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authorhelma@in-silico.ch <helma@in-silico.ch>2018-11-12 17:08:51 +0100
committerhelma@in-silico.ch <helma@in-silico.ch>2018-11-12 17:08:51 +0100
commit6d68a1ca94937a0553f61ebbbbd317dae54ce4e6 (patch)
tree02df42992b8ec3bcd8230826b8ccde5820c35359 /test
parentcf80ed17102a0368df8d65037d113b521cdf6f0c (diff)
PubChem classification download
Diffstat (limited to 'test')
-rw-r--r--test/download.rb22
-rw-r--r--test/use_cases.rb84
2 files changed, 92 insertions, 14 deletions
diff --git a/test/download.rb b/test/download.rb
new file mode 100644
index 0000000..9fd0f40
--- /dev/null
+++ b/test/download.rb
@@ -0,0 +1,22 @@
+require_relative "setup.rb"
+
+class DownloadTest < MiniTest::Test
+
+ def test_pubchem_classification
+ Download.pubchem_classification aid: 1191, active: "carcinogen", inactive: "non-carcinogen", species: "Hamster", endpoint: "Carcinogen"
+ csv = File.join(File.dirname(__FILE__),"..","data","Carcinogen-Hamster.csv")
+ meta_file = File.join(File.dirname(__FILE__),"..","data","Carcinogen-Hamster.json")
+ assert File.exists?(csv)
+ table = CSV.read csv
+ assert_equal 87, table.size
+ assert_equal ["48413129", "CC=O", "carcinogen"], table[1]
+ meta = JSON.parse(File.read(meta_file))
+ assert_equal "Hamster", meta["species"]
+ assert_equal 1, meta["warnings"].size
+ FileUtils.rm(csv)
+ FileUtils.rm(meta_file)
+ end
+
+end
+
+
diff --git a/test/use_cases.rb b/test/use_cases.rb
index 4842a18..59677cb 100644
--- a/test/use_cases.rb
+++ b/test/use_cases.rb
@@ -50,25 +50,81 @@ class UseCasesTest < MiniTest::Test
end
def test_public_models
- skip
+ #skip
+ # TODO clean mongo
+ # PubChem Classification
+ [
+ {
+ :aid => 1205,
+ :species => "Rodents",
+ :endpoint => "Carcinogenicity",
+ :qmrf => {:group => "QMRF 4.12. Carcinogenicity", :name => "OECD 451 Carcinogenicity Studies"}
+ },{
+ :aid => 1208,
+ :species => "Rat",
+ :endpoint => "Carcinogenicity",
+ :qmrf => {:group => "QMRF 4.12. Carcinogenicity", :name => "OECD 451 Carcinogenicity Studies"}
+ },{
+ :aid => 1199,
+ :species => "Mouse",
+ :endpoint => "Carcinogenicity",
+ :qmrf => {:group => "QMRF 4.12. Carcinogenicity", :name => "OECD 451 Carcinogenicity Studies"}
+ }
+ ].each do |assay|
+ Download.pubchem_classification aid: assay[:aid], species: assay[:species], endpoint: assay[:endpoint], active: "carcinogen", inactive: "non-carcinogen", qmrf: qmrf
+ end
+
=begin
- #classification
- aids = [
- 1205, #Rodents (multiple species/sites)
- 1208, # rat carc
- 1199 # mouse
- # Mutagenicity
+ # Mutagenicity
+ kazius = Dataset.from_sdf_file "#{DATA_DIR}/cas_4337.sdf"
+ hansen = Dataset.from_csv_file "#{DATA_DIR}/hansen.csv"
+ efsa = Dataset.from_csv_file "#{DATA_DIR}/efsa.csv"
+ datasets = [kazius,hansen,efsa]
+ map = {"1" => "mutagen", "0" => "nonmutagen"}
+ training_dataset = Dataset.merge datasets: datasets, features: datasets.collect{|d| d.bioactivity_features.first}, value_maps: [nil,map,map], keep_original_features: false, remove_duplicates: true
+ # rename merged feature
+ training_dataset.merged_features.first.name = "Mutagenicity"
+ training_dataset.merged_features.first.save
+ Model::Validation.from_dataset training_dataset: training_dataset, prediction_feature: training_dataset.merged_features.first, species: "Salmonella typhimurium", endpoint: "Mutagenicity"
+
+ # Blood Brain Barrier Penetration
+ bbb = Dataset.from_csv_file "#{DATA_DIR}/bbb.csv"
+ Model::Validation.from_dataset training_dataset: bbb, prediction_feature: bbb.bioactivity_features.first, species: "Human", endpoint: "Blood Brain Barrier Penetration"
+ # PubChem Regression
+ # TODO transformations
+ [
+ {
+ :aid => 1195,
+ :species => "Human",
+ :endpoint => "Maximum Recommended Daily Dose"
+ },{
+ :aid => 1208,
+ :species => "Rat (TD50)",
+ :endpoint => "Carcinogenicity"
+ },{
+ :aid => 1199,
+ :species => "Mouse (TD50)",
+ :endpoint => "Carcinogenicity"
+ },{
+ :aid => 1188,
+ :species => "Fathead minnow",
+ :endpoint => "Acute Toxicity"
+ }
+ ].each do |assay|
+ Model::Validation.from_pubchem_aid aid: assay[:aid], species: assay[;species], endpoint: assay[:endpoint], regression:true
+ end
- 1195 #MRDD
- 1188 #FHM
- 1208, # rat carc td50
- 1199 # mouse td50
-
# daphnia
- # Blood Brain Barrier Penetration
- # Lowest observed adverse effect level (LOAEL)
+ daphnia = Dataset.from_csv_file "#{DATA_DIR}/daphnia.csv"
+ Model::Validation.from_dataset training_dataset: daphnia, prediction_feature: daphnia.bioactivity_features.first, species: "Daphnia magna", endpoint: "Acute toxicity"
+ # LOAEL
+ loael = Dataset.from_csv_file "#{DATA_DIR}/loael.csv"
+ Model::Validation.from_dataset training_dataset: loael, prediction_feature: loael.bioactivity_features.first, species: "Rat", endpoint: "Lowest observed adverse effect level (LOAEL)"
+=end
+
+=begin
# 1204 estrogen receptor
# 1259408, # GENE-TOX
# 1159563 HepG2 cytotoxicity assay