Modified LOAEL scripts.

Added time stamps to outputs. Added argument to set algorithm params.

6 files changed, 62 insertions, 50 deletions

diff --git a/cv/scripts/CV_ds_pctype_algo_rseed_LOAEL.rb b/cv/scripts/CV_ds_pctype_algo_rseed_LOAEL.rb
index 2442b01..b35a86d 100644
--- a/cv/scripts/CV_ds_pctype_algo_rseed_LOAEL.rb
+++ b/cv/scripts/CV_ds_pctype_algo_rseed_LOAEL.rb
@@ -1,9 +1,13 @@
 # Do a 10-fold crossvalidation
 # # Author: Andreas Maunz, David Vorgrimmler
-# # @params: Dataset_name(see dataset_nestle.yaml), pc_type(electronic,cpsa or constitutional ... or nil to disable), prediction_algorithm(local_mlr_prop or local_svm_regression ...)
+# # @params: Dataset_name(see dataset.yaml), pc_type(electronic,cpsa or constitutional ... or nil to disable), prediction_algorithm(local_mlr_prop or local_svm_regression ...), algo_params (e.g. ;param_name1=param_value1;param_name2=param_value2 or nil), random_seed (1, 2, ... or 10), path (e.g. ../data/dataset.yaml)
 
-if ARGV.size != 5 
-  puts "Args: ds_name, pc_type, algo, random_seed, path/to/dataset.yaml"
+require 'rubygems'
+require 'opentox-ruby'
+require 'yaml'
+
+if ARGV.size != 6 
+  puts "Args: ds_name, pc_type, algo, algo_params, random_seed, path/to/dataset.yaml"
   puts ARGV.size
   exit
 end
@@ -11,39 +15,37 @@ end
 #ds_file = "datasets.yaml"
 #pwd=`pwd`
 #path = "#{pwd.chop}/../data/#{ds_file}"
-path = ARGV[4]
+path = ARGV[5]
 ds_file = path.split("/").last
 
 if File.exists?(path)
-  puts "#{ds_file} exists"
+  puts "[#{Time.now.utc.iso8601(4).to_s}] #{ds_file} exists."
 else
   puts "#{ds_file} does not exist."
   exit
 end
 
-require 'rubygems'
-require 'opentox-ruby'
-require 'yaml'
-
 subjectid = nil
 
 ds_name = ARGV[0] # e.g. MOU
 pc_type = ARGV[1] # e.g. electronic,cpsa or nil to disable
 algo = ARGV[2]    # e.g. local_svm_regression, local_mlr_prop
-r_seed = ARGV[3]  # 1, 2, ..., 10
+user_algo_params = ARGV[3] #e.g. ;param_name1=param_value1;param_name2=param_value2
+r_seed = ARGV[4]  # 1, 2, ..., 10
 
 ds = YAML::load_file("#{path}")
 ds_uri = ds[ds_name]["dataset"]
 pc_ds_uri = ds[ds_name][pc_type]
 
 algo_params = "prediction_algorithm=#{algo}"
-algo_params += ";pc_type=#{pc_type}" unless pc_type == "nil" 
-algo_params += ";feature_dataset_uri=#{pc_ds_uri}" unless pc_type == "nil" 
+algo_params += ";pc_type=#{pc_type}" unless (pc_type == "nil") || (pc_ds_uri.include? 'pc_type') 
+algo_params += ";feature_dataset_uri=#{pc_ds_uri}" unless (pc_type == "nil") || (pc_ds_uri.include? 'feature_dataset_uri') 
+algo_params += "#{user_algo_params}" unless user_algo_params == "nil"
 #algo_params += ";min_chisq_significance=0.9"
 #algo_params += ";min_frequency=6"
 #algo_params += ";feature_type=trees"
 
-puts algo_params.to_yaml
+puts "[#{Time.now.utc.iso8601(4).to_s}] #{algo_params.to_yaml}"
 
 prediction_feature = OpenTox::Dataset.find(ds_uri).features.keys.first
 
@@ -56,10 +58,10 @@ cv_args[:algorithm_uri] = "http://toxcreate3.in-silico.ch:8080/algorithm/lazar"
 cv_args[:algorithm_params] = algo_params
 cv_args[:stratified] = false
 cv_args[:random_seed] = r_seed
-puts cv_args.to_yaml
+puts "[#{Time.now.utc.iso8601(4).to_s}] #{cv_args.to_yaml}"
 
 cv = OpenTox::Crossvalidation.create(cv_args).uri
-puts cv
+puts "[#{Time.now.utc.iso8601(4).to_s}] #{cv}"
 
