From b46693c6732558f36aa607d9d2263de896b39527 Mon Sep 17 00:00:00 2001 From: davor Date: Mon, 26 Mar 2012 17:35:59 +0200 Subject: Modified LOAEL scripts. Added time stamps to outputs. Added argument to set algorithm params. --- cv/scripts/CV_ds_pctype_algo_rseed_LOAEL.rb | 34 +++++++++++++------------ cv/scripts/CV_ds_pctype_algo_rseed_LOAEL_loo.rb | 34 +++++++++++++------------ cv/scripts/factors_config_LOAEL | 14 +++++----- cv/scripts/factors_config_LOAEL_loo | 14 +++++----- cv/scripts/wrapper_pc_cv_LOAEL.sh | 8 ++++-- cv/scripts/wrapper_pc_cv_LOAEL_loo.sh | 8 ++++-- 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 -- cgit v1.2.3