bagit upload download enhancement

Author: phuang26

lib/labimotion.rb

@@ -8,7 +8,7 @@ def self.logger
   end
 
   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("version: #{Labimotion::VERSION}; (#{current_user&.id}) \n Exception: #{exception.message}")
     Labimotion.logger.error(exception.backtrace.join("\n"))
   end
 

lib/labimotion/apis/labimotion_hub_api.rb

@@ -19,7 +19,7 @@ class LabimotionHubAPI < Grape::API
         get do
           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 = Labimotion::GenericPublicEntity.represent(list, displayed: params[:with_props], root: 'list')
         rescue StandardError => e
           Labimotion.log_exception(e, current_user)
           []

lib/labimotion/libs/converter.rb

@@ -20,7 +20,10 @@ def self.logger
 
     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'
+      return if att.nil? || att.attachable_id.nil? || att.attachable_type != 'Container' || att.filename.split('.')&.last != 'zip'
+
+      eln_ds = Container.find_by(id: att.attachable_id, container_type: 'dataset')
+      return if eln_ds.nil? || eln_ds.parent.nil? || eln_ds.parent&.container_type != 'analysis'
 
       dsr = []
       ols = nil

lib/labimotion/libs/export_dataset.rb

@@ -40,6 +40,8 @@ def description(ds, id)
       header_style = sheet.styles.add_style(sz: 12, fg_color: 'FFFFFF', bg_color: '00008B', border: { style: :thick, color: 'FF777777', edges: [:bottom] })
       sheet.add_row(['File name', res_name(id)])
       sheet.add_row(['Time', Time.now.strftime("%Y-%m-%d %H:%M:%S %Z")] )
+      sheet.add_row(['(This file is automatically generated by the system.)'])
+      sheet.add_row([''])
       sheet.add_row([''])
       sheet.add_row(['Fields description of sheet:' + ds.dataset_klass.label])
       sheet.add_row(['Fields', 'Field description'], style: header_style)
@@ -49,13 +51,11 @@ def description(ds, id)
       sheet.add_row(['Unit', 'The unit of the field'])
       sheet.add_row(['Name', 'The key of the field, can be used to identify the field'])
       sheet.add_row(['Type', 'The type of the field'])
-      sheet.add_row(['From device?', '[Yes] if the field is from the device, [No] if the field is manually entered by the user, [SYS] if the field is automatically generated by the system'])
-      sheet.add_row(['Device source', 'The source tag of the device file, available only if the ontology term is 1H NMR or 13C NMR'])
-      sheet.add_row(['Device data', 'The original device data, can not be changed after data uploaded'])
-      sheet.add_row([''])
+      sheet.add_row(['Source?', '[Device] from device, [Chemotion] from Chemotion'])
+      sheet.add_row(['Source identifier', 'The source identifier'])
+      sheet.add_row(['Source data', 'The data from Device or Chemotion, cannot be modified once a generic dataset is created'])
       sheet.add_row([''])
       sheet.add_row([''])
-      sheet.add_row(['', '(This file is automatically generated by the system.)'])
     end
 
     def export(id)
@@ -84,29 +84,41 @@ def export(id)
           next if field['type'] == 'dummy'
 
           type = field['type']
-          from_device = field['device'].present? ? 'Yes' : 'No'
-          from_device = field['system'].present? ? 'SYS' : from_device
+          from_device = field['device'].present? ? 'Device' : ''
+          from_device = field['system'].present? ? 'Chemotion' : from_device
           type = "#{field['type']}-#{field['option_layers']}" if field['type'] == 'select' || field['type'] == 'system-defined'
 
           show_value = field['value'] =~ /\A\d+,\d+\z/ ? field['value']&.gsub(',', '.') : field['value']
-          sheet.add_row([' ', field['label'], show_value, field['value_system'], field['field'], type, from_device, field['dkey'], field['system'] || field['device']].freeze)
+          sheet.add_row([' ', field['label'], nil, field['value_system'], field['field'], type, from_device, field['dkey'], nil].freeze)
+
+          if %w[system-defined integer].include? field['type']
+            sheet.rows.last.cells[2].type = :integer
+            sheet.rows.last.cells[8].type = :integer
+          else
+            sheet.rows.last.cells[2].type = :string
+            sheet.rows.last.cells[8].type = :string
+          end
+          sheet.rows.last.cells[2].value = show_value
+          sheet.rows.last.cells[8].value = field['system'] || field['device']
+
+
         end
         # sheet.column_widths nil, nil, nil, nil, 0, 0, 0, 0, 0
       end
     end
 
