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author | Christoph Helma <helma@in-silico.ch> | 2015-08-10 13:26:06 +0200 |
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committer | Christoph Helma <helma@in-silico.ch> | 2015-08-10 13:26:06 +0200 |
commit | b7cd3ebbb858a8891c35c45896f1bdd525f3534e (patch) | |
tree | a9df6b1f4fc15f2f953e9a23c6dd00b74a967754 /test/fminer.rb | |
parent | 23ecfc6fa5ae4913e5cd17b7d58432d1f88d780c (diff) |
algorithm libraries added, fminer tests pass
Diffstat (limited to 'test/fminer.rb')
-rw-r--r-- | test/fminer.rb | 46 |
1 files changed, 46 insertions, 0 deletions
diff --git a/test/fminer.rb b/test/fminer.rb new file mode 100644 index 0000000..17dcbe1 --- /dev/null +++ b/test/fminer.rb @@ -0,0 +1,46 @@ +require_relative "setup.rb" + +class FminerTest < MiniTest::Test + + def test_fminer_bbrc + dataset = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"hamster_carcinogenicity.csv") + refute_nil dataset.id + feature_dataset = OpenTox::Algorithm::Fminer.bbrc dataset + feature_dataset = Dataset.find feature_dataset.id + assert_equal dataset.compounds.size, feature_dataset.compounds.size + assert_equal 54, feature_dataset.features.size + assert_equal "C-C-C=C", feature_dataset.features.first.smarts + compounds = feature_dataset.compounds + smarts = feature_dataset.features + match = OpenTox::Algorithm::Descriptor.smarts_match compounds, smarts + feature_dataset.data_entries.each_with_index do |fingerprint,i| + assert_equal match[i], fingerprint + end + + dataset.delete + feature_dataset.delete + end + + def test_fminer_last + skip "last features have to be activated" + dataset = OpenTox::Dataset.new + dataset.upload File.join(DATA_DIR,"hamster_carcinogenicity.csv") + feature_dataset = OpenTox::Algorithm::Fminer.last :dataset => dataset + assert_equal dataset.compounds.size, feature_dataset.compounds.size + assert_equal 21, feature_dataset.features.size + assert_equal '[#6&A]-[#6&a]:[#6&a]:[#6&a]:[#6&a]:[#6&a]', feature_dataset.features.first.smarts + + compounds = feature_dataset.compounds + smarts = feature_dataset.features.collect{|f| f.smarts} + match = OpenTox::Algorithm::Descriptor.smarts_match compounds, smarts + compounds.each_with_index do |c,i| + smarts.each_with_index do |s,j| + assert_equal match[i][j], feature_dataset.data_entries[i][j].to_i + end + end + + dataset.delete + feature_dataset.delete + end + +end |