labimotion 1.0.18 → 1.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: cb5fd5761e888bf207676bbf97543cf5636dec7ab38fb70ee1d9481bc2fce073
-  data.tar.gz: 99c3efcefccd2c5ac2460c2c1e5b31b4f3aa3740f95511efa9453f04f2218deb
+  metadata.gz: 0c374697be6dd59785865b85ea34a92de6d9e87d8d0fe9d5416b5b58c5f18f11
+  data.tar.gz: 11b8842141477f92d08e50c0fc55c29f82c7a098dc8c08ed9be610b9d037c0ae
 SHA512:
-  metadata.gz: 39cd347d558a49e57931c2d818530ea9cce85ea01e1a8950d04977cbe6794e3f777ec551bb37af058ca773083301a1bbd79d57d85733c882068d081a5d8b527d
-  data.tar.gz: 19c0ededc605def31634b210e0117411841afaad5c7b84dc9f57a96cfcab6177b54d11f5bf70bb0f70752589aebe37d0ed5f53a22bbaa486002a66d2830a3210
+  metadata.gz: 0ebbb6edd334c5f13bbf3196cc7f5b56510019925f516abb35404b0943c9546e21fd16227ffebe5365955d9202b7201b795fac019c72050d0a59f902d4aa70ca
+  data.tar.gz: eded51a9e589660b0a6dcf20187eb715e946448fa9a047263176212c0136d0a648c9015d50a3de0ae06ea39ba6942fcfc23e00b085aecaa583e8faa57e67f1ee

data/lib/labimotion/apis/generic_element_api.rb

@@ -310,7 +310,10 @@ module Labimotion
       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 @@ module Labimotion
               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)
             }

data/lib/labimotion/apis/labimotion_hub_api.rb

@@ -19,7 +19,7 @@ module Labimotion
         get do
           list = "Labimotion::#{params[:klass]}".constantize.where(is_active: true).where.not(released_at: nil)
           list = list.where(is_generic: true) if params[:klass] == 'ElementKlass'
-          entities = Labimotion::GenericPublicEntity.represent(list, displayed: params[:with_props])
+          entities = Labimotion::GenericPublicEntity.represent(list, displayed: params[:with_props], root: 'list')
         rescue StandardError => e
           Labimotion.log_exception(e, current_user)
           []

data/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 @@ module Labimotion
       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

data/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

data/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

data/lib/labimotion/helpers/element_helpers.rb

@@ -92,7 +92,7 @@ module Labimotion
       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 @@ module Labimotion
     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)

data/lib/labimotion/helpers/sample_association_helpers.rb

@@ -6,119 +6,21 @@ module Labimotion
     extend Grape::API::Helpers
 
     def build_sample(sid, cols, current_user, cr_opt)
-      parent_sample = Sample.find(sid)
-
-      case cr_opt
-      when 0
-        subsample = parent_sample
-        collections = Collection.where(id: cols).where.not(id: subsample.collections.pluck(:id))
-        subsample.collections << collections unless collections.empty?
-      when 1
-        subsample = parent_sample.create_subsample(current_user, cols, true)
-      when 2
-        subsample = parent_sample.dup
-        subsample.parent = nil
-        collections = (Collection.where(id: cols) | Collection.where(user_id: current_user.id, label: 'All', is_locked: true))
-        subsample.collections << collections
-        subsample.container = Container.create_root_container
-      else
-        return nil
-      end
-
-      return nil if subsample.nil?
-
-      subsample.save!
-      subsample.reload
-      subsample
+      Labimotion::SampleAssociation.build_sample(sid, cols, current_user, cr_opt)
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       nil
     end
 
