diff options
| author | mr <mr@mrautenberg.de> | 2011-05-23 13:39:56 +0200 |
|---|---|---|
| committer | mr <mr@mrautenberg.de> | 2011-05-23 13:39:56 +0200 |
| commit | 916f715ee52049a0968bc04df5aa6ca0a9a6881d (patch) | |
| tree | 99bbf52ad3b7495114ffe50194b8f9c606f5f248 | |
| parent | 96d500e9691eedbfdd57ec35a2572b59641377f3 (diff) | |
| parent | eb5f8b5da9b247d62abc8a7b9eb2e44fe46a1c79 (diff) | |
Merge branch 'release/2.0.0'v2.0.0
31 files changed, 1453 insertions, 588 deletions
@@ -1,42 +1,6 @@ require 'rubygems' require 'rake' -REPORT_GEMS = [ 'opentox-ruby', 'mime-types', 'ruby-plot', 'rinruby'] #'ar-extensions', 'activerecord', 'activesupport', -VALIDATION_GEMS = [ 'opentox-ruby', 'ruby-plot'] #'ar-extensions', 'activerecord', 'activesupport', - -GEM_VERSIONS = { "ruby-plot" => "= 0.0.2" } -GEM_INSTALL_OPTIONS = {} - -#GEM_VERSIONS = { "activerecord" => "= 2.3.8", "activesupport" => "= 2.3.8", "ar-extensions" => "= 0.9.2", "ruby-plot" => "= 0.0.2" } -## this is needed because otherwihse ar-extensions adds activesupport 3.0.0 which confuses things -#GEM_INSTALL_OPTIONS = { "ar-extensions" => "--ignore-dependencies" } - - -desc "Install required gems" -task :install_gems do - (REPORT_GEMS + VALIDATION_GEMS).uniq.each do |g| - begin - if GEM_VERSIONS.has_key?(g) - print "> gem "+g+", '"+GEM_VERSIONS[g]+"' .. " - gem g, GEM_VERSIONS[g] - else - print "> gem "+g+" .. " - gem g - end - puts "ok" - rescue LoadError => ex - puts "NOT FOUND" - options = "" - options += "--version '"+GEM_VERSIONS[g]+"' " if GEM_VERSIONS.has_key?(g) - options += GEM_INSTALL_OPTIONS[g]+" " if GEM_INSTALL_OPTIONS.has_key?(g) - cmd = "sudo env PATH=$PATH gem install "+options+" "+g - puts "installing gem, this may take some time..." - puts cmd - IO.popen(cmd){ |f| puts f.gets } - end - end -end - desc "Perform unit tests" task :test do require 'test/unit_test.rb' diff --git a/application.rb b/application.rb index ad9653a..10c8fe6 100755 --- a/application.rb +++ b/application.rb @@ -1,16 +1,8 @@ require 'rubygems' -gem "opentox-ruby", "~> 0" -[ 'sinatra', 'sinatra/url_for', 'opentox-ruby' ].each do |lib| +gem "opentox-ruby" +[ 'sinatra', 'sinatra/url_for', 'opentox-ruby', 'benchmark' ].each do |lib| require lib end -['dm-core', 'dm-serializer', 'dm-timestamps', 'dm-types', 'dm-migrations', 'dm-validations' ].each{|lib| require lib } -DataMapper.setup(:default, { - :adapter => CONFIG[:database][:adapter], - :database => CONFIG[:database][:database], - :username => CONFIG[:database][:username], - :password => CONFIG[:database][:password], - :host => CONFIG[:database][:host]}) -set :lock, true #unless(defined? LOGGER) #LOGGER = Logger.new(STDOUT) @@ -37,7 +29,7 @@ end get '/prepare_examples/?' do LOGGER.info "prepare examples" content_type "text/plain" - Example.prepare_example_resources + return_task(Example.prepare_example_resources) end post '/test_examples/?' do diff --git a/data/EPAFHM.csv b/data/EPAFHM.csv new file mode 100644 index 0000000..9092abc --- /dev/null +++ b/data/EPAFHM.csv @@ -0,0 +1,618 @@ +"STRUCTURE_SMILES","LC50_mmol" +"C1=CC(C=O)=CC(OC)=C1OCCCCCC",1.13E-02 +"C1(OC)=C([N+]([O-])=O)C(C=O)=CC(Br)=C1O",2.66E-01 +"CCCCCCCCOC(=O)C1=CC=CC(C(=O)OCCCCCCCC)=C1", +"C1=CC(Cl)=CC=C1OC2=C([N+](=O)[O-])C=CC=C2",7.69E-03 +"CC1=C(NC=O)C=CC=C1Cl",2.75E-01 +"CCCCOC(=O)C1=CC=CC(C(=O)OCCCC)=C1",3.23E-03 +"C(C1=CC=CC=C1)(C2=CC=CC=C2)(O)C#C",5.33E-02 +"CCCSCCSCCC",4.22E-02 +"CCCCCCCCOC(=O)C1=CC=C(C(=O)OCCCCCCCC)C=C1", +"OCCCCOC(=O)C1=CC=CC=C1C(=O)OCCCCOC(=O)C2=CC=CC=C2C(=O)OCCCCO", +"CCCSCCCCSCCC",1.45E-02 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+CCOc1cc(ccc1O)C2CC(=O)N=C3CC(CC(=O)C23)c4cc(OC)ccc4OC,0
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+CCOc1cc(cc(Cl)c1O)C2CC(=O)N=C3CC(CC(=O)C23)c4ccc(OC)cc4,0
+COc1ccc(cc1)C2CC(=O)C3=C(C2)NC(=O)CC3c4ccc(OC)c(OC)c4,0
+CCOc1cc(cc(Cl)c1O)C2CC(=O)N=C3CC(CC(=O)C23)c4ccccc4Cl,0
+Cc1cc(Nc2ccc(Br)c(C)c2)n3nc(C)nc3n1,0
+CCc1nc2nc(C)cc(Nc3ccc(I)cc3)n2n1,0
+COc1ccc(Nc2cc(C)c3ccc(O)cc3n2)cc1,0
+CCOc1ccc(Nc2cc(C)c3ccc(O)cc3n2)cc1,0
+CCc1ccc(Nc2cc(C)c3ccc(O)cc3n2)cc1,0
+CC(C)CN1C(C(C(=O)Nc2ccc(C)c(C)c2)c3ccccc3C1=O)c4cccs4,0
+CCCN(C(=O)C(=O)Nc1ccc2N=C3CCCCCN3C(=O)c2c1)c4ccc(OCC)cc4,0
+CN(C(=O)c1cc2CS(=O)(=O)c3ccccc3c2s1)c4cccc(c4)C(F)(F)F,0
+CCN1N=C(N=C2C(=O)N(C)C(=O)N=C12)c3ccc(cc3)C(F)(F)F,1
+CN1C(=O)N(C)c2cn(c(c3ccc(cc3)C(C)(C)C)c2C1=O)c4cc(Cl)ccc4O,0
+CC(O)(C(CN1CCCCC1)c2ccccc2)c3ccc(Cl)cc3,0
+CC(C)CN1C(C(C(=O)Nc2cccc(c2)C(F)(F)F)c3ccccc3C1=O)c4cccs4,0
+CC(C)CN1C(C(C(=O)Nc2ccc(F)c(Cl)c2)c3ccccc3C1=O)c4cccs4,0
+COc1ccc(NC(=O)C2C(N(CC(C)C)C(=O)c3ccccc23)c4cccs4)cc1Cl,0
+CC(C)CN1C(C(C(=O)Nc2ccc(F)cc2F)c3ccccc3C1=O)c4cccs4,0
+COc1ccc(NC(=O)C2C(N(CC(C)C)C(=O)c3ccccc23)c4cccs4)cc1OC,0
+COc1cccc(NC(=O)C2C(N(CC(C)C)C(=O)c3ccccc23)c4cccs4)c1,0
+COc1cc(OC)c(NC(=O)C2C(N(CC(C)C)C(=O)c3ccccc23)c4cccs4)cc1Cl,0
+CCOc1ccc(NC(=O)C2C(N(CC(C)C)C(=O)c3ccccc23)c4cccs4)cc1,0
+CC(C)CN1C(C(C(=O)Nc2ccc(C)cc2Cl)c3ccccc3C1=O)c4cccs4,0
+CC(C)CN1C(C(C(=O)Nc2cccc(c2)C#N)c3ccccc3C1=O)c4cccs4,0
+CCc1ccccc1NC(=O)C2C(N(CC(C)C)C(=O)c3ccccc23)c4cccs4,0
+COc1ccc(NC(=O)C2C(N(CC(C)C)C(=O)c3ccccc23)c4cccs4)cc1,0
+CC(C)CN1C(C(C(=O)Nc2cccc(c2)C(=O)C)c3ccccc3C1=O)c4cccs4,0
+COC(=O)c1ccc(NC(=O)C2C(N(CC(C)C)C(=O)c3ccccc23)c4cccs4)cc1,0
+COc1ccc(NC(=O)C2C(N(C3CCCC3)C(=O)c4ccccc24)c5cccs5)cc1,0
+CCOC(=O)c1cccc(NC(=O)CC2N(CCC(C)C)C(=O)N(C2=O)c3ccc(F)cc3)c1,0
+CCN(CC)Cc1cc(Nc2ccnc3cc(Cl)ccc23)ccc1O,0
+OC(CNC1CCCCC1)Cn2c3ccc(Cl)cc3c4cc(Cl)ccc24,0
+CC(C)NCC(O)Cn1c2ccc(Cl)cc2c3cc(Cl)ccc13,1
+Cc1ccc(cc1)C2CC(n3nc(cc3N2)C(=O)N4CCN(CC4)C(c5ccccc5)c6ccccc6)C(F)(F)F,0
+Nc1ccc(cc1)c2nc3cc(ccc3[nH]2)c4ccc5[nH]c(nc5c4)c6ccc(N)cc6,1
+OC(CN1C(=N)N(CCN2CCCCC2)c3ccccc13)c4ccc(Cl)c(Cl)c4,1
+CCN1CCN(Cc2c(O)ccc3C(=O)C(=C(Oc23)C(F)(F)F)Oc4ccccc4C(C)C)CC1,0
+CC[n+]1c(\C=C\c2ccc(cc2)N(C)C)ccc3cc(OC)ccc13,1
+CCN(CC)c1ccc(\C=C\c2ccc3ccc(OC)cc3[n+]2CC)cc1,1
+CCN(CC)CCCOC(=O)c1c(C)oc2cc3c(C(=O)OCCCN(CC)CC)c(C)oc3cc12,1
+CCCCCCN1C(=N)N(CC(O)COc2ccccc2C)c3ccccc13,1
+Oc1c(cc(CN2CCN(CC2)c3cccc(c3)C(F)(F)F)c4cccnc14)[N+](=O)[O-],0
+CN1CCN(CC1)c2cc(C)c3cc(NC(=S)NCC4CCN(Cc5cccc(C)c5)CC4)ccc3n2,1
+CN1C(=O)\C(=C/c2ccccc2Cl)\Sc3ccc(cc13)C(=O)NC4CCN(Cc5ccccc5)CC4,0
+C\C=C\c1[n+](C)c2ccccc2n1C,0
+CSc1ccc2ccccc2[n+]1C,0
+Cc1c2[nH]c3ccccc3c2c4CCC(C)(C)Cc4[n+]1C,0
+OC(CNC1CCCC1)Cn2c3ccc(Cl)cc3c4cc(Cl)ccc24,1
+OC(CNC1CCCC1)Cn2c3ccccc3c4ccccc24,0
+Clc1ccc(cc1)S(=O)(=O)N2CCN(CC2)C(=S)NCc3occc3,0
+Cc1ccc(C)c(NC(=O)CC2N(Cc3occc3)C(=S)N(C2=O)c4ccccc4)c1,0
+[O-][N+](=O)c1ccc(cc1)S(=O)(=O)N2CCN(CC2)C(=S)NCc3occc3,0
+CCc1c2ccc(C)n2cc[n+]1CC#C,0
+CC(C)(C)c1cc(cc(c1O)C(C)(C)C)C2C(C#N)C(=N)OC3=C2C(=O)CCC3,1
+COc1ccc(O)c(CN2CCN(CC2)c3cc(C)ccc3C)c1,0
+Oc1ccc(Cl)cc1CN2CCN(CC2)c3cccc(c3)C(F)(F)F,0
+CCOc1ccccc1N2CCN(Cc3cc(Br)cc(OC)c3O)CC2,0
+Cc1cccc(N2CCN(Cc3ccccc3O)CC2)c1C,0
+Cc1cccc(N2CCN(Cc3cc(Br)ccc3O)CC2)c1C,0
+Oc1ccc(Br)cc1CN2CCN(Cc3ccccc3)CC2,0
+Cc1ccc(C)c(c1)N2CCN(Cc3cc(Br)ccc3O)CC2,0
+Cc1ccc(C)c(c1)N2CCN(Cc3cc(Cl)ccc3O)CC2,0
+CCN(C(=O)C)C1=C(N2CCOCC2)C(=O)c3ccccc3C1=O,1
+CCOC(=O)C1=C(C)N=C2S\C(=C/c3cc(Cl)ccc3O)\C(=O)N2C1c4ccc(cc4)N(C)C,0
+Fc1ccc(Nc2nc(NCc3ccccc3)c4ccccc4n2)cc1,1
+CCOc1ccc(Nc2nc(NCc3ccccc3)c4ccccc4n2)cc1,1
+CC(C)c1ccccc1OC2=C(Oc3c(CN4CCN(C)CC4)c(O)ccc3C2=O)C(F)(F)F,0
+ClC(Cl)(Cl)C(=O)Nc1ccccc1N2CCN(CC2)C(=O)c3ccccc3,0
+Clc1cccc(NC(=O)C(Cl)(Cl)Cl)c1N2CCOCC2,0
+CC(C)c1ccc(CNCC(O)c2ccccc2)cc1,0
+CCOC(=O)C1(Cc2cccc(F)c2)CCN(Cc3ccccc3O)CC1,0
+CCOC(=O)C1(Cc2ccc(Cl)cc2)CCN(Cc3ccccc3O)CC1,0
+CCOC(=O)C1(Cc2cccc(c2)C(F)(F)F)CCN(Cc3ccccc3O)CC1,0
+CCOC(=O)C1(Cc2ccccc2)CCN(Cc3cccc(OC)c3O)CC1,0
+CSC(=S)N=NC(c1ccccc1)c2ccccn2,0
+Brc1ccc(cc1)N=C2C(C(=O)c3ccccc3C2=O)n4nnc5ccccc45,0
+CCOC(=O)C1=C(C)N=C2S\C(=C\c3ccccc3O)\C(=O)N2C1c4ccccc4,0
+CC(C)CCNC(=O)c1c(C)oc2C(=O)c3ccccc3C(=O)c12,0
+CCOc1ccc(\C=C\2/Oc3c(CN4CCCCC4)c(O)ccc3C2=O)cc1,0
+COc1ccc(Nc2cc(C)nc(Nc3ccc(NS(=O)(=O)c4ccc(OC)cc4)cc3)n2)cc1,0
+COc1ccccc1Cn2ccnc2SCC(=O)Nc3cc(ccc3Cl)C(F)(F)F,0
+Cc1ccc(cc1)C(O)(CNCc2ccccc2)c3ccc(Br)cc3,0
+CCCCN(CCCC)CC(O)COc1ccccc1C(=O)Nc2ccccc2,0
+Oc1ccc(Br)cc1CN2CCN(CC2)C3CC4CCC3C4,0
+C(Cc1ccccc1)Nc2ccnc3cc4ccccc4cc23,1
+Cc1ccc(cc1)C2(CC2C(=O)Nc3ccc(cc3O)[N+](=O)[O-])c4ccc(C)cc4,0
+Cc1cc(C)nc(N=C(N)Nc2ccccc2O)n1,0
+CC(C)(C)c1cc(cc(c1O)C(C)(C)C)N=NC(=O)c2ccncc2,0
+Oc1ccccc1Cn2c3ccccc3c4cc(ccc24)[N+](=O)[O-],0
+CC(C)(C)NC(=O)C1=CN(C=C(C(=O)NC2CCN(Cc3ccccc3)C2)C1=O)C4CCCCC4,0
+CC(CNC(=O)C1=CN(C=C(C(=O)NC(C)(C)C)C1=O)C2CCCCC2)c3ccccc3,0
@@ -3,11 +3,11 @@ require 'lib/test_util.rb' class Example - @@file=File.new("data/hamster_carcinogenicity.yaml","r") + @@file=File.new("data/hamster_carcinogenicity.csv","r") @@file_type="text/x-yaml" @@model=File.join CONFIG[:services]["opentox-model"],"1" #@@feature= URI.encode("http://local-ot/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)") - @@feature= File.join CONFIG[:services]["opentox-dataset"],"1/feature/hamster_carcinogenicity" + @@feature= File.join CONFIG[:services]["opentox-dataset"],"1/feature/Hamster%2520Carcinogenicity" #@@predicted_feature= URI.encode("http://local-ot/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)_lazar_classification") @@alg = File.join CONFIG[:services]["opentox-algorithm"],"lazar" @@alg_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") @@ -58,12 +58,15 @@ class Example #TODO subjectid = nil + Ohm.flush + task = OpenTox::Task.create("prepare examples", "n/a") do |task| @@summary = "" + #delete validations - log "delete validations" - Lib::Validation.auto_migrate! - Lib::Crossvalidation.auto_migrate! + #log "delete validations" + #Lib::Validation.auto_migrate! + #Lib::Crossvalidation.auto_migrate! #ActiveRecord::Base.logger = Logger.new("/dev/null") #ActiveRecord::Migrator.migrate('db/migrate', 0 ) #ActiveRecord::Migrator.migrate('db/migrate', 1 ) @@ -80,10 +83,7 @@ class Example halt 400,"File not found: "+@@file.path.to_s unless File.exist?(@@file.path) #data = File.read(@@file.path) #data_uri = OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:content_type => @@file_type},data).chomp("\n") - data = File.read(@@file.path) - dataset = OpenTox::Dataset.create - dataset.load_yaml(data) - dataset.save + dataset = OpenTox::Dataset.create_from_csv_file(@@file.path,nil) data_uri = dataset.uri log "-> "+data_uri task.progress(20) @@ -92,7 +92,7 @@ class Example #delete_all(CONFIG[:services]["opentox-model"]) OpenTox::RestClientWrapper.delete CONFIG[:services]["opentox-model"] - split_params = Validation::Util.train_test_dataset_split(data_uri, URI.decode(@@feature), 0.9, 1) + split_params = Validation::Util.train_test_dataset_split(data_uri, URI.decode(@@feature), nil, 0.9, 1) v = Validation::Validation.new :training_dataset_uri => split_params[:training_dataset_uri], :validation_type => "test_set_validation", :test_dataset_uri => split_params[:test_dataset_uri], @@ -102,7 +102,7 @@ class Example v.validate_algorithm( @@alg_params, OpenTox::SubTask.new(task, 20, 40) ) log "crossvalidation" - cv = Validation::Crossvalidation.new({ :dataset_uri => data_uri, :algorithm_uri => @@alg, :num_folds => 5, :stratified => false }) + cv = Validation::Crossvalidation.create({ :dataset_uri => data_uri, :algorithm_uri => @@alg, :num_folds => 5, :stratified => false }) cv.perform_cv( URI.decode(@@feature), @@alg_params, OpenTox::SubTask.new(task, 40, 70) ) log "create validation report" @@ -124,7 +124,7 @@ class Example log "done" @@summary end - return_task(task) + task end # performs all curl calls listed in examples after ">>>", next line is added if line ends with "\" diff --git a/lib/merge.rb b/lib/merge.rb index 527415e..ecbe133 100644 --- a/lib/merge.rb +++ b/lib/merge.rb @@ -20,8 +20,7 @@ module Lib def self.merge_array_objects( array ) return nil if array.size == nil return array[0] if array.size==1 - - m = self.merge_objects(array[0], array[1] ) + m = self.merge_objects(array[0], array[1]) (2..array.size-1).each do |i| m = self.merge_objects(m, array[i] ) end @@ -33,8 +32,7 @@ module Lib end def self.merge_objects( object1, object2 ) - - raise "classes not equal" if object1.class != object2.class + raise "classes not equal : "+object1.class.to_s+" != "+object2.class.to_s if object1.class != object2.class object_class = object1.class raise "register which attributes to merge first, nothing found for class "+object_class.to_s unless merge_attributes_registered?(object_class) raise "not supported, successivly add unmerged object to a merge object" if merge_count(object2)>1 @@ -71,6 +69,11 @@ module Lib variance = nil if (avg=avg_attribute?(object_class, attribute)) || sum_attribute?(object_class, attribute) + # we string to numerics if wanted, value1 is no string anymore if weight>1 + if value2.is_a?(String) and ((weight1==1 and value1.is_a?(String)) or (weight1>1 and value1.is_a?(Numeric))) + value1 = value1.to_f + value2 = value2.to_f + end if (value1==nil and value2==nil ) #do nothing elsif value1.is_a?(Numeric) and value2.is_a?(Numeric) @@ -104,7 +107,8 @@ module Lib end end else - raise "invalid, cannot avg/sum non-numeric content for attribute: "+attribute.to_s+" contents: '"+value1.to_s+"', '"+value2.to_s+"'" + raise "invalid, cannot avg/sum non-numeric content for attribute: "+attribute.to_s+" contents: '"+value1.to_s+"' ("+ + value1.class.to_s+"), '"+value2.to_s+"' ("+value2.class.to_s+")" end elsif non_numeric_attribute?(object_class, attribute) if (value1.is_a?(Hash) and value2.is_a?(Hash)) diff --git a/lib/ohm_util.rb b/lib/ohm_util.rb new file mode 100644 index 0000000..856f9d2 --- /dev/null +++ b/lib/ohm_util.rb @@ -0,0 +1,40 @@ + +module Lib + module OhmUtil + + def self.check_params(model, params) + prop_names = model.attributes.collect{|p| p.to_s} + params.keys.each do |k| + key = k.to_s + if (key == "subjectid" || key == "media") + params.delete(k) + else + unless prop_names.include?(key) + key = key.from_rdf_format + unless prop_names.include?(key) + key = key+"_uri" + unless prop_names.include?(key) + key = key+"s" + unless prop_names.include?(key) + raise OpenTox::BadRequestError.new "no attribute found: '"+k.to_s+"'" + end + end + end + end + params[key.to_sym] = params.delete(k) + end + end + params + end + + def self.find(model, filter_params) + params = check_params(model,filter_params) + if (params.size==0) + model.all + else + model.find(params) + end + end + + end +end
