Class: BEL::Nanopub::Statement

Inherits:
Object
  • Object
show all
Defined in:
lib/bel/translator/plugins/rdf/monkey_patch.rb

Instance Method Summary collapse

Instance Method Details

#to_rdf(graph_name = nil, remap = nil) ⇒ Object 



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# File 'lib/bel/translator/plugins/rdf/monkey_patch.rb', line 227

def to_rdf(graph_name = nil, remap = nil)
  uri        = to_uri
  statements = []

  case
  when subject_only?
    (sub_uri, sub_statements) = @subject.to_rdf(graph_name, remap)
    statements << ::RDF::Statement(uri, BELRDF::BELV.hasSubject, sub_uri, :graph_name => graph_name)
    statements.concat(sub_statements)
  when simple?
    (sub_uri, sub_statements) = @subject.to_rdf(graph_name, remap)
    statements.concat(sub_statements)

    (obj_uri, obj_statements) = @object.to_rdf(graph_name, remap)
    statements.concat(obj_statements)

    rel = BELRDF::RELATIONSHIP_TYPE[@relationship.to_s]
    statements << ::RDF::Statement(uri, BELRDF::BELV.hasSubject, sub_uri,  :graph_name => graph_name)
    statements << ::RDF::Statement(uri, BELRDF::BELV.hasObject, obj_uri,   :graph_name => graph_name)
    statements << ::RDF::Statement(uri, BELRDF::BELV.hasRelationship, rel, :graph_name => graph_name)
  when nested?
    (sub_uri, sub_statements) = @subject.to_rdf(graph_name, remap)
    (nsub_uri, nsub_statements) = @object.subject.to_rdf(graph_name, remap)
    (nobj_uri, nobj_statements) = @object.object.to_rdf(graph_name, remap)
    statements.concat(sub_statements)
    statements.concat(nsub_statements)
    statements.concat(nobj_statements)
    rel = BELRDF::RELATIONSHIP_TYPE[@relationship.to_s]
    nrel = BELRDF::RELATIONSHIP_TYPE[@object.relationship.to_s]
    nuri = BELRDF::BELR["#{strip_prefix(nsub_uri)}_#{nrel}_#{strip_prefix(nobj_uri)}"]

    # inner
    statements << ::RDF::Statement.new(nuri, BELRDF::BELV.hasSubject, nsub_uri,  :graph_name => graph_name)
    statements << ::RDF::Statement.new(nuri, BELRDF::BELV.hasObject, nobj_uri,   :graph_name => graph_name)
    statements << ::RDF::Statement.new(nuri, BELRDF::BELV.hasRelationship, nrel, :graph_name => graph_name)

    # outer
    statements << ::RDF::Statement.new(uri, BELRDF::BELV.hasSubject, sub_uri,  :graph_name => graph_name)
    statements << ::RDF::Statement.new(uri, BELRDF::BELV.hasObject, nuri,      :graph_name => graph_name)
    statements << ::RDF::Statement.new(uri, BELRDF::BELV.hasRelationship, rel, :graph_name => graph_name)
  end

  # common statement triples
  statements << ::RDF::Statement.new(uri, BELRDF::RDF.type, BELRDF::BELV.Statement,     :graph_name => graph_name)
  statements << ::RDF::Statement.new(uri, BELRDF::RDFS.label, to_s.force_encoding('UTF-8'),  :graph_name => graph_name)

  # nanopub
  nanopub    = BELRDF::BELE[BELRDF.generate_uuid]
  statements << ::RDF::Statement.new(nanopub, BELRDF::RDF.type, BELRDF::BELV.Nanopub, :graph_name => graph_name)
  statements << ::RDF::Statement.new(uri, BELRDF::BELV.hasNanopub, nanopub,             :graph_name => graph_name)
  statements << ::RDF::Statement.new(nanopub, BELRDF::BELV.hasStatement, uri,            :graph_name => graph_name)

