diff options
| author | martin <martin@virtual-machine.(none)> | 2012-12-06 17:22:06 +0100 |
|---|---|---|
| committer | martin <martin@virtual-machine.(none)> | 2012-12-06 17:22:06 +0100 |
| commit | 46761d137dc470c6a4ab6b573bd99713a95103d2 (patch) | |
| tree | e50e09daa2b9dd3b12d63b98c32426d6ffb471ed | |
| parent | e4f366398bfbeb8c961183412a15f92923a4e0ae (diff) | |
first step towards new architecture (4store)
37 files changed, 414 insertions, 3419 deletions
@@ -8,3 +8,7 @@ reports public/server.log nightly/nightly_report.html nightly/nightly_report.xml +Gemfile.lock +redis-2.4.4 +redis-2.4.4 redis-2.4.4.tar.gz +redis-2.4.4.tar.gz diff --git a/EXAMPLES b/EXAMPLES deleted file mode 100755 index a27e33b..0000000 --- a/EXAMPLES +++ /dev/null @@ -1,341 +0,0 @@ -API-Definition -=================================================================== - -see http://opentox.org/dev/apis/api-1.1/Validation - - -API-Examples Validation -=================================================================== - -how to -------------------------------------------------------------------- -the examples listed below can be performed with the command line tool curl - - -get list of available validations -------------------------------------------------------------------- - ->>> curl <validation_service> - -result example (accept-header: application/rdf+xml) -<<< not yet supported - -result example (accept-header: text/uri-list) -<<< <validation_service>/<validation_id> -<<< <validation_service>/validation_id_i -<<< <validation_service>/validation_id_j - - -get validation -------------------------------------------------------------------- - ->>> curl <validation_service>/<validation_id> - -supported accept-headers: "text/x-yaml" and "application/rdf+xml" - - -validate model on test-dateset -------------------------------------------------------------------- - ->>> curl -X POST -d model_uri="<model_uri>" \ - -d test_dataset_uri="<test_dataset_uri>" \ - -d test_target_dataset_uri="<dataset_uri>" \ - <validation_service>/test_set_validation - -optional params: -test_target_dataset_uri, default is test_dataset_uri - -result example (accept-header: application/rdf+xml) -<<< not yet supported - -result example (accept-header: text/uri-list) -<<< <validation_service>/id_i - - -validate an algorithm on a training- and test-dataset -------------------------------------------------------------------- - ->>> curl -X POST -d algorithm_uri="<algorithm_uri>" \ - -d training_dataset_uri="<training_dataset_uri>" \ - -d test_dataset_uri="<test_dataset_uri>" \ - -d test_target_dataset_uri="<dataset_uri>" \ - -d prediction_feature="<prediction_feature>" \ - -d algorithm_params="<algorithm_params>" \ - <validation_service>/training_test_validation - -optional params: -algorithm_params, default is empty -test_target_dataset_uri, default is test_dataset_uri - -result example (accept-header: application/rdf+xml) -<<< not yet supported - -result example (accept-header: text/uri-list) -<<< <validation_service>/id_i - - -validate an algorithm on a dataset via training-test-split -------------------------------------------------------------------- - ->>> curl -X POST -d algorithm_uri="<algorithm_uri>" \ - -d dataset_uri="<dataset_uri>" \ - -d prediction_feature="<prediction_feature>" \ - -d algorithm_params="<algorithm_params>" \ - -d split_ratio=0.9 \ - -d random_seed=2 \ - <validation_service>/training_test_split - -optional params: -algorithm_params, default is empty -split_ratio, default is 0.67 -random_seed, default is 1 - -result example (accept-header: application/rdf+xml) -<<< not yet supported - -result example (accept-header: text/uri-list) -<<< <validation_service>/id_i - - -validate an algorithm on a dataset via bootstrapping -------------------------------------------------------------------- - ->>> curl -X POST -d algorithm_uri="<algorithm_uri>" \ - -d dataset_uri="<dataset_uri>" \ - -d prediction_feature="<prediction_feature>" \ - -d algorithm_params="<algorithm_params>" \ - -d random_seed=2 \ - <validation_service>/bootstrapping - -optional params: -algorithm_params, default is empty -random_seed, default is 1 - -result example (accept-header: application/rdf+xml) -<<< not yet supported - -result example (accept-header: text/uri-list) -<<< <validation_service>/id_i - - -get list of available crossvalidations -------------------------------------------------------------------- - ->>> curl <validation_service>/crossvalidation - -result example (accept-header: application/rdf+xml) -<<< not yet supported - -result example (accept-header: text/uri-list) -<<< <validation_service>/crossvalidation/<crossvalidation_id> -<<< <validation_service>/crossvalidation/crossvalidation_id_i -<<< <validation_service>/crossvalidation/crossvalidation_id_j - - -get crossvalidation -------------------------------------------------------------------- - ->>> curl <validation_service>/crossvalidation/<crossvalidation_id> - -supported accept-headers: "text/x-yaml" and "application/rdf+xml" - - -validate an algorithm on a dataset via crossvalidation -(may take a couple of minutes) -------------------------------------------------------------------- - ->>> curl -X POST -d algorithm_uri="<algorithm_uri>" \ - -d dataset_uri="<dataset_uri>" \ - -d prediction_feature="<prediction_feature>" \ - -d algorithm_params="<algorithm_params>" \ - -d num_folds=5 \ - -d random_seed=2 \ - -d stratified=false \ - <validation_service>/crossvalidation - -optional params: -algorithm_params, default is empty -num_folds, default is 10 -random_seed, default is 1 -stratified, default is false - -result example (accept-header: application/rdf+xml) -<<< not yet supported - -result example (accept-header: text/uri-list) -<<< <validation_service>/crossvalidation/id_i - - - -API-Examples Reports -=================================================================== - - -get list of available report types -------------------------------------------------------------------- - ->>> curl <validation_service>/report - -result example (accept-header: application/rdf+xml) -<<< not yet supported - -result example (accept-header: text/uri-list) -<<< <validation_service>/report/validation -<<< <validation_service>/report/crossvalidation -<<< <validation_service>/report/algorithm_comparison - - -get list of available reports of type validation -------------------------------------------------------------------- - ->>> curl <validation_service>/report/validation - -result example (accept-header: application/rdf+xml) -<<< not yet supported - -result example (accept-header: text/uri-list) -<<< <validation_service>/report/validation/<validation_report_id> -<<< <validation_service>/report/validation/id_i -<<< <validation_service>/report/validation/id_j - - -get validation report -------------------------------------------------------------------- - ->>> curl <validation_service>/report/validation/<validation_report_id> - -Supported formats (accept-headers): -* "text/xml" content of report in docbook-article format -* "text/html" report formated with default docbook-article-xsl -* "text/x-yaml" returns report object with meta-info (without the actual report content) -* "application/rdf+xml" returns report object with meta-info (without the actual report content) - -Hint: Visit <validation_service>/report/validation/<validation_report_id> with a browser to see the report in html format - - -create validation report from validation -------------------------------------------------------------------- - ->>> curl -X POST -d validation_uris="<validation_service>/<validation_id>" \ - <validation_service>/report/validation - -result example (accept-header: application/rdf+xml) -<<< not yet supported - -result example (accept-header: text/uri-list) -<<< <validation_service>/report/validation/id_i - - -get list of available reports of type crossvalidation -------------------------------------------------------------------- - ->>> curl <validation_service>/report/crossvalidation - -result example (accept-header: application/rdf+xml) -<<< not yet supported - -result example (accept-header: text/uri-list) -<<< <validation_service>/report/crossvalidation/<crossvalidation_report_id> -<<< <validation_service>/report/crossvalidation/id_i -<<< <validation_service>/report/crossvalidation/id_j - - -get crossvalidation report -------------------------------------------------------------------- - ->>> curl <validation_service>/report/crossvalidation/<crossvalidation_report_id> - -Supported formats (accept-headers): -* "text/xml" content of report in docbook-article format -* "text/html" report formated with default docbook-article-xsl -* "text/x-yaml" returns report object with meta-info (without the actual report content) -* "application/rdf+xml" returns report object with meta-info (without the actual report content) - -Hint: Visit <validation_service>/report/crossvalidation/<crossvalidation_report_id> with a browser to see the report in html format - - -create crossvalidation report from crossvalidation -------------------------------------------------------------------- - ->>> curl -X POST -d validation_uris="<validation_service>/crossvalidation/<crossvalidation_id>" \ - <validation_service>/report/crossvalidation - -result example (accept-header: application/rdf+xml) -<<< not yet supported - -result example (accept-header: text/uri-list) -<<< <validation_service>/report/crossvalidation/id_i - - -manually format html report -------------------------------------------------------------------- - ->>> curl -X POST -d css_style_sheet=<css_file> \ - <validation_service>/report/crossvalidation/<crossvalidation_report_id>/format_html - -This explicity invokes the report convertion to html, with css-style-sheet as parameter. - -result example (accept-header: application/rdf+xml) -<<< not yet supported - -result example (accept-header: text/uri-list) -<<< <validation_service>/report/crossvalidation/id_i - - - -Filter resources -=================================================================== - -It is possible to filter the list of available resources (i.e. validations, crossvalidation, reports) according to property-values. - - -filter available validations for a particular training dataset and model -------------------------------------------------------------------- - ->>> curl <validation_service>?trainingDataset=<training_dataset_uri>\&model=<model_uri> - -alternatively, use property names in (internal) yaml format: - ->>> curl <validation_service>?training_dataset_uri=<training_dataset_uri>\&model_uri=<model_uri> - - -search available validation report for a particular algorithm -------------------------------------------------------------------- - ->>> curl <validation_service>/report/validation?algorithm=lazar - -alternatively, use property names in (internal) yaml format: - ->>> curl <validation_service>/report/validation?algorithm_uris=lazar - - - -Reach reporting -=================================================================== - - -get list of available qmrf report -------------------------------------------------------------------- - ->>> curl <validation_service>/reach_report/qmrf - -result example (accept-header: application/rdf+xml) -<<< not yet supported - -result example (accept-header: text/uri-list) -<<< <validation_service>/reach_report/qmrf/<qmrf_id> -<<< <validation_service>/reach_report/qmrf/report_id_i -<<< <validation_service>/reach_report/qmrf/report_id_j - - -create a QMRF from a model -------------------------------------------------------------------- - ->>> curl -X POST -d model_uri="<model_uri>" \ - <validation_service>/reach_report/qmrf - -result example (accept-header: application/rdf+xml) -<<< not yet supported - -result example (accept-header: text/uri-list) -<<< <validation_service>/reach_report/qmrf/id
\ No newline at end of file @@ -0,0 +1,8 @@ +source :gemcutter +gemspec +gem "opentox-server", :path => "../opentox-server" +gem "opentox-client", :path => "../opentox-client" +gem "emk-sinatra-url-for", "~>0.2.1" +gem "ruby-plot", "~>0.6.0" +gem "ohm", "=0.1.3" +gem "ohm-contrib", "=0.1.1"
\ No newline at end of file @@ -1,61 +1 @@ -require 'rubygems' -require 'rake' - -desc "Perform unit tests" -task :test do - require 'test/unit_test.rb' -end - -=begin - -desc "Installs gems and inits db migration" -task :init => [:install_gems, :migrate] do - #do nothing -end - - -desc "load config" -task :load_config do - require 'yaml' - ENV['RACK_ENV'] = 'production' unless ENV['RACK_ENV'] - basedir = File.join(ENV['HOME'], ".opentox") - config_dir = File.join(basedir, "config") - config_file = File.join(config_dir, "#{ENV['RACK_ENV']}.yaml") - if File.exist?(config_file) - CONFIG = YAML.load_file(config_file) - raise "could not load config, config file: "+config_file.to_s unless CONFIG - end - puts "config loaded" -end - -# USE VERSION 0 instead -#desc "Clear database" -#task :clear_db => :load_config do -# if CONFIG[:database][:adapter]=="mysql" -# clear = nil -# IO.popen("locate clear_mysql.sh"){ |f| clear=f.gets.chomp("\n") } -# raise "clear_mysql.sh not found" unless clear -# cmd = clear+" "+CONFIG[:database][:username]+" "+CONFIG[:database][:password]+" "+CONFIG[:database][:database] -# IO.popen(cmd){ |f| puts f.gets } -# else -# raise "clear not implemented for database-type: "+CONFIG[:database][:adapter] -# end -#end - -desc "Migrate the database through scripts in db/migrate. Target specific version with VERSION=x" -task :migrate => :load_config do - [ 'rubygems', 'active_record', 'logger' ].each{ |l| require l } - puts "database config: "+@@config[:database].inspect.to_s - ActiveRecord::Base.establish_connection( - :adapter => CONFIG[:database][:adapter], - :host => CONFIG[:database][:host], - :database => CONFIG[:database][:database], - :username => CONFIG[:database][:username], - :password => CONFIG[:database][:password] - ) - ActiveRecord::Base.logger = Logger.new($stdout) - ActiveRecord::Migrator.migrate('db/migrate', ENV["VERSION"] ? ENV["VERSION"].to_i : 2 ) -end - -=end - +require "bundler/gem_tasks" @@ -0,0 +1 @@ +1.0.0 diff --git a/application.rb b/application.rb index 10c8fe6..67771f9 100755 --- a/application.rb +++ b/application.rb @@ -1,53 +1,22 @@ require 'rubygems' -gem "opentox-ruby" -[ 'sinatra', 'sinatra/url_for', 'opentox-ruby', 'benchmark' ].each do |lib| +#gem "opentox-ruby" +[ 'sinatra', 'sinatra/url_for', 'ohm', 'benchmark' ].each do |lib| require lib end +class Sinatra::Base + helpers Sinatra::UrlForHelper +end + #unless(defined? LOGGER) #LOGGER = Logger.new(STDOUT) #LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S " #end -#require "error_application.rb" - -require "example.rb" - - -get '/examples/?' do - LOGGER.info "list examples" - - if request.env['HTTP_ACCEPT'] =~ /text\/html/ - content_type "text/html" - OpenTox.text_to_html Example.transform_example,@subjectid - else - content_type "text/plain" - Example.transform_example - end -end - -get '/prepare_examples/?' do - LOGGER.info "prepare examples" - content_type "text/plain" - return_task(Example.prepare_example_resources) -end - -post '/test_examples/?' do - examples = params[:examples] - LOGGER.info "test examples "+examples.to_s - content_type "text/plain" - Example.test_examples(examples) -end - -require "test/test_application.rb" -require "nightly/nightly_application.rb" - -# order is important, first add example methods and reports, than validation -# (otherwise sinatra will try to locate a validation with name examples or report) - -require "report/report_application.rb" -require "reach_reports/reach_application.rb" -require "validation/validation_application.rb" +require "./test/test_application.rb" +require "./report/report_application.rb" +#require "./reach_reports/reach_application.rb" +require "./validation/validation_application.rb" diff --git a/bin/validation-install b/bin/validation-install new file mode 100755 index 0000000..0953c63 --- /dev/null +++ b/bin/validation-install @@ -0,0 +1,127 @@ +#!