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require File.expand_path(File.dirname(__FILE__) + '../../../test_helper')
require 'rbbt/util/tmpfile'
require 'test/unit'
require 'rbbt/knowledge_base'
require 'rbbt/knowledge_base/query'
module Gene
extend Entity
end
class TestKnowledgeBaseSyndicate < Test::Unit::TestCase
EFFECT =StringIO.new <<-END
#: :sep=" "#:type=:double
#SG TG Effect
MDM2 TP53 inhibition
TP53 NFKB1|GLI1 activation|activation true|true
END
EFFECT_OPTIONS = {
:source => "SG=~Associated Gene Name",
:target => "TG=~Associated Gene Name=>Ensembl Gene ID",
:persist => false,
:identifiers => datafile_test('identifiers'),
:undirected => true,
:namespace => "Hsa"
}
EFFECT_TSV = TSV.open EFFECT, EFFECT_OPTIONS.dup
KNOWLEDGE_BASE = KnowledgeBase.new '/tmp/kb.foo2', "Hsa"
KNOWLEDGE_BASE.format = {"Gene" => "Ensembl Gene ID"}
KNOWLEDGE_BASE.entity_options["Gene"] = {:organism => "Mmu", :test_option => "TEST"}
KNOWLEDGE_BASE.register :effects, EFFECT_TSV, EFFECT_OPTIONS.dup
def test_syndicate_entity_options
Gene.add_identifiers datafile_test('identifiers')
kb = KnowledgeBase.new "/tmp/kb.foo3", "Hsa"
kb.format = {"Gene" => "Associated Gene Name"}
kb.syndicate :orig, KNOWLEDGE_BASE
assert_equal "Mmu", KNOWLEDGE_BASE.entity_options_for("Gene", "effects")[:organism]
assert_equal "Mmu", kb.get_index("effects@orig").entity_options["Gene"][:organism]
assert_equal "Mmu", kb.get_database("effects@orig").entity_options["Gene"][:organism]
assert_equal "Mmu", kb.entity_options_for("Gene", "effects@orig")[:organism]
assert_equal "Mmu", kb.children("effects@orig", "TP53").source_entity.organism
end
end
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706 entries across 706 versions & 1 rubygems