labimotion 0.1.6

data/lib/labimotion/entities/application_entity.rb

@@ -0,0 +1,88 @@
+# frozen_string_literal: true
+#
+module Labimotion
+  ## ApplicationEntity
+  class ApplicationEntity < Grape::Entity
+    CUSTOM_ENTITY_OPTIONS = %i[anonymize_below anonymize_with].freeze
+
+    format_with(:eln_timestamp) do |datetime|
+      datetime.present? ? datetime&.strftime('%Y-%m-%d %H:%M:%S %Z')  : nil
+    end
+
+    def self.expose!(*args)
+      fields = args.first
+      options = args.last.is_a?(Hash) ? args.pop : {}
+      options = merge_options(options) # merges additional params set in #with_options
+      expose_fields_with_anonymization!(fields, options)
+    end
+
+    # rubocop:disable Metrics/MethodLength
+    def self.expose_fields_with_anonymization!(fields, options)
+      anonymize_below = options[:anonymize_below] || 0
+      anonymize_with = options.key?(:anonymize_with) ? options[:anonymize_with] : '***'
+
+      Array(fields).each do |field|
+        expose(field, options) do |represented_object, _options|
+          if detail_levels[represented_object.class] < anonymize_below
+            anonymize_with
+          elsif respond_to?(field, true) # Entity has a method with the same name
+            send(field)
+          elsif represented_object.respond_to?(field)
+            represented_object.public_send(field)
+          else
+            represented_object[field] # works both for AR and Hash objects
+          end
+        end
+      end
+    end
+    private_class_method :expose_fields_with_anonymization!
+    # rubocop:enable Metrics/MethodLength
+
+    def self.expose_timestamps(timestamp_fields: %i[created_at updated_at], **additional_args)
+      timestamp_fields.each do |field|
+        expose field, format_with: :eln_timestamp, **additional_args
+      end
+    end
+
+    # overridden method from Grape::Entity to support our custom anonymization options
+    # https://github.com/ruby-grape/grape-entity/blob/v0.7.1/lib/grape_entity/entity.rb#L565
+    def self.valid_options(options)
+      options.each_key do |key|
+        next if OPTIONS.include?(key) || CUSTOM_ENTITY_OPTIONS.include?(key)
+
+        raise ArgumentError, "#{key.inspect} is not a valid option."
+      end
+
+      options[:using] = options.delete(:with) if options.key?(:with)
+      options
+    end
+    private_class_method :valid_options
+
+    private
+
+    def displayed_in_list?
+      options[:displayed_in_list] == true
+    end
+
+    def current_user
+      unless options[:current_user]
+        raise MissingCurrentUserError, "#{self.class} requires a current user to work properly"
+      end
+
+      options[:current_user]
+    end
+
+    def detail_levels
+      maximal_default_levels = Hash.new(10) # every requested detail level will be returned as 10
+      minimal_default_levels = Hash.new(0) # every requested detail level will be returned as 0
+      return maximal_default_levels if !options.key?(:detail_levels) || options[:detail_levels].empty?
+
+      # When explicitly configured detail levels are available, we want to return only those and all other
+      # requests (by using `detail_levels[SomeUnconfiguredModel]`) should return the minimum detail level
+      minimal_default_levels.merge(options[:detail_levels])
+    end
+
+    class MissingCurrentUserError < StandardError
+    end
+  end
+end

data/lib/labimotion/entities/dataset_entity.rb

@@ -0,0 +1,16 @@
+# frozen_string_literal: true
+#
+require 'labimotion/entities/application_entity'
+module Labimotion
+  # Dataset entity
+  class DatasetEntity < ApplicationEntity
+    expose :id, :dataset_klass_id, :properties, :properties_release, :element_id, :element_type, :klass_ols, :klass_label, :klass_uuid
+    def klass_ols
+      object&.dataset_klass&.ols_term_id
+    end
+
+    def klass_label
+      object&.dataset_klass&.label
+    end
+  end
+end

data/lib/labimotion/entities/dataset_klass_entity.rb

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+require 'labimotion/entities/generic_klass_entity'
+module Labimotion
+  class DatasetKlassEntity < GenericKlassEntity
+    expose(
+      :ols_term_id,
+    )
+  end
+end

data/lib/labimotion/entities/element_entity.rb

@@ -0,0 +1,108 @@
+# frozen_string_literal: true
+
+require 'labimotion/entities/application_entity'
+## TODO: Refactor labimotion to use the same entities as chemotion
+module Labimotion
+  class ElementEntity < ApplicationEntity
+    with_options(anonymize_below: 0) do
+      expose! :can_copy
+      expose! :container,                           using: 'Entities::ContainerEntity'
+      expose! :created_by
+      expose! :id
+      expose! :is_restricted
+      expose! :klass_uuid
+      expose! :name
+      expose! :properties
+      expose! :properties_release
+      expose! :short_label
+      expose! :type
+      expose! :uuid
+    end
+
+    with_options(anonymize_below: 10) do
+      expose! :element_klass, anonymize_with: nil,  using: 'Labimotion::ElementKlassEntity'
+      expose! :segments,      anonymize_with: [],   using: 'Labimotion::SegmentEntity'
+      expose! :tag,           anonymize_with: nil,  using: 'Entities::ElementTagEntity'
+    end
+
+    expose_timestamps
+
+
+    private
+
+    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
+    end
+
+    def can_copy
+      true
+    end
+  end
+end

