Class: BEL::Translator::Plugins::Xbel::XBELYielder

Inherits:
Object
  • Object
show all
Defined in:
lib/bel/translator/plugins/xbel/xbel_yielder.rb

Constant Summary collapse

FUNCTIONS = 
::BEL::Language::FUNCTIONS

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(data, options = {}) ⇒ XBELYielder

Returns a new instance of XBELYielder.



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# File 'lib/bel/translator/plugins/xbel/xbel_yielder.rb', line 9

def initialize(data, options = {})
  @data                     = data
  @streaming                = options.fetch(:streaming, false)
  @annotation_reference_map = options.fetch(:annotation_reference_map, nil)
  @namespace_reference_map  = options.fetch(:namespace_reference_map, nil)
  # default BEL version to 2 for default behavior
  @bel_version = 2
end

Class Method Details

.annotation_definitions(list) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/xbel_yielder.rb', line 404

def self.annotation_definitions(list)
  el_ad = REXML::Element.new('bel:annotationDefinitionGroup')
  internal = []
  external = []
  list.each do |annotation|
    case annotation.type.to_sym
    when :url
      el = REXML::Element.new('bel:externalAnnotationDefinition')
      el.add_attribute 'bel:id',  annotation.keyword
      external << el
      if @bel_version == 1
        el.add_attribute 'bel:url', annotation.domain
      else
        url_el = REXML::Element.new('bel:url')
        url_el.text = annotation.domain
        rsrc_el = REXML::Element.new('bel:resource')
        rsrc_el << url_el
        el << rsrc_el
      end
    when :uri
      el = REXML::Element.new('bel:externalAnnotationDefinition')
      el.add_attribute 'bel:id',  annotation.keyword
      external << el
      if @bel_version == 1
        el.add_attribute 'bel:url', annotation.domain
      else
        uri_el = REXML::Element.new('bel:uri')
        uri_el.text = annotation.domain
        rsrc_el = REXML::Element.new('bel:resource')
        rsrc_el << uri_el
        el << rsrc_el
      end
    when :pattern
      el = REXML::Element.new('bel:internalAnnotationDefinition')
      el.add_attribute 'bel:id', annotation.keyword
      el.add_element(REXML::Element.new('bel:description'))
      el.add_element(REXML::Element.new('bel:usage'))

      el_pattern      = REXML::Element.new('bel:patternAnnotation')
      el_pattern.text =
        annotation.domain.respond_to?(:source) ?
          annotation.domain.source : annotation.domain

      el.add_element(el_pattern)
      internal << el
    when :list
      el = REXML::Element.new('bel:internalAnnotationDefinition')
      el.add_attribute 'bel:id', annotation.keyword
      el.add_element(REXML::Element.new('bel:description'))
      el.add_element(REXML::Element.new('bel:usage'))

      el_list = REXML::Element.new('bel:listAnnotation')
      if annotation.domain.respond_to?(:each)
        annotation.domain.each do |value|
          el_list_value      = REXML::Element.new('bel:listValue')
          el_list_value.text = value
          el_list.add_element(el_list_value)
        end
      else
        el_list_value      = REXML::Element.new('bel:listValue')
        el_list_value.text = annotation.domain
        el_list.add_element(el_list_value)
      end

      el.add_element(el_list)
      internal << el
    else
      el = nil
    end
  end

  # first add internal annotation definitions
  internal.each do |internal_element|
    el_ad.add_element(internal_element)
  end

  # second add external annotation definitions
  external.each do |external_element|
    el_ad.add_element(external_element)
  end

  el_ad
end

.annotation_group(nanopub) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/xbel_yielder.rb', line 162

def self.annotation_group(nanopub)
  el_ag = REXML::Element.new('bel:annotationGroup')

  # XBEL citation
  if nanopub.citation && nanopub.citation.valid?
    el_ag.add_element(self.citation(nanopub.citation))
  end

