labimotion 0.3.1 → 0.3.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 5b8192a47d907ab3aab31d14c951ccfe6a9552f04cc57896dffc592d850c90d0
-  data.tar.gz: 54be5a8e125a16ebbb8ee8ac48de31e42678c9473da2c7c2e32394585b746ffa
+  metadata.gz: 1e2976eacd1dbe12aa1caefd59638628b544d64ebd2757b677bc527e18230c1c
+  data.tar.gz: f1ee1381e67ab62bd66b4178f25346988c471b34c1da917e010e7753a83279ca
 SHA512:
-  metadata.gz: 1cb3dd9177e8799a2a07c3454587f6ae7d925e99dd22ce0423a3513cf8992def50d7f900992d9c4db217617473b4ec87b0dcdc02551e3841ba66183efae6159d
-  data.tar.gz: 595b810eee22f50e8ef15db20b2a8b37dc6ad14b2d05d0362568cd235be2cf7358b0ca089722ac09c364a57a5d9e64992fbba5afa342182f9647a602b292467e
+  metadata.gz: e8d3ca3477cfecd469e1d5e1a41be249a5b69da8647478ebd24a6144498dc5a110a4976f6cec56f10bc6fca013872dba164aa47be7402d511219a50d78ce8309
+  data.tar.gz: c6098201eb9ef587b0201e35c56b1146697e19dfead041aad7fb2b515ed4e38db2c00051508b0d631faeb979fc62edb287add0ad9be76c243da30d69d8230949

data/lib/labimotion/{utils → collection}/export.rb

@@ -23,17 +23,20 @@ module Labimotion
     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',
-      })
+      # 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)
+        element, attachments = Labimotion::Export.fetch_properties(data, element, attachments, &fetch_one)
+        fetch_one.call(element, {
+          'element_klass_id' => 'Labimotion::ElementKlass',
+          'created_by' => 'User',
+        })
         fetch_containers.call(element)
         segment, @attachments = Labimotion::Export.fetch_segments(element, attachments, &fetch_one)
         segments += segment if segment.present?
@@ -91,6 +94,15 @@ module Labimotion
           mol = Molecule.find(id) unless id.nil?
           properties['layers'][key]['fields'][idx]['value']['el_id'] = fetch_one.call(mol) unless mol.nil?
         end
+
+        field_samples = layer['fields'].select { |ss| ss['type'] == 'drag_sample' }
+        field_samples.each do |field|
+          # idx = properties['layers'][key]['fields'].index(field)
+          # id = field["value"] && field["value"]["el_id"] unless idx.nil?
+          # ss = Sample.find(id) unless id.nil?
+          # properties['layers'][key]['fields'][idx]['value']['el_id'] = fetch_one.call(ss) unless ss.nil?
+        end
+
         field_uploads = layer['fields'].select { |ss| ss['type'] == 'upload' }
         field_uploads.each do |upload|
           idx = properties['layers'][key]['fields'].index(upload)
@@ -123,7 +135,6 @@ module Labimotion
             end
           end
         end
-
       end
       instance.properties = properties
       [instance, attachments]

data/lib/labimotion/{utils → collection}/import.rb

@@ -1,5 +1,6 @@
 # frozen_string_literal: true
 
+require 'labimotion/utils/import_utils'
 module Labimotion
   class Import
 
@@ -50,7 +51,7 @@ module Labimotion
           element_type = fields.fetch('element_type')
           element = instances.fetch(element_type).fetch(element_uuid)
 
-          dataset_klass = Labimotion::DatasetKlass.find_by(identifier: dk_id)
+          dataset_klass = Labimotion::DatasetKlass.find_by(identifier: dk_id) if dk_id.present?
           next if gt == true && dataset_klass.nil?
 
           dkr = Labimotion::DatasetKlassesRevision.find_by(uuid: fields.fetch('klass_uuid'))
@@ -88,33 +89,21 @@ module Labimotion
           ek_obj = data.fetch('Labimotion::ElementKlass').fetch(sk_obj["element_klass_id"])
           element_klass = Labimotion::ElementKlass.find_by(name: ek_obj['name']) if ek_obj.present?
           next if element_klass.nil? || ek_obj.nil? || ek_obj['is_generic'] == true
+
           element_uuid = fields.fetch('element_id')
           element_type = fields.fetch('element_type')
           element = instances.fetch(element_type).fetch(element_uuid)
-          segment_klass = Labimotion::SegmentKlass.find_by(identifier: sk_id)
-          next if gt == true && segment_klass.nil?
-
-          skr = Labimotion::SegmentKlassesRevision.find_by(uuid: fields.fetch('klass_uuid'))
-          segment_klass = skr.segment_klass if segment_klass.nil? && skr.present?
-
-          # segment_klass = Labimotion::SegmentKlass.create!(sk_obj.slice(
-          #     'label',
-          #     'desc',
-          #     'properties_template',
-          #     'is_active',
-          #     'place',
-          #     'properties_release',
-          #     'uuid',
-          #     'identifier',
-          #     'sync_time'
-          #   ).merge(
-          #     element_klass: element_klass,
-          #     created_by: current_user_id,
-          #     released_at: DateTime.now
-          #   )
-          # ) if segment_klass.nil?
-
-          next if segment_klass.nil?
+          segment_klass = Labimotion::SegmentKlass.find_by(identifier: sk_id) if sk_id.present?
+          segment_klass = Labimotion::SegmentKlass.find_by(uuid: fields.fetch('klass_uuid')) if segment_klass.nil?
+
+          if segment_klass.nil?
+            skr = Labimotion::SegmentKlassesRevision.find_by(uuid: fields.fetch('klass_uuid'))
+            segment_klass = skr.segment_klass if segment_klass.nil? && skr.present?
+          end
+
+          next if segment_klass.nil? || element.nil?
+
+          ## segment_klass = Labimotion::ImportUtils.create_segment_klass(sk_obj, segment_klass, element_klass, current_user_id)
 