data/lib/labimotion/entities/element_klass_entity.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+#
+require 'labimotion/entities/generic_klass_entity'
+
+module Labimotion
+  # ElementKlassEntity
+  class ElementKlassEntity < GenericKlassEntity
+    expose :name, :icon_name, :klass_prefix, :is_generic
+  end
+end

data/lib/labimotion/entities/element_revision_entity.rb

@@ -0,0 +1,57 @@
+# frozen_string_literal: true
+
+require 'labimotion/entities/application_entity'
+module Labimotion
+  # ElementRevisionEntity
+  class ElementRevisionEntity < ApplicationEntity
+    expose :id, :element_id, :uuid, :name, :klass_uuid, :properties, :created_at
+    def created_at
+      object.created_at.strftime('%d.%m.%Y, %H:%M')
+    end
+
+    def properties
+      object.properties['layers']&.keys.each do |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|
+          next unless field['sub_values'].present? && field['sub_fields'].present?
+
+          field_table_molecules = field['sub_fields'].select { |ss| ss['type'] == 'drag_molecule' }
+          next unless field_table_molecules.present?
+
+          col_ids = field_table_molecules.map { |x| x.values[0] }
+          col_ids.each do |col_id|
+            field_table_values = 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 unless find_mol.present?
+
+              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['select_options'] = object.properties_release['select_options']
+      object.properties
+    end
+  end
+end

data/lib/labimotion/entities/eln_element_entity.rb

@@ -0,0 +1,110 @@
+# frozen_string_literal: true
+#
+require 'labimotion/entities/application_entity'
+module Labimotion
+  ## ElementEntity
+  class ElnElementEntity < ApplicationEntity
+    with_options(anonymize_below: 0) do
+      expose! :created_by
+      expose! :id
+      expose! :is_restricted
+      expose! :klass_uuid
+      expose! :name
+      expose! :properties
+      expose! :properties_release
+      expose! :short_label
+      expose! :type
+      expose! :uuid
+    end
+
+    expose(
+      :can_copy, unless: ->(_instance, _options) { displayed_in_list? }
+    )
+
+    private
+
+    def properties
+      (object.properties['layers']&.keys || []).each do |key|
+        # layer = object.properties[key]
+        field_sample_molecules = object.properties['layers'][key]['fields'].select do |ss|
+          ss['type'] == 'drag_sample' || ss['type'] == 'drag_molecule'
+        end
+        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?
+
+          if field['type'] == 'drag_sample'
+            object.properties['layers'][key]['fields'][idx]['value']['el_label'] =
+              el.short_label
+          end
+          if field['type'] == 'drag_sample'
+            object.properties['layers'][key]['fields'][idx]['value']['el_tip'] =
+              el.short_label
+          end
+          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' }
+          if field_table_molecules.present?
+            object.properties['layers'][key]['fields'][idx] =
+              set_table(field, field_table_molecules, 'Molecule')
+          end
+
+          field_table_samples = field['sub_fields'].select { |ss| ss['type'] == 'drag_sample' }
+          if field_table_samples.present?
+            object.properties['layers'][key]['fields'][idx] =
+              set_table(field, field_table_samples, 'Sample')
+          end
+        end
+      end
+      object.properties
+    end
+
+    def type
+      object.element_klass.name
+    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|
+          unless sub_value[col_id].present? && sub_value[col_id]['value'].present? && sub_value[col_id]['value']['el_id'].present?
+            next
+          end
+
+          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

data/lib/labimotion/entities/generic_entity.rb

@@ -0,0 +1,54 @@
+# frozen_string_literal: true
+
+require 'labimotion/entities/application_entity'
+
+# Entity module
+module Labimotion
+  class GenericEntity < Labimotion::ApplicationEntity
+    expose :id, :is_active, :label, :desc, :place, :released_at
+
+    expose :element_klass_id do |obj|
+      obj[:element_klass_id] || 0
+    end
+
+    expose :klass_name do |obj|
+      obj[:name] || ''
+    end
+
+    expose :ols_term_id do |obj|
+      obj[:ols_term_id] || ''
+    end
+
+    expose :icon_name do |obj|
+      obj[:icon_name] || ''
+    end
+
+    expose :klass_prefix do |obj|
+      obj[:klass_prefix] || ''
+    end
+
+    expose :is_generic do |obj|
+      obj[:is_generic] || true
+    end
+
+    expose :uuid do |obj|
+      obj[:uuid] || ''
+    end
+
+    expose :properties_release do |obj|
+      obj[:properties_release] || {}
+    end
+
+    expose :element_klass do |obj|
+      if obj[:element_klass_id]
+        Labimotion::GenericEntity.represent(obj.element_klass)
+      else
+        {}
+      end
+    end
+
+    expose :identifier do |obj|
+      obj[:identifier] || ''
+    end
+  end
+end

