Added feature ds for outl and improved inchi check

2 files changed, 165 insertions, 0 deletions

diff --git a/5x_cv/check_datasets_inchi_equality.rb b/5x_cv/check_datasets_inchi_equality.rb
new file mode 100644
index 0000000..7d38e96
--- /dev/null
+++ b/5x_cv/check_datasets_inchi_equality.rb
@@ -0,0 +1,98 @@
+require 'rubygems'
+require 'opentox-ruby'
+require 'yaml'
+
+@subjectid = nil
+
+
+
+def check_ds(t_ds_uri, f_ds_uri)
+  puts t_ds_uri
+  puts f_ds_uri
+
+  regression_training_dataset = OpenTox::Dataset.find(t_ds_uri, @subjectid)#3963;1572;
+  regression_feature_dataset = OpenTox::Dataset.find(f_ds_uri, @subjectid)#3971;3946;
+
+  train_ds = regression_training_dataset.data_entries.keys
+  train_cmds = regression_training_dataset.compounds
+  feature_ds = regression_feature_dataset.data_entries.keys
+  feature_cmds = regression_feature_dataset.compounds
+
+  puts "----- Check activity inchi -----"
+  match=0
+  mismatch=0
+  train_ds.each { |i| 
+    if feature_ds.include?(i)
+      match = match + 1
+    else
+      mismatch = mismatch + 1
+    end
+  }
+  if  mismatch > 0
+    puts "NOT all training compounds represented in feature dataset!!!" unless mismatch > 0
+    puts "match: #{match}; and mismatch: !!!!!#{mismatch}!!!!!"
+  else
+    puts "All training compounds represented in feature dataset." unless mismatch > 0
+    puts "match: #{match};    mismatch: #{mismatch}"
+    puts "OK!!!"
+  end
+  
+  train_ds.sort!          
+  feature_ds.sort!        
+                          
+  if train_ds == feature_ds
+    puts "train_ds == feature_ds"
+  else                    
+    a = train_ds - feature_ds
+    #puts "d: '#{a}'"
+    puts "train_ds: " + train_ds.size.to_s + ";     feature_ds: "+ feature_ds.size.to_s
+    puts "train_ds =NOT feature_ds"
+  end
+
+
+
+  puts "----- Check compound inchi -----"
+  match=0
+  mismatch=0
+  train_cmds.each { |i|
+    if feature_cmds.include?(i)
+      match = match + 1
+    else
+      mismatch = mismatch + 1
+    end
+  }
+  if  mismatch > 0
+    puts "NOT all training compounds represented in feature dataset!!!" unless mismatch > 0
+    puts "match: #{match}; and mismatch: !!!!!#{mismatch}!!!!!"
+  else
+    puts "All training compounds represented in feature dataset." unless mismatch > 0
+    puts "match: #{match};    mismatch: #{mismatch}"
+    puts "OK!!!"
+  end
+
+
+
+  feature_cmds.sort!      
+  train_cmds.sort!        
