labimotion 0.1.6

data/lib/labimotion/libs/nmr_mapper.rb

@@ -0,0 +1,265 @@
+# frozen_string_literal: true
+
+module Labimotion
+  ## NmrMapper
+  class NmrMapper
+    def self.is_brucker_binary(id)
+      att = Attachment.find(id)
+      if att&.attachment_attacher&.file&.url
+        Zip::File.open(att.attachment_attacher.file.url) do |zip_file|
+          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
+            end
+          end
+        end
+      end
+      nil
+    end
+
+    def self.process(id, content)
+      att = Attachment.find(id)
+      lines = content.split("\n").reject(&:empty?)
+      metadata = {}
+      lines.map do |ln|
+        arr = ln.split(/\s+/)
+        metadata[arr[0]] = arr[1..-1].join(' ') if arr.length > 1
+      end
+      ols = 'CHMO:0000593' if metadata['NUC1'] == '1H'
+      ols = 'CHMO:0000595' if metadata['NUC1'] == '13C'
+      if content.present? && att.present?
+        Labimotion::NmrMapper.ts('write', att.attachable_id,
+                              content: { metadata: metadata, ols: ols })
+      end
+    end
+
+    def self.fetch_content(id)
+      Labimotion::NmrMapper.ts('read', id)
+    end
+
+    def self.generate_ds(id, current_user = {})
+      data = Labimotion::NmrMapper.fetch_content(id)
+      return if data.nil?
+
+      obj = Labimotion::NmrMapper.build_ds(id, data[:content])
+      return if obj.nil? || obj[:ols].nil?
+
+      Labimotion::NmrMapper.update_ds_1h(id, obj, current_user) if obj[:ols] == 'CHMO:0000593'
+      Labimotion::NmrMapper.update_ds_1h(id, obj, current_user) if obj[:ols] == 'CHMO:0000595'
+      Labimotion::NmrMapper.clean(id)
+    end
+
+    def self.update_ds_13c(id, obj)
+      # dataset = obj[:dataset]
+      # metadata = obj[:metadata]
+      # new_prop = dataset.properties
+
+      # dataset.properties = new_prop
+      # dataset.save!
+    end
+
+    def self.set_data(prop, field, idx, layer_name, field_name, value)
+      return if field['field'] != field_name || value&.empty?
+
+      field['value'] = value
+      prop['layers'][layer_name]['fields'][idx] = field
+      prop
+    end
+
+    def self.update_ds_1h(id, obj, current_user)
+      dataset = obj[:dataset]
+      metadata = obj[:metadata]
+      new_prop = dataset.properties
+      new_prop.dig('layers', 'general', 'fields')&.each_with_index do |fi, idx|
+        #  new_prop = set_data(new_prop, fi, idx, 'general', 'title', metadata['NAME'])
+        if fi['field'] == 'title' && metadata['NAME'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['NAME']
+          fi['device'] = metadata['NAME']
+          fi['dkey'] = 'NAME'
+          new_prop['layers']['general']['fields'][idx] = fi
+        end
+
+        if fi['field'] == 'date' && metadata['Date_'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['Date_']
+          fi['device'] = metadata['Date_']
+          fi['dkey'] = 'Date_'
+          new_prop['layers']['general']['fields'][idx] = fi
+        end
+
+        if fi['field'] == 'time' && metadata['Time'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['Time']
+          fi['device'] = metadata['Time']
+          fi['dkey'] = 'Time'
+          new_prop['layers']['general']['fields'][idx] = fi
+        end
+
+        if fi['field'] == 'creator' && current_user.present?