  # XBEL nanopub (::BEL::Nanopub::Support)
  if nanopub.support && nanopub.support.value
    if @bel_version == 1
      xbel_evidence = REXML::Element.new('bel:evidence')
      xbel_evidence.text = nanopub.support.value
      el_ag.add_element(xbel_evidence)
    else
      xbel_support = REXML::Element.new('bel:support')
      xbel_support.text = nanopub.support.value
      el_ag.add_element(xbel_support)
    end
  end

  nanopub.experiment_context.each do |annotation|
    name, value = annotation.values_at(:name, :value)

    if value.respond_to?(:each)
      value.each do |v|
        el_anno      = REXML::Element.new('bel:annotation')
        el_anno.text = v
        el_anno.add_attribute 'bel:refID', name.to_s

        el_ag.add_element(el_anno)
      end
    else
        el_anno      = REXML::Element.new('bel:annotation')
        el_anno.text = value
        el_anno.add_attribute 'bel:refID', name.to_s

        el_ag.add_element(el_anno)
    end
  end

  metadata_keys = nanopub.metadata.keys - [:document_header, :bel_version]
  metadata_keys.each do |k|
    v = nanopub.metadata[k]
    if v.respond_to?(:each)
      v.each do |value|
        el_anno      = REXML::Element.new('bel:annotation')
        el_anno.text = value
        el_anno.add_attribute 'bel:refID', k.to_s

        el_ag.add_element(el_anno)
      end
    else
      el_anno      = REXML::Element.new('bel:annotation')
      el_anno.text = v
      el_anno.add_attribute 'bel:refID', k.to_s

      el_ag.add_element(el_anno)
    end
  end

  el_ag
end

.citation(citation) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/xbel_yielder.rb', line 226

def self.citation(citation)
  el_citation  = REXML::Element.new('bel:citation')

  if citation.type && !citation.type.to_s.empty?
    el_citation.add_attribute 'bel:type', citation.type
  end

  if citation.id && !citation.id.to_s.empty?
    el_reference      = REXML::Element.new('bel:reference')
    el_reference.text = citation.id
    el_citation.add_element(el_reference)
  end

  if citation.name && !citation.name.to_s.empty?
    el_name         = REXML::Element.new('bel:name')
    el_name.text    = citation.name
    el_citation.add_element(el_name)
  end

  if citation.date && !citation.date.to_s.empty?
    el_date         = REXML::Element.new('bel:date')
    el_date.text    = citation.date
    el_citation.add_element(el_date)
  end

  if citation.comment && !citation.comment.to_s.empty?
    el_comment      = REXML::Element.new('bel:comment')
    el_comment.text = citation.comment
    el_citation.add_element(el_comment)
  end

  if citation.authors && !citation.authors.to_s.empty?
    el_author_group = REXML::Element.new('bel:authorGroup')
    citation.authors.each do |author|
      el_author      = REXML::Element.new('bel:author')
      el_author.text = author
      el_author_group.add_element(el_author)
    end
    el_citation.add_element(el_author_group)
  end

  el_citation
end

.document ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/xbel_yielder.rb', line 270

def self.document
  el = REXML::Element.new('bel:document')

  if @bel_version == 1
    el.add_namespace('bel', 'http://belframework.org/schema/1.0/xbel')
    el.add_namespace('xsi', 'http://www.w3.org/2001/XMLSchema-instance')
    el.add_attribute('xsi:schemaLocation', 'http://belframework.org/schema/1.0/xbel http://resource.belframework.org/belframework/1.0/schema/xbel.xsd')
  else
    el.add_namespace('bel', 'http://resources.openbel.org/v2.0/lang/xml-schema/version_2.0/xbel')
    el.add_namespace('xsi', 'http://www.w3.org/2001/XMLSchema-instance')
    el.add_attribute('xsi:schemaLocation', 'http://resources.openbel.org/v2.0/lang/xml-schema/version_2.0/xbel')
  end

  el
end

.header(hash) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/xbel_yielder.rb', line 304

def self.header(hash)
  el_header = REXML::Element.new('bel:header')