\ No newline at end of file diff --git a/lib/ot_predictions.rb b/lib/ot_predictions.rb index f812854..22f9b20 100755 --- a/lib/ot_predictions.rb +++ b/lib/ot_predictions.rb @@ -54,13 +54,20 @@ module Lib @compounds = test_dataset.compounds LOGGER.debug "test dataset size: "+@compounds.size.to_s raise "test dataset is empty "+test_dataset_uri.to_s unless @compounds.size>0 - class_values = feature_type=="classification" ? OpenTox::Feature.find(prediction_feature, subjectid).domain : nil + + if feature_type=="classification" + accept_values = test_target_dataset.features[prediction_feature][OT.acceptValue] + raise "'"+OT.acceptValue.to_s+"' missing/invalid for feature '"+prediction_feature.to_s+"' in dataset '"+ + test_target_dataset_uri.to_s+"', acceptValues are: '"+accept_values.inspect+"'" if accept_values==nil or accept_values.length<2 + else + accept_values=nil + end actual_values = [] @compounds.each do |c| case feature_type when "classification" - actual_values << classification_value(test_target_dataset, c, prediction_feature, class_values) + actual_values << classification_value(test_target_dataset, c, prediction_feature, accept_values) when "regression" actual_values << regression_value(test_target_dataset, c, prediction_feature) end @@ -108,7 +115,7 @@ module Lib case feature_type when "classification" # TODO: remove LAZAR_PREDICTION_DATASET_HACK - predicted_values << classification_value(prediction_dataset, c, no_prediction_feature ? nil : predicted_variable, class_values) + predicted_values << classification_value(prediction_dataset, c, no_prediction_feature ? nil : predicted_variable, accept_values) when "regression" predicted_values << regression_value(prediction_dataset, c, no_prediction_feature ? nil : predicted_variable) end @@ -126,7 +133,7 @@ module Lib end task.progress(80) if task # loaded predicted values and confidence - super(predicted_values, actual_values, confidence_values, feature_type, class_values) + super(predicted_values, actual_values, confidence_values, feature_type, accept_values) raise "illegal num compounds "+num_info if @compounds.size != @predicted_values.size task.progress(100) if task # done with the mathmatics end @@ -143,11 +150,11 @@ module Lib end end - def classification_value(dataset, compound, feature, class_values) + def classification_value(dataset, compound, feature, accept_values) v = value(dataset, compound, feature) - i = class_values.index(v) - raise "illegal class_value of prediction (value is '"+v.to_s+"', class is '"+v.class.to_s+"'), possible values are "+ - class_values.inspect unless v==nil or i!=nil + i = accept_values.index(v.to_s) + raise "illegal class_value of prediction (value is '"+v.to_s+"'), accept values are "+ + accept_values.inspect unless v==nil or i!=nil i end @@ -184,9 +191,9 @@ module Lib res = {} case @feature_type when "classification" - (Lib::VAL_CLASS_PROPS).each{ |s| res[s] = send(s)} + (Validation::VAL_CLASS_PROPS).each{ |s| res[s] = send(s)} when "regression" - (Lib::VAL_REGR_PROPS).each{ |s| res[s] = send(s) } + (Validation::VAL_REGR_PROPS).each{ |s| res[s] = send(s) } end return res end @@ -206,7 +213,7 @@ module Lib begin #a.push( "http://ambit.uni-plovdiv.bg:8080/ambit2/depict/cdk?search="+ # URI.encode(OpenTox::Compound.new(:uri=>p.identifier(i)).smiles) ) if add_pic - a << p.identifier(i)+"/image" + a << p.identifier(i)+"?media=image/png" rescue => ex raise ex #a.push("Could not add pic: "+ex.message) diff --git a/lib/predictions.rb b/lib/predictions.rb index 5850024..420790e 100755 --- a/lib/predictions.rb +++ b/lib/predictions.rb @@ -23,13 +23,13 @@ module Lib actual_values, confidence_values, feature_type, - class_domain=nil ) + accept_values=nil ) @predicted_values = predicted_values @actual_values = actual_values @confidence_values = confidence_values @feature_type = feature_type - @class_domain = class_domain + @accept_values = accept_values @num_classes = 1 #puts "predicted: "+predicted_values.inspect @@ -58,15 +58,15 @@ module Lib case @feature_type when "classification" - raise "class_domain missing while performing classification" unless @class_domain - @num_classes = @class_domain.size + raise "accept_values missing while performing classification" unless @accept_values + @num_classes = @accept_values.size raise "num classes < 2" if @num_classes<2 { "predicted"=>@predicted_values, "actual"=>@actual_values }.each do |s,values| values.each{ |v| raise "illegal "+s+" classification-value ("+v.to_s+"),"+ "has to be either nil or index of predicted-values" if v!=nil and (!v.is_a?(Numeric) or v<0 or v>@num_classes)} end when "regresssion" - raise "class_domain != nil while performing regression" if @class_domain + raise "accept_values != nil while performing regression" if @accept_values { "predicted"=>@predicted_values, "actual"=>@actual_values }.each do |s,values| values.each{ |v| raise "illegal "+s+" regression-value ("+v.to_s+"),"+ "has to be either nil or number" unless v==nil or v.is_a?(Numeric)} @@ -88,8 +88,16 @@ module Lib case @feature_type when "classification" + + # confusion-matrix will contain counts for predictions in a 2d array: + # index of first dim: actual values + # index of second dim: predicited values + # example: + # * summing up over all i with fixed n + # * confusion_matrix[i][n] + # * will give the number of instances that are predicted as n @confusion_matrix = [] - @class_domain.each do |v| + @accept_values.each do |v| @confusion_matrix.push( Array.new( @num_classes, 0 ) ) end @@ -235,8 +243,8 @@ module Lib res = {} (0..@num_classes-1).each do |actual| (0..@num_classes-1).each do |predicted| - res[{:confusion_matrix_actual => @class_domain[actual], - :confusion_matrix_predicted => @class_domain[predicted]}] = @confusion_matrix[actual][predicted] + res[{:confusion_matrix_actual => @accept_values[actual], + :confusion_matrix_predicted => @accept_values[predicted]}] = @confusion_matrix[actual][predicted] end end return res @@ -289,8 +297,8 @@ module Lib def precision(class_index=nil) return prediction_feature_value_map( lambda{ |i| precision(i) } ) if class_index==nil - correct = 0 - total = 0 + correct = 0 # all instances with prediction class_index that are correctly classified + total = 0 # all instances with prediciton class_index (0..@num_classes-1).each do |i| correct += @confusion_matrix[i][class_index] if i == class_index total += @confusion_matrix[i][class_index] @@ -457,7 +465,7 @@ module Lib def mean_absolute_error return 0 if (@num_with_actual_value - @num_unpredicted)==0 - Math.sqrt(@sum_abs_error / (@num_with_actual_value - @num_unpredicted).to_f) + @sum_abs_error / (@num_with_actual_value - @num_unpredicted).to_f end def sum_squared_error @@ -487,21 +495,21 @@ module Lib return @variance_actual end - # data for roc-plots ################################################################################### + # data for (roc-)plots ################################################################################### - def get_roc_values(class_value) + def get_prediction_values(class_value) #puts "get_roc_values for class_value: "+class_value.to_s raise "no confidence values" if @confidence_values==nil - raise "no class-value specified" if class_value==nil + #raise "no class-value specified" if class_value==nil - class_index = @class_domain.index(class_value) - raise "class not found "+class_value.to_s if class_index==nil + class_index = @accept_values.index(class_value) if class_value!=nil + raise "class not found "+class_value.to_s if (class_value!=nil && class_index==nil) c = []; p = []; a = [] (0..@predicted_values.size-1).each do |i| # NOTE: not predicted instances are ignored here - if @predicted_values[i]!=nil and @predicted_values[i]==class_index + if @predicted_values[i]!=nil and (class_index==nil || @predicted_values[i]==class_index) c << @confidence_values[i] p << @predicted_values[i] a << @actual_values[i] @@ -529,7 +537,7 @@ module Lib def predicted_value(instance_index) case @feature_type when "classification" - @predicted_values[instance_index]==nil ? nil : @class_domain[@predicted_values[instance_index]] + @predicted_values[instance_index]==nil ? nil : @accept_values[@predicted_values[instance_index]] when "regression" @predicted_values[instance_index] end @@ -542,7 +550,7 @@ module Lib def actual_value(instance_index) case @feature_type when "classification" - @actual_values[instance_index]==nil ? nil : @class_domain[@actual_values[instance_index]] + @actual_values[instance_index]==nil ? nil : @accept_values[@actual_values[instance_index]] when "regression" @actual_values[instance_index] end @@ -576,7 +584,7 @@ module Lib def prediction_feature_value_map(proc) res = {} (0..@num_classes-1).each do |i| - res[@class_domain[i]] = proc.call(i) + res[@accept_values[i]] = proc.call(i) end return res end diff --git a/lib/validation_db.rb b/lib/validation_db.rb index 0d5db21..e2595c5 100755 --- a/lib/validation_db.rb +++ b/lib/validation_db.rb @@ -4,7 +4,7 @@ #end require "lib/merge.rb" -module Lib +module Validation VAL_PROPS_GENERAL = [ :validation_uri, :validation_type, :model_uri, :algorithm_uri, :training_dataset_uri, :prediction_feature, :test_dataset_uri, :test_target_dataset_uri, :prediction_dataset_uri, :date ] @@ -48,50 +48,62 @@ module Lib VAL_MERGE_AVG = VAL_PROPS_AVG + VAL_CLASS_PROPS_SINGLE_AVG + VAL_CLASS_PROPS_PER_CLASS_AVG + VAL_REGR_PROPS -# class Validation < ActiveRecord::Base -# serialize :classification_statistics -# serialize :regression_statistics -# -# alias_attribute :date, :created_at - - class Validation - include DataMapper::Resource + class Validation < Ohm::Model - property :id, Serial - property :validation_type, String, :length => 512 - property :model_uri, String, :length => 512 - property :algorithm_uri, String, :length => 512 - property :training_dataset_uri, String, :length => 512 - property :test_target_dataset_uri, String, :length => 512 - property :test_dataset_uri, String, :length => 512 - property :prediction_dataset_uri, String, :length => 512 - property :prediction_feature, String, :length => 512 - property :created_at, DateTime - property :num_instances, Integer - property :num_without_class, Integer - property :num_unpredicted, Integer - property :crossvalidation_id, Integer - property :crossvalidation_fold, Integer - property :real_runtime, Float - property :percent_without_class, Float - property :percent_unpredicted, Float - property :classification_statistics, Object - property :regression_statistics, Object - property :finished, Boolean, :default => false + attribute :validation_type + attribute :model_uri + attribute :algorithm_uri + attribute :training_dataset_uri + attribute :test_target_dataset_uri + attribute :test_dataset_uri + attribute :prediction_dataset_uri + attribute :prediction_feature + attribute :date + attribute :num_instances + attribute :num_without_class + attribute :num_unpredicted + attribute :crossvalidation_id + attribute :crossvalidation_fold + attribute :real_runtime + attribute :percent_without_class + attribute :percent_unpredicted + attribute :classification_statistics_yaml + attribute :regression_statistics_yaml + attribute :finished + + index :model_uri + index :validation_type + index :crossvalidation_id attr_accessor :subjectid - after :save, :check_policy - private - def check_policy - OpenTox::Authorization.check_policy(validation_uri, subjectid) + def self.create(params={}) + params[:date] = Time.new + super params end - public - def date - created_at + def classification_statistics + YAML.load(self.classification_statistics_yaml) if self.classification_statistics_yaml + end + + def classification_statistics=(cs) + self.classification_statistics_yaml = cs.to_yaml + end + + def regression_statistics + YAML.load(self.regression_statistics_yaml) if self.regression_statistics_yaml + end + + def regression_statistics=(rs) + self.regression_statistics_yaml = rs.to_yaml + end + + def save + super + OpenTox::Authorization.check_policy(validation_uri, subjectid) end + public def validation_uri raise "no id" if self.id==nil $url_provider.url_for("/"+self.id.to_s, :full) @@ -115,33 +127,36 @@ module Lib end -# class Crossvalidation < ActiveRecord::Base -# alias_attribute :date, :created_at - class Crossvalidation - include DataMapper::Resource + class Crossvalidation < Ohm::Model - property :id, Serial - property :algorithm_uri, String, :length => 512 - property :dataset_uri, String, :length => 512 - property :created_at, DateTime - property :num_folds, Integer, :default => 10 - property :random_seed, Integer, :default => 1 - property :finished, Boolean, :default => false - property :stratified, Boolean, :default => false + attribute :algorithm_uri + attribute :dataset_uri + attribute :date + attribute :num_folds + attribute :random_seed + attribute :finished + attribute :stratified attr_accessor :subjectid - - after :save, :check_policy - private - def check_policy - OpenTox::Authorization.check_policy(crossvalidation_uri, subjectid) + + index :algorithm_uri + index :dataset_uri + index :num_folds + index :random_seed + index :stratified + index :finished + + def self.create(params={}) + params[:date] = Time.new + super params end - public - def date - created_at + def save + super + OpenTox::Authorization.check_policy(crossvalidation_uri, subjectid) end + public def crossvalidation_uri raise "no id" if self.id==nil $url_provider.url_for("/crossvalidation/"+self.id.to_s, :full) if self.id @@ -152,7 +167,7 @@ module Lib # further conditions can be specified in __conditions__ def self.find_all_uniq(conditions={}, subjectid=nil ) #cvs = Lib::Crossvalidation.find(:all, :conditions => conditions) - cvs = Lib::Crossvalidation.all(:conditions => conditions) + cvs = Crossvalidation.find( conditions ) uniq = [] cvs.each do |cv| next if AA_SERVER and !OpenTox::Authorization.authorized?(cv.crossvalidation_uri,"GET",subjectid) @@ -171,8 +186,3 @@ module Lib end end - -Lib::Validation.auto_upgrade! -Lib::Validation.raise_on_save_failure = true -Lib::Crossvalidation.auto_upgrade! -Lib::Crossvalidation.raise_on_save_failure = true diff --git a/public/robots.txt b/public/robots.txt new file mode 100644 index 0000000..1f53798 --- /dev/null +++ b/public/robots.txt @@ -0,0 +1,2 @@ +User-agent: * +Disallow: / diff --git a/reach_reports/reach_persistance.rb b/reach_reports/reach_persistance.rb index 3118809..b90778b 100755 --- a/reach_reports/reach_persistance.rb +++ b/reach_reports/reach_persistance.rb @@ -1,5 +1,8 @@ -require "dm-validations" +['dm-core', 'dm-serializer', 'dm-timestamps', 'dm-types', 'dm-migrations', 'dm-validations' ].each{|lib| require lib } +db_dir = File.join(File.join(ENV['HOME'], ".opentox"), "db") +FileUtils.mkdir_p db_dir +DataMapper::setup(:default, "sqlite3://#{db_dir}/reach_reports.sqlite3") DataMapper::Model.raise_on_save_failure = true diff --git a/reach_reports/reach_service.rb b/reach_reports/reach_service.rb index 53acb62..0cf4172 100755 --- a/reach_reports/reach_service.rb +++ b/reach_reports/reach_service.rb @@ -133,11 +133,11 @@ module ReachReports val_datasets = [] if algorithm - cvs = Lib::Crossvalidation.find_all_uniq({:algorithm_uri => algorithm.uri, :finished => true},r.subjectid) + cvs = Validation::Crossvalidation.find_all_uniq({:algorithm_uri => algorithm.uri, :finished => true},r.subjectid) # PENDING: cv classification/regression hack cvs = cvs.delete_if do |cv| #val = Validation::Validation.first( :all, :conditions => { :crossvalidation_id => cv.id } ) - val = Validation::Validation.first( :crossvalidation_id => cv.id ) + val = Validation::Validation.find( :crossvalidation_id => cv.id ).first raise "should not happen: no validations found for crossvalidation "+cv.id.to_s unless val (val.classification_statistics!=nil) != (feature_type=="classification") end @@ -196,7 +196,7 @@ module ReachReports LOGGER.debug "looking for validations with "+{:model_uri => model.uri}.inspect #vals = Lib::Validation.find(:all, :conditions => {:model_uri => model.uri}) - vals = Lib::Validation.all({:model_uri => model.uri}) + vals = Validation::Validation.find({:model_uri => model.uri}) uniq_vals = [] vals.each do |val| match = false diff --git a/reach_reports/reach_test.rb b/reach_reports/reach_test.rb index 87addfa..43aec28 100755 --- a/reach_reports/reach_test.rb +++ b/reach_reports/reach_test.rb @@ -150,7 +150,7 @@ class ReachTest < Test::Unit::TestCase #model_uri = "http://local-ot/model/104" - model_uri = "http://local-ot/majority/class/model/125" + model_uri = "http://local-ot/model/72" # m = OpenTox::Model::Generic.find(model_uri) diff --git a/report/environment.rb b/report/environment.rb index 12e3272..59465aa 100755 --- a/report/environment.rb +++ b/report/environment.rb @@ -4,7 +4,7 @@ 'rexml/document', 'ruby-plot', 'opentox-ruby' ].each do |g| require g end -gem 'ruby-plot', '= 0.0.2' +gem 'ruby-plot', "~>0.4.0" #R.quit @@ -12,8 +12,7 @@ module Reports end require "lib/ot_predictions.rb" -#require "lib/active_record_setup.rb" -require "lib/data_mapper_util.rb" +require "lib/ohm_util.rb" require "report/plot_factory.rb" require "report/xml_report.rb" diff --git a/report/plot_factory.rb b/report/plot_factory.rb index 43c45fc..a4e415a 100644 --- a/report/plot_factory.rb +++ b/report/plot_factory.rb @@ -77,8 +77,9 @@ module Reports x << x_i y << y_i end - - RubyPlot::plot_points(out_file, "Regression plot", "Predicted values", "Actual values", names, x, y ) + + raise "no predictions performed" if x.size==0 || x[0].size==0 + RubyPlot::regression_point_plot(out_file, "Regression plot", "Predicted values", "Actual values", names, x, y ) end @@ -101,7 +102,7 @@ module Reports tp_rates = [] attribute_values.each do |value| begin - data = transform_predictions(validation_set.filter({split_set_attribute => value}), class_value, false) + data = transform_roc_predictions(validation_set.filter({split_set_attribute => value}), class_value, false) names << value.to_s fp_rates << data[:fp_rate][0] tp_rates << data[:tp_rate][0] @@ -111,11 +112,50 @@ module Reports end RubyPlot::plot_lines(out_file, "ROC-Plot", "False positive rate", "True Positive Rate", names, fp_rates, tp_rates ) else - data = transform_predictions(validation_set, class_value, show_single_curves) + data = transform_roc_predictions(validation_set, class_value, show_single_curves) RubyPlot::plot_lines(out_file, "ROC-Plot", "False positive rate", "True Positive Rate", data[:names], data[:fp_rate], data[:tp_rate], data[:faint] ) end end + + def self.create_confidence_plot( out_file, validation_set, class_value, split_set_attribute=nil, show_single_curves=false ) + + LOGGER.debug "creating confidence plot for '"+validation_set.size.to_s+"' validations, out-file:"+out_file.to_s + + if split_set_attribute + attribute_values = validation_set.get_values(split_set_attribute) + names = [] + confidence = [] + performance = [] + attribute_values.each do |value| + begin + data = transform_confidence_predictions(validation_set.filter({split_set_attribute => value}), class_value, false) + names << value.to_s + confidence << data[:confidence][0] + performance << data[:performance][0] + rescue + LOGGER.warn "could not create confidence plot for "+value.to_s + end + end + #RubyPlot::plot_lines(out_file, "Percent Correct vs Confidence Plot", "Confidence", "Percent Correct", names, fp_rates, tp_rates ) + case validation_set.unique_feature_type + when "classification" + RubyPlot::accuracy_confidence_plot(out_file, "Percent Correct vs Confidence Plot", "Confidence", "Percent Correct", names, confidence, performance) + when "regression" + RubyPlot::accuracy_confidence_plot(out_file, "RMSE vs Confidence Plot", "Confidence", "RMSE", names, confidence, performance, true) + end + else + data = transform_confidence_predictions(validation_set, class_value, show_single_curves) + case validation_set.unique_feature_type + when "classification" + RubyPlot::accuracy_confidence_plot(out_file, "Percent Correct vs Confidence Plot", "Confidence", "Percent Correct", data[:names], data[:confidence], data[:performance]) + when "regression" + RubyPlot::accuracy_confidence_plot(out_file, "RMSE vs Confidence Plot", "Confidence", "RMSE", data[:names], data[:confidence], data[:performance], true) + end + end + end + + def self.create_bar_plot( out_file, validation_set, title_attribute, value_attributes ) LOGGER.debug "creating bar plot, out-file:"+out_file.to_s @@ -127,7 +167,7 @@ module Reports validation_set.validations.each do |v| values = [] value_attributes.each do |a| - validation_set.get_domain_for_attr(a).each do |class_value| + validation_set.get_accept_values_for_attr(a).each do |class_value| value = v.send(a) if value.is_a?(Hash) if class_value==nil @@ -161,7 +201,7 @@ module Reports end - def self.create_ranking_plot( svg_out_file, validation_set, compare_attribute, equal_attribute, rank_attribute, class_value=nil ) + def self.create_ranking_plot( out_file, validation_set, compare_attribute, equal_attribute, rank_attribute, class_value=nil ) #compute ranks #puts "rank attibute is "+rank_attribute.to_s @@ -184,14 +224,14 @@ module Reports ranks, nil, #0.1, validation_set.num_different_values(equal_attribute), - svg_out_file) + out_file) end protected - def self.plot_ranking( title, comparables_array, ranks_array, confidence = nil, numdatasets = nil, svg_out_file = nil ) + def self.plot_ranking( title, comparables_array, ranks_array, confidence = nil, numdatasets = nil, out_file = nil ) (confidence and numdatasets) ? conf = "-q "+confidence.to_s+" -k "+numdatasets.to_s : conf = "" - svg_out_file ? show = "-o" : show = "" + out_file ? show = "-o" : show = "" (title and title.length > 0) ? tit = '-t "'+title+'"' : tit = "" #title = "-t \""+ranking_value_prop+"-Ranking ("+comparables.size.to_s+" "+comparable_prop+"s, "+num_groups.to_s+" "+ranking_group_prop+"s, p < "+p.to_s+")\" " @@ -208,12 +248,12 @@ module Reports end raise "rank plot failed" unless $?==0 - if svg_out_file - f = File.new(svg_out_file, "w") + if out_file + f = File.new(out_file, "w") f.puts res end - svg_out_file ? svg_out_file : res + out_file ? out_file : res end def self.demo_ranking_plot @@ -221,7 +261,7 @@ module Reports end private - def self.transform_predictions(validation_set, class_value, add_single_folds=false) + def self.transform_roc_predictions(validation_set, class_value, add_single_folds=false) if (validation_set.size > 1) @@ -229,7 +269,7 @@ module Reports sum_roc_values = { :predicted_values => [], :actual_values => [], :confidence_values => []} (0..validation_set.size-1).each do |i| - roc_values = validation_set.get(i).get_predictions.get_roc_values(class_value) + roc_values = validation_set.get(i).get_predictions.get_prediction_values(class_value) sum_roc_values[:predicted_values] += roc_values[:predicted_values] sum_roc_values[:confidence_values] += roc_values[:confidence_values] sum_roc_values[:actual_values] += roc_values[:actual_values] @@ -252,24 +292,118 @@ module Reports faint << false return { :names => names, :fp_rate => fp_rate, :tp_rate => tp_rate, :faint => faint } else - roc_values = validation_set.validations[0].get_predictions.get_roc_values(class_value) + roc_values = validation_set.validations[0].get_predictions.get_prediction_values(class_value) tp_fp_rates = get_tp_fp_rates(roc_values) return { :names => ["default"], :fp_rate => [tp_fp_rates[:fp_rate]], :tp_rate => [tp_fp_rates[:tp_rate]] } end end + def self.transform_confidence_predictions(validation_set, class_value, add_single_folds=false) + + if (validation_set.size > 1) + + names = []; performance = []; confidence = []; faint = [] + sum_confidence_values = { :predicted_values => [], :actual_values => [], :confidence_values => []} + + (0..validation_set.size-1).each do |i| + confidence_values = validation_set.get(i).get_predictions.get_prediction_values(class_value) + sum_confidence_values[:predicted_values] += confidence_values[:predicted_values] + sum_confidence_values[:confidence_values] += confidence_values[:confidence_values] + sum_confidence_values[:actual_values] += confidence_values[:actual_values] + + if add_single_folds + begin + pref_conf_rates = get_performance_confidence_rates(confidence_values) + names << "fold "+i.to_s + performance << pref_conf_rates[:performance] + confidence << pref_conf_rates[:confidence] + faint << true + rescue + LOGGER.warn "could not get confidence vals for fold "+i.to_s + end + end + end + pref_conf_rates = get_performance_confidence_rates(sum_confidence_values, validation_set.unique_feature_type) + names << nil # "all" + performance << pref_conf_rates[:performance] + confidence << pref_conf_rates[:confidence] + faint << false + return { :names => names, :performance => performance, :confidence => confidence, :faint => faint } + + else + confidence_values = validation_set.validations[0].get_predictions.get_prediction_values(class_value) + pref_conf_rates = get_performance_confidence_rates(confidence_values, validation_set.unique_feature_type) + return { :names => ["default"], :performance => [pref_conf_rates[:performance]], :confidence => [pref_conf_rates[:confidence]] } + end + end + def self.demo_rock_plot roc_values = {:confidence_values => [0.1, 0.9, 0.5, 0.6, 0.6, 0.6], :predicted_values => [1, 0, 0, 1, 0, 1], :actual_values => [0, 1, 0, 0, 1, 1]} tp_fp_rates = get_tp_fp_rates(roc_values) data = { :names => ["default"], :fp_rate => [tp_fp_rates[:fp_rate]], :tp_rate => [tp_fp_rates[:tp_rate]] } - RubyPlot::plot_lines("/tmp/plot.svg", + RubyPlot::plot_lines("/tmp/plot.png", "ROC-Plot", "False positive rate", "True Positive Rate", data[:names], data[:fp_rate], data[:tp_rate], data[:faint] ) end + def self.get_performance_confidence_rates(roc_values, feature_type) + + c = roc_values[:confidence_values] + p = roc_values[:predicted_values] + a = roc_values[:actual_values] + raise "no prediction values for roc-plot" if p.size==0 + + (0..p.size-2).each do |i| + ((i+1)..p.size-1).each do |j| + if c[i]<c[j] + c.swap!(i,j) + a.swap!(i,j) + p.swap!(i,j) + end + end + end + #puts c.inspect+"\n"+a.inspect+"\n"+p.inspect+"\n\n" + + perf = [] + conf = [] + + case feature_type + when "classification" + count = 0 + correct = 0 + (0..p.size-1).each do |i| + count += 1 + correct += 1 if p[i]==a[i] + if i>0 && (c[i]>=conf[-1]-0.00001) + perf.pop + conf.pop + end + perf << correct/count.to_f * 100 + conf << c[i] + end + when "regression" + count = 0 + sum_squared_error = 0 + (0..p.size-1).each do |i| + count += 1 + sum_squared_error += (p[i]-a[i])**2 + if i>0 && (c[i]>=conf[-1]-0.00001) + perf.pop + conf.pop + end + perf << Math.sqrt(sum_squared_error/count.to_f) + conf << c[i] + end + end + #puts perf.inspect + + return {:performance => perf,:confidence => conf} + end + + def self.get_tp_fp_rates(roc_values) c = roc_values[:confidence_values] diff --git a/report/report_application.rb b/report/report_application.rb index 5a47063..258daa7 100755 --- a/report/report_application.rb +++ b/report/report_application.rb @@ -82,6 +82,8 @@ get '/report/:type/:id' do report = rs.get_report(params[:type],params[:id],accept_header) format = Reports::ReportFormat.get_format(accept_header) content_type format + # default encoding is utf-8, html conversion produces iso-8859-1 encoding + content_type "text/html", 'charset' => 'ISO-8859-1' if format=="text/html" #PENDING: get_report should return file or string, check for result.is_file instead of format if format=="application/x-yaml" or format=="application/rdf+xml" report diff --git a/report/report_content.rb b/report/report_content.rb index 1345e6f..ca04f25 100755 --- a/report/report_content.rb +++ b/report/report_content.rb @@ -8,7 +8,7 @@ class Reports::ReportContent attr_accessor :xml_report, :tmp_files def initialize(title) - @xml_report = Reports::XMLReport.new(title, Time.now.strftime("Created at %m.%d.%Y - %H:%M")) + @xml_report = Reports::XMLReport.new(title, Time.now.strftime("Created at %d.%m.%Y - %H:%M")) @tmp_file_count = 0 @current_section = @xml_report.get_root_element end @@ -147,21 +147,21 @@ class Reports::ReportContent image_caption=nil) image_title = "Regression plot" unless image_title - - section_regr = @xml_report.add_section(@current_section, section_title) + #section_regr = @xml_report.add_section(@current_section, section_title) + section_regr = @current_section prediction_set = validation_set.collect{ |v| v.get_predictions } if prediction_set.size>0 section_text += "\nWARNING: regression plot information not available for all validation results" if prediction_set.size!=validation_set.size @xml_report.add_paragraph(section_regr, section_text) if section_text - plot_file_name = "regr_plot"+@tmp_file_count.to_s+".svg" + plot_file_name = "regr_plot"+@tmp_file_count.to_s+".png" @tmp_file_count += 1 begin plot_file_path = add_tmp_file(plot_file_name) Reports::PlotFactory.create_regression_plot( plot_file_path, prediction_set, name_attribute ) - @xml_report.add_imagefigure(section_regr, image_title, plot_file_name, "SVG", 120, image_caption) - rescue RuntimeError => ex + @xml_report.add_imagefigure(section_regr, image_title, plot_file_name, "PNG", 100, image_caption) + rescue Exception => ex LOGGER.error("Could not create regression plot: "+ex.message) rm_tmp_file(plot_file_name) @xml_report.add_paragraph(section_regr, "could not create regression plot: "+ex.message) @@ -178,7 +178,8 @@ class Reports::ReportContent image_titles=nil, image_captions=nil) - section_roc = @xml_report.add_section(@current_section, section_title) + #section_roc = @xml_report.add_section(@current_section, section_title) + section_roc = @current_section prediction_set = validation_set.collect{ |v| v.get_predictions && v.get_predictions.confidence_values_available? } if prediction_set.size>0 @@ -189,18 +190,18 @@ class Reports::ReportContent end @xml_report.add_paragraph(section_roc, section_text) if section_text - class_domain = validation_set.get_class_domain - class_domain.size.times do |i| - class_value = class_domain[i] + accept_values = validation_set.get_accept_values + accept_values.size.times do |i| + class_value = accept_values[i] image_title = image_titles ? image_titles[i] : "ROC Plot for class-value '"+class_value.to_s+"'" image_caption = image_captions ? image_captions[i] : nil - plot_file_name = "roc_plot"+@tmp_file_count.to_s+".svg" + plot_file_name = "roc_plot"+@tmp_file_count.to_s+".png" @tmp_file_count += 1 begin plot_file_path = add_tmp_file(plot_file_name) Reports::PlotFactory.create_roc_plot( plot_file_path, prediction_set, class_value, split_set_attribute, false )#prediction_set.size>1 ) - @xml_report.add_imagefigure(section_roc, image_title, plot_file_name, "SVG", 120, image_caption) - rescue RuntimeError => ex + @xml_report.add_imagefigure(section_roc, image_title, plot_file_name, "PNG", 100, image_caption) + rescue Exception => ex msg = "WARNING could not create roc plot for class value '"+class_value.to_s+"': "+ex.message LOGGER.error(msg) rm_tmp_file(plot_file_name) @@ -213,6 +214,49 @@ class Reports::ReportContent end + def add_confidence_plot( validation_set, + split_set_attribute = nil, + section_title="Confidence plots", + section_text=nil, + image_titles=nil, + image_captions=nil) + + #section_conf = @xml_report.add_section(@current_section, section_title) + section_conf = @current_section + prediction_set = validation_set.collect{ |v| v.get_predictions && v.get_predictions.confidence_values_available? } + + if prediction_set.size>0 + if prediction_set.size!=validation_set.size + section_text += "\nWARNING: plot information not available for all validation results" + LOGGER.error "WARNING: plot information not available for all validation results:\n"+ + "validation set size: "+validation_set.size.to_s+", prediction set size: "+prediction_set.size.to_s + end + @xml_report.add_paragraph(section_conf, section_text) if section_text + + image_title = image_titles ? image_titles[i] : "Percent Correct vs Confidence Plot" + image_caption = image_captions ? image_captions[i] : nil + plot_file_name = "conf_plot"+@tmp_file_count.to_s+".png" + @tmp_file_count += 1 + + begin + + plot_file_path = add_tmp_file(plot_file_name) + Reports::PlotFactory.create_confidence_plot( plot_file_path, prediction_set, nil, split_set_attribute, false ) + @xml_report.add_imagefigure(section_conf, image_title, plot_file_name, "PNG", 100, image_caption) + + rescue Exception => ex + msg = "WARNING could not create confidence plot: "+ex.message + LOGGER.error(msg) + rm_tmp_file(plot_file_name) + @xml_report.add_paragraph(section_conf, msg) + end + + else + @xml_report.add_paragraph(section_conf, "No prediction-confidence info for confidence plot available.") + end + + end + def add_ranking_plots( validation_set, compare_attribute, equal_attribute, @@ -236,11 +280,11 @@ class Reports::ReportContent image_titles=nil, image_captions=nil) - class_domain = validation_set.get_domain_for_attr(rank_attribute) - puts "ranking plot for "+rank_attribute.to_s+", class values: "+class_domain.to_s + accept_values = validation_set.get_class_values_for(rank_attribute) + puts "ranking plot for "+rank_attribute.to_s+", class values: "+accept_values.to_s - class_domain.size.times do |i| - class_value = class_domain[i] + accept_values.size.times do |i| + class_value = accept_values[i] if image_titles image_title = image_titles[i] else @@ -270,11 +314,11 @@ class Reports::ReportContent section_bar = @xml_report.add_section(@current_section, section_title) @xml_report.add_paragraph(section_bar, section_text) if section_text - plot_file_name = "bar_plot"+@tmp_file_count.to_s+".svg" + plot_file_name = "bar_plot"+@tmp_file_count.to_s+".png" @tmp_file_count += 1 plot_file_path = add_tmp_file(plot_file_name) Reports::PlotFactory.create_bar_plot(plot_file_path, validation_set, title_attribute, value_attributes ) - @xml_report.add_imagefigure(section_bar, image_title, plot_file_name, "SVG", 120, image_caption) + @xml_report.add_imagefigure(section_bar, image_title, plot_file_name, "PNG", 100, image_caption) end private diff --git a/report/report_factory.rb b/report/report_factory.rb index e770d2f..08d9418 100755 --- a/report/report_factory.rb +++ b/report/report_factory.rb @@ -68,15 +68,21 @@ module Reports::ReportFactory case val.feature_type when "classification" report.add_result(validation_set, [:validation_uri] + VAL_ATTR_TRAIN_TEST + VAL_ATTR_CLASS, "Results", "Results") - report.add_roc_plot(validation_set) report.add_confusion_matrix(val) + report.add_section("Plots") + report.add_roc_plot(validation_set) + report.add_confidence_plot(validation_set) + report.end_section when "regression" report.add_result(validation_set, [:validation_uri] + VAL_ATTR_TRAIN_TEST + VAL_ATTR_REGR, "Results", "Results") + report.add_section("Plots") report.add_regression_plot(validation_set, :model_uri) + report.add_confidence_plot(validation_set) + report.end_section end task.progress(90) if task - report.add_result(validation_set, Lib::ALL_PROPS, "All Results", "All Results") + report.add_result(validation_set, Validation::ALL_PROPS, "All Results", "All Results") report.add_predictions( validation_set ) task.progress(100) if task report @@ -89,7 +95,7 @@ module Reports::ReportFactory validation_set.get_values(:crossvalidation_id,false).inspect) if validation_set.unique_value(:crossvalidation_id)==nil validation_set.load_cv_attributes raise OpenTox::BadRequestError.new("num validations ("+validation_set.size.to_s+") is not equal to num folds ("+ - validation_set.unique_value(:num_folds).to_s+")") unless validation_set.unique_value(:num_folds)==validation_set.size + validation_set.unique_value(:num_folds).to_s+")") unless validation_set.unique_value(:num_folds).to_i==validation_set.size raise OpenTox::BadRequestError.new("num different folds is not equal to num validations") unless validation_set.num_different_values(:crossvalidation_fold)==validation_set.size raise OpenTox::BadRequestError.new("validations must have unique feature type, i.e. must be either all regression, "+ +"or all classification validations") unless validation_set.unique_feature_type @@ -104,19 +110,27 @@ module Reports::ReportFactory case validation_set.unique_feature_type when "classification" report.add_result(merged, [:crossvalidation_uri]+VAL_ATTR_CV+VAL_ATTR_CLASS-[:crossvalidation_fold],"Mean Results","Mean Results") - report.add_roc_plot(validation_set, nil, "ROC Plots over all folds") - report.add_roc_plot(validation_set, :crossvalidation_fold) report.add_confusion_matrix(merged.validations[0]) + report.add_section("Plots") + report.add_roc_plot(validation_set) + report.add_roc_plot(validation_set, :crossvalidation_fold) + report.add_confidence_plot(validation_set) + report.add_confidence_plot(validation_set, :crossvalidation_fold) + report.end_section