diff options
Diffstat (limited to 'fminer.rb')
| -rw-r--r-- | fminer.rb | 15 |
1 files changed, 15 insertions, 0 deletions
@@ -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 |