feat: device description - a new element for user to define a device set up (#2281)

Add a new element manageable by users though the Element-list: Device-Description 

It belongs to a device and defines:  
- the purpose of the device using ontology (CHMO)
- how the device is setup (device components description)
- current configuration
- responsible entities /maintenance
- ... 

Backend: 
- AR model DeviceDescription (belongs to Device)
- manageable through collection (has_many collections_device_descriptions, element_permission ...)
- Grape api endpoints and Usecases for CRUD operations
 (NB Labimotion::SegmentKlass dependence /dedicated sql queries for ontologies)
 - DB seed Labimotion::ElementKlass where name: 'device_description'
 
 Frontend:
 - integration for full management by users through element-list/element-detail UI
 - mobx store (element-details)
 - fetchers CRUD, split 
...

Author: beque

app/api/api.rb

@@ -138,7 +138,7 @@ def to_json_camel_case(val)
 
   TARGET = Rails.env.production? ? 'https://www.chemotion-repository.net/' : 'http://localhost:3000/'
 
-  ELEMENTS = %w[research_plan screen wellplate reaction sample cell_line].freeze
+  ELEMENTS = %w[research_plan screen wellplate reaction sample cell_line device_description].freeze
 
   ELEMENT_CLASS = {
     'research_plan' => ResearchPlan,
@@ -147,6 +147,7 @@ def to_json_camel_case(val)
     'reaction' => Reaction,
     'sample' => Sample,
     'cell_line' => CelllineSample,
+    'device_description' => DeviceDescription,
   }.freeze
 
   mount Chemotion::LiteratureAPI
@@ -203,6 +204,7 @@ def to_json_camel_case(val)
   mount Chemotion::AdminDeviceAPI
   mount Chemotion::AdminDeviceMetadataAPI
   mount Chemotion::ChemicalAPI
+  mount Chemotion::DeviceDescriptionAPI
 
   if Rails.env.development?
     add_swagger_documentation(info: {

app/api/chemotion/attachable_api.rb

@@ -48,7 +48,9 @@ class AttachableAPI < Grape::API
             begin
               a.save!
               attach_ary.push(a.id)
-              rp_attach_ary.push(a.id) if a.attachable_type.in?(%w[ResearchPlan Wellplate Labimotion::Element])
+              if a.attachable_type.in?(%w[ResearchPlan Wellplate DeviceDescription Labimotion::Element])
+                rp_attach_ary.push(a.id)
+              end
             ensure
               tempfile.close
               tempfile.unlink

app/api/chemotion/attachment_api.rb

@@ -82,6 +82,7 @@ def remove_duplicated(att)
 
         @attachment = Attachment.find_by(identifier: params[:identifier]) if @attachment.nil? && params[:identifier]
 
+        # rubocop:disable Performance/StringInclude
         case request.env['REQUEST_METHOD']
         when /delete/i
           error!('401 Unauthorized', 401) unless writable?(@attachment)
@@ -101,6 +102,13 @@ def remove_duplicated(att)
               can_dwnld = can_read &&
                           ElementPermissionProxy.new(current_user, element, user_ids).read_dataset?
             end
+          elsif /device_description_analyses/.match?(request.url)
+            @device_description = DeviceDescription.find(params[:device_description_id])
+            if (element = @device_description)
+              can_read = ElementPolicy.new(current_user, element).read?
+              can_dwnld = can_read &&
+                          ElementPermissionProxy.new(current_user, element, user_ids).read_dataset?
+            end
           elsif @attachment
 
             can_dwnld = @attachment.container_id.nil? && @attachment.created_for == current_user.id
@@ -119,6 +127,7 @@ def remove_duplicated(att)
           end
           error!('401 Unauthorized', 401) unless can_dwnld
         end
+        # rubocop:enable Performance/StringInclude
       end
 
       desc 'Bulk Delete Attachments'
@@ -347,20 +356,43 @@ def remove_duplicated(att)
                 end
               end&.flatten&.reduce(:+) || 0
         if tts > 300_000_000
-          DownloadAnalysesJob.perform_later(@sample.id, current_user.id, false)
+          DownloadAnalysesJob.perform_later(@sample.id, current_user.id, false, 'sample')
           nil
         else
           env['api.format'] = :binary
           content_type('application/zip, application/octet-stream')
           filename = CGI.escape("#{@sample.short_label}-analytical-files.zip")
           header('Content-Disposition', "attachment; filename=\"#{filename}\"")
-          zip = DownloadAnalysesJob.perform_now(@sample.id, current_user.id, true)
+          zip = DownloadAnalysesJob.perform_now(@sample.id, current_user.id, true, 'sample')
           zip.rewind
           zip.read
 
         end
       end
 
+      desc 'Download the zip attachment file by device_description_id'
+      get 'device_description_analyses/:device_description_id' do
+        # rubocop:disable Performance/Sum
+        tts = @device_description.analyses&.map do |a|
+                a.children&.map do |d|
+                  d.attachments&.map(&:filesize)
+                end
+              end&.flatten&.reduce(:+) || 0
+        # rubocop:enable Performance/Sum
+        if tts > 300_000_000
+          DownloadAnalysesJob.perform_later(@device_description.id, current_user.id, false, 'device_description')
+          nil
+        else
+          env['api.format'] = :binary
+          content_type('application/zip, application/octet-stream')
+          filename = CGI.escape("#{@device_description.short_label}-analytical-files.zip")
+          header('Content-Disposition', "attachment; filename=\"#{filename}\"")
+          zip = DownloadAnalysesJob.perform_now(@device_description.id, current_user.id, true, 'device_description')
+          zip.rewind
+          zip.read
+        end
+      end
+
       desc 'Return image attachment'
 
