Merge branch 'main' into hide-non-ISA-compliant-elements

.gitignore

@@ -66,6 +66,7 @@ public/javascripts/i18n.js
 public/javascripts/translations.js
 public/stylesheets/*_cached.css
 public/system/
+public/sitemaps/*
 
 public/assets/
 public/assets_dev/

Gemfile

@@ -109,6 +109,7 @@ gem 'ransack'
 
 gem 'terser', '~> 1.1', '>= 1.1.1'
 
+
 # Rails 4 upgrade
 gem 'activerecord-session_store'
 gem 'rails-observers'
@@ -177,6 +178,8 @@ group :development do
 
   gem 'web-console', '>= 4.1.0'
   gem 'rack-mini-profiler', '~> 2.0'
+  gem "flamegraph", "~> 0.9.5"
+  gem "stackprof", "~> 0.2.25"
   gem 'listen', '~> 3.3'
 end
 
@@ -202,3 +205,5 @@ group :test, :development do
   gem 'teaspoon'
   gem 'teaspoon-mocha'
 end
+
+gem "sitemap_generator", "~> 6.3"

Gemfile.lock

@@ -286,6 +286,7 @@ GEM
       loofah (>= 2.3.1)
       sax-machine (>= 1.0)
     ffi (1.15.5)
+    flamegraph (0.9.5)
     fssm (0.2.10)
     gem-licenses (0.2.2)
     gitlab_omniauth-ldap (2.2.0)
@@ -828,6 +829,8 @@ GEM
       simplecov_json_formatter (~> 0.1)
     simplecov-html (0.12.3)
     simplecov_json_formatter (0.1.3)
+    sitemap_generator (6.3.0)
+      builder (~> 3.0)
     slop (3.6.0)
     snaky_hash (2.0.0)
       hashie
@@ -852,6 +855,7 @@ GEM
       activesupport (>= 5.2)
       sprockets (>= 3.0.0)
     sqlite3 (1.4.2)
+    stackprof (0.2.25)
     stringio (3.0.1)
     sunspot (2.6.0)
       pr_geohash (~> 1.0)
@@ -990,6 +994,7 @@ DEPENDENCIES
   exception_notification
   factory_bot (~> 6.2.1)
   feedjira
+  flamegraph (~> 0.9.5)
   fleximage!
   fssm
   gem-licenses
@@ -1073,8 +1078,10 @@ DEPENDENCIES
   seedbank
   simple-spreadsheet-extractor (~> 0.18.0)
   simplecov
+  sitemap_generator (~> 6.3)
   sprockets-rails
   sqlite3 (~> 1.4)
+  stackprof (~> 0.2.25)
   stringio (= 3.0.1)
   sunspot_matchers
   sunspot_rails

app/controllers/assays_controller.rb

@@ -6,6 +6,7 @@ class AssaysController < ApplicationController
   before_action :assays_enabled?
   before_action :find_assets, :only=>[:index]
   before_action :find_and_authorize_requested_item, :only=>[:edit, :update, :destroy, :manage, :manage_update, :show, :new_object_based_on_existing_one]
+  before_action :delete_linked_sample_types, only: [:destroy]
 
   #project_membership_required_appended is an alias to project_membership_required, but is necessary to include the actions
   #defined in the application controller
@@ -18,7 +19,7 @@ class AssaysController < ApplicationController
   api_actions :index, :show, :create, :update, :destroy
 
   def new_object_based_on_existing_one
-    @existing_assay =  Assay.find(params[:id])
+    @existing_assay = Assay.find(params[:id])
     @assay = @existing_assay.clone_with_associations
 
     if @existing_assay.can_view?
@@ -62,9 +63,7 @@ def new_object_based_on_existing_one
       flash[:error]="You do not have the necessary permissions to copy this #{t('assays.assay')}"
       redirect_to @existing_assay
     end
-
-
-   end
+  end
 
   def new
     @assay=setup_new_asset
@@ -112,6 +111,13 @@ def create
     end
   end
 
