drag sample element to segment

lib/labimotion.rb

@@ -22,6 +22,8 @@ def self.log_exception(exception, current_user = nil)
   autoload :ConverterAPI, 'labimotion/apis/converter_api'
 
   ######## Entities
+  autoload :PropertiesEntity, 'labimotion/entities/properties_entity'
+
   autoload :ElementEntity, 'labimotion/entities/element_entity'
   autoload :ElnElementEntity, 'labimotion/entities/eln_element_entity'
 
@@ -56,6 +58,7 @@ def self.log_exception(exception, current_user = nil)
   autoload :NmrMapperRepo, 'labimotion/libs/nmr_mapper_repo' ## for Chemotion Repository
   autoload :TemplateHub, 'labimotion/libs/template_hub'
   autoload :ExportDataset, 'labimotion/libs/export_dataset'
+  autoload :SampleAssociation, 'labimotion/libs/sample_association'
 
   ######## Utils
   autoload :ConState, 'labimotion/utils/con_state'

lib/labimotion/apis/generic_element_api.rb

@@ -310,7 +310,10 @@ class GenericElementAPI < Grape::API
       end
       route_param :id do
         before do
-          error!('401 Unauthorized', 401) unless current_user.matrix_check_by_name('genericElement') && ElementPolicy.new(current_user, Element.find(params[:id])).read?
+          @element_policy = ElementPolicy.new(current_user, Element.find(params[:id]))
+          error!('401 Unauthorized', 401) unless current_user.matrix_check_by_name('genericElement') && @element_policy.read?
+        rescue ActiveRecord::RecordNotFound
+          error!('404 Not Found', 404)
         end
 
         get do
@@ -321,10 +324,12 @@ class GenericElementAPI < Grape::API
               attachments: attach_thumbnail(element&.attachments)
             }
           else
+            #byebug
             {
               element: Labimotion::ElementEntity.represent(
                 element,
                 detail_levels: ElementDetailLevelCalculator.new(user: current_user, element: element).detail_levels,
+                policy: @element_policy
               ),
               attachments: attach_thumbnail(element&.attachments)
             }

lib/labimotion/entities/element_entity.rb

@@ -1,11 +1,13 @@
 # frozen_string_literal: true
 
-require 'labimotion/entities/application_entity'
+require 'labimotion/entities/properties_entity'
 ## TODO: Refactor labimotion to use the same entities as chemotion
 module Labimotion
-  class ElementEntity < ApplicationEntity
+  class ElementEntity < PropertiesEntity
     with_options(anonymize_below: 0) do
-      expose! :can_copy
+      expose! :can_copy,        unless: :displayed_in_list
+      expose! :can_publish,     unless: :displayed_in_list
+      expose! :can_update,      unless: :displayed_in_list
       expose! :container,                           using: 'Entities::ContainerEntity'
       expose! :created_by
       expose! :id
@@ -35,75 +37,21 @@ def is_restricted
       detail_levels[Labimotion::Element] < 10
     end
 
-    # TODO: Refactor this method to something more readable/understandable
-    def properties
-      (object.properties['layers']&.keys || []).each do |key|
-        # layer = object.properties[key]
-        field_sample_molecules = object.properties['layers'][key]['fields'].select { |ss| ss['type'] == 'drag_sample' || ss['type'] == 'drag_molecule' }
-        field_sample_molecules.each do |field|
-          idx = object.properties['layers'][key]['fields'].index(field)
-          sid = field.dig('value', 'el_id')
-          next unless sid.present?
-
-          el = field['type'] == 'drag_sample' ? Sample.find_by(id: sid) : Molecule.find_by(id: sid)
-          next unless el.present?
-          next unless object.properties.dig('layers', key, 'fields', idx, 'value').present?
-
-          object.properties['layers'][key]['fields'][idx]['value']['el_label'] = el.short_label if field['type'] == 'drag_sample'
-          object.properties['layers'][key]['fields'][idx]['value']['el_tip'] = el.short_label if field['type'] == 'drag_sample'
-          object.properties['layers'][key]['fields'][idx]['value']['el_svg'] = field['type'] == 'drag_sample' ? el.get_svg_path : File.join('/images', 'molecules', el.molecule_svg_file)
-        end
-
-        field_tables = object.properties['layers'][key]['fields'].select { |ss| ss['type'] == 'table' }
-        field_tables.each do |field|
-          idx = object.properties['layers'][key]['fields'].index(field)
-          next unless field['sub_values'].present? && field['sub_fields'].present?
-
-          field_table_molecules = field['sub_fields'].select { |ss| ss['type'] == 'drag_molecule' }
-          object.properties['layers'][key]['fields'][idx] = set_table(field, field_table_molecules, 'Molecule') if field_table_molecules.present?
-
-          field_table_samples = field['sub_fields'].select { |ss| ss['type'] == 'drag_sample' }
-          object.properties['layers'][key]['fields'][idx] = set_table(field, field_table_samples, 'Sample') if field_table_samples.present?
-        end
-      end
-      object.properties
-    end
-
     def type
       object.element_klass.name # 'genericEl' #object.type
     end
 
