Class: Labimotion::Converter

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

Class Method Summary collapse

Class Method Details

.auth ⇒ Object 



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

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

.build_ds(att_id, ols) ⇒ Object 



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# File 'lib/labimotion/libs/converter.rb', line 235

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 



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# File 'lib/labimotion/libs/converter.rb', line 311

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

.client_id ⇒ Object 



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

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

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

rubocop: disable Metrics/PerceivedComplexity



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# File 'lib/labimotion/libs/converter.rb', line 126

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

.collect_reaction_converter_metadata(oat, zip_file) ⇒ Object 



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# File 'lib/labimotion/libs/converter.rb', line 99

def self.collect_reaction_converter_metadata(oat, zip_file)
  zip_file.each do |entry|
    next unless entry.name == 'metadata/reaction_variation.json'

    # Create temp file
    tmp_file = Tempfile.new(['reaction_variation', '.json'])
    tmp_file.binmode

    # Write ZIP entry content into temp file
    entry.extract(tmp_file.path) { true }

    # Create attachment
    att = Attachment.create!(
      filename: 'reaction_variation.json',
      file_path: tmp_file.path,
      content_type: 'application/json',
      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?
  end
end

.create_profile(data) ⇒ Object 



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# File 'lib/labimotion/libs/converter.rb', line 327

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 



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# File 'lib/labimotion/libs/converter.rb', line 345

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 



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# File 'lib/labimotion/libs/converter.rb', line 73

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

.delete_profile(id) ⇒ Object 



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# File 'lib/labimotion/libs/converter.rb', line 321

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 



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

def self.extname
  '.jdx'
end

.fetch_dsr(att_id) ⇒ Object 



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# File 'lib/labimotion/libs/converter.rb', line 307

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

.fetch_options ⇒ Object 



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# File 'lib/labimotion/libs/converter.rb', line 315

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 



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# File 'lib/labimotion/libs/converter.rb', line 339

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 



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# File 'lib/labimotion/libs/converter.rb', line 221

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



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# File 'lib/labimotion/libs/converter.rb', line 148

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 



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# File 'lib/labimotion/libs/converter.rb', line 85

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

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



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# File 'lib/labimotion/libs/converter.rb', line 211

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 



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# 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 



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# File 'lib/labimotion/libs/converter.rb', line 391

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



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# File 'lib/labimotion/libs/converter.rb', line 180

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 



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# 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|
    if att.filename.split('.')&.last == 'zip'
      res = Labimotion::Converter.collect_metadata(zip_file, current_user)
      Labimotion::Converter.collect_reaction_converter_metadata(att, zip_file)
    end
    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 



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# File 'lib/labimotion/libs/converter.rb', line 375

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 



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

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

.signature(jbody) ⇒ Object 



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# File 'lib/labimotion/libs/converter.rb', line 77

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 



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# File 'lib/labimotion/libs/converter.rb', line 360

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 



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

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

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



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# File 'lib/labimotion/libs/converter.rb', line 303

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



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# File 'lib/labimotion/libs/converter.rb', line 260

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 



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# File 'lib/labimotion/libs/converter.rb', line 333

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 



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

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

.vor_conv(id) ⇒ Object 



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# File 'lib/labimotion/libs/converter.rb', line 89

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