 cvr = OpenTox::CrossvalidationReport.create( cv , subjectid).uri
-puts cvr
+puts "[#{Time.now.utc.iso8601(4).to_s}] #{cvr}"
diff --git a/cv/scripts/CV_ds_pctype_algo_rseed_LOAEL_loo.rb b/cv/scripts/CV_ds_pctype_algo_rseed_LOAEL_loo.rb
index 34ec4f9..deb78c6 100644
--- a/cv/scripts/CV_ds_pctype_algo_rseed_LOAEL_loo.rb
+++ b/cv/scripts/CV_ds_pctype_algo_rseed_LOAEL_loo.rb
@@ -1,9 +1,13 @@
 # Do a 10-fold crossvalidation
 # # Author: Andreas Maunz, David Vorgrimmler
-# # @params: Dataset_name(see dataset_nestle.yaml), pc_type(electronic,cpsa or constitutional ... or nil to disable), prediction_algorithm(local_mlr_prop or local_svm_regression ...)
+# # @params: Dataset_name(see dataset.yaml), pc_type(electronic,cpsa or constitutional ... or nil to disable), prediction_algorithm(local_mlr_prop or local_svm_regression ...), algo_params (e.g. ;param_name1=param_value1;param_name2=param_value2 or nil), random_seed (1, 2, ... or 10), path (e.g. ../data/dataset.yaml)
 
-if ARGV.size != 5 
-  puts "Args: ds_name, pc_type, algo, random_seed, path/to/dataset.yaml"
+require 'rubygems'
+require 'opentox-ruby'
+require 'yaml'
+
+if ARGV.size != 6 
+  puts "Args: ds_name, pc_type, algo, algo_params, random_seed, path/to/dataset.yaml"
   puts ARGV.size
   exit
 end
@@ -11,39 +15,37 @@ end
 #ds_file = "datasets.yaml"
 #pwd=`pwd`
 #path = "#{pwd.chop}/../data/#{ds_file}"
-path = ARGV[4]
+path = ARGV[5]
 ds_file = path.split("/").last
 
 if File.exists?(path)
-  puts "#{ds_file} exists"
+  puts "[#{Time.now.utc.iso8601(4).to_s}] #{ds_file} exists."
 else
   puts "#{ds_file} does not exist."
   exit
 end
 
-require 'rubygems'
-require 'opentox-ruby'
-require 'yaml'
-
 subjectid = nil
 
 ds_name = ARGV[0] # e.g. MOU
 pc_type = ARGV[1] # e.g. electronic,cpsa or nil to disable
 algo = ARGV[2]    # e.g. local_svm_regression, local_mlr_prop
-r_seed = ARGV[3]  # 1, 2, ..., 10
+user_algo_params = ARGV[3] #e.g. ;param_name1=param_value1;param_name2=param_value2
+r_seed = ARGV[4]  # 1, 2, ..., 10
 
 ds = YAML::load_file("#{path}")
 ds_uri = ds[ds_name]["dataset"]
 pc_ds_uri = ds[ds_name][pc_type]
 
 algo_params = "prediction_algorithm=#{algo}"
-algo_params += ";pc_type=#{pc_type}" unless pc_type == "nil" 
-algo_params += ";feature_dataset_uri=#{pc_ds_uri}" unless pc_type == "nil" 
+algo_params += ";pc_type=#{pc_type}" unless (pc_type == "nil") || (pc_ds_uri.include? 'pc_type') 
+algo_params += ";feature_dataset_uri=#{pc_ds_uri}" unless (pc_type == "nil") || (pc_ds_uri.include? 'feature_dataset_uri') 
+algo_params += "#{user_algo_params}" unless user_algo_params == "nil"
 #algo_params += ";min_chisq_significance=0.9"
 #algo_params += ";min_frequency=6"
 #algo_params += ";feature_type=trees"
 
-puts algo_params.to_yaml
+puts "[#{Time.now.utc.iso8601(4).to_s}] #{algo_params.to_yaml}"
 
 prediction_feature = OpenTox::Dataset.find(ds_uri).features.keys.first
 
@@ -55,10 +57,10 @@ cv_args[:prediction_feature] = prediction_feature
 cv_args[:algorithm_uri] = "http://toxcreate3.in-silico.ch:8080/algorithm/lazar"
 cv_args[:algorithm_params] = algo_params
 cv_args[:loo] = true
-puts cv_args.to_yaml
+puts "[#{Time.now.utc.iso8601(4).to_s}] #{cv_args.to_yaml}"
 
 loo = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-validation"],"crossvalidation/loo"), cv_args )
-puts loo
+puts "[#{Time.now.utc.iso8601(4).to_s}] #{loo}"
 
