Modified scripts for LOAEL Validation

Added argument to set dataset.yaml, added timer.

5 files changed, 43 insertions, 9 deletions

diff --git a/cv/data/utils/check_datasets_inchi_equality.rb b/cv/data/utils/check_datasets_inchi_equality.rb
index 75d6558..ee284f2 100644
--- a/cv/data/utils/check_datasets_inchi_equality.rb
+++ b/cv/data/utils/check_datasets_inchi_equality.rb
@@ -4,7 +4,11 @@ require 'yaml'
 
 @subjectid = nil
 
-
+if ARGV.size != 1
+  puts "Args: path/to/dataset.yaml"
+  puts ARGV.size
+  exit
+end
 
 def check_ds(t_ds_uri, f_ds_uri)
   puts t_ds_uri
@@ -87,9 +91,10 @@ def check_ds(t_ds_uri, f_ds_uri)
 end
 
 
+path = ARGV[0]
+puts path
+ds = YAML::load_file("#{path}")
 
-
-ds = YAML::load_file("../datasets.yaml")
 ds.keys.each { |dataset|
   ds[dataset].keys.each { |pc|
     puts pc
diff --git a/cv/data/utils/create_all_pc_feature_ds.rb b/cv/data/utils/create_all_pc_feature_ds.rb
index 301d28e..6254d29 100644
--- a/cv/data/utils/create_all_pc_feature_ds.rb
+++ b/cv/data/utils/create_all_pc_feature_ds.rb
@@ -4,7 +4,15 @@ require 'yaml'
 
 @subjectid = nil
 
-ds = YAML::load_file("../datasets_new_LOAEL.yaml")
+if ARGV.size != 1
+  puts "Args: path/to/dataset.yaml"
+  puts ARGV.size
+  exit
+end
+
+path = ARGV[0]
+puts path
+ds = YAML::load_file("#{path}")
 #ds.keys.each { |dataset|
 ["LOAEL"].each { |dataset|
   puts "----------------- next dataset -----------------"
diff --git a/cv/data/utils/create_pc_feature_ds.rb b/cv/data/utils/create_pc_feature_ds.rb
index c2ff6aa..00d6845 100644
--- a/cv/data/utils/create_pc_feature_ds.rb
+++ b/cv/data/utils/create_pc_feature_ds.rb
@@ -4,8 +4,17 @@ require 'yaml'
 
 @subjectid = nil
 
-ds = YAML::load_file("../datasets_new_LOAEL.yaml")
-ds.keys.each { |dataset|
+if ARGV.size != 1
+  puts "Args: path/to/dataset.yaml"
+  puts ARGV.size
+  exit
+end
+
+path = ARGV[0]
+puts path
+ds = YAML::load_file("#{path}")
+#ds.keys.each { |dataset|
+["LOAEL"].each { |dataset|
   puts "----------------- next dataset -----------------"
   ["electronic,cpsa", "constitutional", "topological", "hybrid", "joelib"].each { |pc|
     puts "#{dataset}, #{pc}"
diff --git a/cv/data/utils/create_selected_feature_ds.rb b/cv/data/utils/create_selected_feature_ds.rb
index cfc5e28..d5b0c61 100644
--- a/cv/data/utils/create_selected_feature_ds.rb
+++ b/cv/data/utils/create_selected_feature_ds.rb
@@ -4,10 +4,19 @@ require 'yaml'
 
 @subjectid = nil
 
+@subjectid = nil
+
+if ARGV.size != 1
+  puts "Args: path/to/dataset.yaml"
+  puts ARGV.size
+  exit
+end
+
 @dataset = []
 
 def create_f_ds(t_ds_uri, f_ds_uri, del)
 
+  start_time = Time.new
   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)
@@ -24,14 +33,17 @@ def create_f_ds(t_ds_uri, f_ds_uri, del)
 
   result = OpenTox::RestClientWrapper.post( feature_selection_algo_uri, params)
   puts result
+  stop_time = Time.new
+  puts "Duration: #{stop_time - start_time}"
   puts
   result
 end
 
 
+path = ARGV[0]
+puts path
+ds = YAML::load_file("#{path}")
 
-
-ds = YAML::load_file("../datasets_jl1_allnum.yaml")
 #ds.keys.each { |dataset|
 ["LOAEL"].each { |dataset|
   puts "----------------- next dataset -----------------"
diff --git a/cv/data/utils/wrapper_create_selected_feature_ds.sh b/cv/data/utils/wrapper_create_selected_feature_ds.sh
index 5871a24..7e2026c 100755
--- a/cv/data/utils/wrapper_create_selected_feature_ds.sh
+++ b/cv/data/utils/wrapper_create_selected_feature_ds.sh
@@ -20,7 +20,7 @@ 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
+for i in 1 2 3
 do
   otreload
   sleep 5