Class: Labimotion::NmrMapper

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

Overview

NmrMapper

Class Method Summary collapse

Class Method Details

.build_ds(id, content) ⇒ Object 



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# File 'lib/labimotion/libs/nmr_mapper.rb', line 281

def self.build_ds(id, content)
  ds = Container.find_by(id: id)
  return if ds.nil? || content.nil?

  ols = content[:ols]
  metadata = content[:metadata]

  return if ols.nil? || metadata.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'
  dataset = Labimotion::Dataset.create!(
    uuid: uuid,
    dataset_klass_id: klass.id,
    element_type: 'Container',
    element_id: ds.id,
    properties: props,
    properties_release: klass.properties_release,
    klass_uuid: klass.uuid,
  )
  { dataset: dataset, metadata: metadata, ols: ols }
end

.clean(id) ⇒ Object 



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# File 'lib/labimotion/libs/nmr_mapper.rb', line 277

def self.clean(id)
  Labimotion::NmrMapper.ts('delete', id)
end

.fetch_content(id) ⇒ Object 



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# File 'lib/labimotion/libs/nmr_mapper.rb', line 78

def self.fetch_content(id)
  atts = Attachment.where(attachable_id: id)
  return if atts.nil?

  atts.each do |att|
    content = Labimotion::NmrMapper.ts('read', att.id)
    return content if content.present?
  end
end

.generate_ds(id, cid, data, current_user = {}) ⇒ Object 



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

def self.generate_ds(id, cid, data, current_user = {})
  return if data.nil? || cid.nil?

  obj = Labimotion::NmrMapper.build_ds(cid, data[:content])
  return if obj.nil? || obj[:ols].nil?

  Labimotion::NmrMapper.update_ds_1h(cid, obj, current_user) if obj[:ols] == 'CHMO:0000593'
  Labimotion::NmrMapper.update_ds_1h(cid, obj, current_user) if obj[:ols] == 'CHMO:0000595'
end

.is_brucker_binary(id) ⇒ Object 



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# File 'lib/labimotion/libs/nmr_mapper.rb', line 27

def self.is_brucker_binary(id)
  att = Attachment.find_by(id: id, con_state: Labimotion::ConState::NMR)
  return if att.nil?

  if Labimotion::IS_RAILS5 == true
    Zip::File.open(att.store.path) do |zip_file|
      zip_file.each do |entry|
        if entry.name.include?('/pdata/') && entry.name.include?('parm.txt')
          metadata = entry.get_input_stream.read.force_encoding('UTF-8')
          return { is_bagit: false, metadata: metadata }
        elsif entry.name.include?('metadata/') && entry.name.include?('converter.json')
          return { is_bagit: true, metadata: nil }
        end
      end
    end
  else
    if att&.attachment_attacher&.file&.url
      Zip::File.open(att.attachment_attacher.file.url) do |zip_file|
        zip_file.each do |entry|
          if entry.name.include?('/pdata/') && entry.name.include?('parm.txt')
            metadata = entry.get_input_stream.read.force_encoding('UTF-8')
            return { is_bagit: false, metadata: metadata }
          elsif entry.name.include?('metadata/') && entry.name.include?('converter.json')
            return { is_bagit: true, metadata: nil }
          end
        end
      end
    end
  end
  { is_bagit: false, metadata: nil }
end

.process(att, id, content) ⇒ Object 



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# File 'lib/labimotion/libs/nmr_mapper.rb', line 59

def self.process(att, id, content)
  return if att.nil? || content.nil?

  lines = content.split("\n").reject(&:empty?)
  metadata = {}
  lines.map do |ln|
    arr = ln.split(/\s+/)
    metadata[arr[0]] = arr[1..-1].join(' ') if arr.length > 1
  end
  ols = 'CHMO:0000593' if metadata['NUC1'] == '1H'
  ols = 'CHMO:0000595' if metadata['NUC1'] == '13C'

  { content: { metadata: metadata, ols: ols } }
  # if content.present? && att.present?
  #   Labimotion::NmrMapper.ts('write', att.attachable_id,
  #                         content: { metadata: metadata, ols: ols })
  # end
end