+          ## fi['label'] = fi['label']
+          fi['value'] = current_user.name
+          new_prop['layers']['general']['fields'][idx] = fi
+        end
+      end
+      element = Container.find(id)&.root_element
+      element.present? && element&.class&.name == 'Sample' && new_prop.dig('layers', 'sample_details',
+                                                                          'fields')&.each_with_index do |fi, idx|
+        if fi['field'] == 'label'
+          fi['value'] = element.short_label
+          new_prop['layers']['sample_details']['fields'][idx] = fi
+        end
+        if fi['field'] == 'id'
+          fi['value'] = element.id
+          new_prop['layers']['sample_details']['fields'][idx] = fi
+        end
+      end
+
+      new_prop.dig('layers', 'instrument', 'fields')&.each_with_index do |fi, idx|
+        if fi['field'] == 'instrument' && metadata['INSTRUM'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['INSTRUM']
+          fi['device'] = metadata['INSTRUM']
+          fi['dkey'] = 'INSTRUM'
+          new_prop['layers']['instrument']['fields'][idx] = fi
+        end
+      end
+
+      new_prop.dig('layers', 'equipment', 'fields')&.each_with_index do |fi, idx|
+        if fi['field'] == 'probehead' && metadata['PROBHD'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['PROBHD']
+          fi['device'] = metadata['PROBHD']
+          fi['dkey'] = 'PROBHD'
+          new_prop['layers']['equipment']['fields'][idx] = fi
+        end
+      end
+
+      new_prop.dig('layers', 'sample_preparation', 'fields')&.each_with_index do |fi, idx|
+        if fi['field'] == 'solvent' && metadata['SOLVENT'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['SOLVENT']
+          fi['device'] = metadata['SOLVENT']
+          fi['dkey'] = 'SOLVENT'
+          fi['value'] = 'chloroform-D1 (CDCl3)' if metadata['SOLVENT'] == 'CDCl3'
+          new_prop['layers']['sample_preparation']['fields'][idx] = fi
+        end
+      end
+
+      new_prop.dig('layers', 'set', 'fields')&.each_with_index do |fi, idx|
+        if fi['field'] == 'temperature' && metadata['TE'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['TE'].split(/\s+/).first
+          fi['device'] = metadata['TE']
+          fi['dkey'] = 'TE'
+          fi['value_system'] = metadata['TE'].split(/\s+/).last
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+        if fi['field'] == 'ns' && metadata['NS'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['NS']
+          fi['device'] = metadata['NS']
+          fi['dkey'] = 'NS'
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+        if fi['field'] == 'PULPROG' && metadata['PULPROG'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['PULPROG']
+          fi['device'] = metadata['PULPROG']
+          fi['dkey'] = 'PULPROG'
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+        if fi['field'] == 'td' && metadata['TD'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['TD']
+          fi['device'] = metadata['TD']
+          fi['dkey'] = 'TD'
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+        if fi['field'] == 'done' && metadata['D1'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['D1']
+          fi['device'] = metadata['D1']
+          fi['dkey'] = 'D1'
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+        if fi['field'] == 'sf' && metadata['SF'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['SF']
+          fi['device'] = metadata['SF']
+          fi['dkey'] = 'SF'
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+        if fi['field'] == 'sfoone' && metadata['SFO1'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['SFO1']
+          fi['device'] = metadata['SFO1']
+          fi['dkey'] = 'SFO1'
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+        if fi['field'] == 'sfotwo' && metadata['SFO2'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['SFO2']
+          fi['device'] = metadata['SFO2']
+          fi['dkey'] = 'SFO2'
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+        if fi['field'] == 'nucone' && metadata['NUC1'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['NUC1']
+          fi['device'] = metadata['NUC1']
+          fi['dkey'] = 'NUC1'
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+        if fi['field'] == 'nuctwo' && metadata['NUC2'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['NUC2']
+          fi['device'] = metadata['NUC2']
+          fi['dkey'] = 'NUC2'
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+      end
+      dataset.properties = new_prop
+      dataset.save!
+    end
+
+    def self.ts(method, identifier, params = nil)
+      Rails.cache.send(method, "#{Labimotion::NmrMapper.new.class.name}#{identifier}", params)
+    end
+
+    def self.clean(id)
+      Labimotion::NmrMapper.ts('delete', id)
+    end
+
+    def self.build_ds(id, content)
+      ds = Container.find_by(id: id)
+      return if ds.nil? || content.nil?