           segment = Labimotion::Segment.create!(
             fields.slice(
@@ -128,52 +117,7 @@ module Labimotion
             )
           )
 
-          properties = segment.properties
-          properties['layers'].keys.each do |key|
-            layer = properties['layers'][key]
-            field_molecules = layer['fields'].select { |ss| ss['type'] == 'drag_molecule' }
-            field_molecules.each do |field|
-              idx = properties['layers'][key]['fields'].index(field)
-              id = field["value"] && field["value"]["el_id"] unless idx.nil?
-              mol = Molecule.find_or_create_by_molfile(data.fetch('Molecule')[id]['molfile']) unless id.nil?
-              unless mol.nil?
-                properties['layers'][key]['fields'][idx]['value']['el_id'] = mol.id
-                properties['layers'][key]['fields'][idx]['value']['el_tip'] = "#{mol.inchikey}@@#{mol.cano_smiles}"
-                properties['layers'][key]['fields'][idx]['value']['el_label'] = mol.iupac_name
-              end
-            end
-
-            field_tables = layer['fields'].select { |ss| ss['type'] == 'table' }
-            field_tables&.each do |field|
-              tidx = layer['fields'].index(field)
-              next unless field['sub_values'].present? && field['sub_fields'].present?
-
-              field_table_molecules = field['sub_fields'].select { |ss| ss['type'] == 'drag_molecule' }
-              if field_table_molecules.present?
-                col_ids = field_table_molecules.map { |x| x.values[0] }
-                col_ids.each do |col_id|
-                  field['sub_values'].each_with_index do |sub_value, vdx|
-                    next unless sub_value[col_id].present? && sub_value[col_id]['value'].present? && sub_value[col_id]['value']['el_id'].present?
-
-                    svalue = sub_value[col_id]['value']
-                    next unless svalue['el_id'].present? && svalue['el_inchikey'].present?
-
-                    tmol = Molecule.find_or_create_by_molfile(data.fetch('Molecule')[svalue['el_id']]['molfile']) unless svalue['el_id'].nil?
-                    unless tmol.nil?
-                      properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_id'] = tmol.id
-                      properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_tip'] = "#{tmol.inchikey}@@#{tmol.cano_smiles}"
-                      properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_label'] = tmol.cano_smiles
-                      properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_smiles'] = tmol.cano_smiles
-                      properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_iupac'] = tmol.iupac_name
-                      properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_inchikey'] = tmol.inchikey
-                      properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_svg'] = File.join('/images', 'molecules', tmol.molecule_svg_file)
-                      properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_molecular_weight'] = tmol.molecular_weight
-                    end
-                  end
-                end
-              end
-            end
-          end
+          properties = Labimotion::ImportUtils.properties_handler(data, segment.properties)
           segment.update!(properties: properties)
           update_instances.call(uuid, segment)
         end
@@ -182,5 +126,43 @@ module Labimotion
         raise
       end
     end
+
+    def self.import_elements(data, instances, gt, current_user_id, fetch_many, &update_instances)
+      data.fetch('Labimotion::Element', {}).each do |uuid, fields|
+        klass_id = fields["element_klass_id"]
+        ek_obj = data.fetch('Labimotion::ElementKlass', {})[klass_id]
+        ek_id = ek_obj["identifier"]
+        element_klass = Labimotion::ElementKlass.find_by(identifier: ek_id) if ek_id.present?
+        element_klass = Labimotion::ElementKlass.find_by(uuid: fields.fetch('klass_uuid')) if element_klass.nil?
+
+        if element_klass.nil?
+          ekr = Labimotion::ElementKlassesRevision.find_by(uuid: fields.fetch('klass_uuid'))
+          element_klass = ekr.element_klass if element_klass.nil? && ekr.present?
+        end
+        next if element_klass.nil?
+
+        element = Labimotion::Element.create!(
+          fields.slice(
+            'name', 'properties', 'properties_release'
+          ).merge(
+            created_by: current_user_id,
+            element_klass: element_klass,
+            collections: fetch_many.call(
+              'Collection', 'Labimotion::CollectionsElement', 'element_id', 'collection_id', uuid
+            ),
+            uuid: SecureRandom.uuid,
+            klass_uuid: ekr&.uuid || element_klass.uuid
+          )
+        )
+
+        properties = Labimotion::ImportUtils.properties_handler(data, element.properties)
+        element.update!(properties: properties)
+        update_instances.call(uuid, element)
+        element.container = Container.create_root_container
+      end
+    rescue StandardError => e
+      Rails.logger.error(e.backtrace)
+      raise
+    end
   end
 end

