summaryrefslogtreecommitdiff
path: root/test/dataset.rb
diff options
context:
space:
mode:
authorChristoph Helma <helma@in-silico.ch>2019-06-20 22:01:50 +0200
committerChristoph Helma <helma@in-silico.ch>2019-06-20 22:01:50 +0200
commit455da06aa6459da0d25b286ca6cb866ff64c4c34 (patch)
treed0ed8fcf720a02742da781669251f379b8fd07f0 /test/dataset.rb
parent1b44e0cd76f2ead93b8b3fa0f970c85ef32a4b14 (diff)
separate csv serialisations for batch predictions and training data, repeated measurements in mutagenicity dataset fixed, daphnia import fixed, CENTRAL_MONGO_IP removed
Diffstat (limited to 'test/dataset.rb')
-rw-r--r--test/dataset.rb18
1 files changed, 15 insertions, 3 deletions
diff --git a/test/dataset.rb b/test/dataset.rb
index 8e230e0..b978512 100644
--- a/test/dataset.rb
+++ b/test/dataset.rb
@@ -137,7 +137,6 @@ class DatasetTest < MiniTest::Test
d = Dataset.from_csv_file File.join(DATA_DIR,"batch_prediction_#{type}_small.csv")
assert_equal Dataset, d.class
refute_nil d.id
- dataset = Dataset.find d.id
assert_equal 3, d.compounds.size
end
end
@@ -175,10 +174,16 @@ class DatasetTest < MiniTest::Test
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: true, remove_duplicates: true
- assert_equal 8281, dataset.compounds.size
- assert_equal 9, dataset.features.size
+ csv = dataset.to_training_csv
+ rows = csv.split("\n")
+ header = rows.shift
+ assert_equal "Canonical SMILES,Mutagenicity",header
+ values = rows.collect{|r| r.split(",")[1]}.uniq
+ assert_equal 2, values.size
+ assert_equal 8290, dataset.compounds.size
c = Compound.from_smiles("C/C=C/C=O")
assert_equal ["mutagenic"], dataset.values(c,dataset.merged_features.first)
+ assert_equal 9, dataset.features.size
end
# serialisation
@@ -203,6 +208,13 @@ class DatasetTest < MiniTest::Test
end
# special cases/details
+
+ def test_daphnia_import
+ d = Dataset.from_csv_file File.join(File.dirname(__FILE__),"..","data", "Acute_toxicity-Daphnia_magna.csv")
+ assert 3, d.features.size
+ assert 546, d.compounds.size
+ puts d.to_training_csv
+ end
def test_dataset_accessors
d = Dataset.from_csv_file "#{DATA_DIR}/multicolumn.csv"