Added bbrc-sampling test scripts.

4 files changed, 308 insertions, 0 deletions

diff --git a/bbrc-sample/bbrc_sample_dv.rb b/bbrc-sample/bbrc_sample_dv.rb
new file mode 100644
index 0000000..6a7c167
--- /dev/null
+++ b/bbrc-sample/bbrc_sample_dv.rb
@@ -0,0 +1,176 @@
+# # Author: Andreas Maunz, David Vorgrimmler
+
+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"
+  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
+num_boots = ARGV[2] # e.g. electronic,cpsa or nil to disable
+backbone = ARGV[3] # true/false
+min_freq = ARGV[4] # [100, 90, ..., 10]
+method = ARGV[5] # MLE, MEAN, BBRC
+hits = false
+
+ds = YAML::load_file("#{path}")
+ds_uri = ds[ds_name]["dataset"]
+
+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
+
+  # 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_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}"
+
+  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}"
diff --git a/bbrc-sample/factors_config_dv b/bbrc-sample/factors_config_dv
new file mode 100644
index 0000000..41fe9a9
--- /dev/null
+++ b/bbrc-sample/factors_config_dv
@@ -0,0 +1,25 @@
+#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
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
diff --git a/cv/data/datasets_bbrc.yaml b/cv/data/datasets_bbrc.yaml
new file mode 100644
index 0000000..5a3d818
--- /dev/null
+++ b/cv/data/datasets_bbrc.yaml
@@ -0,0 +1,39 @@
+{
+
+  "SAL": {
+    "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/4"
+  },
+  
+  "MOU": {
+    "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/1"
+  },
+  
+  "MCC": {
+    "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/3"
+  },
+
+  "RAT": {
+    "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/2"
+  },
+
+  "BB": {
+    "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/"
+  },
+
+  "NCT": {
+    "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/"
+  },
+
+  "YOSH": {
+    "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/"
+  },
+
+  "YOSH2": {
+    "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/"
+  },
+
+  "KAZ": {
+    "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/5"
+  }
+
+}