Class: Labimotion::Converter

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

Class Method Summary collapse

Class Method Details

.auth ⇒ Object 



65
66
67
 
# File 'lib/labimotion/libs/converter.rb', line 65

def self.auth
  { username: client_id, password: secret_key }
end

.build_ds(att_id, ols) ⇒ Object 



206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
 
# File 'lib/labimotion/libs/converter.rb', line 206

def self.build_ds(att_id, ols)
  cds = Container.find_by(id: att_id)
  dataset = Labimotion::Dataset.find_by(element_type: 'Container', element_id: cds.id)
  return dataset unless dataset.nil?

  klass = Labimotion::DatasetKlass.find_by(ols_term_id: ols)
  return if klass.nil?

  uuid = SecureRandom.uuid
  props = klass.properties_release
  props['uuid'] = uuid
  props['pkg'] = Labimotion::Utils.pkg(props['pkg'])
  props['klass'] = 'Dataset'
  Labimotion::Dataset.create!(
    uuid: uuid,
    dataset_klass_id: klass.id,
    element_type: 'Container',
    element_id: cds.id,
    properties: props,
    properties_release: klass.properties_release,
    klass_uuid: klass.uuid
  )
end

.clean_dsr(att_id) ⇒ Object 



277
278
279
 
# File 'lib/labimotion/libs/converter.rb', line 277

def self.clean_dsr(att_id)
  Labimotion::Converter.ts('delete', att_id)
end

.client_id ⇒ Object 



57
58
59
 
# File 'lib/labimotion/libs/converter.rb', line 57

def self.client_id
  Rails.configuration.converter.profile || ''
end

.collect_metadata(zip_file) ⇒ Object

rubocop: disable Metrics/PerceivedComplexity



95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
 
# File 'lib/labimotion/libs/converter.rb', line 95

def self.collect_metadata(zip_file) # rubocop: disable Metrics/PerceivedComplexity
  dsr = []
  ols = nil
  zip_file.each do |entry|
    next unless entry.name == 'metadata/converter.json'

    metadata = entry.get_input_stream.read.force_encoding('UTF-8')
    jdata = JSON.parse(metadata)

    ols = jdata['ols']
    matches = jdata['matches']
    matches&.each do |match|
      idf = match['identifier']
      idr = match['result']
      if idf&.class == Hash && idr&.class == Hash && !idf['outputLayer'].nil? && !idf['outputKey'].nil? && !idr['value'].nil? # rubocop:disable Layout/LineLength
        dsr.push(layer: idf['outputLayer'], field: idf['outputKey'], value: idr['value'])
      end
    end
  end
  { d: dsr, o: ols }
end

.create_profile(data) ⇒ Object 



293
294
295
296
297
 
# File 'lib/labimotion/libs/converter.rb', line 293

def self.create_profile(data)
  options = { basic_auth: auth, timeout: timeout, body: data.to_json, headers: { 'Content-Type' => 'application/json' } }
  response = HTTParty.post(uri('profiles'), options)
  response.parsed_response if response.code == 201
end

.create_tables(tmpfile) ⇒ Object 



311
312
313
314
315
316
317
318
319
320
321
322
323
324
 
# File 'lib/labimotion/libs/converter.rb', line 311

def self.create_tables(tmpfile)
  res = {}
  File.open(tmpfile.path, 'r') do |file|
    body = { file: file }
    response = HTTParty.post(
      uri('tables'),
      basic_auth: auth,
      body: body,
      timeout: timeout,
    )
    res = response.parsed_response
  end
  res
end

.date_time ⇒ Object 



69
70
71
 
# File 'lib/labimotion/libs/converter.rb', line 69

def self.date_time
  DateTime.now.strftime('%Q')
end

.delete_profile(id) ⇒ Object 



287
288
289
290
291
 
# File 'lib/labimotion/libs/converter.rb', line 287

def self.delete_profile(id)
  options = { basic_auth: auth, timeout: timeout }
  response = HTTParty.delete("#{uri('profiles')}/#{id}", options)
  response.parsed_response if response.code == 200
end

.extname ⇒ Object 



53
54
55
 
# File 'lib/labimotion/libs/converter.rb', line 53

def self.extname
  '.jdx'
end

.fetch_dsr(att_id) ⇒ Object 



273
274
275
 
# File 'lib/labimotion/libs/converter.rb', line 273

def self.fetch_dsr(att_id)
  Labimotion::Converter.ts('read', att_id)
end

.fetch_options ⇒ Object 



281
282
283
284
285
 
# File 'lib/labimotion/libs/converter.rb', line 281

def self.fetch_options
  options = { basic_auth: auth, timeout: timeout }
  response = HTTParty.get(uri('options'), options)
  response.parsed_response if response.code == 200
end

.fetch_profiles ⇒ Object 



305
306
307
308
309
 
# File 'lib/labimotion/libs/converter.rb', line 305

def self.fetch_profiles
  options = { basic_auth: auth, timeout: timeout }
  response = HTTParty.get(uri('profiles'), options)
  response.parsed_response if response.code == 200
end

