Merge branch 'main' of github.com:datadryad/dryad-app into 3480-upgra…

…de-blacklight-and-solr-to-current-versions
datadryad · Dec 11, 2024 · 68a55be · 68a55be
2 parents 89e05d0 + ce5a847
commit 68a55be
Show file tree

Hide file tree

Showing 40 changed files with 328 additions and 172 deletions.
diff --git a/Gemfile b/Gemfile
@@ -8,7 +8,7 @@ source 'https://rubygems.org'
 gem 'irb', '~> 1.4.1'
 gem 'mail', '~> 2.8'
 gem 'mysql2', '~> 0.5.3'
-gem 'rails', '~> 7.0.8.5'
+gem 'rails', '~> 7.0.8.7'
 gem 'react-rails', '~> 2.6.2'
 gem 'shakapacker', '~> 6.0'
 gem 'sprockets', '~> 4.0'

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -17,67 +17,67 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    actioncable (7.0.8.5)
-      actionpack (= 7.0.8.5)
-      activesupport (= 7.0.8.5)
+    actioncable (7.0.8.7)
+      actionpack (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
-    actionmailbox (7.0.8.5)
-      actionpack (= 7.0.8.5)
-      activejob (= 7.0.8.5)
-      activerecord (= 7.0.8.5)
-      activestorage (= 7.0.8.5)
-      activesupport (= 7.0.8.5)
+    actionmailbox (7.0.8.7)
+      actionpack (= 7.0.8.7)
+      activejob (= 7.0.8.7)
+      activerecord (= 7.0.8.7)
+      activestorage (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       mail (>= 2.7.1)
       net-imap
       net-pop
       net-smtp
-    actionmailer (7.0.8.5)
-      actionpack (= 7.0.8.5)
-      actionview (= 7.0.8.5)
-      activejob (= 7.0.8.5)
-      activesupport (= 7.0.8.5)
+    actionmailer (7.0.8.7)
+      actionpack (= 7.0.8.7)
+      actionview (= 7.0.8.7)
+      activejob (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       mail (~> 2.5, >= 2.5.4)
       net-imap
       net-pop
       net-smtp
       rails-dom-testing (~> 2.0)
-    actionpack (7.0.8.5)
-      actionview (= 7.0.8.5)
-      activesupport (= 7.0.8.5)
+    actionpack (7.0.8.7)
+      actionview (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       rack (~> 2.0, >= 2.2.4)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.2.0)
-    actiontext (7.0.8.5)
-      actionpack (= 7.0.8.5)
-      activerecord (= 7.0.8.5)
-      activestorage (= 7.0.8.5)
-      activesupport (= 7.0.8.5)
+    actiontext (7.0.8.7)
+      actionpack (= 7.0.8.7)
+      activerecord (= 7.0.8.7)
+      activestorage (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       globalid (>= 0.6.0)
       nokogiri (>= 1.8.5)
-    actionview (7.0.8.5)
-      activesupport (= 7.0.8.5)
+    actionview (7.0.8.7)
+      activesupport (= 7.0.8.7)
       builder (~> 3.1)
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.1, >= 1.2.0)
-    activejob (7.0.8.5)
-      activesupport (= 7.0.8.5)
+    activejob (7.0.8.7)
+      activesupport (= 7.0.8.7)
       globalid (>= 0.3.6)
-    activemodel (7.0.8.5)
-      activesupport (= 7.0.8.5)
-    activerecord (7.0.8.5)
-      activemodel (= 7.0.8.5)
-      activesupport (= 7.0.8.5)
-    activestorage (7.0.8.5)
-      actionpack (= 7.0.8.5)
-      activejob (= 7.0.8.5)
-      activerecord (= 7.0.8.5)
-      activesupport (= 7.0.8.5)
+    activemodel (7.0.8.7)
+      activesupport (= 7.0.8.7)
+    activerecord (7.0.8.7)
+      activemodel (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
+    activestorage (7.0.8.7)
+      actionpack (= 7.0.8.7)
+      activejob (= 7.0.8.7)
+      activerecord (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       marcel (~> 1.0)
       mini_mime (>= 1.1.0)
-    activesupport (7.0.8.5)
+    activesupport (7.0.8.7)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -407,7 +407,7 @@ GEM
       mime-types-data (~> 3.2015)
     mime-types-data (3.2024.1001)
     mini_mime (1.1.5)
-    minitest (5.25.1)
+    minitest (5.25.4)
     mize (0.6.0)
     mocha (2.4.5)
       ruby2_keywords (>= 0.0.5)
@@ -439,11 +439,11 @@ GEM
     netrc (0.11.0)
     nio4r (2.7.3)
     noid (0.9.0)
-    nokogiri (1.16.7-arm64-darwin)
+    nokogiri (1.17.1-arm64-darwin)
       racc (~> 1.4)
-    nokogiri (1.16.7-x86_64-darwin)
+    nokogiri (1.17.1-x86_64-darwin)
       racc (~> 1.4)
-    nokogiri (1.16.7-x86_64-linux)
+    nokogiri (1.17.1-x86_64-linux)
       racc (~> 1.4)
     notiffany (0.1.3)
       nenv (~> 0.1)
@@ -507,29 +507,29 @@ GEM
       rack
     rack-test (2.1.0)
       rack (>= 1.3)
-    rails (7.0.8.5)
-      actioncable (= 7.0.8.5)
-      actionmailbox (= 7.0.8.5)
-      actionmailer (= 7.0.8.5)
-      actionpack (= 7.0.8.5)
-      actiontext (= 7.0.8.5)
-      actionview (= 7.0.8.5)
-      activejob (= 7.0.8.5)
-      activemodel (= 7.0.8.5)
-      activerecord (= 7.0.8.5)
-      activestorage (= 7.0.8.5)
-      activesupport (= 7.0.8.5)
+    rails (7.0.8.7)
+      actioncable (= 7.0.8.7)
+      actionmailbox (= 7.0.8.7)
+      actionmailer (= 7.0.8.7)
+      actionpack (= 7.0.8.7)
+      actiontext (= 7.0.8.7)
+      actionview (= 7.0.8.7)
+      activejob (= 7.0.8.7)
+      activemodel (= 7.0.8.7)
+      activerecord (= 7.0.8.7)
+      activestorage (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       bundler (>= 1.15.0)
-      railties (= 7.0.8.5)
+      railties (= 7.0.8.7)
     rails-dom-testing (2.2.0)
       activesupport (>= 5.0.0)
       minitest
       nokogiri (>= 1.6)
     rails-html-sanitizer (1.5.0)
       loofah (~> 2.19, >= 2.19.1)
-    railties (7.0.8.5)
-      actionpack (= 7.0.8.5)
-      activesupport (= 7.0.8.5)
+    railties (7.0.8.7)
+      actionpack (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       method_source
       rake (>= 12.2)
       thor (~> 1.0)
@@ -827,7 +827,7 @@ DEPENDENCIES
   puma (= 6.4.3)
   pundit (~> 2.3)
   rack-attack
-  rails (~> 7.0.8.5)
+  rails (~> 7.0.8.7)
   rb-readline
   rdoc (~> 6.1.1)
   react-rails (~> 2.6.2)