data/lib/labimotion/entities/element_entity.rb

@@ -15,6 +15,7 @@ module Labimotion
       expose! :properties
       expose! :properties_release
       expose! :short_label
+      expose! :thumb_svg
       expose! :type
       expose! :uuid
     end

data/lib/labimotion/libs/converter.rb

@@ -14,11 +14,38 @@ require 'labimotion/utils/utils'
 
 module Labimotion
   class Converter
-
     def self.logger
       @@converter_logger ||= Logger.new(Rails.root.join('log/converter.log')) # rubocop:disable Style/ClassVars
     end
 
+    def self.process_ds(id, current_user = {})
+      att = Attachment.find_by(id: id, con_state: Labimotion::ConState::CONVERTED)
+      return if att.nil? || att.attachable_id.nil? || att.attachable_type != 'Container'
+
+      dsr = []
+      ols = nil
+      if Labimotion::IS_RAILS5 == true
+        Zip::File.open(att.store.path) do |zip_file|
+          res = Labimotion::Converter.collect_metadata(zip_file) if att.filename.split('.')&.last == 'zip'
+          ols = res[:o] unless res&.dig(:o).nil?
+          dsr.push(res[:d]) unless res&.dig(:d).nil?
+        end
+      else
+        Zip::File.open(att.attachment_attacher.file.url) do |zip_file|
+          res = Labimotion::Converter.collect_metadata(zip_file) if att.filename.split('.')&.last == 'zip'
+          ols = res[:o] unless res&.dig(:o).nil?
+          dsr.push(res[:d]) unless res&.dig(:d).nil?
+        end
+      end
+      dsr.flatten!
+      dataset = build_ds(att.attachable_id, ols)
+      update_ds(dataset, dsr, current_user) if dataset.present?
+      att.update_column(:con_state, Labimotion::ConState::COMPLETED)
+    rescue StandardError => e
+      Labimotion::Converter.logger.error ["Att ID: #{att&.id}, OLS: #{ols}", "DSR: #{dsr}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
+      raise e
+    end
+
     def self.uri(api_name)
       url = Rails.configuration.converter.url
       "#{url}#{api_name}"
@@ -125,17 +152,7 @@ module Labimotion
           primary_store = Rails.configuration.storage.primary_store
           att.update!(storage: primary_store)
         end
-
-        Zip::File.open(tmp_file.path) do |zip_file|
-          res = Labimotion::Converter.collect_metadata(zip_file) if name.split('.')&.last == 'zip'
-          ols = res[:o] unless res&.dig(:o).nil?
-          dsr.push(res[:d]) unless res&.dig(:d).nil?
-        end
-
-        dsr.flatten!
-        if dsr.length.positive? && name.split('.')&.last == 'zip'
-          Labimotion::Converter.ts('write', att.attachable_id, ols: ols, info: dsr)
-        end
+        process_ds(att.id)
       rescue StandardError => e
         raise e
       ensure
@@ -179,25 +196,22 @@ module Labimotion
     end
 
     def self.jcamp_converter(id)
-      resp = nil
-      begin
-
-        data = Labimotion::Converter.vor_conv(id)
-        return if data.nil?
+      data = Labimotion::Converter.vor_conv(id)
+      return if data.nil?
 
-        Labimotion::Converter.process(data)
-      rescue StandardError => e
-        Labimotion::Converter.logger.error ["jcamp_converter fail: #{id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
-        Labimotion::ConState::ERROR
-      end
+      Labimotion::Converter.process(data)
+    rescue StandardError => e
+      Labimotion::Converter.logger.error ["jcamp_converter fail: #{id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
+      Labimotion::ConState::ERROR
     end
 
     def self.generate_ds(att_id, current_user = {})
       dsr_info = Labimotion::Converter.fetch_dsr(att_id)
       begin
         return unless dsr_info && dsr_info[:info]&.length.positive?
+
         dataset = Labimotion::Converter.build_ds(att_id, dsr_info[:ols])
-        Labimotion::Converter.update_ds(dataset, dsr_info[:info], current_user)
+        Labimotion::Converter.update_ds(dataset, dsr_info[:info], current_user) if dataset.present?
       rescue StandardError => e
         Labimotion::Converter.logger.error ["Att ID: #{att_id}, OLS: #{dsr_info[:ols]}", "DSR: #{dsr_info[:info]}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
       ensure
@@ -325,6 +339,15 @@ module Labimotion
       end
       res
     end
+
+    def self.metadata(id)
+      att = Attachment.find(id)
+      return if att.nil? || att.attachable_id.nil? || att.attachable_type != 'Container'
+
+      ds = Labimotion::Dataset.find_by(element_type: 'Container', element_id: att.attachable_id)
+      att.update_column(:con_state, Labimotion::ConState::COMPLETED) if ds.present?
+      process_ds(att.id) if ds.nil?
+    end
   end
 end
 