-    def build_table_sample(element, field_tables)
-      sds = []
-      field_tables.each do |field|
-        next unless field['sub_values'].present? && field['sub_fields'].present?
-
-        field_table_samples = field['sub_fields'].select { |ss| ss['type'] == 'drag_sample' }
-        next unless field_table_samples.present?
-
-        col_ids = field_table_samples.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?
-
-            svalue = sub_value[col_id]['value']
-            sid = svalue['el_id']
-            next unless sid.present?
-
-            sds << sid unless svalue['is_new']
-            next unless svalue['is_new']
-
-            cr_opt = svalue['cr_opt']
-
-            subsample = build_sample(sid, element.collections, current_user, cr_opt) unless sid.nil? || cr_opt.nil?
-            next if subsample.nil?
-
-            sds << subsample.id
-            sub_value[col_id]['value']['el_id'] = subsample.id
-            sub_value[col_id]['value']['is_new'] = false
-            Labimotion::ElementsSample.find_or_create_by(element_id: element.id, sample_id: subsample.id)
-          end
-        end
-      end
-      sds
+    def build_table_sample(field_tables, current_user, element)
+      Labimotion::SampleAssociation.build_table_sample(field_tables, current_user, element)
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       []
     end
 
-    def update_sample_association(element, properties, current_user)
-      sds = []
-      els = []
-      properties['layers'].keys.each do |key|
-        layer = properties['layers'][key]
-        field_samples = layer['fields'].select { |ss| ss['type'] == 'drag_sample' }
-        field_samples.each do |field|
-          idx = properties['layers'][key]['fields'].index(field)
-          sid = field.dig('value', 'el_id')
-          next if sid.blank?
-
-          sds << sid unless properties.dig('layers', key, 'fields', idx, 'value', 'is_new') == true
-          next unless properties.dig('layers', key, 'fields', idx, 'value', 'is_new') == true
-
-          cr_opt = field.dig('value', 'cr_opt')
-
-          subsample = build_sample(sid, element.collections, current_user, cr_opt) unless sid.nil? || cr_opt.nil?
-          next if subsample.nil?
-
-          sds << subsample.id
-          properties['layers'][key]['fields'][idx]['value']['el_id'] = subsample.id
-          properties['layers'][key]['fields'][idx]['value']['el_label'] = subsample.short_label
-          properties['layers'][key]['fields'][idx]['value']['el_tip'] = subsample.short_label
-          properties['layers'][key]['fields'][idx]['value']['is_new'] = false
-          Labimotion::ElementsSample.find_or_create_by(element_id: element.id, sample_id: subsample.id)
-        end
-        field_tables = properties['layers'][key]['fields'].select { |ss| ss['type'] == 'table' }
-        sds << build_table_sample(element, field_tables)
-
-        field_elements = layer['fields'].select { |ss| ss['type'] == 'drag_element' }
-        field_elements.each do |field|
-          idx = properties['layers'][key]['fields'].index(field)
-          sid = field.dig('value', 'el_id')
-          next if sid.blank? || sid == element.id
-
-          el = Labimotion::Element.find_by(id: sid)
-          next if el.nil?
-
-          Labimotion::ElementsElement.find_or_create_by(parent_id: element.id, element_id: el.id)
-          els << el.id
-        end
-
-      end
-      Labimotion::ElementsSample.where(element_id: element.id).where.not(sample_id: sds)&.destroy_all
-      Labimotion::ElementsElement.where(parent_id: element.id).where.not(element_id: els&.flatten)&.destroy_all
-      properties
+    def update_sample_association(properties, current_user, element)
+      Labimotion::SampleAssociation.update_sample_association(properties, current_user, element)
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
     end

data/lib/labimotion/libs/converter.rb

@@ -20,7 +20,10 @@ module Labimotion
 
     def self.process_ds(id, current_user = {})
       att = Attachment.find_by(id: id, con_state: Labimotion::ConState::CONVERTED)
-      return if att.nil? || att.attachable_id.nil? || att.attachable_type != 'Container'
+      return if att.nil? || att.attachable_id.nil? || att.attachable_type != 'Container' || att.filename.split('.')&.last != 'zip'
+
+      eln_ds = Container.find_by(id: att.attachable_id, container_type: 'dataset')
+      return if eln_ds.nil? || eln_ds.parent.nil? || eln_ds.parent&.container_type != 'analysis'
 
