Class: Etna::Clients::Magma::ModelsOdmXml::Exporter

Inherits:
Object
  • Object
show all
Includes:
Prettify
Defined in:
lib/etna/clients/magma/formatting/models_odm_xml.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Prettify

#prettify, #shorten

Constructor Details

#initialize(project_name:, models:) ⇒ Exporter

Returns a new instance of Exporter.



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# File 'lib/etna/clients/magma/formatting/models_odm_xml.rb', line 31

def initialize(project_name:, models:)
  @project_name = project_name
  @models = models
end

Instance Attribute Details

#models ⇒ Object (readonly)

Returns the value of attribute models.



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# File 'lib/etna/clients/magma/formatting/models_odm_xml.rb', line 29

def models
  @models
end

#project_name ⇒ Object (readonly)

Returns the value of attribute project_name.



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# File 'lib/etna/clients/magma/formatting/models_odm_xml.rb', line 29

def project_name
  @project_name
end

Instance Method Details

#clinical_dictionaries ⇒ Object 



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# File 'lib/etna/clients/magma/formatting/models_odm_xml.rb', line 145

def clinical_dictionaries
  # Our indicator for if something needs a REDCap form will be any
  #   model with a dictionary.
  models.all.select do |model|
    model.template.raw['dictionary']
  end.map do |model|
    model.template.dictionary
  end
end

#data_type_map ⇒ Object 



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# File 'lib/etna/clients/magma/formatting/models_odm_xml.rb', line 36

def data_type_map
  @data_type_map ||= begin
    map = {}
    map[Etna::Clients::Magma::AttributeType::STRING] = 'text'
    map[Etna::Clients::Magma::AttributeType::DATE_TIME] = 'date'
    map[Etna::Clients::Magma::AttributeType::BOOLEAN] = 'text'
    map[Etna::Clients::Magma::AttributeType::FLOAT] = 'float'
    map[Etna::Clients::Magma::AttributeType::INTEGER] = 'integer'

    map
  end
end

#global_variables(xml) ⇒ Object 



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# File 'lib/etna/clients/magma/formatting/models_odm_xml.rb', line 104

def global_variables(xml)
  # Includes general metadata about the project, as well as
  # declarations of all repeating instruments,
  #   which seem like Timepoints to me.
  # NOTE:
  # <redcap:Purpose>0</redcap:Purpose>
  # 0 = Practice / just for fun
  # 1 = Operational Support
  # 2 = Research
  # 3 = Quality Improvement
  # 4 = Other

  xml.GlobalVariables do
    xml.StudyName "#{project_name}"
    xml.StudyDescription "#{project_name} - Data Library integration project"
    xml.ProtocolName "#{project_name}"
    xml.send('redcap:RecordAutonumberingEnabled', 1)
    xml.send('redcap:CustomRecordLabel')
    xml.send('redcap:SecondaryUniqueField')
   xml.send('redcap:SchedulingEnabled', 0)
   xml.send('redcap:SurveysEnabled', 0)
    xml.send('redcap:SurveyInvitationEmailField')
    xml.send('redcap:Purpose', 2) # 2 == research
    xml.send('redcap:PurposeOther')
    xml.send('redcap:ProjectNotes', "Used to easily ingest clinical data for #{project_name} into the Data Library.")
    xml.send('redcap:MissingDataCodes')

    repeating_instruments(xml)
  end
end

#metadata(xml) ⇒ Object 



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# File 'lib/etna/clients/magma/formatting/models_odm_xml.rb', line 176

def metadata(xml)
  # Includes form and field definitions
  xml.MetaDataVersion(
    OID: "Metadata.#{shorten(project_name)}_#{DateTime.now}",
    Name: project_name,
    'redcap:RecordIdField': 'record_id'
  ) do
    clinical_dictionaries.map do |dictionary|
      # Each Magma dictionary needs a FormDef, with
      #   ItemGroupRef children for each form page (?).
      # Each ItemGroupRef requires a corresponding ItemGroupDef
      #   with ItemRef children for each input (?).
      # Each ItemRef requires a correspdonding ItemDef
      #   that defines the label and type, and includes
      #   <Question> as a label (?).
      # Option validations are present as a CodeList (with
      #   CodeListItem children).
      write_form_def(xml, dictionary)
      write_item_group_def(xml, dictionary)
      write_item_def(xml, dictionary)
      write_code_list(xml, dictionary)
    end
  end
end

