From f87c7b3819345aa0880e518d3a83c76eb7198293 Mon Sep 17 00:00:00 2001 From: davor Date: Tue, 20 Mar 2012 15:51:00 +0100 Subject: Added and modified scripts for LOAEL validation. --- cv/data/datasets_jl1_allnum.yaml | 57 ++++++++++++++++++++++ cv/data/utils/create_all_pc_feature_ds.rb | 26 ++++++++++ cv/data/utils/create_pc_feature_ds.rb | 2 +- cv/data/utils/create_selected_feature_ds.rb | 40 +++++++++------ .../utils/wrapper_create_selected_feature_ds.sh | 32 ++++++++++++ 5 files changed, 142 insertions(+), 15 deletions(-) create mode 100644 cv/data/datasets_jl1_allnum.yaml create mode 100644 cv/data/utils/create_all_pc_feature_ds.rb create mode 100755 cv/data/utils/wrapper_create_selected_feature_ds.sh diff --git a/cv/data/datasets_jl1_allnum.yaml b/cv/data/datasets_jl1_allnum.yaml new file mode 100644 index 0000000..7700861 --- /dev/null +++ b/cv/data/datasets_jl1_allnum.yaml @@ -0,0 +1,57 @@ +{ + + "MDD": { + "dataset": "http://toxcreate3.in-silico.ch:8080/dataset/14" #, +# "electronic,cpsa": "http://toxcreate3.in-silico.ch:8080/dataset/", +# "constitutional": "http://toxcreate3.in-silico.ch:8080/dataset/", +# "topological": "http://toxcreate3.in-silico.ch:8080/dataset/", +# "hybrid": "http://toxcreate3.in-silico.ch:8080/dataset/", +# "joelib": "http://toxcreate3.in-silico.ch:8080/dataset/", +# "all_pc": "http://toxcreate3.in-silico.ch:8080/dataset/" + }, + + "FHM": { + "dataset": "http://toxcreate3.in-silico.ch:8080/dataset/6", + "electronic,cpsa": "http://toxcreate3.in-silico.ch:8080/dataset/83", + "constitutional": "http://toxcreate3.in-silico.ch:8080/dataset/87", + "topological": "http://toxcreate3.in-silico.ch:8080/dataset/96", + "hybrid": "http://toxcreate3.in-silico.ch:8080/dataset/100", + "joelib": "http://toxcreate3.in-silico.ch:8080/dataset/84", + "all_pc": "http://toxcreate3.in-silico.ch:8080/dataset/115" + }, + + "RAT": { + "dataset": "http://toxcreate3.in-silico.ch:8080/dataset/7", + "training": "http://toxcreate3.in-silico.ch:8080/dataset/12", + "test": "http://toxcreate3.in-silico.ch:8080/dataset/13", + "electronic,cpsa": "http://toxcreate3.in-silico.ch:8080/dataset/99", + "constitutional": "http://toxcreate3.in-silico.ch:8080/dataset/112", + "topological": "http://toxcreate3.in-silico.ch:8080/dataset/109", + "hybrid": "http://toxcreate3.in-silico.ch:8080/dataset/107", + "joelib": "http://toxcreate3.in-silico.ch:8080/dataset/90", + "all_pc": "http://toxcreate3.in-silico.ch:8080/dataset/3409" + }, + + "MOU": { + "dataset": "http://toxcreate3.in-silico.ch:8080/dataset/8", + "training": "http://toxcreate3.in-silico.ch:8080/dataset/10", + "test": "http://toxcreate3.in-silico.ch:8080/dataset/11", + "electronic,cpsa": "http://toxcreate3.in-silico.ch:8080/dataset/97", + "constitutional": "http://toxcreate3.in-silico.ch:8080/dataset/102", + "topological": "http://toxcreate3.in-silico.ch:8080/dataset/108", + "hybrid": "http://toxcreate3.in-silico.ch:8080/dataset/103", + "joelib": "http://toxcreate3.in-silico.ch:8080/dataset/94", + "all_pc": "http://toxcreate3.in-silico.ch:8080/dataset/2273" + }, + + "LOAEL": { + "dataset": "http://toxcreate3.in-silico.ch:8080/dataset/9", + "electronic,cpsa": "http://toxcreate3.in-silico.ch:8080/dataset/98", + "constitutional": "http://toxcreate3.in-silico.ch:8080/dataset/114", + "topological": "http://toxcreate3.in-silico.ch:8080/dataset/110", + "hybrid": "http://toxcreate3.in-silico.ch:8080/dataset/111", + "joelib": "http://toxcreate3.in-silico.ch:8080/dataset/92", + "all_pc": "http://toxcreate3.in-silico.ch:8080/dataset/1582" + } + +} diff --git a/cv/data/utils/create_all_pc_feature_ds.rb b/cv/data/utils/create_all_pc_feature_ds.rb new file mode 100644 index 0000000..301d28e --- /dev/null +++ b/cv/data/utils/create_all_pc_feature_ds.rb @@ -0,0 +1,26 @@ +require 'rubygems' +require 'opentox-ruby' +require 'yaml' + +@subjectid = nil + +ds = YAML::load_file("../datasets_new_LOAEL.yaml") +#ds.keys.each { |dataset| +["LOAEL"].each { |dataset| + puts "----------------- next dataset -----------------" + ["electronic,cpsa,constitutional,topological,hybrid,joelib"].each { |pc| + puts "#{dataset}, #{pc}" + + args = {} + args[:pc_type] = pc + ds_uri = ds[dataset]["dataset"] + + puts args.to_yaml + + feature_ds = OpenTox::RestClientWrapper.post( File.join(ds_uri,"/pcdesc"), args ) + puts "Result feature dataset:" + puts feature_ds + puts "--------" + } + puts "-----------------" +} diff --git a/cv/data/utils/create_pc_feature_ds.rb b/cv/data/utils/create_pc_feature_ds.rb index 0de64c2..c2ff6aa 100644 --- a/cv/data/utils/create_pc_feature_ds.rb +++ b/cv/data/utils/create_pc_feature_ds.rb @@ -4,7 +4,7 @@ require 'yaml' @subjectid = nil -ds = YAML::load_file("../datasets.yaml") +ds = YAML::load_file("../datasets_new_LOAEL.yaml") ds.keys.each { |dataset| puts "----------------- next dataset -----------------" ["electronic,cpsa", "constitutional", "topological", "hybrid", "joelib"].each { |pc| diff --git a/cv/data/utils/create_selected_feature_ds.rb b/cv/data/utils/create_selected_feature_ds.rb index c30a23e..cfc5e28 100644 --- a/cv/data/utils/create_selected_feature_ds.rb +++ b/cv/data/utils/create_selected_feature_ds.rb @@ -4,14 +4,14 @@ require 'yaml' @subjectid = nil - +@dataset = [] def create_f_ds(t_ds_uri, f_ds_uri, del) regression_training_dataset = OpenTox::Dataset.find(t_ds_uri, @subjectid) prediction_feature = regression_training_dataset.features.keys.first regression_feature_dataset = OpenTox::Dataset.find(f_ds_uri, @subjectid) - + params = {} params[:dataset_uri] = regression_training_dataset.uri params[:prediction_feature_uri] = prediction_feature @@ -20,29 +20,41 @@ def create_f_ds(t_ds_uri, f_ds_uri, del) puts params.to_yaml feature_selection_algo_uri = File.join(CONFIG[:services]["opentox-algorithm"],"feature_selection/rfe") puts feature_selection_algo_uri + puts "--- Feature dataset is: ---" result = OpenTox::RestClientWrapper.post( feature_selection_algo_uri, params) - puts "--- Feature dataset is: ---" puts result - puts + result end -ds = YAML::load_file("../datasets.yaml") -ds.keys.each { |dataset| +ds = YAML::load_file("../datasets_jl1_allnum.yaml") +#ds.keys.each { |dataset| +["LOAEL"].each { |dataset| puts "----------------- next dataset -----------------" + @dataset << "\"#{dataset}\": {" ds[dataset].keys.each { |pc| - puts pc unless (pc == "dataset") || (pc == "test") || (pc == "training") - #[false, true].each { |del_missing| - [false].each { |del_missing| #false is default - begin - create_f_ds(ds[dataset]["dataset"], ds[dataset][pc], del_missing) unless (pc == "dataset") || (pc == "test") || (pc == "training") - rescue - end - } + if !((pc == "dataset") || (pc == "test") || (pc == "training") || (pc == "hybrid")) + puts pc + #[false, true].each { |del_missing| + [false].each { |del_missing| #false is default + begin + result = create_f_ds(ds[dataset]["dataset"], ds[dataset][pc], del_missing) + @dataset << " \"#{pc}\": \"#{result}\"," + rescue + end + } + else + @dataset << " \"#{pc}\": \"#{ds[dataset][pc]}\"," + + end puts "-----------------" unless pc == "dataset" } + @dataset << "}," } + +puts @dataset + diff --git a/cv/data/utils/wrapper_create_selected_feature_ds.sh b/cv/data/utils/wrapper_create_selected_feature_ds.sh new file mode 100755 index 0000000..5871a24 --- /dev/null +++ b/cv/data/utils/wrapper_create_selected_feature_ds.sh @@ -0,0 +1,32 @@ +#!/bin/bash +# Wrapper Skript +# Creates selected feature ds from datasets.yaml +# David Vorgrimmler, 2012 + +PWD=`pwd` +echo $PWD +if [ ! -f $PWD/../datasets.yaml ] +then + echo "datasets.yaml does not exist." + exit +fi + +# Configure basics +source $HOME/.bash_aliases +otconfig +THIS_DATE=`date +%Y%m%d_%H_` +SFD="create_selected_feature_ds.rb" + +# Don't start when running +while ps x | grep $SFD | grep -v grep >/dev/null 2>&1; do sleep 5; done + +for i in 1 #2 3 +do + otreload + sleep 5 + LOGFILE=""$THIS_DATE""$i"_boot_150_sfd.log" + #rm "$LOGFILE" >/dev/null 2>&1 + echo "Start "$i"" + echo "ruby $SFD" >> $LOGFILE 2>&1 + ruby $SFD >> $LOGFILE 2>&1 +done -- cgit v1.2.3