labimotion 0.2.0 → 0.2.1

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: f80c183c86ccc07a012df8b1aaafdcd4fee0bf2663e1c6096d02792bf42b91d0
+  data.tar.gz: 23bcd1152eed5ceb0d7596e7f60ae6f302d6bef48d2c6972f450ff9b205e0a6f
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+  data.tar.gz: fb8118dc73c028fd4fe693cf4fbacf8124d474f4ecdbf0c14412deef615ef52648d2ce6b0d919087d72f564e24d22e78cebb0a8cc0ae6b521a8747dee074d762

data/lib/labimotion/helpers/dataset_helpers.rb

@@ -15,7 +15,7 @@ module Labimotion
 
     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') # .except(:id, :is_active, :place, :created_by, :created_at, :updated_at)
+      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_template'] = response['properties_release']
       attributes['place'] = ((Labimotion::DatasetKlass.all.length * 10) || 0) + 10
       attributes['is_active'] = false
@@ -27,8 +27,9 @@ module Labimotion
         ds.update!(attributes)
       else
         attributes['created_by'] = current_user.id
-        Labimotion::DatasetKlass.create!(attributes)
+        ds = Labimotion::DatasetKlass.create!(attributes)
       end
+      ds.create_klasses_revision(current_user.id)
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       # { error: e.message }

data/lib/labimotion/helpers/element_helpers.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 require 'grape'
-require 'labimotion/version'
+require 'labimotion/utils/utils'
 # require 'labimotion/models/element_klass'
 module Labimotion
   ## ElementHelpers
@@ -20,11 +20,12 @@ module Labimotion
       uuid = SecureRandom.uuid
       template = { uuid: uuid, layers: {}, select_options: {} }
       attributes = declared(params, include_missing: false)
-      attributes[:properties_template]['uuid'] = uuid if attributes[:properties_template].present?
-      attributes[:properties_template] = template unless attributes[:properties_template].present?
-      attributes[:properties_template]['eln'] = Chemotion::Application.config.version if attributes[:properties_template].present?
-      attributes[:properties_template]['labimotion'] = Labimotion::VERSION if attributes[:properties_template].present?
-      attributes[:properties_template]['klass'] = 'ElementKlass' if attributes[:properties_template].present?
+      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[:is_active] = false
       attributes[:uuid] = uuid
       attributes[:released_at] = DateTime.now
@@ -34,7 +35,7 @@ module Labimotion
       new_klass = Labimotion::ElementKlass.create!(attributes)
       new_klass.reload
       new_klass.create_klasses_revision(current_user.id)
-      klass_names_file = Rails.root.join('config', 'klasses.json')
+      klass_names_file = Rails.root.join('app/packs/klasses.json')
       klasses = Labimotion::ElementKlass.where(is_active: true)&.pluck(:name) || []
       File.write(klass_names_file, klasses)
       klasses
@@ -68,11 +69,11 @@ module Labimotion
       uuid = SecureRandom.uuid
       params[:properties]['uuid'] = uuid
       params[:properties]['klass_uuid'] = klass[:uuid]
-      params[:properties]['eln'] = Chemotion::Application.config.version
-      params[:properties]['labimotion'] = Labimotion::VERSION
+      params[:properties]['pkg'] = Labimotion::Utils.pkg(params[:properties]['pkg'])
       params[:properties]['klass'] = 'Element'
       properties = params[:properties]
       properties.delete('flow') unless properties['flow'].nil?
+      properties.delete('flowObject') unless properties['flowObject'].nil?
       properties.delete('select_options') unless properties['select_options'].nil?
       attributes = {
         name: params[:name],
@@ -109,14 +110,14 @@ module Labimotion
       params.delete(:container)
       params.delete(:properties)
       attributes = declared(params.except(:segments), include_missing: false)
-      properties['eln'] = Chemotion::Application.config.version
-      properties['labimotion'] = Labimotion::VERSION
+      properties['pkg'] = Labimotion::Utils.pkg(properties['pkg'])
       if element.klass_uuid != properties['klass_uuid'] || element.properties != properties || element.name != params[:name]
         properties['klass'] = 'Element'
         uuid = SecureRandom.uuid
         properties['uuid'] = uuid
 
         properties.delete('flow') unless properties['flow'].nil?
+        properties.delete('flowObject') unless properties['flowObject'].nil?
         properties.delete('select_options') unless properties['select_options'].nil?
 