#odm_headers ⇒ Object 



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# File 'lib/etna/clients/magma/formatting/models_odm_xml.rb', line 86

def odm_headers
  {
    xmlns: "http://www.cdisc.org/ns/odm/v1.3",
    'xmlns:ds': "http://www.w3.org/2000/09/xmldsig#",
    'xmlns:xsi': "http://www.w3.org/2001/XMLSchema-instance",
    'xmlns:redcap': "https://projectredcap.org",
    'xsi:schemaLocation': "http://www.cdisc.org/ns/odm/v1.3 schema/odm/ODM1-3-1.xsd",
    ODMVersion: "1.3.2",
    FileOID: "000-00-0000",
    FileType: "Snapshot",
    Description: project_name,
    AsOfDateTime: DateTime.now,
    CreationDateTime: DateTime.now,
    SourceSystem: "Magma",
    SourceSystemVersion: DateTime.now
  }
end

#redcap_field_type_map ⇒ Object 



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# File 'lib/etna/clients/magma/formatting/models_odm_xml.rb', line 49

def redcap_field_type_map
  @redcap_field_type_map ||= begin
    map = {}
    map[Etna::Clients::Magma::AttributeType::STRING] = 'textarea'
    map[Etna::Clients::Magma::AttributeType::DATE_TIME] = 'text'
    map[Etna::Clients::Magma::AttributeType::BOOLEAN] = 'radio'
    map[Etna::Clients::Magma::AttributeType::FLOAT] = 'text'
    map[Etna::Clients::Magma::AttributeType::INTEGER] = 'text'

    map
  end
end

#redcap_text_validation_map ⇒ Object 



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# File 'lib/etna/clients/magma/formatting/models_odm_xml.rb', line 62

def redcap_text_validation_map
  @redcap_text_validation_map ||= begin
    map = {}
    map[Etna::Clients::Magma::AttributeType::DATE_TIME] = 'date_mdy'
    map[Etna::Clients::Magma::AttributeType::FLOAT] = 'float'
    map[Etna::Clients::Magma::AttributeType::INTEGER] = 'int'

    map
  end
end

#repeating_attribute_types ⇒ Object 



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# File 'lib/etna/clients/magma/formatting/models_odm_xml.rb', line 135

def repeating_attribute_types
  # We don't have a good indicator for what is a repeating
  #   attribute for REDCap...
  # Will this work for models without timepoint, that go
  #   straight from subject -> sample?
  models.model('subject').template.attributes.all.select do |attribute|
    Etna::Clients::Magma::AttributeType::COLLECTION == attribute.attribute_type
  end
end

#repeating_instruments(xml) ⇒ Object 



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# File 'lib/etna/clients/magma/formatting/models_odm_xml.rb', line 155

def repeating_instruments(xml)
  # Now we get into repeating instruments and events.
  # From a Magma model perspective, this should be
  #   Timepoint that hangs off of
  #   a Subject model.
  xml.send('redcap:RepeatingInstrumentsAndEvents') do
    repeating_attribute_types.map do |repeating_attribute|
      write_repeating_instrument_xml(xml, repeating_attribute)
    end
  end
end

#write_code_list(xml, dictionary) ⇒ Object 



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# File 'lib/etna/clients/magma/formatting/models_odm_xml.rb', line 265

def write_code_list(xml, dictionary)
  model_attributes = models.model(dictionary.model_name).template.attributes
  dictionary.attributes.keys.map do |attribute_name|
    attribute = model_attributes.attribute(attribute_name)
    if attribute.validation && Etna::Clients::Magma::AttributeValidationType::ARRAY == attribute.validation['type']
      xml.CodeList(
        OID: "#{dictionary.model_name}.#{attribute_name}.choices",
        Name: "#{attribute_name}",
        DataType: "text",
        'redcap:Variable': attribute_name
      ) do
        attribute.validation['value'].map do |option|
          xml.CodeListItem(
            CodedValue: option
          ) do
            xml.Decode() do
              xml.send('TranslatedText', option)
            end
          end
        end
      end
    end
  end
end