data/lib/labimotion/libs/export_dataset.rb

@@ -27,7 +27,7 @@ module Labimotion
       name = ds.dataset_klass.label
 
       match = name.match(/\((.*?)\)/)
-      name = match && match.length > 2 ? match[1] : name
+      name = match && match.length > 1 ? match[1] : name
 
       name = '1H NMR' if ds.dataset_klass.ols_term_id == 'CHMO:0000593'
       name = '13C NMR' if ds.dataset_klass.ols_term_id == 'CHMO:0000595'
@@ -99,9 +99,14 @@ module Labimotion
       wb = @xfile.workbook
       gds = Labimotion::Dataset.find_by(element_id: id, element_type: 'Container')
       cds = Container.find(id)
-      cds.attachments.where(aasm_state: 'csv').each do |att|
+      cds_csv = cds.attachments.where(aasm_state: 'csv')
+      csv_length = cds_csv.length
+      return if csv_length.zero?
+      cds_csv.each_with_index do |att, idx|
         name = File.basename(att.filename, '.csv')
-        sheet = @xfile.workbook.add_worksheet(name: name.slice(0, 25))
+        name = name.slice(0, (25 - csv_length.to_s.length - 1))
+        sheet_name = "#{name}_#{idx}"
+        sheet = @xfile.workbook.add_worksheet(name: sheet_name)
 
         if Labimotion::IS_RAILS5 == true
           File.open(att.store.path) do |fi|

data/lib/labimotion/libs/nmr_mapper.rb

@@ -6,8 +6,24 @@ require 'labimotion/utils/utils'
 module Labimotion
   ## NmrMapper
   class NmrMapper
+    def self.process_ds(id, current_user = {})
+      att = Attachment.find_by(id: id, con_state: Labimotion::ConState::NMR)
+      return if att.nil?
+
+      content = is_brucker_binary(id)
+      if content.nil?
+        Labimotion::ConState::NONE
+      else
+        data = process(att, id, content)
+        generate_ds(id, att.attachable_id, data, current_user)
+        Labimotion::ConState::COMPLETED
+      end
+    end
+
     def self.is_brucker_binary(id)
-      att = Attachment.find(id)
+      att = Attachment.find_by(id: id, con_state: Labimotion::ConState::NMR)
+      return if att.nil?
+
       if Labimotion::IS_RAILS5 == true
         Zip::File.open(att.store.path) do |zip_file|
           zip_file.each do |entry|
@@ -32,8 +48,9 @@ module Labimotion
       nil
     end
 
-    def self.process(id, content)
-      att = Attachment.find(id)
+    def self.process(att, id, content)
+      return if att.nil? || content.nil?
+
       lines = content.split("\n").reject(&:empty?)
       metadata = {}
       lines.map do |ln|
@@ -42,26 +59,33 @@ module Labimotion
       end
       ols = 'CHMO:0000593' if metadata['NUC1'] == '1H'
       ols = 'CHMO:0000595' if metadata['NUC1'] == '13C'
-      if content.present? && att.present?
-        Labimotion::NmrMapper.ts('write', att.attachable_id,
-                              content: { metadata: metadata, ols: ols })
-      end
+
+      { content: { metadata: metadata, ols: ols } }
+      # if content.present? && att.present?
+      #   Labimotion::NmrMapper.ts('write', att.attachable_id,
+      #                         content: { metadata: metadata, ols: ols })
+      # end
     end
 
     def self.fetch_content(id)
-      Labimotion::NmrMapper.ts('read', id)
+      atts = Attachment.where(attachable_id: id)
+      return if atts.nil?
+
+      atts.each do |att|
+        content = Labimotion::NmrMapper.ts('read', att.id)
+        return content if content.present?
+      end
     end
 
-    def self.generate_ds(id, current_user = {})
-      data = Labimotion::NmrMapper.fetch_content(id)
-      return if data.nil?
 
-      obj = Labimotion::NmrMapper.build_ds(id, data[:content])
+    def self.generate_ds(id, cid, data, current_user = {})
+      return if data.nil? || cid.nil?
+
+      obj = Labimotion::NmrMapper.build_ds(cid, data[:content])
       return if obj.nil? || obj[:ols].nil?
 
-      Labimotion::NmrMapper.update_ds_1h(id, obj, current_user) if obj[:ols] == 'CHMO:0000593'
-      Labimotion::NmrMapper.update_ds_1h(id, obj, current_user) if obj[:ols] == 'CHMO:0000595'
-      Labimotion::NmrMapper.clean(id)
+      Labimotion::NmrMapper.update_ds_1h(cid, obj, current_user) if obj[:ols] == 'CHMO:0000593'
+      Labimotion::NmrMapper.update_ds_1h(cid, obj, current_user) if obj[:ols] == 'CHMO:0000595'
     end
 
     def self.update_ds_13c(id, obj)

