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# # Author: Andreas Maunz, David Vorgrimmler
require 'rubygems'
require 'opentox-ruby'
require 'yaml'
if ARGV.size != 7
puts "Args: path/to/dataset.yaml ds_name num_boots backbone min_frequency method find_min_frequency"
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,RAT
num_boots = ARGV[2] # integer, 100 recommended
backbone = ARGV[3] # true/false
min_freq = ARGV[4] # integer
method = ARGV[5] # mle, mean, bbrc
find_min_frequency = ARGV[6] # true/false
hits = false
ds = YAML::load_file("#{path}")
ds_uri = ds[ds_name]["dataset"]
result1 = []
result2 = []
metadata = []
begin
for i in 1..50
puts
puts "--------------------------- Round: #{i} ---------------------------"
#################################
# SPLIT
#################################
puts " ----- split ds -----"
split_params = {}
split_params["dataset_uri"] = ds_uri
split_params["prediction_feature"] = (ds_uri.to_s + "/feature/1")
split_params["stratified"] = true
split_params["split_ratio"] = 0.5
split_params["random_seed"] = i
puts "[#{Time.now.iso8601(4).to_s}] Split params: #{split_params.to_yaml}"
split_result = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-validation"],"plain_training_test_split"), split_params)
datasets = {}
datasets[:training_ds] = split_result.inspect.gsub(/"/,'').split("\\n")[0]
datasets[:test_ds] = split_result.inspect.gsub(/"/,'').split("\\n")[1]
puts "[#{Time.now.iso8601(4).to_s}] Split result: #{datasets.to_yaml}"
puts
#################################
# FIND "good" min_frequency
#################################
if find_min_frequency.to_s == "true"
min_params = {}
min_params["dataset_uri"] = datasets[:training_ds]
ds = OpenTox::Dataset.find(datasets[:training_ds])
ds_nr_com = ds.compounds.size
min_params["backbone"] = backbone
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
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
end
# puts
# puts "----- Main phase: -----"
max_duration = durations[0] +(ds_nr_com.to_f * 0.003) # this is only an experience value.
min_params["min_frequency"] = y
y = y_old
found = false
cnt = 0
min_f = min_params["min_frequency"]
# Search for min_frequency with following heuristic procedure. If no good min_frequency found the delivered value(from the arguments) is used.
while found == false || cnt == 4 do
if min_f == min_params["min_frequency"]
cnt = cnt + 1
end
min_f = 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
# Check if number of features is max half and min one-tenth of the number of compounds and performed in accaptable amount of time
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
min_freq = min_params["min_frequency"]
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
end
#################################
# BBRC SAMPLE
#################################
puts " ----- bbrc feature calulation -----"
algo_params = {}
algo_params["dataset_uri"] = datasets[:training_ds]
algo_params["backbone"] = backbone
algo_params["min_frequency"] = min_freq
algo_params["nr_hits"] = hits
algo_params["method"] = method
t = Time.now
if method == "bbrc"
puts "[#{Time.now.iso8601(4).to_s}] BBRC params: #{algo_params.to_yaml}"
feature_dataset_uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc"), algo_params )
else
algo_params["num_boots"] = num_boots
algo_params["random_seed"] = i
puts "[#{Time.now.iso8601(4).to_s}] BBRC params: #{algo_params.to_yaml}"
feature_dataset_uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc/sample"), algo_params )
end
duration = Time.now - t
puts "[#{Time.now.iso8601(4).to_s}] BBRC duration: #{duration}"
puts "[#{Time.now.iso8601(4).to_s}] BBRC result: #{feature_dataset_uri}"
puts
#################################
# MATCH
#################################
puts " ----- bbrc match -----"
match_params = {}
match_params["feature_dataset_uri"] = "#{feature_dataset_uri}"
match_params["dataset_uri"] = datasets[:test_ds]
match_params["min_frequency"] = min_freq
match_params["nr_hits"] = hits
puts "[#{Time.now.iso8601(4).to_s}] Match params: #{match_params.to_yaml}"
matched_dataset_uri = OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-algorithm"],"fminer","bbrc","match"),match_params)
puts "[#{Time.now.iso8601(4).to_s}] BBRC match result: #{matched_dataset_uri}"
puts
#################################
# COMPARE pValues
#################################
puts " ----- pValue comparision -----"
bbrc_ds = OpenTox::Dataset.find(feature_dataset_uri)
bbrc_smarts_pValues = {}
bbrc_ds.features.each do |f, values|
if values[RDF::type].include?(OT.Substructure)
bbrc_smarts_pValues[values[OT::smarts]] = values[OT::pValue]
end
end
match_ds = OpenTox::Dataset.find(matched_dataset_uri)
matched_smarts_pValues = {}
match_ds.features.each do |f, values|
if values[RDF::type].include?(OT.Substructure)
matched_smarts_pValues[values[OT::smarts]] = values[OT::pValue]
end
end
sum_E1 = 0.0
sum_E2 = 0.0
bbrc_smarts_pValues.each do |s, p|
if matched_smarts_pValues.include?(s)
dif = (p.to_f - matched_smarts_pValues[s].to_f).abs
sum_E1 = sum_E1 + dif
sum_E2 = sum_E2 + dif**2
end
end
puts "[#{Time.now.iso8601(4).to_s}] Sum pValue difference (E1): #{sum_E1}"
puts "[#{Time.now.iso8601(4).to_s}] Squared sum pValue difference (E2): #{sum_E2}"
#################################
# SAVE data
#################################
result1 << sum_E1
result2 << sum_E2
info = []
info << { :ds_name => ds_name, :nr_features => bbrc_ds.features.size}
info << split_params
info << algo_params
info << match_params
metadata << info
puts
end
puts "############################################"
puts "############# FINAL RESULTS ################"
puts "############################################"
puts
puts "[#{Time.now.iso8601(4).to_s}] metadata: #{metadata.to_yaml}"
puts
puts "[#{Time.now.iso8601(4).to_s}] result1: #{result1.to_yaml}"
puts
puts "[#{Time.now.iso8601(4).to_s}] result2: #{result2.to_yaml}"
rescue Exception => e
LOGGER.debug "#{e.class}: #{e.message}"
LOGGER.debug "Backtrace:\n\t#{e.backtrace.join("\n\t")}"
puts "############################################"
puts "############ RESULTS befor error ###########"
puts "############################################"
puts
puts "[#{Time.now.iso8601(4).to_s}] metadata: #{metadata.to_yaml}"
puts
puts "[#{Time.now.iso8601(4).to_s}] result1: #{result1.to_yaml}"
puts
puts "[#{Time.now.iso8601(4).to_s}] result2: #{result2.to_yaml}"
end
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