Module: Linnaeus

Defined in:

lib/rbbt/ner/linnaeus.rb

Constant Summary

ARGS =

["--properties", Rbbt.software.opt.Linnaeus["species-proxy/properties.conf"].find]

Class Method Summary

• .init ⇒ Object
• .match(text) ⇒ Object

Class Method Details

.init ⇒ Object

# File 'lib/rbbt/ner/linnaeus.rb', line 13

def self.init
  begin
    @@ArgParser    = Rjb::import('martin.common.ArgParser')
    @@Args         = @@ArgParser.new(ARGS)
    @@Loggers      = Rjb::import('martin.common.Loggers')
    @@Logger       = @@Loggers.getDefaultLogger(@@Args)
    @@EntityTagger = Rjb::import('uk.ac.man.entitytagger.EntityTagger')
    @@Matcher      = @@EntityTagger.getMatcher(@@Args, @@Logger)
  rescue
    if $!.message =~ /heap space/i
      Log.warn "Heap Space seems too low. Make sure Linnaeus is loaded before other Java wrappers so that it has the chance to init the Java Bridge with sufficient heap space"
    end
    raise $!
  end
end

.match(text) ⇒ Object

# File 'lib/rbbt/ner/linnaeus.rb', line 29

def self.match(text)

  init unless defined? @@Matcher

  @@Matcher.match(text).toArray().collect do |mention|
    NamedEntity.setup(mention.text(), mention.start(), "Organism", mention.ids(), mention.probabilities())
  end
end