1.4.0

lib/labimotion.rb

@@ -1,6 +1,7 @@
 # In your_gem_name.rb or main Ruby file
 module Labimotion
 
+  autoload :CONF, 'labimotion/conf'
   autoload :VERSION, 'labimotion/version'
 
   def self.logger
@@ -62,6 +63,7 @@ def self.log_exception(exception, current_user = nil)
   autoload :ExportDataset, 'labimotion/libs/export_dataset'
   autoload :SampleAssociation, 'labimotion/libs/sample_association'
   autoload :PropertiesHandler, 'labimotion/libs/properties_handler'
+  autoload :AttachmentHandler, 'labimotion/libs/attachment_handler'
 
   ######## Utils
   autoload :Prop, 'labimotion/utils/prop'

lib/labimotion/apis/generic_element_api.rb

@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 
-require 'labimotion/version'
+require 'labimotion/conf'
 require 'labimotion/libs/export_element'
 
 module Labimotion
@@ -10,12 +10,26 @@ class GenericElementAPI < Grape::API
     helpers ContainerHelpers
     helpers ParamsHelpers
     helpers CollectionHelpers
+    helpers UserLabelHelpers
     helpers Labimotion::SampleAssociationHelpers
     helpers Labimotion::GenericHelpers
     helpers Labimotion::ElementHelpers
     helpers Labimotion::ParamHelpers
 
     resource :generic_elements do
+      # might be removed because the file is moved to public folder
+      namespace :current do
+        desc 'Return serialized elements of current user'
+        get do
+          klasses_json_path = Labimotion::KLASSES_JSON # Rails.root.join('app/packs/klasses.json')
+          klasses = JSON.parse(File.read(klasses_json_path))
+          { klasses: klasses }
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          { klasses: [] }
+        end
+      end
+
       namespace :klass do
         desc 'get klass info'
         params do
@@ -327,7 +341,7 @@ class GenericElementAPI < Grape::API
           Labimotion.log_exception(e, current_user)
           { error: e.message }
         end
-      end      
+      end
 
       desc 'Return serialized elements of current user'
       params do
@@ -336,6 +350,7 @@ class GenericElementAPI < Grape::API
         optional :el_type, type: String, desc: 'element klass name'
         optional :from_date, type: Integer, desc: 'created_date from in ms'
         optional :to_date, type: Integer, desc: 'created_date to in ms'
+        optional :user_label, type: Integer, desc: 'user label'
         optional :filter_created_at, type: Boolean, desc: 'filter by created at or updated at'
         optional :sort_column, type: String, desc: 'sort by updated_at or selected layers property'
       end
@@ -426,7 +441,7 @@ class GenericElementAPI < Grape::API
             raise e
           end
         end
-      end      
+      end
     end
   end
 end

lib/labimotion/collection/import.rb

@@ -47,8 +47,12 @@ def self.import_datasets(data, instances, gt, current_user_id, &update_instances
       begin
         data.fetch('Labimotion::Dataset', {}).each do |uuid, fields|
           klass_id = fields['dataset_klass_id']
-          dk_obj = data.fetch('Labimotion::DatasetKlass', {})[klass_id]
-          dk_id = dk_obj['identifier']
+          next if data.fetch('Labimotion::DatasetKlass', {}).empty?
+
+          dk_obj = data.fetch('Labimotion::DatasetKlass', {}) && data.fetch('Labimotion::DatasetKlass', {})[klass_id]
+          next if dk_obj.nil?
+
+          dk_id = dk_obj && dk_obj['identifier']
           element_uuid = fields.fetch('element_id')
           element_type = fields.fetch('element_type')
           element = instances.fetch(element_type).fetch(element_uuid)
@@ -78,7 +82,7 @@ def self.import_datasets(data, instances, gt, current_user_id, &update_instances
         end
       rescue StandardError => e
         Labimotion.log_exception(e)
-        raise
+        # raise
       end
     end
 

