labimotion 0.1.12 → 0.1.15

checksums.yaml

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

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module Labimotion
   ## Generic Dataset API
   class GenericDatasetAPI < Grape::API

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
 
@@ -160,6 +187,33 @@ 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')
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          []
+        end
+      end
+
+      namespace :create_repo_klass do
+        desc 'create Generic Element Klass'
+        params do
+          requires :identifier, type: String, desc: 'Identifier'
+        end
+        post do
+          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 }
         end
       end
 
@@ -176,6 +230,9 @@ module Labimotion
         end
         post do
           deactivate_klass(params)
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          raise e
         end
       end
 
@@ -188,6 +245,9 @@ module Labimotion
         delete ':id' do
           delete_klass(params)
           status 201
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          raise e
         end
       end
 
@@ -197,14 +257,17 @@ module Labimotion
           requires :klass, type: String, desc: 'Klass', values: %w[ElementKlass SegmentKlass DatasetKlass]
           requires :id, type: Integer, desc: 'Klass ID'
           requires :properties_template, type: Hash
-          optional :is_release, type: Boolean, default: false
+          optional :release, type: String, default: 'draft', desc: 'release status', values: %w[draft major minor patch]
         end
         after_validation do
           authenticate_admin!(params[:klass].gsub(/(Klass)/, 's').downcase)
           @klz = fetch_klass(params[:klass], params[:id])
         end
         post do
-          update_template(params)
+          update_template(params, current_user)
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
+          raise e
         end
       end
 
@@ -216,10 +279,10 @@ module Labimotion
         optional :from_date, type: Integer, desc: 'created_date from in ms'
         optional :to_date, type: Integer, desc: 'created_date to in ms'
         optional :filter_created_at, type: Boolean, desc: 'filter by created at or updated at'
+        optional :sort_column, type: String, desc: 'sort by updated_at or selected layers property'
       end
       paginate per_page: 7, offset: 0, max_per_page: 100
       get do
-
         scope = list_serialized_elements(params, current_user)
 
         reset_pagination_page(scope)
@@ -235,6 +298,9 @@ 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'
@@ -262,6 +328,8 @@ module Labimotion
               attachments: Entities::AttachmentEntity.represent(element.attachments),
             }
           end
+        rescue StandardError => e
+          Labimotion.log_exception(e, current_user)
         end
       end
 

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/entities/generic_klass_entity.rb

@@ -4,7 +4,7 @@ require 'labimotion/entities/application_entity'
 module Labimotion
   # GenericKlassEntity
   class GenericKlassEntity < ApplicationEntity
-    expose :id, :uuid, :label, :desc, :properties_template, :properties_release, :is_active,
+    expose :id, :uuid, :label, :desc, :properties_template, :properties_release, :is_active, :version,
           :place, :released_at, :identifier, :sync_time, :created_by, :updated_by, :created_at, :updated_at
     expose_timestamps(timestamp_fields: [:released_at])
     expose_timestamps(timestamp_fields: [:created_at])

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/entities/klass_revision_entity.rb

@@ -3,7 +3,7 @@
 module Labimotion
   # KlassRevisionEntity
   class KlassRevisionEntity < ApplicationEntity
-    expose :id, :uuid, :properties_release, :released_at
+    expose :id, :uuid, :properties_release, :version, :released_at
 
     expose :klass_id do |object|
       klass_id = object.element_klass_id if object.respond_to? :element_klass_id

data/lib/labimotion/helpers/dataset_helpers.rb

@@ -15,8 +15,9 @@ 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['properties_template'] = response['properties_release']
+      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']
       attributes['place'] = ((Labimotion::DatasetKlass.all.length * 10) || 0) + 10
       attributes['is_active'] = false
       attributes['updated_by'] = current_user.id
@@ -27,8 +28,9 @@ 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)
     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 +20,10 @@ 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?
+      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
@@ -33,8 +32,8 @@ 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')
+      new_klass.create_klasses_revision(current_user)
+      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 +67,12 @@ 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'
+      params[:properties]['identifier'] = klass[:identifier]
       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 +109,14 @@ 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
@@ -168,8 +168,8 @@ module Labimotion
       (attach_ary << att_ary).flatten! unless att_ary&.empty?
 
