labimotion 1.4.0.1 → 1.5.0.rc1

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: fb234cedd28a03695520718330ec4b35e7ad7512dce48ccd82919a917f249c52
+  data.tar.gz: 06c95920f9e0c88705f6c1d3fac27dbc516d57f1025d4798876870cc48a51ddd
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+  data.tar.gz: cb91684b0d3c8b0b4eb03b43adee712bb16d2a7d402d08fd319e7fbf162dbf7cc2c4438e64429e3fe9d9fc82bbbab703544d924086539628348af0960c58c268

data/lib/labimotion/apis/generic_element_api.rb

@@ -12,6 +12,7 @@ module Labimotion
     helpers CollectionHelpers
     helpers UserLabelHelpers
     helpers Labimotion::SampleAssociationHelpers
+    helpers Labimotion::VocabularyHelpers
     helpers Labimotion::GenericHelpers
     helpers Labimotion::ElementHelpers
     helpers Labimotion::ParamHelpers

data/lib/labimotion/apis/generic_klass_api.rb

@@ -6,7 +6,7 @@ require 'labimotion/libs/export_element'
 module Labimotion
   # Generic Element API
   class GenericKlassAPI < Grape::API
-    
+
     resource :generic_klass do
       namespace :download_klass do
         desc 'export klass'
@@ -28,7 +28,8 @@ module Labimotion
           Labimotion.log_exception(e, current_user)
           {}
         end
-      end      
+      end
+
     end
   end
 end

data/lib/labimotion/apis/labimotion_api.rb

@@ -0,0 +1,13 @@
+# app/api/labimotion/central_api.rb
+module Labimotion
+  class LabimotionAPI < Grape::API
+    mount Labimotion::ConverterAPI
+    mount Labimotion::GenericKlassAPI
+    mount Labimotion::GenericElementAPI
+    mount Labimotion::GenericDatasetAPI
+    mount Labimotion::SegmentAPI
+    mount Labimotion::LabimotionHubAPI
+    mount Labimotion::StandardLayerAPI
+    mount Labimotion::VocabularyAPI
+  end
+end

data/lib/labimotion/apis/standard_api.rb

@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+
+require 'labimotion/version'
+require 'labimotion/libs/export_element'
+
+module Labimotion
+  # Generic Element API
+  class StandardAPI < Grape::API
+    resource :standards do
+      namespace :create_std_layer do
+        desc 'create standard layer'
+        params do
+          use :create_std_layer_params
+        end
+        post do
+          # authenticate_admin!('elements')
+          # create_element_klass(current_user, params)
+          create_std_layer(current_user, params)
+          status 201
+        rescue ActiveRecord::RecordInvalid => e
+          { error: e.message }
+        end
+      end
+    end
+  end
+end

data/lib/labimotion/apis/standard_layer_api.rb

@@ -0,0 +1,100 @@
+# frozen_string_literal: true
+
+require 'labimotion/version'
+
+module Labimotion
+  # Generic Element API
+  class StandardLayerAPI < Grape::API
+    include Grape::Kaminari
+    helpers Labimotion::ParamHelpers
+
+    resource :layers do
+      namespace :get_all_layers do
+        desc 'get all standard layers for designer'
+        get do
+          list = Labimotion::StdLayer.all.sort_by { |e| e.name }
+          # present list, with: Labimotion::StdLayer, root: 'klass'
+          # data = Labimotion::StdLayer.represent(col_tree, serializable: true)
+          return { mc: 'ss00', data: list }
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          { mc: 'se00', msg: e.message, data: [] }
+        end
+      end
+
+      namespace :get_standard_layer do
+        desc 'get standard layer by id'
+        # params do
+        #   requires :id, type: Integer, desc: 'Layer id'
+        # end
+        route_param :id do
+          before do
+          #   @element_policy = ElementPolicy.new(current_user, Labimotion::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
+            entity = Labimotion::StdLayer.find(params[:id])
+            return { mc: 'ss00', data: entity }
+          rescue StandardError => e
+            Labimotion.log_exception(e, current_user)
+            { mc: 'se00', msg: e.message, data: {} }
+          end
+        end
+      end
+
+      namespace :save_standard_layer do
+        desc 'create Generic Element Klass'
+        params do
+          use :std_layer_save
+        end
+        before do
+          cur_layer = Labimotion::StdLayer.find_by(name: params[:key])
+          error!('Error! duplicate name', 409) if cur_layer.present?
+          # @element_policy = ElementPolicy.new(current_user, Labimotion::Element.find(params[:id]))
+          # error!('401 Unauthorized', 401) unless current_user.matrix_check_by_name('genericElement') && @element_policy.read?
+        # rescue ActiveRecord::RecordNotFound
+        #   Labimotion.log_exception(e, current_user)
+        #   error!('404 Not Found', 404)
+        end
+        post do
+          attributes = {
+            name: params[:key],
+            label: params[:label],
+            description: params[:description],
+            identifier: SecureRandom.uuid,
+            created_by: current_user.id,
+            properties: declared(params, include_missing: false)
+          }
+          layer = Labimotion::StdLayer.new(attributes)
+          layer.save!
+          { mc: 'ss00', data: layer }
+        rescue ActiveRecord::RecordInvalid => e
+          Labimotion.log_exception(e, current_user)
+          { mc: 'se00', msg: e.message, data: {} }
+        end
+      end
+
+      namespace :delete_standard_layer do
+        desc 'delete standard layer by id'
+        params do
+          requires :id, type: Integer, desc: 'Standard layer id'
+        end
+        route_param :id do
+          before do
+            # error!('401 Unauthorized', 401) unless ElementPolicy.new(current_user, StdLayer.find(params[:id])).destroy?
+          end
+          delete do
+            entity = Labimotion::StdLayer.find(params[:id])
+            entity.destroy
+            return { mc: 'ss00', data: {} }
+          rescue StandardError => e
+            Labimotion.log_exception(e, current_user)
+            { mc: 'se00', msg: e.message, data: [] }
+          end
+        end
+      end
+    end
+  end
+end