         attributes['properties'] = properties
@@ -267,7 +268,7 @@ module Labimotion
 
     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') # .except(:id, :is_active, :place, :created_by, :created_at, :updated_at)
+      attributes = response.slice('name', 'label', 'desc', 'icon_name', 'klass_prefix', 'is_generic', 'identifier', 'properties_release', 'version') # .except(:id, :is_active, :place, :created_by, :created_at, :updated_at)
       attributes['properties_template'] = response['properties_release']
       attributes['place'] = ((Labimotion::DatasetKlass.all.length * 10) || 0) + 10
       attributes['is_active'] = false
@@ -280,8 +281,9 @@ module Labimotion
         element_klass.update!(attributes)
       else
         attributes['created_by'] = current_user.id
-        Labimotion::ElementKlass.create!(attributes)
+        element_klass = Labimotion::ElementKlass.create!(attributes)
       end
+      element_klass.create_klasses_revision(current_user.id)
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       # { error: e.message }

data/lib/labimotion/helpers/generic_helpers.rb

@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 require 'grape'
-require 'labimotion/version'
+require 'labimotion/utils/utils'
 # Helper for associated sample
 module Labimotion
   ## Generic Helpers
@@ -45,34 +45,13 @@ module Labimotion
       klz = fetch_klass(params[:klass], params[:id])
       uuid = SecureRandom.uuid
       properties = params[:properties_template]
-      if Labimotion::IS_RAILS5 == false
-        properties['uuid'] = uuid unless params[:release] != 'draft' && @klz.identifier.present?
-      else
-        properties['uuid'] = uuid
-      end
-
-      klz.version =
-        case params[:release]
-        when 'draft'
-          klz.version
-        when 'major'
-          if klz.version.nil? || klz.version&.split('.').length < 2
-            '1.0'
-          else
-            "#{klz.version&.split('.').first.to_i + 1}.0"
-          end
-        when 'minor'
-          if klz.version.nil? || klz.version&.split('.').length < 2
-            '0.1'
-          else
-            "#{klz.version.split('.').first.to_i.to_s}.#{klz.version.split('.').last.to_i + 1}"
-          end
-        end
+      properties['uuid'] = uuid
 
+      klz.version = Labimotion::Utils.next_version(params[:release], klz.version)
       properties['version'] = klz.version
-      properties['eln'] = Chemotion::Application.config.version
-      properties['labimotion'] = Labimotion::VERSION
-      properties['klass'] = @klz.class.name.split('::').last
+      properties['pkg'] = Labimotion::Utils.pkg(params['pkg'] || klz.properties_template['pkg'])
+      properties['klass'] = klz.class.name.split('::').last
+      properties.delete('eln') if properties['eln'].present?
       klz.updated_by = current_user.id
       klz.properties_template = properties
       klz.save!
@@ -117,12 +96,8 @@ module Labimotion
 
 
     ###############
-
-
     def generate_klass_file
-      klass_dir = File.join(Rails.root, 'data')
-      !File.directory?(klass_dir) && FileUtils.mkdir_p(klass_dir)
-      klass_names_file = File.join(klass_dir, 'klasses.json')
+      klass_names_file = Rails.root.join('app/packs/klasses.json')
       klasses = Labimotion::ElementKlass.where(is_active: true)&.pluck(:name) || []
       File.write(klass_names_file, klasses)
     rescue StandardError => e
@@ -266,7 +241,7 @@ module Labimotion
       filter_list || []
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
-      raise e
+      { error: 'Cannot connect to Chemotion Repository' }
     end
   end
 end