/bin/sh + +# Installs Opentox Webservice. +# Author: Christoph Helma, Andreas Maunz, Martin Gütlein + +SELF=$(basename $0 -install) +[ "`id -u`" = "0" ] && echo "This script must be run as non-root." 1>&2 && exit 1 + +SILENT=false +if [ -n "$1" ] +then + if [ "$1" = "silent" ] + then + SILENT=true + fi +fi + +if [ $SILENT = false ]; then + echo + echo "Welcome to service installation (<Return> to continue)." + read delete_me +fi + +# check wd is root of service +DIR=`pwd` +if echo $DIR | grep "$SELF/bin" >/dev/null 2>&1 ; then cd ..; fi +SELF_DIR=`pwd` + + +# # # Boot the script + +# load base config, helper funs, environment +OT_CONFIG_DIR="$HOME/.opentox" +! [ -f "$OT_CONFIG_DIR/config/install/config.sh" ] && echo "config.sh not found." 1>&2 && exit 1 || . $OT_CONFIG_DIR/config/install/config.sh +! [ -f "$OT_PREFIX/install/utils.sh" ] && echo "utils.sh not found." 1>&2 && exit 1 || . $OT_PREFIX/install/utils.sh +[ -f $OT_CONFIG_DIR/opentox-ui.sh ] && . $OT_CONFIG_DIR/opentox-ui.sh # should have been done by user already +RUBY_DIR="$HOME/.rbenv/versions/$RUBY_NUM_VER" + + +# # # Install + +check_utils "rbenv find" +check_log $SELF + +if [ "$OT_BRANCH" = "development" ]; then + cmd="test -d $OT_PREFIX/opentox-server" && run_cmd "$cmd" "Opentox-server" + cmd="test -d $OT_PREFIX/opentox-client" && run_cmd "$cmd" "Opentox-client" +fi + + +# log directory for this service +[ -d $OT_CONFIG_DIR/config/$SELF ] || cmd="mkdir -p $OT_CONFIG_DIR/config/$SELF" && run_cmd "$cmd" "Config directory" + +# Adjust ruby version here! +RUBY_NUM_VER="1.9.3-p194" + +# ruby +install_ruby + +# self +echo +install_with_bundler + +# config +[ -f $OT_CONFIG_DIR/config/$SELF.rb ] || touch $OT_CONFIG_DIR/config/$SELF.rb +if ! cat "$OT_CONFIG_DIR/config/$SELF.rb" | grep "four_store">/dev/null 2>&1; then echo '$four_store = { :uri => "http://localhost:9088", :user => "", :password => "" }' >> $OT_CONFIG_DIR/config/$SELF.rb; fi +if ! cat "$OT_CONFIG_DIR/config/$SELF.rb" | grep "aa">/dev/null 2>&1; then echo '$aa = { :uri => nil }' >> $OT_CONFIG_DIR/config/$SELF.rb; fi +if ! cat "$OT_DEFAULT_CONF" | grep "$SELF">/dev/null 2>&1; then echo '$validation = { :uri => "http://localhost:8087/validation" }' >> $OT_DEFAULT_CONF; fi + +#install redis +WGET="`which wget`" +if [ ! -e "$WGET" ]; then + echo "'wget' missing. Install 'wget' first. Aborting..." + exit 1 +fi +REDIS_VER="2.4.4" +REDIS_DEST="$SELF_DIR/redis-$REDIS_VER" +REDIS_SERVER_CONF="$REDIS_DEST/redis.conf" +LOG="redis-log.txt" +echo +echo "Redis (log: '$LOG', dir: '$REDIS_DEST'):" +REDIS_DONE=false +mkdir "$REDIS_DEST" >/dev/null 2>&1 +if [ ! -d "$REDIS_DEST" ]; then + echo "Install directory '$REDIS_DEST' is not available! Aborting..." + exit 1 +else + if ! rmdir "$REDIS_DEST" >/dev/null 2>&1; then # if not empty this will fail + REDIS_DONE=true + fi +fi +if ! $REDIS_DONE; then + echo "vm.overcommit_memory = 1" | sudo tee -a /etc/sysctl.conf >>$LOG 2>&1 + URI="http://redis.googlecode.com/files/redis-$REDIS_VER.tar.gz" + if ! [ -d "redis-$REDIS_VER" ]; then + cmd="$WGET $URI" && run_cmd "$cmd" "Download" + cmd="tar zxf redis-$REDIS_VER.tar.gz" && run_cmd "$cmd" "Unpack" + fi + cd redis-$REDIS_VER >>$LOG 2>&1 + cmd="make" && run_cmd "$cmd" "Make" + if ! grep "daemonize yes" $REDIS_SERVER_CONF >>$LOG 2>&1 ; then + echo "daemonize yes" > $REDIS_SERVER_CONF 2>$LOG + fi + if ! grep "dir `pwd`" $REDIS_SERVER_CONF >>$LOG 2>&1 ; then + echo "dir `pwd`" >> $REDIS_SERVER_CONF 2>$LOG + fi + if ! grep "save 900 1" $REDIS_SERVER_CONF >>$LOG 2>&1 ; then + echo "save 900 1" >> $REDIS_SERVER_CONF 2>$LOG + fi +else + echo "redis already installed" +fi +if [ ! -f $REDIS_CONF ]; then + echo "if ! echo \"\$PATH\" | grep \"$REDIS_DEST\">/dev/null 2>&1; then export PATH=$REDIS_DEST/src:\$PATH; fi" >> "$REDIS_CONF" + echo "Redis configuration has been stored in '$REDIS_CONF'." + #if ! grep ". \"$REDIS_CONF\"" $OT_UI_CONF; then + # echo ". \"$REDIS_CONF\"" >> $OT_UI_CONF + #fi +fi + + +if [ $SILENT = false ]; then + notify +fi + +# return to wd +cd "$DIR" @@ -1,7 +1,5 @@ -require 'rubygems' -require 'sinatra' -require 'application.rb' -require 'config/config_ru' -run Sinatra::Application -set :raise_errors, false -set :show_exceptions, false
\ No newline at end of file +SERVICE = "validation" +require 'bundler' +Bundler.require +require './application.rb' +run run Sinatra::Application diff --git a/example.rb b/example.rb deleted file mode 100755 index 636579e..0000000 --- a/example.rb +++ /dev/null @@ -1,212 +0,0 @@ - -require 'lib/test_util.rb' - -class Example - - @@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%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") - @@data=File.join CONFIG[:services]["opentox-dataset"],"1" - @@train_data=File.join CONFIG[:services]["opentox-dataset"],"2" - @@test_data=File.join CONFIG[:services]["opentox-dataset"],"3" - @@prediction_data=File.join CONFIG[:services]["opentox-dataset"],"5" - @@css_file="http://apps.ideaconsult.net:8080/ToxPredict/style/global.css" - - @@summary="" - - # replaces placeholdes ( in <> brackets ) in EXAMPLE file with uris and ids - def self.transform_example - - file = File.new("EXAMPLES", "r") - res = "" - while (line = file.gets) - res += line - end - file.close - - sub = { "validation_service" => CONFIG[:services]["opentox-validation"].chomp("/"), - "validation_id" => "1", - "model_uri" => @@model, - "dataset_uri" => @@data, - "training_dataset_uri" => @@train_data, - "test_dataset_uri" => @@test_data, - "prediction_feature" => @@feature, - "algorithm_uri" => @@alg, - "algorithm_params" => @@alg_params, - "crossvalidation_id" => "1", - "validation_report_id" => "1", - "crossvalidation_report_id" => "2", - "css_file" => @@css_file, - "prediction_dataset_uri" => @@prediction_data, - #"predicted_feature" => @@predicted_feature, - "qmrf_id" => "1"} - - sub.each do |k,v| - res.gsub!(/<#{k}>/,v) - end - res - end - - # creates the resources that are requested by the examples - def self.prepare_example_resources - - #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! - #ActiveRecord::Base.logger = Logger.new("/dev/null") - #ActiveRecord::Migrator.migrate('db/migrate', 0 ) - #ActiveRecord::Migrator.migrate('db/migrate', 1 ) - #ActiveRecord::Migrator.migrate('db/migrate', 2 ) - - #delete all qmrf reports - ReachReports::QmrfReport.auto_migrate! - - #delete_all(CONFIG[:services]["opentox-dataset"]) - log OpenTox::RestClientWrapper.delete CONFIG[:services]["opentox-dataset"] - task.progress(10) - - log "upload dataset" - raise OpenTox::BadRequestError.new"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") - dataset = OpenTox::Dataset.create_from_csv_file(@@file.path,nil) - data_uri = dataset.uri - log "-> "+data_uri - task.progress(20) - - 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), 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], - :test_target_dataset_uri => data_uri, - :prediction_feature => URI.decode(@@feature), - :algorithm_uri => @@alg - v.validate_algorithm( @@alg_params, OpenTox::SubTask.new(task, 20, 40) ) - - log "crossvalidation" - 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" - rep = Reports::ReportService.instance(File.join(CONFIG[:services]["opentox-validation"],"report")) - rep.delete_all_reports("validation", subjectid) - rep.create_report("validation",v.validation_uri) - task.progress(80) - - log "create crossvalidation report" - rep.delete_all_reports("crossvalidation", subjectid) - rep.create_report("crossvalidation",cv.crossvalidation_uri) - task.progress(90) - - log "build qmrf" - t = ReachReports.create_report("QMRF",{:model_uri=>@@model}) - Lib::TestUtil.wait_for_task(t) - task.progress(100) - - log "done" - @@summary - end - task - end - - # performs all curl calls listed in examples after ">>>", next line is added if line ends with "\" - def self.test_examples(example_uri=nil) - - if (example_uri) - examples = OpenTox::RestClientWrapper.get(example_uri) - else - examples = transform_example # use local examples - end - - lines = examples.split("\n") - curl_call = false - curl_calls = [] - - lines.each do |line| - if line =~ /^\s*>>>\s*.*/ - line.gsub!(/^\s*>>>\s*/,"") - if line =~ /.*\s*\\s*$/ - curl_call = true - line.gsub!(/\s*\\s*$/," ") - else - curl_call = false - end - curl_calls.push( line ) - elsif curl_call - if line =~ /.*\s*\\s*$/ - curl_call = true - line.gsub!(/\s*\\s*$/," ") - else - curl_call = false - end - curl_calls[-1] = curl_calls[-1]+line - end - end - - Spork.spork(:logger => LOGGER) do - @@summary = "" - num = 0 - suc = 0 - curl_calls.each do |cmd| - num += 1 - log "testing: "+cmd - result = "" - IO.popen(cmd.to_s+" 2> /dev/null") do |f| - while line = f.gets - result += line if result.size<50 - end - end - result.chomp! - result.gsub!(/\n/, " \\n ") - if ($?==0) - if result.task_uri? - log "wait for task: "+result - result = Lib::TestUtil.wait_for_task(result) - end - log "ok ( " +result.to_s[0,50]+" )" - suc += 1 - else - log "failed ( " +result.to_s[0,50]+" )" - end - end - log suc.to_s+"/"+num.to_s+" curls succeeded" - @@summary - end - "testing in background, check log for results" - end - - private - # deletes resources listed by service - def self.delete_all(uri_list_service) - uri_list = OpenTox::RestClientWrapper.get(uri_list_service) - LOGGER.debug "deleting: "+uri_list.inspect - uri_list.split("\n").each do |uri| - OpenTox::RestClientWrapper.delete(uri) - end - end - - # logs string and and adds to summary - def self.log(log_string) - LOGGER.info "EXAMPLE: "+log_string - @@summary += log_string+"\n" - end - -end diff --git a/lib/active_record_setup.rb b/lib/active_record_setup.rb deleted file mode 100755 index 5f081af..0000000 --- a/lib/active_record_setup.rb +++ /dev/null @@ -1,50 +0,0 @@ - -#gem "activerecord", "= 2.3.8" -#gem "ar-extensions", "= 0.9.2" -['rubygems', 'logger', 'active_record', 'opentox-ruby' ].each do |g| #'ar-extensions', - require g -end - -unless ActiveRecord::Base.connected? - ActiveRecord::Base.establish_connection( - :adapter => CONFIG[:database][:adapter], - :host => CONFIG[:database][:host], - :database => CONFIG[:database][:database], - :username => CONFIG[:database][:username], - :password => CONFIG[:database][:password] - ) - ActiveRecord::Base.logger = Logger.new("/dev/null") -end - -class ActiveRecord::Base - - def self.find_like(filter_params) - - raise "find like removed" - - #puts "params before "+filter_params.inspect - filter_params.keys.each do |k| - key = k.to_s - unless self.column_names.include?(key) - key = key.from_rdf_format - unless self.column_names.include?(key) - key = key+"_uri" - unless self.column_names.include?(key) - key = key+"s" - unless self.column_names.include?(key) - err = "no attribute found: '"+k.to_s+"'" -# if $sinatra -# $sinatra.raise OpenTox::BadRequestError.newerr -# else - raise err -# end - end - end - end - end - filter_params[key+"_like"] = filter_params.delete(k) - end - #puts "params after "+filter_params.inspect - self.find(:all, :conditions => filter_params) - end -end diff --git a/lib/data_mapper_util.rb b/lib/data_mapper_util.rb deleted file mode 100644 index 23f52f5..0000000 --- a/lib/data_mapper_util.rb +++ /dev/null @@ -1,37 +0,0 @@ - -#DataObjects::Mysql.logger = DataObjects::Logger.new(STDOUT, 0) - -module Lib - module DataMapperUtil - - def self.check_params(model, params) - prop_names = model.properties.collect{|p| p.name.to_s if p.is_a?DataMapper::Property::Object} - params.keys.each do |k| - key = k.to_s - if (key == "subjectid") - 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.all(model, filter_params) - model.all(check_params(model,filter_params)) - end - - end -end