data/lib/labimotion/apis/vocabulary_api.rb

@@ -0,0 +1,109 @@
+# frozen_string_literal: true
+
+require 'labimotion/version'
+
+module Labimotion
+  # Generic Element API
+  class VocabularyAPI < Grape::API
+    include Grape::Kaminari
+    helpers Labimotion::ParamHelpers
+
+    resource :vocab do
+      namespace :save_vocabulary do
+        desc 'Save vocabularies'
+        params do
+          use :vocab_save
+        end
+        before do
+          # error!('Error! duplicate record', 409) if ???.present?
+        rescue ActiveRecord::RecordNotFound
+          error!('404 Not Found', 404)
+        end
+        post do
+          attributes = {
+            name: params[:name],
+            label: params[:label],
+            field_type: params[:field_type],
+            opid: 8,
+            term_id: params[:term_id],
+            source: params[:source],
+            source_id: params[:source_id],
+            layer_id: params[:layer_id],
+            field_id: params[:name],
+            identifier: params[:source_id],
+            created_by: current_user.id,
+            properties: declared(params, include_missing: false),
+          }
+          voc = Labimotion::Vocabulary.new(attributes)
+          voc.save!
+          { mc: 'ss00', data: voc }
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          { mc: 'se00', msg: e.message, data: {} }
+        end
+      end
+
+      namespace :get_all_vocabularies do
+        desc 'get all standard layers for designer'
+        get do
+          # merged_data = []
+          # Dir.glob(Rails.public_path.join('generic', 'vocabularies', '*.json')).each do |file_path|
+          #   file_content = File.read(file_path)
+          #   json_data = JSON.parse(file_content)
+          #   merged_data.concat(json_data)
+          # end
+
+          # list = Labimotion::Vocabulary.all.sort_by { |e| e.name }
+          # present list, with: Labimotion::StdLayer, root: 'klass'
+          vocabularies = Labimotion::VocabularyHandler.load_all_vocabularies
+          combined_data = Labimotion::VocabularyEntity.represent(vocabularies, serializable: true)
+          return { mc: 'ss00', data: combined_data }
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          { mc: 'se00', msg: e.message, data: [] }
+        end
+      end
+
+      namespace :field_klasses do
+        desc 'get all field klasses for admin function'
+        get do
+          # Dir.glob(Rails.public_path.join('generic', 'vocabularies', '*.json')).each do |file_path|
+          #   file_content = File.read(file_path)
+          #   json_data = JSON.parse(file_content)
+          #   merged_data.concat(json_data)
+          # end
+          vocabularies = Labimotion::VocabularyHandler.load_app_vocabularies
+          merged_data = Labimotion::FieldKlassEntity.represent(vocabularies, serializable: true)
+          # byebug
+          # list = Labimotion::Vocabulary.all.sort_by { |e| e.name }
+          # present list, with: Labimotion::VocabularyEntity, root: 'klass'
+          # byebug
+          merged_data
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          []
+        end
+      end
+
+      namespace :delete_vocabulary do
+        desc 'delete vocabulary by id'
+        params do
+          requires :id, type: Integer, desc: 'Vocabulary id'
+        end
+        route_param :id do
+          before do
+            # error!('401 Unauthorized', 401) unless ElementPolicy.new(current_user, Vocabulary.find(params[:id])).destroy?
+          end
+          delete do
+            entity = Labimotion::Vocabulary.find(params[:id])
+            entity.destroy
+            return { mc: 'ss00', data: {} }
+          rescue StandardError => e
+            Labimotion.log_exception(e, current_user)
+            { mc: 'se00', msg: e.message, data: [] }
+          end
+        end
+      end
+    end
+  end
+end

