Added feature datasets (pc_all) and updated scripts.

7 files changed, 1950 insertions, 11 deletions

diff --git a/cv/data/csv/FHM_all_pc.csv b/cv/data/csv/FHM_all_pc.csv
new file mode 100644
index 0000000..04b92ba
--- /dev/null
+++ b/cv/data/csv/FHM_all_pc.csv
@@ -0,0 +1,536 @@
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\ No newline at end of file
diff --git a/cv/data/csv/LOAEL_all_pc.csv b/cv/data/csv/LOAEL_all_pc.csv
new file mode 100644
index 0000000..b600e52
--- /dev/null
+++ b/cv/data/csv/LOAEL_all_pc.csv
@@ -0,0 +1,440 @@
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\ No newline at end of file
diff --git a/cv/data/csv/MOU_all_pc.csv b/cv/data/csv/MOU_all_pc.csv
new file mode 100644
index 0000000..b08e08d
--- /dev/null
+++ b/cv/data/csv/MOU_all_pc.csv
@@ -0,0 +1,402 @@
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\ No newline at end of file
diff --git a/cv/data/csv/RAT_all_pc.csv b/cv/data/csv/RAT_all_pc.csv
new file mode 100644
index 0000000..e40a409
--- /dev/null
+++ b/cv/data/csv/RAT_all_pc.csv
@@ -0,0 +1,512 @@
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+InChI%3D1S%2FC6H7N%2Fc7-6-4-2-1-3-5-6%2Fh1-5H%2C7H2,,4.0,1.0,34.5055999755859,,0.00881668832153082,0.0,0.0,0.371587008237839,,,5.14285714285714,0.0,2.34375,,1.5,6.9924488067627,,5.0,0.219979539513588,6.08364343643188,0.0,,3.04182171821594,0.0,0.0,0.322327673435211,0.0,0.0,0.0,0.0,-0.184992119669914,4.97105360031128,,0.494464188814163,0.0,-0.0360544472932816,0.0,,5.14285707473755,0.102062076330185,1.2688,28.2429008483887,0.0,2.34375,0.102062076330185,-16.2093238830566,0.0,0.0,0.0,1.5,-3.15915203094482,0.0,,0.0,0.0,7.0,0.275611728429794,21.8537044525146,,,0.0978959873318672,0.0,0.0,,59.3787994384766,7.0,7.33338356018066,3.96410155296326,14.003077507019,30.0,,2.19935870170593,16.3275508880615,0.0,0.0738276764750481,34.0790138244629,1.41068363189697,154.009994506836,-0.302463263273239,200.597534179688,,4.64573574066162,0.799572467803955,115.128059387207,5.40718269348145,0.453038930892944,15.6945419311523,,3.80735492706299,11.8500003814697,5.11288404464722,0.256600111722946,0.48710572719574,0.530342638492584,,3.3938467502594,1.3004184961319,0.0,0.0370370373129845,,274.155914306641,2.74318218231201,14.0,0.0,7.0,1.89384686946869,2.00999999046326,,3.11505794525146,0.0,,0.216230019927025,0.288675129413605,1.30671286582947,1.0,0.926172316074371,0.0,,0.0,0.901047587394714,0.0,1.0,0.0,0.0,0.20412415266037,0.0,0.25,0.0,0.0,0.0,0.0,0.0,,0.0,,1.0,0.0,26.0200004577637,0.0,,0.0,0.0,42.0,0.0,0.0,0.535000026226044,,0.333333343267441,,,0.0,0.0,,1.0,0.0320750139653683,0.0,,7.0,0.0185185186564922,1.0,6.0,0.677672326564789,0.0,0.0,,0.0,0.0,,0.388933509588242,0.0427248887717724,0.0530203767120838,7.35998821258545,6.46722555160522,7.16618537902832,,0.0,0.0,0.00177360558882356,8.33237075805664,26.02,0.40824830532074,0.0,,7.0,5.33237028121948,0.433012694120407,,,1.16618525981903,300.981719970703,6.0,,0.0,0.40824830532074,,,311.011962890625,0.0962250456213951,105.185432434082,,344.347229003906,0.0,0.526972889900208,169.887512207031,1.0,0.0,,0.0,205.845489501953,0.0,26.3670063018799,0.0,34.5240516662598,,0.0,0.0,0.0153829231858253,0.0,,-0.00502963690087199,,0.0,0.0,-0.00247410940937698,10.8196048736572,6.0,,-0.000180991701199673,,0.0,1.0,0.0,5.7978196144104,-6.7234004745842e-06,0.0,,,0.0,6.0,0.0,0.0,0.0,0.0,0.206699997186661,0.0,,,45.0,0.0,30.0,3.0,0.0,86.072998046875,,0.111111111938953,11.5163097381592,0.0962250456213951,95.4121017456055,0.0740740746259689,,-54.759449005127,0.0,,,0.0,-10.6724643707275,,5.0,,30.8544,1.84717881679535,,
