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 40

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 194

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

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

  uuid = SecureRandom.uuid
  props = klass.properties_release
  props['uuid'] = uuid
  props['eln'] = Chemotion::Application.config.version
  props['klass'] = 'Dataset'
  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 264

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

.client_id ⇒ Object 



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# File 'lib/labimotion/libs/converter.rb', line 32

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 70

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 280

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 298

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 44

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

.delete_profile(id) ⇒ Object 



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

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 28

def self.extname
  '.jdx'
end

.fetch_dsr(att_id) ⇒ Object 



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

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

.fetch_options ⇒ Object 



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# File 'lib/labimotion/libs/converter.rb', line 268

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 292

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 180

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

    dataset = Analyses::Converter.build_ds(att_id, dsr_info[:ols])
    Analyses::Converter.update_ds(dataset, dsr_info[:info], current_user)
  rescue StandardError => e
    Analyses::Converter.logger.error ["Att ID: #{att_id}, OLS: #{dsr_info[:ols]}", "DSR: #{dsr_info[:info]}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
  ensure
    Analyses::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 92

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',
      created_by: oat.created_by,
      created_for: oat.created_for,
    )
    # att.attachment_attacher.attach(tmp_file)

    if att.valid?
      # att.attachment_attacher.create_derivatives
      att.save!
    end
    Zip::File.open(tmp_file.path) do |zip_file|
      res = Analyses::Converter.collect_metadata(zip_file) if name.split('.')&.last == 'zip'
      ols = res[:o] unless res&.dig(:o).nil?
      dsr.push(res[:d]) unless res&.dig(:d).nil?
    end

    dsr.flatten!
    if dsr.length.positive? && name.split('.')&.last == 'zip'
      Analyses::Converter.ts('write', att.attachable_id, ols: ols, info: dsr)
    end
  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 56

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

.jcamp_converter(id) ⇒ Object 



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# File 'lib/labimotion/libs/converter.rb', line 165

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

    resp = Analyses::Converter.process(data)
    resp&.success? ? 'done' : 'failure'
  rescue StandardError => e
    Analyses::Converter.logger.error ["jcamp_converter fail: #{id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
  ensure
    resp&.success? ? 'done' : 'failure'
  end
end

.logger ⇒ Object 



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# File 'lib/labimotion/libs/converter.rb', line 15

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

.process(data) ⇒ Object 



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# File 'lib/labimotion/libs/converter.rb', line 137

def self.process(data)
  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?
      Analyses::Converter.handle_response(data[:a], response)
    else
      Analyses::Converter.logger.error ["Converter Response Error: id: [#{data[:a]&.id}], filename: [#{data[:a]&.filename}], response: #{response}"].join($INPUT_RECORD_SEPARATOR)
    end
    response
  rescue StandardError => e
    raise e
  ensure
    FileUtils.rm_f(ofile)
  end
end

.secret_key ⇒ Object 



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# File 'lib/labimotion/libs/converter.rb', line 36

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

.signature(jbody) ⇒ Object 



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

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 24

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 256

def self.ts(method, identifier, params = nil)
  Rails.cache.send(method, "#{Analyses::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 218

def self.update_ds(dataset, dsr, current_user = nil) # rubocop: disable Metrics/PerceivedComplexity
  layers = dataset.properties['layers'] || {}
  new_prop = dataset.properties
  dsr.each do |ds|
    layer = layers[ds[:layer]]
    fields = layer['fields'].select{ |f| f['field'] == ds[:field] }
    fi = fields&.first
    idx = layer['fields'].find_index(fi)
    fi['value'] = ds[:value]
    fi['device'] = ds[:device] || ds[:value]
    new_prop['layers'][ds[:layer]]['fields'][idx] = fi
  end
  new_prop.dig('layers', 'general', 'fields')&.each_with_index do |fi, idx|
    if fi['field'] == 'creator' && current_user.present?
      fi['label'] = fi['label']
      fi['value'] = current_user.name
      fi['system'] = current_user.name
      new_prop['layers']['general']['fields'][idx] = fi
    end
  end
  element = Container.find(dataset.element_id)&.root_element
  element.present? && element&.class&.name == 'Sample' && new_prop.dig('layers', 'sample_details', 'fields')&.each_with_index do |fi, idx|
    if fi['field'] == 'id'
      fi['value'] = element.id
      fi['system'] = element.id
      new_prop['layers']['general']['fields'][idx] = fi
    end

    if fi['field'] == 'label'
      fi['value'] = element.short_label
      fi['system'] = element.short_label
      new_prop['layers']['general']['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 286

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 19

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 60

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