       dsr = []
       ols = nil

data/lib/labimotion/libs/export_dataset.rb

@@ -40,6 +40,8 @@ module Labimotion
       header_style = sheet.styles.add_style(sz: 12, fg_color: 'FFFFFF', bg_color: '00008B', border: { style: :thick, color: 'FF777777', edges: [:bottom] })
       sheet.add_row(['File name', res_name(id)])
       sheet.add_row(['Time', Time.now.strftime("%Y-%m-%d %H:%M:%S %Z")] )
+      sheet.add_row(['(This file is automatically generated by the system.)'])
+      sheet.add_row([''])
       sheet.add_row([''])
       sheet.add_row(['Fields description of sheet:' + ds.dataset_klass.label])
       sheet.add_row(['Fields', 'Field description'], style: header_style)
@@ -49,13 +51,11 @@ module Labimotion
       sheet.add_row(['Unit', 'The unit of the field'])
       sheet.add_row(['Name', 'The key of the field, can be used to identify the field'])
       sheet.add_row(['Type', 'The type of the field'])
-      sheet.add_row(['From device?', '[Yes] if the field is from the device, [No] if the field is manually entered by the user, [SYS] if the field is automatically generated by the system'])
-      sheet.add_row(['Device source', 'The source tag of the device file, available only if the ontology term is 1H NMR or 13C NMR'])
-      sheet.add_row(['Device data', 'The original device data, can not be changed after data uploaded'])
-      sheet.add_row([''])
+      sheet.add_row(['Source?', '[Device] from device, [Chemotion] from Chemotion'])
+      sheet.add_row(['Source identifier', 'The source identifier'])
+      sheet.add_row(['Source data', 'The data from Device or Chemotion, cannot be modified once a generic dataset is created'])
       sheet.add_row([''])
       sheet.add_row([''])
-      sheet.add_row(['', '(This file is automatically generated by the system.)'])
     end
 
     def export(id)
@@ -84,29 +84,41 @@ module Labimotion
           next if field['type'] == 'dummy'
 
           type = field['type']
-          from_device = field['device'].present? ? 'Yes' : 'No'
-          from_device = field['system'].present? ? 'SYS' : from_device
+          from_device = field['device'].present? ? 'Device' : ''
+          from_device = field['system'].present? ? 'Chemotion' : from_device
           type = "#{field['type']}-#{field['option_layers']}" if field['type'] == 'select' || field['type'] == 'system-defined'
 
           show_value = field['value'] =~ /\A\d+,\d+\z/ ? field['value']&.gsub(',', '.') : field['value']
-          sheet.add_row([' ', field['label'], show_value, field['value_system'], field['field'], type, from_device, field['dkey'], field['system'] || field['device']].freeze)
+          sheet.add_row([' ', field['label'], nil, field['value_system'], field['field'], type, from_device, field['dkey'], nil].freeze)
+
+          if %w[system-defined integer].include? field['type']
+            sheet.rows.last.cells[2].type = :integer
+            sheet.rows.last.cells[8].type = :integer
+          else
+            sheet.rows.last.cells[2].type = :string
+            sheet.rows.last.cells[8].type = :string
+          end
+          sheet.rows.last.cells[2].value = show_value
+          sheet.rows.last.cells[8].value = field['system'] || field['device']
+
+
         end
         # sheet.column_widths nil, nil, nil, nil, 0, 0, 0, 0, 0
       end
     end
 
     def spectra(id)
+      name_mapping = []
       wb = @xfile.workbook
       gds = Labimotion::Dataset.find_by(element_id: id, element_type: 'Container')
       cds = Container.find(id)
-      cds_csv = cds.attachments.where(aasm_state: 'csv')
+      cds_csv = cds.attachments.where(aasm_state: 'csv').order(:filename)
       csv_length = cds_csv.length
       return if csv_length.zero?
       cds_csv.each_with_index do |att, idx|
-        name = File.basename(att.filename, '.csv')
-        name = name.slice(0, (25 - csv_length.to_s.length - 1))
-        sheet_name = "#{name}_#{idx}"
+        sheet_name = "Sheet#{idx+1}"
         sheet = @xfile.workbook.add_worksheet(name: sheet_name)
+        name_mapping.push([sheet_name, att.filename])
 
