labimotion 0.1.11 → 0.1.14

data/lib/labimotion/libs/converter.rb

@@ -5,6 +5,7 @@ require 'uri'
 require 'json'
 require 'date'
 require 'labimotion/version'
+require 'labimotion/utils/utils'
 
 # rubocop: disable Metrics/AbcSize
 # rubocop: disable Metrics/MethodLength
@@ -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
 
@@ -209,8 +216,7 @@ 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,
@@ -228,6 +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
@@ -101,9 +102,18 @@ module Labimotion
       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(','))
+
+        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

@@ -1,12 +1,15 @@
 # frozen_string_literal: true
 
+require 'labimotion/version'
+require 'labimotion/utils/utils'
+
 module Labimotion
   ## NmrMapper
   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')
@@ -14,6 +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
@@ -247,8 +261,7 @@ 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

@@ -1,17 +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
 
@@ -245,8 +261,7 @@ 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 || {}
+      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}")
+      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}")
+      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/attachment_converter.rb

@@ -9,7 +9,7 @@ module Labimotion
       before_create :init_converter
       after_update :exec_converter
       def init_converter
-        return if con_state.present?
+        return if self.has_attribute?(:con_state) == false || con_state.present?
         if Rails.configuration.try(:converter).try(:url) && ACCEPTED_FORMATS.include?(File.extname(filename&.downcase))
           self.con_state = Labimotion::ConState::WAIT
         end
@@ -23,7 +23,7 @@ module Labimotion
 
       def exec_converter
         #return if attachable_id.nil?
-        return if con_state.nil? || con_state == Labimotion::ConState::NONE
+        return if self.has_attribute?(:con_state) == false || con_state.nil? || con_state == Labimotion::ConState::NONE
         case con_state
         when Labimotion::ConState::NMR
           content = Labimotion::NmrMapperRepo.is_brucker_binary(id)
@@ -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

@@ -1,6 +1,7 @@
 # frozen_string_literal: true
 
 # Datasetable concern
+require 'labimotion/utils/utils'
 
 module Labimotion
   ## Datasetable concern
@@ -21,23 +22,18 @@ 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['identifier'] = klass.identifier
+      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

@@ -1,34 +1,42 @@
 # frozen_string_literal: true
 
 module Labimotion
-    module GenericKlassRevisions
+  ## Generic Klass Revisions Helpers
+  module GenericKlassRevisions
     extend ActiveSupport::Concern
     included do
       # has_many :element_klasses_revisions, dependent: :destroy
     end
 
-    def create_klasses_revision(user_id=0)
+    def create_klasses_revision(current_user)
       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
+      klass_attributes = {
+        uuid: properties_template['uuid'],
+        properties_template: properties_release,
+        properties_release: properties_release,
+        released_at: DateTime.now,
+        updated_by: current_user&.id,
+        released_by: current_user&.id,
+      }
 
-      self.update!({ uuid: properties_template['uuid'], properties_release: properties_release, released_at: DateTime.now })
+      self.update!(klass_attributes)
       reload
       attributes = {
-        released_by: user_id,
+        released_by: released_by,
         uuid: uuid,
+        version: version,
         properties_release: properties_release,
         released_at: released_at
       }

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 +47,18 @@ 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['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'])
         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/concerns/workflow.rb

@@ -0,0 +1,27 @@
+module Labimotion
+  # Segmentable concern
+  module Workflow
+    extend ActiveSupport::Concern
+
+    def split_workflow(properties)
+      return if properties['flow'].nil?
+
+      if properties['flow'].present?
+        properties['flowObject'] = {}
+        elements = properties['flow']['elements'] || {}
+        properties['flowObject']['nodes'] = elements.select { |obj| obj['source'].nil? }
+        properties['flowObject']['edges'] = elements.select { |obj| obj['source'] && obj['source'] != obj['target'] }.map do |obj|
+          obj['markerEnd'] = { 'type': 'arrowclosed' }
+          obj
+        end
+        properties['flowObject']['viewport'] = {
+          "x": properties['flow']['position'][0] || 0,
+          "y": properties['flow']['position'][1] || 0,
+          "zoom": properties['flow']['zoom'] || 1
+        }
+        properties.delete('flow')
+      end
+      properties
+    end
+  end
+end

data/lib/labimotion/models/element.rb

@@ -1,16 +1,19 @@
 # frozen_string_literal: true
 require 'labimotion/models/concerns/generic_revisions'
 require 'labimotion/models/concerns/segmentable'
+require 'labimotion/models/concerns/workflow'
 
 module Labimotion
   class Element < ApplicationRecord
     acts_as_paranoid
     self.table_name = :elements
-    include PgSearch
+    include PgSearch if Labimotion::IS_RAILS5 == true
+    include PgSearch::Model if Labimotion::IS_RAILS5 == false
     include ElementUIStateScopes
     include Collectable
     ## include AnalysisCodes
     include Taggable
+    include Workflow
     include Segmentable
     include GenericRevisions
 