report.add_result(validation_set, VAL_ATTR_CV+VAL_ATTR_CLASS-[:num_folds], "Results","Results",nil,"validation") when "regression" report.add_result(merged, [:crossvalidation_uri]+VAL_ATTR_CV+VAL_ATTR_REGR-[:crossvalidation_fold],"Mean Results","Mean Results") + report.add_section("Plots") report.add_regression_plot(validation_set, :crossvalidation_fold) + report.add_confidence_plot(validation_set) + report.add_confidence_plot(validation_set, :crossvalidation_fold) + report.end_section report.add_result(validation_set, VAL_ATTR_CV+VAL_ATTR_REGR-[:num_folds], "Results","Results") end task.progress(90) if task - report.add_result(validation_set, Lib::ALL_PROPS, "All Results", "All Results") + report.add_result(validation_set, Validation::ALL_PROPS, "All Results", "All Results") report.add_predictions( validation_set ) #, [:crossvalidation_fold] ) task.progress(100) if task report @@ -194,7 +208,25 @@ module Reports::ReportFactory end when "regression" - raise OpenTox::BadRequestError.new("algorithm comparison for regression not yet implemented") + + attributes = VAL_ATTR_CV+VAL_ATTR_REGR-[:crossvalidation_fold] + attributes = ([ :dataset_uri ] + attributes).uniq + + dataset_grouping.each do |validations| + + set = Reports::ValidationSet.create(validations) + + dataset = validations[0].dataset_uri + merged = set.merge([:algorithm_uri, :dataset_uri, :crossvalidation_id, :crossvalidation_uri]) + merged.sort(:dataset_uri) + + report.add_section("Dataset: "+dataset) + report.add_result(merged,attributes, + "Mean Results","Mean Results",nil,"crossvalidation") + report.add_paired_ttest_table(set, :algorithm_uri, :r_square) + report.end_section + end + end task.progress(100) if task report diff --git a/report/report_persistance.rb b/report/report_persistance.rb index df4930c..c85ad68 100755 --- a/report/report_persistance.rb +++ b/report/report_persistance.rb @@ -188,28 +188,29 @@ module Reports # serialize :model_uris # alias_attribute :date, :created_at - class ReportData - include DataMapper::Resource + class ReportData < Ohm::Model - property :id, Serial - property :report_type, String, :length => 255 - property :created_at, DateTime - property :validation_uris, Object - property :crossvalidation_uris, Object - property :model_uris, Object - property :algorithm_uris, Object + attribute :report_type + attribute :date + attribute :validation_uris + attribute :crossvalidation_uris + attribute :model_uris + attribute :algorithm_uris + + index :report_type + index :validation_uris + index :crossvalidation_uris attr_accessor :subjectid - after :save, :check_policy - private - def check_policy - OpenTox::Authorization.check_policy(report_uri, subjectid) + def self.create(params={}) + params[:date] = Time.new + super params end - public - def date - created_at + def save + super + OpenTox::Authorization.check_policy(report_uri, subjectid) end def report_uri @@ -241,36 +242,24 @@ module Reports def new_report(report_content, type, meta_data, uri_provider, subjectid=nil) raise "report meta data missing" unless meta_data - report = ReportData.new(meta_data) + meta_data[:report_type] = type + report = ReportData.create(meta_data) report.subjectid = subjectid - report.report_type = type - report.save + OpenTox::Authorization.check_policy(report.report_uri, subjectid) new_report_with_id(report_content, type, report.id) end def list_reports(type, filter_params={}) - filter_params["report_type"]=type unless filter_params.has_key?("report_type") - #ReportData.find_like(filter_params).delete_if{|r| r.report_type!=type}.collect{ |r| r.id } - - filter_params = Lib::DataMapperUtil.check_params(ReportData, filter_params) - # unfortunately, datamapper does not allow searching in Objects - # do filtering for list = Object params manually - list_params = {} - [:validation_uris, :crossvalidation_uris, :algorithm_uris, :model_uris].each do |l| - list_params[l] = filter_params.delete(l) if filter_params.has_key?(l) - end - - reports = ReportData.all(filter_params).delete_if{|r| r.report_type!=type} - list_params.each do |k,v| - reports = reports.delete_if{ |r| !r.send(k).include?(v) } - end + LOGGER.debug "find reports for params: "+filter_params.inspect + reports = Lib::OhmUtil.find( ReportData, filter_params ) reports.collect{ |r| r.id } end def get_report(type, id, format, force_formating, params) - report = ReportData.first({:id => id, :report_type => type}) - raise OpenTox::NotFoundError.new("Report with id='"+id.to_s+"' and type='"+type.to_s+"' not found.") unless report + report = ReportData[id] + raise OpenTox::NotFoundError.new("Report with id='"+id.to_s+"' and type='"+type.to_s+"' not found.") if + report==nil or report.report_type!=type # begin # report = ReportData.find(:first, :conditions => {:id => id, :report_type => type}) # rescue ActiveRecord::RecordNotFound @@ -294,9 +283,10 @@ module Reports # raise OpenTox::NotFoundError.new("Report with id='"+id.to_s+"' and type='"+type.to_s+"' not found.") # end # ReportData.delete(id) - report = ReportData.first({:id => id, :report_type => type}) - raise OpenTox::NotFoundError.new("Report with id='"+id.to_s+"' and type='"+type.to_s+"' not found.") unless report - report.destroy + report = ReportData[id] + raise OpenTox::NotFoundError.new("Report with id='"+id.to_s+"' and type='"+type.to_s+"' not found.") if + report==nil || report.report_type!=type + report.delete if (subjectid) begin res = OpenTox::Authorization.delete_policies_from_uri(report.report_uri, subjectid) @@ -310,9 +300,6 @@ module Reports end end -Reports::ReportData.auto_upgrade! -Reports::ReportData.raise_on_save_failure = true - #module Reports # def self.check_filter_params(model, filter_params) # prop_names = model.properties.collect{|p| p.name.to_s} diff --git a/report/report_service.rb b/report/report_service.rb index 91eefe8..722c3d6 100644 --- a/report/report_service.rb +++ b/report/report_service.rb @@ -83,6 +83,9 @@ module Reports LOGGER.debug "report persisted with id: '"+id.to_s+"'" task.progress(100) if task + #HACK - format to html right after creation, as dynamically create html may cause deadlocks + get_report(type, id, "text/html") + return get_uri(type, id) end diff --git a/report/validation_access.rb b/report/validation_access.rb index 53ecc46..e9b6e19 100755 --- a/report/validation_access.rb +++ b/report/validation_access.rb @@ -21,11 +21,11 @@ class Reports::ValidationDB # rescue => ex # raise "could not access crossvalidation with id "+validation_id.to_s+", error-msg: "+ex.message # end - cv = Lib::Crossvalidation.get( cv_id ) + cv = Validation::Crossvalidation.get( cv_id ) raise OpenTox::NotFoundError.new "crossvalidation with id "+cv_id.to_s+" not found" unless cv raise OpenTox::BadRequestError.new("crossvalidation with id '"+cv_id.to_s+"' not finished") unless cv.finished - #res += Lib::Validation.find( :all, :conditions => { :crossvalidation_id => cv_id } ).collect{|v| v.validation_uri.to_s} - res += Lib::Validation.all( :crossvalidation_id => cv_id ).collect{|v| v.validation_uri.to_s } + #res += Validation::Validation.find( :all, :conditions => { :crossvalidation_id => cv_id } ).collect{|v| v.validation_uri.to_s} + res += Validation::Validation.find( :crossvalidation_id => cv_id ).collect{|v| v.validation_uri.to_s } else res += [u.to_s] end @@ -42,16 +42,16 @@ class Reports::ValidationDB v = nil raise OpenTox::NotAuthorizedError.new "Not authorized: GET "+uri.to_s if AA_SERVER and !OpenTox::Authorization.authorized?(uri,"GET",subjectid) - v = Lib::Validation.get(validation_id) + v = Validation::Validation.get(validation_id) raise OpenTox::NotFoundError.new "validation with id "+validation_id.to_s+" not found" unless v raise OpenTox::BadRequestError.new "validation with id "+validation_id.to_s+" is not finished yet" unless v.finished - (Lib::VAL_PROPS + Lib::VAL_CV_PROPS).each do |p| + (Validation::VAL_PROPS + Validation::VAL_CV_PROPS).each do |p| validation.send("#{p.to_s}=".to_sym, v.send(p)) end - {:classification_statistics => Lib::VAL_CLASS_PROPS, - :regression_statistics => Lib::VAL_REGR_PROPS}.each do |subset_name,subset_props| + {:classification_statistics => Validation::VAL_CLASS_PROPS, + :regression_statistics => Validation::VAL_REGR_PROPS}.each do |subset_name,subset_props| subset = v.send(subset_name) subset_props.each{ |prop| validation.send("#{prop.to_s}=".to_sym, subset[prop]) } if subset end @@ -60,11 +60,11 @@ class Reports::ValidationDB def init_cv(validation) #cv = Lib::Crossvalidation.find(validation.crossvalidation_id) - cv = Lib::Crossvalidation.get(validation.crossvalidation_id) + cv = Validation::Crossvalidation.get(validation.crossvalidation_id) raise OpenTox::BadRequestError.new "no crossvalidation found with id "+validation.crossvalidation_id.to_s unless cv - Lib::CROSS_VAL_PROPS.each do |p| - validation.send("#{p.to_s}=".to_sym, cv[p]) + Validation::CROSS_VAL_PROPS.each do |p| + validation.send("#{p.to_s}=".to_sym, cv.send(p.to_s)) end end @@ -74,8 +74,13 @@ class Reports::ValidationDB validation.predicted_variable, subjectid, task) end - def get_class_domain( validation ) - OpenTox::Feature.new( validation.prediction_feature ).domain + def get_accept_values( validation, subjectid=nil ) + # PENDING So far, one has to load the whole dataset to get the accept_value from ambit + d = OpenTox::Dataset.find( validation.test_target_dataset_uri, subjectid ) + accept_values = d.features[validation.prediction_feature][OT.acceptValue] + raise "cannot get accept values from dataset "+validation.test_target_dataset_uri.to_s+" for feature "+ + validation.prediction_feature+":\n"+d.features[validation.prediction_feature].to_yaml unless accept_values!=nil + accept_values end def feature_type( validation, subjectid=nil ) diff --git a/report/validation_data.rb b/report/validation_data.rb index 15d51ec..42b179b 100755 --- a/report/validation_data.rb +++ b/report/validation_data.rb @@ -51,13 +51,13 @@ end module Reports - # = Reports::Validation + # = ReportValidation # # contains all values of a validation object # - class Validation + class ReportValidation - @@validation_access = Reports::ValidationDB.new + @@validation_access = ValidationDB.new # for overwriting validation source (other than using webservices) def self.reset_validation_access(validation_access) @@ -69,7 +69,7 @@ module Reports end # create member variables for all validation properties - @@validation_attributes = Lib::ALL_PROPS + + @@validation_attributes = Validation::ALL_PROPS + VAL_ATTR_VARIANCE.collect{ |a| (a.to_s+"_variance").to_sym } + VAL_ATTR_RANKING.collect{ |a| (a.to_s+"_ranking").to_sym } @@validation_attributes.each{ |a| attr_accessor a } @@ -85,7 +85,7 @@ module Reports # returns/creates predictions, cache to save rest-calls/computation time # # call-seq: - # get_predictions => Reports::Predictions + # get_predictions => Predictions # def get_predictions( task=nil ) if @predictions @@ -104,9 +104,9 @@ module Reports # returns the predictions feature values (i.e. the domain of the class attribute) # - def get_class_domain() - @class_domain = @@validation_access.get_class_domain(self) unless @class_domain - @class_domain + def get_accept_values() + @accept_values = @@validation_access.get_accept_values(self, @subjectid) unless @accept_values + @accept_values end # is classification/regression validation? cache to save rest-calls @@ -127,13 +127,13 @@ module Reports @@validation_access.init_cv(self) end - @@persistance = Reports::ReportService.persistance + @@persistance = ReportService.persistance def validation_report_uri #puts "searching for validation report: "+self.validation_uri.to_s return @validation_report_uri if @validation_report_uri!