         if Labimotion::IS_RAILS5 == true
           File.open(att.store.path) do |fi|
@@ -122,10 +134,22 @@ module Labimotion
           end
         end
       end
+
+      if name_mapping.length > 1
+        first_sheet = @xfile.workbook.worksheets&.first
+        header_style = first_sheet&.styles.add_style(sz: 12, fg_color: 'FFFFFF', bg_color: '00008B', border: { style: :thick, color: 'FF777777', edges: [:bottom] })
+        first_sheet&.add_row(['Sheet name', 'File name'], style: header_style)
+        name_mapping&.each do |mapping|
+          next if mapping.length < 2
+
+          @xfile.workbook.worksheets&.first&.add_row([mapping[0].to_s, mapping[1].to_s])
+        end
+      end
+
     end
 
     def header
-      ['Layer Label', 'Field Label', 'Value', 'Unit', 'Name', 'Type', 'from device?', 'Device source', 'Device data'].freeze
+      ['Layer Label', 'Field Label', 'Value', 'Unit', 'Name', 'Type', 'Source?', 'Source identifier', 'Source data'].freeze
     end
 
     def read

data/lib/labimotion/libs/nmr_mapper.rb

@@ -10,8 +10,12 @@ module Labimotion
       att = Attachment.find_by(id: id, con_state: Labimotion::ConState::NMR)
       return if att.nil?
 
-      content = is_brucker_binary(id)
-      if content.nil?
+      result = is_brucker_binary(id)
+      if result[:is_bagit] == true
+        att.update_column(:con_state, Labimotion::ConState::CONVERTED)
+        Labimotion::Converter.metadata(id)
+        Labimotion::ConState::COMPLETED
+      elsif result[:metadata] == nil
         Labimotion::ConState::NONE
       else
         data = process(att, id, content)
@@ -29,7 +33,9 @@ module Labimotion
           zip_file.each do |entry|
             if entry.name.include?('/pdata/') && entry.name.include?('parm.txt')
               metadata = entry.get_input_stream.read.force_encoding('UTF-8')
-              return metadata
+              return { is_bagit: false, metadata: metadata }
+            elsif entry.name.include?('metadata/') && entry.name.include?('converter.json')
+              return { is_bagit: true, metadata: nil }
             end
           end
         end
@@ -39,13 +45,15 @@ module Labimotion
             zip_file.each do |entry|
               if entry.name.include?('/pdata/') && entry.name.include?('parm.txt')
                 metadata = entry.get_input_stream.read.force_encoding('UTF-8')
-                return metadata
+                return { is_bagit: false, metadata: metadata }
+              elsif entry.name.include?('metadata/') && entry.name.include?('converter.json')
+                return { is_bagit: true, metadata: nil }
               end
             end
           end
         end
       end
-      nil
+      { is_bagit: false, metadata: nil }
     end
 
     def self.process(att, id, content)

