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.



10
11
12
13
14
 
# File 'lib/labimotion/libs/export_dataset.rb', line 10

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 



36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
 
# File 'lib/labimotion/libs/export_dataset.rb', line 36

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 



60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
 
# File 'lib/labimotion/libs/export_dataset.rb', line 60

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 



112
113
114
 
# File 'lib/labimotion/libs/export_dataset.rb', line 112

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

#ols_name(id) ⇒ Object 



22
23
24
25
26
27
28
29
30
31
32
33
34
 
# File 'lib/labimotion/libs/export_dataset.rb', line 22

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 > 2 ? 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 



116
117
118
 
# File 'lib/labimotion/libs/export_dataset.rb', line 116

def read
  @xfile.to_stream.read
end

#res_name(id) ⇒ Object 



16
17
18
19
20
 
# File 'lib/labimotion/libs/export_dataset.rb', line 16

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 



97
98
99
100
101
102
103
104
105
106
107
108
109
110
 
# File 'lib/labimotion/libs/export_dataset.rb', line 97

def spectra(id)
  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|
    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(','))
      end
    end
  end
end