labimotion 0.2.2 → 0.3.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/labimotion/apis/generic_dataset_api.rb

@@ -30,7 +30,7 @@ module Labimotion
       namespace :fetch_repo do
         desc 'fetch Generic Dataset Klass from Chemotion Repository'
         get do
-          fetch_repo('DatasetKlass')
+          fetch_repo('DatasetKlass', current_user)
         end
       end
 
@@ -40,8 +40,9 @@ module Labimotion
           requires :identifier, type: String, desc: 'Identifier'
         end
         post do
-          create_repo_klass(params, current_user)
-          present DatasetKlass.all, with: Labimotion::DatasetKlassEntity, root: 'klass'
+          msg = create_repo_klass(params, current_user, request.headers['Origin'])
+          klass = Labimotion::DatasetKlassEntity.represent(DatasetKlass.all)
+          { status: msg[:status], message: msg[:message], klass: klass }
         rescue StandardError => e
           Labimotion.log_exception(e, current_user)
           { error: e.message }

data/lib/labimotion/apis/generic_element_api.rb

@@ -21,6 +21,9 @@ module Labimotion
         get do
           ek = Labimotion::ElementKlass.find_by(name: params[:name])
           present ek, with: Labimotion::ElementKlassEntity, root: 'klass'
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          { klass: [] }
         end
       end
 
@@ -32,6 +35,9 @@ module Labimotion
         get do
           list = klass_list(params[:generic_only])
           present list, with: Labimotion::ElementKlassEntity, root: 'klass'
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          { klass: [] }
         end
       end
 
@@ -67,6 +73,9 @@ module Labimotion
         post do
           authenticate_admin!('elements')
           update_element_klass(current_user, params)
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          raise e
         end
       end
 
@@ -79,6 +88,9 @@ module Labimotion
         get do
           list = list_klass_revisions(params)
           present list, with: Labimotion::KlassRevisionEntity, root: 'revisions'
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          []
         end
       end
 
@@ -90,6 +102,9 @@ module Labimotion
         get do
           list = element_revisions(params)
           present list, with: Labimotion::ElementRevisionEntity, root: 'revisions'
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          []
         end
       end
 
@@ -104,6 +119,9 @@ module Labimotion
           authenticate_admin!(params[:klass].gsub(/(Klass)/, 's').downcase)
           delete_klass_revision(params)
           status 201
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          raise e
         end
       end
 
@@ -117,6 +135,9 @@ module Labimotion
         post do
           delete_revision(params)
           status 201
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          raise e
         end
       end
 
@@ -129,6 +150,9 @@ module Labimotion
           klass = Labimotion::Segment.find(params[:id])
           list = klass.segments_revisions unless klass.nil?
           present list&.sort_by(&:created_at).reverse, with: Labimotion::SegmentRevisionEntity, root: 'revisions'
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          []
         end
       end
 
@@ -152,6 +176,9 @@ module Labimotion
         post do
           upload_generics_files(current_user, params)
           true
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          raise e
         end
       end
 
@@ -160,13 +187,19 @@ module Labimotion
         get do
           list = Labimotion::ElementKlass.all.sort_by { |e| e.place }
           present list, with: Labimotion::ElementKlassEntity, root: 'klass'
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          []
         end
       end
 
       namespace :fetch_repo do
         desc 'fetch Generic Element Klass from Chemotion Repository'
         get do
-          fetch_repo('ElementKlass')
+          fetch_repo('ElementKlass', current_user)
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          []
         end
       end
 
@@ -176,8 +209,9 @@ module Labimotion
           requires :identifier, type: String, desc: 'Identifier'
         end
         post do
-          create_repo_klass(params, current_user)
-          present ElementKlass.all, with: Labimotion::ElementKlassEntity, root: 'klass'
+          msg = create_repo_klass(params, current_user, request.headers['Origin'])
+          klass = Labimotion::ElementKlassEntity.represent(ElementKlass.all)
+          { status: msg[:status], message: msg[:message], klass: klass }
         rescue StandardError => e
           Labimotion.log_exception(e, current_user)
           { error: e.message }
@@ -197,6 +231,9 @@ module Labimotion
         end
         post do
           deactivate_klass(params)
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          raise e
         end
       end
 
@@ -209,6 +246,9 @@ module Labimotion
         delete ':id' do
           delete_klass(params)
           status 201
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          raise e
         end
       end
 