-    def set_table(field, field_table_objs, obj)
-      col_ids = field_table_objs.map { |x| x.values[0] }
-      col_ids.each do |col_id|
-        field['sub_values'].each do |sub_value|
-          next unless sub_value[col_id].present? && sub_value[col_id]['value'].present? && sub_value[col_id]['value']['el_id'].present?
-
-          find_obj = obj.constantize.find_by(id: sub_value[col_id]['value']['el_id'])
-          next unless find_obj.present?
-
-          case obj
-          when 'Molecule'
-            sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_obj.molecule_svg_file)
-            sub_value[col_id]['value']['el_inchikey'] = find_obj.inchikey
-            sub_value[col_id]['value']['el_smiles'] = find_obj.cano_smiles
-            sub_value[col_id]['value']['el_iupac'] = find_obj.iupac_name
-            sub_value[col_id]['value']['el_molecular_weight'] = find_obj.molecular_weight
-          when 'Sample'
-            sub_value[col_id]['value']['el_svg'] = find_obj.get_svg_path
-            sub_value[col_id]['value']['el_label'] = find_obj.short_label
-            sub_value[col_id]['value']['el_short_label'] = find_obj.short_label
-            sub_value[col_id]['value']['el_name'] = find_obj.name
-            sub_value[col_id]['value']['el_external_label'] = find_obj.external_label
-            sub_value[col_id]['value']['el_molecular_weight'] = find_obj.decoupled ? find_obj.molecular_mass : find_obj.molecule.molecular_weight
-          end
-        end
-      end
-      field
+    def can_update
+      self.options[:policy].try(:update?) || false
     end
 
     def can_copy
-      true
+      self.options[:policy].try(:copy?) || false
     end
+
+    def can_publish
+      self.options[:policy].try(:destroy?) || false
+    end
+
   end
 end

lib/labimotion/entities/properties_entity.rb

@@ -0,0 +1,72 @@
+require 'labimotion/entities/application_entity'
+
+# Entity module
+module Labimotion
+  class PropertiesEntity < Labimotion::ApplicationEntity
+
+    # TODO: Refactor this method to something more readable/understandable
+    def properties
+      (object&.properties.is_a?(Hash) && object.properties['layers']&.keys || []).each do |key|
+        # layer = object.properties[key]
+        field_sample_molecules = object.properties['layers'][key]['fields'].select { |ss| ss['type'] == 'drag_sample' || ss['type'] == 'drag_molecule' }
+        field_sample_molecules.each do |field|
+          idx = object.properties['layers'][key]['fields'].index(field)
+          sid = field.dig('value', 'el_id')
+          next unless sid.present?
+
+          el = field['type'] == 'drag_sample' ? Sample.find_by(id: sid) : Molecule.find_by(id: sid)
+          next unless el.present?
+          next unless object.properties.dig('layers', key, 'fields', idx, 'value').present?
+
+          object.properties['layers'][key]['fields'][idx]['value']['el_label'] = el.short_label if field['type'] == 'drag_sample'
+          object.properties['layers'][key]['fields'][idx]['value']['el_tip'] = el.short_label if field['type'] == 'drag_sample'
+          object.properties['layers'][key]['fields'][idx]['value']['el_svg'] = field['type'] == 'drag_sample' ? el.get_svg_path : File.join('/images', 'molecules', el.molecule_svg_file)
+        end
+
+        field_tables = object.properties['layers'][key]['fields'].select { |ss| ss['type'] == 'table' }
+        field_tables.each do |field|
+          idx = object.properties['layers'][key]['fields'].index(field)
+          next unless field['sub_values'].present? && field['sub_fields'].present?
+
+          field_table_molecules = field['sub_fields'].select { |ss| ss['type'] == 'drag_molecule' }
+          object.properties['layers'][key]['fields'][idx] = set_table(field, field_table_molecules, 'Molecule') if field_table_molecules.present?
+
+          field_table_samples = field['sub_fields'].select { |ss| ss['type'] == 'drag_sample' }
+          object.properties['layers'][key]['fields'][idx] = set_table(field, field_table_samples, 'Sample') if field_table_samples.present?
+        end
+      end
+      object.properties
+    end
+
+
+    def set_table(field, field_table_objs, obj)
+      col_ids = field_table_objs.map { |x| x.values[0] }
+      col_ids.each do |col_id|
+        field['sub_values'].each do |sub_value|
+          next unless sub_value[col_id].present? && sub_value[col_id]['value'].present? && sub_value[col_id]['value']['el_id'].present?
+
+          find_obj = obj.constantize.find_by(id: sub_value[col_id]['value']['el_id'])
+          next unless find_obj.present?
+
+          case obj
+          when 'Molecule'
+            sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_obj.molecule_svg_file)
+            sub_value[col_id]['value']['el_inchikey'] = find_obj.inchikey
+            sub_value[col_id]['value']['el_smiles'] = find_obj.cano_smiles
+            sub_value[col_id]['value']['el_iupac'] = find_obj.iupac_name
+            sub_value[col_id]['value']['el_molecular_weight'] = find_obj.molecular_weight
+          when 'Sample'
+            sub_value[col_id]['value']['el_svg'] = find_obj.get_svg_path
+            sub_value[col_id]['value']['el_label'] = find_obj.short_label
+            sub_value[col_id]['value']['el_short_label'] = find_obj.short_label
+            sub_value[col_id]['value']['el_name'] = find_obj.name
+            sub_value[col_id]['value']['el_external_label'] = find_obj.external_label
+            sub_value[col_id]['value']['el_molecular_weight'] = find_obj.decoupled ? find_obj.molecular_mass : find_obj.molecule.molecular_weight
+          end
+        end
+      end
+      field
+    end
+
+  end
+end