=nil ids = @@persistance.list_reports("validation",{:validation_uris=>validation_uri }) - @validation_report_uri = Reports::ReportService.instance.get_uri("validation",ids[-1]) if ids and ids.size>0 + @validation_report_uri = ReportService.instance.get_uri("validation",ids[-1]) if ids and ids.size>0 end def cv_report_uri @@ -142,7 +142,7 @@ module Reports raise "no cv uri "+to_yaml unless self.crossvalidation_uri ids = @@persistance.list_reports("crossvalidation",{:crossvalidation=>self.crossvalidation_uri.to_s }) #puts "-> "+ids.inspect - @cv_report_uri = Reports::ReportService.instance.get_uri("crossvalidation",ids[-1]) if ids and ids.size>0 + @cv_report_uri = ReportService.instance.get_uri("crossvalidation",ids[-1]) if ids and ids.size>0 end def clone_validation @@ -160,9 +160,9 @@ module Reports def initialize(validation_uris=nil, subjectid=nil) @unique_values = {} - validation_uris = Reports::Validation.resolve_cv_uris(validation_uris, subjectid) if validation_uris + validation_uris = ReportValidation.resolve_cv_uris(validation_uris, subjectid) if validation_uris @validations = Array.new - validation_uris.each{|u| @validations.push(Reports::Validation.new(u, subjectid))} if validation_uris + validation_uris.each{|u| @validations.push(ReportValidation.new(u, subjectid))} if validation_uris end @@ -233,7 +233,7 @@ module Reports # def get_true_prediction_feature_value # if all_classification? -# class_values = get_class_domain +# class_values = get_accept_values # if class_values.size == 2 # (0..1).each do |i| # return class_values[i] if (class_values[i].to_s.downcase == "true" || class_values[i].to_s.downcase == "active") @@ -243,21 +243,23 @@ module Reports # return nil # end - def get_class_domain( ) - return unique_value("get_class_domain") + def get_accept_values( ) + return unique_value("get_accept_values") end - def get_domain_for_attr( attribute ) - class_domain = get_class_domain() - if Lib::Validation.classification_property?(attribute) and - !Lib::Validation.depends_on_class_value?(attribute) - [ nil ] - elsif Lib::Validation.classification_property?(attribute) and - class_domain.size==2 and - Lib::Validation.complement_exists?(attribute) - [ class_domain[0] ] + def get_accept_values_for_attr( attribute ) + if !Validation::Validation.classification_property?(attribute) + [] else - class_domain + accept_values = get_accept_values() + if !Validation::Validation.depends_on_class_value?(attribute) + [ nil ] + elsif accept_values.size==2 and + Validation::Validation.complement_exists?(attribute) + [ accept_values[0] ] + else + accept_values + end end end @@ -270,10 +272,10 @@ module Reports # returns a new set with all validation that have values as specified in the map # # call-seq: - # filter(map) => Reports::ValidationSet + # filter(map) => ValidationSet # def filter(map) - new_set = Reports::ValidationSet.new + new_set = ValidationSet.new validations.each{ |v| new_set.validations.push(v) if v.has_values?(map) } return new_set end @@ -282,10 +284,10 @@ module Reports # e.g. create set with predictions: collect{ |validation| validation.get_predictions!=null } # # call-seq: - # filter_proc(proc) => Reports::ValidationSet + # filter_proc(proc) => ValidationSet # def collect - new_set = Reports::ValidationSet.new + new_set = ValidationSet.new validations.each{ |v| new_set.validations.push(v) if yield(v) } return new_set end @@ -298,10 +300,10 @@ module Reports #puts col_values.inspect # get domain for classification attribute, i.e. ["true","false"] - class_domain = get_domain_for_attr(attribute_val) + accept_values = get_accept_values_for_attr(attribute_val) # or the attribute has a complementary value, i.e. true_positive_rate # -> domain is reduced to one class value - first_value_elem = (class_domain.size==1 && class_domain[0]!=nil) + first_value_elem = (accept_values.size==1 && accept_values[0]!=nil) cell_values = {} row_values.each do |row| @@ -311,7 +313,7 @@ module Reports if v.send(attribute_row)==row and v.send(attribute_col)==col raise "two validation have equal row and column values"if val!=nil val = v.send(attribute_val) - val = val[class_domain[0]] if first_value_elem + val = val[accept_values[0]] if first_value_elem val = val.to_nice_s end end @@ -357,13 +359,13 @@ module Reports else attribute_not_nil[index] = true if remove_nil_attributes - class_domain = get_domain_for_attr(a) + accept_values = get_accept_values_for_attr(a) # get domain for classification attribute, i.e. ["true","false"] - if class_domain.size==1 && class_domain[0]!=nil + if accept_values.size==1 && accept_values[0]!=nil # or the attribute has a complementary value, i.e. true_positive_rate # -> domain is reduced to one class value raise "illegal state, value for "+a.to_s+" is no hash: '"+val.to_s+"'" unless (val.is_a?(Hash)) - val = val[class_domain[0]] + val = val[accept_values[0]] end if variance @@ -398,19 +400,19 @@ module Reports # to_array(attributes) => array # def merge(equal_attributes) - new_set = Reports::ValidationSet.new + new_set = ValidationSet.new # unique values stay unique when merging # derive unique values before, because model dependent props cannot be accessed later (when mergin validations from different models) new_set.unique_values = @unique_values #compute grouping - grouping = Reports::Util.group(@validations, equal_attributes) + grouping = Util.group(@validations, equal_attributes) #puts "groups "+grouping.size.to_s - Lib::MergeObjects.register_merge_attributes( Reports::Validation, - Lib::VAL_MERGE_AVG,Lib::VAL_MERGE_SUM,Lib::VAL_MERGE_GENERAL) unless - Lib::MergeObjects.merge_attributes_registered?(Reports::Validation) + Lib::MergeObjects.register_merge_attributes( ReportValidation, + Validation::VAL_MERGE_AVG,Validation::VAL_MERGE_SUM,Validation::VAL_MERGE_GENERAL) unless + Lib::MergeObjects.merge_attributes_registered?(ReportValidation) #merge grouping.each do |g| @@ -438,12 +440,12 @@ module Reports def compute_ranking(equal_attributes, ranking_attribute, class_value=nil ) #puts "compute_ranking("+equal_attributes.inspect+", "+ranking_attribute.inspect+", "+class_value.to_s+" )" - new_set = Reports::ValidationSet.new + new_set = ValidationSet.new (0..@validations.size-1).each do |i| new_set.validations.push(@validations[i].clone_validation) end - grouping = Reports::Util.group(new_set.validations, equal_attributes) + grouping = Util.group(new_set.validations, equal_attributes) grouping.each do |group| # put indices and ranking values for current group into hash diff --git a/report/xml_report.rb b/report/xml_report.rb index 4b9a11a..4fbfae3 100755 --- a/report/xml_report.rb +++ b/report/xml_report.rb @@ -184,7 +184,7 @@ module Reports row = Element.new("row") r.each do |v| entry = Element.new("entry") - if auto_link_urls && v.to_s =~ /depict/ || v.to_s =~ /image$/ #PENDING + if auto_link_urls && v.to_s =~ /depict/ || v.to_s =~ /image\/png$/ #PENDING add_image(entry, v.to_s) elsif auto_link_urls && v.to_s =~ /^http(s?):\/\// add_url(entry, v.to_s, v.to_s) diff --git a/test/test_examples.rb b/test/test_examples.rb index 3c6f00e..49d7838 100755 --- a/test/test_examples.rb +++ b/test/test_examples.rb @@ -85,7 +85,7 @@ module ValidationExamples class EPAFHMCrossvalidation < CrossValidation def initialize - @dataset_file = File.new("data/EPAFHM.csv","r") + @dataset_file = File.new("data/EPAFHM.mini.csv","r") #@prediction_feature = "http://ot-dev.in-silico.ch/toxcreate/feature#IRIS%20unit%20risk" @num_folds = 10 end diff --git a/test/unit_test.rb b/test/unit_test.rb deleted file mode 100644 index 11b0759..0000000 --- a/test/unit_test.rb +++ /dev/null @@ -1,189 +0,0 @@ -#TEST_USER = "mgtest" -#TEST_PW = "mgpasswd" -#ENV['RACK_ENV'] = 'test' - -require "rubygems" -require "sinatra" -require "uri" -require "yaml" -require 'application.rb' -require 'test/unit' -require 'rack/test' -require 'lib/test_util.rb' -require 'test/test_examples.rb' - -TEST_USER = "guest" -TEST_PW = "guest" - -#LOGGER = OTLogger.new(STDOUT) -#LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S " -#LOGGER.formatter = Logger::Formatter.new - -module Sinatra - set :raise_errors, false - set :show_exceptions, false -end - -class Exception - def message - errorCause ? errorCause.to_yaml : to_s - end -end - -class ValidationTest < Test::Unit::TestCase - include Rack::Test::Methods - include Lib::TestUtil - - def global_setup - puts "login and upload datasets" - if AA_SERVER - @@subjectid = OpenTox::Authorization.authenticate(TEST_USER,TEST_PW) - raise "could not log in" unless @@subjectid - puts "logged in: "+@@subjectid.to_s - else - puts "AA disabled" - @@subjectid = nil - end - f = File.new("data/hamster_carcinogenicity.mini.csv") - @@data_class_mini = ValidationExamples::Util.upload_dataset(f, @@subjectid) - @@feat_class_mini = ValidationExamples::Util.prediction_feature_for_file(f) - end - - def global_teardown - puts "delete and logout" - OpenTox::Dataset.find(@@data_class_mini,@@subjectid).delete(@@subjectid) if defined?@@data_class_mini - @@cv.delete(@@subjectid) if defined?@@cv - @@report.delete(@@subjectid) if defined?@@report - @@qmrfReport.delete(@@subjectid) if defined?@@qmrfReport - OpenTox::Authorization.logout(@@subjectid) if AA_SERVER - end - - def test_crossvalidation - puts "test_crossvalidation" - #assert_rest_call_error OpenTox::NotFoundError do - # OpenTox::Crossvalidation.find(File.join(CONFIG[:services]["opentox-validation"],"crossvalidation/noexistingid")) - #end - p = { - :dataset_uri => @@data_class_mini, - :algorithm_uri => File.join(CONFIG[:services]["opentox-algorithm"],"lazar"), - :algorithm_params => "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc"), - :prediction_feature => @@feat_class_mini, - :num_folds => 2 } - t = OpenTox::SubTask.new(nil,0,1) - def t.progress(pct) - if !defined?@last_msg or @last_msg+3<Time.new - puts "waiting for crossvalidation: "+pct.to_s - @last_msg=Time.new - end - end - def t.waiting_for(task_uri); end - cv = OpenTox::Crossvalidation.create(p, @@subjectid, t) - assert cv.uri.uri? - if @@subjectid - assert_rest_call_error OpenTox::NotAuthorizedError do - OpenTox::Crossvalidation.find(cv.uri) - end - end - cv = OpenTox::Crossvalidation.find(cv.uri, @@subjectid) - assert cv.uri.uri? - if @@subjectid - assert_rest_call_error OpenTox::NotAuthorizedError do - cv.summary(cv) - end - end - summary = cv.summary(@@subjectid) - assert_kind_of Hash,summary - @@cv = cv - end - - def test_crossvalidation_report - #@@cv = OpenTox::Crossvalidation.find("http://local-ot/validation/crossvalidation/48", @@subjectid) - - puts "test_crossvalidation_report" - assert defined?@@cv,"no crossvalidation defined" - assert_kind_of OpenTox::Crossvalidation,@@cv - #assert_rest_call_error OpenTox::NotFoundError do - # OpenTox::CrossvalidationReport.find_for_crossvalidation(@@cv.uri) - #end - if @@subjectid - assert_rest_call_error OpenTox::NotAuthorizedError do - OpenTox::CrossvalidationReport.create(@@cv.uri) - end - end - report = OpenTox::CrossvalidationReport.create(@@cv.uri,@@subjectid) - assert report.uri.uri? - if @@subjectid - assert_rest_call_error OpenTox::NotAuthorizedError do - OpenTox::CrossvalidationReport.find(report.uri) - end - end - report = OpenTox::CrossvalidationReport.find(report.uri,@@subjectid) - assert report.uri.uri? - report2 = OpenTox::CrossvalidationReport.find_for_crossvalidation(@@cv.uri,@@subjectid) - assert_equal report.uri,report2.uri - report3_uri = @@cv.find_or_create_report(@@subjectid) - assert_equal report.uri,report3_uri - @report = report2 - end - - def test_qmrf_report - #@@cv = OpenTox::Crossvalidation.find("http://local-ot/validation/crossvalidation/47", @@subjectid) - - puts "test_qmrf_report" - assert defined?@@cv,"no crossvalidation defined" - - validations = @@cv.metadata[OT.validation] - assert_kind_of Array,validations - assert validations.size==@@cv.metadata[OT.numFolds] - - val = OpenTox::Validation.find(validations[0], @@subjectid) - model_uri = val.metadata[OT.model] - model = OpenTox::Model::Generic.find(model_uri, @@subjectid) - assert model!=nil - - #assert_rest_call_error OpenTox::NotFoundError do - # OpenTox::QMRFReport.find_for_model(model_uri, @@subjectid) - #end - - @@qmrfReport = OpenTox::QMRFReport.create(model_uri, @@subjectid) - end - - ################### utils and overrides ########################## - - def app - Sinatra::Application - end - - # checks RestCallError type - def assert_rest_call_error( ex ) - if ex==OpenTox::NotAuthorizedError and @@subjectid==nil - puts "AA disabled: skipping test for not authorized" - return - end - begin - yield - rescue OpenTox::RestCallError => e - report = e.errorCause - while report.errorCause - report = report.errorCause - end - assert_equal report.errorType,ex.to_s - end - end - - # hack to have a global_setup and global_teardown - def teardown - if((@@expected_test_count-=1) == 0) - global_teardown - end - end - def setup - unless defined?