\ No newline at end of file diff --git a/lib/ot_predictions.rb b/lib/ot_predictions.rb index 2752fcc..8ddf364 100755 --- a/lib/ot_predictions.rb +++ b/lib/ot_predictions.rb @@ -1,6 +1,6 @@ -require "lib/prediction_data.rb" -require "lib/predictions.rb" +require "./lib/prediction_data.rb" +require "./lib/predictions.rb" module Lib diff --git a/lib/prediction_data.rb b/lib/prediction_data.rb index d387d24..f42cd9f 100644 --- a/lib/prediction_data.rb +++ b/lib/prediction_data.rb @@ -1,6 +1,7 @@ module Lib + class PredictionData CHECK_VALUES = ENV['RACK_ENV'] =~ /debug|test/ @@ -53,17 +54,14 @@ module Lib @compounds end - def self.create( feature_type, test_dataset_uris, test_target_dataset_uris, - prediction_feature, prediction_dataset_uris, predicted_variables, predicted_confidences, - subjectid=nil, task=nil ) + def self.create( feature_type, test_dataset_uris, prediction_feature, prediction_dataset_uris, + predicted_variables, predicted_confidences, subjectid=nil, task=nil ) test_dataset_uris = [test_dataset_uris] unless test_dataset_uris.is_a?(Array) - test_target_dataset_uris = [test_target_dataset_uris] unless test_target_dataset_uris.is_a?(Array) prediction_dataset_uris = [prediction_dataset_uris] unless prediction_dataset_uris.is_a?(Array) predicted_variables = [predicted_variables] unless predicted_variables.is_a?(Array) predicted_confidences = [predicted_confidences] unless predicted_confidences.is_a?(Array) LOGGER.debug "loading prediction -- test-dataset: "+test_dataset_uris.inspect - LOGGER.debug "loading prediction -- test-target-datset: "+test_target_dataset_uris.inspect LOGGER.debug "loading prediction -- prediction-dataset: "+prediction_dataset_uris.inspect LOGGER.debug "loading prediction -- predicted_variable: "+predicted_variables.inspect LOGGER.debug "loading prediction -- predicted_confidence: "+predicted_confidences.inspect @@ -84,7 +82,6 @@ module Lib test_dataset_uris.size.times do |i| test_dataset_uri = test_dataset_uris[i] - test_target_dataset_uri = test_target_dataset_uris[i] prediction_dataset_uri = prediction_dataset_uris[i] predicted_variable = predicted_variables[i] predicted_confidence = predicted_confidences[i] @@ -94,35 +91,18 @@ module Lib test_dataset = Lib::DatasetCache.find test_dataset_uri,subjectid raise "test dataset not found: '"+test_dataset_uri.to_s+"'" unless test_dataset - if test_target_dataset_uri == nil || test_target_dataset_uri.strip.size==0 || test_target_dataset_uri==test_dataset_uri - test_target_dataset_uri = test_dataset_uri - test_target_dataset = test_dataset - raise "prediction_feature not found in test_dataset, specify a test_target_dataset\n"+ - "prediction_feature: '"+prediction_feature.to_s+"'\n"+ - "test_dataset: '"+test_target_dataset_uri.to_s+"'\n"+ - "available features are: "+test_target_dataset.features.inspect if test_target_dataset.features.keys.index(prediction_feature)==nil - else - test_target_dataset = Lib::DatasetCache.find test_target_dataset_uri,subjectid - raise "test target datset not found: '"+test_target_dataset_uri.to_s+"'" unless test_target_dataset - if CHECK_VALUES - test_dataset.compounds.each do |c| - raise "test compound not found on test class dataset "+c.to_s unless test_target_dataset.compounds.include?(c) - end - end - raise "prediction_feature not found in test_target_dataset\n"+ - "prediction_feature: '"+prediction_feature.to_s+"'\n"+ - "test_target_dataset: '"+test_target_dataset_uri.to_s+"'\n"+ - "available features are: "+test_target_dataset.features.inspect if test_target_dataset.features.keys.index(prediction_feature)==nil - end + raise "prediction_feature not found in test_dataset\n"+ + "prediction_feature: '"+prediction_feature.to_s+"'\n"+ + "test_dataset: '"+test_dataset_uri.to_s+"'\n"+ + "available features are: "+test_dataset.features.inspect if test_dataset.features.keys.index(prediction_feature)==nil - 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 + LOGGER.debug "test dataset size: "+test_dataset.compounds.size.to_s + raise "test dataset is empty "+test_dataset_uri.to_s unless test_dataset.compounds.size>0 if feature_type=="classification" - av = test_target_dataset.accept_values(prediction_feature) + av = test_dataset.accept_values(prediction_feature) raise "'"+OT.acceptValue.to_s+"' missing/invalid for feature '"+prediction_feature.to_s+"' in dataset '"+ - test_target_dataset_uri.to_s+"', acceptValues are: '"+av.inspect+"'" if av==nil or av.length<2 + test_dataset_uri.to_s+"', acceptValues are: '"+av.inspect+"'" if av==nil or av.length<2 if accept_values==nil accept_values=av else @@ -131,20 +111,15 @@ module Lib end actual_values = [] - tmp_compounds = [] - compounds.each do |c| + test_dataset.compounds.size.times do |c_idx| case feature_type when "classification" - vals = classification_vals(test_target_dataset, c, prediction_feature, accept_values) + actual_values << classification_val(test_dataset, c_idx, prediction_feature, accept_values) when "regression" - vals = regression_vals(test_target_dataset, c, prediction_feature) - end - vals.each do |v| - actual_values << v - tmp_compounds << c + actual_values << numeric_val(test_dataset, c_idx, prediction_feature) end + #raise "WTF #{c_idx} #{test_dataset.compounds[c_idx]} #{actual_values[-1]} #{actual_values[-2]}" if c_idx>0 and test_dataset.compounds[c_idx]==test_dataset.compounds[c_idx-1] and actual_values[-1]!=actual_values[-2] end - compounds = tmp_compounds task.progress( task_status += task_step ) if task # loaded actual values prediction_dataset = Lib::DatasetCache.find prediction_dataset_uri,subjectid @@ -160,41 +135,42 @@ module Lib "prediction_dataset: '"+prediction_dataset_uri.to_s+"'\n"+ "available features are: "+prediction_dataset.features.inspect if predicted_confidence and prediction_dataset.features.keys.index(predicted_confidence)==nil and prediction_dataset.compounds.size>0 - raise "more predicted than test compounds, #test: "+compounds.size.to_s+" < #prediction: "+ + raise "more predicted than test compounds, #test: "+test_dataset.compounds.size.to_s+" < #prediction: "+ prediction_dataset.compounds.size.to_s+", test-dataset: "+test_dataset_uri.to_s+", prediction-dataset: "+ - prediction_dataset_uri if compounds.size < prediction_dataset.compounds.size + prediction_dataset_uri if test_dataset.compounds.size < prediction_dataset.compounds.size if CHECK_VALUES prediction_dataset.compounds.each do |c| raise "predicted compound not found in test dataset:\n"+c+"\ntest-compounds:\n"+ - compounds.collect{|c| c.to_s}.join("\n") if compounds.index(c)==nil + test_dataset.compounds.collect{|c| c.to_s}.join("\n") unless test_dataset.compounds.include?(c) end end predicted_values = [] confidence_values = [] - count = 0 - compounds.each do |c| - if prediction_dataset.compounds.index(c)==nil + + test_dataset.compounds.size.times do |test_c_idx| + c = test_dataset.compounds[test_c_idx] + pred_c_idx = prediction_dataset.compound_index(test_dataset,test_c_idx) + if pred_c_idx==nil + raise "internal error: mapping failed" if prediction_dataset.compounds.include?(c) predicted_values << nil confidence_values << nil else + raise "internal error: mapping failed" unless c==prediction_dataset.compounds[pred_c_idx] case feature_type when "classification" - vals = classification_vals(prediction_dataset, c, predicted_variable, accept_values) + predicted_values << classification_val(prediction_dataset, pred_c_idx, predicted_variable, accept_values) when "regression" - vals = regression_vals(prediction_dataset, c, predicted_variable) + predicted_values << numeric_val(prediction_dataset, pred_c_idx, predicted_variable) end - raise "not yet implemented: more than one prediction for one compound" if vals.size>1 - predicted_values << vals[0] if predicted_confidence - confidence_values << confidence_val(prediction_dataset, c, predicted_confidence) + confidence_values << numeric_val(prediction_dataset, pred_c_idx, predicted_confidence) else confidence_values << nil end end - count += 1 end - all_compounds += compounds + all_compounds += test_dataset.compounds all_predicted_values += predicted_values all_actual_values += actual_values all_confidence_values += confidence_values @@ -237,61 +213,23 @@ module Lib end private - def self.regression_vals(dataset, compound, feature) - v_num = [] - values(dataset, compound, feature).each do |v| - if v==nil or v.is_a?(Numeric) - v_num << v - else - begin - v_num << v.to_f - rescue - LOGGER.warn "no numeric value for regression: '"+v.to_s+"'" - v_num << nil - end - end - end - v_num - end - - def self.confidence_val(dataset, compound, confidence) - v = values(dataset, compound, confidence) - raise "not yet implemented: duplicate conf value" if v.size>1 + def self.numeric_val(dataset, compound_index, feature) + v = dataset.data_entry_value(compound_index, feature) begin - v = v[0] v = v.to_f unless v==nil or v.is_a?(Numeric) v rescue - LOGGER.warn "no numeric value for confidence '"+v.to_s+"'" + LOGGER.warn "no numeric value for feature '#{feature}' : '#{v}'" nil end end - def self.classification_vals(dataset, compound, feature, accept_values) - v_indices = [] - values(dataset, compound, feature).each do |v| - i = accept_values.index(v) - raise "illegal class_value of prediction (value is '"+v.to_s+"'), accept values are "+ - accept_values.inspect unless v==nil or i!=nil - v_indices << i - end - v_indices + def self.classification_val(dataset, compound_index, feature, accept_values) + v = dataset.data_entry_value(compound_index, feature) + i = accept_values.index(v) + 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 - - def self.values(dataset, compound, feature) - return [nil] if dataset.data_entries[compound]==nil - if feature==nil - v = dataset.data_entries[compound].values[0] - else - v = dataset.data_entries[compound][feature] - end - return [nil] if v==nil - # sanitiy checks - raise "no array "+v.class.to_s+" : '"+v.to_s+"'" unless v.is_a?(Array) - v.each{|vv| raise "array-elem is array" if vv.is_a?(Array)} - # replace empty strings with nil - v_mod = v.collect{|vv| (vv.to_s().size==0 ? nil : vv)} - v_mod - end end end diff --git a/lib/predictions.rb b/lib/predictions.rb index d929f1a..9f62d31 100755 --- a/lib/predictions.rb +++ b/lib/predictions.rb @@ -1,5 +1,5 @@ -require "lib/prediction_data.rb" +require "./lib/prediction_data.rb" module Lib @@ -805,8 +805,8 @@ module Lib end def self.test_r_square - require "rubygems" - require "opentox-ruby" + #require "rubygems" + #require "opentox-ruby" max_deviation = rand * 0.9 avg_deviation = max_deviation * 0.5 diff --git a/lib/validation_db.rb b/lib/validation_db.rb index 086853e..e486a62 100755 --- a/lib/validation_db.rb +++ b/lib/validation_db.rb @@ -2,13 +2,12 @@ #[ 'rubygems', 'datamapper' ].each do |lib| # require lib #end -require "lib/merge.rb" +require "./lib/merge.rb" module Validation VAL_PROPS_GENERAL = [ :validation_uri, :validation_type, :model_uri, :algorithm_uri, :algorithm_params, - :training_dataset_uri, :prediction_feature, :test_dataset_uri, :test_target_dataset_uri, - :prediction_dataset_uri, :date ] + :training_dataset_uri, :prediction_feature, :test_dataset_uri, :prediction_dataset_uri, :date ] VAL_PROPS_SUM = [ :num_instances, :num_without_class, :num_unpredicted ] VAL_PROPS_AVG = [:real_runtime, :percent_without_class, :percent_unpredicted ] VAL_PROPS = VAL_PROPS_GENERAL + VAL_PROPS_SUM + VAL_PROPS_AVG @@ -59,7 +58,6 @@ module Validation attribute :algorithm_uri attribute :algorithm_params attribute :training_dataset_uri - attribute :test_target_dataset_uri attribute :test_dataset_uri attribute :prediction_dataset_uri attribute :prediction_feature diff --git a/nightly/nightly.rb b/nightly/nightly.rb deleted file mode 100755 index 07cd11a..0000000 --- a/nightly/nightly.rb +++ /dev/null @@ -1,218 +0,0 @@ - -require 'test/test_examples.rb' - -class Nightly - - NIGHTLY_REP_DIR = File.join(FileUtils.pwd,"nightly") - NIGHTLY_REPORT_XML = "nightly_report.xml" - NIGHTLY_REPORT_HTML = "nightly_report.html" - - def self.get_nightly - LOGGER.info("Accessing nightly report.") - if File.exist?(File.join(NIGHTLY_REP_DIR,NIGHTLY_REPORT_HTML)) - return File.new(File.join(NIGHTLY_REP_DIR,NIGHTLY_REPORT_HTML)) - else - return "Nightly report not available, try again later" - end - end - - def self.build_nightly(select=nil, dry_run=false) - - validationExamples = ValidationExamples.select(select) - return "please \"select\" validation examples:\n"+ValidationExamples.list if validationExamples.size==0 - - task = OpenTox::Task.create("Build nightly","nightly-validation-test-service") do |task| #,{:select => select, :dry_run => dry_run}) - LOGGER.info("Building nightly report") - - benchmarks = validationExamples.collect{ |e| ValidationBenchmark.new(e) } - - running = [] - report = Reports::XMLReport.new("Nightly Validation", Time.now.strftime("Created at %m.%d.%Y - %H:%M")) - count = 1 - benchmarks.each do |b| - id = "["+count.to_s+"]-"+b.title - count += 1 - running << id - Thread.new do - begin - b.build() - rescue => ex - LOGGER.error "uncaught nightly build error: "+ex.message - ensure - running.delete id - end - end - end - wait = 0 - while running.size>0 - LOGGER.debug "Nightly report waiting for "+running.inspect if wait%60==0 - wait += 1 - sleep 1 - end - LOGGER.debug "Nightly report, all benchmarks done "+running.inspect - - section_about = report.add_section(report.get_root_element, "About this report") - report.add_paragraph(section_about, - "This a opentox internal test report. Its purpose is to maintain interoperability between the OT validation web service "+ - "and other OT web services. If you have any comments, remarks, or wish your service/test-case to be added, please email "+ - "to guetlein@informatik.uni-freiburg.de or use the issue tracker at http://opentox.informatik.uni-freiburg.de/simple_ot_stylesheet.css") - - benchmarks.each do |b| - section = report.add_section(report.get_root_element, b.title) - - section_info = report.add_section(section, "Info") - info_table = b.info_table - report.add_table(section_info, "Validation info", info_table) if info_table - - section_results = report.add_section(section, "Results") - report.add_table(section_results, "Valdation results", b.result_table) - - if (b.comparison_report) - report.add_table(section_results, "Validation comparison report", [[b.comparison_report]], false) - end - - section_errors = report.add_section(section, "Errors") - - if b.errors and b.errors.size>0 - b.errors.each do |k,v| - elem = report.add_section(section_errors,k) - report.add_paragraph(elem,v,true) - end - else - report.add_paragraph(section_errors,"no errors occured") - end - - end - - unless dry_run - report.write_to(File.new(File.join(NIGHTLY_REP_DIR,NIGHTLY_REPORT_XML), "w")) - Reports::ReportFormat.format_report_to_html(NIGHTLY_REP_DIR, - NIGHTLY_REPORT_XML, - NIGHTLY_REPORT_HTML, - nil) - #"http://www.opentox.org/portal_css/Opentox%20Theme/base-cachekey7442.css") - #"http://apps.ideaconsult.net:8080/ToxPredict/style/global.css") - LOGGER.info("Nightly report completed") - else - LOGGER.info("Nightly report completed - DRY RUN, no report creation") - end - - #benchmarks.collect{|b| b.uris}.join(",") - File.join(CONFIG[:services]["opentox-validation"],"nightly") - end - return_task(task) - end - - class ValidationBenchmark - - attr_accessor :errors, :comparison_report - - def comparable - if @comp == nil - @comp = @validation_examples[0].algorithm_uri==nil ? :model_uri : :algorithm_uri - end - @comp - end - - def uris - @validation_examples.collect{|v| v.validation_uri}.join(",") - end - - def initialize(validationExamples) - @validation_examples = [] - validationExamples.each do |v| - example = v.new - @validation_examples << example - end - end - - def title - if @validation_examples.size==0 - @validation_examples[0].class.humanize - else - @validation_examples[0].class.superclass.humanize - end - end - - def result_table - t = [] - row = [comparable.to_s, "validation", "report"] - t << row - @validation_examples.each do |e| - row = [ e.send(comparable), - (e.validation_error!=nil ? "error, see below" : e.validation_uri), - (e.report_error!