data/lib/labimotion/entities/dataset_entity.rb

@@ -3,7 +3,7 @@
 require 'labimotion/entities/application_entity'
 module Labimotion
   # Dataset entity
-  class DatasetEntity < ApplicationEntity
+  class DatasetEntity < PropertiesEntity
     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

data/lib/labimotion/entities/properties_entity.rb

@@ -8,6 +8,27 @@ module Labimotion
     def properties
       (object&.properties.is_a?(Hash) && object.properties[Labimotion::Prop::LAYERS]&.keys || []).each do |key|
         # layer = object.properties[key]
+
+#         field_vocabularies = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['is_vocabulary'] == true}
+#         field_vocabularies.each do |field|
+#           idx = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
+#           if field['identifier'] == '7c30cd4f-aef4-433a-946e-d0f81f8918f1'
+#             if properties['klass'] == 'Dataset'
+#               container = object&.element_type.constantize.find_by(id: object&.element_id)
+#               element = container.root.containable
+#               if field['source'] == 'Segment'
+#                 byebug
+#                 segments = element.segments.joins(:segment_klass).find_by('segment_klasses.identifier = ?', field['source_id'])
+#                 seg_prop = segments.properties
+#                 fields = seg_prop[Labimotion::Prop::LAYERS][field['layer_id']][Labimotion::Prop::FIELDS].select { |ss| ss['field'] == field['field_id'] }
+#                 val = fields.first['value']
+#                 object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value'] = val
+#               end
+#             end
+# #            object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value'] = Time.now.strftime('%d/%m/%Y %H:%M')
+#           end
+#         end
+
         field_sample_molecules = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].select { |ss| ss['type'] == Labimotion::FieldType::DRAG_SAMPLE || ss['type'] == Labimotion::FieldType::DRAG_MOLECULE }
         field_sample_molecules.each do |field|
           idx = object.properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)

data/lib/labimotion/entities/vocabulary_entity.rb

@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+#
+require 'labimotion/entities/application_entity'
+module Labimotion
+  # Dataset entity
+  class VocabularyEntity < ApplicationEntity
+    expose :id, :identifier, :name, :label, :field_type, :opid, :term_id,
+           :field_id, :properties, :source, :source_id, :layer_id
+    # expose :source do |obj|
+    #   (obj[:properties] && obj[:properties]['voc'] && obj[:properties]['voc']['source']) || ''
+    # end
+    # expose :source_id do |obj|
+    #   (obj[:properties] && obj[:properties]['voc'] && obj[:properties]['voc']['source_id']) || ''
+    # end
+    # expose :layer_id do |obj|
+    #   (obj[:properties] && obj[:properties]['voc'] && obj[:properties]['voc']['layer_id']) || ''
+    # end
+
+    expose :voc do |obj|
+      (obj[:properties] && obj[:properties]['voc']) || {}
+    end
+    expose :ontology do |obj|
+      (obj[:properties] && obj[:properties]['ontology']) || {}
+    end
+  end
+end

data/lib/labimotion/helpers/element_helpers.rb

@@ -93,7 +93,8 @@ module Labimotion
       all_coll = Collection.get_all_collection_for_user(current_user.id)
       element.collections << all_coll
       element.save!
-      element.properties = update_sample_association(params[:properties], current_user, element)
+      _properties = update_sample_association(params[:properties], current_user, element)
+      element.properties = update_vocabularies(_properties, current_user, element)
       element.container = update_datamodel(params[:container], current_user)
       element.save!
       update_element_labels(element, params[:user_labels], current_user.id)
@@ -321,7 +322,6 @@ module Labimotion
           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 }
@@ -351,7 +351,9 @@ module Labimotion
         _att
       end
       attachments
+    rescue StandardError => e
+      Labimotion.log_exception(e)
+      attachments
     end
-
   end
 end