@@expected_test_count - @@expected_test_count = (self.class.instance_methods.reject{|method| method[0..3] != 'test'}).length - global_setup - end - end - -end - - diff --git a/validation/validation_application.rb b/validation/validation_application.rb index e07acf0..4bcd07d 100755 --- a/validation/validation_application.rb +++ b/validation/validation_application.rb @@ -9,10 +9,7 @@ require 'validation/validation_service.rb' get '/crossvalidation/?' do LOGGER.info "list all crossvalidations" - #uri_list = Validation::Crossvalidation.all.collect{ |cv| cv.crossvalidation_uri }.join("\n")+"\n" - uri_list = Lib::DataMapperUtil.all(Validation::Crossvalidation,params).collect{ |cv| cv.crossvalidation_uri }.join("\n")+"\n" - - #uri_list = Validation::Crossvalidation.find_like(params).collect{ |cv| cv.crossvalidation_uri }.join("\n")+"\n" + uri_list = Lib::OhmUtil.find( Validation::Crossvalidation, params ).collect{|v| v.crossvalidation_uri}.join("\n") + "\n" if request.env['HTTP_ACCEPT'] =~ /text\/html/ related_links = "Single validations: "+url_for("/",:full)+"\n"+ @@ -41,7 +38,7 @@ post '/crossvalidation/?' do cv_params = { :dataset_uri => params[:dataset_uri], :algorithm_uri => params[:algorithm_uri] } [ :num_folds, :random_seed, :stratified ].each{ |sym| cv_params[sym] = params[sym] if params[sym] } - cv = Validation::Crossvalidation.new cv_params + cv = Validation::Crossvalidation.create cv_params cv.subjectid = @subjectid cv.perform_cv( params[:prediction_feature], params[:algorithm_params], task ) cv.crossvalidation_uri @@ -62,7 +59,7 @@ post '/crossvalidation/cleanup/?' do deleted << cv.crossvalidation_uri #Validation::Crossvalidation.delete(cv.id) cv.subjectid = @subjectid - cv.delete + cv.delete_crossvalidation #end end LOGGER.info "crossvalidation cleanup, deleted "+deleted.size.to_s+" cvs" @@ -124,13 +121,19 @@ get '/crossvalidation/:id/statistics' do raise OpenTox::BadRequestError.new "Crossvalidation '"+params[:id].to_s+"' not finished" unless crossvalidation.finished Lib::MergeObjects.register_merge_attributes( Validation::Validation, - Lib::VAL_MERGE_AVG,Lib::VAL_MERGE_SUM,Lib::VAL_MERGE_GENERAL-[:date,:validation_uri,:crossvalidation_uri]) unless + Validation::VAL_MERGE_AVG,Validation::VAL_MERGE_SUM,Validation::VAL_MERGE_GENERAL-[:date,:validation_uri,:crossvalidation_uri]) unless Lib::MergeObjects.merge_attributes_registered?(Validation::Validation) #v = Lib::MergeObjects.merge_array_objects( Validation::Validation.find( :all, :conditions => { :crossvalidation_id => params[:id] } ) ) - v = Lib::MergeObjects.merge_array_objects( Validation::Validation.all( :crossvalidation_id => params[:id] ) ) - v.created_at = nil - v.id = nil + # convert ohm:set into array, as ohm:set[0]=nil(!) + vals = Validation::Validation.find( :crossvalidation_id => params[:id] ).collect{|x| x} +# LOGGER.debug vals.collect{|v| v.validation_uri}.join("\n") +# LOGGER.debug vals.size +# LOGGER.debug vals.class + raise "could not load all validations for crossvalidation" if vals.include?(nil) + v = Lib::MergeObjects.merge_array_objects( vals ) + v.date = nil + #v.id = nil case request.env['HTTP_ACCEPT'].to_s when /text\/html/ @@ -159,7 +162,7 @@ delete '/crossvalidation/:id/?' do cv = Validation::Crossvalidation.get(params[:id]) cv.subjectid = @subjectid raise OpenTox::NotFoundError.new "Crossvalidation '#{params[:id]}' not found." unless cv - cv.delete + cv.delete_crossvalidation end #get '/crossvalidation/:id/validations' do @@ -184,8 +187,7 @@ get '/crossvalidation/:id/predictions' do raise OpenTox::BadRequestError.new "Crossvalidation '"+params[:id].to_s+"' not finished" unless crossvalidation.finished content_type "application/x-yaml" - #validations = Validation::Validation.find( :all, :conditions => { :crossvalidation_id => params[:id] } ) - validations = Validation::Validation.all( :crossvalidation_id => params[:id] ) + validations = Validation::Validation.find( :crossvalidation_id => params[:id] ) p = Lib::OTPredictions.to_array( validations.collect{ |v| v.compute_validation_stats_with_model(nil, true) } ).to_yaml case request.env['HTTP_ACCEPT'].to_s @@ -206,11 +208,7 @@ end get '/?' do LOGGER.info "list all validations, params: "+params.inspect - #uri_list = Validation::Validation.find_like(params).collect{ |v| v.validation_uri }.join("\n")+"\n" - #uri_list = Validation::Validation.all(params).collect{ |v| v.validation_uri }.join("\n")+"\n" - uri_list = Lib::DataMapperUtil.all(Validation::Validation,params).collect{ |v| v.validation_uri }.join("\n")+"\n" - - + uri_list = Lib::OhmUtil.find( Validation::Validation, params ).collect{|v| v.validation_uri}.join("\n") + "\n" if request.env['HTTP_ACCEPT'] =~ /text\/html/ related_links = "To perform a validation:\n"+ @@ -241,7 +239,7 @@ post '/test_set_validation' do LOGGER.info "creating test-set-validation "+params.inspect if params[:model_uri] and params[:test_dataset_uri] and !params[:training_dataset_uri] and !params[:algorithm_uri] task = OpenTox::Task.create( "Perform test-set-validation", url_for("/", :full) ) do |task| #, params - v = Validation::Validation.new :validation_type => "test_set_validation", + v = Validation::Validation.create :validation_type => "test_set_validation", :model_uri => params[:model_uri], :test_dataset_uri => params[:test_dataset_uri], :test_target_dataset_uri => params[:test_target_dataset_uri], @@ -262,8 +260,9 @@ get '/test_set_validation' do #uri_list = Validation::Validation.find( :all, :conditions => { :validation_type => "test_set_validation" } ).collect{ |v| v.validation_uri }.join("\n")+"\n" #uri_list = Validation::Validation.all( :validation_type => "test_set_validation" ).collect{ |v| v.validation_uri }.join("\n")+"\n" - params[:validation_type] = "test_set_validation" - uri_list = Lib::DataMapperUtil.all(Validation::Validation,params).collect{ |v| v.validation_uri }.join("\n")+"\n" + #params[:validation_type] = "test_set_validation" + #uri_list = Lib::DataMapperUtil.all(Validation::Validation,params).collect{ |v| v.validation_uri }.join("\n")+"\n" + uri_list = Validation::Validation.find(:validation_type => "test_set_validation").collect{|v| v.validation_uri}.join("\n") + "\n" if request.env['HTTP_ACCEPT'] =~ /text\/html/ related_links = @@ -285,7 +284,7 @@ post '/training_test_validation/?' do LOGGER.info "creating training-test-validation "+params.inspect if params[:algorithm_uri] and params[:training_dataset_uri] and params[:test_dataset_uri] and params[:prediction_feature] and !params[:model_uri] task = OpenTox::Task.create( "Perform training-test-validation", url_for("/", :full) ) do |task| #, params - v = Validation::Validation.new :validation_type => "training_test_validation", + v = Validation::Validation.create :validation_type => "training_test_validation", :algorithm_uri => params[:algorithm_uri], :training_dataset_uri => params[:training_dataset_uri], :test_dataset_uri => params[:test_dataset_uri], @@ -306,8 +305,9 @@ get '/training_test_validation' do LOGGER.info "list all training-test-validations, params: "+params.inspect #uri_list = Validation::Validation.find( :all, :conditions => { :validation_type => "training_test_validation" } ).collect{ |v| v.validation_uri }.join("\n")+"\n" #uri_list = Validation::Validation.all( :validation_type => "training_test_validation" ).collect{ |v| v.validation_uri }.join("\n")+"\n" - params[:validation_type] = "training_test_validation" - uri_list = Lib::DataMapperUtil.all(Validation::Validation,params).collect{ |v| v.validation_uri }.join("\n")+"\n" + #params[:validation_type] = "training_test_validation" + #uri_list = Lib::DataMapperUtil.all(Validation::Validation,params).collect{ |v| v.validation_uri }.join("\n")+"\n" + uri_list = Validation::Validation.find(:validation_type => "training_test_validation").collect{|v| v.validation_uri}.join("\n") + "\n" if request.env['HTTP_ACCEPT'] =~ /text\/html/ related_links = @@ -340,7 +340,7 @@ post '/bootstrapping' do params.merge!( Validation::Util.bootstrapping( params[:dataset_uri], params[:prediction_feature], @subjectid, params[:random_seed], OpenTox::SubTask.create(task,0,33)) ) - v = Validation::Validation.new :validation_type => "bootstrapping", + v = Validation::Validation.create :validation_type => "bootstrapping", :test_target_dataset_uri => params[:dataset_uri], :prediction_feature => params[:prediction_feature], :algorithm_uri => params[:algorithm_uri] @@ -355,8 +355,9 @@ get '/bootstrapping' do LOGGER.info "list all bootstrapping-validations, params: "+params.inspect #uri_list = Validation::Validation.find( :all, :conditions => { :validation_type => "bootstrapping" } ).collect{ |v| v.validation_uri }.join("\n")+"\n" #uri_list = Validation::Validation.all( :validation_type => "bootstrapping" ).collect{ |v| v.validation_uri }.join("\n")+"\n" - params[:validation_type] = "bootstrapping" - uri_list = Lib::DataMapperUtil.all(Validation::Validation,params).collect{ |v| v.validation_uri }.join("\n")+"\n" + #params[:validation_type] = "bootstrapping" + #uri_list = Lib::DataMapperUtil.all(Validation::Validation,params).collect{ |v| v.validation_uri }.join("\n")+"\n" + uri_list = Validation::Validation.find(:validation_type => "bootstrapping").collect{|v| v.validation_uri}.join("\n") + "\n" if request.env['HTTP_ACCEPT'] =~ /text\/html/ related_links = @@ -388,7 +389,7 @@ post '/training_test_split' do params.merge!( Validation::Util.train_test_dataset_split(params[:dataset_uri], params[:prediction_feature], @subjectid, params[:split_ratio], params[:random_seed], OpenTox::SubTask.create(task,0,33))) - v = Validation::Validation.new :validation_type => "training_test_split", + v = Validation::Validation.create :validation_type => "training_test_split", :training_dataset_uri => params[:training_dataset_uri], :test_dataset_uri => params[:test_dataset_uri], :test_target_dataset_uri => params[:dataset_uri], @@ -406,8 +407,9 @@ get '/training_test_split' do LOGGER.info "list all training-test-split-validations, params: "+params.inspect #uri_list = Validation::Validation.find( :all, :conditions => { :validation_type => "training_test_split" } ).collect{ |v| v.validation_uri }.join("\n")+"\n" #uri_list = Validation::Validation.all( :validation_type => "training_test_split" ).collect{ |v| v.validation_uri }.join("\n")+"\n" - params[:validation_type] = "training_test_split" - uri_list = Lib::DataMapperUtil.all(Validation::Validation,params).collect{ |v| v.validation_uri }.join("\n")+"\n" + #params[:validation_type] = "training_test_split" + #uri_list = Lib::DataMapperUtil.all(Validation::Validation,params).collect{ |v| v.validation_uri }.join("\n")+"\n" + uri_list = Validation::Validation.find(:validation_type => "training_test_split").collect{|v| v.validation_uri}.join("\n") + "\n" if request.env['HTTP_ACCEPT'] =~ /text\/html/ related_links = @@ -440,7 +442,7 @@ post '/cleanup/?' do deleted << val.validation_uri #Validation::Validation.delete(val.id) val.subjectid = @subjectid - val.delete + val.delete_validation end LOGGER.info "validation cleanup, deleted "+deleted.size.to_s+" validations" deleted.join("\n")+"\n" @@ -463,7 +465,7 @@ post '/validate_datasets' do params[:validation_type] = "validate_datasets" if params[:model_uri] - v = Validation::Validation.new params + v = Validation::Validation.create params v.subjectid = @subjectid v.compute_validation_stats_with_model(nil,false,task) else @@ -475,7 +477,7 @@ post '/validate_datasets' do predicted_feature = params.delete("predicted_feature") feature_type = "classification" if params.delete("classification")!=nil feature_type = "regression" if params.delete("regression")!=nil - v = Validation::Validation.new params + v = Validation::Validation.create params v.subjectid = @subjectid v.compute_validation_stats(feature_type,predicted_feature,nil,nil,false,task) end @@ -532,7 +534,7 @@ get '/:id' do # rescue ActiveRecord::RecordNotFound => ex # raise OpenTox::NotFoundError.new "Validation '#{params[:id]}' not found." # end - validation = Validation::Validation.get(params[:id]) + validation = Validation::Validation[params[:id]] raise OpenTox::NotFoundError.new "Validation '#{params[:id]}' not found." unless validation case request.env['HTTP_ACCEPT'].to_s @@ -566,5 +568,5 @@ delete '/:id' do validation.subjectid = @subjectid raise OpenTox::NotFoundError.new "Validation '#{params[:id]}' not found." unless validation content_type "text/plain" - validation.delete + validation.delete_validation end
