Class: Labimotion::Converter

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

Class Method Summary collapse

Class Method Details

.auth ⇒ Object 



66
67
68
 
# File 'lib/labimotion/libs/converter.rb', line 66

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

.build_ds(att_id, ols) ⇒ Object 



205
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 205

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,
    metadata: klass.metadata
  )
end

.clean_dsr(att_id) ⇒ Object 



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

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

.client_id ⇒ Object 



58
59
60
 
# File 'lib/labimotion/libs/converter.rb', line 58

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

.collect_metadata(zip_file, current_user = {}) ⇒ Object

rubocop: disable Metrics/PerceivedComplexity



96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
 
# File 'lib/labimotion/libs/converter.rb', line 96

def self.collect_metadata(zip_file, current_user = {}) # 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 



297
298
299
300
301
 
# File 'lib/labimotion/libs/converter.rb', line 297

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 



315
316
317
318
319
320
321
322
323
324
325
326
327
328
 
# File 'lib/labimotion/libs/converter.rb', line 315

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 



70
71
72
 
# File 'lib/labimotion/libs/converter.rb', line 70

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

.delete_profile(id) ⇒ Object 



291
292
293
294
295
 
# File 'lib/labimotion/libs/converter.rb', line 291

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 



54
55
56
 
# File 'lib/labimotion/libs/converter.rb', line 54

def self.extname
  '.jdx'
end

.fetch_dsr(att_id) ⇒ Object 



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

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

.fetch_options ⇒ Object 



285
286
287
288
289
 
# File 'lib/labimotion/libs/converter.rb', line 285

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 



309
310
311
312
313
 
# File 'lib/labimotion/libs/converter.rb', line 309

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 



191
192
193
194
195
196
197
198
199
200
201
202
203
 
# File 'lib/labimotion/libs/converter.rb', line 191

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, current_user = {}) ⇒ Object

rubocop: disable Metrics/PerceivedComplexity



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
 
# File 'lib/labimotion/libs/converter.rb', line 118

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

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

    filename = oat.filename
    name = "#{File.basename(filename, '.*')}#{File.extname(filename) == '.zip' ? '.bagit.zip' : '.zip'}"
    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, current_user)
  rescue StandardError => e
    raise e
  ensure
    tmp_file&.close
  end
end

.header(opt = {}) ⇒ Object 



82
83
84
 
# File 'lib/labimotion/libs/converter.rb', line 82

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

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



181
182
183
184
185
186
187
188
189
 
# File 'lib/labimotion/libs/converter.rb', line 181

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

  Labimotion::Converter.process(data, current_user)
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 



18
19
20
 
# File 'lib/labimotion/libs/converter.rb', line 18

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

.metadata(id, current_user) ⇒ Object 



361
362
363
364
365
366
367
368
 
# File 'lib/labimotion/libs/converter.rb', line 361

def self.metadata(id, current_user)
  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, current_user) if ds.nil?
end

.process(data, current_user = {}) ⇒ Object

rubocop: disable Metrics/PerceivedComplexity



150
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
 
# File 'lib/labimotion/libs/converter.rb', line 150

def self.process(data, current_user = {}) # rubocop: disable Metrics/PerceivedComplexity
  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, current_user)
      Labimotion::ConState::PROCESSED
    else
      Labimotion::Converter.logger.error ["Converter Response Error: id: [#{data[:a]&.id}], filename: [#{data[:a]&.filename}], response: #{response}"].join($INPUT_RECORD_SEPARATOR)
      Labimotion::ConState::ERROR
    end
  rescue StandardError => e
    Labimotion::Converter.logger.error ["process fail: #{data[:a]&.id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
    Labimotion::ConState::ERROR
  ensure
    FileUtils.rm_f(ofile)
  end
end

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



22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
 
# File 'lib/labimotion/libs/converter.rb', line 22

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, current_user) 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

.restore(profile_id, version, hard) ⇒ Object 



345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
 
# File 'lib/labimotion/libs/converter.rb', line 345

def self.restore(profile_id, version, hard)
  body = { hard: hard }
  response = HTTParty.post(
    uri("profiles/restore/#{profile_id}/#{version}"),
    headers: {
      "Content-Type" => "application/json"
    },
    basic_auth: auth,
    body: body.to_json,
    timeout: timeout,
  )
  res = response.parsed_response

  res
end

.secret_key ⇒ Object 



62
63
64
 
# File 'lib/labimotion/libs/converter.rb', line 62

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

.signature(jbody) ⇒ Object 



74
75
76
77
78
79
80
 
# File 'lib/labimotion/libs/converter.rb', line 74

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

.test_conversions(tmpfile, format) ⇒ Object 



330
331
332
333
334
335
336
337
338
339
340
341
342
343
 
# File 'lib/labimotion/libs/converter.rb', line 330

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

.timeout ⇒ Object 



50
51
52
 
# File 'lib/labimotion/libs/converter.rb', line 50

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

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



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

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
268
269
270
271
 
# 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

  container = dataset.element

  # Extract and update general description fields
  general_dsr = dsr.select { |ds| ds[:layer] == 'general' }
  if general_dsr.present?
    date = general_dsr.find { |ds| ds[:field] == 'date' }&.dig(:value)
    time = general_dsr.find { |ds| ds[:field] == 'time' }&.dig(:value)
    Labimotion::ConverterHelpers.update_general_description(container, current_user, date: date, time: time)
  else
    Labimotion::ConverterHelpers.update_general_description(container, current_user)
  end

  dsr.each do |ds|
    layer = layers[ds[:layer]]
    next if layer.blank? || layer[Labimotion::Prop::FIELDS].blank?
    is_unit = ds[:field].start_with?(Prop::CONVERTER_FIELD_UINT_PREFIX)
    next if is_unit && ds[:value].nil?

    field_name = ds[:field].delete_prefix(Prop::CONVERTER_FIELD_UINT_PREFIX)

    fields = layer[Labimotion::Prop::FIELDS].select{ |f| f['field'] == field_name }
    fi = fields&.first
    next if fi.blank?

    idx = layer[Labimotion::Prop::FIELDS].find_index(fi)
    if is_unit
      fi['value_system'] = ds[:value]
    else
      fi['value'] = ds[:value]
      fi['device'] = ds[:device] || ds[:value]
    end
    new_prop[Labimotion::Prop::LAYERS][ds[:layer]][Labimotion::Prop::FIELDS][idx] = fi
  end
  element = Container.find(dataset.element_id)&.root_element
  new_prop = Labimotion::VocabularyHandler.update_vocabularies(new_prop, current_user, element)
  dataset.properties = new_prop
  dataset.save!
end

.update_profile(data) ⇒ Object 



303
304
305
306
307
 
# File 'lib/labimotion/libs/converter.rb', line 303

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 



45
46
47
48
 
# File 'lib/labimotion/libs/converter.rb', line 45

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

.vor_conv(id) ⇒ Object 



86
87
88
89
90
91
92
93
94
 
# File 'lib/labimotion/libs/converter.rb', line 86

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