  # citation
  citation = @annotations.delete('Citation')
  if citation
    value = citation.value.map{|x| x.gsub('"', '')}
    if citation and value[0] == 'PubMed'
      pid = value[2]
      statements << ::RDF::Statement.new(nanopub, BELRDF::BELV.hasCitation, BELRDF::PUBMED[pid], :graph_name => graph_name)
    end
  end

  # nanopub
  support = @annotations.delete('Support')
  if support
    value = support.value.gsub('"', '').force_encoding('UTF-8')
    statements << ::RDF::Statement.new(nanopub, BELRDF::BELV.hasSupport, value, :graph_name => graph_name)
  end

  # annotations
  @annotations.each do |_, anno|
    name = anno.name.gsub('"', '')

    # update annotations resource
    anno_rdf_uri = nil
    if remap && remap['annotations']
      ro_ind = remap['annotations'].index { |mapping|
        mapping['remap'] && mapping['remap'].is_a?(Hash) &&
        mapping['remap']['from'] && mapping['remap']['from'].is_a?(Hash) &&
        mapping['remap']['from']['keyword'] == name && (mapping['remap']['from']['type'] == 'url' ||
        mapping['remap']['from']['type'] == 'list' &&
        mapping['remap']['from']['domain'] && mapping['remap']['from']['domain'].is_a?(Array) &&
        mapping['remap']['from']['domain'].include?(anno.value))
      }
      if ro_ind
        anno_rdf_uri = remap['annotations'][ro_ind]['remap']['to']['rdf_uri']
        anno_rdf_uri << '/' unless anno_rdf_uri.end_with?('/')
      end
    end

    if anno_rdf_uri or BELRDF::const_defined? name
      annotation_scheme = anno_rdf_uri ? anno_rdf_uri : BELRDF::const_get(name)
      [anno.value].flatten.map{|x| x.gsub('"', '')}.each do |val|
        value_uri = BELRDF::RDF::URI(URI.encode(annotation_scheme + val.to_s))
        statements << ::RDF::Statement.new(nanopub, BELRDF::BELV.hasAnnotation, value_uri, :graph_name => graph_name)
      end
    end
  end

  [uri, statements]
end

#to_uri ⇒ Object 



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# File 'lib/bel/translator/plugins/rdf/monkey_patch.rb', line 191

def to_uri
  case
  when simple?
    sub_id = @subject.to_s.squeeze(')').gsub(/[")\[\]]/, '').gsub(/[(:, ]/, '_')
    obj_id = @object.to_s.squeeze(')').gsub(/[")\[\]]/, '').gsub(/[(:, ]/, '_')
    rel = BELRDF::RELATIONSHIP_TYPE[@relationship.to_s]
    if rel
      rel = rel.path.split('/')[-1]
    else
      rel = @relationship.to_s
    end
    BELRDF::BELR[URI::encode("#{sub_id}_#{rel}_#{obj_id}")]
  when nested?
    sub_id = @subject.to_s.squeeze(')').gsub(/[")\[\]]/, '').gsub(/[(:, ]/, '_')
    nsub_id = @object.subject.to_s.squeeze(')').gsub(/[")\[\]]/, '').gsub(/[(:, ]/, '_')
    nobj_id = @object.object.to_s.squeeze(')').gsub(/[")\[\]]/, '').gsub(/[(:, ]/, '_')
    rel = BELRDF::RELATIONSHIP_TYPE[@relationship.to_s]
    if rel
      rel = rel.path.split('/')[-1]
    else
      rel = @relationship.to_s
    end
    nrel = BELRDF::RELATIONSHIP_TYPE[@object.relationship.to_s]
    if nrel
      nrel = nrel.path.split('/')[-1]
    else
      nrel = @object.relationship.to_s
    end
    BELRDF::BELR[URI::encode("#{sub_id}_#{rel}_#{nsub_id}_#{nrel}_#{nobj_id}")]
  else
    # Interpret as subject only BEL statement.
    tid = @subject.to_s.squeeze(')').gsub(/[")\[\]]/, '').gsub(/[(:, ]/, '_')
    BELRDF::BELR[URI::encode(tid)]
  end
end