data/lib/labimotion/helpers/segment_helpers.rb

@@ -1,6 +1,8 @@
 # frozen_string_literal: true
 require 'grape'
 require 'labimotion/models/segment_klass'
+require 'labimotion/utils/utils'
+
 module Labimotion
   ## ElementHelpers
   module SegmentHelpers
@@ -26,8 +28,7 @@ module Labimotion
       attributes = declared(params, include_missing: false)
       attributes[:properties_template]['uuid'] = uuid if attributes[:properties_template].present?
       template = (attributes[:properties_template].presence || template)
-      template['eln'] = Chemotion::Application.config.version
-      template['labimotion'] = Labimotion::VERSION
+      template['pkg'] = Labimotion::Utils.pkg(template['pkg'])
       template['klass'] = 'SegmentKlass'
       attributes.merge!(properties_template: template, element_klass: @klass, created_by: current_user.id,
                         place: place)
@@ -64,7 +65,7 @@ module Labimotion
 
     def create_repo_klass(params, current_user)
       response = Labimotion::TemplateHub.fetch_identifier('SegmentKlass', params[:identifier])
-      attributes = response.slice('label', 'desc', 'uuid', 'identifier', 'released_at') # .except(:id, :is_active, :place, :created_by, :created_at, :updated_at)
+      attributes = response.slice('label', 'desc', 'uuid', 'identifier', 'released_at', 'properties_release', 'version') # .except(:id, :is_active, :place, :created_by, :created_at, :updated_at)
       attributes['properties_template'] = response['properties_release']
       attributes['place'] = ((Labimotion::SegmentKlass.all.length * 10) || 0) + 10
       attributes['is_active'] = false
@@ -86,8 +87,9 @@ module Labimotion
         segment_klass.update!(attributes)
       else
         attributes['created_by'] = current_user.id
-        Labimotion::SegmentKlass.create!(attributes)
+        segment_klass = Labimotion::SegmentKlass.create!(attributes)
       end
+      segment_klass.create_klasses_revision(current_user.id)
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       raise e

data/lib/labimotion/libs/converter.rb

@@ -4,7 +4,7 @@ require 'net/http'
 require 'uri'
 require 'json'
 require 'date'
-require 'labimotion/version'
+require 'labimotion/utils/utils'
 
 # rubocop: disable Metrics/AbcSize
 # rubocop: disable Metrics/MethodLength
@@ -209,8 +209,7 @@ module Labimotion
       uuid = SecureRandom.uuid
       props = klass.properties_release
       props['uuid'] = uuid
-      props['eln'] = Chemotion::Application.config.version
-      props['labimotion'] = Labimotion::VERSION
+      props['pkg'] = Labimotion::Utils.pkg(props['pkg'])
       props['klass'] = 'Dataset'
       Labimotion::Dataset.create!(
         uuid: uuid,

data/lib/labimotion/libs/nmr_mapper.rb

@@ -1,5 +1,7 @@
 # frozen_string_literal: true
 
+require 'labimotion/utils/utils'
+
 module Labimotion
   ## NmrMapper
   class NmrMapper
@@ -247,8 +249,7 @@ module Labimotion
       uuid = SecureRandom.uuid
       props = klass.properties_release
       props['uuid'] = uuid
-      props['eln'] = Chemotion::Application.config.version
-      props['labimotion'] = Labimotion::VERSION
+      props['pkg'] = Labimotion::Utils.pkg(props['pkg'])
       props['klass'] = 'Dataset'
       dataset = Labimotion::Dataset.create!(
         uuid: uuid,

data/lib/labimotion/libs/nmr_mapper_repo.rb

@@ -1,4 +1,5 @@
 # frozen_string_literal: true
+require 'labimotion/utils/utils'
 
 module Labimotion
   class NmrMapperRepo
@@ -245,8 +246,7 @@ module Labimotion
       uuid = SecureRandom.uuid
       props = klass.properties_release
       props['uuid'] = uuid
-      props['eln'] = Chemotion::Application.config.version
-      props['labimotion'] = Labimotion::VERSION
+      props['pkg'] = Labimotion::Utils.pkg(props['pkg'])
       props['klass'] = 'Dataset'
       dataset = Labimotion::Dataset.create!(
         uuid: uuid,

