1 files changed, 66 insertions, 0 deletions
diff --git a/LOAEL/CV_ds_pctype_algo_rseed_LOAEL_loo.rb b/LOAEL/CV_ds_pctype_algo_rseed_LOAEL_loo.rb
new file mode 100644
index 0000000..d969164
--- /dev/null
+++ b/LOAEL/CV_ds_pctype_algo_rseed_LOAEL_loo.rb
@@ -0,0 +1,66 @@
+# Do a 10-fold crossvalidation
+# # Author: Andreas Maunz, David Vorgrimmler
+# # @params: Dataset_name(see dataset.yaml), pc_type(electronic,cpsa or constitutional ... or nil to disable), prediction_algorithm(local_mlr_prop or local_svm_regression ...), algo_params (e.g. ;param_name1=param_value1;param_name2=param_value2 or nil), random_seed (1, 2, ... or 10), path (e.g. ../data/dataset.yaml)
+
+require 'rubygems'
+require 'opentox-ruby'
+require 'yaml'
+
+if ARGV.size != 6 
+  puts "Args: ds_name, pc_type, algo, algo_params, random_seed, path/to/dataset.yaml"
+  puts ARGV.size
+  exit
+end
+
+#ds_file = "datasets.yaml"
+#pwd=`pwd`
+#path = "#{pwd.chop}/../data/#{ds_file}"
+path = ARGV[5]
+ds_file = path.split("/").last
+
+if File.exists?(path)
+  puts "[#{Time.now.utc.iso8601(4).to_s}] #{ds_file} exists."
+else
+  puts "#{ds_file} does not exist."
+  exit
+end
+
+subjectid = nil
+
+ds_name = ARGV[0] # e.g. MOU
+pc_type = ARGV[1] # e.g. electronic,cpsa or nil to disable
+algo = ARGV[2]    # e.g. local_svm_regression, local_mlr_prop
+user_algo_params = ARGV[3] #e.g. ;param_name1=param_value1;param_name2=param_value2
+r_seed = ARGV[4]  # 1, 2, ..., 10
+
+ds = YAML::load_file("#{path}")
+ds_uri = ds[ds_name]["dataset"]
+pc_ds_uri = ds[ds_name][pc_type]
+
+algo_params = "prediction_algorithm=#{algo}"
+algo_params += ";pc_type=#{pc_type}" unless (pc_type == "nil") || (pc_ds_uri.include? 'pc_type') 
+algo_params += ";feature_dataset_uri=#{pc_ds_uri}" unless (pc_type == "nil") || (pc_ds_uri.include? 'feature_dataset_uri') 
+algo_params += "#{user_algo_params}" unless user_algo_params == "nil"
+#algo_params += ";min_chisq_significance=0.9"
+#algo_params += ";min_frequency=6"
+#algo_params += ";feature_type=trees"
+
+puts "[#{Time.now.utc.iso8601(4).to_s}] #{algo_params.to_yaml}"
+
+prediction_feature = OpenTox::Dataset.find(ds_uri).features.keys.first
+
+
+# Ready
+cv_args = {}
+cv_args[:dataset_uri] = ds_uri
+cv_args[:prediction_feature] = prediction_feature
+cv_args[:algorithm_uri] = "http://toxcreate3.in-silico.ch:8085/algorithm/lazar"
+cv_args[:algorithm_params] = algo_params
+cv_args[:loo] = true
+puts "[#{Time.now.utc.iso8601(4).to_s}] #{cv_args.to_yaml}"
+
+loo = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-validation"],"crossvalidation/loo"), cv_args )
+puts "[#{Time.now.utc.iso8601(4).to_s}] #{loo}"
+
+cvr = OpenTox::CrossvalidationReport.create( loo , subjectid).uri
+puts "[#{Time.now.utc.iso8601(4).to_s}] #{cvr}"