From 6e9d20a1417ad2f4548194d226f6b3f2b3c47036 Mon Sep 17 00:00:00 2001 From: root Date: Thu, 3 Mar 2011 12:16:51 +0000 Subject: contradicting multiple measurements ignored --- lib/ot_predictions.rb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/lib/ot_predictions.rb b/lib/ot_predictions.rb index eb80205..f812854 100755 --- a/lib/ot_predictions.rb +++ b/lib/ot_predictions.rb @@ -162,8 +162,12 @@ module Lib raise "no array "+v.class.to_s+" : '"+v.to_s+"'" unless v.is_a?(Array) if v.size>1 v.uniq! - raise "not yet implemented: multiple non-equal values "+compound.to_s+" "+v.inspect if v.size>1 - v = v[0] + if v.size>1 + v = nil + LOGGER.warn "not yet implemented: multiple non-equal values "+compound.to_s+" "+v.inspect + else + v = v[0] + end elsif v.size==1 v = v[0] else -- cgit v1.2.3 From d0dbdc711cddff823db456136a2604ab1912ee53 Mon Sep 17 00:00:00 2001 From: root Date: Thu, 3 Mar 2011 12:36:10 +0000 Subject: remaining merge conflicts removed --- application.rb | 8 +++++ db/migrate/000_drop_validations.rb | 13 -------- db/migrate/001_init_validation.rb | 65 -------------------------------------- db/migrate/002_init_reports.rb | 36 --------------------- example.rb | 39 ----------------------- report/report_test.rb | 2 +- test/test_examples.rb | 8 ----- test/test_examples_util.rb | 8 ----- 8 files changed, 9 insertions(+), 170 deletions(-) delete mode 100755 db/migrate/000_drop_validations.rb delete mode 100755 db/migrate/001_init_validation.rb delete mode 100755 db/migrate/002_init_reports.rb diff --git a/application.rb b/application.rb index f543167..ad9653a 100755 --- a/application.rb +++ b/application.rb @@ -3,6 +3,14 @@ gem "opentox-ruby", "~> 0" [ 'sinatra', 'sinatra/url_for', 'opentox-ruby' ].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) diff --git a/db/migrate/000_drop_validations.rb b/db/migrate/000_drop_validations.rb deleted file mode 100755 index fb70967..0000000 --- a/db/migrate/000_drop_validations.rb +++ /dev/null @@ -1,13 +0,0 @@ - -class DropValidations < ActiveRecord::Migration - def self.up - # drop_table :validations if table_exists? :validations - # drop_table :crossvalidations if table_exists? :crossvalidations - end - - def self.down - #drop_table :validations if table_exists? :validations - #drop_table :crossvalidations if table_exists? :crossvalidations - end -end - diff --git a/db/migrate/001_init_validation.rb b/db/migrate/001_init_validation.rb deleted file mode 100755 index 2189568..0000000 --- a/db/migrate/001_init_validation.rb +++ /dev/null @@ -1,65 +0,0 @@ - -class InitValidation < ActiveRecord::Migration - def self.up - - create_table :crossvalidations do |t| - - [:algorithm_uri, - :dataset_uri ].each do |p| - t.column p, :string, :limit => 255 - end - - [:created_at ].each do |p| - t.column p, :datetime - end - - [:num_folds, - :random_seed ].each do |p| - t.column p, :integer, :null => false - end - - [ :stratified, :finished ].each do |p| - t.column p, :boolean, :null => false - end - end - - create_table :validations do |t| - - [:validation_type, - :model_uri, - :algorithm_uri, - :training_dataset_uri, - :test_target_dataset_uri, - :test_dataset_uri, - :prediction_dataset_uri, - :prediction_feature].each do |p| - t.column p, :string, :limit => 255 - end - - [:created_at ].each do |p| - t.column p, :datetime - end - - [:real_runtime, :num_instances, :num_without_class, :num_unpredicted, :crossvalidation_id, :crossvalidation_fold ].each do |p| - t.column p, :integer - end - - [:real_runtime, :percent_without_class, :percent_unpredicted ].each do |p| - t.column p, :float - end - - [:classification_statistics, :regression_statistics].each do |p| - t.column(p, :text, :limit => 16320) - end - - [ :finished ].each do |p| - t.column p, :boolean, :null => false - end - end - end - - def self.down - drop_table :validations if table_exists? :validations - drop_table :crossvalidations if table_exists? :crossvalidations - end -end diff --git a/db/migrate/002_init_reports.rb b/db/migrate/002_init_reports.rb deleted file mode 100755 index dcf44a1..0000000 --- a/db/migrate/002_init_reports.rb +++ /dev/null @@ -1,36 +0,0 @@ - -class InitReports < ActiveRecord::Migration - def self.up - - create_table :report_datum do |t| - - [:report_uri, - :report_type - ].each do |p| - t.column p, :string, :limit => 255 - end - - [:created_at ].each do |p| - t.column p, :datetime - end - - [:validation_uris, :crossvalidation_uris, :model_uris, :algorithm_uris].each do |p| - t.column(p, :text, :limit => 16320) - end - end - end - - def self.down - drop_table :report_datum if table_exists? :report_datum - if CONFIG[:reports] and CONFIG[:reports][:report_dir] - ["validation", "crossvalidation", "algorithm_comparison"].each do |t| - dir = File.join(CONFIG[:reports][:report_dir],t) - if File.exist?