jquery (>= 1.7)
-    rails-assets-vue (2.1.10)
-    rails-assets-x-editable (1.5.1)
-      rails-assets-jquery (>= 1.6)
     rails-controller-testing (1.0.2)
       actionpack (~> 5.x, >= 5.0.1)
       actionview (~> 5.x, >= 5.0.1)
@@ -634,7 +613,7 @@ GEM
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.2.4)
+    rexml (3.2.5)
     rfc-822 (0.4.1)
     rmagick (2.15.2)
     ro-bundle (0.2.5)
@@ -903,15 +882,6 @@ DEPENDENCIES
   puma (>= 3.12.6)
   rack-attack (~> 5.0.1)
   rails (~> 5.2.4)
-  rails-assets-bootstrap-multiselect (~> 0.9.13)!
-  rails-assets-bootstrap-tagsinput (~> 0.8.0)!
-  rails-assets-chartjs (~> 2.7.2)!
-  rails-assets-clipboard (~> 1.5.12)!
-  rails-assets-eonasdan-bootstrap-datetimepicker (~> 4.17.42)!
-  rails-assets-lightbox2 (~> 2.10.0)!
-  rails-assets-typeahead.js (~> 0.10.5)!
-  rails-assets-vue (~> 2.1.8)!
-  rails-assets-x-editable (~> 1.5.1)!
   rails-controller-testing
   rails-html-sanitizer
   rails-observers

app/assets/javascripts/sharing.js.erb

@@ -77,7 +77,7 @@ var Sharing = {
   },
 
   requestInstitutionsUrl: '<%= Rails.application.routes.url_helpers.request_institutions_projects_path %>',
-  requestAllInstitutionsUrl: '<%= Rails.application.routes.url_helpers.request_all_institutions_path %>',
+  requestAllInstitutionsUrl: '<%= Rails.application.routes.url_helpers.request_all_sharing_form_institutions_path %>',
 
   accessTypes: {
     noAccess: <%= Policy::NO_ACCESS %>,

app/controllers/admin_controller.rb

@@ -98,6 +98,7 @@ def update_features_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]
+    Seek::Config.programmes_open_for_projects_enabled = string_to_boolean params[:programmes_open_for_projects_enabled]
     Seek::Config.publications_enabled = string_to_boolean params[:publications_enabled]
     Seek::Config.samples_enabled = string_to_boolean params[:samples_enabled]
     Seek::Config.workflows_enabled = string_to_boolean params[:workflows_enabled]    
@@ -186,6 +187,7 @@ def update_rebrand
 
     Seek::Config.dm_project_name = params[:dm_project_name]
     Seek::Config.dm_project_link = params[:dm_project_link]
+    Seek::Config.issue_tracker = params[:issue_tracker]
 
     Seek::Config.application_name = params[:application_name]
 

app/controllers/homes_controller.rb

@@ -2,7 +2,7 @@ class HomesController < ApplicationController
   helper HumanDiseasesHelper
 
   before_action :redirect_to_sign_up_when_no_user
-  before_action :login_required, only: %i[feedback send_feedback create_or_join_project]
+  before_action :login_required, only: %i[feedback send_feedback create_or_join_project report_issue]
   before_action :redirect_to_create_or_join_if_no_member, only: %i[index]
 
   respond_to :html, only: [:index]
@@ -25,6 +25,12 @@ def feedback
     end
   end
 
+  def report_issue
+    respond_to do |format|
+      format.html
+    end
+  end
+
   def isa_colours
     respond_to do |format|
       format.html

app/controllers/institutions_controller.rb

@@ -127,6 +127,16 @@ def request_all
     end
   end
 
+  # request all institutions, but specific to the sharing form which expects an array
+  def request_all_sharing_form
+    institution_list = Institution.order(:id).collect{ |institution| [institution.title, institution.id] }
+    respond_to do |format|
+      format.json do       
+        render json: { status: 200, institution_list: institution_list }       
+      end
+    end
+  end
+
   private
 
   def institution_params

app/controllers/projects_controller.rb

@@ -76,7 +76,12 @@ def administer_join_request
     details = JSON.parse(@message_log.details)
     @comments = details['comments']
     @institution = Institution.new(details['institution'])
-    @institution = Institution.find(@institution.id) unless @institution.id.nil?
+    if @institution.id
+      @institution = Institution.find(@institution.id)
+    else
+      # override with existing institution if already exists with same title, it could have been created since the request was made
+      @institution = Institution.find_by(title: @institution.title) if Institution.find_by(title: @institution.title)
+    end
 
     respond_to do |format|
       format.html
@@ -726,9 +731,13 @@ def parse_message_log_details
     @project = Project.find(@project.id) unless @project.id.nil?
 
     @institution = Institution.new(details['institution'])
-    @institution = Institution.find(@institution.id) unless @institution.id.nil?
-
 
+    if @institution.id
+      @institution = Institution.find(@institution.id)
+    else
+      # override with existing institution if already exists with same title, it could have been created since the request was made
+      @institution = Institution.find_by(title: @institution.title) if Institution.find_by(title: @institution.title)
+    end 
   end
 
   # check programme permissions for responding to a MesasgeLog

app/controllers/sessions_controller.rb

@@ -44,6 +44,13 @@ def create
     password_authentication
   end
 
+  def omniauth_failure
+    flash[:error] = "#{t("login.#{params[:strategy]}")} authentication failure (Invalid username/password?)"
+    respond_to do |format|
+      format.html { render :new }
+    end
+  end
+
   def destroy
     logout_user
     flash[:notice] = 'You have been logged out.'

app/helpers/sessions_helper.rb

@@ -36,7 +36,7 @@ def show_omniauth_login?
     Seek::Config.omniauth_enabled && Seek::Config.omniauth_providers.any?
   end
 
