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.



11
12
13
14
15
 
# 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 



37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
 
# 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(['(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([''])
end

#export(id) ⇒ Object 



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
96
97
98
99
100
101
102
103
104
105
106
107
108
 
# 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? ? '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'], 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

#header ⇒ Object 



151
152
153
 
# File 'lib/labimotion/libs/export_dataset.rb', line 151

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

#ols_name(id) ⇒ Object 



23
24
25
26
27
28
29
30
31
32
33
34
35
 
# 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 



155
156
157
 
# File 'lib/labimotion/libs/export_dataset.rb', line 155

def read
  @xfile.to_stream.read
end

#res_name(id) ⇒ Object 



17
18
19
20
21
 
# 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 



110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
 
# File 'lib/labimotion/libs/export_dataset.rb', line 110

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])

    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

  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