+
+  if train_cmds == feature_cmds
+    puts "train_cmds == feature_cmds"
+  else
+    b = train_cmds - feature_cmds
+    #puts "d: '#{b}'"
+    puts "train_cmds: " + train_cmds.size.to_s + ";     feature_cmds: " + feature_cmds.size.to_s
+    puts "train_cmds =NOT feature_cmds"
+  end 
+  puts
+end
+
+
+
+
+ds = YAML::load_file("datasets_nestle.yaml")
+ds.keys.each { |dataset|
+  ds[dataset].keys.each { |pc|
+    puts pc
+    check_ds(ds[dataset]["dataset"], ds[dataset][pc])
+  }
+}
diff --git a/5x_cv/datasets_nestle_outl.yaml b/5x_cv/datasets_nestle_outl.yaml
new file mode 100644
index 0000000..d6308f5
--- /dev/null
+++ b/5x_cv/datasets_nestle_outl.yaml
@@ -0,0 +1,67 @@
+{
+
+  "MDD": {
+    "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/1571",
+    "electronic,cpsa": "http://toxcreate3.in-silico.ch:8086/dataset/4007",
+    "constitutional": "http://toxcreate3.in-silico.ch:8086/dataset/4006",
+#    "geometrical":  "http://toxcreate3.in-silico.ch:8086/dataset/1905",
+#    "topological": "http://toxcreate3.in-silico.ch:8086/dataset/1906",
+#    "hybrid": "http://toxcreate3.in-silico.ch:8086/dataset/1907",
+    "constitutional,electronic,cpsa": "http://toxcreate3.in-silico.ch:8086/dataset/5265"
+  },
+  
+  "FHM": {
+    "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/1572",
+    "electronic,cpsa": "http://toxcreate3.in-silico.ch:8086/dataset/4019",
+    "constitutional": "http://toxcreate3.in-silico.ch:8086/dataset/4008" #,
+#    "geometrical":  "http://toxcreate3.in-silico.ch:8086/dataset/1908",
+#    "topological": "http://toxcreate3.in-silico.ch:8086/dataset/1909",
+#    "hybrid": "http://toxcreate3.in-silico.ch:8086/dataset/1910"
+  },
+  
+  "RAT": {
+    "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/1573",
+    "electronic,cpsa": "http://toxcreate3.in-silico.ch:8086/dataset/4077",
+    "constitutional": "http://toxcreate3.in-silico.ch:8086/dataset/4020" #,
+#    "geometrical":  "http://toxcreate3.in-silico.ch:8086/dataset/1911",
+#    "topological": "http://toxcreate3.in-silico.ch:8086/dataset/1912",
+#    "hybrid": "http://toxcreate3.in-silico.ch:8086/dataset/1913"
+  },
+  
+  "MOU": {
+    "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/1574",
+    "electronic,cpsa": "http://toxcreate3.in-silico.ch:8086/dataset/4115",
+    "constitutional": "http://toxcreate3.in-silico.ch:8086/dataset/4101" #,
+#    "geometrical":  "http://toxcreate3.in-silico.ch:8086/dataset/1914",
+#    "topological": "http://toxcreate3.in-silico.ch:8086/dataset/1915",
+#    "hybrid": "http://toxcreate3.in-silico.ch:8086/dataset/1916"
+  },
+
+#  "MDD2": {
+#    "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/",
+#    "electronic,cpsa": "http://toxcreate3.in-silico.ch:8086/dataset/",
+#    "constitutional": "http://toxcreate3.in-silico.ch:8086/dataset/",
+#    "constitutional,electronic,cpsa": "http://toxcreate3.in-silico.ch:8086/dataset/"
+#  },
+#  
+  "FHM2": {
+    "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/4975",
+    "electronic,cpsa": "http://toxcreate3.in-silico.ch:8086/dataset/5263",
+    "constitutional": "http://toxcreate3.in-silico.ch:8086/dataset/5262",
+    "constitutional,electronic,cpsa": "http://toxcreate3.in-silico.ch:8086/dataset/5266"
+  },
+  
+  "RAT2": {
+    "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/4977",
+    "electronic,cpsa": "http://toxcreate3.in-silico.ch:8086/dataset/5253",
+    "constitutional": "http://toxcreate3.in-silico.ch:8086/dataset/5246",
+    "constitutional,electronic,cpsa": "http://toxcreate3.in-silico.ch:8086/dataset/5254"
+  },
+  
+  "MOU2": {
+    "dataset": "http://toxcreate3.in-silico.ch:8086/dataset/4976",
+    "electronic,cpsa": "http://toxcreate3.in-silico.ch:8086/dataset/4115",
+    "constitutional": "http://toxcreate3.in-silico.ch:8086/dataset/5264",
+    "constitutional,electronic,cpsa": "http://toxcreate3.in-silico.ch:8086/dataset/5198"
+  }
+}