 cvr = OpenTox::CrossvalidationReport.create( loo , subjectid).uri
-puts cvr
+puts "[#{Time.now.utc.iso8601(4).to_s}] #{cvr}"
diff --git a/cv/scripts/factors_config_LOAEL b/cv/scripts/factors_config_LOAEL
index 4254011..ca8cca1 100644
--- a/cv/scripts/factors_config_LOAEL
+++ b/cv/scripts/factors_config_LOAEL
@@ -27,10 +27,10 @@
 #MOU joelib local_svm_regression
 #MOU all_pc local_svm_regression
 #MOU nil local_svm_regression
-LOAEL constitutional local_svm_regression
-LOAEL electronic,cpsa local_svm_regression
-LOAEL topological local_svm_regression
-#LOAEL hybrid local_svm_regression
-LOAEL joelib local_svm_regression
-LOAEL all_pc local_svm_regression
-#LOAEL nil local_svm_regression
+LOAEL constitutional local_svm_regression nil
+LOAEL electronic,cpsa local_svm_regression nil
+LOAEL topological local_svm_regression nil
+#LOAEL hybrid local_svm_regression nil
+LOAEL joelib local_svm_regression nil
+LOAEL all_pc local_svm_regression nil
+#LOAEL nil local_svm_regression nil
diff --git a/cv/scripts/factors_config_LOAEL_loo b/cv/scripts/factors_config_LOAEL_loo
index 4254011..ca8cca1 100644
--- a/cv/scripts/factors_config_LOAEL_loo
+++ b/cv/scripts/factors_config_LOAEL_loo
@@ -27,10 +27,10 @@
 #MOU joelib local_svm_regression
 #MOU all_pc local_svm_regression
 #MOU nil local_svm_regression
-LOAEL constitutional local_svm_regression
-LOAEL electronic,cpsa local_svm_regression
-LOAEL topological local_svm_regression
-#LOAEL hybrid local_svm_regression
-LOAEL joelib local_svm_regression
-LOAEL all_pc local_svm_regression
-#LOAEL nil local_svm_regression
+LOAEL constitutional local_svm_regression nil
+LOAEL electronic,cpsa local_svm_regression nil
+LOAEL topological local_svm_regression nil
+#LOAEL hybrid local_svm_regression nil
+LOAEL joelib local_svm_regression nil
+LOAEL all_pc local_svm_regression nil
+#LOAEL nil local_svm_regression nil
diff --git a/cv/scripts/wrapper_pc_cv_LOAEL.sh b/cv/scripts/wrapper_pc_cv_LOAEL.sh
index e4f5685..ce0bfca 100755
--- a/cv/scripts/wrapper_pc_cv_LOAEL.sh
+++ b/cv/scripts/wrapper_pc_cv_LOAEL.sh
@@ -25,10 +25,14 @@ CV="CV_ds_pctype_algo_rseed_LOAEL.rb"
 FACTORS="$1"
 
 # Don't start when running
-while ps x | grep $CV | grep -v grep >/dev/null 2>&1; do sleep 3; done
+while ps x | grep $CV | grep -v grep >/dev/null 2>&1; do sleep 30; done
 
 LOGFILE="$THIS_DATE""$USER""_wrapper_pc_cv_LOAEL.log"
-rm "$LOGFILE" >/dev/null 2>&1
+#rm "$LOGFILE" >/dev/null 2>&1
+if [ -f $LOGFILE ]
+then
+  LOGFILE="$LOGFILE`date +%M%S`"
+fi
 
 
 cat $FACTORS | while read factor; do
diff --git a/cv/scripts/wrapper_pc_cv_LOAEL_loo.sh b/cv/scripts/wrapper_pc_cv_LOAEL_loo.sh
index f75f385..bf36a89 100755
--- a/cv/scripts/wrapper_pc_cv_LOAEL_loo.sh
+++ b/cv/scripts/wrapper_pc_cv_LOAEL_loo.sh
@@ -25,10 +25,14 @@ CV="CV_ds_pctype_algo_rseed_LOAEL_loo.rb"
 FACTORS="$1"
 
 # Don't start when running
-while ps x | grep $CV | grep -v grep >/dev/null 2>&1; do sleep 3; done
+while ps x | grep $CV | grep -v grep >/dev/null 2>&1; do sleep 30; done
 
 LOGFILE="$THIS_DATE""$USER""_wrapper_pc_cv_LOAEL_loo.log"
-rm "$LOGFILE" >/dev/null 2>&1
+#rm "$LOGFILE" >/dev/null 2>&1
+if [ -f $LOGFILE ]
+then
+  LOGFILE="$LOGFILE`date +%M%S`"
+fi
 
 
 cat $FACTORS | while read factor; do