+InChI%3D1S%2FC7H6N2O4%2Fc1-5-6%288%2810%2911%293-2-4-7%285%299%2812%2913%2Fh2-4H%2C1H3,0.0,6.0,0.0,11.273699760437,0.0,0.25259917974472,0.0,0.0,0.439710050821304,0.0,0.0,11.0769230769231,0.0,4.48148148148148,0.0,2.47933884297521,9.0712423324585,0.0,19.0,0.142386898398399,2.38110160827637,0.25,0.0,4.58575630187988,0.0,0.0,0.57096141576767,0.0,0.0,0.0,0.153846153846154,-0.377651870250702,6.80724048614502,0.0,0.498851299285889,0.0,-0.062790684401989,0.0,0.0,11.0769233703613,0.0680413842201233,2.8578,85.5254440307617,0.0,4.48148155212402,0.146608799695969,-56.5692253112793,0.0,0.0,0.0,2.47933888435364,-9.40554141998291,0.0,0.0,1.0,0.0,12.0,0.349990248680115,0.0,0.0,0.0,0.164609462022781,0.0,2.0,0.0,64.2665481567383,13.0,8.60916996002197,6.75947093963623,15.9979257583618,62.0,0.0,3.42152738571167,21.7287578582764,0.0,0.0,42.5079193115234,2.43548393249512,205.059997558594,-0.132685780525208,166.050674438477,0.0,3.30752015113831,1.67000353336334,109.831153869629,3.71671867370605,1.0071976184845,8.54590797424316,0.0,4.70043992996216,11.8900003433228,10.0080718994141,0.484665840864182,0.704401254653931,0.472289383411407,0.0,6.03658103942871,1.32113099098206,0.0,0.183000296354294,0.0,387.029693603516,5.60576343536377,19.0,0.07236647605896,13.0,4.13821697235107,1.57000005245209,0.0,3.56142926216125,0.0,0.0,0.198885351419449,1.13128232955933,3.31346035003662,4.0,1.0,0.0,0.0,0.0,1.93341875076294,0.0,0.0,0.0,0.429300367832184,1.08348917961121,0.908560276031494,0.5,0.0,0.0,0.0,0.54997193813324,1.88988161087036,0.0,0.0,0.0,0.0,0.0,68.2799987792969,0.0,2.0,0.0,0.0,234.0,0.0,0.0,2.68199992179871,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0240562614053488,0.0,0.0,13.0,0.0455728359520435,0.0,6.0,0.42903858423233,0.0,0.0,0.0,0.0,0.0,0.0,0.28377965092659,0.301181435585022,0.0220807529985905,16.8178520202637,0.600448906421661,15.5462341308594,0.0,0.0,2.0,0.0371074303984642,21.5420475006104,91.64,2.51677393913269,0.0,0.0,13.0,22.6538467407227,3.77983808517456,0.0,0.0,20.6774616241455,529.473999023438,6.0,0.0,0.0,4.35032272338867,0.0,0.0,603.23193359375,0.328635036945343,-54.9283409118652,0.0,803.134460449219,0.0,0.191561058163643,255.99365234375,1.0,0.0,0.0,0.0,762.645141601562,0.086066298186779,32.8477668762207,0.0,485.518005371094,0.0,0.0,0.0,0.113428935408592,0.0,0.0,0.00162364356219769,0.0,0.0,0.0,-0.00144386710599065,21.8157863616943,5.0,0.0,0.00485660415142775,0.0,1.44224953651428,3.0,0.0,12.3158092498779,-0.084684431552887,0.0,0.0,0.0,2.38110160827637,6.0,2.0,0.0,1.0,0.0,0.548799991607666,0.0,0.0,0.0,119.0,2.0,62.0,5.0,1.0,176.086996078491,4.0,0.710035920143127,8.74507331848145,0.826527535915375,220.979019165039,0.74670273065567,0.0,-146.162490844727,0.0,0.0,0.0,0.0,-24.3018608093262,0.0,3.0,0.0,48.823,2.9932119846344,0.0,0.0
\ No newline at end of file
diff --git a/cv/data/datasets.yaml b/cv/data/datasets.yaml
index ccc491a..7700861 100644
--- a/cv/data/datasets.yaml
+++ b/cv/data/datasets.yaml
@@ -16,8 +16,8 @@
     "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"
+    "joelib": "http://toxcreate3.in-silico.ch:8080/dataset/84",
+    "all_pc": "http://toxcreate3.in-silico.ch:8080/dataset/115"
   },
   
