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 42

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(['(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)
  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(['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([''])
rescue StandardError => e
  Labimotion.log_exception(e)
end

#export(id) ⇒ Object 



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# File 'lib/labimotion/libs/export_dataset.rb', line 68

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[Labimotion::Prop::LAYERS] || {}
  options = ds.properties[Labimotion::Prop::SEL_OPTIONS]
  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[Labimotion::Prop::FIELDS].sort_by { |obj| obj['position'] }
    sorted_fields.each do |field|
      next if field['type'] == 'dummy'

      type = field['type']
      from_device = field['device'].present? ? 'Device' : ''
      from_device = field['system'].present? ? 'Chemotion' : from_device
      type = "#{field['type']}-#{field['option_layers']}" if field['type'] == Labimotion::FieldType::SELECT || field['type'] == Labimotion::FieldType::SYSTEM_DEFINED

      show_value = field['value'] =~ /\A\d+,\d+\z/ ? field['value']&.gsub(',', '.') : field['value']
      ols_short_form = (field['ontology'] && field['ontology']['short_form']) || ''
      ols_label = (field['ontology'] && field['ontology']['label']) || ''
      ols_iri = (field['ontology'] && field['ontology']['iri']) || ''
      sheet.add_row([' ', field['label'], nil, field['value_system'], field['field'], type, from_device, field['dkey'], nil, ols_short_form, ols_label, ols_iri].freeze)

      case field['type']
      when Labimotion::FieldType::SELECT
        sheet.rows.last.cells[2].type = :string
        sheet.rows.last.cells[8].type = :string
        show_value = opt_value(field, options) if show_value.present?
      when Labimotion::FieldType::SYSTEM_DEFINED, Labimotion::FieldType::INTEGER
        sheet.rows.last.cells[2].type = :float
        sheet.rows.last.cells[8].type = :float
      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
rescue StandardError => e
  Labimotion.log_exception(e)
end

#header ⇒ Object 



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# File 'lib/labimotion/libs/export_dataset.rb', line 171

def header
  ['Layer Label', 'Field Label', 'Value', 'Unit', 'Name', 'Type', 'Source?', 'Source identifier', 'Source data', 'Ontology', 'Ontology Label', 'iri'].freeze
end

#ols_name(id) ⇒ Object 



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# File 'lib/labimotion/libs/export_dataset.rb', line 25

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)
rescue StandardError => e
  Labimotion.log_exception(e)
  'ols_name'
end

#opt_value(field, options) ⇒ Object 



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# File 'lib/labimotion/libs/export_dataset.rb', line 128

def opt_value(field, options)
  return nil if field.nil? || options.nil? || field['value']&.empty? || field['option_layers']&.empty?
  return nil unless opts = options.fetch(field['option_layers'], nil)&.fetch('options', nil)

  selected = opts&.find { |ss| ss['key'] == field['value'] }
  selected&.fetch('label', nil) || field['value']
rescue StandardError => e
  Labimotion.log_exception(e)
  field['value']
end

#read ⇒ Object 



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# File 'lib/labimotion/libs/export_dataset.rb', line 175

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"
rescue StandardError => e
  Labimotion.log_exception(e)
end

#spectra(id) ⇒ Object 



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# File 'lib/labimotion/libs/export_dataset.rb', line 139

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').order(:filename)
  csv_length = cds_csv.length
  return if csv_length.zero?
  cds_csv.each_with_index do |att, idx|
    sheet_name = "Sheet#{idx+1}"
    sheet = @xfile.workbook.add_worksheet(name: sheet_name)
    name_mapping.push([sheet_name, att.filename])
    File.open(att.attachment_url) do |fi|
      fi.each_line do |line|
        sheet.add_row(line.split(','))
      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