data/lib/labimotion/helpers/param_helpers.rb

@@ -6,94 +6,149 @@ module Labimotion
   ## Generic Helpers
   module ParamHelpers
     extend Grape::API::Helpers
-       ## Element Klass Params
-      params :upload_element_klass_params do
-        requires :name, type: String, desc: 'Klass Name'
-        optional :label, type: String, desc: 'Klass label'
-        optional :desc, type: String, desc: 'Klass desc'
-        optional :klass_prefix, type: String, desc: 'Klass klass_prefix'
-        optional :icon_name, type: String, desc: 'Klass icon_name'
-        requires :properties_template, type: Hash, desc: 'Klass template'
-        optional :properties_release, type: Hash, desc: 'Klass release'
-        optional :released_at, type: DateTime, desc: 'Klass released_at'
-        requires :uuid, type: String, desc: 'Klass uuid'
-        requires :place, type: Integer, desc: 'Klass place'
-        requires :identifier, type: String, desc: 'Klass identifier'
-        optional :sync_time, type: DateTime, desc: 'Klass sync_time'
-        optional :version, type: String, desc: 'Klass version'
-      end
+    ## Element Klass Params
+    params :upload_element_klass_params do
+      requires :name, type: String, desc: 'Klass Name'
+      optional :label, type: String, desc: 'Klass label'
+      optional :desc, type: String, desc: 'Klass desc'
+      optional :klass_prefix, type: String, desc: 'Klass klass_prefix'
+      optional :icon_name, type: String, desc: 'Klass icon_name'
+      requires :properties_template, type: Hash, desc: 'Klass template'
+      optional :properties_release, type: Hash, desc: 'Klass release'
+      optional :released_at, type: DateTime, desc: 'Klass released_at'
+      requires :uuid, type: String, desc: 'Klass uuid'
+      requires :place, type: Integer, desc: 'Klass place'
+      requires :identifier, type: String, desc: 'Klass identifier'
+      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'
-        requires :klass_prefix, type: String, desc: 'Element Klass Short Label Prefix'
-        optional :icon_name, type: String, desc: 'Element Klass Icon Name'
-        optional :desc, type: String, desc: 'Element Klass Desc'
-        optional :properties_template, type: Hash, desc: 'Element Klass properties template'
-      end
+    params :create_element_klass_params do
+      requires :name, type: String, desc: 'Element Klass Name'
+      requires :label, type: String, desc: 'Element Klass Label'
+      requires :klass_prefix, type: String, desc: 'Element Klass Short Label Prefix'
+      optional :icon_name, type: String, desc: 'Element Klass Icon Name'
+      optional :desc, type: String, desc: 'Element Klass Desc'
+      optional :properties_template, type: Hash, desc: 'Element Klass properties template'
+    end
 
-      params :update_element_klass_params do
-        requires :id, type: Integer, desc: 'Element Klass ID'
-        optional :label, type: String, desc: 'Element Klass Label'
-        optional :klass_prefix, type: String, desc: 'Element Klass Short Label Prefix'
-        optional :icon_name, type: String, desc: 'Element Klass Icon Name'
-        optional :desc, type: String, desc: 'Element Klass Desc'
-        optional :place, type: String, desc: 'Element Klass Place'
-      end
+    params :update_element_klass_params do
+      requires :id, type: Integer, desc: 'Element Klass ID'
+      optional :label, type: String, desc: 'Element Klass Label'
+      optional :klass_prefix, type: String, desc: 'Element Klass Short Label Prefix'
+      optional :icon_name, type: String, desc: 'Element Klass Icon Name'
+      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
-        requires :name, type: String
-        optional :properties, type: Hash
-        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
+    ## Element Params
+    params :create_element_params do
+      requires :element_klass, type: Hash
+      requires :name, type: String
+      optional :properties, type: Hash
+      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
+    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'
-        optional :desc, type: String, desc: 'Klass desc'
-        requires :properties_template, type: Hash, desc: 'Klass template'
-        optional :properties_release, type: Hash, desc: 'Klass release'
-        optional :released_at, type: DateTime, desc: 'Klass released_at'
-        requires :uuid, type: String, desc: 'Klass uuid'
-        requires :place, type: Integer, desc: 'Klass place'
-        requires :identifier, type: String, desc: 'Klass identifier'
-        optional :sync_time, type: DateTime, desc: 'Klass sync_time'
-        optional :version, type: String, desc: 'Klass version'
-        requires :element_klass, type: Hash do
-          use :upload_element_klass_params
-        end
+    ## Segment Klass Params
+    params :upload_segment_klass_params do
+      requires :label, type: String, desc: 'Klass label'
+      optional :desc, type: String, desc: 'Klass desc'
+      requires :properties_template, type: Hash, desc: 'Klass template'
+      optional :properties_release, type: Hash, desc: 'Klass release'
+      optional :released_at, type: DateTime, desc: 'Klass released_at'
+      requires :uuid, type: String, desc: 'Klass uuid'
+      requires :place, type: Integer, desc: 'Klass place'
+      requires :identifier, type: String, desc: 'Klass identifier'
+      optional :sync_time, type: DateTime, desc: 'Klass sync_time'
+      optional :version, type: String, desc: 'Klass version'
+      requires :element_klass, type: Hash do
+        use :upload_element_klass_params
       end
+    end
 
-      params :update_segment_klass_params do
-        requires :id, type: Integer, desc: 'Segment Klass ID'
-        optional :label, type: String, desc: 'Segment Klass Label'
-        optional :desc, type: String, desc: 'Segment Klass Desc'
-        optional :place, type: String, desc: 'Segment Klass Place', default: '100'
-        optional :identifier, type: String, desc: 'Segment Identifier'
-      end
+    params :update_segment_klass_params do
+      requires :id, type: Integer, desc: 'Segment Klass ID'
+      optional :label, type: String, desc: 'Segment Klass Label'
+      optional :desc, type: String, desc: 'Segment Klass Desc'
+      optional :place, type: String, desc: 'Segment Klass Place', default: '100'
+      optional :identifier, type: String, desc: 'Segment Identifier'
+    end
 