+
+  def delete_linked_sample_types
+    return unless is_single_page_assay?
+
+    @assay.sample_type.destroy
+  end
+
   def update
     update_assay_organisms @assay, params
     update_assay_human_diseases @assay, params
@@ -177,4 +183,10 @@ def assay_params
       assay_params[:model_ids].select! { |id| Model.find_by_id(id).try(:can_view?) } if assay_params.key?(:model_ids)
     end
   end
+
+  def is_single_page_assay?
+    return false unless params.key?(:return_to)
+
+    params[:return_to].start_with? '/single_pages/'
+  end
 end

app/controllers/studies_controller.rb

@@ -6,6 +6,7 @@ class StudiesController < ApplicationController
   before_action :studies_enabled?
   before_action :find_assets, only: [:index]
   before_action :find_and_authorize_requested_item, only: %i[edit update destroy manage manage_update show new_object_based_on_existing_one]
+  before_action :delete_linked_sample_types, only: [:destroy]
 
   # project_membership_required_appended is an alias to project_membership_required, but is necesary to include the actions
   # defined in the application controller
@@ -88,6 +89,16 @@ def update
     end
   end
 
+  def delete_linked_sample_types
+    return unless is_single_page_study?
+
+    # The study sample types must be destroyed in reversed order
+    # otherwise the first sample type won't be removed becaused it is linked from the second
+    study_st_ids = @study.sample_types.map(&:id).sort { |a, b| b <=> a }
+    SampleType.destroy(study_st_ids)
+  end
+
+
   def show
     @study = Study.find(params[:id])
 
@@ -201,7 +212,7 @@ def batch_create
       study_params = {
         title: params[:studies][:title][index],
         description: params[:studies][:description][index],
-        investigation_id: params[:study][:investigation_id],        
+        investigation_id: params[:study][:investigation_id],
         custom_metadata: CustomMetadata.new(
           custom_metadata_type: metadata_types,
           data: metadata
@@ -351,3 +362,9 @@ def study_params
                                   { custom_metadata_attributes: determine_custom_metadata_keys })
   end
 end
+
+def is_single_page_study?
+  return false unless params.key?(:return_to)
+
+  params[:return_to].start_with? '/single_pages/'
+end

app/controllers/templates_controller.rb

@@ -87,7 +87,7 @@ def task_status
 
   def populate_template
     uploaded_file = params[:template_json_file]
-    dir = Rails.root.join('config', 'default_data', 'source_types')
+    dir = Seek::Config.append_filestore_path('source_types')
 
     if Dir.exist?(dir)
       `rm #{dir}/*`
@@ -146,11 +146,11 @@ def set_status
   end
 
   def lockfile
-    Rails.root.join('tmp', 'populate_templates.lock')
+    Rails.root.join(Seek::Config.temporary_filestore_path, 'populate_templates.lock')
   end
 
   def resultfile
-    Rails.root.join('tmp', 'populate_templates.result')
+    Rails.root.join(Seek::Config.temporary_filestore_path, 'populate_templates.result')
   end
 
   def running!

app/models/assay.rb

@@ -77,7 +77,7 @@ def short_description
   end
 
   def state_allows_delete?(*args)
-    assets.empty? && publications.empty? && super
+    assets.empty? && publications.empty? && associated_samples_through_sample_type.empty? && super
   end
 
   # returns true if this is a modelling class of assay
@@ -90,6 +90,10 @@ def is_experimental?
     !assay_class.nil? && assay_class.key == 'EXP'
   end
 
+  def associated_samples_through_sample_type
+    (sample_type.nil? || sample_type.samples.nil?) ? [] : sample_type.samples
+  end
+
   # Create or update relationship of this assay to another, with a specific relationship type and version
   def associate(asset, options = {})
     if asset.is_a?(Organism)

app/models/study.rb

@@ -2,7 +2,7 @@ class Study < ApplicationRecord
 
   enum status: [:planned, :running, :completed, :cancelled, :failed]
   belongs_to :assignee, class_name: 'Person'
-  
+
   searchable(:auto_index => false) do
     text :experimentalists
   end if Seek::Config.solr_enabled
@@ -22,7 +22,7 @@ class Study < ApplicationRecord
   has_many :sop_versions, through: :assays
 
   has_one :external_asset, as: :seek_entity, dependent: :destroy
-  
+
   has_and_belongs_to_many :sops
 
