labimotion 0.3.1 → 1.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 5b8192a47d907ab3aab31d14c951ccfe6a9552f04cc57896dffc592d850c90d0
-  data.tar.gz: 54be5a8e125a16ebbb8ee8ac48de31e42678c9473da2c7c2e32394585b746ffa
+  metadata.gz: 387a4b4a47a140008970b10f005472e8ba882c80ddaab99863ced5acdb0dfa29
+  data.tar.gz: 90f5839a92d045e45861a2354354bf5ef1542799a484cda94fa9c1263c206d5e
 SHA512:
-  metadata.gz: 1cb3dd9177e8799a2a07c3454587f6ae7d925e99dd22ce0423a3513cf8992def50d7f900992d9c4db217617473b4ec87b0dcdc02551e3841ba66183efae6159d
-  data.tar.gz: 595b810eee22f50e8ef15db20b2a8b37dc6ad14b2d05d0362568cd235be2cf7358b0ca089722ac09c364a57a5d9e64992fbba5afa342182f9647a602b292467e
+  metadata.gz: cca4c43074754aefbe3f2b3ca09b55af69d25ebf2a4b7f456990bc692ee7ab19905020aed4505d6360b720d94e497e91ab5910b8c50d4b5b914a01d23e840796
+  data.tar.gz: 5280180e034e2bd2a38000b62e8001ebee247cae2dd29e30f5b66eb3292d11e0e9f0566986c5eb918e6f6dcfc9d95024553204d834da44e7a1aee2b13500d454

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

data/lib/labimotion/apis/generic_element_api.rb

@@ -21,9 +21,6 @@ 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
 
@@ -35,9 +32,6 @@ 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
 
@@ -73,9 +67,6 @@ 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
 
@@ -88,9 +79,6 @@ 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
 
@@ -102,9 +90,6 @@ 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
 
@@ -119,9 +104,6 @@ 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
 
@@ -135,9 +117,6 @@ module Labimotion
         post do
           delete_revision(params)
           status 201
-        rescue StandardError => e
-          Labimotion.log_exception(e, current_user)
-          raise e
         end
       end
 
@@ -150,9 +129,6 @@ 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
 
@@ -176,9 +152,6 @@ module Labimotion
         post do
           upload_generics_files(current_user, params)
           true
-        rescue StandardError => e
-          Labimotion.log_exception(e, current_user)
-          raise e
         end
       end
 
@@ -187,19 +160,13 @@ 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', current_user)
-        rescue StandardError => e
-          Labimotion.log_exception(e, current_user)
-          []
+          fetch_repo('ElementKlass')
         end
       end
 
@@ -209,9 +176,8 @@ module Labimotion
           requires :identifier, type: String, desc: 'Identifier'
         end
         post do
-          msg = create_repo_klass(params, current_user, request.headers['Origin'])
-          klass = Labimotion::ElementKlassEntity.represent(ElementKlass.all)
-          { status: msg[:status], message: msg[:message], klass: klass }
+          create_repo_klass(params, current_user)
+          present ElementKlass.all, with: Labimotion::ElementKlassEntity, root: 'klass'
         rescue StandardError => e
           Labimotion.log_exception(e, current_user)
           { error: e.message }
@@ -231,9 +197,6 @@ module Labimotion
         end
         post do
           deactivate_klass(params)
-        rescue StandardError => e
-          Labimotion.log_exception(e, current_user)
-          raise e
         end
       end
 
@@ -246,9 +209,6 @@ module Labimotion
         delete ':id' do
           delete_klass(params)
           status 201
-        rescue StandardError => e
-          Labimotion.log_exception(e, current_user)
-          raise e
         end
       end
 
@@ -266,9 +226,6 @@ module Labimotion
         end
         post do
           update_template(params, current_user)
-        rescue StandardError => e
-          Labimotion.log_exception(e, current_user)
-          raise e
         end
       end
 
@@ -299,9 +256,6 @@ 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'
@@ -318,7 +272,7 @@ module Labimotion
           if Labimotion::IS_RAILS5 == true
             {
               element: ElementPermissionProxy.new(current_user, element, user_ids).serialized,
-              attachments: attach_thumbnail(element&.attachments)
+              attachments: Entities::AttachmentEntity.represent(element.attachments)
             }
           else
             {
@@ -326,11 +280,9 @@ module Labimotion
                 element,
                 detail_levels: ElementDetailLevelCalculator.new(user: current_user, element: element).detail_levels,
               ),
-              attachments: attach_thumbnail(element&.attachments)
+              attachments: Entities::AttachmentEntity.represent(element.attachments),
             }
           end
-        rescue StandardError => e
-          Labimotion.log_exception(e, current_user)
         end
       end
 