-      params :create_segment_klass_params do
-        requires :label, type: String, desc: 'Segment Klass Label'
-        requires :element_klass, type: Integer, desc: 'Element Klass Id'
-        optional :desc, type: String, desc: 'Segment Klass Desc'
-        optional :place, type: String, desc: 'Segment Klass Place', default: '100'
-        optional :properties_template, type: Hash, desc: 'Element Klass properties template'
-      end
+    params :create_segment_klass_params do
+      requires :label, type: String, desc: 'Segment Klass Label'
+      requires :element_klass, type: Integer, desc: 'Element Klass Id'
+      optional :desc, type: String, desc: 'Segment Klass Desc'
+      optional :place, type: String, desc: 'Segment Klass Place', default: '100'
+      optional :properties_template, type: Hash, desc: 'Element Klass properties template'
+    end
+
+    params :create_std_layer_params do
+      requires :name, type: String, desc: 'Element Klass Name'
+      requires :label, type: String, desc: 'Element Klass Label'
+      requires :klass_prefix, type: String, desc: 'Element Klass Short Label Prefix'
+      optional :icon_name, type: String, desc: 'Element Klass Icon Name'
+      optional :desc, type: String, desc: 'Element Klass Desc'
+      optional :properties_template, type: Hash, desc: 'Element Klass properties template'
+    end
+
+    params :std_layer_save do
+      requires :key, type: String, desc: 'key'
+      requires :cols, type: Integer, desc: 'key'
+      requires :label, type: String, desc: 'Label'
+      optional :position, type: Integer, desc: 'position'
+      optional :wf_position, type: Integer, desc: 'wf position'
+      optional :fields, type: Array, desc: 'fields'
+      optional :select_options, type: Hash, desc: 'selections'
+    end
+
+    params :std_layer_criteria do
+      requires :name, type: String, desc: 'Layer name'
+    end
+
+    params :vocab_save do
+      optional :name, type: String, desc: 'field'
+      optional :label, type: String, desc: 'Label'
+      optional :term_id, type: String, desc: 'ontology term_id'
+      requires :ontology, type: Hash, desc: 'ontology'
+      optional :source, type: String, desc: 'source'
+      optional :source_id, type: String, desc: 'source_id'
+      optional :layer_id, type: String, desc: 'layer_id'
+      optional :sub_fields, type: Array, desc: 'sub_fields'
+      optional :text_sub_fields, type: Array, desc: 'text_sub_fields'
+      requires :field_type, type: String, desc: 'field type'
+      requires :voc, type: Hash, desc: 'vocabulary references'
+      optional :select_options, type: Hash, desc: 'selections'
+      optional :option_layers, type: String, desc: 'option'
+    end
+
+    # params :vocabulary_save do
+    #   requires :type, type: String, desc: 'type'
+    #   requires :field, type: String, desc: 'field'
+    #   optional :default, type: String, desc: 'default'
+    #   optional :description, type: String, desc: 'description'
+    #   optional :label, type: String, desc: 'label'
+    #   optional :position, type: Integer, desc: 'position'
+    #   optional :ontology, type: Hash, desc: 'ontology'
+    #   optional :required, type: Boolean, desc: 'is required?'
+    #   optional :sub_fields, type: Array, desc: 'sub_fields'
+    #   optional :text_sub_fields, type: Array, desc: 'text_sub_fields'
+    #   optional :source_type, type: String, desc: 'source type'
+    #   optional :source_id, type: String, desc: 'source id'
+    #   optional :layer_id, type: String, desc: 'layer id'
+    # end
   end
-end
+end

data/lib/labimotion/helpers/vocabulary_helpers.rb

@@ -0,0 +1,16 @@
+# frozen_string_literal: true
+
+module Labimotion
+  # Helper for associated sample
+  module VocabularyHelpers
+    extend Grape::API::Helpers
+
+    def update_vocabularies(properties, current_user, element)
+      Labimotion::VocabularyHandler.update_vocabularies(properties, current_user, element)
+    rescue StandardError => e
+      Labimotion.log_exception(e, current_user)
+      properties
+    end
+
+  end
+end

data/lib/labimotion/libs/converter.rb

@@ -232,10 +232,12 @@ module Labimotion
       new_prop = dataset.properties
       dsr.each do |ds|
         layer = layers[ds[:layer]]
-        next if layer.nil? || layer[Labimotion::Prop::FIELDS].nil?
+        next if layer.blank? || layer[Labimotion::Prop::FIELDS].blank?
 