diff --git a/app/controllers/health_controller.rb b/app/controllers/health_controller.rb
@@ -1,42 +1,69 @@
 class HealthController < ApplicationController
 
   def check
-    health_status = { status: 'OK' }
+    @health_status = {}
+    populate_statuses
 
+    status_code = @health_status.map { |_k, v| v[:status] }.include?('not connected') ? :service_unavailable : :ok
+    notify_health_status_change(status_code, @health_status)
+
+    render json: { status: status_code }.merge(@health_status), status: status_code and return if params.key?(:advanced)
+
+    render json: { status: status_code }.merge(simple_response_hash), status: status_code
+  end
+
+  private
+
+  def simple_response_hash
+    return @simple_response_hash if @simple_response_hash
+
+    @simple_response_hash = @health_status.each_with_object({}) do |(key, value), result|
+      result[key] = value[:status]
+    end
+  end
+
+  def populate_statuses
     # Check database connectivity
+    @health_status[:database] = {}
     begin
       StashEngine::Identifier.last
-      health_status[:database] = 'connected'
+      @health_status[:database][:status] = 'connected'
     rescue StandardError => e
-      health_status[:database] = 'not connected'
-      health_status[:database_error] = e.message if params[:advanced]
+      @health_status[:database][:status] = 'not connected'
+      @health_status[:database][:error] = e.message
     end
 
     # Check Solr connectivity
+    @health_status[:solr] = {}
     begin
       solr = RSolr.connect(url: Blacklight.connection_config[:url])
       solr.get('select', params: { fl: 'dc_identifier_s', rows: 1 })
-      health_status[:solr] = 'connected'
+      @health_status[:solr][:status] = 'connected'
     rescue StandardError => e
-      health_status[:solr] = 'not connected'
-      health_status[:solr_error] = e.message if params[:advanced]
+      @health_status[:solr][:status] = 'not connected'
+      @health_status[:solr][:error] = e.message
     end
 
     # Check AWS S3 connectivity
+    @health_status[:aws_s3] = {}
     begin
       if Stash::Aws::S3.new.exists?(s3_key: 's3_status_check.txt')
-        health_status[:aws_s3] = 'connected'
+        @health_status[:aws_s3][:status] = 'connected'
       else
-        health_status[:aws_s3] = 'not connected'
-        health_status[:aws_s3_error] = 'file does not exist' if params[:advanced]
+        @health_status[:aws_s3][:status] = 'not connected'
+        @health_status[:aws_s3][:error] = 'file does not exist'
       end
     rescue StandardError => e
-      health_status[:aws_s3] = 'not connected'
-      health_status[:aws_s3_error] = e.message if params[:advanced]
+      @health_status[:aws_s3][:status] = 'not connected'
+      @health_status[:aws_s3][:error] = e.message
     end
+  end
+
+  def notify_health_status_change(status_code, health_status)
+    old_statuses = Rails.cache.read('health_status')
+    Rails.cache.write('health_status', simple_response_hash, expires_in: 10.minute)
+    return if old_statuses == simple_response_hash
 
