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 73

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 225

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 



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# File 'lib/labimotion/libs/converter.rb', line 296

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 65

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

.collect_metadata(zip_file) ⇒ Object

rubocop: disable Metrics/PerceivedComplexity



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# File 'lib/labimotion/libs/converter.rb', line 103

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 



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# File 'lib/labimotion/libs/converter.rb', line 312

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 330

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 77

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

.delete_profile(id) ⇒ Object 



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# File 'lib/labimotion/libs/converter.rb', line 306

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 61

def self.extname
  '.jdx'
end

.fetch_dsr(att_id) ⇒ Object 



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# File 'lib/labimotion/libs/converter.rb', line 292

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 300

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 324

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 211

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



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# File 'lib/labimotion/libs/converter.rb', line 125

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.attachment_attacher.attach(tmp_file)
    if att.valid? && Labimotion::IS_RAILS5 == false
      ## att.attachment_attacher.create_derivatives
      att.save!
    end
    if att.valid? && Labimotion::IS_RAILS5 == true
      att.save!
      primary_store = Rails.configuration.storage.primary_store
      att.update!(storage: primary_store)
    end
    process_ds(att.id)
  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 89

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

.jcamp_converter(id) ⇒ Object 



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# File 'lib/labimotion/libs/converter.rb', line 201

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 



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# 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 



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

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 



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# File 'lib/labimotion/libs/converter.rb', line 166

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)
    if Labimotion::IS_RAILS5 == true
      FileUtils.cp(data[:a].store.path, ofile)
    else
      FileUtils.cp(data[:a].attachment_url, ofile)
    end

    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 



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# 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
  if Labimotion::IS_RAILS5 == true
    Zip::File.open(att.store.path) 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
  else
    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
  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 



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

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

.signature(jbody) ⇒ Object 



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

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 



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

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 288

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 249

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 



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# File 'lib/labimotion/libs/converter.rb', line 318

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 52

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 93

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