lib/labimotion/conf.rb

@@ -0,0 +1,6 @@
+# frozen_string_literal: true
+
+## Labimotion Configuration
+module Labimotion
+  KLASSES_JSON = Rails.root.join('public', 'klasses.json').to_s.freeze # Rails.root.join('app/packs/klasses.json').to_s.freeze
+end

lib/labimotion/entities/element_revision_entity.rb

@@ -23,7 +23,7 @@ def properties
 
           object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_label'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
           object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_tip'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
-          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el.molecule_svg_file)
+          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el&.molecule_svg_file || 'nosvg')
         end
 
         field_tables = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::TABLE }
@@ -41,7 +41,7 @@ def properties
               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_svg'] = File.join('/images', 'molecules', find_mol.molecule_svg_file) if find_mol&.molecule_svg_file&.present?
               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

lib/labimotion/entities/eln_element_entity.rb

@@ -47,7 +47,7 @@ def properties
               el.short_label
           end
           object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] =
-            field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el.molecule_svg_file)
+            field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el&.molecule_svg_file || 'nosvg')
         end
 
         field_tables = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::TABLE }
@@ -88,7 +88,7 @@ def set_table(field, field_table_objs, obj)
 
           case obj
           when Labimotion::Prop::MOLECULE
-            sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_obj.molecule_svg_file)
+            sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_obj.molecule_svg_file) if find_obj&.molecule_svg_file&.present?
             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

lib/labimotion/entities/properties_entity.rb

@@ -20,7 +20,27 @@ def properties
 
           object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_label'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
           object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_tip'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
-          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el.molecule_svg_file)
+          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el&.molecule_svg_file || 'nosvg')
+        end
+
+        field_sys_reactions = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::SYS_REACTION }
+        field_sys_reactions.each do |field|
+          idx = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
+          sid = field.dig('value', 'el_id')
+          next unless sid.present?
+
+          el = Reaction.find_by(id: sid)
+          if el.blank?
+            object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_tip'] = 'ERROR'
+            object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] = ''
+          end
+
+          next unless el.present?
+          next unless object.properties.dig(Labimotion::Prop::LAYERS, key, Labimotion::Prop::FIELDS, idx, 'value').present?
+
+          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_label'] = el.short_label
+          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_tip'] = el.short_label
+          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] =  el.reaction_svg_file
         end
 
         field_tables = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::TABLE }
@@ -49,7 +69,7 @@ def set_table(field, field_table_objs, obj)
 
           case obj
           when Labimotion::Prop::MOLECULE
-            sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_obj.molecule_svg_file)
+            sub_value[col_id]['value']['el_svg'] = File.join('/images', 'molecules', find_obj.molecule_svg_file) if find_obj&.molecule_svg_file&.present?
             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

lib/labimotion/entities/segment_revision_entity.rb

@@ -22,7 +22,7 @@ def properties
 
           object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_label'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
           object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_tip'] = el.short_label if field['type'] == Labimotion::FieldType::DRAG_SAMPLE
-          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el.molecule_svg_file)
+          object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']['el_svg'] = field['type'] == Labimotion::FieldType::DRAG_SAMPLE ? el.get_svg_path : File.join('/images', 'molecules', el&.molecule_svg_file || 'nosvg')
         end
 
         field_tables = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::TABLE }
@@ -40,7 +40,7 @@ def properties
               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_svg'] = File.join('/images', 'molecules', find_mol.molecule_svg_file) if find_mol&.molecule_svg_file&.present?
               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