  # normalize hash keys
  hash = Hash[
    hash.map { |k, v|
      k = k.to_s.dup
      k.downcase!
      k.gsub!(/[-_ .]/, '')
      [k, v]
    }
  ]

  (%w(name description version copyright) & hash.keys).each do |field|
    el      = REXML::Element.new("bel:#{field}")
    el.text = hash[field]
    el_header.add_element(el)
  end

  # add contactinfo with different element name (contactInfo)
  if hash.has_key?('contactinfo')
    el      = REXML::Element.new('bel:contactInfo')
    el.text = hash['contactinfo']
    el_header.add_element(el)
  end

  # add bel_version with different element name (belVersion)
  if hash.has_key?('belversion')
    el = REXML::Element.new('bel:belVersion')
    el.text = hash['belversion']
    el_header.add_element(el)
  else
    # apply defaults
    el = REXML::Element.new('bel:belVersion')
    el.text = '2.0'
    el_header.add_element(el)
  end

  # handle grouping for authors and licenses
  if hash.has_key?('authors')
    authors  = hash['authors']
    el_group = REXML::Element.new('bel:authorGroup')

    [authors].flatten.each do |author|
      el      = REXML::Element.new('bel:author')
      el.text = author.to_s
      el_group.add_element(el)
    end
    el_header.add_element(el_group)
  end
  if hash.has_key?('licenses')
    licenses = hash['licenses']
    el_group = REXML::Element.new('bel:licenseGroup')

    [licenses].flatten.each do |license|
      el      = REXML::Element.new('bel:license')
      el.text = license.to_s
      el_group.add_element(el)
    end
    el_header.add_element(el_group)
  end

  el_header
end

.namespace_definitions(list) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/xbel_yielder.rb', line 369

def self.namespace_definitions(list)
  el_nd = REXML::Element.new('bel:namespaceGroup')
  list.each do |namespace|
    if namespace.url?
      el = REXML::Element.new('bel:namespace')
      el.add_attribute 'bel:prefix', namespace.keyword
      if @bel_version == 1
        el.add_attribute 'bel:resourceLocation', namespace.uri
      else
        url_el = REXML::Element.new('bel:url')
        url_el.text = namespace.uri
        rsrc_el = REXML::Element.new('bel:resource')
        rsrc_el << url_el
        el << rsrc_el
      end
      el_nd.add_element(el)
    elsif namespace.uri?
      el = REXML::Element.new('bel:namespace')
      el.add_attribute 'bel:prefix', namespace.keyword
      if @bel_version == 1
        el.add_attribute 'bel:resourceLocation', namespace.uri
      else
        uri_el = REXML::Element.new('bel:uri')
        uri_el.text = namespace.uri
        rsrc_el = REXML::Element.new('bel:resource')
        rsrc_el << uri_el
        el << rsrc_el
      end
      el_nd.add_element(el)
    end
  end

  el_nd
end

.nanopub(nanopub) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/xbel_yielder.rb', line 90

def self.nanopub(nanopub)
  statement    = nanopub.bel_statement
  el_statement = REXML::Element.new('bel:statement')

  el_statement.add_element(self.annotation_group(nanopub))
  self.statement(statement, el_statement)

  el_statement
end

.object(object) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/xbel_yielder.rb', line 125

def self.object(object)
  el_object = REXML::Element.new('bel:object')

  case object
  when ::BELParser::Expression::Model::Term
    el_object.add_element(self.term(object))
  when ::BELParser::Expression::Model::Statement
    el_statement = REXML::Element.new('bel:statement')
    el_object.add_element(el_statement)
    self.statement(object, el_statement)
  end
  el_object
end

.parameter(parameter) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/xbel_yielder.rb', line 154

def self.parameter(parameter)
  el_parameter      = REXML::Element.new('bel:parameter')
  el_parameter.text = parameter.value
  keyword           = parameter.namespace && parameter.namespace.keyword
  el_parameter.add_attribute 'bel:ns', keyword
  el_parameter
end