@@ -226,6 +266,9 @@ module Labimotion
         end
         post do
           update_template(params, current_user)
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          raise e
         end
       end
 
@@ -256,6 +299,9 @@ module Labimotion
           end
         end
         { generic_elements: generic_elements }
+      rescue StandardError => e
+        Labimotion.log_exception(e, current_user)
+        { generic_elements: [] }
       end
 
       desc 'Return serialized element by id'
@@ -272,7 +318,7 @@ module Labimotion
           if Labimotion::IS_RAILS5 == true
             {
               element: ElementPermissionProxy.new(current_user, element, user_ids).serialized,
-              attachments: Entities::AttachmentEntity.represent(element.attachments)
+              attachments: attach_thumbnail(element&.attachments)
             }
           else
             {
@@ -280,9 +326,11 @@ module Labimotion
                 element,
                 detail_levels: ElementDetailLevelCalculator.new(user: current_user, element: element).detail_levels,
               ),
-              attachments: Entities::AttachmentEntity.represent(element.attachments),
+              attachments: attach_thumbnail(element&.attachments)
             }
           end
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
         end
       end
 
@@ -302,7 +350,7 @@ module Labimotion
           if Labimotion::IS_RAILS5 == true
             {
               element: ElementPermissionProxy.new(current_user, element, user_ids).serialized,
-              attachments: Entities::AttachmentEntity.represent(element.attachments)
+              attachments: attach_thumbnail(element&.attachments)
             }
           else
             present(
@@ -338,7 +386,7 @@ module Labimotion
             if Labimotion::IS_RAILS5 == true
               {
                 element: ElementPermissionProxy.new(current_user, element, user_ids).serialized,
-                attachments: Entities::AttachmentEntity.represent(element.attachments)
+                attachments: attach_thumbnail(element&.attachments)
               }
             else
               {
@@ -346,7 +394,7 @@ module Labimotion
                   element,
                   detail_levels: ElementDetailLevelCalculator.new(user: current_user, element: element).detail_levels,
                 ),
-                attachments: Entities::AttachmentEntity.represent(element.attachments),
+                attachments: attach_thumbnail(element&.attachments),
               }
             end
           rescue StandardError => e

data/lib/labimotion/apis/labimotion_hub_api.rb

@@ -1,6 +1,7 @@
 # frozen_string_literal: true
 
 require 'open-uri'
+require 'labimotion/models/hub_log'
 
 # Belong to Chemotion module
 module Labimotion
@@ -19,20 +20,25 @@ module Labimotion
           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.length > 1 ? de_encode_json(entities) : []
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          []
         end
       end
       namespace :fetch do
         desc "get active generic templates"
         params do
           requires :klass, type: String, desc: 'Klass', values: %w[ElementKlass SegmentKlass DatasetKlass]
-          # requires :fqdn, type: Integer, desc: 'FQDN'
+          requires :origin, type: String, desc: 'origin'
           requires :identifier, type: String, desc: 'Identifier'
         end
-        get do
+        post do
           entity = "Labimotion::#{params[:klass]}".constantize.find_by(identifier: params[:identifier])
+          Labimotion::HubLog.create(klass: entity, origin: params[:origin], uuid: entity.uuid, version: entity.version)
           "Labimotion::#{params[:klass]}Entity".constantize.represent(entity)
-          # entities.length > 1 ? de_encode_json(entities) : []
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          raise e
         end
       end
 
@@ -45,6 +51,9 @@ module Labimotion
           list = Labimotion::ElementKlass.where(is_active: true) if params[:generic_only].present? && params[:generic_only] == true
           list = Labimotion::ElementKlass.where(is_active: true) unless params[:generic_only].present? && params[:generic_only] == true
           list.pluck(:name)
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          []
         end
       end
 

data/lib/labimotion/apis/segment_api.rb

@@ -118,7 +118,7 @@ module Labimotion
       namespace :fetch_repo do
         desc 'fetch Generic Segment Klass from Chemotion Repository'
         get do
-          fetch_repo('SegmentKlass')
+          fetch_repo('SegmentKlass', current_user)
         rescue StandardError => e
           Labimotion.log_exception(e, current_user)
           { error: e.message }
@@ -131,8 +131,9 @@ module Labimotion
           requires :identifier, type: String, desc: 'Identifier'
         end
         post do
-          create_repo_klass(params, current_user)
-          present SegmentKlass.all, with: Labimotion::SegmentKlassEntity, root: 'klass'
+          msg = create_repo_klass(params, current_user, request.headers['Origin'])
+          klass = Labimotion::SegmentKlassEntity.represent(SegmentKlass.all)
+          { status: msg[:status], message: msg[:message], klass: klass }
         rescue StandardError => e
           Labimotion.log_exception(e, current_user)
           ## { error: e.message }

