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Contents
require 'bel/quoting'
# Serializing of common {BEL::Nanopub::Nanopub nanopub} components to BEL
# Script syntax.
#
# @abstract
module BEL::Translator::Plugins::BelScript::NanopubSerialization
include BEL::Quoting
# Serialize the {BEL::Nanopub::Nanopub nanopub} to a BEL Script string.
#
# @param [BEL::Nanopub::Nanopub] nanopub the nanopub to serialize
# @return [String] the BEL Script string
# @abstract Include and override {#to_bel} to implement serialization
# {BEL::Nanopub::Nanopub nanopub} to BEL Script
def to_bel(nanopub)
end
# Return BEL Script syntax that completes the BEL Script document.
#
# @abstract
def epilogue
raise NotImplementedError.new("#{self.class}#epilogue")
end
protected
def citation_value(nanopub)
citation = nanopub.citation
return nil unless citation && citation.valid?
values = citation.to_a
values.map! { |v|
v ||= ""
if v.respond_to?(:each)
%Q{"#{v.join('|')}"}
else
%Q{"#{v}"}
end
}
values.join(', ')
end
def support_value(nanopub)
support = nanopub.support
return nil unless support && support.value
value = support.value
value.gsub!("\n", "")
value.gsub!('"', %Q{\\"})
value
end
def annotation_values(nanopub)
experiment_context = nanopub.experiment_context
return {} unless experiment_context
Hash[
experiment_context.
sort_by { |obj| obj[:name].to_sym }.
map { |obj|
name = obj[:name].to_sym
value = obj[:value]
value_s =
if value.respond_to? :map
"{#{value.map { |v| quote(v) }.join(', ')}}"
else
quote(value)
end
[name, value_s]
}
]
end
end
Version data entries
82 entries across 82 versions & 1 rubygems