Class: Labimotion::ExportDataset

Inherits:
Object
  • Object
show all
Defined in:
lib/labimotion/libs/export_dataset.rb

Overview

ExportDataset

Constant Summary collapse

DEFAULT_ROW_WIDTH = 
100
DEFAULT_ROW_HEIGHT = 
20

Instance Method Summary collapse

Constructor Details

#initialize(**args) ⇒ ExportDataset

Returns a new instance of ExportDataset.



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# File 'lib/labimotion/libs/export_dataset.rb', line 11

def initialize(**args)
  @xfile = Axlsx::Package.new
  @file_extension = 'xlsx'
  @xfile.workbook.styles.fonts.first.name = 'Calibri'
end

Instance Method Details

#description(ds, id) ⇒ Object 



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# File 'lib/labimotion/libs/export_dataset.rb', line 37

def description(ds, id)
  wb = @xfile.workbook
  sheet = @xfile.workbook.add_worksheet(name: 'Description')
  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([''])
  sheet.add_row(['Fields description of sheet:' + ds.dataset_klass.label])
  sheet.add_row(['Fields', 'Field description'], style: header_style)
  sheet.add_row(['Layer Label', 'The label of the layer'])
  sheet.add_row(['Field Label', 'The label of the field'])
  sheet.add_row(['Value', 'The current value of the field'])
  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([''])
  sheet.add_row([''])
  sheet.add_row(['', '(This file is automatically generated by the system.)'])
end

#export(id) ⇒ Object 



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# File 'lib/labimotion/libs/export_dataset.rb', line 61

def export(id)
  ds = Labimotion::Dataset.find_by(element_id: id, element_type: 'Container')
  return if ds.nil?

  description(ds, id)

  wb = @xfile.workbook
  name = ols_name(id)
  return if name.nil?

  sheet = @xfile.workbook.add_worksheet(name: name)
  sheet.add_row([ds.dataset_klass.label])
  header_style = sheet.styles.add_style(sz: 12, fg_color: 'FFFFFF', bg_color: '00008B', border: { style: :thick, color: 'FF777777', edges: [:bottom] })
  layer_style = sheet.styles.add_style(b: true, bg_color: 'CEECF5')
  sheet.add_row(header, style: header_style)

  layers = ds.properties['layers'] || {}
  layer_keys = layers.keys.sort_by { |key| layers[key]['position'] }
  layer_keys.each do |key|
    layer = layers[key]
    sheet.add_row([layer['label'], ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' '], style: layer_style)
    sorted_fields = layer['fields'].sort_by { |obj| obj['position'] }
    sorted_fields.each do |field|
      next if field['type'] == 'dummy'

      type = field['type']
      from_device = field['device'].present? ? 'Yes' : 'No'
      from_device = field['system'].present? ? 'SYS' : 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)
    end
    # sheet.column_widths nil, nil, nil, nil, 0, 0, 0, 0, 0
  end
end

#header ⇒ Object 



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# File 'lib/labimotion/libs/export_dataset.rb', line 127

def header
  ['Layer Label', 'Field Label', 'Value', 'Unit', 'Name', 'Type', 'from device?', 'Device source', 'Device data'].freeze
end

#ols_name(id) ⇒ Object 



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# File 'lib/labimotion/libs/export_dataset.rb', line 23

def ols_name(id)
  ds = Labimotion::Dataset.find_by(element_id: id, element_type: 'Container')
  return nil if ds.nil?

  name = ds.dataset_klass.label

  match = name.match(/\((.*?)\)/)
  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'
  name.slice(0, 26)
end

#read ⇒ Object 



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# File 'lib/labimotion/libs/export_dataset.rb', line 131

def read
  @xfile.to_stream.read
end

#res_name(id) ⇒ Object 



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# File 'lib/labimotion/libs/export_dataset.rb', line 17

def res_name(id)
  element_name = Container.find(id)&.root_element&.short_label
  ols = ols_name(id)
  "#{element_name}_#{ols.gsub(' ', '_')}.xlsx"
end

#spectra(id) ⇒ Object 



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# File 'lib/labimotion/libs/export_dataset.rb', line 98

def spectra(id)
  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')
  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 = @xfile.workbook.add_worksheet(name: sheet_name)

    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
end