data/lib/labimotion/libs/template_hub.rb

@@ -20,7 +20,7 @@ module Labimotion
 
 
     def self.header(opt = {})
-      opt || { :timeout => 10,  :headers => {'Content-Type' => 'text/json'}  }
+      opt || { timeout: 10, headers: { 'Content-Type' => 'text/json' } }
     end
 
     def self.handle_response(oat, response) # rubocop: disable Metrics/PerceivedComplexity
@@ -35,16 +35,22 @@ module Labimotion
 
     def self.list(klass)
       body = { klass: klass }
-      response = HTTParty.get("#{uri('list')}?klass=#{klass}", header)
+      response = HTTParty.get("#{uri('list')}?klass=#{klass}", timeout: 10)
       # response.parsed_response if response.code == 200
       JSON.parse(response.body) if response.code == 200
+    rescue StandardError => e
+      Labimotion.log_exception(e)
+      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}", header)
+      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 == 200
+    rescue StandardError => e
+      Labimotion.log_exception(e)
+      error!('Cannot connect to Chemotion Repository', 401)
     end
   end
 end

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

@@ -1,6 +1,7 @@
 # frozen_string_literal: true
 
 # Datasetable concern
+require 'labimotion/utils/utils'
 
 module Labimotion
   ## Datasetable concern
@@ -21,23 +22,17 @@ module Labimotion
       klass = Labimotion::DatasetKlass.find_by(id: args[:dataset_klass_id])
       uuid = SecureRandom.uuid
       props = args[:properties]
-      props['eln'] = Chemotion::Application.config.version
-      props['labimotion'] = Labimotion::VERSION
+      props['pkg'] = Labimotion::Utils.pkg(props['pkg'])
+      props['uuid'] = uuid
+      props['klass'] = 'Dataset'
+
       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)
-        props['uuid'] = uuid
-        props['eln'] = Chemotion::Application.config.version
-        props['labimotion'] = Labimotion::VERSION
-        props['klass'] = 'Dataset'
         ds.update!(properties_release: klass.properties_release, uuid: uuid, dataset_klass_id: args[:dataset_klass_id], properties: props, klass_uuid: props['klass_uuid'])
       end
       return if ds.present?
 
-      props['uuid'] = uuid
       props['klass_uuid'] = klass.uuid
-      props['eln'] = Chemotion::Application.config.version
-      props['labimotion'] = Labimotion::VERSION
-      props['klass'] = 'Dataset'
       Labimotion::Dataset.create!(properties_release: klass.properties_release, uuid: uuid, dataset_klass_id: args[:dataset_klass_id], element_type: self.class.name, element_id: id, properties: props, klass_uuid: klass.uuid)
     end
 

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

@@ -9,22 +9,20 @@ module Labimotion
 
     def create_klasses_revision(user_id=0)
       properties_release = properties_template
-      # (properties_release['layers'] || {}).keys.each do |key|
-      #   properties_release['layers'][key]['layer'] = properties_release['layers'][key]['key']
-      # end
+      migrate_workflow if properties_release['flow'].present?
 
-      if properties_release['flow'].present?
-        elements = (properties_release['flow']['elements'] || []).map do |el|
+      if properties_release['flowObject'].present?
+        elements = (properties_release['flowObject']['nodes'] || []).map do |el|
           if el['data'].present? && el['data']['lKey'].present?
             layer = properties_release['layers'][el['data']['lKey']]
             el['data']['layer'] = layer if layer.present?
           end
           el
         end
-        properties_release['flow']['elements'] = elements
+        properties_release['flowObject']['nodes'] = elements
       end
 
-      self.update!({ uuid: properties_template['uuid'], properties_release: properties_release, released_at: DateTime.now })
+      self.update!({ uuid: properties_template['uuid'], properties_template: properties_release, properties_release: properties_release, released_at: DateTime.now })
       reload
       attributes = {
         released_by: user_id,

