Added and modified scripts for LOAEL validation.

5 files changed, 142 insertions, 15 deletions

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