Merge remote-tracking branch 'upstream/main' into Third-Party-Apps

.gitignore

@@ -98,6 +98,10 @@
 
 /public/json/*
 !/public/json/schema.json
+!/public/json/precautionaryPhrases.json
+!/public/json/hazardPhrases.json
+!/public/json/pictograms.json
+
 
 /public/zip/*
 !/public/zip/.keep

CHANGELOG.md

@@ -2,6 +2,17 @@
 # Chemotion_ELN Changelog
 
 
+## [v1.6.1]
+> 2023-06-19
+
+* Fixes
+  * scan result calculation [PR1325](https://github.com/ComPlat/chemotion_ELN/pull/1325)
+  * Load the correct url of nmrium wrapper [#1339](https://github.com/ComPlat/chemotion_ELN/pull/1339)
+  * Zooming in chemspectra on firefox [#1346](https://github.com/ComPlat/chemotion_ELN/pull/1346)
+  * AdminUI: Datacollector setting [#1344](https://github.com/ComPlat/chemotion_ELN/pull/1344)
+  * nmrium: display preview image after saving [#1356](https://github.com/ComPlat/chemotion_ELN/pull/1356)
+
+
 ## [v1.6.0] 
 > 2023-05-09
 

app/api/chemotion/admin_api.rb

@@ -235,30 +235,18 @@ class AdminAPI < Grape::API
         end
 
         namespace :name do
-          desc 'Find top 3 matched user names by type'
+          desc 'Find top 4 matched user names by type'
           params do
-            requires :type, type: String
-            requires :name, type: String
+            requires :type, type: String, values: %w[Group Device User Person Admin]
+            requires :name, type: String, desc: 'user name'
           end
           get do
-            if params[:name].present?
-              users = User.where(type: params[:type])
-                          .by_name(params[:name])
-                          .limit(3)
-                          .select(
-                            'first_name',
-                            'last_name',
-                            'name',
-                            'id',
-                            'name_abbreviation',
-                            'name_abbreviation as abb',
-                            'type as user_type')
-                          .map(&:attributes)
-
-              { users: users }
-            else
-              { users: [] }
-            end
+            return { users: [] } if params[:name].blank?
+
+            users = User.where(type: params[:type])
+                        .by_name(params[:name])
+                        .limit(4)
+            present users, with: Entities::UserSimpleEntity, root: 'users'
           end
         end
 

app/api/chemotion/attachment_api.rb

@@ -44,8 +44,8 @@ def upload_chunk_error_message
       error!(message, 404)
     end
 
-    resource :attachments do # rubocop:disable Metrics/BlockLength
-      before do # rubocop:disable Metrics/BlockLength
+    resource :attachments do
+      before do
         @attachment = Attachment.find_by(id: params[:attachment_id])
 
         @attachment = Attachment.find_by(identifier: params[:identifier]) if @attachment.nil? && params[:identifier]
@@ -163,7 +163,9 @@ def upload_chunk_error_message
 
         env['api.format'] = :binary
         store = @attachment.attachment.storage.directory
-        file_location = store.join(@attachment.attachment_data['derivatives']['annotation']['annotated_file_location'] ||'not available')
+        file_location = store.join(
+          @attachment.attachment_data['derivatives']['annotation']['annotated_file_location'] || 'not available',
+        )
 
         uploaded_file = if file_location.present? && File.file?(file_location)
                           extension_of_annotation = File.extname(@attachment.filename)
@@ -238,20 +240,30 @@ def upload_chunk_error_message
       end
 
       desc 'Download the zip attachment file'
-      get 'zip/:container_id' do # rubocop:disable Metrics/BlockLength
+      get 'zip/:container_id' do
         env['api.format'] = :binary
         content_type('application/zip, application/octet-stream')
         filename = CGI.escape("#{@container.parent&.name&.gsub(/\s+/, '_')}-#{@container.name.gsub(/\s+/, '_')}.zip")
         header('Content-Disposition', "attachment; filename=\"#{filename}\"")
         zip = Zip::OutputStream.write_buffer do |zip| # rubocop:disable Lint/ShadowingOuterLocalVariable
+          file_text = ''
           @container.attachments.each do |att|
             zip.put_next_entry att.filename
             zip.write att.read_file
-          end
-          file_text = ''
-          @container.attachments.each do |att|
             file_text += "#{att.filename} #{att.checksum}\n"
+            next unless att.annotated?
+
+            begin
+              annotated_file_name = "#{File.basename(att.filename, '.*')}_annotated#{File.extname(att.filename)}"
+              zip.put_next_entry annotated_file_name
+              file = File.open(att.annotated_file_location)
+              zip.write file.read
+              file_text += "#{annotated_file_name} #{file.size}\n"
+            ensure
+              file.close
+            end
           end
+
           hyperlinks_text = ''
           JSON.parse(@container.extended_metadata.fetch('hyperlinks', '[]')).each do |link|
             hyperlinks_text += "#{link} \n"