+
+      ols = content[:ols]
+      metadata = content[:metadata]
+
+      return if ols.nil? || metadata.nil?
+
+      klass = Labimotion::DatasetKlass.find_by(ols_term_id: ols)
+      return if klass.nil?
+
+      uuid = SecureRandom.uuid
+      props = klass.properties_release
+      props['uuid'] = uuid
+      props['eln'] = Chemotion::Application.config.version
+      props['labimotion'] = Labimotion::VERSION
+      props['klass'] = 'Dataset'
+      dataset = Labimotion::Dataset.create!(
+        uuid: uuid,
+        dataset_klass_id: klass.id,
+        element_type: 'Container',
+        element_id: ds.id,
+        properties: props,
+        properties_release: klass.properties_release,
+        klass_uuid: klass.uuid,
+      )
+      { dataset: dataset, metadata: metadata, ols: ols }
+    end
+  end
+end

data/lib/labimotion/libs/nmr_mapper_repo.rb

@@ -0,0 +1,263 @@
+# frozen_string_literal: true
+
+module Labimotion
+  class NmrMapperRepo
+    def self.is_brucker_binary(id)
+      att = Attachment.find(id)
+      Zip::File.open(att.store.path) do |zip_file|
+        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
+          end
+        end
+      end
+      nil
+    end
+
+    def self.process(id, content)
+      att = Attachment.find(id)
+      lines = content.split("\n").reject(&:empty?)
+      metadata = {}
+      lines.map do |ln|
+        arr = ln.split(/\s+/)
+        metadata[arr[0]] = arr[1..-1].join(' ') if arr.length > 1
+      end
+      ols = 'CHMO:0000593' if metadata['NUC1'] == '1H'
+      ols = 'CHMO:0000595' if metadata['NUC1'] == '13C'
+      if content.present? && att.present?
+        Labimotion::NmrMapper.ts('write', att.attachable_id,
+                              content: { metadata: metadata, ols: ols })
+      end
+    end
+
+    def self.fetch_content(id)
+      Labimotion::NmrMapper.ts('read', id)
+    end
+
+    def self.generate_ds(id, current_user = {})
+      data = Labimotion::NmrMapper.fetch_content(id)
+      return if data.nil?
+
+      obj = Labimotion::NmrMapper.build_ds(id, data[:content])
+      return if obj.nil? || obj[:ols].nil?
+
+      Labimotion::NmrMapper.update_ds_1h(id, obj, current_user) if obj[:ols] == 'CHMO:0000593'
+      Labimotion::NmrMapper.update_ds_1h(id, obj, current_user) if obj[:ols] == 'CHMO:0000595'
+      Labimotion::NmrMapper.clean(id)
+    end
+
+    def self.update_ds_13c(id, obj)
+      # dataset = obj[:dataset]
+      # metadata = obj[:metadata]
+      # new_prop = dataset.properties
+
+      # dataset.properties = new_prop
+      # dataset.save!
+    end
+
+    def self.set_data(prop, field, idx, layer_name, field_name, value)
+      return if field['field'] != field_name || value&.empty?
+
+      field['value'] = value
+      prop['layers'][layer_name]['fields'][idx] = field
+      prop
+    end
+
+    def self.update_ds_1h(id, obj, current_user)
+      dataset = obj[:dataset]
+      metadata = obj[:metadata]
+      new_prop = dataset.properties
+      new_prop.dig('layers', 'general', 'fields')&.each_with_index do |fi, idx|
+      #  new_prop = set_data(new_prop, fi, idx, 'general', 'title', metadata['NAME'])
+        if fi['field'] == 'title' && metadata['NAME'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['NAME']
+          fi['device'] = metadata['NAME']
+          fi['dkey'] = 'NAME'
+          new_prop['layers']['general']['fields'][idx] = fi
+        end
+
+        if fi['field'] == 'date' && metadata['Date_'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['Date_']
+          fi['device'] = metadata['Date_']
+          fi['dkey'] = 'Date_'
+          new_prop['layers']['general']['fields'][idx] = fi
+        end
+
+        if fi['field'] == 'time' && metadata['Time'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['Time']
+          fi['device'] = metadata['Time']
+          fi['dkey'] = 'Time'
+          new_prop['layers']['general']['fields'][idx] = fi
+        end
+
+        if fi['field'] == 'creator' && current_user.present?