-    status_code = health_status.values.include?('not connected') ? :service_unavailable : :ok
-    health_status[:status] = status_code
-    render json: health_status, status: status_code
+    StashEngine::NotificationsMailer.health_status_change(status_code, health_status).deliver_now
   end
 end
diff --git a/app/controllers/stash_engine/admin_dashboard_controller.rb b/app/controllers/stash_engine/admin_dashboard_controller.rb
@@ -347,10 +347,10 @@ def load
     end
 
     def curation_activity_change
-      return publishing_error if @resource.id != @identifier.last_submitted_resource.id &&
+      return publishing_error if @resource.id != @identifier.last_submitted_resource&.id &&
         %w[embargoed published].include?(params.dig(:curation_activity, :status))
 
-      return state_error unless CurationActivity.allowed_states(@last_state).include?(@status)
+      return state_error unless CurationActivity.allowed_states(@last_state, current_user).include?(@status)
 
       decipher_curation_activity
       @note = params.dig(:curation_activity, :note)

diff --git a/app/controllers/stash_engine/admin_datasets_controller.rb b/app/controllers/stash_engine/admin_datasets_controller.rb
@@ -58,6 +58,17 @@ def create_salesforce_case
       redirect_to(sf_url, allow_other_host: true)
     end
 
+    def destroy
+      identifier = Identifier.find(params[:id])
+      authorize identifier
+
+      if identifier.destroy
+        redirect_to admin_dashboard_path, notice: "Dataset with DOI #{identifier.identifier} has been deleted."
+      else
+        redirect_to activity_log_path(identifier.id), alert: 'Dataset could not be deleted. Please try again later.'
+      end
+    end
+
     private
 
     def load

diff --git a/app/helpers/stash_engine/admin_datasets_helper.rb b/app/helpers/stash_engine/admin_datasets_helper.rb
@@ -15,7 +15,7 @@ def status_select(statuses = [])
     end
 
     def filter_status_select(current_status)
-      statuses = StashEngine::CurationActivity.allowed_states(current_status)
+      statuses = StashEngine::CurationActivity.allowed_states(current_status, current_user)
 
       statuses.delete(current_status) # because we don't show the current state as an option, it is implied by leaving state blank
 

diff --git a/app/helpers/stash_engine/dashboard_helper.rb b/app/helpers/stash_engine/dashboard_helper.rb
diff --git a/app/helpers/stash_engine/edit_histories_helper.rb b/app/helpers/stash_engine/edit_histories_helper.rb
diff --git a/app/helpers/stash_engine/embargoes_helper.rb b/app/helpers/stash_engine/embargoes_helper.rb
diff --git a/app/helpers/stash_engine/file_uploads_helper.rb b/app/helpers/stash_engine/file_uploads_helper.rb
diff --git a/app/helpers/stash_engine/pages_helper.rb b/app/helpers/stash_engine/pages_helper.rb
diff --git a/app/helpers/stash_engine/resources_helper.rb b/app/helpers/stash_engine/resources_helper.rb
diff --git a/app/helpers/stash_engine/searches_helper.rb b/app/helpers/stash_engine/searches_helper.rb
diff --git a/app/helpers/stash_engine/shares_helper.rb b/app/helpers/stash_engine/shares_helper.rb
diff --git a/app/helpers/stash_engine/tenants_helper.rb b/app/helpers/stash_engine/tenants_helper.rb
diff --git a/app/helpers/stash_engine/zenodo_queue_helper.rb b/app/helpers/stash_engine/zenodo_queue_helper.rb
diff --git a/app/mailers/stash_engine/notifications_mailer.rb b/app/mailers/stash_engine/notifications_mailer.rb
@@ -0,0 +1,13 @@
+module StashEngine
+
+  # Mails users about submissions
+  class NotificationsMailer < ApplicationMailer
+
+    def health_status_change(status_code, health_status)
+      @status_code = status_code
+      @health_status = health_status
+
+      mail(to: 'devs@datadryad.org', subject: "#{rails_env}Health check status changed - #{status_code}")
+    end
+  end
+end
diff --git a/app/models/stash_engine/curation_activity.rb b/app/models/stash_engine/curation_activity.rb
@@ -181,8 +181,10 @@ def first_time_in_status?
       resource.curation_activities.where('id < ?', id).where(status: status).empty?
     end
 
-    def self.allowed_states(current_state)
-      CURATOR_ALLOWED_STATES[current_state].dup
+    def self.allowed_states(current_state, current_user)
+      statuses = CURATOR_ALLOWED_STATES[current_state].dup
+      statuses << 'withdrawn' if current_user.superuser? # superusers can withdraw a datasets from any status
+      statuses.uniq
     end
 
     # Private methods