#write_form_def(xml, dictionary) ⇒ Object 



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# File 'lib/etna/clients/magma/formatting/models_odm_xml.rb', line 201

def write_form_def(xml, dictionary)
  xml.FormDef(
    OID: "Form.#{dictionary.model_name}",
    Name: dictionary.model_name.capitalize,
    Repeating: "No",
    'redcap:FormName': dictionary.model_name
  ) do
    # Assume a single item group
    xml.ItemGroupRef(
      ItemGroupOID: "#{dictionary.model_name}.attributes",
      Mandatory: "No"
    ) do
    end
  end
end

#write_item_def(xml, dictionary) ⇒ Object 



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# File 'lib/etna/clients/magma/formatting/models_odm_xml.rb', line 234

def write_item_def(xml, dictionary)
  model_attributes = models.model(dictionary.model_name).template.attributes
  dictionary.attributes.keys.map do |attribute_name|
    attribute = model_attributes.attribute(attribute_name)
    attribute_type = attribute.attribute_type
    params = {
      OID: "#{dictionary.model_name}.#{attribute_name}", # Does this need to be unique across all items?
      Name: attribute_name,
      DataType: data_type_map[attribute_type] || 'text',
      'redcap:Variable': attribute_name,
      'redcap:FieldType': redcap_field_type_map[attribute_type] || 'text',
      Length: '999' # How could we infer shorter values?
    }

    params['redcap:TextValidationType'] = redcap_text_validation_map[attribute_type] if redcap_text_validation_map[attribute_type]
    params['redcap:FieldNote'] = attribute.description if attribute.description
    xml.ItemDef(params) do
      xml.Question do
        xml.send('TranslatedText', attribute_name.capitalize)
      end

      if attribute.validation && Etna::Clients::Magma::AttributeValidationType::ARRAY == attribute.validation['type']
        xml.CodeListRef(
          CodeListOID: "#{dictionary.model_name}.#{attribute_name}.choices"
        ) do
        end
      end
    end
  end
end

#write_item_group_def(xml, dictionary) ⇒ Object 



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# File 'lib/etna/clients/magma/formatting/models_odm_xml.rb', line 217

def write_item_group_def(xml, dictionary)
  xml.ItemGroupDef(
    OID: "#{dictionary.model_name}.attributes",
    Name: "#{dictionary.model_name.capitalize} Attributes",
    Repeating: "No"
  ) do
    dictionary.attributes.keys.map do |attribute_name|
      xml.ItemRef(
        ItemOID: "#{dictionary.model_name}.#{attribute_name}", # Does this need to be unique across all items?
        Mandatory: "No",
        'redcap:Variable': attribute_name # Does this need to be unique?
      ) do
      end
    end
  end
end

#write_models(output_io: nil, filename: nil) ⇒ Object 



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# File 'lib/etna/clients/magma/formatting/models_odm_xml.rb', line 73

def write_models(output_io: nil, filename: nil)
  @document = Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
    xml.ODM(odm_headers) do
      xml.Study(OID: "Project.#{shorten(project_name)}") do
      end
      global_variables(xml)
      metadata(xml)
    end
  end

  @document.to_xml
end

#write_repeating_instrument_xml(xml, instrument) ⇒ Object 



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# File 'lib/etna/clients/magma/formatting/models_odm_xml.rb', line 167

def write_repeating_instrument_xml(xml, instrument)
  node = xml.send('redcap:RepeatingInstrument')
  node['redcap:UniqueEventName'] = 'event_1_arm_1'
  node['redcap:RepeatInstrument'] = instrument.attribute_name
  node['redcap:CustomLabel'] = instrument.display_name || instrument.attribute_name.capitalize

  node
end