-  def show_elixir_login?
+  def show_elixir_aai_login?
     Seek::Config.omniauth_elixir_aai_enabled
   end
 

app/jobs/auth_lookup_update_job.rb

@@ -32,8 +32,6 @@ def perform_job(item)
   end
 
   def gather_items
-    # including item_type in the order, encourages assets to be processed before users (since they are much quicker), due to the happy coincidence
-    # that User falls last alphabetically. Its not that important if a new authorized type is added after User in the future.
     AuthLookupUpdateQueue.dequeue(Seek::Config.auth_lookup_update_batch_size)
   end
 

app/jobs/reindexing_job.rb

@@ -16,7 +16,7 @@ def perform_job(item)
   end
 
   def gather_items
-    ReindexingQueue.dequeue(BATCHSIZE)
+    ReindexingQueue.dequeue(BATCHSIZE).compact
   end
 
   def follow_on_job?

app/models/concerns/resource_queue.rb

@@ -12,6 +12,9 @@ def queue_enabled?
     end
 
     def prioritized
+      # including item_type in the order, encourages assets to be processed before users
+      #  (since they are much quicker, in the case of auth lookup processing), due to the happy coincidence that User
+      #  falls last alphabetically. Its not that important if a new authorized type is added after User in the future.
       order(:priority, :item_type, :id)
     end
 

app/models/programme.rb

@@ -105,7 +105,7 @@ def can_activate?(user = User.current_user)
   end
 
   def allows_user_projects?
-    open_for_projects?
+    open_for_projects? && Seek::Config.programmes_open_for_projects_enabled
   end
 
   def self.can_create?

app/models/user.rb

@@ -351,7 +351,7 @@ def queue_update_auth_table
 
   def remove_from_auth_tables
     Seek::Util.authorized_types.each do |type|
-      type.lookup_class.where(user: id).delete_all
+      type.lookup_class.where(user: id).in_batches(of:1000).delete_all
     end
   end
 

app/views/admin/_doi_settings.html.erb

@@ -10,7 +10,7 @@
 
 
   <%= admin_text_setting(:datacite_url, Seek::Config.datacite_url,
-                         'Datacite URL', "The root URL for the Datacite rest service. If it is not set, #{Seek::Config.default_datacite_url} will be used. You can also set the test url, https://test.datacite.org/mds/, for generating test DOIs.") %>
+                         'Datacite URL', "The root URL for the Datacite rest service. If it is not set, #{Seek::Config.default_datacite_url} will be used. You can also set the test url, https://mds.test.datacite.org/, for generating test DOIs.") %>
 
   <%= admin_text_setting(:doi_prefix, Seek::Config.doi_prefix,
                          'DOI prefix', 'The DOI prefix that will have been provided to you by DataCite for your organization.') %>

app/views/admin/features_enabled.html.erb

@@ -28,6 +28,9 @@
                                "Site mananaged #{t('programme')}",
                                "The #{t('programme')} the users can request to have a #{t('project')} created and associated with, without the need to create and manage their own",
                                include_blank:'None') %>
+    <%= admin_checkbox_setting(:programmes_open_for_projects_enabled, 1, Seek::Config.programmes_open_for_projects_enabled,
+        "#{t('programme').pluralize} open for #{t(:project).pluralize} enabled",
+        "When enabled, gives the ability for individual #{t(:programme).pluralize} to be configured to allow any other registered user to create a #{t(:project)} linked to that #{t(:programme)} without requiring approval or admin rights. Use with care if open user registration is enabled, as it could allow any user to register, create a project and start adding content to that Programme.") %>  
   </div>
   <%= admin_checkbox_setting(:samples_enabled, 1, Seek::Config.samples_enabled,
                              "Samples enabled", "Whether the Samples framework is enabled. The framework allows users to create their own custom Sample types to describe their biological samples and other metadata.",:onchange=>toggle_appear_javascript('sample_type_pa_only')) %>

app/views/admin/rebrand.html.erb

@@ -25,6 +25,9 @@
   <%= admin_text_setting(:dm_project_link, Seek::Config.dm_project_link,
                          "Data management #{t('project')} link", "A URL that is used in links to the data management #{t('project')}.") %>
 
+  <%= admin_text_setting(:issue_tracker, Seek::Config.issue_tracker,
+                         "Issue tracker link", "A URL for an issue tracker, which users can use to report bugs or other issues. Leave blank if not required") %>
+
   <%= admin_checkbox_setting(:header_image_enabled, 1, Seek::Config.header_image_enabled,
                              "Header logo image enabled", "Whether a header logo image appears on the right in the header.",
                              :onchange => toggle_appear_javascript('header_image_details')) %>

app/views/assays/show.html.erb

@@ -58,9 +58,7 @@
 
         <% if Seek::Config.organisms_enabled %>
             <%= list_assay_organisms("Organisms", @assay.assay_organisms,{:id=>"organism"}) %>
-        <% end %>
-
-        <%= render partial: 'custom_metadata/custom_metadata_attribute_values', locals: {resource: @assay} %>
+        <% end %>        
 
         <% if Seek::Config.human_diseases_enabled %>
             <%= list_assay_human_diseases("Human Diseases", @assay.assay_human_diseases,{:id=>"human_disease"}) %>
@@ -74,6 +72,9 @@
         </div>
       </div>
     <% end %>
+
+    <%= render partial: 'custom_metadata/custom_metadata_attribute_values', locals: {resource: @assay} %>
+
     <% if ((@assay.is_modelling?) && !@assay.models.empty? && !@assay.data_files.empty?) %><%#MODELLING ASSAY %>
         <div class="data_model_relationship">
           <% unless @assay.models.empty? %>