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-rw-r--r--test/fminer.rb52
1 files changed, 0 insertions, 52 deletions
diff --git a/test/fminer.rb b/test/fminer.rb
deleted file mode 100644
index 16e1f9e..0000000
--- a/test/fminer.rb
+++ /dev/null
@@ -1,52 +0,0 @@
-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
- # TODO: fminer calculates 62 instead of 54 features
- # it is unclear which commit changed the numbers (occurs with old libraries/mongodb branch too
- # modification of Compound to use smiles instead of inchis seems to have no effect
- #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
- smarts.each do |smart|
- assert smart.p_value.round(2) >= 0.95
- end
- 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