data/lib/labimotion/libs/sample_association.rb

@@ -0,0 +1,125 @@
+# frozen_string_literal: true
+
+module Labimotion
+  class SampleAssociation
+    def self.build_sample(sid, cols, current_user, cr_opt)
+      parent_sample = Sample.find(sid)
+      case cr_opt
+      when 0
+        subsample = parent_sample
+        collections = Collection.where(id: cols).where.not(id: subsample.collections.pluck(:id))
+        subsample.collections << collections unless collections.empty?
+      when 1
+        subsample = parent_sample.create_subsample(current_user, cols, true)
+      when 2
+        subsample = parent_sample.dup
+        subsample.parent = nil
+        collections = (Collection.where(id: cols) | Collection.where(user_id: current_user.id, label: 'All', is_locked: true))
+        subsample.collections << collections
+        subsample.container = Container.create_root_container
+      else
+        return nil
+      end
+
+      return nil if subsample.nil?
+
+      subsample.save!
+      subsample.reload
+      subsample
+    rescue StandardError => e
+      Labimotion.log_exception(e, current_user)
+      nil
+    end
+
+    def self.build_table_sample(field_tables, current_user, element = nil)
+      sds = []
+      field_tables.each do |field|
+        next unless field['sub_values'].present? && field['sub_fields'].present?
+
+        field_table_samples = field['sub_fields'].select { |ss| ss['type'] == 'drag_sample' }
+        next unless field_table_samples.present?
+
+        col_ids = field_table_samples.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?
+
+            svalue = sub_value[col_id]['value']
+            sid = svalue['el_id']
+            next unless sid.present?
+
+            sds << sid unless svalue['is_new']
+            next unless svalue['is_new']
+
+            cr_opt = svalue['cr_opt']
+            next if element.nil?
+
+            subsample = Labimotion::SampleAssociation.build_sample(sid, element.collections, current_user, cr_opt) unless sid.nil? || cr_opt.nil?
+            next if subsample.nil?
+
+            sds << subsample.id
+            sub_value[col_id]['value']['el_id'] = subsample.id
+            sub_value[col_id]['value']['is_new'] = false
+            Labimotion::ElementsSample.find_or_create_by(element_id: element.id, sample_id: subsample.id)
+          end
+        end
+      end
+      sds
+    rescue StandardError => e
+      Labimotion.log_exception(e, current_user)
+      []
+    end
+
+    def self.update_sample_association(properties, current_user, element = nil)
+      sds = []
+      els = []
+      properties['layers'].keys.each do |key|
+        layer = properties['layers'][key]
+        field_samples = layer['fields'].select { |ss| ss['type'] == 'drag_sample' }
+        field_samples.each do |field|
+          idx = properties['layers'][key]['fields'].index(field)
+          sid = field.dig('value', 'el_id')
+          next if sid.blank?
+
+          sds << sid unless properties.dig('layers', key, 'fields', idx, 'value', 'is_new') == true
+          next unless properties.dig('layers', key, 'fields', idx, 'value', 'is_new') == true
+
+          cr_opt = field.dig('value', 'cr_opt')
+          subsample = Labimotion::SampleAssociation.build_sample(sid, element&.collections, current_user, cr_opt) unless sid.nil? || cr_opt.nil?
+          next if subsample.nil?
+
+          sds << subsample.id
+          properties['layers'][key]['fields'][idx]['value']['el_id'] = subsample.id
+          properties['layers'][key]['fields'][idx]['value']['el_label'] = subsample.short_label
+          properties['layers'][key]['fields'][idx]['value']['el_tip'] = subsample.short_label
+          properties['layers'][key]['fields'][idx]['value']['is_new'] = false
+          Labimotion::ElementsSample.find_or_create_by(element_id: element.id, sample_id: subsample.id) if element.present?
+        end
+        field_tables = properties['layers'][key]['fields'].select { |ss| ss['type'] == 'table' }
+        sds << Labimotion::SampleAssociation.build_table_sample(field_tables, current_user, element) if element.present?
+        field_elements = layer['fields'].select { |ss| ss['type'] == 'drag_element' }
+        field_elements.each do |field|
+          idx = properties['layers'][key]['fields'].index(field)
+          sid = field.dig('value', 'el_id')
+          next if element.nil? || sid.blank? || sid == element.id
+
+          el = Labimotion::Element.find_by(id: sid)
+          next if el.nil?
+
+          Labimotion::ElementsElement.find_or_create_by(parent_id: element.id, element_id: el.id)
+          els << el.id
+        end
+
+      end
+      if element.present?
+        es_list = Labimotion::ElementsSample.where(element_id: element.id).where.not(sample_id: sds)
+        ee_list = Labimotion::ElementsElement.where(parent_id: element.id).where.not(element_id: els&.flatten)
+        es_list.destroy_all if es_list.present?
+        ee_list.destroy_all if ee_list.present?
+      end
+      properties
+    rescue StandardError => e
+      Labimotion.log_exception(e, current_user)
+    end
+  end
+end

