From dcd8379fcd2448b83f1b390fc74bb0b4025f8dd8 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Mon, 7 May 2012 08:36:18 +0200
Subject: Embedded R code

---
 application.rb |  1 +
 bbrc-sample    |  2 +-
 fminer.rb      | 15 +++++++++++++++
 last-utils     |  2 +-
 4 files changed, 18 insertions(+), 2 deletions(-)

diff --git a/application.rb b/application.rb
index b00ba9f..ee1bf65 100644
--- a/application.rb
+++ b/application.rb
@@ -20,6 +20,7 @@ require File.join(File.expand_path(File.dirname(__FILE__)), 'last-utils/lu.rb')
 gem "opentox-ruby", "~> 3"
 require 'opentox-ruby'
 require 'rjb'
+require 'rinruby'
 
 
 # main
diff --git a/bbrc-sample b/bbrc-sample
index 0043519..fc4ae7d 160000
--- a/bbrc-sample
+++ b/bbrc-sample
@@ -1 +1 @@
-Subproject commit 00435190a8f49e43fc5194a024156300472294e3
+Subproject commit fc4ae7d22a60838a62747069660542c304ce2f12
diff --git a/fminer.rb b/fminer.rb
index 53985ab..cec902e 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -345,10 +345,25 @@ post '/fminer/bbrc/sample/?' do
 
     raise "No compounds in dataset #{fminer.training_dataset.uri}" if fminer.compounds.size==0
 
+
     # run bbrc-sample, obtain smarts and p-values
     features = Set.new
     task.progress 10
 
+    @r = RinRuby.new(true,false) # global R instance leads to Socket errors after a large number of requests
+    @r.assign "dataset.uri", params[:dataset_uri]
+    @r.assign "prediction.feature.uri", fminer.prediction_feature.uri
+    @r.assign "num.boots", num_boots
+    @r.assign "min.frequency.per.sample", fminer.minfreq
+    @r.assign "min.sampling.support", min_sampling_support
+    @r.assign "bbrc.service", File.join(CONFIG[:services]["opentox-algorithm"], "fminer/bbrc")
+    @r.assign "dataset.service", CONFIG[:services]["opentox-dataset"]
+    
+    @r.eval "source(\"bbrc-sample/bbrc-sample.R\")"
+    @r.eval "bootBbrc(dataset.uri, prediction.feature.uri, num.boots, min.frequency.per.sample, min.sampling.support, NULL, bbrc.service, dataset.service, F)"
+    
+    smarts = (@r.pull "ans.patterns").collect! { |id| id.gsub(/\'/,"") } # remove extra quotes
+    r_p_values = @r.pull "ans.p.values"
 
     # matching
     task.progress 90
diff --git a/last-utils b/last-utils
index efcc3f4..8a3dd9b 160000
--- a/last-utils
+++ b/last-utils
@@ -1 +1 @@
-Subproject commit efcc3f41dd9e2f590a1520dfee3bf709120b2e41
+Subproject commit 8a3dd9bb550f0ea264c2f4e844f664f0a42ca16f
-- 
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