From 6f203f40ba5e500d695eb4146eab11e60e03d01c Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Fri, 4 May 2012 13:58:53 +0200 Subject: Cleaner parameter handling for sampling --- fminer.rb | 19 ++++--------------- last-utils | 2 +- 2 files changed, 5 insertions(+), 16 deletions(-) diff --git a/fminer.rb b/fminer.rb index fd32043..53985ab 100644 --- a/fminer.rb +++ b/fminer.rb @@ -57,7 +57,7 @@ end # Get RDF/XML representation of fminer bbrc algorithm # @return [application/rdf+xml] OWL-DL representation of fminer bbrc algorithm -get "/fminer/bbrc/sample?" do +get "/fminer/bbrc/sample/?" do algorithm = OpenTox::Algorithm::Generic.new(url_for('/fminer/bbrc/sample',:full)) algorithm.metadata = { DC.title => 'fminer backbone refinement class representatives, obtained from samples of a dataset', @@ -293,7 +293,7 @@ end post '/fminer/bbrc/sample/?' do fminer=OpenTox::Algorithm::Fminer.new - fminer.check_params(params,80,@subjectid) + fminer.check_params(params,100,@subjectid) # AM: 100 per-mil (10%) as default minfreq # num_boots unless params[:num_boots] @@ -313,17 +313,6 @@ post '/fminer/bbrc/sample/?' do min_sampling_support= params[:min_sampling_support].to_i.ceil end - # re-set min_frequency - unless params[:min_frequency] - min_frequency = (fminer.training_dataset.compounds.size * 0.1).ceil - LOGGER.debug "Set min_frequency to default value #{fminer.minfreq}" - else - raise OpenTox::BadRequestError.new "min_frequency is not numeric" unless OpenTox::Algorithm.numeric? params[:min_frequency] - min_frequency= params[:min_frequency].to_i.ceil - end - - fminer.training_dataset.compounds.size - task = OpenTox::Task.create("Mining BBRC sample features", url_for('/fminer',:full)) do |task| if fminer.prediction_feature.feature_type == "regression" raise OpenTox::BadRequestError.new "BBRC sampling is only for classification" @@ -352,11 +341,11 @@ post '/fminer/bbrc/sample/?' do fminer.smi = [] # AM LAST: needed for matching the patterns back # Add data to fminer - fminer.add_fminer_data(@@last, @value_map) + fminer.add_fminer_data(nil, @value_map) # AM: 'nil' as instance to only fill in administrative data raise "No compounds in dataset #{fminer.training_dataset.uri}" if fminer.compounds.size==0 - # run bbrc-sample + # run bbrc-sample, obtain smarts and p-values features = Set.new task.progress 10 diff --git a/last-utils b/last-utils index cf02384..efcc3f4 160000 --- a/last-utils +++ b/last-utils @@ -1 +1 @@ -Subproject commit cf0238477127e54509b6ab8b5c38f50dd6ffce08 +Subproject commit efcc3f41dd9e2f590a1520dfee3bf709120b2e41 -- cgit v1.2.3