.generate_ds(att_id, current_user = {}) ⇒ Object 



192
193
194
195
196
197
198
199
200
201
202
203
204
 
# File 'lib/labimotion/libs/converter.rb', line 192

def self.generate_ds(att_id, current_user = {})
  dsr_info = Labimotion::Converter.fetch_dsr(att_id)
  begin
    return unless dsr_info && dsr_info[:info]&.length.positive?

    dataset = Labimotion::Converter.build_ds(att_id, dsr_info[:ols])
    Labimotion::Converter.update_ds(dataset, dsr_info[:info], current_user) if dataset.present?
  rescue StandardError => e
    Labimotion::Converter.logger.error ["Att ID: #{att_id}, OLS: #{dsr_info[:ols]}", "DSR: #{dsr_info[:info]}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
  ensure
    Labimotion::Converter.clean_dsr(att_id)
  end
end

.handle_response(oat, response) ⇒ Object

rubocop: disable Metrics/PerceivedComplexity



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/converter.rb', line 117

def self.handle_response(oat, response) # rubocop: disable Metrics/PerceivedComplexity
  dsr = []
  ols = nil

  begin
    tmp_file = Tempfile.new(encoding: 'ascii-8bit')
    tmp_file.write(response.parsed_response)
    tmp_file.rewind

    name = response&.headers && response&.headers['content-disposition']&.split('=')&.last
    filename = oat.filename
    name = "#{File.basename(filename, '.*')}.zip" if name.nil?

    att = Attachment.new(
      filename: name,
      file_path: tmp_file.path,
      ## content_type: file[:type],
      attachable_id: oat.attachable_id,
      attachable_type: 'Container',
      con_state: Labimotion::ConState::CONVERTED,
      created_by: oat.created_by,
      created_for: oat.created_for,
    )

    att.save! if att.valid?

    process_ds(att.id)
  rescue StandardError => e
    raise e
  ensure
    tmp_file&.close
  end
end

.header(opt = {}) ⇒ Object 



81
82
83
 
# File 'lib/labimotion/libs/converter.rb', line 81

def self.header(opt = {})
  opt || {}
end

.jcamp_converter(id) ⇒ Object 



182
183
184
185
186
187
188
189
190
 
# File 'lib/labimotion/libs/converter.rb', line 182

def self.jcamp_converter(id)
  data = Labimotion::Converter.vor_conv(id)
  return if data.nil?

  Labimotion::Converter.process(data)
rescue StandardError => e
  Labimotion::Converter.logger.error ["jcamp_converter fail: #{id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
  Labimotion::ConState::ERROR
end

.logger ⇒ Object 



17
18
19
 
# File 'lib/labimotion/libs/converter.rb', line 17

def self.logger
  @@converter_logger ||= Logger.new(Rails.root.join('log/converter.log')) # rubocop:disable Style/ClassVars
end

.metadata(id) ⇒ Object 



326
327
328
329
330
331
332
333
 
# File 'lib/labimotion/libs/converter.rb', line 326

def self.metadata(id)
  att = Attachment.find(id)
  return if att.nil? || att.attachable_id.nil? || att.attachable_type != Labimotion::Prop::CONTAINER

  ds = Labimotion::Dataset.find_by(element_type: Labimotion::Prop::CONTAINER, element_id: att.attachable_id)
  att.update_column(:con_state, Labimotion::ConState::COMPLETED) if ds.present?
  process_ds(att.id) if ds.nil?
end

.process(data) ⇒ Object 



151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
 
# File 'lib/labimotion/libs/converter.rb', line 151

def self.process(data)
  return data[:a].con_state if data[:a]&.attachable_type != 'Container'
  response = nil
  begin
    ofile = Rails.root.join(data[:f], data[:a].filename)
    FileUtils.cp(data[:a].attachment_url, ofile)

    File.open(ofile, 'r') do |f|
      body = { file: f }
      response = HTTParty.post(
        uri('conversions'),
        basic_auth: auth,
        body: body,
        timeout: timeout,
      )
    end
    if response.ok?
      Labimotion::Converter.handle_response(data[:a], response)
      Labimotion::ConState::PROCESSED
    else
      Labimotion::Converter.logger.error ["Converter Response Error: id: [#{data[:a]&.id}], filename: [#{data[:a]&.filename}], response: #{response}"].join($INPUT_RECORD_SEPARATOR)
      Labimotion::ConState::ERROR
    end
  rescue StandardError => e
    Labimotion::Converter.logger.error ["process fail: #{id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
    Labimotion::ConState::ERROR
  ensure
    FileUtils.rm_f(ofile)
  end
end