         fields = layer[Labimotion::Prop::FIELDS].select{ |f| f['field'] == ds[:field] }
         fi = fields&.first
+        next if fi.blank?
+
         idx = layer[Labimotion::Prop::FIELDS].find_index(fi)
         fi['value'] = ds[:value]
         fi['device'] = ds[:device] || ds[:value]
@@ -262,6 +264,7 @@ module Labimotion
           new_prop[Labimotion::Prop::LAYERS]['sample_details'][Labimotion::Prop::FIELDS][idx] = fi
         end
       end
+      new_prop = Labimotion::VocabularyHandler.update_vocabularies(new_prop, current_user, element)
       dataset.properties = new_prop
       dataset.save!
     end

data/lib/labimotion/libs/nmr_mapper.rb

@@ -256,6 +256,7 @@ module Labimotion
           new_prop[Labimotion::Prop::LAYERS]['set'][Labimotion::Prop::FIELDS][idx] = fi
         end
       end
+      new_prop = Labimotion::VocabularyHandler.update_vocabularies(new_prop, current_user, element)
       dataset.properties = new_prop
       dataset.save!
     end

data/lib/labimotion/libs/vocabulary_handler.rb

@@ -0,0 +1,91 @@
+# frozen_string_literal: true
+
+module Labimotion
+  class VocabularyHandler
+
+    def self.update_vocabularies(properties, current_user, element)
+      properties[Labimotion::Prop::LAYERS].keys.each do |key|
+        layer = properties[Labimotion::Prop::LAYERS][key]
+        field_vocabularies = layer[Labimotion::Prop::FIELDS].select { |ss| ss['is_vocabulary'] == true && ss['opid'] == 9}
+        field_vocabularies.each do |field|
+          idx = properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS].index(field)
+          val = ''
+          orig_val = properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value']
+          case field['source']
+          when 'System'
+            val = Time.now.strftime('%d/%m/%Y %H:%M') if field['identifier'] == 'dateTime.update'
+            val = Time.now.strftime('%d/%m/%Y %H:%M') if field['identifier'] == 'dateTime.create' && orig_val.blank?
+          when 'User'
+            val = current_user.name if field['identifier'] == 'user.name' && current_user.present?
+          when 'Element'
+            val = element.id.to_s if field['identifier'] == 'element.id'
+            val = element.short_label if element.has_attribute?(:short_label) && field['identifier'] == 'element.short_label'
+          when 'Segment'
+            segments = element.segments.joins(:segment_klass).find_by('segment_klasses.identifier = ?', field['source_id'])
+            next if segments.nil?
+
+            seg_prop = segments.properties
+            fields = seg_prop[Labimotion::Prop::LAYERS][field['layer_id']][Labimotion::Prop::FIELDS].select { |ss| ss['field'] == field['field_id'] }
+            val = fields.first['value']
+          when 'Dataset'
+            byebug
+          end
+          # case field['identifier']
+          # when 'dateTime.now'
+          #   val = Time.now.strftime('%d/%m/%Y %H:%M')
+          # when 'user.name'
+          #   val = current_user.name
+          # when 'element.id'
+          #   val = element.id.to_s
+          # when 'element.short_label'
+          #   val = element.short_label
+          # end
+          # ontology = {
+          #   id: "ncit:class:http://purl.obolibrary.org/obo/#{field['term_id']}",
+          #   iri: "http://purl.obolibrary.org/obo/#{field['term_id']}",
+          #   type: "class",
+          #   label: field['name'],
+          #   obo_id: field['term_id'],
+          #   short_form: field['term_id'],
+          #   description: field['label'],
+          # }
+          # properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['ontology'] = ontology if ontology.present?
+          properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['value'] = val if val.present?
+          ## properties[Labimotion::Prop::LAYERS][key][Labimotion::Prop::FIELDS][idx]['placeholder'] = val if val.present?
+        end
+      end
+      properties
+    rescue StandardError => e
+      Labimotion.log_exception(e, current_user)
+      properties
+    end
+
+    def self.load_all_vocabularies
+      file_data = load_from_files
+      db_data = load_from_database
+      file_data + db_data
+    end
+
+    def self.load_app_vocabularies
+      load_from_files
+    end
+
+    def self.load_from_files
+      merged_data = []
+      dir_path = Rails.root.join('lib', 'labimotion', 'libs', 'data', 'vocab')
+      Dir.glob(dir_path.join('*.json')).each do |file_path|
+        file_content = File.read(file_path)
+        json_data = JSON.parse(file_content)
+        merged_data.concat(json_data)
+      end
+      merged_data
+    end
+
+    def self.load_from_database
+      Labimotion::Vocabulary.all.sort_by(&:name)
+      # Labimotion::VocabularyEntity.represent(Labimotion::Vocabulary.all.sort_by(&:name), serializable: true)
+    end
+
+    private_class_method :load_from_files, :load_from_database
+  end
+end