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



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# File 'lib/labimotion/libs/nmr_mapper.rb', line 9

def self.process_ds(id, current_user = {})
  att = Attachment.find_by(id: id, con_state: Labimotion::ConState::NMR)
  return if att.nil?

  result = is_brucker_binary(id)
  if result[:is_bagit] == true
    att.update_column(:con_state, Labimotion::ConState::CONVERTED)
    Labimotion::Converter.metadata(id)
    Labimotion::ConState::COMPLETED
  elsif result[:metadata] == nil
    Labimotion::ConState::NONE
  else
    data = process(att, id, result[:metadata])
    generate_ds(id, att.attachable_id, data, current_user)
    Labimotion::ConState::COMPLETED
  end
end

.set_data(prop, field, idx, layer_name, field_name, value) ⇒ Object 



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# File 'lib/labimotion/libs/nmr_mapper.rb', line 108

def self.set_data(prop, field, idx, layer_name, field_name, value)
  return if field['field'] != field_name || value&.empty?

  field['value'] = value
  prop['layers'][layer_name]['fields'][idx] = field
  prop
end

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



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# File 'lib/labimotion/libs/nmr_mapper.rb', line 273

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

.update_ds_13c(id, obj) ⇒ Object 



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

def self.update_ds_13c(id, obj)
  # dataset = obj[:dataset]
  # metadata = obj[:metadata]
  # new_prop = dataset.properties

  # dataset.properties = new_prop
  # dataset.save!
end

.update_ds_1h(id, obj, current_user) ⇒ Object 



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# File 'lib/labimotion/libs/nmr_mapper.rb', line 116

def self.update_ds_1h(id, obj, current_user)
  dataset = obj[:dataset]
  metadata = obj[:metadata]
  new_prop = dataset.properties
  new_prop.dig('layers', 'general', 'fields')&.each_with_index do |fi, idx|
    #  new_prop = set_data(new_prop, fi, idx, 'general', 'title', metadata['NAME'])
    if fi['field'] == 'title' && metadata['NAME'].present?
      ## fi['label'] = fi['label']
      fi['value'] = metadata['NAME']
      fi['device'] = metadata['NAME']
      fi['dkey'] = 'NAME'
      new_prop['layers']['general']['fields'][idx] = fi
    end

    if fi['field'] == 'date' && metadata['Date_'].present?
      ## fi['label'] = fi['label']
      fi['value'] = metadata['Date_']
      fi['device'] = metadata['Date_']
      fi['dkey'] = 'Date_'
      new_prop['layers']['general']['fields'][idx] = fi
    end

    if fi['field'] == 'time' && metadata['Time'].present?
      ## fi['label'] = fi['label']
      fi['value'] = metadata['Time']
      fi['device'] = metadata['Time']
      fi['dkey'] = 'Time'
      new_prop['layers']['general']['fields'][idx] = fi
    end

    if fi['field'] == 'creator' && current_user.present?
      ## fi['label'] = fi['label']
      fi['value'] = current_user.name
      new_prop['layers']['general']['fields'][idx] = fi
    end
  end
  element = Container.find(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'] == 'label'
      fi['value'] = element.short_label
      new_prop['layers']['sample_details']['fields'][idx] = fi
    end
    if fi['field'] == 'id'
      fi['value'] = element.id
      new_prop['layers']['sample_details']['fields'][idx] = fi
    end
  end

  new_prop.dig('layers', 'instrument', 'fields')&.each_with_index do |fi, idx|
    if fi['field'] == 'instrument' && metadata['INSTRUM'].present?
      ## fi['label'] = fi['label']
      fi['value'] = metadata['INSTRUM']
      fi['device'] = metadata['INSTRUM']
      fi['dkey'] = 'INSTRUM'
      new_prop['layers']['instrument']['fields'][idx] = fi
    end
  end

  new_prop.dig('layers', 'equipment', 'fields')&.each_with_index do |fi, idx|
    if fi['field'] == 'probehead' && metadata['PROBHD'].present?
      ## fi['label'] = fi['label']
      fi['value'] = metadata['PROBHD']
      fi['device'] = metadata['PROBHD']
      fi['dkey'] = 'PROBHD'
      new_prop['layers']['equipment']['fields'][idx] = fi
    end
  end