+          ## fi['label'] = fi['label']
+          fi['value'] = current_user.name
+          new_prop['layers']['general']['fields'][idx] = fi
+        end
+      end
+      element = Container.find(id)&.root_element
+      element.present? && element&.class&.name == 'Sample' && new_prop.dig('layers', 'sample_details', 'fields')&.each_with_index do |fi, idx|
+        if fi['field'] == 'label'
+          fi['value'] = element.short_label
+          new_prop['layers']['sample_details']['fields'][idx] = fi
+        end
+        if fi['field'] == 'id'
+          fi['value'] = element.id
+          new_prop['layers']['sample_details']['fields'][idx] = fi
+        end
+      end
+
+      new_prop.dig('layers', 'instrument', 'fields')&.each_with_index do |fi, idx|
+        if fi['field'] == 'instrument' && metadata['INSTRUM'].present?
+          # fi['label'] = fi['label']
+          fi['value'] = metadata['INSTRUM']
+          fi['device'] = metadata['INSTRUM']
+          fi['dkey'] = 'INSTRUM'
+          new_prop['layers']['instrument']['fields'][idx] = fi
+        end
+      end
+
+
+      new_prop.dig('layers', 'equipment', 'fields')&.each_with_index do |fi, idx|
+        if fi['field'] == 'probehead' && metadata['PROBHD'].present?
+          # fi['label'] = fi['label']
+          fi['value'] = metadata['PROBHD']
+          fi['device'] = metadata['PROBHD']
+          fi['dkey'] = 'PROBHD'
+          new_prop['layers']['equipment']['fields'][idx] = fi
+        end
+      end
+
+      new_prop.dig('layers', 'sample_preparation', 'fields')&.each_with_index do |fi, idx|
+        if fi['field'] == 'solvent' && metadata['SOLVENT'].present?
+          # fi['label'] = fi['label']
+          fi['value'] = metadata['SOLVENT']
+          fi['device'] = metadata['SOLVENT']
+          fi['dkey'] = 'SOLVENT'
+          fi['value'] = 'chloroform-D1 (CDCl3)' if metadata['SOLVENT'] == 'CDCl3'
+          new_prop['layers']['sample_preparation']['fields'][idx] = fi
+        end
+      end
+
+
+      new_prop.dig('layers', 'set', 'fields')&.each_with_index do |fi, idx|
+        if fi['field'] == 'temperature' && metadata['TE'].present?
+          # fi['label'] = fi['label']
+          fi['value'] = metadata['TE'].split(/\s+/).first
+          fi['device'] = metadata['TE']
+          fi['dkey'] = 'TE'
+          fi['value_system'] = metadata['TE'].split(/\s+/).last
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+        if fi['field'] == 'ns' && metadata['NS'].present?
+          # fi['label'] = fi['label']
+          fi['value'] = metadata['NS']
+          fi['device'] = metadata['NS']
+          fi['dkey'] = 'NS'
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+        if fi['field'] == 'PULPROG' && metadata['PULPROG'].present?
+          # fi['label'] = fi['label']
+          fi['value'] = metadata['PULPROG']
+          fi['device'] = metadata['PULPROG']
+          fi['dkey'] = 'PULPROG'
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+        if fi['field'] == 'td' && metadata['TD'].present?
+          # fi['label'] = fi['label']
+          fi['value'] = metadata['TD']
+          fi['device'] = metadata['TD']
+          fi['dkey'] = 'TD'
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+        if fi['field'] == 'done' && metadata['D1'].present?