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

@@ -25,14 +25,15 @@ module Labimotion
       def exec_converter
         return if self.has_attribute?(:con_state) == false || self.con_state.nil? || self.con_state == Labimotion::ConState::NONE
 
-        return if attachable_id.nil? && self.con_state != Labimotion::ConState::WAIT
+        return if attachable_id.nil? && con_state != Labimotion::ConState::WAIT
 
+        current_user = User.find_by(id: created_by)
         case con_state
         when Labimotion::ConState::NMR
-          self.con_state = Labimotion::NmrMapper.process_ds(id)
+          self.con_state = Labimotion::NmrMapper.process_ds(id, current_user)
           update_column(:con_state, con_state)
         when Labimotion::ConState::WAIT
-          self.con_state = Labimotion::Converter.jcamp_converter(id)
+          self.con_state = Labimotion::Converter.jcamp_converter(id, current_user)
           update_column(:con_state, con_state)
         when Labimotion::ConState::CONVERTED
           Labimotion::Converter.metadata(id)

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

@@ -42,6 +42,7 @@ module Labimotion
       props['identifier'] = klass.identifier if klass.identifier.present?
       props['uuid'] = uuid
       props['klass'] = 'Dataset'
+      props = Labimotion::VocabularyHandler.update_vocabularies(props, args[:current_user], args[:element])
 
       ds = Labimotion::Dataset.find_by(element_type: self.class.name, element_id: id)
       if ds.present? && (ds.klass_uuid != props['klass_uuid'] || ds.properties != props)

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

@@ -59,6 +59,8 @@ module Labimotion
         props['uuid'] = uuid
         props['klass'] = 'Segment'
         props = Labimotion::SampleAssociation.update_sample_association(props, args[:current_user_id])
+        current_user = User.find_by(id: args[:current_user_id])
+        props = Labimotion::VocabularyHandler.update_vocabularies(props, current_user, self)
         segment = Labimotion::Segment.where(element_type: self.class.name, element_id: self.id, segment_klass_id: seg['segment_klass_id']).order(id: :desc).first
         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/models/std_layer.rb

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+
+module Labimotion
+  class StdLayer < ApplicationRecord
+    acts_as_paranoid
+    self.table_name = :l_s_lyrs
+    has_many :l_s_lyrs_tracks, primary_key: 'identifier', foreign_key: 'identifier', class_name: 'Labimotion::StdLayersRevision'
+  end
+end

data/lib/labimotion/models/std_layers_revision.rb

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+
+module Labimotion
+  class StdLayersRevision < ApplicationRecord
+    acts_as_paranoid
+    self.table_name = :l_s_lyrs_tracks
+    belongs_to :l_s_lyrs, primary_key: 'identifier', foreign_key: 'identifier', class_name: 'Labimotion::StdLayer'
+  end
+end

data/lib/labimotion/models/vocabulary.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+require 'labimotion/models/concerns/generic_klass_revisions'
+require 'labimotion/models/concerns/workflow'
+
+module Labimotion
+  class Vocabulary < ApplicationRecord
+    self.table_name = :vocabularies
+    acts_as_paranoid
+
+
+  end
+end

data/lib/labimotion/version.rb

@@ -2,5 +2,5 @@
 
 ## Labimotion Version
 module Labimotion
-  VERSION = '1.4.0.1'
+  VERSION = '1.5.0.rc1'
 end

data/lib/labimotion.rb

@@ -16,12 +16,15 @@ module Labimotion
   autoload :Utils, 'labimotion/utils/utils'
 
   ######## APIs
+  autoload :LabimotionAPI, 'labimotion/apis/labimotion_api'
   autoload :GenericKlassAPI, 'labimotion/apis/generic_klass_api'
   autoload :GenericElementAPI, 'labimotion/apis/generic_element_api'
   autoload :GenericDatasetAPI, 'labimotion/apis/generic_dataset_api'
   autoload :SegmentAPI, 'labimotion/apis/segment_api'
   autoload :LabimotionHubAPI, 'labimotion/apis/labimotion_hub_api'
   autoload :ConverterAPI, 'labimotion/apis/converter_api'
+  autoload :StandardLayerAPI, 'labimotion/apis/standard_layer_api'
+  autoload :VocabularyAPI, 'labimotion/apis/vocabulary_api'
 
   ######## Entities
   autoload :PropertiesEntity, 'labimotion/entities/properties_entity'
@@ -43,6 +46,7 @@ module Labimotion
   autoload :ElementRevisionEntity, 'labimotion/entities/element_revision_entity'
   autoload :SegmentRevisionEntity, 'labimotion/entities/segment_revision_entity'
   ## autoload :DatasetRevisionEntity, 'labimotion/entities/dataset_revision_entity'
+  autoload :VocabularyEntity, 'labimotion/entities/vocabulary_entity'
 