   has_and_belongs_to_many :sample_types
@@ -41,7 +41,16 @@ def assets
   end
 
   def state_allows_delete? *args
-    assays.empty? && super
+    assays.empty? && associated_samples_through_sample_type.empty? && super
+  end
+
+  def associated_samples_through_sample_type
+    return [] if sample_types.nil?
+    st_samples = []
+    sample_types.map do |st|
+      st.samples.map { |sts| st_samples.push sts }
+    end
+    st_samples
   end
 
   def clone_with_associations

app/views/general/_index.html.erb

@@ -5,10 +5,14 @@
   show_new_button = true unless local_assigns.has_key?(:show_new_button)
   title ||= nil
   subtitle ||= nil
+	isa_templates_enabled = Seek::Config.sample_type_template_enabled && Seek::Config.project_single_page_advanced_enabled
 %>
 
 <div class="pull-right">
   <% if show_new_button && controller_model.can_create? %>
+    <% if isa_templates_enabled %>
+      <%= link_to "Query by #{t('template').pluralize}", query_form_samples_path, class: "btn btn-default btn" %>
+    <% end %>
     <%= button_link_to(new_item_label, "new", new_item_path) %>
   <% end %>
 

app/views/programmes/activation_review.html.erb

@@ -1,4 +1,4 @@
-<%= render :partial => "general/item_title",:locals => {:item=>@programme, :title_prefix=>"Acitivation required for: "} %>
+<%= render :partial => "general/item_title",:locals => {:item=>@programme, :title_prefix=>"Activation required for: "} %>
 
 <p>
   A <%= t('programme') %> has been created by a user, and requires activation. The <%= t('programme') %> created is <%= link_to @programme.title, @programme %>.

config/schedule.rb

@@ -71,6 +71,11 @@ def offset(off_hours)
   runner "Seek::BioSchema::DataDump.generate_dumps"
 end
 
+# Generate a new sitemap...
+every 1.day, at: '12:45 am' do
+  rake "-s sitemap:refresh"
+end
+
 # not safe to automatically add in a non containerised environment
 if Seek::Docker.using_docker?
   every 10.minutes do

config/sitemap.rb

@@ -0,0 +1,19 @@
+# https://github.com/kjvarga/sitemap_generator#sitemapgenerator
+SitemapGenerator::Sitemap.sitemaps_path = "sitemaps"
+SitemapGenerator::Sitemap.create_index = "auto"
+SitemapGenerator::Sitemap.compress = false
+SitemapGenerator::Sitemap.default_host = URI.parse(Seek::Config.site_base_url)
+
+SitemapGenerator::Sitemap.create do
+  Seek::Util.searchable_types.each do |type|
+    add  polymorphic_path(type), lastmod: type.maximum(:updated_at), changefreq: 'daily', priority: 0.7
+  end
+end
+
+Seek::Util.searchable_types.each do |type|
+  SitemapGenerator::Sitemap.create(filename: type.table_name, include_root: false) do
+    type.authorized_for('view', nil).find_all do |obj|
+      add polymorphic_path(obj), lastmod: obj.updated_at, changefreq: 'daily', priority: 0.7
+    end
+  end
+end

lib/seek/isa_templates/template_extractor.rb

@@ -12,7 +12,7 @@ def self.extract_templates
         disable_authorization_checks do
           client = Ebi::OlsClient.new
           project = Project.find_or_create_by(title: 'Default Project')
-          directory = Rails.root.join('config', 'default_data', 'source_types')
+          directory = Seek::Config.append_filestore_path('source_types')
           directory_files = Dir.exist?(directory) ? Dir.glob("#{directory}/*.json") : []
           raise '<ul><li>Make sure to upload files that have the ".json" extension.</li></ul>' if directory_files == []
 
@@ -172,11 +172,11 @@ def self.seed_isa_tags
       end
 
       def self.lockfile
-        Rails.root.join('tmp', 'populate_templates.lock')
+        Rails.root.join(Seek::Config.temporary_filestore_path, 'populate_templates.lock')
       end
 
       def self.resultfile
-        Rails.root.join('tmp', 'populate_templates.result')
+        Rails.root.join(Seek::Config.temporary_filestore_path, 'populate_templates.result')
       end
     end
   end