diff options
Diffstat (limited to 'bbrc-sample/find_pm.rb')
-rw-r--r-- | bbrc-sample/find_pm.rb | 68 |
1 files changed, 68 insertions, 0 deletions
diff --git a/bbrc-sample/find_pm.rb b/bbrc-sample/find_pm.rb new file mode 100644 index 0000000..a541793 --- /dev/null +++ b/bbrc-sample/find_pm.rb @@ -0,0 +1,68 @@ +# # Author: Andreas Maunz, David Vorgrimmler + +require 'rubygems' +require 'opentox-ruby' +require 'yaml' + +if ARGV.size != 2 + puts "Args: path/to/dataset.yaml ds_name" + puts ARGV.size + exit +end + +path = ARGV[0] +ds_file = path.split("/").last + +if File.exists?(path) + puts "[#{Time.now.iso8601(4).to_s}] #{ds_file} exists." +else + puts "#{ds_file} does not exist." + exit +end + +subjectid = nil + +ds_name = ARGV[1] # e.g. MOU + +ds = YAML::load_file("#{path}") +ds_uri = ds[ds_name]["dataset"] + +algo_params = {} +algo_params["dataset_uri"] = ds_uri + + +ds = OpenTox::Dataset.find(ds_uri) +ds_nr_de = ds.data_entries.size +ds_nr_com = ds.compounds.size + +[true,false].each do |bb| + min_freq = 110 + duration = 0.0 + while duration < 60.0 && min_freq > 10 do + min_freq = min_freq - 10 + algo_params["min_frequency"] = min_freq.to_s + "pm" + algo_params["backbone"] = bb + #algo_params["nr_hits"] = false + #algo_params["feature_type"] = true + + + puts "[#{Time.now.iso8601(4).to_s}] #{algo_params.to_yaml}" + t = Time.now + result_uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc/"), algo_params ) + duration = Time.now - t + ds_result = OpenTox::Dataset.find(result_uri) + ds_result_nr_de = ds_result.data_entries.size + ds_result_nr_com = ds_result.compounds.size + ds_result_nr_f = ds_result.features.size + + puts + puts "[#{Time.now.iso8601(4).to_s}] Bbrc result: #{result_uri}" + puts "[#{Time.now.iso8601(4).to_s}] nr dataentries: #{ds_result_nr_de} , (of #{ds_nr_de} ), #{(ds_result_nr_de/(ds_nr_de/100)).to_f.round}%" + puts "[#{Time.now.iso8601(4).to_s}] nr compounds: #{ds_result_nr_com} , (of #{ds_nr_com} ), #{(ds_result_nr_com/(ds_nr_com/100)).to_f.round}%" + puts "[#{Time.now.iso8601(4).to_s}] nr features: #{ds_result_nr_f}, , #{(ds_result_nr_f/(ds_nr_de/100)).to_f.round}%" + puts "[#{Time.now.iso8601(4).to_s}] Duration: #{duration}" + puts "------------------------" + puts + end + puts +end |