lib/labimotion/helpers/element_helpers.rb

@@ -1,6 +1,7 @@
 # frozen_string_literal: true
 
 require 'grape'
+require 'labimotion/conf'
 require 'labimotion/utils/utils'
 # require 'labimotion/models/element_klass'
 module Labimotion
@@ -33,7 +34,7 @@ def create_element_klass(current_user, params)
       new_klass = Labimotion::ElementKlass.create!(attributes)
       new_klass.reload
       new_klass.create_klasses_revision(current_user)
-      klass_names_file = Rails.root.join('app/packs/klasses.json')
+      klass_names_file = Labimotion::KLASSES_JSON # Rails.root.join('app/packs/klasses.json')
       klasses = Labimotion::ElementKlass.where(is_active: true)&.pluck(:name) || []
       File.write(klass_names_file, klasses)
       klasses
@@ -95,6 +96,7 @@ def create_element(current_user, params)
       element.properties = update_sample_association(params[:properties], current_user, element)
       element.container = update_datamodel(params[:container], current_user)
       element.save!
+      update_element_labels(element, params[:user_labels], current_user.id)
       element.save_segments(segments: params[:segments], current_user_id: current_user.id)
       element
     rescue StandardError => e
@@ -108,6 +110,9 @@ def update_element_by_id(current_user, params)
       properties = update_sample_association(params[:properties], current_user, element)
       params.delete(:container)
       params.delete(:properties)
+      update_element_labels(element, params[:user_labels], current_user.id)
+      params.delete(:user_labels)
+
       attributes = declared(params.except(:segments), include_missing: false)
       properties['pkg'] = Labimotion::Utils.pkg(properties['pkg'])
       if element.klass_uuid != properties['klass_uuid'] || element.properties != properties || element.name != params[:name]
@@ -288,6 +293,7 @@ def list_serialized_elements(params, current_user)
       scope = scope.elements_created_time_to(Time.at(to) + 1.day) if to && by_created_at
       scope = scope.elements_updated_time_from(Time.at(from)) if from && !by_created_at
       scope = scope.elements_updated_time_to(Time.at(to) + 1.day) if to && !by_created_at
+      scope = scope.by_user_label(params[:user_label]) if params[:user_label]
       scope
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
@@ -315,7 +321,7 @@ def validate_klass(attributes)
           return { status: 'success', message: "The element: #{attributes['name']} has been created using version: #{attributes['version']}!" }
         end
       end
-      
+
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       return { status: 'error', message: e.message }

lib/labimotion/helpers/generic_helpers.rb

@@ -1,5 +1,6 @@
 # frozen_string_literal: true
 require 'grape'
+require 'labimotion/conf'
 require 'labimotion/utils/utils'
 # Helper for associated sample
 module Labimotion
@@ -23,7 +24,7 @@ def fetch_klass(name, id)
     def deactivate_klass(params)
       klz = fetch_klass(params[:klass], params[:id])
       klz&.update!(is_active: params[:is_active])
-      generate_klass_file unless klz.class.name != 'ElementKlass'
+      generate_klass_file unless klz.class.name != 'Labimotion::ElementKlass'
       klz
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
@@ -34,7 +35,7 @@ def delete_klass(params)
       authenticate_admin!(params[:klass].gsub(/(Klass)/, 's').downcase)
       klz = fetch_klass(params[:klass], params[:id])
       klz&.destroy!
-      generate_klass_file unless klz.class.name != 'ElementKlass'
+      generate_klass_file unless klz.class.name != 'Labimotion::ElementKlass'
       status 201
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
@@ -97,7 +98,7 @@ def list_klass_revisions(params)
 
     ###############
     def generate_klass_file
-      klass_names_file = Rails.root.join('app/packs/klasses.json')
+      klass_names_file = Labimotion::KLASSES_JSON # Rails.root.join('app/packs/klasses.json')
       klasses = Labimotion::ElementKlass.where(is_active: true)&.pluck(:name) || []
       File.write(klass_names_file, klasses)
     rescue StandardError => e