.process_ds(id, current_user = {}) ⇒ Object 



21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
 
# File 'lib/labimotion/libs/converter.rb', line 21

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' || 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
  Zip::File.open(att.attachment_attacher.file.url) do |zip_file|
    res = Labimotion::Converter.collect_metadata(zip_file) if att.filename.split('.')&.last == 'zip'
    ols = res[:o] unless res&.dig(:o).nil?
    dsr.push(res[:d]) unless res&.dig(:d).nil?
  end
  dsr.flatten!
  dataset = build_ds(att.attachable_id, ols)
  update_ds(dataset, dsr, current_user) if dataset.present?
  att.update_column(:con_state, Labimotion::ConState::COMPLETED)
rescue StandardError => e
  Labimotion::Converter.logger.error ["Att ID: #{att&.id}, OLS: #{ols}", "DSR: #{dsr}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
  raise e
end

.secret_key ⇒ Object 



61
62
63
 
# File 'lib/labimotion/libs/converter.rb', line 61

def self.secret_key
  Rails.configuration.converter.secret_key || ''
end

.signature(jbody) ⇒ Object 



73
74
75
76
77
78
79
 
# File 'lib/labimotion/libs/converter.rb', line 73

def self.signature(jbody)
  md5 = Digest::MD5.new
  md5.update jbody
  mdhex = md5.hexdigest
  mdall = mdhex << secret_key
  @signature = Digest::SHA1.hexdigest mdall
end

.timeout ⇒ Object 



49
50
51
 
# File 'lib/labimotion/libs/converter.rb', line 49

def self.timeout
  Rails.configuration.try(:converter).try(:timeout) || 30
end

.ts(method, identifier, params = nil) ⇒ Object 



269
270
271
 
# File 'lib/labimotion/libs/converter.rb', line 269

def self.ts(method, identifier, params = nil)
  Rails.cache.send(method, "#{Labimotion::Converter.new.class.name}#{identifier}", params)
end

.update_ds(dataset, dsr, current_user = nil) ⇒ Object

rubocop: disable Metrics/PerceivedComplexity



230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
 
# File 'lib/labimotion/libs/converter.rb', line 230

def self.update_ds(dataset, dsr, current_user = nil) # rubocop: disable Metrics/PerceivedComplexity
  layers = dataset.properties[Labimotion::Prop::LAYERS] || {}
  new_prop = dataset.properties
  dsr.each do |ds|
    layer = layers[ds[:layer]]
    next if layer.nil? || layer[Labimotion::Prop::FIELDS].nil?

    fields = layer[Labimotion::Prop::FIELDS].select{ |f| f['field'] == ds[:field] }
    fi = fields&.first
    idx = layer[Labimotion::Prop::FIELDS].find_index(fi)
    fi['value'] = ds[:value]
    fi['device'] = ds[:device] || ds[:value]
    new_prop[Labimotion::Prop::LAYERS][ds[:layer]][Labimotion::Prop::FIELDS][idx] = fi
  end
  new_prop.dig(Labimotion::Prop::LAYERS, 'general', Labimotion::Prop::FIELDS)&.each_with_index do |fi, idx|
    if fi['field'] == 'creator' && current_user.present?
      fi['value'] = current_user.name
      fi['system'] = current_user.name
      new_prop[Labimotion::Prop::LAYERS]['general'][Labimotion::Prop::FIELDS][idx] = fi
    end
  end
  element = Container.find(dataset.element_id)&.root_element
  element.present? && element&.class&.name == 'Sample' && new_prop.dig(Labimotion::Prop::LAYERS, 'sample_details', Labimotion::Prop::FIELDS)&.each_with_index do |fi, idx|
    if fi['field'] == 'id'
      fi['value'] = element.id
      fi['system'] = element.id
      new_prop[Labimotion::Prop::LAYERS]['sample_details'][Labimotion::Prop::FIELDS][idx] = fi
    end

    if fi['field'] == 'label'
      fi['value'] = element.short_label
      fi['system'] = element.short_label
      new_prop[Labimotion::Prop::LAYERS]['sample_details'][Labimotion::Prop::FIELDS][idx] = fi
    end
  end
  dataset.properties = new_prop
  dataset.save!
end

.update_profile(data) ⇒ Object 



299
300
301
302
303
 
# File 'lib/labimotion/libs/converter.rb', line 299

def self.update_profile(data)
  options = { basic_auth: auth, timeout: timeout, body: data.to_json, headers: { 'Content-Type' => 'application/json' } }
  response = HTTParty.put("#{uri('profiles')}/#{data[:id]}", options)
  response.parsed_response if response.code == 200
end

.uri(api_name) ⇒ Object 



44
45
46
47
 
# File 'lib/labimotion/libs/converter.rb', line 44

def self.uri(api_name)
  url = Rails.configuration.converter.url
  "#{url}#{api_name}"
end

.vor_conv(id) ⇒ Object 



85
86
87
88
89
90
91
92
93
 
# File 'lib/labimotion/libs/converter.rb', line 85

def self.vor_conv(id)
  conf = Rails.configuration.try(:converter).try(:url)
  oa = Attachment.find(id)
  folder = Rails.root.join('tmp/uploads/converter')
  FileUtils.mkdir_p(folder)
  return nil if conf.nil? || oa.nil?

  { a: oa, f: folder }
end