       params do

app/api/chemotion/code_log_api.rb

@@ -27,15 +27,16 @@ class CodeLogAPI < Grape::API
         get do
           code = params[:code]
           s = code&.size || 0
-          code_log = if s >= 39
-                       CodeLog.find(CodeCreator.digit_to_uuid(code))
-                     elsif s >= 8
-                       # TODO: use where instead of find_by ?
-                       CodeLog.where('value ~ ?', "\\A0#{code}").first
-                     elsif s == 6
-                       # TODO: use where instead of find_by ?
-                       CodeLog.find_by(value_xs: code.to_i)
-                     end
+          code_log =
+            if s >= 39
+              CodeLog.find(CodeCreator.digit_to_uuid(code))
+            elsif s >= 8
+              # TODO: use where instead of find_by ?
+              CodeLog.where('value ~ ?', "\\A0#{code}").first
+            elsif s == 6
+              # TODO: use where instead of find_by ?
+              CodeLog.find_by(value_xs: code.to_i)
+            end
 
           if code_log.nil?
             error!("Element with #{code.size}-digit code #{params[:code]} not found", 404)
@@ -48,7 +49,7 @@ class CodeLogAPI < Grape::API
       namespace :print_codes do
         desc 'Build PDF with element bar & qr code'
         params do
-          requires :element_type, type: String, values: %w[sample reaction wellplate screen]
+          requires :element_type, type: String, values: %w[sample reaction wellplate screen device_description]
           # TODO: check coerce with  type Array[Integer] not working with before do
           requires :ids, type: Array # , coerce_with: ->(val) { val.split(/,/).map(&:to_i) }
           requires :width, type: Integer
@@ -97,7 +98,7 @@ class CodeLogAPI < Grape::API
       namespace :print_analyses_codes do
         desc 'Build PDF with analyses codes of one analysis type'
         params do
-          requires :element_type, type: String, values: %w[sample reaction wellplate screen]
+          requires :element_type, type: String, values: %w[sample reaction wellplate screen device_description]
           requires :id, type: Integer, desc: 'Element id'
           requires :analyses_ids, type: Array[String]
           requires :size, type: String, values: %w[small big]
@@ -118,7 +119,7 @@ class CodeLogAPI < Grape::API
           content_type('application/pdf')
           header 'Content-Disposition', "attachment; filename*=UTF-8''analysis_codes_#{params[:size]}.pdf"
           env['api.format'] = :binary
-          # TODO: check container type/info  instead
+          # TODO: check container type/info instead
           # case params[:type]
           # when "nmr_analysis"
           #   body AnalysisNmrPdf.new(elements).render

app/api/chemotion/collection_api.rb

@@ -193,6 +193,9 @@ class CollectionAPI < Grape::API
             optional :cell_line, type: Hash do
               use :ui_state_params
             end
+            optional :device_description, type: Hash do
+              use :ui_state_params
+            end
           end
           requires :collection_attributes, type: Hash do
             requires :permission_level, type: Integer
@@ -221,6 +224,9 @@ class CollectionAPI < Grape::API
           cell_lines = CelllineSample.by_collection_id(@cid)
                                      .by_ui_state(params[:elements_filter][:cell_line])
                                      .for_user_n_groups(user_ids)
+          device_descriptions = DeviceDescription.by_collection_id(@cid)
+                                                 .by_ui_state(params[:elements_filter][:device_description])
+                                                 .for_user_n_groups(user_ids)
           elements = {}
           Labimotion::ElementKlass.find_each do |klass|
             elements[klass.name] = Labimotion::Element.by_collection_id(@cid).by_ui_state(params[:elements_filter][klass.name]).for_user_n_groups(user_ids)
@@ -237,6 +243,7 @@ class CollectionAPI < Grape::API
           share_screens = ElementsPolicy.new(current_user, screens).share?
           share_research_plans = ElementsPolicy.new(current_user, research_plans).share?
           share_cell_lines = ElementsPolicy.new(current_user, cell_lines).share?
+          share_device_descriptions = ElementsPolicy.new(current_user, device_descriptions).share?
           share_elements = !(elements&.length > 0)
           elements.each do |k, v|
             share_elements = ElementsPolicy.new(current_user, v).share?
@@ -249,6 +256,7 @@ class CollectionAPI < Grape::API
                             share_screens &&
                             share_research_plans &&
                             share_cell_lines &&
+                            share_device_descriptions &&
                             share_elements
           error!('401 Unauthorized', 401) if (!sharing_allowed || is_top_secret)
 
@@ -258,6 +266,7 @@ class CollectionAPI < Grape::API
           @screen_ids = screens.pluck(:id)
           @research_plan_ids = research_plans.pluck(:id)
           @cell_line_ids = cell_lines.pluck(:id)
+          @device_description_ids = device_descriptions.pluck(:id)
           @element_ids = elements&.transform_values { |v| v && v.pluck(:id) }
         end
 
@@ -280,6 +289,7 @@ class CollectionAPI < Grape::API
             screen_ids: @screen_ids,
             research_plan_ids: @research_plan_ids,
             cell_line_ids: @cell_line_ids,
+            device_description_ids: @device_description_ids,
             element_ids: @element_ids,
             collection_attributes: params[:collection_attributes].merge(shared_by_id: current_user.id)
           ).execute!

app/api/chemotion/comment_api.rb

@@ -100,6 +100,7 @@ def find_commentable(commentable_type, commentable_id)
                          Comment.wellplate_sections.values +
                          Comment.screen_sections.values +
                          Comment.research_plan_sections.values +
+                         Comment.device_description_sections.values +
                          Comment.header_sections.values
       end