data/lib/labimotion/entities/generic_public_entity.rb

@@ -5,6 +5,7 @@ require 'labimotion/entities/application_entity'
 # Entity module
 module Labimotion
   class GenericPublicEntity < Labimotion::ApplicationEntity
+    expose! :uuid
     expose! :name
     expose! :desc
     expose! :icon_name
@@ -12,6 +13,7 @@ module Labimotion
     expose! :klass_name
     expose! :label
     expose! :identifier
+    expose! :version
     expose! :released_at
     expose! :properties_release, if: :displayed
     expose :element_klass do |obj|

data/lib/labimotion/helpers/dataset_helpers.rb

@@ -13,8 +13,8 @@ module Labimotion
       end
     end
 
-    def create_repo_klass(params, current_user)
-      response = Labimotion::TemplateHub.fetch_identifier('DatasetKlass', params[:identifier])
+    def create_repo_klass(params, current_user, origin)
+      response = Labimotion::TemplateHub.fetch_identifier('DatasetKlass', params[:identifier], origin)
       attributes = response.slice('ols_term_id', 'label', 'desc', 'uuid', 'identifier', 'properties_release', 'version') # .except(:id, :is_active, :place, :created_by, :created_at, :updated_at)
       attributes['properties_release']['identifier'] = attributes['identifier']
       attributes['properties_template'] = attributes['properties_release']
@@ -23,14 +23,22 @@ module Labimotion
       attributes['updated_by'] = current_user.id
       attributes['sync_by'] = current_user.id
       attributes['sync_time'] = DateTime.now
-      if Labimotion::DatasetKlass.find_by(ols_term_id: attributes['ols_term_id']).present?
-        ds = Labimotion::DatasetKlass.find_by(ols_term_id: attributes['ols_term_id'])
-        ds.update!(attributes)
+      dataset_klass = Labimotion::DatasetKlass.find_by(ols_term_id: attributes['ols_term_id'])
+      if dataset_klass.present?
+        if dataset_klass['uuid'] == attributes['uuid'] && dataset_klass['version'] == attributes['version']
+          { status: 'success', message: "This dataset: #{attributes['label']} has the latest version!" }
+        else
+          ds = Labimotion::DatasetKlass.find_by(ols_term_id: attributes['ols_term_id'])
+          ds.update!(attributes)
+          ds.create_klasses_revision(current_user)
+          { status: 'success', message: "This dataset: [#{attributes['label']}] has been upgraded to the version: #{attributes['version']}!" }
+        end
       else
         attributes['created_by'] = current_user.id
         ds = Labimotion::DatasetKlass.create!(attributes)
+        ds.create_klasses_revision(current_user)
+        { status: 'success', message: "The dataset: #{attributes['label']} has been created using version: #{attributes['version']}!" }
       end
-      ds.create_klasses_revision(current_user)
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       # { error: e.message }

data/lib/labimotion/helpers/element_helpers.rb

@@ -20,12 +20,10 @@ module Labimotion
       uuid = SecureRandom.uuid
       template = { uuid: uuid, layers: {}, select_options: {} }
       attributes = declared(params, include_missing: false)
-      if attributes[:properties_template].present?
-        attributes[:properties_template]['uuid'] = uuid
-        attributes[:properties_template] = template
-        attributes[:properties_template]['pkg'] = Labimotion::Utils.pkg(attributes[:properties_template]['pkg'])
-        attributes[:properties_template]['klass'] = 'ElementKlass'
-      end
+      attributes[:properties_template] = template if attributes[:properties_template].nil?
+      attributes[:properties_template]['uuid'] = uuid
+      attributes[:properties_template]['pkg'] = Labimotion::Utils.pkg(attributes[:properties_template]['pkg'])
+      attributes[:properties_template]['klass'] = 'ElementKlass'
       attributes[:is_active] = false
       attributes[:uuid] = uuid
       attributes[:released_at] = DateTime.now
@@ -161,7 +159,7 @@ module Labimotion
         att_ary = create_attachments(
           params[:attfiles],
           params[:delfiles],
-          params[:att_type],
+          "Labimotion::#{params[:att_type]}",
           params[:att_id],
           params[:attfilesIdentifier],
           current_user.id
@@ -176,8 +174,7 @@ module Labimotion
       true
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
-      ## false
-      raise e
+      false
     end
 
     def element_revisions(params)
@@ -292,9 +289,9 @@ module Labimotion
       raise e
     end
 