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

@@ -10,6 +10,7 @@ module Labimotion
       after_update :exec_converter
       def init_converter
         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
@@ -22,21 +23,20 @@ module Labimotion
       end
 
       def exec_converter
-        #return if attachable_id.nil?
-        return if self.has_attribute?(:con_state) == false || con_state.nil? || con_state == Labimotion::ConState::NONE
+        return if self.has_attribute?(:con_state) == false || self.con_state.nil? || self.con_state == Labimotion::ConState::NONE
+
+        return if attachable_id.nil? && self.con_state != Labimotion::ConState::WAIT
+
         case con_state
         when Labimotion::ConState::NMR
-          content = Labimotion::NmrMapperRepo.is_brucker_binary(id)
-          if content.nil?
-            self.con_state = Labimotion::ConState::NONE
-          else
-            Labimotion::NmrMapperRepo.process(id, content)
-            self.con_state = Labimotion::ConState::PROCESSED
-          end
+          self.con_state = Labimotion::NmrMapper.process_ds(id)
+          update_column(:con_state, con_state)
         when Labimotion::ConState::WAIT
           self.con_state = Labimotion::Converter.jcamp_converter(id)
+          update_column(:con_state, con_state)
+        when Labimotion::ConState::CONVERTED
+          Labimotion::Converter.metadata(id)
         end
-        update_column(:con_state, con_state)
       end
     end
   end

data/lib/labimotion/models/element.rb

@@ -101,13 +101,20 @@ module Labimotion
     end
 
     def thumb_svg
-      image_atts = attachments.select do |a_img|
-        a_img&.content_type&.match(Regexp.union(%w[jpg jpeg png tiff tif]))
-      end
+      if Labimotion::IS_RAILS5 == true
+        image_atts = attachments.select do |a_img|
+          a_img&.content_type&.match(Regexp.union(%w[jpg jpeg png tiff tif]))
+        end
 
-      attachment = image_atts[0] || attachments[0]
-      preview = attachment.read_thumbnail if attachment
-      preview && Base64.encode64(preview) || 'not available'
+        attachment = image_atts[0] || attachments[0]
+        preview = attachment.read_thumbnail if attachment
+        preview && Base64.encode64(preview) || 'not available'
+      else
+        image_atts = attachments.select(&:type_image?)
+        attachment = image_atts[0] || attachments[0]
+        preview = attachment&.read_thumbnail
+        (preview && Base64.encode64(preview)) || 'not available'
+      end
     end
 
 

data/lib/labimotion/utils/import_utils.rb

@@ -0,0 +1,116 @@
+# frozen_string_literal: true
+
+module Labimotion
+  ## Import Utils
+  class ImportUtils
+    def self.proc_sample(layer, key, data, properties)
+      field_samples = layer['fields'].select { |ss| ss['type'] == 'drag_sample' }
+      field_samples.each do |field|
+        idx = properties['layers'][key]['fields'].index(field)
+        id = field["value"] && field["value"]["el_id"] unless idx.nil?
+
+        # mol = Molecule.find_or_create_by_molfile(data.fetch('Molecule')[id]['molfile']) unless id.nil?
+        # unless mol.nil?
+        #   properties['layers'][key]['fields'][idx]['value']['el_id'] = mol.id
+        #   properties['layers'][key]['fields'][idx]['value']['el_tip'] = "#{mol.inchikey}@@#{mol.cano_smiles}"
+        #   properties['layers'][key]['fields'][idx]['value']['el_label'] = mol.iupac_name
+        # end
+      end
+      properties
+    rescue StandardError => e
+      Rails.logger.error(e.backtrace)
+      raise
+    end
+
+    def self.proc_molecule(layer, key, data, properties)
+      field_molecules = layer['fields'].select { |ss| ss['type'] == 'drag_molecule' }
+      field_molecules.each do |field|
+        idx = properties['layers'][key]['fields'].index(field)
+        id = field["value"] && field["value"]["el_id"] unless idx.nil?
+        mol = Molecule.find_or_create_by_molfile(data.fetch('Molecule')[id]['molfile']) unless id.nil?
+        unless mol.nil?
+          properties['layers'][key]['fields'][idx]['value']['el_id'] = mol.id
+          properties['layers'][key]['fields'][idx]['value']['el_tip'] = "#{mol.inchikey}@@#{mol.cano_smiles}"
+          properties['layers'][key]['fields'][idx]['value']['el_label'] = mol.iupac_name
+        end
+      end
+      properties
+    rescue StandardError => e
+      Rails.logger.error(e.backtrace)
+      raise
+    end
+
+    def self.proc_table(layer, key, data, properties)
+      field_tables = layer['fields'].select { |ss| ss['type'] == 'table' }
+      field_tables&.each do |field|
+        tidx = layer['fields'].index(field)
+        next unless field['sub_values'].present? && field['sub_fields'].present?
+
+        field_table_molecules = field['sub_fields'].select { |ss| ss['type'] == 'drag_molecule' }
+        if field_table_molecules.present?
+          col_ids = field_table_molecules.map { |x| x.values[0] }
+          col_ids.each do |col_id|
+            field['sub_values'].each_with_index do |sub_value, vdx|
+              next unless sub_value[col_id].present? && sub_value[col_id]['value'].present? && sub_value[col_id]['value']['el_id'].present?
+
+              svalue = sub_value[col_id]['value']
+              next unless svalue['el_id'].present? && svalue['el_inchikey'].present?
+
+              tmol = Molecule.find_or_create_by_molfile(data.fetch('Molecule')[svalue['el_id']]['molfile']) unless svalue['el_id'].nil?
+              unless tmol.nil?
+                properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_id'] = tmol.id
+                properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_tip'] = "#{tmol.inchikey}@@#{tmol.cano_smiles}"
+                properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_label'] = tmol.cano_smiles
+                properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_smiles'] = tmol.cano_smiles
+                properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_iupac'] = tmol.iupac_name
+                properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_inchikey'] = tmol.inchikey
+                properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_svg'] = File.join('/images', 'molecules', tmol.molecule_svg_file)
+                properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_molecular_weight'] = tmol.molecular_weight
+              end
+            end
+          end
+        end
+      end
+      properties
+    rescue StandardError => e
+      Rails.logger.error(e.backtrace)
+      raise
+    end
+
+    def self.properties_handler(data, properties)
+      properties && properties['layers'] && properties['layers'].keys&.each do |key|
+        layer = properties['layers'][key]
+        properties = proc_molecule(layer, key, data, properties)
+        properties = proc_table(layer, key, data, properties)
+        # properties = proc_sample(layer, key, data, properties)
+      end
+      properties
+    rescue StandardError => e
+      Rails.logger.error(e.backtrace)
+      raise
+    end
+
+    def self.create_segment_klass(sk_obj, segment_klass, element_klass, current_user_id)
+      return if segment_klass.present? || element_klass.nil? || sk_obj.nil?
+
+      segment_klass = Labimotion::SegmentKlass.create!(sk_obj.slice(
+          'label',
+          'desc',
+          'properties_template',
+          'is_active',
+          'place',
+          'properties_release',
+          'uuid',
+          'identifier',
+          'sync_time'
+        ).merge(
+          element_klass: element_klass,
+          created_by: current_user_id,
+          released_at: DateTime.now
+        )
+      )
+
+      segment_klass
+    end
+  end
+end

