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require File.join(File.expand_path(File.dirname(__FILE__)), '../../test_helper.rb')
require 'rbbt/workflow'
require 'rbbt/entity'
Workflow.require_workflow "Genomics"
Workflow.require_workflow "TextMining"
require 'rbbt/entity/pmid'
require 'rbbt/entity/document'
require 'rbbt/corpus'
require 'test/unit'
module Document
self.corpus = Persist.open_tokyocabinet("/tmp/corpus", false, :string, "BDB")
property :banner => :single do |*args|
normalize, organism = args
TextMining.job(:gene_mention_recognition, "Factoid", :text => text, :method => :banner, :normalize => normalize, :organism => organism).exec.each{|e| SegmentWithDocid.setup(e, self.docid)}
end
property :abner => :single do |*args|
normalize, organism = args
TextMining.job(:gene_mention_recognition, "Factoid", :text => text, :method => :abner, :normalize => normalize, :organism => organism).exec.each{|e| SegmentWithDocid.setup(e, self.docid)}
end
persist :abner, :annotations, :dir => Rbbt.tmp.test.find(:user).entity_property
end
class TestDocument < Test::Unit::TestCase
def _test_pmid
pmid = "21904853"
PMID.setup(pmid)
assert_match /^PMID/, pmid.id
assert_match /TET2/, pmid.text
end
def _test_abner
pmid = "21904853"
PMID.setup(pmid)
genes = pmid.abner.reject{|ne| ne.offset.nil?}
genes.each do |ne|
orig = ne
orig_range = ne.range
ne.mask
assert ne.masked?
assert ne =~ /^MASKED/
assert_equal orig_range, ne.range
assert_equal ne, ne.unmask
end
assert pmid.abner.include? "TET2"
end
def test_free_text
text = "Free text including a mention to TET2."
Document.setup(text)
assert text.abner.include? "TET2"
docid = text.docid
assert_match /TET2/, Document.setup(docid).text
assert Document.setup(docid).abner.include? "TET2"
end
end
Version data entries
18 entries across 18 versions & 1 rubygems