-    def create_repo_klass(params, current_user)
-      response = Labimotion::TemplateHub.fetch_identifier('ElementKlass', params[:identifier])
-      attributes = response.slice('name', 'label', 'desc', 'icon_name', 'klass_prefix', 'is_generic', 'identifier', 'properties_release', 'version')
+    def create_repo_klass(params, current_user, origin)
+      response = Labimotion::TemplateHub.fetch_identifier('ElementKlass', params[:identifier], origin)
+      attributes = response.slice('name', 'label', 'desc', 'icon_name', 'uuid', 'klass_prefix', 'is_generic', 'identifier', 'properties_release', 'version')
       attributes['properties_release']['identifier'] = attributes['identifier']
       attributes['properties_template'] = attributes['properties_release']
       attributes['place'] = ((Labimotion::DatasetKlass.all.length * 10) || 0) + 10
@@ -305,17 +302,38 @@ module Labimotion
 
       element_klass = Labimotion::ElementKlass.find_by(identifier: attributes['identifier'])
       if element_klass.present?
-        element_klass.update!(attributes)
+        if element_klass['uuid'] == attributes['uuid'] && element_klass['version'] == attributes['version']
+          { status: 'success', message: "This element: #{attributes['name']} has the latest version!" }
+        else
+          element_klass.update!(attributes)
+          element_klass.create_klasses_revision(current_user)
+          { status: 'success', message: "This element: [#{attributes['name']}] has been upgraded to the version: #{attributes['version']}!" }
+        end
       else
-        attributes['created_by'] = current_user.id
-        element_klass = Labimotion::ElementKlass.create!(attributes)
+        exist_klass = Labimotion::ElementKlass.find_by(name: attributes['name'])
+        if exist_klass.present?
+          { status: 'error', message: "The name [#{attributes['name']}] is already in use." }
+        else
+          attributes['created_by'] = current_user.id
+          element_klass = Labimotion::ElementKlass.create!(attributes)
+          element_klass.create_klasses_revision(current_user)
+          { status: 'success', message: "The element: #{attributes['name']} has been created using version: #{attributes['version']}!" }
+        end
       end
-      element_klass.create_klasses_revision(current_user)
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       # { error: e.message }
       raise e
     end
 
+    def attach_thumbnail(_attachments)
+      attachments = _attachments&.map do |attachment|
+        _att = Entities::AttachmentEntity.represent(attachment, serializable: true)
+        _att[:thumbnail] = attachment.thumb ? Base64.encode64(attachment.read_thumbnail) : nil
+        _att
+      end
+      attachments
+    end
+
   end
 end

data/lib/labimotion/helpers/generic_helpers.rb

@@ -46,10 +46,9 @@ module Labimotion
       uuid = SecureRandom.uuid
       properties = params[:properties_template]
       properties['uuid'] = uuid
-
       klz.version = Labimotion::Utils.next_version(params[:release], klz.version)
       properties['version'] = klz.version
-      properties['pkg'] = Labimotion::Utils.pkg(params['pkg'] || klz.properties_template['pkg'])
+      properties['pkg'] = Labimotion::Utils.pkg(params['pkg'] || (klz.properties_template && klz.properties_template['pkg']))
       properties['klass'] = klz.class.name.split('::').last
       properties['identifier'] = klz.identifier
       properties.delete('eln') if properties['eln'].present?
@@ -189,37 +188,37 @@ module Labimotion
       raise e
     end
 
-    def create_attachments(files, del_files, type, id, user_id)
+    def create_attachments(files, del_files, type, id, identifier, user_id)
       attach_ary = []
-      (files || []).each do |file|
+      (files || []).each_with_index do |file, index|
         next unless (tempfile = file[:tempfile])
 
