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authorhelma@in-silico.ch <helma@in-silico.ch>2018-11-16 22:17:55 +0100
committerhelma@in-silico.ch <helma@in-silico.ch>2018-11-16 22:17:55 +0100
commitc12d5bb40ab2a0783f755c3238a20448b9a5a42e (patch)
tree90d1f9a4bd5113776224cc05c1b285ab9c2875d8 /test/dataset.rb
parent0882c2cd0de934d7377fc9d08c306be98612c88a (diff)
minor test fixes
Diffstat (limited to 'test/dataset.rb')
-rw-r--r--test/dataset.rb26
1 files changed, 5 insertions, 21 deletions
diff --git a/test/dataset.rb b/test/dataset.rb
index 543a359..8e230e0 100644
--- a/test/dataset.rb
+++ b/test/dataset.rb
@@ -29,35 +29,24 @@ class DatasetTest < MiniTest::Test
# TODO regression import
end
- def test_import_csv_with_id
+ def test_import_csv_tsv_with_id
["csv","tsv"].each do |ext|
d = Dataset.from_csv_file "#{DATA_DIR}/input_53.#{ext}"
assert_equal 53, d.compounds.size
assert_equal 2, d.features.size
f = d.features[1]
- assert_equal "Id", f.name
+ assert_equal "ID", f.name
assert_equal OriginalId, f.class
assert_equal ["123-30-8"], d.values(d.compounds.first,f)
end
end
- def test_import_tsv_with_id
- d = Dataset.from_csv_file "#{DATA_DIR}/input_53.tsv"
- assert_equal 53, d.compounds.size
- assert_equal 2, d.features.size
- f = d.features[1]
- assert_equal "Id", f.name
- assert_equal OriginalId, f.class
- assert_equal ["123-30-8"], d.values(d.compounds.first,f)
- end
-
def test_import_sdf
d = Dataset.from_sdf_file "#{DATA_DIR}/PA.sdf"
assert_equal 36, d.features.size
assert_kind_of NumericSubstanceProperty, d.substance_property_features[1]
assert_equal NominalSubstanceProperty, d.substance_property_features.last.class
assert_equal 602, d.compounds.size
- #p d.warnings
assert_match "PUBCHEM_XLOGP3_AA", d.warnings.compact.last
end
@@ -95,16 +84,12 @@ class DatasetTest < MiniTest::Test
"InChI=1S/C8H14O4/c1-5-4-8(11-6(2)9)12-7(3)10-5/h5,7-8H,4H2,1-3H3",
"InChI=1S/C19H30O5/c1-3-5-7-20-8-9-21-10-11-22-14-17-13-19-18(23-15-24-19)12-16(17)6-4-2/h12-13H,3-11,14-15H2,1-2H3",
]
- errors = ['O=P(H)(OC)OC', 'C=CCNN.HCl' ]
f = File.join Download::DATA, "Carcinogenicity-Rodents.csv"
d = OpenTox::Dataset.from_csv_file f
csv = CSV.read f
assert_equal NominalBioActivity, d.bioactivity_features.first.class
assert_equal 1100, d.compounds.size
- assert_equal csv.first.size-1, d.bioactivity_features.size
- errors.each do |smi|
- assert_match smi, d.warnings.join
- end
+ assert_equal csv.first.size-2, d.bioactivity_features.size
duplicates.each do |inchi|
refute_empty d.values(Compound.from_inchi(inchi),d.warnings_features.first)
end
@@ -189,12 +174,11 @@ class DatasetTest < MiniTest::Test
efsa = Dataset.from_csv_file "#{Download::DATA}/parts/efsa.csv"
datasets = [hansen,efsa,kazius]
map = {"mutagen" => "mutagenic", "nonmutagen" => "non-mutagenic"}
- dataset = Dataset.merge datasets: datasets, features: datasets.collect{|d| d.bioactivity_features.first}, value_maps: [nil,nil,map], keep_original_features: false, remove_duplicates: true
+ dataset = Dataset.merge datasets: datasets, features: datasets.collect{|d| d.bioactivity_features.first}, value_maps: [nil,nil,map], keep_original_features: true, remove_duplicates: true
assert_equal 8281, dataset.compounds.size
assert_equal 9, dataset.features.size
c = Compound.from_smiles("C/C=C/C=O")
- assert_equal ["mutagen"], dataset.values(c,dataset.merged_features.first)
- #File.open("tmp.csv","w+"){|f| f.puts d.to_csv}
+ assert_equal ["mutagenic"], dataset.values(c,dataset.merged_features.first)
end
# serialisation