Class: Labimotion::NmrMapperRepo

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

Class Method Summary collapse

Class Method Details

.build_ds(id, content) ⇒ Object 



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# File 'lib/labimotion/libs/nmr_mapper_repo.rb', line 226

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 = 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 = 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_repo.rb', line 222

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

.fetch_content(id) ⇒ Object 



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

def self.fetch_content(id)
  Analyses::NmrMapper.ts('read', id)
end

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



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

def self.generate_ds(id, current_user={})
  data = Analyses::NmrMapper.fetch_content(id)
  return if data.nil?

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

  Analyses::NmrMapper.update_ds_1h(id, obj, current_user) if obj[:ols] == 'CHMO:0000593'
  Analyses::NmrMapper.update_ds_1h(id, obj, current_user) if obj[:ols] == 'CHMO:0000595'
  Analyses::NmrMapper.clean(id)
end

.is_brucker_binary(id) ⇒ Object 



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# File 'lib/labimotion/libs/nmr_mapper_repo.rb', line 5

def self.is_brucker_binary(id)
  att = Attachment.find(id)
  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 metadata
      end
    end
  end
  nil
end

.process(id, content) ⇒ Object 



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# File 'lib/labimotion/libs/nmr_mapper_repo.rb', line 18

def self.process(id, content)
  att = Attachment.find(id)
  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'

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

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



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

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_repo.rb', line 219

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

.update_ds_13c(id, obj) ⇒ Object 



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

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_repo.rb', line 65

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|
    fi['id'] = element.id
    fi['label'] = element.short_label
    new_prop['layers']['general']['fields'][idx] = fi
  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