-        a = Attachment.new(
+        att = Attachment.new(
           bucket: file[:container_id],
           filename: file[:filename],
           con_state: Labimotion::ConState::NONE,
           file_path: file[:tempfile],
           created_by: user_id,
           created_for: user_id,
+          identifier: identifier[index],
           content_type: file[:type],
           attachable_type: type,
           attachable_id: id,
         )
         begin
-          a.save!
-          attach_ary.push(a.id)
+          att.save!
+          attach_ary.push(att.id)
         ensure
           tempfile.close
           tempfile.unlink
         end
       end
       unless (del_files || []).empty?
-        Attachment.where('id IN (?) AND attachable_type = (?)', del_files.map!(&:to_i),
-                        type).update_all(attachable_id: nil)
+        Attachment.where('id IN (?) AND attachable_type = (?)', del_files.map!(&:to_i), type).update_all(attachable_id: nil)
       end
       attach_ary
     rescue StandardError => e
-      Labimotion.log_exception(e, current_user)
+      Labimotion.log_exception(e)
       raise e
     end
 
@@ -231,15 +230,16 @@ module Labimotion
       Chemotion::Generic::Fetch::Template.list(API::TARGET, name)
     end
 
-    def fetch_repo(name)
-      current_klasses = "Labimotion::#{name}".constantize.where.not(identifier: nil)&.pluck(:identifier) || []
+    def fetch_repo(name, current_user)
+      # current_klasses = "Labimotion::#{name}".constantize.where.not(identifier: nil)&.pluck(:identifier) || []
       response = Labimotion::TemplateHub.list(name)
-      if response && response['list'].present? && response['list'].length.positive?
-        filter_list = response['list']&.reject do |ds|
-          current_klasses.include?(ds['identifier'])
-        end || []
-      end
-      filter_list || []
+      # if response && response['list'].present? && response['list'].length.positive?
+        # filter_list = response['list']&.reject do |ds|
+        #   current_klasses.include?(ds['identifier'])
+        # end || []
+      # end
+      # filter_list || []
+      (response && response['list']) || []
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       { error: 'Cannot connect to Chemotion Repository' }

data/lib/labimotion/helpers/segment_helpers.rb

@@ -63,8 +63,8 @@ module Labimotion
       raise e
     end
 
-    def create_repo_klass(params, current_user)
-      response = Labimotion::TemplateHub.fetch_identifier('SegmentKlass', params[:identifier])
+    def create_repo_klass(params, current_user, origin)
+      response = Labimotion::TemplateHub.fetch_identifier('SegmentKlass', params[:identifier], origin)
       attributes = response.slice('label', 'desc', 'uuid', 'identifier', 'released_at', 'properties_release', 'version')
       attributes['properties_release']['identifier'] = attributes['identifier']
       attributes['properties_template'] = attributes['properties_release']
@@ -75,8 +75,8 @@ module Labimotion
       attributes['sync_time'] = DateTime.now
 
       element_klass = Labimotion::ElementKlass.find_by(identifier: response['element_klass']['identifier'])
-      element_klass = Labimotion::ElementKlass.find_by(name: response['element_klass']['name']) if element_klass.nil?
-      return { error: 'ElementKlass not found' } if element_klass.nil?
+      element_klass = Labimotion::ElementKlass.find_by(name: response['element_klass']['name'], is_generic: false) if element_klass.nil?
+      return { status: 'error', message: "The element [#{response['element_klass']['name']}] does not exist in this instance" } if element_klass.nil?
 
       # el_attributes = response['element_klass'].slice('name', 'label', 'desc', 'uuid', 'identifier', 'icon_name', 'klass_prefix', 'is_generic', 'released_at')
       # el_attributes['properties_template'] = response['element_klass']['properties_release']
@@ -85,12 +85,24 @@ module Labimotion
       attributes['element_klass_id'] = element_klass.id
       segment_klass = Labimotion::SegmentKlass.find_by(identifier: attributes['identifier'])
       if segment_klass.present?
-        segment_klass.update!(attributes)
+        if segment_klass['uuid'] == attributes['uuid'] && segment_klass['version'] == attributes['version']
+          { status: 'success', message: "This segment: #{attributes['label']} has the latest version!" }
+        else
+          segment_klass.update!(attributes)
+          segment_klass.create_klasses_revision(current_user)
+          { status: 'success', message: "This segment: [#{attributes['label']}] has been upgraded to the version: #{attributes['version']}!" }
+        end
       else
-        attributes['created_by'] = current_user.id
-        segment_klass = Labimotion::SegmentKlass.create!(attributes)
+        exist_klass = Labimotion::SegmentKlass.find_by(label: attributes['label'], element_klass_id: element_klass.id)
+        if exist_klass.present?
+          { status: 'error', message: "The segment [#{attributes['label']}] is already in use." }
+        else
+          attributes['created_by'] = current_user.id
+          segment_klass = Labimotion::SegmentKlass.create!(attributes)
+          segment_klass.create_klasses_revision(current_user)
+          { status: 'success', message: "The segment: #{attributes['label']} has been created using version: #{attributes['version']}!" }
+        end
       end
-      segment_klass.create_klasses_revision(current_user)
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       raise e