   "RAT": {
@@ -28,8 +28,8 @@
     "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/"
+    "joelib": "http://toxcreate3.in-silico.ch:8080/dataset/90",
+    "all_pc": "http://toxcreate3.in-silico.ch:8080/dataset/3409"
   },
 
   "MOU": {
@@ -40,8 +40,8 @@
     "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/"
+    "joelib": "http://toxcreate3.in-silico.ch:8080/dataset/94",
+    "all_pc": "http://toxcreate3.in-silico.ch:8080/dataset/2273"
   },
 
   "LOAEL": {
@@ -50,8 +50,8 @@
     "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/"
+    "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/count_features.rb b/cv/data/utils/count_features.rb
new file mode 100644
index 0000000..1e272ac
--- /dev/null
+++ b/cv/data/utils/count_features.rb
@@ -0,0 +1,48 @@
+require 'rubygems'
+require 'opentox-ruby'
+require 'yaml'
+
+@subjectid = nil
+
+
+
+def count_features(ds_uri)
+  puts ds_uri
+
+  dataset = OpenTox::Dataset.find(ds_uri, @subjectid)
+
+  features = dataset.features.keys
+  puts "# all features: #{features.size}"
+  
+  delete_features = []
+  features.each{ |fn|
+    dataset.features[fn][RDF.type].each { |typestr|
+      if typestr.include? "MissingFeature"
+        delete_features << fn 
+        @missing_features << dataset.features[fn][DC.title]
+      end
+    }
+  }
+  puts "# Missingfeatures: #{delete_features.size}"
+  features = features - delete_features
+  puts "# numeric features: #{features.size}"
+  puts "-----"
+end
+
+
+@missing_features = []
+
+ds = YAML::load_file("../datasets.yaml")
+ds.keys.each { |dataset|
+  puts "----------"
+  puts dataset
+  ds[dataset].keys.each { |pc|
+    puts pc unless (pc == "dataset") || (pc == "test") || (pc == "training")
+    count_features(ds[dataset][pc]) unless (pc == "dataset") || (pc == "test") || (pc == "training") 
+  }
+  puts "----------"
+  puts
+}
+puts
+puts "Missing features over all datasets:"
+puts @missing_features.uniq!.to_yaml 
diff --git a/cv/data/utils/create_selected_feature_ds.rb b/cv/data/utils/create_selected_feature_ds.rb
index 0e5f063..c30a23e 100644
--- a/cv/data/utils/create_selected_feature_ds.rb
+++ b/cv/data/utils/create_selected_feature_ds.rb
@@ -35,10 +35,11 @@ ds = YAML::load_file("../datasets.yaml")
 ds.keys.each { |dataset|
   puts "----------------- next dataset -----------------"
   ds[dataset].keys.each { |pc|
-    puts pc unless pc == "dataset"
-    [false, true].each { |del_missing|
+    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"
+        create_f_ds(ds[dataset]["dataset"], ds[dataset][pc], del_missing) unless (pc == "dataset") || (pc == "test") || (pc == "training")
       rescue
       end
     }