data/lib/labimotion/version.rb

@@ -1,7 +1,11 @@
 # frozen_string_literal: true
 
+## Labimotion Version
 module Labimotion
   IS_RAILS5 = true
-  VERSION = '0.3.1' if Labimotion::IS_RAILS5 == true
-  VERSION = '1.0.7' if Labimotion::IS_RAILS5 == false
+  VERSION_ELN = '1.0.17'
+  VERSION_REPO = '0.3.3'
+
+  VERSION = Labimotion::VERSION_REPO if Labimotion::IS_RAILS5 == true
+  VERSION = Labimotion::VERSION_ELN if Labimotion::IS_RAILS5 == false
 end

data/lib/labimotion.rb

@@ -61,8 +61,11 @@ module Labimotion
   autoload :ConState, 'labimotion/utils/con_state'
   autoload :Serializer, 'labimotion/utils/serializer'
   autoload :Search, 'labimotion/utils/search'
-  autoload :Export, 'labimotion/utils/export'
-  autoload :Import, 'labimotion/utils/import'
+
+
+  ######## Collection
+  autoload :Export, 'labimotion/collection/export'
+  autoload :Import, 'labimotion/collection/import'
 
   ######## Models
   autoload :Element, 'labimotion/models/element'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: labimotion
 version: !ruby/object:Gem::Version
-  version: 0.3.1
+  version: 0.3.3
 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: 2023-10-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -34,12 +34,13 @@ extensions: []
 extra_rdoc_files: []
 files:
 - lib/labimotion.rb
-- lib/labimotion/api.rb
 - lib/labimotion/apis/converter_api.rb
 - lib/labimotion/apis/generic_dataset_api.rb
 - lib/labimotion/apis/generic_element_api.rb
 - lib/labimotion/apis/labimotion_hub_api.rb
 - lib/labimotion/apis/segment_api.rb
+- lib/labimotion/collection/export.rb
+- lib/labimotion/collection/import.rb
 - lib/labimotion/entities/application_entity.rb
 - lib/labimotion/entities/dataset_entity.rb
 - lib/labimotion/entities/dataset_klass_entity.rb
@@ -65,7 +66,6 @@ files:
 - lib/labimotion/libs/converter.rb
 - lib/labimotion/libs/export_dataset.rb
 - lib/labimotion/libs/nmr_mapper.rb
-- lib/labimotion/libs/nmr_mapper_repo.rb
 - lib/labimotion/libs/template_hub.rb
 - lib/labimotion/models/collections_element.rb
 - lib/labimotion/models/concerns/attachment_converter.rb
@@ -90,15 +90,14 @@ files:
 - lib/labimotion/models/segment_klasses_revision.rb
 - lib/labimotion/models/segments_revision.rb
 - lib/labimotion/utils/con_state.rb
-- lib/labimotion/utils/export.rb
-- lib/labimotion/utils/import.rb
+- lib/labimotion/utils/import_utils.rb
 - lib/labimotion/utils/search.rb
 - lib/labimotion/utils/serializer.rb
 - lib/labimotion/utils/utils.rb
 - lib/labimotion/version.rb
-homepage: https://github.com/phuang26/labimotion
+homepage: https://gitlab.kit.edu/kit/labimotion/labimotion
 licenses:
-- MIT
+- GPL-3.0
 metadata: {}
 post_install_message: 
 rdoc_options: []