.statement(statement, el_statement) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/xbel_yielder.rb', line 100

def self.statement(statement, el_statement)
  if statement.relationship
    el_statement.add_attribute 'bel:relationship', statement.relationship.to_s(:long)
  end

  if statement.subject
    el_subject = self.subject(statement.subject)
    el_statement.add_element(el_subject)
  end

  if statement.object
    el_object = self.object(statement.object)
    el_statement.add_element(el_object)
  end

  el_statement
end

.statement_group(declare_namespaces = false) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/xbel_yielder.rb', line 286

def self.statement_group(declare_namespaces = false)
  el = REXML::Element.new('bel:statementGroup')

  if declare_namespaces
    if @bel_version == 1
      el.add_namespace('bel', 'http://belframework.org/schema/1.0/xbel')
      el.add_namespace('xsi', 'http://www.w3.org/2001/XMLSchema-instance')
      el.add_attribute('xsi:schemaLocation', 'http://belframework.org/schema/1.0/xbel http://resource.belframework.org/belframework/1.0/schema/xbel.xsd')
    else
      el.add_namespace('bel', 'http://resources.openbel.org/v2.0/lang/xml-schema/version_2.0/xbel')
      el.add_namespace('xsi', 'http://www.w3.org/2001/XMLSchema-instance')
      el.add_attribute('xsi:schemaLocation', 'http://resources.openbel.org/v2.0/lang/xml-schema/version_2.0/xbel')
    end
  end

  el
end

.subject(subject) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/xbel_yielder.rb', line 118

def self.subject(subject)
  el_subject = REXML::Element.new('bel:subject')
  el_subject.add_element(self.term(subject))

  el_subject
end

.term(term) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/xbel_yielder.rb', line 139

def self.term(term)
  el_term   = REXML::Element.new('bel:term')
  el_term.add_attribute 'bel:function', term.function.to_s(:long)

  term.arguments.each do |arg|
    case arg
    when ::BELParser::Expression::Model::Term
      el_term.add_element(self.term(arg))
    when ::BELParser::Expression::Model::Parameter
      el_term.add_element(self.parameter(arg))
    end
  end
  el_term
end

Instance Method Details

#each ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/xbel_yielder.rb', line 18

def each
  if block_given?
    combiner =
      if @streaming
        BEL::Nanopub::StreamingNanopubCombiner.new(@data)
      elsif @annotation_reference_map && @namespace_reference_map
        BEL::Nanopub::MapReferencesCombiner.new(
          @data,
          BEL::Nanopub::HashMapReferences.new(
            @annotation_reference_map,
            @namespace_reference_map
          )
        )
      else
        BEL::Nanopub::BufferingNanopubCombiner.new(@data)
      end

    header_flag = true

    # yield <document>
    el_document = XBELYielder.document
    yield start_element_string(el_document)

    el_statement_group = nil
    nanopub_count = 0
    combiner.each { |nanopub|
      # is BEL version 1.0?
      if nanopub.metadata.bel_version == '1.0'
        @bel_version = 1
      end
      if header_flag
        # document header
        el_statement_group = XBELYielder.statement_group

        yield element_string(
          XBELYielder.header(nanopub.metadata.document_header)
        )
        yield element_string(
          XBELYielder.namespace_definitions(combiner.namespace_references)
        )
        yield element_string(
          XBELYielder.annotation_definitions(combiner.annotation_references)
        )

        yield start_element_string(el_statement_group)

        header_flag = false
      end

      yield element_string(XBELYielder.nanopub(nanopub))
      nanopub_count += 1
    }

    if nanopub_count > 0
      yield end_element_string(el_statement_group)
    else
      # empty head sections; required for XBEL schema

      empty_header = Hash[%w(name description version).map { |element|
        [element, ""]
      }]
      yield element_string(XBELYielder.header(empty_header))
      yield element_string(XBELYielder.namespace_definitions([]))
      yield element_string(XBELYielder.annotation_definitions([]))
      yield element_string(XBELYielder.statement_group)
    end
    yield end_element_string(el_document)
  else
    to_enum(:each)
  end
end