data/lib/labimotion/entities/generic_klass_entity.rb

@@ -0,0 +1,14 @@
+# frozen_string_literal: true
+#
+require 'labimotion/entities/application_entity'
+module Labimotion
+  # GenericKlassEntity
+  class GenericKlassEntity < ApplicationEntity
+    expose :id, :uuid, :label, :desc, :properties_template, :properties_release, :is_active,
+          :place, :released_at, :identifier, :sync_time, :created_by, :updated_by, :created_at, :updated_at
+    expose_timestamps(timestamp_fields: [:released_at])
+    expose_timestamps(timestamp_fields: [:created_at])
+    expose_timestamps(timestamp_fields: [:updated_at])
+    expose_timestamps(timestamp_fields: [:sync_time])
+  end
+end

data/lib/labimotion/entities/generic_public_entity.rb

@@ -0,0 +1,25 @@
+# frozen_string_literal: true
+
+require 'labimotion/entities/application_entity'
+
+# Entity module
+module Labimotion
+  class GenericPublicEntity < Labimotion::ApplicationEntity
+    expose! :name
+    expose! :desc
+    expose! :icon_name
+    expose! :klass_prefix
+    expose! :klass_name
+    expose! :label
+    expose! :identifier
+    expose! :released_at
+    expose! :properties_release, if: :displayed
+    expose :element_klass do |obj|
+      if obj[:element_klass_id]
+        { :label => obj.element_klass.label, :icon_name => obj.element_klass.icon_name }
+      else
+        {}
+      end
+    end
+  end
+end

data/lib/labimotion/entities/klass_revision_entity.rb

@@ -0,0 +1,20 @@
+# frozen_string_literal: true
+
+module Labimotion
+  # KlassRevisionEntity
+  class KlassRevisionEntity < ApplicationEntity
+    expose :id, :uuid, :properties_release, :released_at
+
+    expose :klass_id do |object|
+      klass_id = object.element_klass_id if object.respond_to? :element_klass_id
+      klass_id = object.segment_klass_id if object.respond_to? :segment_klass_id
+      klass_id = object.dataset_klass_id if object.respond_to? :dataset_klass_id
+      klass_id
+    end
+
+    def released_at
+      object.released_at&.strftime('%d.%m.%Y, %H:%M')
+    end
+  end
+end
+

data/lib/labimotion/entities/segment_entity.rb

@@ -0,0 +1,62 @@
+# frozen_string_literal: true
+
+require 'labimotion/entities/application_entity'
+module Labimotion
+  ## Segment entity
+  class SegmentEntity < ApplicationEntity
+    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

data/lib/labimotion/entities/segment_klass_entity.rb

@@ -0,0 +1,8 @@
+# frozen_string_literal: true
+require 'labimotion/entities/generic_klass_entity'
+require 'labimotion/entities/element_klass_entity'
+module Labimotion
+  class SegmentKlassEntity < Labimotion::GenericKlassEntity
+    expose :element_klass, using: Labimotion::ElementKlassEntity
+  end
+end

data/lib/labimotion/entities/segment_revision_entity.rb

@@ -0,0 +1,55 @@
+# frozen_string_literal: true
+#
+require 'labimotion/entities/application_entity'
+module Labimotion
+  class SegmentRevisionEntity < ApplicationEntity
+    expose :id, :segment_id, :uuid, :klass_uuid, :properties, :created_at
+    def created_at
+      object.created_at.strftime('%d.%m.%Y, %H:%M')
+    end
+
+    def properties
+      object.properties['layers']&.keys.each do |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|
+          next unless field['sub_values'].present? && field['sub_fields'].present?
+
+          field_table_molecules = field['sub_fields'].select { |ss| ss['type'] == 'drag_molecule' }
+          next unless field_table_molecules.present?
+
+          col_ids = field_table_molecules.map { |x| x.values[0] }
+          col_ids.each do |col_id|
+            field_table_values = 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 unless find_mol.present?
+
+              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

data/lib/labimotion/helpers/converter_helpers.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+require 'grape'
+
+module Labimotion
+  ## ElementHelpers
+  module ConverterHelpers
+    extend Grape::API::Helpers
+
+    def demo(params)
+      ### TODO: implement demo
+    end
+  end
+end