   ######## Helpers
   autoload :GenericHelpers, 'labimotion/helpers/generic_helpers'
@@ -54,6 +58,7 @@ module Labimotion
   autoload :ConverterHelpers, 'labimotion/helpers/converter_helpers'
   autoload :SampleAssociationHelpers, 'labimotion/helpers/sample_association_helpers'
   autoload :RepositoryHelpers, 'labimotion/helpers/repository_helpers'
+  autoload :VocabularyHelpers, 'labimotion/helpers/vocabulary_helpers'
 
   ######## Libs
   autoload :Converter, 'labimotion/libs/converter'
@@ -64,6 +69,7 @@ module Labimotion
   autoload :SampleAssociation, 'labimotion/libs/sample_association'
   autoload :PropertiesHandler, 'labimotion/libs/properties_handler'
   autoload :AttachmentHandler, 'labimotion/libs/attachment_handler'
+  autoload :VocabularyHandler, 'labimotion/libs/vocabulary_handler'
 
   ######## Utils
   autoload :Prop, 'labimotion/utils/prop'
@@ -84,6 +90,7 @@ module Labimotion
   autoload :ElementKlass, 'labimotion/models/element_klass'
   autoload :SegmentKlass, 'labimotion/models/segment_klass'
   autoload :DatasetKlass, 'labimotion/models/dataset_klass'
+  autoload :Vocabulary, 'labimotion/models/vocabulary'
 
   autoload :ElementsRevision, 'labimotion/models/elements_revision'
   autoload :SegmentsRevision, 'labimotion/models/segments_revision'
@@ -97,6 +104,9 @@ module Labimotion
   autoload :ElementsElement, 'labimotion/models/elements_element'
   autoload :CollectionsElement, 'labimotion/models/collections_element'
 
+  autoload :StdLayer, 'labimotion/models/std_layer'
+  autoload :StdLayersRevision, 'labimotion/models/std_layers_revision'
+
   ######## Models/Concerns
   autoload :GenericKlassRevisions, 'labimotion/models/concerns/generic_klass_revisions'
   autoload :GenericRevisions, 'labimotion/models/concerns/generic_revisions'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 1.4.0.1
+  version: 1.5.0.rc1
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-08-22 00:00:00.000000000 Z
+date: 2024-09-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -38,8 +38,12 @@ files:
 - lib/labimotion/apis/generic_dataset_api.rb
 - lib/labimotion/apis/generic_element_api.rb
 - lib/labimotion/apis/generic_klass_api.rb
+- lib/labimotion/apis/labimotion_api.rb
 - lib/labimotion/apis/labimotion_hub_api.rb
 - lib/labimotion/apis/segment_api.rb
+- lib/labimotion/apis/standard_api.rb
+- lib/labimotion/apis/standard_layer_api.rb
+- lib/labimotion/apis/vocabulary_api.rb
 - lib/labimotion/collection/export.rb
 - lib/labimotion/collection/import.rb
 - lib/labimotion/conf.rb
@@ -58,6 +62,7 @@ files:
 - lib/labimotion/entities/segment_entity.rb
 - lib/labimotion/entities/segment_klass_entity.rb
 - lib/labimotion/entities/segment_revision_entity.rb
+- lib/labimotion/entities/vocabulary_entity.rb
 - lib/labimotion/helpers/converter_helpers.rb
 - lib/labimotion/helpers/dataset_helpers.rb
 - lib/labimotion/helpers/element_helpers.rb
@@ -67,6 +72,7 @@ files:
 - lib/labimotion/helpers/sample_association_helpers.rb
 - lib/labimotion/helpers/search_helpers.rb
 - lib/labimotion/helpers/segment_helpers.rb
+- lib/labimotion/helpers/vocabulary_helpers.rb
 - lib/labimotion/libs/attachment_handler.rb
 - lib/labimotion/libs/converter.rb
 - lib/labimotion/libs/export_dataset.rb
@@ -75,6 +81,7 @@ files:
 - lib/labimotion/libs/properties_handler.rb
 - lib/labimotion/libs/sample_association.rb
 - lib/labimotion/libs/template_hub.rb
+- lib/labimotion/libs/vocabulary_handler.rb
 - lib/labimotion/models/collections_element.rb
 - lib/labimotion/models/concerns/attachment_converter.rb
 - lib/labimotion/models/concerns/datasetable.rb
@@ -98,6 +105,9 @@ files:
 - lib/labimotion/models/segment_klass.rb
 - lib/labimotion/models/segment_klasses_revision.rb
 - lib/labimotion/models/segments_revision.rb
+- lib/labimotion/models/std_layer.rb
+- lib/labimotion/models/std_layers_revision.rb
+- lib/labimotion/models/vocabulary.rb
 - lib/labimotion/utils/con_state.rb
 - lib/labimotion/utils/export_utils.rb
 - lib/labimotion/utils/field_type.rb
@@ -123,9 +133,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - ">"
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.3.1
 requirements: []
 rubygems_version: 3.1.6
 signing_key: