lib/mspire/mzml/instrument_configuration.rb
require 'mspire/paramable'
require 'mspire/mzml/component'
require 'mspire/mzml/list'
module Mspire
class Mzml
class InstrumentConfiguration
include Mspire::Paramable
extend Mspire::Mzml::List
# (required) the id that this guy can be referenced from
attr_accessor :id
# a list of Source, Analyzer, Detector objects (optional)
attr_accessor :components
# a single software object associated with the instrument (optional)
attr_accessor :software
def initialize(id, components=[])
@id, @components = id, components
params_init
yield(self) if block_given?
end
def to_xml(builder)
builder.instrumentConfiguration(id: @id) do |inst_conf_n|
super(builder)
Mspire::Mzml::Component.list_xml(components, inst_conf_n)
inst_conf_n.softwareRef(ref: @software.id) if @software
end
builder
end
def self.from_xml(xml, link)
obj = self.new(xml[:id])
next_n = obj.describe_from_xml!(xml, link[:ref_hash])
if next_n && (next_n.name == 'componentList')
obj.components = next_n.children.map do |component_n|
if component_n.is_a?(Nokogiri::XML::Text)
# TODO: this is a fix for when there is an empty component list but
# Nokogiri returns a text node. Really this needs to be fixed
# in our xml writer!
nil
else
Mspire::Mzml.const_get(component_n.name.capitalize).new.describe_self_from_xml!(component_n, link[:ref_hash])
end
end.compact
next_n = next_n.next
end
if next_n && next_n.name == 'softwareRef'
obj.software = link[:software_hash][next_n[:ref]]
end
obj
end
end
end
end