data/lib/labimotion/models/concerns/segmentable.rb

@@ -41,6 +41,7 @@ module Labimotion
 
     def save_segments(**args) # rubocop:disable Metrics/AbcSize, Metrics/CyclomaticComplexity
       return if args[:segments].nil?
+
       segments = []
       args[:segments]&.each do |seg|
         klass = Labimotion::SegmentKlass.find_by(id: seg['segment_klass_id'])
@@ -50,6 +51,7 @@ module Labimotion
         props['identifier'] = klass.identifier if klass.identifier.present?
         props['uuid'] = uuid
         props['klass'] = 'Segment'
+        props = Labimotion::SampleAssociation.update_sample_association(props, args[:current_user_id])
         segment = Labimotion::Segment.find_by(element_type: Labimotion::Utils.element_name(self.class.name), element_id: self.id, segment_klass_id: seg['segment_klass_id'])
         if segment.present? && (segment.klass_uuid != props['klass_uuid'] || segment.properties != props)
           segment.update!(properties_release: klass.properties_release, properties: props, uuid: uuid, klass_uuid: props['klass_uuid'])

data/lib/labimotion/version.rb

@@ -3,9 +3,5 @@
 ## Labimotion Version
 module Labimotion
   IS_RAILS5 = false
-  VERSION_ELN = '1.0.18'
-  VERSION_REPO = '0.3.1'
-
-  VERSION = Labimotion::VERSION_REPO if Labimotion::IS_RAILS5 == true
-  VERSION = Labimotion::VERSION_ELN if Labimotion::IS_RAILS5 == false
+  VERSION = '1.1.0'
 end

data/lib/labimotion.rb

@@ -8,7 +8,7 @@ module Labimotion
   end
 
   def self.log_exception(exception, current_user = nil)
-    Labimotion.logger.error("version: #{Labimotion::VERSION}; #{Labimotion::IS_RAILS5}, (#{current_user&.id}) \n Exception: #{exception.message}")
+    Labimotion.logger.error("version: #{Labimotion::VERSION}; (#{current_user&.id}) \n Exception: #{exception.message}")
     Labimotion.logger.error(exception.backtrace.join("\n"))
   end
 
@@ -22,6 +22,8 @@ module Labimotion
   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 @@ module Labimotion
   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'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 1.0.18
+  version: 1.1.0
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-10-20 00:00:00.000000000 Z
+date: 2024-01-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -52,6 +52,7 @@ files:
 - lib/labimotion/entities/generic_klass_entity.rb
 - lib/labimotion/entities/generic_public_entity.rb
 - lib/labimotion/entities/klass_revision_entity.rb
+- lib/labimotion/entities/properties_entity.rb
 - lib/labimotion/entities/segment_entity.rb
 - lib/labimotion/entities/segment_klass_entity.rb
 - lib/labimotion/entities/segment_revision_entity.rb
@@ -66,6 +67,7 @@ files:
 - lib/labimotion/libs/converter.rb
 - lib/labimotion/libs/export_dataset.rb
 - lib/labimotion/libs/nmr_mapper.rb
+- lib/labimotion/libs/sample_association.rb
 - lib/labimotion/libs/template_hub.rb
 - lib/labimotion/models/collections_element.rb
 - lib/labimotion/models/concerns/attachment_converter.rb
@@ -97,7 +99,7 @@ files:
 - lib/labimotion/version.rb
 homepage: https://gitlab.kit.edu/kit/labimotion/labimotion
 licenses:
-- GPL-3.0
+- AGPL-3.0
 metadata: {}
 post_install_message: 
 rdoc_options: []
@@ -114,7 +116,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.4.18
+rubygems_version: 3.1.6
 signing_key: 
 specification_version: 4
 summary: Chemotion LabIMotion