+          # fi['label'] = fi['label']
+          fi['value'] = metadata['D1']
+          fi['device'] = metadata['D1']
+          fi['dkey'] = 'D1'
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+        if fi['field'] == 'sf' && metadata['SF'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['SF']
+          fi['device'] = metadata['SF']
+          fi['dkey'] = 'SF'
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+        if fi['field'] == 'sfoone' && metadata['SFO1'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['SFO1']
+          fi['device'] = metadata['SFO1']
+          fi['dkey'] = 'SFO1'
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+        if fi['field'] == 'sfotwo' && metadata['SFO2'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['SFO2']
+          fi['device'] = metadata['SFO2']
+          fi['dkey'] = 'SFO2'
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+        if fi['field'] == 'nucone' && metadata['NUC1'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['NUC1']
+          fi['device'] = metadata['NUC1']
+          fi['dkey'] = 'NUC1'
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+        if fi['field'] == 'nuctwo' && metadata['NUC2'].present?
+          ## fi['label'] = fi['label']
+          fi['value'] = metadata['NUC2']
+          fi['device'] = metadata['NUC2']
+          fi['dkey'] = 'NUC2'
+          new_prop['layers']['set']['fields'][idx] = fi
+        end
+      end
+      dataset.properties = new_prop
+      dataset.save!
+    end
+
+
+    def self.ts(method, identifier, params = nil)
+      Rails.cache.send(method, "#{Labimotion::NmrMapper.new.class.name}#{identifier}", params)end
+
+    def self.clean(id)
+      Labimotion::NmrMapper.ts('delete', id)
+    end
+
+    def self.build_ds(id, content)
+      ds = Container.find_by(id: id)
+      return if ds.nil? || content.nil?
+
+      ols = content[:ols]
+      metadata = content[:metadata]
+
+      return if ols.nil? || metadata.nil?
+
+      klass = Labimotion::DatasetKlass.find_by(ols_term_id: ols)
+      return if klass.nil?
+
+      uuid = SecureRandom.uuid
+      props = klass.properties_release
+      props['uuid'] = uuid
+      props['eln'] = Chemotion::Application.config.version
+      props['labimotion'] = Labimotion::VERSION
+      props['klass'] = 'Dataset'
+      dataset = Labimotion::Dataset.create!(
+        uuid: uuid,
+        dataset_klass_id: klass.id,
+        element_type: 'Container',
+        element_id: ds.id,
+        properties: props,
+        properties_release: klass.properties_release,
+        klass_uuid: klass.uuid
+      )
+      { dataset: dataset, metadata: metadata, ols: ols }
+    end
+  end
+end

data/lib/labimotion/libs/template_hub.rb

@@ -0,0 +1,55 @@
+# frozen_string_literal: true
+
+require 'net/http'
+require 'uri'
+require 'json'
+require 'date'
+
+# rubocop: disable Metrics/AbcSize
+# rubocop: disable Metrics/MethodLength
+
+module Labimotion
+  ## TemplateHub
+  class TemplateHub
+    TARGET = Rails.env.production? ? 'https://www.chemotion-repository.net/' : 'http://localhost:3000/'
+
+    def self.uri(api_name)
+      url = TARGET
+      "#{url}api/v1/labimotion_hub/#{api_name}"
+    end
+
+
+    def self.header(opt = {})
+      opt || {}
+    end
+
+    def self.handle_response(oat, response) # rubocop: disable Metrics/PerceivedComplexity
+      begin
+        response&.success? ? 'OK' : 'ERROR'
+      rescue StandardError => e
+        raise e
+      ensure
+        ## oat.update(status: response&.success? ? 'done' : 'failure')
+      end
+    end
+
+    def self.list(klass)
+      body = { klass: klass }
+      response = HTTParty.get("#{uri('list')}?klass=#{klass}")
+      # response.parsed_response if response.code == 200
+      JSON.parse(response.body) if response.code == 200
+    end
+
