Updated scripts and added comments.

2 files changed, 228 insertions, 232 deletions

diff --git a/bbrc-sample/bbrc_sample_dv.rb b/bbrc-sample/bbrc_sample_dv.rb
index 923469e..4f68cd3 100644
--- a/bbrc-sample/bbrc_sample_dv.rb
+++ b/bbrc-sample/bbrc_sample_dv.rb
@@ -4,8 +4,8 @@ require 'rubygems'
 require 'opentox-ruby'
 require 'yaml'
 
-if ARGV.size != 6 
-  puts "Args: path/to/dataset.yaml ds_name num_boots backbone min_frequency method"
+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
@@ -22,11 +22,12 @@ end
 
 subjectid = nil
 
-ds_name = ARGV[1] # e.g. MOU
-num_boots = ARGV[2] # e.g. electronic,cpsa or nil to disable
+ds_name = ARGV[1] # e.g. MOU,RAT
+num_boots = ARGV[2] # integer, 100 recommended
 backbone = ARGV[3] # true/false
-min_freq = ARGV[4] # [100, 90, ..., 10]
-method = ARGV[5] # MLE, MEAN, BBRC
+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}")
@@ -36,218 +37,207 @@ result1 = []
 result2 = []
 metadata = []
 
-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
+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
 
-  # Find "good" min_frequency
-  
-  min_params = {}
-  min_params["dataset_uri"] = datasets[:training_ds]
-
-  ds = OpenTox::Dataset.find(datasets[:training_ds])
-#  ds_nr_de = ds.data_entries.size
-  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
-#    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
+    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
-    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
-        min_freq = min_params["min_frequency"]
-      else
-        x = min_params["min_frequency"]
-        min_params["min_frequency"] = ((min_params["min_frequency"]+y)/2).to_i
+    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
-    else
-      y = min_params["min_frequency"]
-      min_params["min_frequency"] = ((x+min_params["min_frequency"])/2).to_i
     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 )
+    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
-  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 "############################################"
+  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}"
 
-  # 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_E1 + 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
-
-  #  ds = OpenTox::Dataset.find(datasets[:training_ds])
-  #  ds_nr_de = ds.data_entries.size
-  #  ds_nr_com = ds.compounds.size
-  #
-  #  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
-  #
-  #  min_sampling_support = ds_result.metadata[OT::parameters][2][OT::paramValue]
-  #  num_boots = ds_result.metadata[OT::parameters][3][OT::paramValue] 
-  #  min_frequency_per_sample = ds_result.metadata[OT::parameters][4][OT::paramValue]
-  #  nr_hits = ds_result.metadata[OT::parameters][5][OT::paramValue]
-  #  merge_time = ds_result.metadata[OT::parameters][6][OT::paramValue]
-  #  n_stripped_mss = ds_result.metadata[OT::parameters][7][OT::paramValue]
-  #  n_stripped_cst = ds_result.metadata[OT::parameters][8][OT::paramValue]
-  #  random_seed = ds_result.metadata[OT::parameters][9][OT::paramValue]
-  #
-  #  puts "[#{Time.now.iso8601(4).to_s}] nr dataentries: #{ds_result_nr_de} , (of #{ds_nr_de} )"
-  #  puts "[#{Time.now.iso8601(4).to_s}] nr dataentries: #{ds_result_nr_com} , (of #{ds_nr_com} )"
-  #  puts "[#{Time.now.iso8601(4).to_s}] nr features: #{ds_result_nr_f}"
-  #  puts "[#{Time.now.iso8601(4).to_s}] Merge time: #{merge_time}"
-  #
-  #  puts "=hyperlink(\"#{ds_uri}\";\"#{ds_name}\"),#{num_boots},#{min_sampling_support},#{min_frequency_per_sample},#{nr_hits},=hyperlink(\"#{result_uri}\";\"bbrc_result\"),#{ds_result_nr_com},#{ds_nr_com},#{ds_result_nr_f},#{duration},#{merge_time},#{n_stripped_mss},#{n_stripped_cst},#{random_seed}"
+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
 
-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}"
diff --git a/bbrc-sample/factors_config_dv b/bbrc-sample/factors_config_dv
index 41fe9a9..76e089e 100644
--- a/bbrc-sample/factors_config_dv
+++ b/bbrc-sample/factors_config_dv
@@ -1,25 +1,31 @@
-#Dataset num_boots backbone min_frequence 
-#MOU 100 true
-#MOU 100 false
-#RAT 100 true
-#RAT 100 false
-#MCC 100 true
-#MCC 100 false
-SAL 100 true 40pm mle
-SAL 100 true 40pm mean
-SAL 100 true 40pm bbrc
-#SAL 100 false
-#KAZ 100 true
-#KAZ 100 false
-#BB 300
-#BB 200
-#BB 150
-#BB 100
-#NCT 300
-#NCT 200
-#NCT 150
-#NCT 100
-#YOSH 300
-#YOSH 200
-#YOSH 150
-#YOSH 100
+#Dataset num_boots backbone min_frequence method find_min_frequency
+#MOU 100 true 20pm mle true
+#MOU 100 true 20pm mean true
+#MOU 100 true 20pm bbrc true
+#MOU 100 false 30pm mle true
+#MOU 100 false 30pm mean true
+#MOU 100 false 30pm bbrc  true
+#RAT 100 true 20pm mle true
+#RAT 100 true 20pm mean true
+#RAT 100 true 20pm bbrc true
+#RAT 100 false 40pm mle true
+#RAT 100 false 40pm mean true
+#RAT 100 false 40pm bbrc true
+#MCC 100 true 20pm mle  true
+#MCC 100 true 20pm mean true
+#MCC 100 true 20pm bbrc true
+#MCC 100 false 50pm mle  true
+#MCC 100 false 50pm mean true
+#MCC 100 false 50pm bbrc true
+#SAL 100 true 40pm mle true
+#SAL 100 true 40pm mean true
+#SAL 100 true 40pm bbrc true
+#SAL 100 false 70pm mle true
+#SAL 100 false 70pm mean true
+#SAL 100 false 70pm bbrc true
+#KAZ 100 true 30pm mle true
+#KAZ 100 true 30pm mean true
+#KAZ 100 true 30pm bbrc true
+#KAZ 100 false 90pm mle true
+#KAZ 100 false 90pm mean true
+#KAZ 100 false 90pm bbrc true