data/lib/labimotion/libs/converter.rb

@@ -4,6 +4,7 @@ require 'net/http'
 require 'uri'
 require 'json'
 require 'date'
+require 'labimotion/version'
 require 'labimotion/utils/utils'
 
 # rubocop: disable Metrics/AbcSize
@@ -116,7 +117,7 @@ module Labimotion
         )
         # att.attachment_attacher.attach(tmp_file)
         if att.valid? && Labimotion::IS_RAILS5 == false
-          att.attachment_attacher.create_derivatives
+          ## att.attachment_attacher.create_derivatives
           att.save!
         end
         if att.valid? && Labimotion::IS_RAILS5 == true
@@ -143,12 +144,16 @@ module Labimotion
     end
 
     def self.process(data)
-      return if data[:a]&.attachable_type != 'Container'
-
+      return data[:a].con_state if data[:a]&.attachable_type != 'Container'
       response = nil
       begin
         ofile = Rails.root.join(data[:f], data[:a].filename)
-        FileUtils.cp(data[:a].store.path, ofile)
+        if Labimotion::IS_RAILS5 == true
+          FileUtils.cp(data[:a].store.path, ofile)
+        else
+          FileUtils.cp(data[:a].attachment_url, ofile)
+        end
+
         File.open(ofile, 'r') do |f|
           body = { file: f }
           response = HTTParty.post(
@@ -160,12 +165,14 @@ module Labimotion
         end
         if response.ok?
           Labimotion::Converter.handle_response(data[:a], response)
+          Labimotion::ConState::PROCESSED
         else
           Labimotion::Converter.logger.error ["Converter Response Error: id: [#{data[:a]&.id}], filename: [#{data[:a]&.filename}], response: #{response}"].join($INPUT_RECORD_SEPARATOR)
+          Labimotion::ConState::ERROR
         end
-        response
       rescue StandardError => e
-        raise e
+        Labimotion::Converter.logger.error ["process fail: #{id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
+        Labimotion::ConState::ERROR
       ensure
         FileUtils.rm_f(ofile)
       end
@@ -174,14 +181,14 @@ module Labimotion
     def self.jcamp_converter(id)
       resp = nil
       begin
+
         data = Labimotion::Converter.vor_conv(id)
         return if data.nil?
 
-        resp = Labimotion::Converter.process(data)
-        resp&.success? ? Labimotion::ConState::PROCESSED : Labimotion::ConState::ERROR
+        Labimotion::Converter.process(data)
       rescue StandardError => e
-        Labimotion::ConState::ERROR
         Labimotion::Converter.logger.error ["jcamp_converter fail: #{id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
+        Labimotion::ConState::ERROR
       end
     end
 
@@ -227,6 +234,8 @@ module Labimotion
       new_prop = dataset.properties
       dsr.each do |ds|
         layer = layers[ds[:layer]]
+        next if layer.nil? || layer['fields'].nil?
+
         fields = layer['fields'].select{ |f| f['field'] == ds[:field] }
         fi = fields&.first
         idx = layer['fields'].find_index(fi)

data/lib/labimotion/libs/export_dataset.rb

@@ -1,5 +1,6 @@
 # frozen_string_literal: true
 require 'export_table'
+require 'labimotion/version'
 
 module Labimotion
   ## ExportDataset
@@ -100,10 +101,19 @@ module Labimotion
       cds = Container.find(id)
       cds.attachments.where(aasm_state: 'csv').each do |att|
         name = File.basename(att.filename, '.csv')
-        sheet = @xfile.workbook.add_worksheet(name: name)
-        File.open(att.store.path) do |fi|
-          fi.each_line do |line|
-            sheet.add_row(line.split(','))
+        sheet = @xfile.workbook.add_worksheet(name: name.slice(0, 25))
+
+        if Labimotion::IS_RAILS5 == true
+          File.open(att.store.path) do |fi|
+            fi.each_line do |line|
+              sheet.add_row(line.split(','))
+            end
+          end
+        else
+          File.open(att.attachment_url) do |fi|
+            fi.each_line do |line|
+              sheet.add_row(line.split(','))
+            end
           end
         end
       end