(dir) - puts "deleting dir "+dir.to_s - FileUtils.rm_rf(dir) - end - end - end - end -end - diff --git a/example.rb b/example.rb index c691375..07151a8 100755 --- a/example.rb +++ b/example.rb @@ -58,44 +58,6 @@ class Example #TODO subjectid = nil -<<<<<<< HEAD - #delete_all(CONFIG[:services]["opentox-dataset"]) - log OpenTox::RestClientWrapper.delete CONFIG[:services]["opentox-dataset"] - - log "upload dataset" - 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") - - log "train-test-validation" - #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) - v = Validation::Validation.new :training_dataset_uri => split_params[:training_dataset_uri], - :test_dataset_uri => split_params[:test_dataset_uri], - :test_target_dataset_uri => data_uri, - :prediction_feature => URI.decode(@@feature), - :algorithm_uri => @@alg - v.validate_algorithm( @@alg_params ) - - log "crossvalidation" - cv = Validation::Crossvalidation.new({ :dataset_uri => data_uri, :algorithm_uri => @@alg, :num_folds => 5, :stratified => false }) - cv.create_cv_datasets( URI.decode(@@feature) ) - cv.perform_cv( @@alg_params ) - - log "create validation report" - rep = Reports::ReportService.new(File.join(CONFIG[:services]["opentox-validation"],"report")) - rep.delete_all_reports("validation") - rep.create_report("validation",v.validation_uri) - - log "create crossvalidation report" - rep.delete_all_reports("crossvalidation") - rep.create_report("crossvalidation",cv.crossvalidation_uri) - - log "done" - @@summary -======= task = OpenTox::Task.create("prepare examples", "n/a") do |task| @@summary = "" #delete validations @@ -163,7 +125,6 @@ class Example @@summary end return_task(task) ->>>>>>> mguetlein/test end # performs all curl calls listed in examples after ">>>", next line is added if line ends with "\" diff --git a/report/report_test.rb b/report/report_test.rb index 57e867b..571d6d8 100755 --- a/report/report_test.rb +++ b/report/report_test.rb @@ -344,4 +344,4 @@ end # # end # -#end +#end \ No newline at end of file diff --git a/test/test_examples.rb b/test/test_examples.rb index 9476ed7..3c6f00e 100755 --- a/test/test_examples.rb +++ b/test/test_examples.rb @@ -188,11 +188,7 @@ module ValidationExamples class LazarHamsterTrainingTest < HamsterTrainingTest def initialize @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") -<<<<<<< HEAD - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer") -======= @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") ->>>>>>> mguetlein/test super end end @@ -220,11 +216,7 @@ module ValidationExamples class LazarHamsterCrossvalidation < HamsterCrossvalidation def initialize @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") -<<<<<<< HEAD - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer") -======= @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") ->>>>>>> mguetlein/test super end end diff --git a/test/test_examples_util.rb b/test/test_examples_util.rb index 56bee6b..a5f2867 100755 --- a/test/test_examples_util.rb +++ b/test/test_examples_util.rb @@ -66,11 +66,7 @@ module ValidationExamples $test_case.post uri,params return wait($test_case.last_response.body) else -<<<<<<< HEAD - return OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],uri),params) -======= return OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],uri),params,nil,waiting_task).to_s ->>>>>>> mguetlein/test end end @@ -93,11 +89,7 @@ module ValidationExamples $test_case.delete uri,{:subjectid => SUBJECTID},'HTTP_ACCEPT' => accept_header return wait($test_case.last_response.body) else -<<<<<<< HEAD - return OpenTox::RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"],uri),{:accept => accept_header}) -======= return OpenTox::RestClientWrapper.delete(File.join(CONFIG[:services]["opentox-validation"],uri),{:accept => accept_header,:subjectid => SUBJECTID}) ->>>>>>> mguetlein/test end end -- cgit v1.2.3