data/lib/labimotion/api.rb

@@ -1,19 +0,0 @@
-# frozen_string_literal: true
-
-## This is the first version of the dataset class
-module Labimotion
-  ## This is the first version of the dataset class
-  class Api
-    def initialize
-      # Initialization code
-    end
-
-    def gget_data
-      'Hello, worlddddddddddddddddddddd!'
-    end
-
-    def self.hello
-      'Hellooooooooooooooooooooo!'
-    end
-  end
-end

data/lib/labimotion/libs/nmr_mapper_repo.rb

@@ -1,278 +0,0 @@
-# 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)
-      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
-
-    def self.process(id, content)
-      att = Attachment.find(id)
-      lines = content.split("\n").reject(&:empty?)
-      metadata = {}
-      lines.map do |ln|
-        arr = ln.split(/\s+/)
-        metadata[arr[0]] = arr[1..-1].join(' ') if arr.length > 1
-      end
-      ols = 'CHMO:0000593' if metadata['NUC1'] == '1H'
-      ols = 'CHMO:0000595' if metadata['NUC1'] == '13C'
-      if content.present? && att.present?
-        Labimotion::NmrMapper.ts('write', att.attachable_id,
-                              content: { metadata: metadata, ols: ols })
-      end
-    end
-
-    def self.fetch_content(id)
-      Labimotion::NmrMapper.ts('read', id)
-    end
-
-    def self.generate_ds(id, current_user = {})
-      data = Labimotion::NmrMapper.fetch_content(id)
-      return if data.nil?
-
-      obj = Labimotion::NmrMapper.build_ds(id, data[:content])
-      return if obj.nil? || obj[:ols].nil?
-
-      Labimotion::NmrMapper.update_ds_1h(id, obj, current_user) if obj[:ols] == 'CHMO:0000593'
-      Labimotion::NmrMapper.update_ds_1h(id, obj, current_user) if obj[:ols] == 'CHMO:0000595'
-      Labimotion::NmrMapper.clean(id)
-    end
-
-    def self.update_ds_13c(id, obj)
-      # dataset = obj[:dataset]
-      # metadata = obj[:metadata]
-      # new_prop = dataset.properties
-
-      # dataset.properties = new_prop
-      # dataset.save!
-    end
-
-    def self.set_data(prop, field, idx, layer_name, field_name, value)
-      return if field['field'] != field_name || value&.empty?
-
-      field['value'] = value
-      prop['layers'][layer_name]['fields'][idx] = field
-      prop
-    end
-
-    def self.update_ds_1h(id, obj, current_user)
-      dataset = obj[:dataset]
-      metadata = obj[:metadata]
-      new_prop = dataset.properties
-      new_prop.dig('layers', 'general', 'fields')&.each_with_index do |fi, idx|
-      #  new_prop = set_data(new_prop, fi, idx, 'general', 'title', metadata['NAME'])
-        if fi['field'] == 'title' && metadata['NAME'].present?
-          ## fi['label'] = fi['label']
-          fi['value'] = metadata['NAME']
-          fi['device'] = metadata['NAME']
-          fi['dkey'] = 'NAME'
-          new_prop['layers']['general']['fields'][idx] = fi
-        end
-
-        if fi['field'] == 'date' && metadata['Date_'].present?
-          ## fi['label'] = fi['label']
-          fi['value'] = metadata['Date_']
-          fi['device'] = metadata['Date_']
-          fi['dkey'] = 'Date_'
-          new_prop['layers']['general']['fields'][idx] = fi
-        end
-
-        if fi['field'] == 'time' && metadata['Time'].present?
-          ## fi['label'] = fi['label']
-          fi['value'] = metadata['Time']
-          fi['device'] = metadata['Time']
-          fi['dkey'] = 'Time'
-          new_prop['layers']['general']['fields'][idx] = fi
-        end
-
-        if fi['field'] == 'creator' && current_user.present?
-          ## fi['label'] = fi['label']
-          fi['value'] = current_user.name
-          new_prop['layers']['general']['fields'][idx] = fi
-        end
-      end
-      element = Container.find(id)&.root_element
-      element.present? && element&.class&.name == 'Sample' && new_prop.dig('layers', 'sample_details', 'fields')&.each_with_index do |fi, idx|
-        if fi['field'] == 'label'
-          fi['value'] = element.short_label
-          new_prop['layers']['sample_details']['fields'][idx] = fi
-        end
-        if fi['field'] == 'id'
-          fi['value'] = element.id
-          new_prop['layers']['sample_details']['fields'][idx] = fi
-        end
-      end
-
-      new_prop.dig('layers', 'instrument', 'fields')&.each_with_index do |fi, idx|
-        if fi['field'] == 'instrument' && metadata['INSTRUM'].present?
-          # fi['label'] = fi['label']
-          fi['value'] = metadata['INSTRUM']
-          fi['device'] = metadata['INSTRUM']
-          fi['dkey'] = 'INSTRUM'
-          new_prop['layers']['instrument']['fields'][idx] = fi
-        end
-      end
-
-
-      new_prop.dig('layers', 'equipment', 'fields')&.each_with_index do |fi, idx|
-        if fi['field'] == 'probehead' && metadata['PROBHD'].present?
-          # fi['label'] = fi['label']