lib/labimotion/helpers/param_helpers.rb

@@ -22,7 +22,7 @@ module ParamHelpers
         optional :sync_time, type: DateTime, desc: 'Klass sync_time'
         optional :version, type: String, desc: 'Klass version'
       end
-      
+
       params :create_element_klass_params do
         requires :name, type: String, desc: 'Element Klass Name'
         requires :label, type: String, desc: 'Element Klass Label'
@@ -40,7 +40,7 @@ module ParamHelpers
         optional :desc, type: String, desc: 'Element Klass Desc'
         optional :place, type: String, desc: 'Element Klass Place'
       end
-      
+
       ## Element Params
       params :create_element_params do
         requires :element_klass, type: Hash
@@ -49,18 +49,20 @@ module ParamHelpers
         optional :properties_release, type: Hash
         optional :collection_id, type: Integer
         requires :container, type: Hash
+        optional :user_labels, type: Array
         optional :segments, type: Array, desc: 'Segments'
       end
-      
+
       params :update_element_params do
         requires :id, type: Integer, desc: 'element id'
         optional :name, type: String
         requires :properties, type: Hash
         optional :properties_release, type: Hash
         requires :container, type: Hash
+        optional :user_labels, type: Array
         optional :segments, type: Array, desc: 'Segments'
       end
-      
+
       ## Segment Klass Params
       params :upload_segment_klass_params do
         requires :label, type: String, desc: 'Klass label'

lib/labimotion/helpers/segment_helpers.rb

@@ -107,9 +107,9 @@ def create_repo_klass(params, current_user, origin)
       attributes['updated_by'] = current_user.id
       attributes['sync_by'] = current_user.id
       attributes['sync_time'] = DateTime.now
-      attr_klass = response.dig('element_klass', {})        # response['element_klass']
+      attr_klass = response['element_klass']    ## response.dig('element_klass', {})        # response['element_klass']
       validate_klass(attributes, attr_klass)
-      
+
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       raise e

lib/labimotion/libs/attachment_handler.rb

@@ -0,0 +1,29 @@
+# frozen_string_literal: true
+require 'labimotion/version'
+
+module Labimotion
+  ## ExportDataset
+  class AttachmentHandler
+    def self.copy(original_attach, element_id, element_type, current_user_id)
+      copy_attach = Attachment.new(
+        attachable_id: element_id,
+        attachable_type: element_type,
+        aasm_state: original_attach.aasm_state,
+        created_by: current_user_id,
+        created_for: current_user_id,
+        filename: original_attach.filename,
+      )
+      copy_attach.save
+
+      copy_io = original_attach.attachment_attacher.get.to_io
+      attacher = copy_attach.attachment_attacher
+      attacher.attach copy_io
+      copy_attach.file_path = copy_io.path
+      copy_attach.save
+
+      Usecases::Attachments::Copy.update_annotation(original_attach.id, copy_attach.id) if (original_attach.attachment_data && original_attach.attachment_data['derivatives'])
+      copy_attach
+    end
+
+  end
+end

lib/labimotion/libs/export_dataset.rb

@@ -97,7 +97,10 @@ def export(id)
           type = "#{field['type']}-#{field['option_layers']}" if field['type'] == Labimotion::FieldType::SELECT || field['type'] == Labimotion::FieldType::SYSTEM_DEFINED
 
           show_value = field['value'] =~ /\A\d+,\d+\z/ ? field['value']&.gsub(',', '.') : field['value']
-          sheet.add_row([' ', field['label'], nil, field['value_system'], field['field'], type, from_device, field['dkey'], nil].freeze)
+          ols_short_form = (field['ontology'] && field['ontology']['short_form']) || ''
+          ols_label = (field['ontology'] && field['ontology']['label']) || ''
+          ols_iri = (field['ontology'] && field['ontology']['iri']) || ''
+          sheet.add_row([' ', field['label'], nil, field['value_system'], field['field'], type, from_device, field['dkey'], nil, ols_short_form, ols_label, ols_iri].freeze)
 
           case field['type']
           when Labimotion::FieldType::SELECT
@@ -166,7 +169,7 @@ def spectra(id)
     end
 
     def header
-      ['Layer Label', 'Field Label', 'Value', 'Unit', 'Name', 'Type', 'Source?', 'Source identifier', 'Source data'].freeze
+      ['Layer Label', 'Field Label', 'Value', 'Unit', 'Name', 'Type', 'Source?', 'Source identifier', 'Source data', 'Ontology', 'Ontology Label', 'iri'].freeze
     end
 
     def read