app/api/chemotion/chemical_api.rb

@@ -0,0 +1,159 @@
+# frozen_string_literal: true
+
+module Chemotion
+  class ChemicalAPI < Grape::API
+    include Grape::Kaminari
+    resource :chemicals do
+      desc 'update chemicals'
+      params do
+        requires :chemical_data, type: Array[Hash], desc: 'chemical data'
+        optional :cas, type: String, desc: 'cas number'
+      end
+      route_param :sample_id do
+        put do
+          Chemotion::ChemicalsService.handle_exceptions do
+            attributes = declared(params, include_missing: false)
+            if params[:chemical_data].present? || params[:cas].present?
+              Chemical.find_by(sample_id: params[:sample_id]).update!(attributes)
+            else
+              status 204
+            end
+          end
+        end
+      end
+
+      desc 'Return chemical by sample_id'
+      params do
+        requires :sample_id, type: Integer, desc: 'sample id'
+      end
+
+      get do
+        Chemotion::ChemicalsService.handle_exceptions do
+          Chemical.find_by(sample_id: params[:sample_id]) || Chemical.new
+        end
+      end
+
+      resource :create do
+        desc 'Create a Chemical Entry'
+        params do
+          requires :chemical_data, type: Array[Hash], desc: 'chemical data'
+          requires :cas, type: String
+          requires :sample_id, type: Integer
+        end
+
+        post do
+          Chemotion::ChemicalsService.handle_exceptions do
+            attributes = declared(params, include_missing: false)
+            Chemical.create!(attributes)
+          end
+        end
+      end
+
+      resource :fetch_safetysheet do
+        desc 'fetch safety data sheet'
+        route_param :id do
+          params do
+            requires :data, type: Hash, desc: 'params'
+          end
+          get do
+            Chemotion::ChemicalsService.handle_exceptions do
+              data = params[:data]
+              molecule = Molecule.find(params[:id])
+              vendor = data[:vendor]
+              language = data[:language]
+              case data[:option]
+              when 'Common Name'
+                name = data[:searchStr] || molecule.names[0]
+              when 'CAS'
+                name = data[:searchStr] || molecule.cas[0]
+              end
+              case vendor
+              when 'Merck'
+                { merck_link: Chemotion::ChemicalsService.merck(name, language) }
+              when 'Thermofisher'
+                { alfa_link: Chemotion::ChemicalsService.alfa(name, language) }
+              else
+                {
+                  alfa_link: Chemotion::ChemicalsService.alfa(name, language),
+                  merck_link: Chemotion::ChemicalsService.merck(name, language),
+                }
+              end
+            end
+          end
+        end
+      end
+
+      resource :save_safety_datasheet do
+        desc 'save safety data sheet'
+
+        params do
+          requires :sample_id, type: Integer, desc: 'sample id'
+          requires :cas, type: String
+          requires :chemical_data, type: Array[Hash]
+          optional :vendor_product, type: String
+        end
+        post do
+          Chemotion::ChemicalsService.handle_exceptions do
+            chemical = Chemical.find_by(sample_id: params[:sample_id])
+            product_info = params[:chemical_data][0][params[:vendor_product]]
+            if chemical.present?
+              chemical.update!(chemical_data: params[:chemical_data])
+            else
+              Chemical.create!(sample_id: params[:sample_id], cas: params[:cas], chemical_data: params[:chemical_data])
+            end
+            file_path = "#{product_info['productNumber']}_#{product_info['vendor']}.pdf"
+            Chemotion::ChemicalsService.create_sds_file(file_path, product_info['sdsLink'])
+          end
+        end
+      end
+
+      resources :safety_phrases do
+        desc 'H and P safety phrases'
+
+        params do
+          requires :vendor, type: String, desc: 'params'
+        end
+
+        route_param :sample_id do
+          get do
+            Chemotion::ChemicalsService.handle_exceptions do
+              chemical = Chemical.find_by(sample_id: params[:sample_id]) || Chemical.new
+              if chemical.chemical_data.present?
+                if params[:vendor] == 'thermofischer' && chemical.chemical_data[0]['alfaProductInfo']
+                  product_number = chemical.chemical_data[0]['alfaProductInfo']['productNumber']
+                  Chemotion::ChemicalsService.safety_phrases_thermofischer(product_number)
+                elsif params[:vendor] == 'merck' && chemical.chemical_data[0]['merckProductInfo']
+                  product_link = chemical.chemical_data[0]['merckProductInfo']['productLink']
+                  Chemotion::ChemicalsService.safety_phrases_merck(product_link)
+                else
+                  err_body = 'Please fetch and save corresponding safety data sheet first'
+                  err_body
+                end
+              else
+                status 204
+              end
+            end
+          end
+        end
+      end
+
+      resources :chemical_properties do
+        desc 'additional chemical properties'
+
+        params do
+          requires :link, type: String, desc: 'vendor product link'
+        end
+
+        get do
+          Chemotion::ChemicalsService.handle_exceptions do
+            if params[:link].include? 'alfa'
+              Chemotion::ChemicalsService.chemical_properties_alfa(params[:link])
+            elsif params[:link].include? 'sigmaaldrich'
+              Chemotion::ChemicalsService.chemical_properties_merck(params[:link])
+            end
+          end
+        end
+      end
+    end
+  end
+end