=nil ? "error, see below" : e.report_uri) ] - t << row - end - t - end - - def info_table - t = [] - t << ["param", "uri"] - - (@validation_examples[0].params+@validation_examples[0].opt_params).each do |p| - map = {} - @validation_examples.each{|e| map[e.send(p).to_s]=nil } - - if map.size==1 && map.keys[0].size==0 - #omit - elsif map.size==1 #values equal - t << [p.to_s, map.keys[0]] - else - count = 1 - @validation_examples.each do |e| - t << [p.to_s+" ["+count.to_s+"]", e.send(p)] - count += 1 - end - end - end - t - end - - def build() - - @errors = {} - - running = [] - count = 1 - - @validation_examples.each do |v| - - id = "["+count.to_s+"]-"+v.title - count += 1 - running << id - LOGGER.debug "Uploading datasets: "+v.title - v.upload_files - v.check_requirements - - Thread.new do - - LOGGER.debug "Validate: "+v.title - v.validate - if v.validation_error!=nil - @errors["Error validating "+v.title] = v.validation_error - else - LOGGER.debug "Building report: "+v.title - v.report - if v.report_error!=nil - @errors["Error building report for "+v.title] = v.report_error - end - end - running.delete(id) - end - end - - wait = 0 - while running.size>0 - LOGGER.debug self.title+" waiting for "+running.inspect if wait%20==0 - wait += 1 - sleep 1 - end - - LOGGER.debug self.class.to_s.gsub(/Nightly::/, "")+": build comparison report" - @comparison_report = ValidationExamples::Util.build_compare_report(@validation_examples) - end - end - -end diff --git a/nightly/nightly_application.rb b/nightly/nightly_application.rb deleted file mode 100644 index 69b4614..0000000 --- a/nightly/nightly_application.rb +++ /dev/null @@ -1,22 +0,0 @@ -require "nightly/nightly.rb" - -post '/build_nightly/?' do - dry_run = params[:dry_run]!=nil and params[:dry_run] - Nightly.build_nightly(params["select"],dry_run) -end - -get '/css_style_sheet/?' do - perform do |rs| - "@import \""+params[:css_style_sheet]+"\";" - end -end - -get '/nightly/?' do - content_type "text/html" - rep = Nightly.get_nightly - if rep.is_a?(File) - result = body(rep) - else - result = rep - end -end diff --git a/reach_reports/reach_application.rb b/reach_reports/reach_application.rb deleted file mode 100755 index b380c92..0000000 --- a/reach_reports/reach_application.rb +++ /dev/null @@ -1,269 +0,0 @@ - -[ 'rubygems', 'sinatra', 'sinatra/url_for', 'opentox-ruby' ].each do |lib| - require lib -end - -QMRF_EDITOR_URI = "http://ortona.informatik.uni-freiburg.de/qmrfedit/OT_QMRFEditor.jnlp" - -# hack for as long as mysql lite is used -def mysql_lite_retry( n_times=15 ) - n_times.times do - begin - yield - return - rescue => ex - LOGGER.warn "datamapper error, wait and retry : "+ex.message - sleep(1+rand(3)) # wait 1-3 seconds - end - end - yield # try a last time -end - -require 'reach_reports/reach_persistance.rb' -require 'reach_reports/reach_service.rb' - -require "lib/format_util.rb" - -def extract_type(params) - raise OpenTox::BadRequestError.new "illegal type, neither QMRF nor QPRF: "+params[:type] unless params[:type] && params[:type] =~ /(?i)Q(M|P)RF/ - params.delete("type") -end - -get '/reach_report' do - uri_list = url_for('/reach_report/QMRF', :full)+"\n"+url_for('/reach_report/QPRF', :full)+"\n" - if request.env['HTTP_ACCEPT'] =~ /text\/html/ - content_type "text/html" - related_links = - "All validations: "+url_for("/",:full)+"\n"+ - "Validation reporting: "+url_for("/report",:full) - description = - "A list of all suported REACH reporting types." - OpenTox.text_to_html uri_list,related_links,description, @subjectid - else - content_type "text/uri-list" - uri_list - end -end - -get '/reach_report/:type' do - type = extract_type(params) - LOGGER.info "list all "+type+" reports" - uris = ReachReports.list_reports(type,params[:model] || params[:model_uri]) - if request.env['HTTP_ACCEPT'] =~ /text\/html/ - content_type "text/html" - related_links = - "All REACH reporting types: "+url_for("/reach_report",:full) - description = - "A list of "+type+" reports." - post_command = nil - case type - when /(?i)QMRF/ - related_links += "\n"+ - "OpenTox version of QMRF editor: "+QMRF_EDITOR_URI - description += "\n"+ - "To create a QMRF report use the POST method." - post_command = OpenTox::PostCommand.new request.url,"Create QMRF report" - post_command.attributes << OpenTox::PostAttribute.new("model_uri") - when /(?i)QPRF/ - #TODO - end - OpenTox.text_to_html uris,@subjectid,related_links,description,post_command - else - content_type "text/uri-list" - uris - end -end - -post '/reach_report/:type' do - - type = extract_type(params) - content_type "text/uri-list" - - LOGGER.info "creating "+type+" report "+params.inspect - raise OpenTox::BadRequestError.new "model_uri missing" if type=~/(?i)QMRF/ and - params[:model_uri]!=nil and params[:model_uri].to_s.size==0 - - #puts "creating "+type+" report "+params.inspect - result_uri = ReachReports.create_report(type,params,@subjectid,request.env["rack.input"]) - - if result_uri and result_uri.task_uri? - halt 202,result_uri+"\n" - else - result_uri+"\n" - end -end - -get '/reach_report/:type/:id' do - - type = extract_type(params) - LOGGER.info "get "+type+" report with id '"+params[:id].to_s+"' "+request.env['HTTP_ACCEPT'].to_s+"'" - rep = ReachReports.get_report(type, params[:id]) - - case request.env['HTTP_ACCEPT'].to_s - when "application/rdf+xml" - raise OpenTox::BadRequestError.new "application/rdf+xml not yet supported" - owl = OpenTox::Owl.create(type+"Report",rep.report_uri) - owl.set_data( rep.get_content.keys_to_rdf_format ) - owl.rdf - when "application/qmrf-xml" - content_type "application/qmrf-xml" - rep.to_xml - #f = File.new("/home/martin/info_home/.public_html/qmrf.out.xml","w") - #f.puts result - when /text\/html/ - content_type "text/html" - related_links = - "Open report in QMRF editor: "+rep.report_uri+"/editor"+"\n"+ - "All "+type+" reports: "+url_for("/reach_report/"+type,:full) - description = - "A QMRF report." - OpenTox.text_to_html rep.to_yaml,@subjectid,related_links,description - when /application\/x-yaml|\*\/\*|^$/ # matches 'application/x-yaml', '*/*', '' - content_type "application/x-yaml" - rep.to_yaml - else - raise OpenTox::BadRequestError.new "MIME type '"+request.env['HTTP_ACCEPT'].to_s+"' not supported, valid Accept-Headers are \"application/rdf+xml\", \"application/x-yaml\", \"application/qmrf-xml\"." - end -end - -post '/reach_report/:type/:id' do - - type = extract_type(params) - LOGGER.info "Post to "+type+" report with id "+params[:id].to_s+"' "+request.env['HTTP_ACCEPT'].to_s+"'" - rep = ReachReports.get_report(type, params[:id]) - - input = request.env["rack.input"].read - raise OpenTox::BadRequestError.new "no xml data specified" unless input && input.to_s.size>0 - LOGGER.debug "size of posted data: "+input.to_s.size.to_s - - ReachReports::QmrfReport.from_xml(rep,input) - - #f = File.new("/home/martin/info_home/.public_html/qmrf.out.xml","w") - #f.puts rep.to_xml -end - -delete '/reach_report/:type/:id' do - type = extract_type(params) - LOGGER.info "delete "+type+" report with id '"+params[:id].to_s+"'" - ReachReports.delete_report(type, params[:id], @subjectid) -end - - -#get '/reach_report/:type/:id/:section' do -# -# type = extract_type(params) -# LOGGER.info "get "+type+" report section '"+params[:section].to_s+"', with id "+params[:id].to_s+"' "+request.env['HTTP_ACCEPT'].to_s+"'" -# ReachReports.get_report(type, params[:id], params[:section]).to_yaml -#end -# -#get '/reach_report/:type/:id/:section/:subsection' do -# -# type = extract_type(params) -# LOGGER.info "get "+type+" report subsection '"+params[:subsection].to_s+"', section '"+params[:section].to_s+"', with id "+params[:id].to_s+"' "+request.env['HTTP_ACCEPT'].to_s+"'" -# ReachReports.get_report(type, params[:id], params[:section], params[:subsection]).to_yaml -#end - -get '/reach_report/:type/:id/editor' do - - type = extract_type(params) - LOGGER.info "editor for "+type+" report with id '"+params[:id].to_s+"' "+params.inspect - - jnlp = <<EOF -<?xml version ="1.0" encoding="utf-8"?> -<jnlp spec="1.0+" codebase="http://opentox.informatik.uni-freiburg.de/" href="qmrfedit/OT_QMRFEditor.jnlp" > -<information> -<title>QMRF Editor</title> -<vendor>www.opentox.org</vendor> -<description>(Q)SAR Model Reporting Format Editor</description> -<description kind="short">(Q)SAR Model Reporting Format Editor</description> -<icon href="qmrfedit/OTLogo.png" /> -</information> -<resources> -<j2se version="1.6+" java-vm-args="-Xincgc"/> - -<jar href="qmrfedit/OT_QMRFEditor.jar" download="eager" main="true"/> -<jar href="qmrfedit/OT_QMRFEditor_lib/xercesImpl.jar" download="eager"/> -<jar href="qmrfedit/OT_QMRFEditor_lib/itext-1.4.5.jar" download="lazy"/> -<jar href="qmrfedit/OT_QMRFEditor_lib/poi-3.0.jar" download="lazy"/> -<jar href="qmrfedit/OT_QMRFEditor_lib/poi-contrib.jar" download="lazy"/> -<jar href="qmrfedit/OT_QMRFEditor_lib/poi-scratchpad.jar" download="lazy"/> -<jar href="qmrfedit/OT_QMRFEditor_lib/commons-lang-2.3.jar" download="lazy"/> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-applications.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-builder3d.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-charges.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-core.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-datadebug.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-data.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-experimental.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-extra.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-forcefield.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-interfaces.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-io.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-jchempaint.applet.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-jchempaint.application.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-jchempaint.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-libio-cml.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-libio-weka.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-nonotify.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-pdb-cml.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-pdb.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-qsar-cml.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-qsar.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/cdk-qsar-pdb.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/commons-cli-1.0.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/commons-io-1.1.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/commons-logging-1.0.4.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/commons-codec-1.3.jar" download="eager" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/fop.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/jai_codec.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/jai_core.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/jgrapht-0.6.0.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/jh.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/l2fprod-common-all.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/libfonts-0.1.4.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/log4j-1.2.8.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/log4j.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/mysql-connector-java-5.0.5-bin.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/naming-factory-dbcp.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/naming-factory.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/naming-resources.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/opsin-big-0.1.0.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/org.restlet.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/swing-layout-1.0.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/xmlgraphics-commons-1.1.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/xom-1.1b2.jar" download="lazy" /> -<jar href="qmrfedit/OT_QMRFEditor_lib/xom-1.1.jar" download="lazy" /> - - -</resources> -<application-desc main-class="ambit.applications.qmrf.QMRFEditor"> -<argument>-x -EOF - jnlp.chomp! - jnlp += File.join(url_for("/reach_report/QMRF",:full),params[:id]) - - if @subjectid.to_s.size>0 - jnlp += <<EOF -</argument> -<argument>--subjectid= -EOF - jnlp.chomp! - jnlp += @subjectid.to_s - end - - jnlp += <<EOF -</argument> -<argument>-d http://opentox.informatik.uni-freiburg.de/qmrfedit/qmrf.dtd</argument> -<argument>-t http://opentox.informatik.uni-freiburg.de/qmrfedit/verdana.ttf</argument> - -</application-desc> -<security> - <all-permissions/> -</security> -</jnlp> -EOF - - content_type "application/x-java-jnlp-file" - jnlp -end - diff --git a/reach_reports/reach_persistance.rb b/reach_reports/reach_persistance.rb deleted file mode 100755 index 1226d95..0000000 --- a/reach_reports/reach_persistance.rb +++ /dev/null @@ -1,1216 +0,0 @@ - -['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 - -module REXML - - class Element - def self.find_or_create(parent_node, name) - if parent_node.elements[name] - parent_node.elements[name] - else - node = Element.new(name) - parent_node << node - node - end - end - end - - class TextElement < Element - def initialize(name, text) - super(name) - self.text = text - end - - def self.find_or_create(parent_node, name, text) - elem = Element.find_or_create(parent_node, name) - elem.text = text - elem - end - end -end - - -class Symbol - - XML_ALIAS = { - :qsar_identifier => "QSAR_identifier", :qsar_title => "QSAR_title", :qsar_software => "QSAR_software", - :qsar_models => "QSAR_models", :qsar_general_information => "QSAR_General_information", - :qsar_endpoint => "QSAR_Endpoint", :qmrf_author => "qmrf_authors", :qsar_algorithm => "QSAR_Algorithm", - :qsar_applicability_domain => "QSAR_Applicability_domain", :qsar_robustness => "QSAR_Robustness", - :qsar_predictivity => "QSAR_Predictivity", :qsar_interpretation => "QSAR_Interpretation", - :qsar_miscellaneous => "QSAR_Miscelaneous", :qmrf_summary => "QMRF_Summary", :qmrf_number => "QMRF_number" } - - def xml_alias - XML_ALIAS[self] ? XML_ALIAS[self] : self.to_s - end -end - -class DataMapper::Associations::OneToMany::Relationship - def get_child_model - @child_model - end -end - -module DataMapper::Resource - - def association_class( property ) - relationship = relationships[property] - raise "no relationship found for "+property.to_s+" "+relationships.inspect unless relationship - raise "not a many-to-one or one-to-one association for "+property.to_s+" "+relationship.inspect unless - relationship.is_a?