+    def self.fetch_identifier(klass, identifier)
+      # body = { klass: klass, identifier: identifier }
+      response = HTTParty.get("#{uri('fetch')}?klass=#{klass}&identifier=#{identifier}")
+      # response.parsed_response if response.code == 200
+      JSON.parse(response.body) if response.code == 200
+    end
+  end
+end
+
+# rubocop: enable Metrics/AbcSize
+# rubocop: enable Metrics/MethodLength
+# rubocop: enable Metrics/ClassLength
+# rubocop: enable Metrics/CyclomaticComplexity

data/lib/labimotion/models/collections_element.rb

@@ -0,0 +1,42 @@
+# frozen_string_literal: true
+
+module Labimotion
+  class CollectionsElement < ApplicationRecord
+    acts_as_paranoid
+    self.table_name = :collections_elements
+    belongs_to :collection
+    belongs_to :element, class_name: 'Labimotion::Element'
+
+    include Tagging
+    include Collecting
+
+    def self.get_elements_by_collection_type(collection_ids, type)
+      self.where(collection_id: collection_ids, element_type: type).pluck(:element_id).compact.uniq
+    end
+
+    def self.remove_in_collection(eids, from_col_ids)
+      element_ids = Labimotion::Element.get_associated_elements(eids)
+      sample_ids = Labimotion::Element.get_associated_samples(element_ids)
+      delete_in_collection(element_ids, from_col_ids)
+      update_tag_by_element_ids(element_ids)
+      CollectionsSample.remove_in_collection(sample_ids, from_col_ids)
+    end
+
+    def self.move_to_collection(eids, from_col_ids, to_col_ids, element_type='')
+      element_ids = Labimotion::Element.get_associated_elements(eids)
+      sample_ids = Labimotion::Element.get_associated_samples(element_ids)
+      delete_in_collection(element_ids, from_col_ids)
+      static_create_in_collection(element_ids, to_col_ids)
+      CollectionsSample.move_to_collection(sample_ids, from_col_ids, to_col_ids)
+      update_tag_by_element_ids(element_ids)
+    end
+
+    def self.create_in_collection(eids, to_col_ids, element_type='')
+      element_ids = Labimotion::Element.get_associated_elements(eids)
+      sample_ids = Labimotion::Element.get_associated_samples(element_ids)
+      static_create_in_collection(element_ids, to_col_ids)
+      CollectionsSample.create_in_collection(sample_ids, to_col_ids)
+      update_tag_by_element_ids(element_ids)
+    end
+  end
+end

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

@@ -0,0 +1,42 @@
+# frozen_string_literal: true
+
+module Labimotion
+  module AttachmentConverter
+    ACCEPTED_FORMATS = (Rails.configuration.try(:converter).try(:ext) || []).freeze
+    extend ActiveSupport::Concern
+
+    included do
+      before_create :init_converter
+      after_update :exec_converter
+      def init_converter
+        return if con_state.present?
+        if Rails.configuration.try(:converter).try(:url) && ACCEPTED_FORMATS.include?(File.extname(filename&.downcase))
+          self.con_state = Labimotion::ConState::WAIT
+        end
+
+        if File.extname(filename&.downcase) == '.zip' && attachable&.dataset.nil?
+          self.con_state = Labimotion::ConState::NMR
+        end
+
+        self.con_state = Labimotion::ConState::NONE if con_state.nil?
+      end
+
+      def exec_converter
+        #return if attachable_id.nil?
+        return if con_state.nil? || con_state == Labimotion::ConState::NONE
+        case con_state
+        when Labimotion::ConState::NMR
+          content = Labimotion::NmrMapperRepo.is_brucker_binary(id)
+          if content.nil?
+            self.con_state = Labimotion::ConState::NONE
+          else
+            Labimotion::NmrMapperRepo.process(id, content)
+            self.con_state = Labimotion::ConState::PROCESSED
+          end
+        when Labimotion::ConState::WAIT
+          self.con_state = Labimotion::Converter.jcamp_converter(id)
+        end
+      end
+    end
+  end
+end