data/lib/labimotion/libs/nmr_mapper.rb

@@ -1,5 +1,6 @@
 # frozen_string_literal: true
 
+require 'labimotion/version'
 require 'labimotion/utils/utils'
 
 module Labimotion
@@ -7,8 +8,8 @@ module Labimotion
   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|
+      if Labimotion::IS_RAILS5 == true
+        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')
@@ -16,6 +17,17 @@ module Labimotion
             end
           end
         end
+      else
+        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
       end
       nil
     end

data/lib/labimotion/libs/nmr_mapper_repo.rb

@@ -1,18 +1,33 @@
 # frozen_string_literal: true
+require 'labimotion/version'
 require 'labimotion/utils/utils'
 
 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
+      if Labimotion::IS_RAILS5 == true
+        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
+      else
+        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
       end
+
       nil
     end
 

data/lib/labimotion/libs/template_hub.rb

@@ -43,11 +43,15 @@ module Labimotion
       error!('Cannot connect to Chemotion Repository', 401)
     end
 
-    def self.fetch_identifier(klass, identifier)
-      # body = { klass: klass, identifier: identifier }
-      response = HTTParty.get("#{uri('fetch')}?klass=#{klass}&identifier=#{identifier}", timeout: 10)
+    def self.fetch_identifier(klass, identifier, origin)
+      body = { klass: klass, identifier: identifier, origin: origin }
+      response = HTTParty.post(
+        uri('fetch'),
+        body: body,
+        timeout: 10
+      )
       # response.parsed_response if response.code == 200
-      JSON.parse(response.body) if response.code == 200
+      JSON.parse(response.body) if response.code == 201
     rescue StandardError => e
       Labimotion.log_exception(e)
       error!('Cannot connect to Chemotion Repository', 401)

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

@@ -36,6 +36,7 @@ module Labimotion
         when Labimotion::ConState::WAIT
           self.con_state = Labimotion::Converter.jcamp_converter(id)
         end
+        update_column(:con_state, con_state)
       end
     end
   end

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

@@ -23,7 +23,7 @@ module Labimotion
       uuid = SecureRandom.uuid
       props = args[:properties]
       props['pkg'] = Labimotion::Utils.pkg(props['pkg'])
-      props['identifier'] = klass.identifier
+      props['identifier'] = klass.identifier if klass.identifier.present?
       props['uuid'] = uuid
       props['klass'] = 'Dataset'
 

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

@@ -41,14 +41,13 @@ module Labimotion
 
     def save_segments(**args) # rubocop:disable Metrics/AbcSize, Metrics/CyclomaticComplexity
       return if args[:segments].nil?
-
       segments = []
-      args[:segments].each do |seg|
+      args[:segments]&.each do |seg|
         klass = Labimotion::SegmentKlass.find_by(id: seg['segment_klass_id'])
         uuid = SecureRandom.uuid
         props = seg['properties']
         props['pkg'] = Labimotion::Utils.pkg(props['pkg'])
-        props['identifier'] = identifier
+        props['identifier'] = klass.identifier if klass.identifier.present?
         props['uuid'] = uuid
         props['klass'] = 'Segment'
         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'])
@@ -59,7 +58,7 @@ module Labimotion
         next if segment.present?
 
         props['klass_uuid'] = klass.uuid
-        segment = Labimotion::Segment.create!(properties_release: klass.properties_release, segment_klass_id: seg['segment_klass_id'], element_type: Labimotion::Utils.element_name(self.class.name), element_id: self.id, properties: props, created_by: args[:current_user_id], uuid: uuid, klass_uuid: klass.uuid)
+        segment = Labimotion::Segment.create!(properties_release: klass.properties_release, segment_klass_id: seg['segment_klass_id'], element_type: self.class.name, element_id: self.id, properties: props, created_by: args[:current_user_id], uuid: uuid, klass_uuid: klass.uuid)
         segments.push(segment)
       end
       segments