     def spectra(id)
+      name_mapping = []
       wb = @xfile.workbook
       gds = Labimotion::Dataset.find_by(element_id: id, element_type: 'Container')
       cds = Container.find(id)
-      cds_csv = cds.attachments.where(aasm_state: 'csv')
+      cds_csv = cds.attachments.where(aasm_state: 'csv').order(:filename)
       csv_length = cds_csv.length
       return if csv_length.zero?
       cds_csv.each_with_index do |att, idx|
-        name = File.basename(att.filename, '.csv')
-        name = name.slice(0, (25 - csv_length.to_s.length - 1))
-        sheet_name = "#{name}_#{idx}"
+        sheet_name = "Sheet#{idx+1}"
         sheet = @xfile.workbook.add_worksheet(name: sheet_name)
+        name_mapping.push([sheet_name, att.filename])
 
         if Labimotion::IS_RAILS5 == true
           File.open(att.store.path) do |fi|
@@ -122,10 +134,22 @@ def spectra(id)
           end
         end
       end
+
+      if name_mapping.length > 1
+        first_sheet = @xfile.workbook.worksheets&.first
+        header_style = first_sheet&.styles.add_style(sz: 12, fg_color: 'FFFFFF', bg_color: '00008B', border: { style: :thick, color: 'FF777777', edges: [:bottom] })
+        first_sheet&.add_row(['Sheet name', 'File name'], style: header_style)
+        name_mapping&.each do |mapping|
+          next if mapping.length < 2
+
+          @xfile.workbook.worksheets&.first&.add_row([mapping[0].to_s, mapping[1].to_s])
+        end
+      end
+
     end
 
     def header
-      ['Layer Label', 'Field Label', 'Value', 'Unit', 'Name', 'Type', 'from device?', 'Device source', 'Device data'].freeze
+      ['Layer Label', 'Field Label', 'Value', 'Unit', 'Name', 'Type', 'Source?', 'Source identifier', 'Source data'].freeze
     end
 
     def read

lib/labimotion/libs/nmr_mapper.rb

@@ -10,8 +10,12 @@ 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?
+      result = is_brucker_binary(id)
+      if result[:is_bagit] == true
+        att.update_column(:con_state, Labimotion::ConState::CONVERTED)
+        Labimotion::Converter.metadata(id)
+        Labimotion::ConState::COMPLETED
+      elsif result[:metadata] == nil
         Labimotion::ConState::NONE
       else
         data = process(att, id, content)
@@ -29,7 +33,9 @@ def self.is_brucker_binary(id)
           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
+              return { is_bagit: false, metadata: metadata }
+            elsif entry.name.include?('metadata/') && entry.name.include?('converter.json')
+              return { is_bagit: true, metadata: nil }
             end
           end
         end
@@ -39,13 +45,15 @@ def self.is_brucker_binary(id)
             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
+                return { is_bagit: false, metadata: metadata }
+              elsif entry.name.include?('metadata/') && entry.name.include?('converter.json')
+                return { is_bagit: true, metadata: nil }
               end
             end
           end
         end
       end
-      nil
+      { is_bagit: false, metadata: nil }
     end
 
     def self.process(att, id, content)

lib/labimotion/version.rb

@@ -3,9 +3,5 @@
 ## Labimotion Version
 module Labimotion
   IS_RAILS5 = false
-  VERSION_ELN = '1.0.19'
-  VERSION_REPO = '0.3.1'
-
-  VERSION = Labimotion::VERSION_REPO if Labimotion::IS_RAILS5 == true
-  VERSION = Labimotion::VERSION_ELN if Labimotion::IS_RAILS5 == false
+  VERSION = '1.1.0'
 end