(DataMapper::Associations::OneToMany::Relationship) or - relationship.is_a?(DataMapper::Associations::OneToOne::Relationship) - relationship.get_child_model - end - - def from_xml(node) - - raise "node is nil ("+self.class.to_s+".from_xml)" unless node - #puts "FROM xml: "+self.class.to_s #+", NODE: "+node.to_s - - dbg_check = { :attributes => Set.new(), :nodes => Set.new(), :subnodes => Set.new() } - - xml_infos.each do |xml_info| - - if xml_info.is_a?(ReachReports::TextNodeProperty) - text_node = node.elements[ xml_info.xml_prop ] - raise "node not found: "+ xml_info.xml_prop+" ("+self.class.to_s+".from_xml)" unless text_node - self.send( xml_info.prop.to_s+"=", text_node.text ) - dbg_check[:nodes] << text_node.name - - elsif xml_info.is_a?(ReachReports::CatalogReference) - root_node = node.elements[ xml_info.xml_prop ] - raise "node not found: "+ xml_info.xml_prop+" ("+self.class.to_s+".from_xml)" unless root_node - dbg_check[:nodes] << root_node.name - - self.send(xml_info.prop).each{ |s| s.destroy } if self.send(xml_info.prop) - self.send(xml_info.prop).clear() #otherwise the content is tmp still here - - catalog_node = $catalogs_node.elements[xml_info.catalog_name] - - root_node.each_element(xml_info.catalog_element+"_ref") do |n| - ref = nil - catalog_node.each_element_with_attribute("id", n.attribute("idref").to_s) do |e| - ref = e - break - end - raise "referenced node not found for "+xml_info.xml_prop+" in catalog "+xml_info.catalog_name+" ref-node was "+n.to_s unless ref - dbg_check[:subnodes] << n - - entry = self.association_class(xml_info.prop).new - entry.from_xml( ref ) - self.send(xml_info.prop) << entry - end - - elsif xml_info.is_a?(ReachReports::AttributeProperty) - #puts "attr "+xml_info.prop.to_s - self.send(xml_info.prop.to_s+"=", node.attribute(xml_info.xml_prop)) - dbg_check[:attributes] << xml_info.prop - - elsif xml_info.is_a?(ReachReports::TextSubnodeProperty) - parent_node = node.elements[ xml_info.parent_prop.xml_alias ] - raise "parent node not found: '"+ xml_info.parent_prop.xml_alias+"' ("+self.class.to_s+".from_xml)" unless parent_node - text_node = parent_node.elements[ xml_info.xml_prop ] - raise "node not found: "+ xml_info.xml_prop+" ("+self.class.to_s+".from_xml)" unless text_node - self.send( xml_info.prop.to_s+"=", text_node.text ) - dbg_check[:nodes] << parent_node.name - dbg_check[:subnodes] << text_node - - elsif xml_info.is_a?(ReachReports::SingleAttributeNodeProperty) - attr_node = node.elements[ xml_info.xml_prop ] - self.send(xml_info.prop.to_s+"=", attr_node.attribute(xml_info.attribute)) - dbg_check[:nodes] << attr_node.name - - elsif xml_info.is_a?(ReachReports::AttributeNodeProperty) - attr_node = node.elements[ xml_info.xml_prop ] - entry = self.association_class( xml_info.prop ).new - entry.from_xml(attr_node) - self.send(xml_info.prop.to_s+"=",entry) - dbg_check[:nodes] << attr_node.name - - elsif xml_info.is_a?(ReachReports::AttributeSubNodeListProperty) - - parent_node = node.elements[ xml_info.parent_prop.xml_alias ] - raise "parent node not found: '"+ xml_info.parent_prop.xml_alias+"' ("+self.class.to_s+".from_xml)" unless parent_node - #puts "parent node "+xml_info.parent_prop.xml_alias - prop_node = parent_node.elements[ xml_info.xml_prop ] - if prop_node - #puts "prop node "+xml_info.xml_prop.to_s - prop_node.each_element do |n| - #puts "elem node "+n.name.to_s - raise "illegal node '"+n.name.to_s+"' should be '"+xml_info.list_element.to_s+"'" unless n.name==xml_info.list_element.to_s - entry = self.association_class( xml_info.prop ).new - entry.from_xml( n ) - self.send(xml_info.prop) << entry - end - dbg_check[:subnodes] << prop_node - end - dbg_check[:nodes] << parent_node.name - - else - raise "type not supported yet: "+xml_info.inspect - end - end - - ##raise "not a qsar_identifier" unless qsar_identifier.is_a?(QsarIdentifier) - - #puts node.elements.inspect - #puts "there we go: "+qsar_identifier.qsar_software.to_s - #qsar_identifier.qsar_software = QsarSoftware.new - #puts "there we go: "+qsar_identifier.qsar_software.to_s - #exit - - # if defined?(self.class.text_properties) -# self.class.text_properties.each do |p| -# puts "set "+p.to_s -# raise "node not found: "+p.xml_alias.to_s+" ("+self.class.to_s+".from_xml)" unless node.elements[p.xml_alias] -# #puts "set "+p.to_s+" to: "+node.elements[p.xml_alias].text.to_s -# self.send(p.to_s+"=", node.elements[p.xml_alias].text) -# #qsar_identifier.qsar_models = node.elements["qsar_models".xml_alias].text -# dbg_check[:nodes] << node.elements[p.xml_alias].name -# end -# - - -# if defined?(self.class.subsection_properties) -# self.class.subsection_properties.each do |section_p, subsection_p| -# #puts "set "+p.to_s -# #raise "node not found: "+p.xml_alias.to_s+" ("+self.class.to_s+".from_xml)" unless node.elements[p.xml_alias] -# #puts "set "+p.to_s+" to: "+node.elements[p.xml_alias].text.to_s -# section = node.elements[section_p.xml_alias] -# subsection = section.elements[subsection_p.xml_alias] -# self.send(subsection_p.to_s+"=", subsection.text) -# -# dbg_check[:nodes] << section.name -# dbg_check[:subnodes] << subsection -# -# #qsar_identifier.qsar_models = node.elements["qsar_models".xml_alias].text -# #dbg_check[:text_nodes] << node.elements[p.xml_alias].name -# end -# end - -# if defined?(self.class.attribute_properties) -# self.class.attribute_properties.each do |p| -# puts "read attribute "+p.to_s -# #self.update(p => node.attribute(p.xml_alias)) -# self.send(p.to_s+"=", node.attribute(p.xml_alias)) -# dbg_check[:attributes] << p -# #qsar_identifier.qsar_models = node.elements["qsar_models".xml_alias].text -# end -# end - - #qsar_identifier.qsar_title = node.elements["qsar_title".xml_alias].text - #qsar_identifier.qsar_models = node.elements["qsar_models".xml_alias].text - - - - ignore_attribs =[ "id", "name", "help", "chapter" ] - node.attributes.each do |a,v| - unless (ignore_attribs.include?(a.to_s)) || dbg_check[:attributes].include?(a.to_sym) - raise "not handled : attribute '"+a.to_s+"' -> '"+v.to_s+"'" + - "\n("+self.class.to_s+".from_xml)" + - "\nchecked:\n"+dbg_check[:attributes].to_yaml+ - "\nnode-attribtues:\n"+node.attributes.to_yaml - end - end - - node.each_element do |n| -# if n.text!=nil and n.text.to_s.size>0 and -# !dbg_check[:text_nodes].include?(n.name) and -# (!dbg_check[:catalog_nodes].has_key?(n.name)) - - valid = dbg_check[:nodes].include?(n.name) - if (valid) - refs = dbg_check[:subnodes] - #puts "sub "+refs.inspect - n.each_element do |nn| - #puts "lookin for ref "+nn.to_s - unless refs.include?(nn) - valid = false - break - end - end - end - - unless valid - raise puts "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\nXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\nnot handled node : "+n.to_s+ - "\n("+self.class.to_s+".from_xml)" -# raise "not handled node : "+n.to_s+ -# "\n("+self.class.to_s+".from_xml)" + -# "\nchecked text nodes:\n"+dbg_check[:text_nodes].to_yaml+ -# "\nchecked catalog nodes:\n"+dbg_check[:catalog_nodes].to_yaml+ -# "\nnode-attribtues:\n"+n.attributes.to_yaml - end - end - - - #self.save! - #self.reload -# unless self.save -# self.errors.each do |e| -# puts "Error: "+e.to_s -# end -# end - #puts "self id: "+self.id.to_s - -# qsar_identifier.qsar_software.each{ |s| s.destroy } if qsar_identifier.qsar_software -# qsar_identifier.qsar_software.update({}) #otherwise the content is tmp still here -# -# catalog_node = $catalogs_node.elements["software_catalog"] -# -# node.elements[:qsar_software.xml_alias].each_element do |n| -# -# puts "reading software ref "+n.to_s -# ref = nil -# catalog_node.each_element_with_attribute("id", n.attribute("idref").to_s) do |e| -# ref = e -# break -# end -# software = QsarSoftware.new -# QsarSoftware.from_xml( software, ref ) -# qsar_identifier.qsar_software << software -# end -# #qsar_identifier.qsar_software = QsarSoftware.new unless qsar_identifier.qsar_software -# #QsarSoftware.from_xml( qsar_identifier.qsar_software, node.elements["qsar_software".xml_alias] ) - - end - - def to_XML(node, chapter=nil ) - - xml_infos.each do |xml_info| - if xml_info.is_a?(ReachReports::TextNodeProperty) - new_node = REXML::TextElement.find_or_create(node, xml_info.xml_prop,self.send(xml_info.prop)) - - elsif xml_info.is_a?(ReachReports::CatalogReference) - - new_node = REXML::Element.find_or_create( node, xml_info.xml_prop ) - catalog_node = $catalogs_node.elements[ xml_info.catalog_name ] - - self.send(xml_info.prop.to_s+"=",[self.association_class(xml_info.prop).new]) unless self.send(xml_info.prop) and self.send(xml_info.prop).size>0 - - self.send( xml_info.prop ).each do |elem| - elem_node = REXML::Element.new(xml_info.catalog_element ) - elem.to_XML( elem_node ) - # if not saved, i.e. the element was only created for a complete xml, count elements in catalog for id - element_id = xml_info.catalog_element+"_"+(elem.id ? elem.id.to_s : (catalog_node.elements.size+1).to_s) - elem_node.add_attribute("id",element_id) - catalog_node << elem_node - - ref_node = REXML::Element.new(xml_info.catalog_element+"_ref" ) - ref_node.add_attributes("idref"=>element_id,"catalog"=>xml_info.catalog_name) - new_node << ref_node - end - - elsif xml_info.is_a?(ReachReports::AttributeProperty) - node.add_attribute( xml_info.xml_prop, self.send(xml_info.prop).to_s ) - - elsif xml_info.is_a?(ReachReports::TextSubnodeProperty) - new_node = REXML::Element.find_or_create( node, xml_info.parent_prop.xml_alias) - REXML::TextElement.find_or_create( new_node, xml_info.xml_prop,self.send(xml_info.prop)) - - elsif xml_info.is_a?(ReachReports::SingleAttributeNodeProperty) - new_node = REXML::Element.find_or_create(node, xml_info.xml_prop) - new_node.add_attribute(xml_info.attribute, self.send(xml_info.prop).to_s) - - elsif xml_info.is_a?(ReachReports::AttributeNodeProperty) - new_node = REXML::Element.find_or_create(node, xml_info.xml_prop) - self.send(xml_info.prop.to_s+"=",self.association_class(xml_info.prop).new) unless self.send(xml_info.prop) - self.send(xml_info.prop).to_XML(new_node) - - elsif xml_info.is_a?(ReachReports::AttributeSubNodeListProperty) - new_node = REXML::Element.find_or_create( node, xml_info.parent_prop.xml_alias ) - #puts "new parent "+xml_info.parent_prop.xml_alias - prop_node = REXML::Element.find_or_create( new_node, xml_info.xml_prop ) - #puts "new prop "+xml_info.xml_prop - self.send( xml_info.prop ).each do |elem| - #puts "elem "+elem.to_yaml - elem_node = REXML::Element.new( xml_info.list_element.xml_alias ) - elem.to_XML( elem_node ) - prop_node << elem_node - end - - else - raise "type not supported yet: "+xml_info.inspect - end - - new_node.add_attribute("chapter", chapter.to_s+"."+node.elements.size.to_s) if chapter and new_node and new_node.attribute("chapter")==nil - end - -# if defined?(self.class.text_properties) -# self.class.text_properties.each do |p| -# node << REXML::TextElement.new(p.xml_alias,self.send(p)) -# end -# end - #node << REXML::TextElement.new(:qsar_title.xml_alias,qsar_title) - #node << REXML::TextElement.new(:qsar_models.xml_alias,qsar_models) - -# if defined?(self.class.catalog_entries) -# self.class.catalog_entries.each do |p| #,associatedClass| -# -# assoc_node = REXML::Element.new( p.xml_alias ) -# self.send(p).each{ |s| s.to_XML( assoc_node ) } -# node << assoc_node -# end -# end -# -# if defined?(self.class.catalog_name) -# catalog_node = $catalogs_node.elements[self.class.catalog_name] -# node_ref = REXML::Element.new(self.class.catalog_element+"_ref") -# -# raise "id is nil" if self.id==nil || self.id.to_s.size==0 -# element_id = self.class.catalog_element+"_"+self.id.to_s -# node_ref.add_attributes("idref"=>element_id,"catalog"=>self.class.catalog_name) -# -# content_node = REXML::Element.new(self.class.catalog_element) -# content_node.add_attribute("id",element_id) -# self.class.attribute_properties.each do |p| -# content_node.add_attribute p.xml_alias,send(p) -# end -# catalog_node << content_node -# node << node_ref -# -## def catalog_to_xml(node, catalog_name, element_name, attributes) -## catalog_node = $catalogs_node.elements[catalog_name] -## node_ref = REXML::Element.new(element_name+"_ref") -## attributes["id"] = element_name+"_"+attributes.delete("id").to_s -## node_ref.add_attributes("idref"=>attributes["id"],"catalog"=>catalog_name) -## content_node = REXML::Element.new(element_name) -## #puts "my attribts: "+attributes.inspect -## attributes.each do |k,v| -## content_node.add_attribute k,v.to_s -## end -## catalog_node << content_node -## node << node_ref -## end -# end - - -# node << REXML::TextElement.new(:qsar_title.xml_alias,qsar_title) -# node << REXML::TextElement.new(:qsar_models.xml_alias,qsar_models) -# qsar_software_node = REXML::Element.new(:qsar_software.xml_alias) -# qsar_software.each{ |s| s.to_xml( qsar_software_node ) } -# node << qsar_software_node - end - -end - - -module ReachReports - - def self.get_uri( report ) - raise "internal error, id not set "+to_yaml if report.id==nil - return $url_provider.url_for("/"+File.join(report.type,report.id.to_s), :full).to_s - end - - - - -# module CatalogEntry -# -# def catalog_to_xml(node, catalog_name, element_name, attributes) -# catalog_node = $catalogs_node.elements[catalog_name] -# node_ref = REXML::Element.new(element_name+"_ref") -# attributes["id"] = element_name+"_"+attributes.delete("id").to_s -# node_ref.add_attributes("idref"=>attributes["id"],"catalog"=>catalog_name) -# content_node = REXML::Element.new(element_name) -# #puts "my attribts: "+attributes.inspect -# attributes.each do |k,v| -# content_node.add_attribute k,v.to_s -# end -# catalog_node << content_node -# node << node_ref -# end -# end - -# class QsarSoftware -# include DataMapper::Resource #, CatalogEntry -# -# property :id, Serial -# property :contact, String, :length => 255 -# property :description, String, :length => 255 -# property :name, String, :length => 255 -# property :number, String, :length => 255 -# property :url, String, :length => 255 -# -# def self.attribute_properties -# [ :contact, :description, :name, :number, :url ] -# end -# -# def self.catalog_name -# "software_catalog" -# end -# -# def self.catalog_element -# "software" -# end -# -# belongs_to :qsar_identifier -# end - - class Software - include DataMapper::Resource #, CatalogEntry - - property :id, Serial - property :contact, String, :length => 255 - property :description, String, :length => 255 - property :name, String, :length => 255 - property :number, String, :length => 255 - property :url, String, :length => 255 - - def xml_infos - [ AttributeProperty.new(:contact), - AttributeProperty.new(:description), - AttributeProperty.new(:name), - AttributeProperty.new(:number), - AttributeProperty.new(:url) ] - end - end - - class QsarSoftware < Software - #belongs_to :qsar_identifier, :key => false - property :qsar_identifier_id, Integer - end - - class XmlInfo - - attr_accessor :prop - - protected - def initialize( prop ) - @prop = prop - end - - public - def xml_prop - @prop.xml_alias - end - end - - class TextNodeProperty < XmlInfo - - end - - class TextSubnodeProperty < XmlInfo - attr_accessor :parent_prop - - def initialize( prop, parent_prop ) - super(prop) - @parent_prop = parent_prop - end - end - - class AttributeProperty < XmlInfo - - end - - class AttributeNodeProperty < XmlInfo - - end - - class AttributeSubNodeListProperty < XmlInfo - - attr_accessor :list_element, :parent_prop - - def initialize( prop, list_element, parent_prop ) - super(prop) - @list_element = list_element - @parent_prop = parent_prop - end - end - - class SingleAttributeNodeProperty < XmlInfo - attr_accessor :attribute - - def initialize( prop, attribute ) - super(prop) - @attribute = attribute - end - end - - class CatalogReference < XmlInfo - attr_accessor :catalog_name, :catalog_element - - def initialize( prop, catalog_name, catalog_element ) - super(prop) - @catalog_name = catalog_name - @catalog_element = catalog_element - end - end - - - class QsarIdentifier - include DataMapper::Resource - - property :id, Serial - property :qsar_title, Text - property :qsar_models, Text - - has n, :qsar_software - - def xml_infos - [ TextNodeProperty.new(:qsar_title), - TextNodeProperty.new(:qsar_models), - CatalogReference.new(:qsar_software, "software_catalog", "software") ] - end - - belongs_to :qmrf_report - end - - class Author - include DataMapper::Resource - - property :id, Serial - property :affiliation, String, :length => 255 - property :contact, String, :length => 255 - property :email, String, :length => 255 - property :name, String, :length => 255 - property :number, String, :length => 255 - property :url, String, :length => 255 - - def xml_infos - [ AttributeProperty.new(:affiliation), - AttributeProperty.new(:contact), - AttributeProperty.new(:email), - AttributeProperty.new(:name), - AttributeProperty.new(:number), - AttributeProperty.new(:url) ] - end - - belongs_to :qsar_general_information - end - - class QmrfAuthor < Author - property :type, String, :default => "QmrfAuthor" - end - - class ModelAuthor < Author - property :type, String, :default => "ModelAuthor" - end - - class Publication - include DataMapper::Resource - - property :id, Serial - property :title, Text - property :url, String, :length => 255 - - def xml_infos - [ AttributeProperty.new(:title), - AttributeProperty.new(:url) ] - end - end - - class Reference < Publication - #belongs_to :qsar_general_information - property :qsar_general_information_id, Integer - end - - - class QsarGeneralInformation - include DataMapper::Resource - - property :id, Serial - property :qmrf_date, Text #String, :length => 255 #PENDING -> datetime - property :model_date, Text #String, :length => 255 #PENDING -> datetime - property :qmrf_date_revision, Text #String, :length => 255 #PENDING -> datetime - property :qmrf_revision, Text - property :model_date, Text - property :info_availability, Text - property :related_models, Text - - # type is needed to distinguish between authors - # (the datamapper creates a table "Authors", the relation is defined by QsarGeneral.id and Author.id) - has n, :qmrf_authors, :type => "QmrfAuthor" - has n, :model_authors, :type => "ModelAuthor" - has n, :references - - def xml_infos - [ TextNodeProperty.new(:qmrf_date), - CatalogReference.new(:qmrf_authors, "authors_catalog", "author"), - TextNodeProperty.new(:qmrf_date_revision), - TextNodeProperty.new(:qmrf_revision), - CatalogReference.new(:model_authors, "authors_catalog", "author"), - TextNodeProperty.new(:model_date), - CatalogReference.new(:references, "publications_catalog", "publication"), - TextNodeProperty.new(:info_availability), - TextNodeProperty.new(:related_models) ] - end - - belongs_to :qmrf_report - end - - class ModelEndpoint - include DataMapper::Resource - - property :id, Serial - property :group, String, :length => 255 - property :name, String, :length => 255 - property :subgroup, String, :length => 255 - - def xml_infos - [ AttributeProperty.new(:group), - AttributeProperty.new(:name), - AttributeProperty.new(:subgroup) ] - end - - belongs_to :qsar_endpoint - end - - class QsarEndpoint - include DataMapper::Resource - - property :id, Serial - property :endpoint_variable, Text - property :model_species, Text - property :endpoint_comments, Text - property :endpoint_units, Text - property :endpoint_protocol, Text - property :endpoint_data_quality, Text - - has n, :model_endpoint - - def xml_infos - [ TextNodeProperty.new(:model_species), - CatalogReference.new(:model_endpoint, "endpoints_catalog", "endpoint"), - TextNodeProperty.new(:endpoint_comments), - TextNodeProperty.new(:endpoint_units), - TextNodeProperty.new(:endpoint_variable), - TextNodeProperty.new(:endpoint_protocol), - TextNodeProperty.new(:endpoint_data_quality) ] - end - - belongs_to :qmrf_report - end - - class AlgorithmExplicit - include DataMapper::Resource - - property :id, Serial - property :definition, Text - property :description, Text - property :publication_ref, Text - - def xml_infos - [ AttributeProperty.new(:definition), - AttributeProperty.new(:description), - AttributeProperty.new(:publication_ref) ] - end - - belongs_to :qsar_algorithm - end - - class AlgorithmsDescriptor - include DataMapper::Resource - - property :id, Serial - property :description, Text - property :name, Text - property :publication_ref, Text - property :units, Text - - def xml_infos - [ AttributeProperty.new(:description), - AttributeProperty.new(:name), - AttributeProperty.new(:publication_ref), - AttributeProperty.new(:units) ] - end - - belongs_to :qsar_algorithm - end - - class DescriptorsGenerationSoftware < Software - - #belongs_to :qsar_algorithm, :key => false - property :qsar_algorithm_id, Integer - end - - class QsarAlgorithm - include DataMapper::Resource - - property :id, Serial - - property :algorithm_type, Text - property :descriptors_selection, Text - property :descriptors_generation, Text - property :descriptors_chemicals_ratio, Text - property :equation, Text - - has n, :algorithm_explicit - has n, :algorithms_descriptors - has n, :descriptors_generation_software - - def xml_infos - [ TextNodeProperty.new(:algorithm_type), - CatalogReference.new(:algorithm_explicit, "algorithms_catalog", "algorithm"), - TextSubnodeProperty.new(:equation, :algorithm_explicit), - CatalogReference.new(:algorithms_descriptors, "descriptors_catalog", "descriptor"), - TextNodeProperty.new(:descriptors_selection), - TextNodeProperty.new(:descriptors_generation), - CatalogReference.new(:descriptors_generation_software, "software_catalog", "software"), - TextNodeProperty.new(:descriptors_chemicals_ratio), - ] - end - - belongs_to :qmrf_report - end - - class AppDomainSoftware < Software - - #belongs_to :qsar_algorithm, :key => false - property :qsar_applicability_domain_id, Integer - end - - class QsarApplicabilityDomain - include DataMapper::Resource - - property :id, Serial - property :app_domain_description, Text - property :app_domain_method, Text - property :applicability_limits, Text - - has n,:app_domain_software - - def xml_infos - [ TextNodeProperty.new(:app_domain_description), - TextNodeProperty.new(:app_domain_method), - CatalogReference.new(:app_domain_software, "software_catalog", "software"), - TextNodeProperty.new(:applicability_limits), ] - end - - belongs_to :qmrf_report - - end - - class DatasetData - include DataMapper::Resource - - property :id, Serial - property :chemname, String, :default => "No" - property :cas, String, :default => "No" - property :smiles, String, :default => "No" - property :inchi, String, :default => "No" - property :mol, String, :default => "No" - property :formula, String, :default => "No" - - def xml_infos - [ AttributeProperty.new(:chemname), - AttributeProperty.new(:cas), - AttributeProperty.new(:smiles), - AttributeProperty.new(:inchi), - AttributeProperty.new(:mol), - AttributeProperty.new(:formula) ] - end - - end - - class TrainingSetData < DatasetData - - #belongs_to :qsar_robustness - property :qsar_robustness_id, Integer - end - - - class QsarRobustness - include DataMapper::Resource - - property :id, Serial - property :training_set_availability, String, :default => "No" - property :training_set_descriptors, String, :default => "No" - property :dependent_var_availability, String, :default => "No" - property :other_info, Text - property :preprocessing, Text - property :goodness_of_fit, Text - property :loo, Text - property :lmo, Text - property :yscrambling, Text - property :bootstrap, Text - property :other_statistics, Text - - has 1, :training_set_data, :model => "TrainingSetData" - - def xml_infos - [ SingleAttributeNodeProperty.new(:training_set_availability, "answer"), - AttributeNodeProperty.new(:training_set_data), - SingleAttributeNodeProperty.new(:training_set_descriptors, "answer"), - SingleAttributeNodeProperty.new(:dependent_var_availability, "answer"), - TextNodeProperty.new(:other_info), - TextNodeProperty.new(:preprocessing), - TextNodeProperty.new(:goodness_of_fit), - TextNodeProperty.new(:loo), - TextNodeProperty.new(:lmo), - TextNodeProperty.new(:yscrambling), - TextNodeProperty.new(:bootstrap), - TextNodeProperty.new(:other_statistics), - ] - end - - belongs_to :qmrf_report - - end - - - class ValidationSetData < DatasetData - - #belongs_to :qsar_predictivity - property :qsar_predictivity_id, Integer - end - - class QsarPredictivity - include DataMapper::Resource - - property :id, Serial - - property :validation_set_availability, String, :default => "No" - property :validation_set_descriptors, String, :default => "No" - property :validation_dependent_var_availability, String, :default => "No" - property :validation_other_info, Text - property :experimental_design, Text - property :validation_predictivity, Text - property :validation_assessment, Text - property :validation_comments, Text - - has 1, :validation_set_data, :model => "ValidationSetData" - - def xml_infos - [ SingleAttributeNodeProperty.new(:validation_set_availability, "answer"), - AttributeNodeProperty.new(:validation_set_data), - SingleAttributeNodeProperty.new(:validation_set_descriptors, "answer"), - SingleAttributeNodeProperty.new(:validation_dependent_var_availability, "answer"), - TextNodeProperty.new(:validation_other_info), - TextNodeProperty.new(:experimental_design), - TextNodeProperty.new(:validation_predictivity), - TextNodeProperty.new(:validation_assessment), - TextNodeProperty.new(:validation_comments), - ] - end - - belongs_to :qmrf_report - end - - class QsarInterpretation - include DataMapper::Resource - - property :id, Serial - property :mechanistic_basis, Text - property :mechanistic_basis_comments, Text - property :mechanistic_basis_info, Text - - def xml_infos - [ TextNodeProperty.new(:mechanistic_basis), - TextNodeProperty.new(:mechanistic_basis_comments), - TextNodeProperty.new(:mechanistic_basis_info), - ] - end - - belongs_to :qmrf_report - end - - class Bibliography < Publication - - #belongs_to :qsar_miscellaneous - property :qsar_miscellaneous_id, Integer - end - - class Attachment - include DataMapper::Resource - - property :id, Serial - property :description, Text - property :filetype, String - property :url, String, :length => 255 - - def xml_infos - [ AttributeProperty.new(:description), - AttributeProperty.new(:filetype), - AttributeProperty.new(:url), - ] - end - - belongs_to :qsar_miscellaneous - end - - class AttachmentTrainingData < Attachment - property :type, String, :default => "AttachmentTrainingData" - end - - class AttachmentValidationData < Attachment - property :type, String, :default => "AttachmentValidationData" - end - - class AttachmentDocument < Attachment - property :type, String, :default => "AttachmentDocument" - end - - - class QsarMiscellaneous - include DataMapper::Resource - - property :id, Serial - property :comments, Text - - has n, :bibliography, Text - - # type is needed to distinguish between attachments - # (the datamapper creates a table "Attachments", the relation is defined by QsarMisc.id and Attachment.id) - has n, :attachment_training_data, :model => "AttachmentValidationData", :type => "AttachmentTrainingData" - has n, :attachment_validation_data, :model => "AttachmentValidationData", :type => "AttachmentValidationData" - has n, :attachment_documents, :type => "AttachmentDocument" - - def xml_infos - [ TextNodeProperty.new(:comments), - CatalogReference.new(:bibliography,"publications_catalog", "publication"), - AttributeSubNodeListProperty.new(:attachment_training_data, :molecules, :attachments), - AttributeSubNodeListProperty.new(:attachment_validation_data, :molecules, :attachments), - AttributeSubNodeListProperty.new(:attachment_documents, :documents, :attachments), - ] - end - - belongs_to :qmrf_report - end - - class QmrfSummary - include DataMapper::Resource - - property :id, Serial - property :qmrf_number, Text - property :date_publication, Text - property :keywords, Text - property :summary_comments, Text - - def xml_infos - [ TextNodeProperty.new(:qmrf_number), - TextNodeProperty.new(:date_publication), - TextNodeProperty.new(:keywords), - TextNodeProperty.new(:summary_comments), - ] - end - - belongs_to :qmrf_report - end - - class QmrfReport - include DataMapper::Resource, REXML - - property :id, Serial - property :model_uri, String, :length => 255 - - CHAPTERS = [ :qsar_identifier, :qsar_general_information, :qsar_endpoint, :qsar_algorithm, - :qsar_applicability_domain, :qsar_robustness, :qsar_predictivity, :qsar_interpretation, - :qsar_miscellaneous, :qmrf_summary ] - - CHAPTERS.each{ |c,clazz| has 1, c } - - attr_accessor :subjectid - - after :save, :check_policy - private - def check_policy - raise "no id" unless @id - #raise "no subjectid" unless subjectid - OpenTox::Authorization.check_policy(report_uri, subjectid) - end - - public - def to_yaml - super(:methods => CHAPTERS) - end - - def report_uri - return $url_provider.url_for("/reach_report/QMRF/"+@id.to_s, :full).to_s - end - - def self.from_xml(report, xml_data) - - raise "xml data size < 255, probably no qmrf report : '"+xml_data.to_s+"'" if xml_data.to_s.size<255 - doc = Document.new xml_data - - root = doc.elements["QMRF"] - raise "no QMRF node found" unless root - chapters = root.elements["QMRF_chapters"] - raise "no chapter node found" unless chapters - $catalogs_node = root.elements["Catalogs"] - raise "catalogs not found" unless $catalogs_node - - CHAPTERS.each do |p| #, chapterClass| - #unless report.send(p) - report.send(p).destroy if report.send(p) - c = report.association_class(p).new #chapterClass.new - #c.save - report.send(p.to_s+"=",c) - #end - report.send(p).from_xml( chapters.elements[p.xml_alias] ) - end - - #raise "already exists" if report.qsar_identifier - #report.qsar_general_information.destroy if report.qsar_general_information - #report.qsar_identifier.clear - #report.qsar_general_information = QsarGeneralInformation.new - #report.qsar_general_information.qmrf_date = "DateTime.now" - #report.qsar_general_information.model_authors << ModelAuthor.new - #report.qsar_general_information.qmrf_authors << QmrfAuthor.new - - #report.qsar_identifier = QsarIdentifier.new unless report.qsar_identifier - #report.qsar_identifier.from_xml( chapters.elements[:qsar_identifier.xml_alias] ) - - #report.qsar_general_information = QsarGeneralInformation.new unless report.qsar_general_information - #report.qsar_general_information.from_xml( chapters.elements[:qsar_general_information.xml_alias] ) - - - #QsarGeneralInformation.from_xml( report.qsar_general_information, chapters.elements["qsar_general_information".xml_alias] ) - - #puts "set qsar_identifier to "+report.qsar_identifier.class.to_s - -# begin - report.save -# rescue DataObjects::SQLError => e -# puts e.message -# exit -# rescue DataObjects::DataError => e -# puts e.message -# exit -# rescue DataMapper::SaveFailureError => e -# puts e.resource.errors.inspect -# exit -# end - -# puts "XXXXXXXxxxxx" -# -# puts "1" -# puts report.qsar_miscellaneous.attachment_training_data.inspect -# puts "2" -# puts report.qsar_miscellaneous.attachment_validation_data.inspect -# puts "3" -# puts report.qsar_miscellaneous.attachment_documents.inspect -# -# -# r = QmrfReport.get(report.id) -# -# puts "1" -# puts r.qsar_miscellaneous.attachment_training_data.inspect -# puts "2" -# puts r.qsar_miscellaneous.attachment_validation_data.inspect -# puts "3" -# puts r.qsar_miscellaneous.attachment_documents.inspect -# -# exit - - - end - - def to_xml - #puts "now qsar_identifier is "+self.qsar_identifier.class.to_s - - doc = Document.new - decl = XMLDecl.new - decl.encoding = "UTF-8" - doc << decl - type = DocType.new('QMRF SYSTEM "http://ambit.sourceforge.net/qmrf/jws/qmrf.dtd"') - doc << type - - root = Element.new("QMRF") - root.add_attributes( "version" => 1.2, "schema_version" => 1.0, "name" => "(Q)SAR Model Reporting Format", - "author" => "Joint Research Centre, European Commission", "contact" => "Joint Research Centre, European Commission", - "date" => "July 2007", "email" => "qsardb@jrc.it", "url" => "http://ecb.jrc.ec.europa.eu/qsar/" ) - - catalogs = Element.new("Catalogs") - [ "software_catalog", "algorithms_catalog", "descriptors_catalog", - "endpoints_catalog", "publications_catalog", "authors_catalog"].each do |c| - catalogs << Element.new(c) - end - $catalogs_node = catalogs - - chapters = Element.new("QMRF_chapters") - chapter_count = 1 - - CHAPTERS.each do |p| - node = Element.new( p.xml_alias ) - node.add_attribute("chapter",chapter_count) - self.send(p.to_s+"=", self.association_class(p).new) unless self.send(p) # create empy chapter, as xml must be complete - self.send(p).to_XML( node, chapter_count ) - chapters << node - chapter_count += 1 - end - -# qsar_identifier_node = Element.new(:qsar_identifier.xml_alias) -# self.qsar_identifier.to_XML( qsar_identifier_node ) -# chapters << qsar_identifier_node -# -# qsar_general_information_node = Element.new(:qsar_general_information.xml_alias) -# self.qsar_general_information.to_XML( qsar_general_information_node ) -# chapters << qsar_general_information_node - - - -# [ @qsar_identifier, @qsar_general_information, @qsar_endpoint ].each do |c| -# n = c.to_xml -# raise "no node "+n.to_s+" "+n.class.to_s unless n.is_a?(Element) -# chapters << n -# end - - root << chapters - root << catalogs - doc << root - - s = "" - doc.write(s, 2, false, false) - return s - - end - end - -#Profile2.auto_upgrade! - -# class QmrfReport < ActiveRecord::Base -# -# alias_attribute :date, :created_at -# -# QmrfProperties.serialized_properties.each do |p| -# serialize p -# end -# -# def type -# "QMRF" -# end -# -# def report_uri -# ReachReports.get_uri(self) -# end -# -# def get_content -# hash = {} -# [ :model_uri, :date ].each{ |p| hash[p] = self.send(p) } -# QmrfProperties.properties.each{ |p| hash[p] = self.send(p) } -# return hash -# end -# end -# -# -# class QprfReport < ActiveRecord::Base -# -# alias_attribute :date, :created_at -# -# def report_uri -# ReachReports.get_uri(self) -# end -# -# def type -# "QPRF" -# end -# end - - mysql_lite_retry do - [ QsarSoftware, QsarIdentifier, QmrfAuthor, ModelAuthor, Reference, QsarGeneralInformation, ModelEndpoint, QsarEndpoint, AlgorithmExplicit, - AlgorithmsDescriptor, DescriptorsGenerationSoftware, QsarAlgorithm, AppDomainSoftware, QsarApplicabilityDomain, TrainingSetData, - QsarRobustness, ValidationSetData, QsarPredictivity, QsarInterpretation, Bibliography, AttachmentTrainingData, AttachmentValidationData, - AttachmentDocument, QsarMiscellaneous, QmrfSummary, QmrfReport ].each do |model| - model.auto_upgrade! - model.raise_on_save_failure = true - end - - end - -end
\ No newline at end of file diff --git a/reach_reports/reach_service.rb b/reach_reports/reach_service.rb deleted file mode 100755 index 5dd68e1..0000000 --- a/reach_reports/reach_service.rb +++ /dev/null @@ -1,328 +0,0 @@ - -class Array - - def to_html - return "" unless size>0 - s = "<html>\n<head>\n</head>\n<body>\n" - s += join(" <br>\n") - s += "</body>\n</html>\n" - return s - end -end - -module ReachReports - - def self.list_reports(type, model_uri=nil) - case type - when /(?i)QMRF/ - params = {} - params[:model_uri]=model_uri if model_uri - ReachReports::QmrfReport.all(params).collect{ |r| r.report_uri }.join("\n")+"\n" - when /(?i)QPRF/ - ReachReports::QprfReport.all.collect{ |r| r.report_uri }.join("\n")+"\n" - end - end - - def self.create_report( type, params, subjectid, xml_data=nil ) - - case type - when /(?i)QMRF/ - if params[:model_uri] - task = OpenTox::Task.create( "Create "+type+" report", - $url_provider.url_for("/reach_report/"+type, :full) ) do |task| #, params - - report = ReachReports::QmrfReport.new :model_uri => params[:model_uri] - report.subjectid = subjectid - build_qmrf_report(report, task) - report.report_uri - end - result_uri = task.uri - elsif xml_data and (input = xml_data.read).to_s.size>0 - report = ReachReports::QmrfReport.new - report.subjectid = subjectid - ReachReports::QmrfReport.from_xml(report,input) - result_uri = report.report_uri - else - raise OpenTox::BadRequestError.new "illegal parameters for qmrf-report creation, either\n"+ - "* give 'model_uri' as param\n"+ - "* provide xml file\n"+ - "params given: "+params.inspect - end - when /(?i)QPRF/ - raise OpenTox::BadRequestError.new "qprf report creation not yet implemented" - if params[:compound_uri] - #report = ReachReports::QprfReport.new :compound_uri => params[:compound_uri] - else - raise OpenTox::BadRequestError.new "illegal parameters for qprf-report, use either\n"+ - "* compound-uri\n"+ - "params given: "+params.inspect - end - end - result_uri - end - - def self.build_qmrf_report(r, task=nil) - - #puts r.model_uri - model = OpenTox::Model::Generic.find(r.model_uri, r.subjectid) - feature_type = model.feature_type(r.subjectid) - - # chapter 1 - r.qsar_identifier = QsarIdentifier.new - r.qsar_identifier.qsar_title = model.metadata[DC.title] - # TODO QSAR_models -> sparql same endpoint - r.qsar_identifier.qsar_software << QsarSoftware.new( :url => model.uri, - :name => model.metadata[DC.title], :contact => model.metadata[DC.creator] ) - algorithm = OpenTox::Algorithm::Generic.find(model.metadata[OT.algorithm], r.subjectid) if model.metadata[OT.algorithm] - r.qsar_identifier.qsar_software << QsarSoftware.new( :url => algorithm.uri, :name => algorithm.metadata[DC.title] ) - task.progress(10) if task - - #chpater 2 - r.qsar_general_information = QsarGeneralInformation.new - r.qsar_general_information.qmrf_date = DateTime.now.to_s - # EMPTY: qmrf_authors, qmrf_date_revision, qmrf_revision - # TODO: model_authors ? - r.qsar_general_information.model_date = model.metadata[DC.date].to_s - # TODO: references? - # EMPTY: info_availablity - # TODO: related_models = find qmrf reports for QSAR_models - task.progress(20) if task - - # chapter 3 - # TODO "model_species" ? - r.qsar_endpoint = QsarEndpoint.new - model.metadata[OT.predictedVariables].each do |p| - r.qsar_endpoint.model_endpoint << ModelEndpoint.new( :name => p ) - end if model.metadata[OT.predictedVariables] - # TODO "endpoint_comments" => "3.3", "endpoint_units" => "3.4", - r.qsar_endpoint.endpoint_variable = model.metadata[OT.dependentVariables] if model.metadata[OT.dependentVariables] - # TODO "endpoint_protocol" => "3.6", "endpoint_data_quality" => "3.7", - task.progress(30) if task - - # chapter 4 - # TODO algorithm_type (='type of model') - # TODO algorithm_explicit.equation - # TODO algorithm_explicit.algorithms_catalog - # TODO algorithms_descriptors, descriptors_selection, descriptors_generation, descriptors_generation_software, descriptors_chemicals_ratio - task.progress(40) if task - - # chapter 5 - # TODO app_domain_description, app_domain_method, app_domain_software, applicability_limits - - #training_dataset = model.trainingDataset ? OpenTox::Dataset.find(model.trainingDataset+"/metadata") : nil - if ( OpenTox::Dataset.exist?(model.metadata[OT.trainingDataset], r.subjectid) ) - training_dataset = OpenTox::Dataset.new( model.metadata[OT.trainingDataset], r.subjectid ) - training_dataset.load_metadata( r.subjectid ) - else - training_dataset = nil - LOGGER.warn "build qmrf: training_dataset not found "+model.metadata[OT.trainingDataset].to_s - end - task.progress(50) if task - - # chapter 6 - r.qsar_robustness = QsarRobustness.new - if training_dataset - r.qsar_robustness.training_set_availability = "Yes" - r.qsar_robustness.training_set_data = TrainingSetData.new(:chemname => "Yes", :cas => "Yes", - :smiles => "Yes", :inchi => "Yes", :mol => "Yes", :formula => "Yes") - end - - #TODO "training_set_data" => "6.2", - # "training_set_descriptors" => "6.3", - # "dependent_var_availability" => "6.4", "other_info" => "6.5", "preprocessing" => "6.6", "goodness_of_fit" => "6.7", - # "loo" => "6.8", - - val_datasets = [] - - if algorithm - 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.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 - - lmo = [ "found "+cvs.size.to_s+" crossvalidation/s for algorithm '"+algorithm.uri.to_s+"'" ] - if cvs.size>0 - cvs_same_data = [] - cvs_other_data = [] - cvs.each do |cv| - if cv.dataset_uri == model.metadata[OT.trainingDataset] - cvs_same_data << cv - else - cvs_other_data << cv - end - end - lmo << cvs_same_data.size.to_s+" crossvalidations/s where performed on the training dataset of the model ("+ - model.metadata[OT.trainingDataset].to_s+")" - lmo << cvs_other_data.size.to_s+" crossvalidations/s where performed on the other datasets" - lmo << "" - - {cvs_same_data => "training dataset", cvs_other_data => "other datasets"}.each do |cvs,desc| - next if cvs.size==0 - lmo << "crossvalidation/s on "+desc - cvs.each do |cv| - begin - lmo << "crossvalidation: "+cv.crossvalidation_uri - lmo << "dataset (see 9.3 Validation data): "+cv.dataset_uri - val_datasets << cv.dataset_uri - lmo << "settings: num-folds="+cv.num_folds.to_s+", random-seed="+cv.random_seed.to_s+", stratified:"+cv.stratified.to_s - - val = YAML.load( OpenTox::RestClientWrapper.get(File.join(cv.crossvalidation_uri,"statistics"),{:subjectid => r.subjectid}) ) - case feature_type - when "classification" - lmo << "percent_correct: "+val[OT.classificationStatistics][OT.percentCorrect].to_s - lmo << "weighted AUC: "+val[OT.classificationStatistics][OT.weightedAreaUnderRoc].to_s - when "regression" - lmo << "root_mean_squared_error: "+val[OT.regressionStatistics][OT.rootMeanSquaredError].to_s - lmo << "r_square "+val[OT.regressionStatistics][OT.rSquare].to_s - end - reports = OpenTox::RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"], - "report/crossvalidation?crossvalidation_uris="+cv.crossvalidation_uri),{:subjectid => r.subjectid}) - if reports and reports.chomp.size>0 - lmo << "for more info see report: "+reports.split("\n")[0] - else - lmo << "for more info see report: not yet created for '"+cv.crossvalidation_uri+"'" - end - rescue => ex - LOGGER.warn "could not add cv "+cv.crossvalidation_uri+" : "+ex.message - end - end - lmo << "" - end - end - else - lmo = [ "no prediction algortihm for model found, crossvalidation not possible" ] - end - r.qsar_robustness.lmo = lmo.to_html - # "lmo" => "6.9", "yscrambling" => "6.10", "bootstrap" => "6.11", "other_statistics" => "6.12", - - LOGGER.debug "looking for validations with "+{:model_uri => model.uri}.inspect - #vals = Lib::Validation.find(:all, :conditions => {:model_uri => model.uri}) - vals = Validation::Validation.find({:model_uri => model.uri}) - uniq_vals = [] - vals.each do |val| - match = false - uniq_vals.each do |val2| - if val.test_dataset_uri == val2.test_dataset_uri - match = true - break - end - end - uniq_vals << val unless match - end - - r.qsar_predictivity = QsarPredictivity.new - if uniq_vals.size > 0 - r.qsar_predictivity.validation_set_availability = "Yes" - r.qsar_predictivity.validation_set_data = ValidationSetData.new(:chemname => "Yes", :cas => "Yes", - :smiles => "Yes", :inchi => "Yes", :mol => "Yes", :formula => "Yes") - - v = [ "found '"+uniq_vals.size.to_s+"' test-set validations of model '"+model.uri+"'" ] - v << "" - uniq_vals.each do |validation| - v << "validation: "+validation.validation_uri - v << "dataset (see 9.3 Validation data): "+validation.test_dataset_uri - val_datasets << validation.test_dataset_uri - case feature_type - when "classification" - v << "percent_correct: "+validation.classification_statistics[:percent_correct].to_s - v << "average AUC: "+validation.classification_statistics[:average_area_under_roc].to_s - when "regression" - v << "root_mean_squared_error: "+validation.regression_statistics[:root_mean_squared_error].to_s - v << "r_square "+validation.regression_statistics[:r_square].to_s - end - report = OpenTox::ValidationReport.find_for_validation(validation.validation_uri,r.subjectid) - #reports = OpenTox::RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"], - # "report/validation?validation_uris="+validation.validation_uri),{:subjectid => r.subjectid}) - if report - v << "for more info see report: "+report.uri - else - v << "for more info see report: not yet created for '"+validation.validation_uri+"'" - end - v << "" - end - else - v = [ "no validation for model '"+model.uri+"' found" ] - end - r.qsar_predictivity.validation_predictivity = v.to_html - task.progress(60) if task - - # chapter 7 - # "validation_set_availability" => "7.1", "validation_set_data" => "7.2", "validation_set_descriptors" => "7.3", - # "validation_dependent_var_availability" => "7.4", "validation_other_info" => "7.5", "experimental_design" => "7.6", - # "validation_predictivity" => "7.7", "validation_assessment" => "7.8", "validation_comments" => "7.9", - task.progress(70) if task - - # chapter 8 - # "mechanistic_basis" => "8.1", "mechanistic_basis_comments" => "8.2", "mechanistic_basis_info" => "8.3", - task.progress(80) if task - - # chapter 9 - # "comments" => "9.1", "bibliography" => "9.2", "attachments" => "9.3", - - r.qsar_miscellaneous = QsarMiscellaneous.new - - r.qsar_miscellaneous.attachment_training_data << AttachmentTrainingData.new( - { :description => training_dataset.title, - :filetype => "owl-dl", - :url => training_dataset.uri} ) if training_dataset - - val_datasets.each do |data_uri| - if OpenTox::Dataset.exist?