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

@@ -23,5 +23,14 @@ module Labimotion
       end
       properties
     end
+
+    def migrate_workflow
+      return if properties_template.nil? || properties_release.nil?
+
+      return if properties_template['flow'].nil? && properties_release['flow'].nil?
+
+      update_column(:properties_template, split_workflow(properties_template)) if properties_template['flow']
+      update_column(:properties_release, split_workflow(properties_release)) if properties_release['flow']
+    end
   end
 end

data/lib/labimotion/models/element.rb

@@ -7,10 +7,12 @@ module Labimotion
   class Element < ApplicationRecord
     acts_as_paranoid
     self.table_name = :elements
-    include PgSearch::Model
+    include PgSearch if Labimotion::IS_RAILS5 == true
+    include PgSearch::Model if Labimotion::IS_RAILS5 == false
     include ElementUIStateScopes
     include Collectable
     ## include AnalysisCodes
+    include ElementCodes
     include Taggable
     include Workflow
     include Segmentable
@@ -57,7 +59,7 @@ module Labimotion
 
 
     def attachments
-      Attachment.where(attachable_id: self.id, attachable_type: 'Element')
+      Attachment.where(attachable_id: self.id, attachable_type: self.class.name)
     end
 
     def self.get_associated_samples(element_ids)

data/lib/labimotion/models/element_klass.rb

@@ -23,13 +23,5 @@ module Labimotion
       )
     end
 
-    def migrate_workflow
-      return if properties_template.nil? || properties_release.nil?
-
-      return if properties_template['flow'].nil? && properties_release['flow'].nil?
-
-      update_column(:properties_template, split_workflow(properties_template)) if properties_template['flow']
-      update_column(:properties_release, split_workflow(properties_release)) if properties_release['flow']
-    end
   end
 end

data/lib/labimotion/models/hub_log.rb

@@ -0,0 +1,8 @@
+# frozen_string_literal: true
+
+module Labimotion
+  class HubLog < ApplicationRecord
+    self.table_name = :hub_logs
+    belongs_to :klass, polymorphic: true, optional: true
+  end
+end

data/lib/labimotion/models/segment_klass.rb

@@ -6,6 +6,7 @@ module Labimotion
     self.table_name = :segment_klasses
     acts_as_paranoid
     include GenericKlassRevisions
+    include Workflow
     belongs_to :element_klass, class_name: 'Labimotion::ElementKlass'
     has_many :segments, dependent: :destroy, class_name: 'Labimotion::Segment'
     has_many :segment_klasses_revisions, dependent: :destroy, class_name: 'Labimotion::SegmentKlassesRevision'

data/lib/labimotion/utils/export.rb

@@ -22,6 +22,26 @@ module Labimotion
       fetch_many.call(klasses, {'created_by' => 'User'})
     end
 
+    def self.fetch_elements(collection, segments, attachments, fetch_many, fetch_one, fetch_containers)
+      fetch_many.call(collection.elements, {
+        'element_klass_id' => 'Labimotion::ElementKlass',
+        'created_by' => 'User',
+      })
+      fetch_many.call(collection.collections_elements, {
+              'collection_id' => 'Collection',
+              'element_id' => 'Labimotion::Element',
+      })
+      collection.elements.each do |element|
+
+        element, attachments = Labimotion::Export.fetch_properties(element, attachments, &fetch_one)
+        fetch_containers.call(element)
+        segment, @attachments = Labimotion::Export.fetch_segments(element, attachments, &fetch_one)
+        segments += segment if segment.present?
+      end
+
+      [segments, attachments]
+
+    end
 
     def self.fetch_segments(element, attachments, &fetch_one)
       element_type = element.class.name

data/lib/labimotion/version.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 module Labimotion
-  # VERSION = '0.1.4'
-  VERSION = '0.2.2'
-  IS_RAILS5 = false
+  IS_RAILS5 = true
+  VERSION = '0.3.0' if Labimotion::IS_RAILS5 == true
+  VERSION = '1.0.6' if Labimotion::IS_RAILS5 == false
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 0.2.2
+  version: 0.3.0
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-08-23 00:00:00.000000000 Z
+date: 2023-09-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -17,14 +17,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 6.1.7
+        version: 5.2.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 6.1.7
+        version: 5.2.0
 description: 
 email:
 - chia-lin.lin@kit.edu
@@ -84,6 +84,7 @@ files:
 - lib/labimotion/models/elements_element.rb
 - lib/labimotion/models/elements_revision.rb
 - lib/labimotion/models/elements_sample.rb
+- lib/labimotion/models/hub_log.rb
 - lib/labimotion/models/segment.rb
 - lib/labimotion/models/segment_klass.rb
 - lib/labimotion/models/segment_klasses_revision.rb