@@ -350,7 +302,7 @@ module Labimotion
           if Labimotion::IS_RAILS5 == true
             {
               element: ElementPermissionProxy.new(current_user, element, user_ids).serialized,
-              attachments: attach_thumbnail(element&.attachments)
+              attachments: Entities::AttachmentEntity.represent(element.attachments)
             }
           else
             present(
@@ -386,7 +338,7 @@ module Labimotion
             if Labimotion::IS_RAILS5 == true
               {
                 element: ElementPermissionProxy.new(current_user, element, user_ids).serialized,
-                attachments: attach_thumbnail(element&.attachments)
+                attachments: Entities::AttachmentEntity.represent(element.attachments)
               }
             else
               {
@@ -394,7 +346,7 @@ module Labimotion
                   element,
                   detail_levels: ElementDetailLevelCalculator.new(user: current_user, element: element).detail_levels,
                 ),
-                attachments: attach_thumbnail(element&.attachments),
+                attachments: Entities::AttachmentEntity.represent(element.attachments),
               }
             end
           rescue StandardError => e

data/lib/labimotion/apis/labimotion_hub_api.rb

@@ -1,7 +1,6 @@
 # frozen_string_literal: true
 
 require 'open-uri'
-require 'labimotion/models/hub_log'
 
 # Belong to Chemotion module
 module Labimotion
@@ -20,25 +19,20 @@ 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])
-        rescue StandardError => e
-          Labimotion.log_exception(e, current_user)
-          []
+          # entities.length > 1 ? de_encode_json(entities) : []
         end
       end
       namespace :fetch do
         desc "get active generic templates"
         params do
           requires :klass, type: String, desc: 'Klass', values: %w[ElementKlass SegmentKlass DatasetKlass]
-          requires :origin, type: String, desc: 'origin'
+          # requires :fqdn, type: Integer, desc: 'FQDN'
           requires :identifier, type: String, desc: 'Identifier'
         end
-        post do
+        get 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)
-        rescue StandardError => e
-          Labimotion.log_exception(e, current_user)
-          raise e
+          # entities.length > 1 ? de_encode_json(entities) : []
         end
       end
 
@@ -51,9 +45,6 @@ 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', current_user)
+          fetch_repo('SegmentKlass')
         rescue StandardError => e
           Labimotion.log_exception(e, current_user)
           { error: e.message }
@@ -131,9 +131,8 @@ module Labimotion
           requires :identifier, type: String, desc: 'Identifier'
         end
         post do
-          msg = create_repo_klass(params, current_user, request.headers['Origin'])
-          klass = Labimotion::SegmentKlassEntity.represent(SegmentKlass.all)
-          { status: msg[:status], message: msg[:message], klass: klass }
+          create_repo_klass(params, current_user)
+          present SegmentKlass.all, with: Labimotion::SegmentKlassEntity, root: 'klass'
         rescue StandardError => e
           Labimotion.log_exception(e, current_user)
           ## { error: e.message }

data/lib/labimotion/entities/generic_public_entity.rb

@@ -5,7 +5,6 @@ require 'labimotion/entities/application_entity'
 # Entity module
 module Labimotion
   class GenericPublicEntity < Labimotion::ApplicationEntity
-    expose! :uuid
     expose! :name
     expose! :desc
     expose! :icon_name
@@ -13,7 +12,6 @@ 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, origin)
-      response = Labimotion::TemplateHub.fetch_identifier('DatasetKlass', params[:identifier], origin)
+    def create_repo_klass(params, current_user)
+      response = Labimotion::TemplateHub.fetch_identifier('DatasetKlass', params[:identifier])
       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']
@@ -23,22 +23,14 @@ module Labimotion
       attributes['updated_by'] = current_user.id
       attributes['sync_by'] = current_user.id
       attributes['sync_time'] = DateTime.now
-      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
+      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)
       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

@@ -159,7 +159,7 @@ module Labimotion
         att_ary = create_attachments(
           params[:attfiles],
           params[:delfiles],
-          "Labimotion::#{params[:att_type]}",
+          params[:att_type],
           params[:att_id],
           params[:attfilesIdentifier],
           current_user.id
@@ -174,7 +174,8 @@ module Labimotion
       true
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
-      false
+      ## false
+      raise e
     end
 
     def element_revisions(params)
@@ -289,9 +290,9 @@ module Labimotion
       raise e
     end
 
-    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')
+    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')
       attributes['properties_release']['identifier'] = attributes['identifier']
       attributes['properties_template'] = attributes['properties_release']
       attributes['place'] = ((Labimotion::DatasetKlass.all.length * 10) || 0) + 10
@@ -302,38 +303,17 @@ module Labimotion
 
       element_klass = Labimotion::ElementKlass.find_by(identifier: attributes['identifier'])
       if element_klass.present?
-        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
+        element_klass.update!(attributes)
       else
-        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
+        attributes['created_by'] = current_user.id
+        element_klass = Labimotion::ElementKlass.create!(attributes)
       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

@@ -193,7 +193,7 @@ module Labimotion
       (files || []).each_with_index do |file, index|
         next unless (tempfile = file[:tempfile])
 