@@ -106,6 +109,16 @@ module Labimotion
       preview && Base64.encode64(preview) || 'not available'
     end
 
+
+    def migrate_workflow
+      return if properties.nil? || properties_release.nil?
+
+      return if properties['flow'].nil? && properties_release['flow'].nil?
+
+      update_column(:properties, split_workflow(properties)) if properties['flow']
+      update_column(:properties_release, split_workflow(properties_release)) if properties_release['flow']
+    end
+
     private
 
     def delete_attachment

data/lib/labimotion/models/element_klass.rb

@@ -1,11 +1,13 @@
 # frozen_string_literal: true
 require 'labimotion/models/concerns/generic_klass_revisions'
+require 'labimotion/models/concerns/workflow'
 
 module Labimotion
   class ElementKlass < ApplicationRecord
-    acts_as_paranoid
     self.table_name = :element_klasses
+    acts_as_paranoid
     include GenericKlassRevisions
+    include Workflow
     has_many :elements, dependent: :destroy, class_name: 'Labimotion::Element'
     has_many :segment_klasses, dependent: :destroy, class_name: 'Labimotion::SegmentKlass'
     has_many :element_klasses_revisions, dependent: :destroy, class_name: 'Labimotion::ElementKlassesRevision'
@@ -16,10 +18,18 @@ module Labimotion
       klasses = []
     ensure
       File.write(
-        Rails.root.join('config', 'klasses.json'),
+        Rails.root.join('app/packs/klasses.json'),
         klasses&.to_json || []
       )
     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_klasses_revision.rb

@@ -1,9 +1,19 @@
 # frozen_string_literal: true
 
+require 'labimotion/models/concerns/workflow'
+
 module Labimotion
   class ElementKlassesRevision < ApplicationRecord
     acts_as_paranoid
     self.table_name = :element_klasses_revisions
+    include Workflow
     has_one :element_klass, class_name: 'Labimotion::ElementKlass'
+
+
+    def migrate_workflow
+      return if properties_release.nil? || properties_release['flow'].nil?
+
+      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/utils/utils.rb

@@ -1,6 +1,8 @@
 # frozen_string_literal: true
 
+require 'labimotion/version'
 module Labimotion
+  ## Generic Utils
   class Utils
     def self.klass_by_collection(name)
       names = name.split('::')
@@ -53,5 +55,36 @@ 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)
+      pkg = {} if pkg.nil?
+      pkg['eln'] = Chemotion::Application.config.version
+      pkg['labimotion'] = Labimotion::VERSION
+      pkg
+    end
   end
 end

data/lib/labimotion/version.rb

@@ -1,6 +1,7 @@
 # frozen_string_literal: true
 
 module Labimotion
-  VERSION = '0.1.11'
   IS_RAILS5 = true
+  VERSION = '0.1.14' if Labimotion::IS_RAILS5 == true
+  VERSION = '1.0.1' if Labimotion::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: 0.1.11
+  version: 0.1.14
 platform: ruby
 authors:
 - Chia-Lin Lin
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-08-16 00:00:00.000000000 Z
+date: 2023-08-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -73,6 +73,7 @@ files:
 - lib/labimotion/models/concerns/generic_klass_revisions.rb
 - lib/labimotion/models/concerns/generic_revisions.rb
 - lib/labimotion/models/concerns/segmentable.rb
+- lib/labimotion/models/concerns/workflow.rb
 - lib/labimotion/models/dataset.rb
 - lib/labimotion/models/dataset_klass.rb
 - lib/labimotion/models/dataset_klasses_revision.rb
@@ -83,6 +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
@@ -113,7 +115,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.9
+rubygems_version: 3.4.18
 signing_key: 
 specification_version: 4
 summary: Chemotion LabIMotion