app/api/chemotion/container_api.rb

@@ -47,7 +47,7 @@ class ContainerAPI < Grape::API
           # NB: attachments are destroy through container (DJ in production)
           # NB: attachments are not paranoidized so cannot be restored)
         @container.self_and_descendants.each(&:destroy)
-        status 200
+        status 204
       end
 
       desc 'Update Container Content'

app/api/chemotion/inbox_api.rb

@@ -2,17 +2,51 @@
 
 module Chemotion
   class InboxAPI < Grape::API
+    helpers ParamsHelpers
+
     resource :inbox do
       params do
         requires :cnt_only, type: Boolean, desc: 'return count number only'
       end
+
+      paginate per_page: 20, offset: 0, max_per_page: 50
+
       get do
         current_user.container = Container.create(name: 'inbox', container_type: 'root') unless current_user.container
 
         if params[:cnt_only]
-          present current_user.container, with: Entities::InboxEntity, root: :inbox, only: [:inbox_count]
+          present current_user.container, with: Entities::InboxEntity,
+                                          root_container: true,
+                                          root: :inbox,
+                                          only: [:inbox_count]
         else
-          present current_user.container, with: Entities::InboxEntity, root: :inbox
+          scope = current_user.container.children.order(created_at: :desc)
+
+          reset_pagination_page(scope)
+
+          device_boxes = paginate(scope).map do |device_box|
+            Entities::InboxEntity.represent(device_box, root_container: true)
+          end
+
+          inbox_service = InboxService.new(current_user.container)
+          present inbox_service.to_hash(device_boxes)
+        end
+      end
+
+      desc 'Return files by subcontainer ID'
+      params do
+        requires :container_id, type: Integer, desc: 'subcontainer ID'
+        optional :dataset_page, type: Integer, desc: 'Pagination number'
+      end
+
+      get 'containers/:container_id' do
+        if current_user.container.present?
+          container = current_user.container.children.find params[:container_id]
+
+          Entities::InboxEntity.represent(container,
+                                          root_container: false,
+                                          dataset_page: params[:dataset_page],
+                                          root: :inbox)
         end
       end
 

app/api/chemotion/sample_api.rb

@@ -2,6 +2,7 @@
 #require './helpers'
 
 module Chemotion
+  # rubocop:disable Metrics/ClassLength
   class SampleAPI < Grape::API
     include Grape::Kaminari
     helpers ContainerHelpers
@@ -53,7 +54,9 @@ class SampleAPI < Grape::API
           col_id = ui_state[:currentCollectionId]
           sample_ids = Sample.for_user(current_user.id).for_ui_state_with_collection(ui_state[:sample], CollectionsSample, col_id)
           Sample.where(id: sample_ids).each do |sample|
-            subsample = sample.create_subsample current_user, col_id, true
+            # rubocop:disable Lint/UselessAssignment
+            subsample = sample.create_subsample(current_user, col_id, true, 'sample')
+            # rubocop:enable Lint/UselessAssignment
           end
 
           {} # JS layer does not use the reply
@@ -319,6 +322,7 @@ class SampleAPI < Grape::API
         requires :container, type: Hash
         optional :user_labels, type: Array
         optional :decoupled, type: Boolean, desc: 'Sample is decoupled from structure?', default: false
+        optional :inventory_sample, type: Boolean, default: false
         optional :molecular_mass, type: Float
         optional :sum_formula, type: String
         #use :root_container_params
@@ -431,6 +435,7 @@ class SampleAPI < Grape::API
         optional :molecule_id, type: Integer
         requires :container, type: Hash
         optional :decoupled, type: Boolean, desc: 'Sample is decoupled from structure?', default: false
+        optional :inventory_sample, type: Boolean, default: false
         optional :molecular_mass, type: Float
         optional :sum_formula, type: String
       end
@@ -462,6 +467,7 @@ class SampleAPI < Grape::API
           stereo: params[:stereo],
           molecule_name_id: params[:molecule_name_id],
           decoupled: params[:decoupled],
+          inventory_sample: params[:inventory_sample],
           molecular_mass: params[:molecular_mass],
           sum_formula: params[:sum_formula]
         }
@@ -557,3 +563,4 @@ class SampleAPI < Grape::API
     end
   end
 end
+# rubocop:enable Metrics/ClassLength