\ No newline at end of file diff --git a/validation/validation_format.rb b/validation/validation_format.rb index f69ceac..6fdea61 100755 --- a/validation/validation_format.rb +++ b/validation/validation_format.rb @@ -4,15 +4,15 @@ require "lib/format_util.rb" module Validation # adding to_yaml and to_rdf functionality to validation - class Validation < Lib::Validation + class Validation # builds hash for valiation, as the internal presentation differs from the owl-object # the hash is directly printed in to_yaml, or added to the owl-structure def get_content_as_hash() h = {} - (Lib::VAL_PROPS - [:validation_uri]).each do |p| - h[p] = self.send(p) + (VAL_PROPS - [:validation_uri]).each do |p| + h[p] = self.send(p.to_s) end if crossvalidation_id!=nil cv = {:type => OT.CrossvalidationInfo} @@ -22,13 +22,14 @@ module Validation h[:crossvalidation_info] = cv end if classification_statistics - raise "classification_statistics is no has: "+classification_statistics.class.to_s unless classification_statistics.is_a?(Hash) + raise "classification_statistics is no hash: "+classification_statistics.class.to_s+" -> '"+ + classification_statistics.to_s+"'" unless classification_statistics.is_a?(Hash) clazz = { :type => OT.ClassificationStatistics } - Lib::VAL_CLASS_PROPS_SINGLE.each{ |p| clazz[p] = classification_statistics[p] } + VAL_CLASS_PROPS_SINGLE.each{ |p| clazz[p] = classification_statistics[p] } # transpose results per class class_values = {} - Lib::VAL_CLASS_PROPS_PER_CLASS.each do |p| + VAL_CLASS_PROPS_PER_CLASS.each do |p| raise "missing classification statitstics: "+p.to_s+" "+classification_statistics.inspect if classification_statistics[p]==nil classification_statistics[p].each do |class_value, property_value| class_values[class_value] = {:class_value => class_value, :type => OT.ClassValueStatistics} unless class_values.has_key?(class_value) @@ -54,7 +55,7 @@ module Validation h[:classification_statistics] = clazz elsif regression_statistics regr = {:type => OT.RegressionStatistics } - Lib::VAL_REGR_PROPS.each{ |p| regr[p] = regression_statistics[p]} + VAL_REGR_PROPS.each{ |p| regr[p] = regression_statistics[p]} h[:regression_statistics] = regr end return h @@ -72,17 +73,17 @@ module Validation end - class Crossvalidation < Lib::Crossvalidation + class Crossvalidation def get_content_as_hash h = {} - (Lib::CROSS_VAL_PROPS_REDUNDANT - [:crossvalidation_uri]).each do |p| + (CROSS_VAL_PROPS_REDUNDANT - [:crossvalidation_uri]).each do |p| h[p] = self.send(p) end v = [] #Validation.find( :all, :conditions => { :crossvalidation_id => self.id } ).each do |val| - Validation.all( :crossvalidation_id => self.id ).each do |val| + Validation.find( :crossvalidation_id => self.id ).each do |val| v.push( val.validation_uri.to_s ) end h[:validation_uris] = v diff --git a/validation/validation_service.rb b/validation/validation_service.rb index a1efba5..dcfb8d7 100755 --- a/validation/validation_service.rb +++ b/validation/validation_service.rb @@ -30,7 +30,7 @@ end module Validation - class Validation < Lib::Validation + class Validation # constructs a validation object, Rsets id und uri #def initialize( params={} ) @@ -43,7 +43,7 @@ module Validation # deletes a validation # PENDING: model and referenced datasets are deleted as well, keep it that way? - def delete( delete_all=true ) + def delete_validation( delete_all=true ) if (delete_all) to_delete = [:model_uri, :training_dataset_uri, :test_dataset_uri, :test_target_dataset_uri, :prediction_dataset_uri ] case self.validation_type @@ -72,7 +72,7 @@ module Validation end end end - self.destroy + self.delete if (subjectid) begin res = OpenTox::Authorization.delete_policies_from_uri(validation_uri, subjectid) @@ -222,17 +222,13 @@ module Validation # :percent_unpredicted => prediction.percent_unpredicted, # :finished => true} # self.save! - self.attributes= {:num_instances => prediction.num_instances, + self.update :num_instances => prediction.num_instances, :num_without_class => prediction.num_without_class, :percent_without_class => prediction.percent_without_class, :num_unpredicted => prediction.num_unpredicted, :percent_unpredicted => prediction.percent_unpredicted, - :finished => true} - begin - self.save - rescue DataMapper::SaveFailureError => e - raise "could not save validation: "+e.resource.errors.inspect - end + :finished => true + raise unless self.valid? end task.progress(100) if task @@ -240,7 +236,7 @@ module Validation end end - class Crossvalidation < Lib::Crossvalidation + class Crossvalidation # constructs a crossvalidation, id and uri are set #def initialize( params={} ) @@ -262,12 +258,12 @@ module Validation end # deletes a crossvalidation, all validations are deleted as well - def delete - Validation.all(:crossvalidation_id => self.id).each do |v| + def delete_crossvalidation + Validation.find(:crossvalidation_id => self.id).each do |v| v.subjectid = self.subjectid - v.delete + v.delete_validation end - self.destroy + self.delete if (subjectid) begin res = OpenTox::Authorization.delete_policies_from_uri(crossvalidation_uri, subjectid) @@ -281,6 +277,9 @@ module Validation # creates the cv folds def create_cv_datasets( prediction_feature, task=nil ) + self.random_seed = 1 unless self.random_seed + self.num_folds = 10 unless self.num_folds + self.stratified = false unless self.stratified if copy_cv_datasets( prediction_feature ) # dataset folds of a previous crossvalidaiton could be used task.progress(100) if task @@ -296,7 +295,7 @@ module Validation i = 0 task_step = 100 / self.num_folds.to_f; @tmp_validations.each do | val | - validation = Validation.new val + validation = Validation.create val validation.subjectid = self.subjectid validation.validate_algorithm( algorithm_params, OpenTox::SubTask.create(task, i * task_step, ( i + 1 ) * task_step) ) @@ -316,8 +315,7 @@ module Validation # copies datasets from an older crossvalidation on the same dataset and the same folds # returns true if successfull, false otherwise def copy_cv_datasets( prediction_feature ) - - cvs = Crossvalidation.all( { + cvs = Crossvalidation.find( { :dataset_uri => self.dataset_uri, :num_folds => self.num_folds, :stratified => self.stratified, @@ -326,13 +324,13 @@ module Validation cvs.each do |cv| next if AA_SERVER and !OpenTox::Authorization.authorized?(cv.crossvalidation_uri,"GET",self.subjectid) tmp_val = [] - Validation.all( :crossvalidation_id => cv.id ).each do |v| + Validation.find( :crossvalidation_id => cv.id ).each do |v| break unless v.prediction_feature == prediction_feature and OpenTox::Dataset.exist?(v.training_dataset_uri,self.subjectid) and OpenTox::Dataset.exist?(v.test_dataset_uri,self.subjectid) #make sure self.id is set - self.save if self.new? + #self.save if self.new? tmp_val << { :validation_type => "crossvalidation", :training_dataset_uri => v.training_dataset_uri, :test_dataset_uri => v.test_dataset_uri, @@ -342,7 +340,7 @@ module Validation :prediction_feature => prediction_feature, :algorithm_uri => self.algorithm_uri } end - if tmp_val.size == self.num_folds + if tmp_val.size == self.num_folds.to_i @tmp_validations = tmp_val LOGGER.debug "copied dataset uris from cv "+cv.crossvalidation_uri.to_s #+":\n"+tmp_val.inspect return true @@ -354,23 +352,22 @@ module Validation # creates cv folds (training and testdatasets) # stores uris in validation objects def create_new_cv_datasets( prediction_feature, task = nil ) - - raise "random seed not set "+self.inspect unless self.random_seed LOGGER.debug "creating datasets for crossvalidation" orig_dataset = OpenTox::Dataset.find(self.dataset_uri,self.subjectid) raise OpenTox::NotFoundError.new "Dataset not found: "+self.dataset_uri.to_s unless orig_dataset shuffled_compounds = orig_dataset.compounds.shuffle( self.random_seed ) - unless self.stratified - split_compounds = shuffled_compounds.chunk( self.num_folds ) + unless self.stratified + split_compounds = shuffled_compounds.chunk( self.num_folds.to_i ) else class_compounds = {} # "inactive" => compounds[], "active" => compounds[] .. - shuffled_compounds.each do |c| - orig_dataset.features(c).each do |a| - value = OpenTox::Feature.new(:uri => a.uri).value(prediction_feature).to_s - class_compounds[value] = [] unless class_compounds.has_key?(value) - class_compounds[value].push(c) + accept_values = orig_dataset.features[prediction_feature][OT.acceptValue] + accept_values.each do |value| + class_compounds[value] = [] + shuffled_compounds.each do |c| + #PENDING accept values are type string, data_entries may be boolean + class_compounds[value] << c if orig_dataset.data_entries[c][prediction_feature].collect{|v| v.to_s}.include?(value) end end LOGGER.debug "stratified cv: different class values: "+class_compounds.keys.join(", ") @@ -378,7 +375,7 @@ module Validation split_class_compounds = [] # inactive_compounds[fold_i][], active_compounds[fold_i][], .. class_compounds.values.each do |compounds| - split_class_compounds.push( compounds.chunk( self.num_folds ) ) + split_class_compounds << compounds.chunk( self.num_folds.to_i ) end LOGGER.debug "stratified cv: splits for class values: "+split_class_compounds.collect{ |c| c.collect{ |cc| cc.size }.join("/") }.join(", ") @@ -389,7 +386,7 @@ module Validation # step 1: sort current split in ascending order split_comp.sort!{|x,y| x.size <=> y.size } # step 2: add splits - (0..self.num_folds-1).each do |i| + (0..self.num_folds.to_i-1).each do |i| unless split_compounds[i] split_compounds[i] = split_comp[i] else @@ -406,7 +403,7 @@ module Validation @tmp_validations = [] - (1..self.num_folds).each do |n| + (1..self.num_folds.to_i).each do |n| datasetname = 'cv'+self.id.to_s + #'_d'+orig_dataset.name.to_s + @@ -418,7 +415,7 @@ module Validation test_compounds = [] train_compounds = [] - (1..self.num_folds).each do |nn| + (1..self.num_folds.to_i).each do |nn| compounds = split_compounds.at(nn-1) if n == nn @@ -428,8 +425,9 @@ module Validation end end - raise "internal error, num test compounds not correct" unless (shuffled_compounds.size/self.num_folds - test_compounds.size).abs <= 1 - raise "internal error, num train compounds not correct" unless shuffled_compounds.size - test_compounds.size == train_compounds.size + raise "internal error, num test compounds not correct" unless (shuffled_compounds.size/self.num_folds.to_i - test_compounds.size).abs <= 1 + raise "internal error, num train compounds not correct, should be '"+(shuffled_compounds.size-test_compounds.size).to_s+ + "', is '"+train_compounds.size.to_s+"'" unless shuffled_compounds.size - test_compounds.size == train_compounds.size LOGGER.debug "training set: "+datasetname+"_train, compounds: "+train_compounds.size.to_s #train_dataset_uri = orig_dataset.create_new_dataset( train_compounds, orig_dataset.features, datasetname + '_train', source ) @@ -442,7 +440,7 @@ module Validation { DC.title => datasetname + '_test', DC.creator => source }, self.subjectid ).uri #make sure self.id is set - self.save if self.new? + #self.save if self.new? tmp_validation = { :validation_type => "crossvalidation", :training_dataset_uri => train_dataset_uri, :test_dataset_uri => test_dataset_uri, @@ -551,9 +549,10 @@ module Validation # splits a dataset into test and training dataset # returns map with training_dataset_uri and test_dataset_uri def self.train_test_dataset_split( orig_dataset_uri, prediction_feature, subjectid, split_ratio=nil, random_seed=nil, task=nil ) - split_ratio=0.67 unless split_ratio + split_ratio = split_ratio.to_f random_seed=1 unless random_seed + random_seed = random_seed.to_i orig_dataset = OpenTox::Dataset.find orig_dataset_uri, subjectid orig_dataset.load_all subjectid diff --git a/validation/validation_test.rb b/validation/validation_test.rb index ffb25c4..efa8ad5 100755 --- a/validation/validation_test.rb +++ b/validation/validation_test.rb @@ -184,13 +184,13 @@ class ValidationTest < Test::Unit::TestCase #ambit_service = "https://ambit.uni-plovdiv.bg:8443/ambit2" #https%3A%2F%2Fambit.uni-plovdiv.bg%3A8443%2Fambit2 - + # post "/validate_datasets",{ -# :test_dataset_uri=>ambit_service+"/dataset/R401577?max=50", -# :prediction_dataset_uri=>ambit_service+"/dataset/R401577?max=50&feature_uris[]="+CGI.escape(ambit_service)+"%2Fmodel%2F35194%2Fpredicted", -# #:test_target_dataset_uri=>ambit_service+"/dataset/R401560", -# :prediction_feature=>ambit_service+"/feature/26221", -# :predicted_feature=>ambit_service+"/feature/218699", +# :test_dataset_uri=>"http://local-ot/dataset/94", +# :prediction_dataset_uri=>'http://local-ot/dataset/96', +# :test_target_dataset_uri=>'http://local-ot/dataset/92', +# :prediction_feature=>'http://local-ot/dataset/92/feature/Hamster%20Carcinogenicity', +# :predicted_feature=>"", # :classification=>"true", # :subjectid=>SUBJECTID} # #:model_uri=>"http://local-ot/model/31"} @@ -199,8 +199,8 @@ class ValidationTest < Test::Unit::TestCase # uri = last_response.body # val = wait_for_task(uri) # puts val -# #get "/"+val.split("/")[-1] - +# get "/"+val.split("/")[-1] +# puts last_response.body # d = OpenTox::Dataset.find("https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/R545",SUBJECTID) # puts d.compounds.inspect @@ -257,7 +257,9 @@ class ValidationTest < Test::Unit::TestCase #delete "/1",:subjectid=>SUBJECTID - run_test("19i") + prepare_examples() + + #run_test("1a") #,{:validation_uri => "http://local-ot/validation/crossvalidation/1"}) #run_test("3a","http://local-ot/validation/crossvalidation/4") #run_test("3b","http://local-ot/validation/crossvalidation/3") |