-        att = Attachment.new(
+        a = Attachment.new(
           bucket: file[:container_id],
           filename: file[:filename],
           con_state: Labimotion::ConState::NONE,
@@ -205,7 +205,7 @@ module Labimotion
           attachable_type: type,
           attachable_id: id,
         )
-        begin
+        ActiveRecord::Base.transaction do
           att.save!
           attach_ary.push(att.id)
         ensure
@@ -214,11 +214,12 @@ module Labimotion
         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)
+      Labimotion.log_exception(e, current_user)
       raise e
     end
 
@@ -230,16 +231,15 @@ module Labimotion
       Chemotion::Generic::Fetch::Template.list(API::TARGET, name)
     end
 
-    def fetch_repo(name, current_user)
-      # current_klasses = "Labimotion::#{name}".constantize.where.not(identifier: nil)&.pluck(:identifier) || []
+    def fetch_repo(name)
+      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 || []
-      (response && response['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 || []
     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, origin)
-      response = Labimotion::TemplateHub.fetch_identifier('SegmentKlass', params[:identifier], origin)
+    def create_repo_klass(params, current_user)
+      response = Labimotion::TemplateHub.fetch_identifier('SegmentKlass', params[:identifier])
       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'], 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?
+      element_klass = Labimotion::ElementKlass.find_by(name: response['element_klass']['name']) if element_klass.nil?
+      return { error: 'ElementKlass not found' } 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']
@@ -85,24 +85,12 @@ module Labimotion
       attributes['element_klass_id'] = element_klass.id
       segment_klass = Labimotion::SegmentKlass.find_by(identifier: attributes['identifier'])
       if segment_klass.present?
-        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
+        segment_klass.update!(attributes)
       else
-        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
+        attributes['created_by'] = current_user.id
+        segment_klass = Labimotion::SegmentKlass.create!(attributes)
       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

@@ -144,7 +144,8 @@ module Labimotion
     end
 
     def self.process(data)
-      return data[:a].con_state if data[:a]&.attachable_type != 'Container'
+      return if data[:a]&.attachable_type != 'Container'
+
       response = nil
       begin
         ofile = Rails.root.join(data[:f], data[:a].filename)
@@ -165,14 +166,12 @@ 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($INPUT_RECORD_SEPARATOR)
-          Labimotion::ConState::ERROR
         end
+        response
       rescue StandardError => e
-        Labimotion::Converter.logger.error ["process fail: #{id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
-        Labimotion::ConState::ERROR
+        raise e
       ensure
         FileUtils.rm_f(ofile)
       end
@@ -181,14 +180,14 @@ module Labimotion
     def self.jcamp_converter(id)
       resp = nil
       begin
-
         data = Labimotion::Converter.vor_conv(id)
         return if data.nil?
 
-        Labimotion::Converter.process(data)
+        resp = Labimotion::Converter.process(data)
+        resp&.success? ? Labimotion::ConState::PROCESSED : Labimotion::ConState::ERROR
       rescue StandardError => e
-        Labimotion::Converter.logger.error ["jcamp_converter fail: #{id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
         Labimotion::ConState::ERROR
+        Labimotion::Converter.logger.error ["jcamp_converter fail: #{id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
       end
     end
 
@@ -234,8 +233,6 @@ 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

@@ -101,7 +101,7 @@ 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.slice(0, 25))
+        sheet = @xfile.workbook.add_worksheet(name: name)
 
         if Labimotion::IS_RAILS5 == true
           File.open(att.store.path) do |fi|

data/lib/labimotion/libs/template_hub.rb

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

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

@@ -36,7 +36,6 @@ 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 if klass.identifier.present?
+      props['identifier'] = klass.identifier
       props['uuid'] = uuid
       props['klass'] = 'Dataset'
 

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

@@ -41,13 +41,14 @@ 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'] = klass.identifier if klass.identifier.present?
+        props['identifier'] = identifier
         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'])
@@ -58,7 +59,7 @@ 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: 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: 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)
         segments.push(segment)
       end
       segments

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

@@ -23,14 +23,5 @@ 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

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

data/lib/labimotion/models/element_klass.rb

@@ -23,5 +23,13 @@ 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/segment_klass.rb

@@ -1,13 +1,11 @@
 # frozen_string_literal: true
 require 'labimotion/models/concerns/generic_klass_revisions'
-require 'labimotion/models/concerns/workflow'
 
 module Labimotion
   class SegmentKlass < ApplicationRecord
     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

@@ -22,26 +22,6 @@ 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
-  IS_RAILS5 = true
-  VERSION = '0.3.1' if Labimotion::IS_RAILS5 == true
-  VERSION = '1.0.7' if Labimotion::IS_RAILS5 == false
+  # VERSION = '0.1.4'
+  VERSION = '1.0.0'
+  IS_RAILS5 = false
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 0.3.1
+  version: 1.0.0
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-09-10 00:00:00.000000000 Z
+date: 2023-08-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -17,14 +17,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 5.2.0
+        version: 6.1.7
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 5.2.0
+        version: 6.1.7
 description: 
 email:
 - chia-lin.lin@kit.edu
@@ -84,7 +84,6 @@ 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

data/lib/labimotion/models/hub_log.rb

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