From 731e65f87d1ae3c4c8a676202f3fefcb7224159d Mon Sep 17 00:00:00 2001 From: mr Date: Tue, 5 Jul 2011 12:35:30 +0200 Subject: fix gitmodules from http to git protocol --- .gitmodules | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitmodules b/.gitmodules index 75218e9..61a4b92 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,6 +1,6 @@ [submodule "libfminer"] path = libfminer - url = http://github.com/amaunz/fminer2.git + url = git://github.com/amaunz/fminer2.git [submodule "last-utils"] path = last-utils url = git://github.com/amaunz/last-utils.git -- cgit v1.2.3 From 048a738b1e0a51d2bc5d08d87611580fb2996cb5 Mon Sep 17 00:00:00 2001 From: mr Date: Tue, 5 Jul 2011 12:36:05 +0200 Subject: fix gitmodules from http to git protocol --- .gitmodules | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitmodules b/.gitmodules index 75218e9..61a4b92 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,6 +1,6 @@ [submodule "libfminer"] path = libfminer - url = http://github.com/amaunz/fminer2.git + url = git://github.com/amaunz/fminer2.git [submodule "last-utils"] path = last-utils url = git://github.com/amaunz/last-utils.git -- cgit v1.2.3 From 686011c826bcef8c26b8c5fd30eafc8c8630e701 Mon Sep 17 00:00:00 2001 From: mguetlein Date: Mon, 11 Jul 2011 16:10:23 +0200 Subject: setting task percentage completed for fminer and lazar model creation --- fminer.rb | 13 +++++++++---- lazar.rb | 6 ++++-- 2 files changed, 13 insertions(+), 6 deletions(-) diff --git a/fminer.rb b/fminer.rb index ad3c7f9..45751fc 100644 --- a/fminer.rb +++ b/fminer.rb @@ -99,7 +99,7 @@ post '/fminer/bbrc/?' do fminer=OpenTox::Algorithm::Fminer.new fminer.check_params(params,5) - task = OpenTox::Task.create("Mining BBRC features", url_for('/fminer',:full)) do + task = OpenTox::Task.create("Mining BBRC features", url_for('/fminer',:full)) do |task| @@bbrc.Reset if fminer.prediction_feature.feature_type == "regression" @@bbrc.SetRegression(true) # AM: DO NOT MOVE DOWN! Must happen before the other Set... operations! @@ -140,12 +140,14 @@ post '/fminer/bbrc/?' do g_median=OpenTox::Algorithm.median(g_array) raise "No compounds in dataset #{fminer.training_dataset.uri}" if fminer.compounds.size==0 - + task.progress 10 + step_width = 80 / @@bbrc.GetNoRootNodes().to_f features = Set.new + # run @@bbrc (0 .. @@bbrc.GetNoRootNodes()-1).each do |j| - results = @@bbrc.MineRoot(j) + task.progress 10+step_width*(j+1) results.each do |result| f = YAML.load(result)[0] smarts = f[0] @@ -223,7 +225,7 @@ post '/fminer/last/?' do fminer=OpenTox::Algorithm::Fminer.new fminer.check_params(params,80) - task = OpenTox::Task.create("Mining LAST features", url_for('/fminer',:full)) do + task = OpenTox::Task.create("Mining LAST features", url_for('/fminer',:full)) do |task| @@last.Reset if fminer.prediction_feature.feature_type == "regression" @@last.SetRegression(true) # AM: DO NOT MOVE DOWN! Must happen before the other Set... operations! @@ -265,9 +267,12 @@ post '/fminer/last/?' do # run @@last features = Set.new xml = "" + task.progress 10 + step_width = 80 / @@last.GetNoRootNodes().to_f (0 .. @@last.GetNoRootNodes()-1).each do |j| results = @@last.MineRoot(j) + task.progress 10+step_width*(j+1) results.each do |result| xml << result end diff --git a/lazar.rb b/lazar.rb index e81c1ba..e2dde9a 100644 --- a/lazar.rb +++ b/lazar.rb @@ -72,7 +72,7 @@ post '/lazar/?' do elsif prediction_feature.feature_type == "regression" lazar.prediction_algorithm = "Neighbors.local_svm_regression" end - + task.progress 10 if params[:feature_dataset_uri] feature_dataset_uri = params[:feature_dataset_uri] @@ -95,7 +95,7 @@ post '/lazar/?' do if prediction_feature.feature_type == "regression" && feature_generation_uri.match(/fminer/) params[:feature_type] = "paths" end - feature_dataset_uri = OpenTox::Algorithm::Generic.new(feature_generation_uri).run(params).to_s + feature_dataset_uri = OpenTox::Algorithm::Generic.new(feature_generation_uri).run(params, OpenTox::SubTask.new(task,10,70)).to_s training_features = OpenTox::Dataset.new(feature_dataset_uri) end @@ -140,6 +140,7 @@ post '/lazar/?' do end end end + task.progress 80 # AM: allow prediction_algorithm override by user for classification AND regression lazar.prediction_algorithm = "Neighbors.#{params[:prediction_algorithm]}" unless params[:prediction_algorithm].nil? @@ -163,6 +164,7 @@ post '/lazar/?' do end end end + task.progress 90 lazar.metadata[DC.title] = "lazar model for #{URI.decode(File.basename(prediction_feature.uri))}" lazar.metadata[OT.dependentVariables] = prediction_feature.uri -- cgit v1.2.3 From 309f3d5e1ce60c96128b5e13ae22656c6d6eb4be Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Tue, 12 Jul 2011 13:02:08 +0200 Subject: Fixed effects calculation: Reversed and using internal values for classification --- fminer.rb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/fminer.rb b/fminer.rb index ad3c7f9..0126fe2 100644 --- a/fminer.rb +++ b/fminer.rb @@ -153,8 +153,8 @@ post '/fminer/bbrc/?' do if (!@@bbrc.GetRegression) id_arrs = f[2..-1].flatten - max = OpenTox::Algorithm.effect(f[2..-1].reverse, fminer.db_class_sizes) - effect = @value_map[(f[2..-1].size-max)].to_s + max = OpenTox::Algorithm.effect(f[2..-1], fminer.db_class_sizes) + effect = f[2..-1].size-max else #regression part id_arrs = f[2] # DV: effect calculation @@ -290,7 +290,7 @@ post '/fminer/last/?' do @value_map.each { |y,act| g[y-1]=Array.new } feat_hash.each { |x,y| g[y-1].push(x) } max = OpenTox::Algorithm.effect(g, fminer.db_class_sizes) - effect = @value_map[(g.size-max)].to_s + effect = g.size-max end feature_uri = File.join feature_dataset.uri,"feature","last", features.size.to_s unless features.include? smarts -- cgit v1.2.3