  new_prop.dig('layers', 'sample_preparation', 'fields')&.each_with_index do |fi, idx|
    if fi['field'] == 'solvent' && metadata['SOLVENT'].present?
      ## fi['label'] = fi['label']
      fi['value'] = metadata['SOLVENT']
      fi['device'] = metadata['SOLVENT']
      fi['dkey'] = 'SOLVENT'
      fi['value'] = 'chloroform-D1 (CDCl3)' if metadata['SOLVENT'] == 'CDCl3'
      new_prop['layers']['sample_preparation']['fields'][idx] = fi
    end
  end

  new_prop.dig('layers', 'set', 'fields')&.each_with_index do |fi, idx|
    if fi['field'] == 'temperature' && metadata['TE'].present?
      ## fi['label'] = fi['label']
      fi['value'] = metadata['TE'].split(/\s+/).first
      fi['device'] = metadata['TE']
      fi['dkey'] = 'TE'
      fi['value_system'] = metadata['TE'].split(/\s+/).last
      new_prop['layers']['set']['fields'][idx] = fi
    end
    if fi['field'] == 'ns' && metadata['NS'].present?
      ## fi['label'] = fi['label']
      fi['value'] = metadata['NS']
      fi['device'] = metadata['NS']
      fi['dkey'] = 'NS'
      new_prop['layers']['set']['fields'][idx] = fi
    end
    if fi['field'] == 'PULPROG' && metadata['PULPROG'].present?
      ## fi['label'] = fi['label']
      fi['value'] = metadata['PULPROG']
      fi['device'] = metadata['PULPROG']
      fi['dkey'] = 'PULPROG'
      new_prop['layers']['set']['fields'][idx] = fi
    end
    if fi['field'] == 'td' && metadata['TD'].present?
      ## fi['label'] = fi['label']
      fi['value'] = metadata['TD']
      fi['device'] = metadata['TD']
      fi['dkey'] = 'TD'
      new_prop['layers']['set']['fields'][idx] = fi
    end
    if fi['field'] == 'done' && metadata['D1'].present?
      ## fi['label'] = fi['label']
      fi['value'] = metadata['D1']
      fi['device'] = metadata['D1']
      fi['dkey'] = 'D1'
      new_prop['layers']['set']['fields'][idx] = fi
    end
    if fi['field'] == 'sf' && metadata['SF'].present?
      ## fi['label'] = fi['label']
      fi['value'] = metadata['SF']
      fi['device'] = metadata['SF']
      fi['dkey'] = 'SF'
      new_prop['layers']['set']['fields'][idx] = fi
    end
    if fi['field'] == 'sfoone' && metadata['SFO1'].present?
      ## fi['label'] = fi['label']
      fi['value'] = metadata['SFO1']
      fi['device'] = metadata['SFO1']
      fi['dkey'] = 'SFO1'
      new_prop['layers']['set']['fields'][idx] = fi
    end
    if fi['field'] == 'sfotwo' && metadata['SFO2'].present?
      ## fi['label'] = fi['label']
      fi['value'] = metadata['SFO2']
      fi['device'] = metadata['SFO2']
      fi['dkey'] = 'SFO2'
      new_prop['layers']['set']['fields'][idx] = fi
    end
    if fi['field'] == 'nucone' && metadata['NUC1'].present?
      ## fi['label'] = fi['label']
      fi['value'] = metadata['NUC1']
      fi['device'] = metadata['NUC1']
      fi['dkey'] = 'NUC1'
      new_prop['layers']['set']['fields'][idx] = fi
    end
    if fi['field'] == 'nuctwo' && metadata['NUC2'].present?
      ## fi['label'] = fi['label']
      fi['value'] = metadata['NUC2']
      fi['device'] = metadata['NUC2']
      fi['dkey'] = 'NUC2'
      new_prop['layers']['set']['fields'][idx] = fi
    end
  end
  dataset.properties = new_prop
  dataset.save!
end