Module: BEL::Nanopub

Included in:
BELRDF::Reader::NanopubYielder, Translator::Plugins::Xbel::NanopubHandler, BELRDF::Reader::NanopubYielder
Defined in:
lib/bel/nanopub/util.rb,
lib/bel/nanopub/nanopub.rb,
lib/bel/nanopub/support.rb,
lib/bel/nanopub/citation.rb,
lib/bel/nanopub/metadata.rb,
lib/bel/nanopub/references.rb,
lib/bel/nanopub/map_references.rb,
lib/bel/nanopub/experiment_context.rb,
lib/bel/nanopub/hash_map_references.rb,
lib/bel/nanopub/map_references_combiner.rb,
lib/bel/nanopub/buffering_nanopub_combiner.rb,
lib/bel/nanopub/streaming_nanopub_combiner.rb

Defined Under Namespace

Modules: MapReferences Classes: BufferingNanopubCombiner, Citation, ExperimentContext, HashMapReferences, MapReferencesCombiner, Metadata, Nanopub, Parameter, References, Statement, StreamingNanopubCombiner, Support, Term

Class Method Summary collapse

Class Method Details

.union_annotation_references(destination, source, suffix = 'incr') ⇒ Object 



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# File 'lib/bel/nanopub/util.rb', line 12

def self.union_annotation_references(destination, source, suffix = 'incr')
  BEL::Nanopub.union_by_keyword(
    destination,
    source,
    suffix
  )
end

.union_by_keyword(destination, source, suffix = 'incr') ⇒ Array<Array<Hash>,Hash>

Combines annotation/namespace references together by disambiguating the keywords. The references in @source@ are combined into @destination@.

Parameters:

  • destination (Array<Hash>) —

    existing references to merge with; may be an empty @[]@ array

  • source (Array<Hash>) —

    references to union with @destination@

  • suffix (String) (defaults to: 'incr') —

    the suffix to apply to reference keywords in @source@ for disambiguation

Returns:

  • (Array<Array<Hash>,Hash>) —

    array where the first item is and Array of combined references and the second item is a Hash that remaps references from source



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# File 'lib/bel/nanopub/util.rb', line 32

def self.union_by_keyword(destination, source, suffix = 'incr')
  # find new
  new            = source - destination
  suffix_pattern = /#{Regexp.escape(suffix)}([0-9]+)$/
  remap_result   = {}

  combined = destination + new.map { |new_obj|
    new_key = new_obj.keyword

    # find a match where the keyword differs
    match_by_value = destination.find { |dest|
      new_obj.domain_equal?(dest)
    }

    rewrite_key =
      if match_by_value
        match_by_value.keyword
      else
        # find max suffix match
        max_suffix = destination.map { |dest|
          key, suffix_number = dest.keyword.to_s.split(suffix_pattern)
          if new_key == key
            suffix_number
          else
            nil
          end
        }.compact.max { |suffix_number|
          suffix_number.to_i
        }

        if max_suffix
          new_key + suffix + max_suffix.next
        else
          if destination.any? { |dest| dest.keyword == new_key }
            "#{new_key}#{suffix}1"
          else
            new_key
          end
        end
      end

    rewrite_obj           = new_obj.dup
    rewrite_obj.keyword   = rewrite_key
    remap_result[new_obj] = rewrite_obj
    rewrite_obj
  }
  combined.uniq!

  [combined, remap_result]
end

.union_namespace_references(destination, source, suffix = 'incr') ⇒ Object 



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# File 'lib/bel/nanopub/util.rb', line 4

def self.union_namespace_references(destination, source, suffix = 'incr')
  BEL::Nanopub.union_by_keyword(
    destination,
    source,
    suffix
  )
end