Module: BEL::BELRDF::Reader::NanopubYielder

Includes:
Nanopub, Quoting
Included in:
BufferedNanopubYielder, UnbufferedNanopubYielder
Defined in:
lib/bel/translator/plugins/rdf2/reader.rb

Constant Summary

Constants included from Quoting

Quoting::KeywordMatcher, Quoting::Keywords, Quoting::LenientQuotedMatcher, Quoting::NonWordMatcher, Quoting::QuoteNotEscapedMatcher, Quoting::StrictQuotedMatcher

Instance Method Summary collapse

Methods included from Quoting

#always_quote, #ensure_quotes, #identifier_value?, #quote, #quote_if_needed, #quoted?, #quotes_required?, #remove_quotes, #string_value?, #unquote, #unquoted?

Methods included from Nanopub

union_annotation_references, union_by_keyword, union_namespace_references

Instance Method Details

#describe(resource, graph) ⇒ Hash

Describes an RDF resource contained within graph. Describing an RDF resource will retrieve the neighborhood of RDF statements with resource in the subject position.

Parameters:

  • resource (::RDF::Resource) —

    the RDF resource to describe

  • graph (::RDF::Graph) —

    the RDF graph to query

Returns:

  • (Hash) —

    a hash of predicate to object in the neighborhood of resource



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# File 'lib/bel/translator/plugins/rdf2/reader.rb', line 31

def describe(resource, graph)
  graph.query([resource, nil, nil]).reduce({}) { |hash, statement|
    hash[statement.predicate] = statement.object
    hash
  }
end

#make_nanopub(nanopub_hash, graph) ⇒ Nanopub

Create an Nanopub::Nanopub object from RDF statements found in the graph.

Parameters:

  • nanopub (Hash) —

    a hash of predicate to object representing the described nanopub

  • graph (::RDF::Graph) —

    the RDF graph to query

Returns:



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# File 'lib/bel/translator/plugins/rdf2/reader.rb', line 58

def make_nanopub(nanopub_hash, graph)
  statement     = describe(nanopub_hash[BELV.hasStatement], graph)

  # values
  bel_statement = statement[::RDF::RDFS.label].value
  support_text  = nanopub_hash[BELV.hasSupport]
  citation      = nanopub_hash[BELV.hasCitation]

  # model
  nanopub               = Nanopub.new
  nanopub.bel_statement = ::BEL::Script.parse(bel_statement)
                             .find { |obj|
                               obj.is_a? Statement
                             }
  nanopub.support       = Support.new(support_text.value) if support_text

  if citation.respond_to?(:value)
    nanopub.citation =
      case citation.value
      when /pubmed:(\d+)$/
        pubmed_id = $1.to_i
        Citation.new({
          :type => 'PubMed',
          :id   => pubmed_id,
          :name => "PubMed Citation - #{pubmed_id}"
        })
      else
        nil
      end
  end

  nanopub
end

#nanopub_yielder(graph) {|::BEL::Nanopub::Nanopub| ... } ⇒ Object

Iterate the BELV.Nanopub predicated statements, from the graph, and yield those correspdonding Nanopub::Nanopub objects.

Parameters:

  • graph (::RDF::Graph) —

    the RDF graph to query

Yields:



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# File 'lib/bel/translator/plugins/rdf2/reader.rb', line 44

def nanopub_yielder(graph)
  resources_of_type(BELV.Nanopub, graph).each do |nanopub|

    yield make_nanopub(nanopub, graph)
  end
end

#resources_of_type(type, graph) ⇒ Enumerator

Find described resources by type in graph.

Parameters:

  • type (::RDF::Resource) —

    the RDF type to find instances for

  • graph (::RDF::Graph) —

    the RDF graph to query

Returns:

  • (Enumerator) —

    an enumerator of described resource instances



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# File 'lib/bel/translator/plugins/rdf2/reader.rb', line 15

def resources_of_type(type, graph)
  graph.query([nil, ::RDF.type, type])
    .lazy
    .map { |rdf_statement|
      describe(rdf_statement.subject, graph)
    }
end