-          fi['value'] = metadata['PROBHD']
-          fi['device'] = metadata['PROBHD']
-          fi['dkey'] = 'PROBHD'
-          new_prop['layers']['equipment']['fields'][idx] = fi
-        end
-      end
-
-      new_prop.dig('layers', 'sample_preparation', 'fields')&.each_with_index do |fi, idx|
-        if fi['field'] == 'solvent' && metadata['SOLVENT'].present?
-          # fi['label'] = fi['label']
-          fi['value'] = metadata['SOLVENT']
-          fi['device'] = metadata['SOLVENT']
-          fi['dkey'] = 'SOLVENT'
-          fi['value'] = 'chloroform-D1 (CDCl3)' if metadata['SOLVENT'] == 'CDCl3'
-          new_prop['layers']['sample_preparation']['fields'][idx] = fi
-        end
-      end
-
-
-      new_prop.dig('layers', 'set', 'fields')&.each_with_index do |fi, idx|
-        if fi['field'] == 'temperature' && metadata['TE'].present?
-          # fi['label'] = fi['label']
-          fi['value'] = metadata['TE'].split(/\s+/).first
-          fi['device'] = metadata['TE']
-          fi['dkey'] = 'TE'
-          fi['value_system'] = metadata['TE'].split(/\s+/).last
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-        if fi['field'] == 'ns' && metadata['NS'].present?
-          # fi['label'] = fi['label']
-          fi['value'] = metadata['NS']
-          fi['device'] = metadata['NS']
-          fi['dkey'] = 'NS'
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-        if fi['field'] == 'PULPROG' && metadata['PULPROG'].present?
-          # fi['label'] = fi['label']
-          fi['value'] = metadata['PULPROG']
-          fi['device'] = metadata['PULPROG']
-          fi['dkey'] = 'PULPROG'
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-        if fi['field'] == 'td' && metadata['TD'].present?
-          # fi['label'] = fi['label']
-          fi['value'] = metadata['TD']
-          fi['device'] = metadata['TD']
-          fi['dkey'] = 'TD'
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-        if fi['field'] == 'done' && metadata['D1'].present?
-          # fi['label'] = fi['label']
-          fi['value'] = metadata['D1']
-          fi['device'] = metadata['D1']
-          fi['dkey'] = 'D1'
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-        if fi['field'] == 'sf' && metadata['SF'].present?
-          ## fi['label'] = fi['label']
-          fi['value'] = metadata['SF']
-          fi['device'] = metadata['SF']
-          fi['dkey'] = 'SF'
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-        if fi['field'] == 'sfoone' && metadata['SFO1'].present?
-          ## fi['label'] = fi['label']
-          fi['value'] = metadata['SFO1']
-          fi['device'] = metadata['SFO1']
-          fi['dkey'] = 'SFO1'
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-        if fi['field'] == 'sfotwo' && metadata['SFO2'].present?
-          ## fi['label'] = fi['label']
-          fi['value'] = metadata['SFO2']
-          fi['device'] = metadata['SFO2']
-          fi['dkey'] = 'SFO2'
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-        if fi['field'] == 'nucone' && metadata['NUC1'].present?
-          ## fi['label'] = fi['label']
-          fi['value'] = metadata['NUC1']
-          fi['device'] = metadata['NUC1']
-          fi['dkey'] = 'NUC1'
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-        if fi['field'] == 'nuctwo' && metadata['NUC2'].present?
-          ## fi['label'] = fi['label']
-          fi['value'] = metadata['NUC2']
-          fi['device'] = metadata['NUC2']
-          fi['dkey'] = 'NUC2'
-          new_prop['layers']['set']['fields'][idx] = fi
-        end
-      end
-      dataset.properties = new_prop
-      dataset.save!
-    end
-
-
-    def self.ts(method, identifier, params = nil)
-      Rails.cache.send(method, "#{Labimotion::NmrMapper.new.class.name}#{identifier}", params)end
-
-    def self.clean(id)
-      Labimotion::NmrMapper.ts('delete', id)
-    end
-
-    def self.build_ds(id, content)
-      ds = Container.find_by(id: id)
-      return if ds.nil? || content.nil?
-
-      ols = content[:ols]
-      metadata = content[:metadata]
-
-      return if ols.nil? || metadata.nil?
-
-      klass = Labimotion::DatasetKlass.find_by(ols_term_id: ols)
-      return if klass.nil?
-
-      uuid = SecureRandom.uuid
-      props = klass.properties_release
-      props['uuid'] = uuid
-      props['pkg'] = Labimotion::Utils.pkg(props['pkg'])
-      props['klass'] = 'Dataset'
-      dataset = Labimotion::Dataset.create!(
-        uuid: uuid,
-        dataset_klass_id: klass.id,
-        element_type: 'Container',
-        element_id: ds.id,
-        properties: props,
-        properties_release: klass.properties_release,
-        klass_uuid: klass.uuid
-      )
-      { dataset: dataset, metadata: metadata, ols: ols }
-    end
-  end
-end