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

@@ -1,5 +1,7 @@
 # frozen_string_literal: true
 
+require 'labimotion/utils/utils'
+
 module Labimotion
   # Segmentable concern
   module Segmentable
@@ -45,25 +47,17 @@ module Labimotion
         klass = Labimotion::SegmentKlass.find_by(id: seg['segment_klass_id'])
         uuid = SecureRandom.uuid
         props = seg['properties']
-        props['eln'] = Chemotion::Application.config.version
-        props['labimotion'] = Labimotion::VERSION
+        props['pkg'] = Labimotion::Utils.pkg(props['pkg'])
+        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'])
         if segment.present? && (segment.klass_uuid != props['klass_uuid'] || segment.properties != props)
-          props['uuid'] = uuid
-          props['eln'] = Chemotion::Application.config.version
-          props['labimotion'] = Labimotion::VERSION
-          props['klass'] = 'Segment'
-
           segment.update!(properties_release: klass.properties_release, properties: props, uuid: uuid, klass_uuid: props['klass_uuid'])
           segments.push(segment)
         end
         next if segment.present?
 
-        props['uuid'] = uuid
         props['klass_uuid'] = klass.uuid
-        props['eln'] = Chemotion::Application.config.version
-        props['labimotion'] = Labimotion::VERSION
-        props['klass'] = 'Segment'
         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

data/lib/labimotion/models/element_klass.rb

@@ -23,7 +23,6 @@ module Labimotion
       )
     end
 
-
     def migrate_workflow
       return if properties_template.nil? || properties_release.nil?
 
@@ -32,8 +31,5 @@ module Labimotion
       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
-
-    private
-
   end
 end

data/lib/labimotion/utils/utils.rb

@@ -1,5 +1,6 @@
 # frozen_string_literal: true
 
+require 'labimotion/version'
 module Labimotion
   ## Generic Utils
   class Utils
@@ -54,5 +55,37 @@ module Labimotion
     def self.element_name_dc(name)
       Labimotion::Utils.element_name(name)&.downcase
     end
+
+    def self.next_version(release, current_version)
+      case release
+      when 'draft'
+        current_version
+      when 'major'
+        if current_version.nil? || current_version.split('.').length < 2
+          '1.0'
+        else
+          "#{current_version&.split('.').first.to_i + 1}.0"
+        end
+      when 'minor'
+        if current_version.nil? || current_version&.split('.').length < 2
+          '0.1'
+        else
+          "#{current_version&.split('.').first.to_i.to_s}.#{current_version&.split('.').last.to_i + 1}"
+        end
+      else
+        current_version
+      end
+    rescue StandardError => e
+      Labimotion.log_exception(e)
+      current_version
+    end
+
+    def self.pkg(pkg)
+byebug
+      pkg = {} if pkg.nil?
+      pkg['eln'] = Chemotion::Application.config.version
+      pkg['labimotion'] = Labimotion::VERSION
+      pkg
+    end
   end
 end

data/lib/labimotion/version.rb

@@ -2,6 +2,6 @@
 
 module Labimotion
   # VERSION = '0.1.4'
-  VERSION = '0.2.0'
+  VERSION = '0.2.1'
   IS_RAILS5 = false
 end

data/lib/labimotion.rb

@@ -7,7 +7,7 @@ module Labimotion
     @@labimotion_logger ||= Logger.new(Rails.root.join('log/labimotion.log')) # rubocop:disable Style/ClassVars
   end
 
-  def self.log_exception(exception, current_user = {})
+  def self.log_exception(exception, current_user = nil)
     Labimotion.logger.error("version: #{Labimotion::VERSION}; #{Labimotion::IS_RAILS5}, (#{current_user&.id}) \n Exception: #{exception.message}")
     Labimotion.logger.error(exception.backtrace.join("\n"))
   end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.2.1
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-08-22 00:00:00.000000000 Z
+date: 2023-08-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -114,7 +114,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.6
+rubygems_version: 3.4.18
 signing_key: 
 specification_version: 4
 summary: Chemotion LabIMotion