       if Labimotion::IS_RAILS5 == true
-        TransferThumbnailToPublicJob.set(queue: "transfer_thumbnail_to_public_#{current_user.id}").perform_later(attach_ary) unless attach_ary.empty?
-        TransferFileFromTmpJob.set(queue: "transfer_file_from_tmp_#{current_user.id}").perform_later(attach_ary) unless attach_ary.empty?
+        TransferThumbnailToPublicJob.set(queue: "transfer_thumbnail_to_public_#{current_user.id}").perform_now(attach_ary) unless attach_ary.empty?
+        TransferFileFromTmpJob.set(queue: "transfer_file_from_tmp_#{current_user.id}").perform_now(attach_ary) unless attach_ary.empty?
       end
       true
     rescue StandardError => e
@@ -180,7 +180,7 @@ module Labimotion
     def element_revisions(params)
       klass = Labimotion::Element.find(params[:id])
       list = klass.elements_revisions unless klass.nil?
-      list&.sort_by(&:created_at)&.reverse
+      list&.sort_by(&:created_at)&.reverse&.first(10)
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       raise e
@@ -245,7 +245,7 @@ module Labimotion
           .where(
             element_klasses: { name: params[:el_type] },
             collections_elements: { collection_id: collection_id },
-          ).includes(:tag, collections: :sync_collections_users).order('created_at DESC')
+          ).includes(:tag, collections: :sync_collections_users)
       else
         Labimotion::Element.none
       end
@@ -254,14 +254,65 @@ module Labimotion
       from = params[:from_date]
       to = params[:to_date]
       by_created_at = params[:filter_created_at] || false
-      scope = scope.created_time_from(Time.at(from)) if from && by_created_at
-      scope = scope.created_time_to(Time.at(to) + 1.day) if to && by_created_at
-      scope = scope.updated_time_from(Time.at(from)) if from && !by_created_at
-      scope = scope.updated_time_to(Time.at(to) + 1.day) if to && !by_created_at
+      if params[:sort_column]&.include?('.')
+        layer, field = params[:sort_column].split('.')
+
+        element_klass = Labimotion::ElementKlass.find_by(name: params[:el_type])
+        allowed_fields = element_klass.properties_release.dig('layers', layer, 'fields')&.pluck('field') || []
+
+        if field.in?(allowed_fields)
+          query = ActiveRecord::Base.sanitize_sql(
+            [
+              "LEFT JOIN LATERAL(
+                SELECT field->'value' AS value
+                FROM jsonb_array_elements(properties->'layers'->:layer->'fields') a(field)
+                WHERE field->>'field' = :field
+              ) a ON true",
+              { layer: layer, field: field },
+            ],
+          )
+          scope = scope.joins(query).order('value ASC NULLS FIRST')
+        else
+          scope = scope.order(updated_at: :desc)
+        end
+      else
+        scope = scope.order(updated_at: :desc)
+      end
+
+      scope = scope.elements_created_time_from(Time.at(from)) if from && by_created_at
+      scope = scope.elements_created_time_to(Time.at(to) + 1.day) if to && by_created_at
+      scope = scope.elements_updated_time_from(Time.at(from)) if from && !by_created_at
+      scope = scope.elements_updated_time_to(Time.at(to) + 1.day) if to && !by_created_at
       scope
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       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')
+      attributes['properties_release']['identifier'] = attributes['identifier']
+      attributes['properties_template'] = attributes['properties_release']
+      attributes['place'] = ((Labimotion::DatasetKlass.all.length * 10) || 0) + 10
+      attributes['is_active'] = false
+      attributes['updated_by'] = current_user.id
+      attributes['sync_by'] = current_user.id
+      attributes['sync_time'] = DateTime.now
+
+      element_klass = Labimotion::ElementKlass.find_by(identifier: attributes['identifier'])
+      if element_klass.present?
+        element_klass.update!(attributes)
+      else
+        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
+
   end
 end

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
@@ -41,23 +41,22 @@ module Labimotion
       raise e
     end
 
-    def update_template(params)
+    def update_template(params, current_user)
       klz = fetch_klass(params[:klass], params[:id])
       uuid = SecureRandom.uuid
       properties = params[:properties_template]
-      if Labimotion::IS_RAILS5 == false
-        properties['uuid'] = uuid unless params[:is_release] == true && @klz.identifier.present?
-      else
-        properties['uuid'] = uuid
-      end
-      properties['eln'] = Chemotion::Application.config.version
-      properties['labimotion'] = Labimotion::VERSION
-      properties['klass'] = @klz.class.name
+      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 && klz.properties_template['pkg']))
+      properties['klass'] = klz.class.name.split('::').last
+      properties['identifier'] = klz.identifier
+      properties.delete('eln') if properties['eln'].present?
       klz.updated_by = current_user.id
       klz.properties_template = properties
       klz.save!
       klz.reload
-      klz.create_klasses_revision(current_user.id) if params[:is_release] == true
+      klz.create_klasses_revision(current_user) if params[:release] != 'draft'
       klz
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
@@ -89,7 +88,7 @@ module Labimotion
     def list_klass_revisions(params)
       klass = "Labimotion::#{params[:klass]}".constantize.find_by(id: params[:id])
       list = klass.send("#{params[:klass].underscore}es_revisions") unless klass.nil?
-      list.sort_by(&:released_at).reverse
+      list&.order(released_at: :desc)&.limit(10)
     rescue StandardError => e
       Labimotion.log_exception(e, current_user)
       raise e
@@ -97,12 +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
@@ -193,37 +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
 
@@ -246,7 +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