lib/labimotion/entities/segment_entity.rb

@@ -3,60 +3,12 @@
 require 'labimotion/entities/application_entity'
 module Labimotion
   ## Segment entity
-  class SegmentEntity < ApplicationEntity
+  class SegmentEntity < PropertiesEntity
     expose :id, :segment_klass_id, :element_type, :element_id, :properties, :properties_release, :uuid, :klass_uuid, :klass_label
 
     def klass_label
       object.segment_klass.label
     end
 
-    def properties # rubocop:disable Metrics/PerceivedComplexity, Metrics/CyclomaticComplexity, Metrics/AbcSize, Metrics/MethodLength
-      return unless object.respond_to?(:properties)
-
-      return if object&.properties.dig('layers').blank?
-
-      object&.properties['layers'].each_key do |key|  # rubocop:disable Metrics/BlockLength
-        next if object&.properties.dig('layers', key, 'fields').blank?
-
-        field_sample_molecules = object&.properties['layers'][key]['fields'].select { |ss| ss['type'] == 'drag_molecule' }
-        field_sample_molecules.each do |field|
-          idx = object&.properties['layers'][key]['fields'].index(field)
-          sid = field.dig('value', 'el_id')
-          next if sid.blank?
-
-          el = Molecule.find_by(id: sid)
-          next if el.blank?
-
-          next if object&.properties.dig('layers', key, 'fields', idx, 'value').blank?
-
-          object&.properties['layers'][key]['fields'][idx]['value']['el_svg'] = File.join('/images', 'molecules', el.molecule_svg_file)
-        end
-
-        field_tables = object.properties['layers'][key]['fields'].select { |ss| ss['type'] == 'table' }
-        field_tables.each do |field|
-          next unless field['sub_values'].present? && field['sub_fields'].present?
-
-          field_table_molecules = field['sub_fields'].select { |ss| ss['type'] == 'drag_molecule' }
-          next if field_table_molecules.blank?
-
-          col_ids = field_table_molecules.map { |x| x.values[0] }
-          col_ids.each do |col_id|
-            field['sub_values'].each do |sub_value|
-              next unless sub_value[col_id].present? && sub_value[col_id]['value'].present? && sub_value[col_id]['value']['el_id'].present?
-
-              find_mol = Molecule.find_by(id: sub_value[col_id]['value']['el_id'])
-              next if find_mol.blank?
-
-              sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_mol.molecule_svg_file)
-              sub_value[col_id]['value']['el_inchikey'] = find_mol.inchikey
-              sub_value[col_id]['value']['el_smiles'] = find_mol.cano_smiles
-              sub_value[col_id]['value']['el_iupac'] = find_mol.iupac_name
-              sub_value[col_id]['value']['el_molecular_weight'] = find_mol.molecular_weight
-            end
-          end
-        end
-      end
-      object&.properties
-    end
   end
 end

lib/labimotion/helpers/element_helpers.rb

@@ -92,7 +92,7 @@ def create_element(current_user, params)
       all_coll = Collection.get_all_collection_for_user(current_user.id)
       element.collections << all_coll
       element.save!
-      element.properties = update_sample_association(element, params[:properties], current_user)
+      element.properties = update_sample_association(params[:properties], current_user, element)
       element.container = update_datamodel(params[:container], current_user)
       element.save!
       element.save_segments(segments: params[:segments], current_user_id: current_user.id)
@@ -105,7 +105,7 @@ def create_element(current_user, params)
     def update_element_by_id(current_user, params)
       element = Labimotion::Element.find(params[:id])
       update_datamodel(params[:container], current_user)
-      properties = update_sample_association(element, params[:properties], current_user)
+      properties = update_sample_association(params[:properties], current_user, element)
       params.delete(:container)
       params.delete(:properties)
       attributes = declared(params.except(:segments), include_missing: false)