diff options
Diffstat (limited to 'bbrc-sample/find_pm.rb')
-rw-r--r-- | bbrc-sample/find_pm.rb | 115 |
1 files changed, 115 insertions, 0 deletions
diff --git a/bbrc-sample/find_pm.rb b/bbrc-sample/find_pm.rb new file mode 100644 index 0000000..761e538 --- /dev/null +++ b/bbrc-sample/find_pm.rb @@ -0,0 +1,115 @@ +# # 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"] + +min_params = {} +min_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_params["backbone"] = bb + #min_freq = 110 + durations = [] + x = ds_nr_com + ds_result_nr_f = 0 + y = x + y_old = 0 + puts + puts "----- Initialization: -----" + while ds_result_nr_f < (ds_nr_com/4).to_i do + y_old = y + y = x + x = (x/2).to_i + min_params["min_frequency"] = x + puts "[#{Time.now.iso8601(4).to_s}] min_freq #{x}" + t = Time.now + result_uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc/"), min_params ) + durations << Time.now - t + ds_result = OpenTox::Dataset.find(result_uri) + ds_result_nr_f = ds_result.features.size + puts "[#{Time.now.iso8601(4).to_s}] nr features #{ds_result_nr_f}" + puts "[#{Time.now.iso8601(4).to_s}] duration #{durations.last}" + puts "-------------" + puts + end + puts "----- Main phase: -----" + puts + max_duration = durations[0] +(ds_nr_com.to_f * 0.003) + puts "max duration: #{max_duration}" + puts + min_params["min_frequency"] = y + y = y_old + found = false + cnt = 0 + min_f = min_params["min_frequency"] + while found == false || cnt == 4 do + if min_f == min_params["min_frequency"] + cnt = cnt + 1 + end + min_f = min_params["min_frequency"] + puts "[#{Time.now.iso8601(4).to_s}] min_freq #{min_params["min_frequency"]}" + t = Time.now + result_uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc/"), min_params ) + durations << Time.now - t + ds_result = OpenTox::Dataset.find(result_uri) + ds_result_nr_f = ds_result.features.size + ds_result_nr_de = ds_result.data_entries.size + ds_result_nr_com = ds_result.compounds.size + puts "[#{Time.now.iso8601(4).to_s}] nr features #{ds_result_nr_f}" + puts "[#{Time.now.iso8601(4).to_s}] duration #{durations.last}" + puts "-------------" + puts + puts "smaller than #{(ds_nr_com*0.45).to_i} and larger than #{(ds_nr_com/10).to_i}" + puts "x #{x}, y #{y}, min_freq #{min_params["min_frequency"]}" + if ds_result_nr_f.to_i < (ds_nr_com/2).to_i && ds_result_nr_f.to_i > (ds_nr_com/10).to_i + if durations.last < max_duration + found = true + else + x = min_params["min_frequency"] + min_params["min_frequency"] = ((min_params["min_frequency"]+y)/2).to_i + end + else + y = min_params["min_frequency"] + min_params["min_frequency"] = ((x+min_params["min_frequency"])/2).to_i + end + end + + 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: #{durations.last}" + puts "------------------------" + puts +end |