(data_uri, r.subjectid) - d = OpenTox::Dataset.new(data_uri, r.subjectid) - d.load_metadata( r.subjectid) - r.qsar_miscellaneous.attachment_validation_data << AttachmentValidationData.new( - { :description => d.title, - :filetype => "owl-dl", - :url => data_uri} ) - end - end - task.progress(90) if task - - mysql_lite_retry do - r.save - end - task.progress(100) if task - end - -# def self.get_report_content(type, id, *keys) -# -# report_content = get_report(type, id).get_content -# keys.each do |k| -# $sinatra.raise OpenTox::BadRequestError.new type+" unknown report property '#{key}'" unless report_content.is_a?(Hash) and report_content.has_key?(k) -# report_content = report_content[k] -# end -# report_content -# end - - def self.get_report(type, id) - report = nil - mysql_lite_retry(3) do - case type - when /(?i)QMRF/ - report = ReachReports::QmrfReport.get(id) - when /(?i)QPRF/ - report = ReachReports::QprfReport.get(id) - end - raise OpenTox::NotFoundError.new type+" report with id '#{id}' not found." unless report - end - return report - end - - def self.delete_report(type, id, subjectid=nil) - - case type - when /(?i)QMRF/ - report = ReachReports::QmrfReport.get(id) - when /(?i)QPRF/ - report = ReachReports::QprfReport.get(id) - end - raise OpenTox::NotFoundError.new type+" report with id '#{id}' not found." unless report - OpenTox::Authorization.delete_policies_from_uri(report.report_uri, subjectid) if subjectid - return report.destroy - end - -end diff --git a/reach_reports/reach_test.rb b/reach_reports/reach_test.rb deleted file mode 100755 index 43aec28..0000000 --- a/reach_reports/reach_test.rb +++ /dev/null @@ -1,284 +0,0 @@ - -require "rubygems" -require "sinatra" -before { - request.env['HTTP_HOST']="local-ot/validation" - request.env["REQUEST_URI"]=request.env["PATH_INFO"] -} - -require "uri" -require "yaml" -ENV['RACK_ENV'] = 'test' -require 'application.rb' -require 'test/unit' -require 'rack/test' -require 'lib/test_util.rb' -require 'test/test_examples.rb' - -LOGGER = OTLogger.new(STDOUT) -LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S " -LOGGER.formatter = Logger::Formatter.new - -if AA_SERVER - #TEST_USER = "mgtest" - #TEST_PW = "mgpasswd" - TEST_USER = "guest" - TEST_PW = "guest" - 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 - -#Rack::Test::DEFAULT_HOST = "local-ot/validation" -module Sinatra - module UrlForHelper - BASE = "http://local-ot/validation" - def url_for url_fragment, mode=:path_only - case mode - when :path_only - raise "not impl" - when :full - end - "#{BASE}#{url_fragment}" - end - end - set :raise_errors, false - set :show_exceptions, false -end - - -#DataMapper::Model.raise_on_save_failure = true -# -#class TestResourceX -# include DataMapper::Resource -# -# property :id, Serial -# -# has 1, :test_resource -#end -# -#class DataMapper::Associations::ManyToOne::Relationship -# def get_parent_model -# @parent_model -# end -#end -# -#class TestResource -# include DataMapper::Resource -# -# property :id, Serial -# property :time, DateTime -# property :body, Text -# -# def self.info -# relationships.each do |k,v| -# puts k -# puts v.inspect -# puts v.get_parent_model -# -# end -# end -# #validates_format_of :time -# #validates_length_of :body, :minimum => 1000 -# -# belongs_to :test_resource_x -#end -# -#TestResourceX.auto_upgrade! -#TestResource.auto_upgrade! - -class ReachTest < Test::Unit::TestCase - include Rack::Test::Methods - include Lib::TestUtil - - def app - Sinatra::Application - end - - def test_it - - begin - - # delete '/reach_report/QMRF/3' - # puts last_response.body - - #exit -# testResource = TestResource.new -# -# TestResource.info -# exit - -# p = nil -# #puts TestResource.properties.inspect -# TestResource.properties.each do |pp| -# p = pp if pp.name==:time -# end -# #puts p -# val = "no time" #DateTime.new -# testResource.time = val -# #puts p.valid?(val) -# -# #puts "test restource: "+testResource.valid?.to_s -# -# #puts testResource.time.to_s + " " + testResource.time.class.to_s -# begin -# testResource.save -# rescue DataMapper::SaveFailureError => e -# puts e.message -# puts e.resource.errors.inspect -# end -# exit - - #$test_case = self - -# #file = File.new("qmrf-report.xml") -# file = File.new("/home/martin/win/home/test2.xml") -# raise "File not found: "+file.path.to_s unless File.exist?(file.path) -# data = File.read(file.path) -# #puts "data found "+data.to_s[0..1000] -# puts OpenTox::RestClientWrapper.post("http://local-ot/validation/reach_report/qmrf/20",{:content_type => "application/qmrf-xml"},data).to_s.chomp - -# post "/reach_report/qmrf/8" -# puts last_response.body - - #model_uri = "http://ambit.uni-plovdiv.bg:8080/ambit2/model/173393" - - #model_uri = "http://local-ot/majority/class/model/58" - - - #model_uri = "http://local-ot/model/104" - model_uri = "http://local-ot/model/72" - - -# m = OpenTox::Model::Generic.find(model_uri) -# puts m.metadata[OT.algorithm] if m -# a = OpenTox::Algorithm::Generic.find(m.metadata[OT.algorithm]) -# puts a.metadata.inspect -# exit - - puts SUBJECTID - -# model_uri = "http://local-ot/model/1" - #http://local-ot/majority/class/model/15 - #model_uri = "http://local-ot/majority/class/model/15" - # model_uri = "http://local-ot/majority/class/model/91" - #model_uri = "http://apps.ideaconsult.net:8080/ambit2/model/2" - post '/reach_report/qmrf',{:model_uri=>model_uri, :subjectid => SUBJECTID} #http://local-ot/model/1" - ##post '/reach_report/qprf',:compound_uri=>"http://local-ot/compound/XYZ" - uri = last_response.body - puts "task: "+uri.to_s - uri = Lib::TestUtil.wait_for_task(uri) - if uri - id = uri.split("/")[-1] - puts uri - end - -# id = "8" - - #get '/reach_report/qmrf' - #puts last_response.body - -# get '/reach_report/qmrf/'+id.to_s,nil,'HTTP_ACCEPT'=>"application/x-yaml" -# puts "YAML" -# puts last_response.body - -# get '/reach_report/qmrf/'+id.to_s,nil,'HTTP_ACCEPT'=>"application/rdf+xml" -# puts "RDF" -# puts last_response.body - - #get '/reach_report/qmrf/'+id,nil,'HTTP_ACCEPT' => "application/qmrf-xml" - #puts "XML" - #puts last_response.body - - - #r = ReachReports::QmrfReport.find_like( :QSAR_title => "Hamster") - #puts r.collect{|rr| "report with id:"+rr.id.to_s}.inspect - - #File.new("/home/martin/tmp/qmr_rep_del_me.xml","w").puts last_response.body - #File.new("/home/martin/win/home/qmr_rep_del_me.xml","w").puts last_response.body - #File.new("/home/martin/info_home/.public_html/qmr_rep_del_me.xml","w").puts last_response.body - - rescue => ex - rep = OpenTox::ErrorReport.create(ex, "") - puts rep.to_yaml - end - - - end -end - - -# query = <<EOF -#PREFIX ot:<http://www.opentox.org/api/1.1#> -#PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> -#select ?model -#where { -#?model rdf:type ot:Model -#} -#EOF -# puts OpenTox::RestClientWrapper.post("http://apps.ideaconsult.net:8080/ontology/",{:accept => "application/rdf+xml", :query => query}) -# exit - -#class Person -# include DataMapper::Resource -# -# property :id, Serial -# -# has 1, :profile -# has 1, :profile2 -# end -# -# class Profile -# include DataMapper::Resource -# -# property :id, Serial -# property :val, Text -# -# belongs_to :person -# end -# -# class Profile2 -# include DataMapper::Resource -# -# property :id, Serial -# property :val, Text -# -# belongs_to :person -# end -# -#Person.auto_upgrade! -#Profile.auto_upgrade! -#Profile2.auto_upgrade! -# -# A.auto_upgrade! -# ValTest.auto_upgrade! - #A.auto_migrate! - #ValTest.auto_migrate! - -# class ReachTest < Test::Unit::TestCase -# include Rack::Test::Methods -# include Lib::TestUtil -# -# -# def app -# Sinatra::Application -# end -# -# def test_datamapper -# -# # Assigning a resource to a one-to-one relationship -# puts Person.all.collect{|v| v.id}.inspect -# -# person = Person.create -# person.profile = Profile.new -# person.profile2 = Profile2.new -# person.profile2.val = "bla" -# person.save -# -# p = Person.get(11) -## puts p.profile2 -# puts p.profile2.val - diff --git a/report/environment.rb b/report/environment.rb index 7addc45..58c3b2b 100755 --- a/report/environment.rb +++ b/report/environment.rb @@ -1,9 +1,8 @@ ['rubygems', 'logger', 'fileutils', 'sinatra', 'sinatra/url_for', 'rest_client', 'yaml', 'fileutils', 'mime/types', 'abbrev', - 'rexml/document', 'ruby-plot', 'opentox-ruby' ].each do |g| + 'rexml/document', 'ruby-plot' ].each do |g| require g end -gem 'ruby-plot', "~>0.6.0" module Reports @@ -21,24 +20,24 @@ module Reports end -require "lib/ot_predictions.rb" -require "lib/ohm_util.rb" - -require "report/plot_factory.rb" -require "report/xml_report.rb" -require "report/xml_report_util.rb" -require "report/report_persistance.rb" -require "report/report_content.rb" -require "report/report_factory.rb" -require "report/report_service.rb" -require "report/report_format.rb" -require "report/validation_access.rb" -require "report/validation_data.rb" -require "report/util.rb" -require "report/statistical_test.rb" - -ICON_ERROR = File.join(CONFIG[:services]["opentox-validation"],"resources/error.png") -ICON_OK = File.join(CONFIG[:services]["opentox-validation"],"resources/ok.png") +require "./lib/ot_predictions.rb" +require "./lib/ohm_util.rb" + +require "./report/plot_factory.rb" +require "./report/xml_report.rb" +require "./report/xml_report_util.rb" +require "./report/report_persistance.rb" +require "./report/report_content.rb" +require "./report/report_factory.rb" +require "./report/report_service.rb" +require "./report/report_format.rb" +require "./report/validation_access.rb" +require "./report/validation_data.rb" +require "./report/util.rb" +require "./report/statistical_test.rb" + +ICON_ERROR = File.join($validation[:uri],"resources/error.png") +ICON_OK = File.join($validation[:uri],"resources/ok.png") diff --git a/report/plot_factory.rb b/report/plot_factory.rb index 6e90dbc..6c90594 100644 --- a/report/plot_factory.rb +++ b/report/plot_factory.rb @@ -106,14 +106,13 @@ module Reports train = [] test = [] validation_set.validations.each do |v| - [[v.test_dataset_uri, test, v.test_target_dataset_uri], - [v.training_dataset_uri, train, v.training_dataset_uri]].each do |uri,array,uri2| + [[v.test_dataset_uri, test], + [v.training_dataset_uri, train]].each do |uri,array| d = Lib::DatasetCache.find(uri, validation_set.validations[0].subjectid) - d2 = Lib::DatasetCache.find((uri2 ? uri2 : uri), validation_set.validations[0].subjectid) d.compounds.each do |c| - d2.data_entries[c][v.prediction_feature].each do |val| + d.data_entries[c][v.prediction_feature].each do |val| array << val - end if d2.data_entries[c] and d2.data_entries[c][v.prediction_feature] + end if d.data_entries[c] and d.data_entries[c][v.prediction_feature] end end end @@ -671,8 +670,8 @@ module Reports end end -#require "rubygems" -#require "ruby-plot" +#require "./rubygems" +#require "./ruby-plot" ###Reports::PlotFactory::demo_ranking_plot #class Array # def sum diff --git a/report/report_application.rb b/report/report_application.rb index 5fec6d1..f7528b6 100755 --- a/report/report_application.rb +++ b/report/report_application.rb @@ -1,4 +1,4 @@ -require "report/environment.rb" +require "./report/environment.rb" def perform @@report_service = Reports::ReportService.instance( url_for("/report", :full) ) unless defined?@@report_service diff --git a/report/report_format.rb b/report/report_format.rb index d64bf57..d216782 100644 --- a/report/report_format.rb +++ b/report/report_format.rb @@ -4,7 +4,7 @@ ENV['JAVA_HOME'] = "/usr/bin" unless ENV['JAVA_HOME'] ENV['PATH'] = ENV['JAVA_HOME']+":"+ENV['PATH'] unless ENV['PATH'].split(":").index(ENV['JAVA_HOME']) ENV['SAXON_JAR'] = "saxonhe9-2-0-3j/saxon9he.jar" unless ENV['SAXON_JAR'] -OT_STYLESHEET = File.join(CONFIG[:services]["opentox-validation"],"resources/simple_ot_stylesheet.css") +OT_STYLESHEET = File.join($validation[:uri],"resources/simple_ot_stylesheet.css") # = Reports::ReportFormat # diff --git a/report/report_persistance.rb b/report/report_persistance.rb index ccdebad..447ea16 100755 --- a/report/report_persistance.rb +++ b/report/report_persistance.rb @@ -1,6 +1,6 @@ REPORT_DIR = File.join(Dir.pwd,'/reports') -require "lib/format_util.rb" +require "./lib/format_util.rb" # = Reports::ReportPersistance # diff --git a/report/report_test.rb b/report/report_test.rb index 571d6d8..6989896 100755 --- a/report/report_test.rb +++ b/report/report_test.rb @@ -1,9 +1,9 @@ require "fileutils" ENV['RACK_ENV'] = 'test' -require 'report/report_application.rb' +require './report/report_application.rb' require 'test/unit' require 'rack/test' -require "lib/test_util.rb" +require "./lib/test_util.rb" LOGGER = Logger.new(STDOUT) LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S " @@ -129,12 +129,12 @@ end #class Reports::ReportServiceTest < Test::Unit::TestCase # include Lib::TestUtil # -# WS_VAL = CONFIG[:services]["opentox-validation"] -# WS_DATA=CONFIG[:services]["opentox-dataset"] +# WS_VAL = $validation[:uri] +# WS_DATA=$dataset[:uri] # FILE=File.new("data/hamster_carcinogenicity.owl","r") # -# WS_CLASS_ALG=File.join(CONFIG[:services]["opentox-algorithm"],"lazar") -# WS_FEATURE_ALG=File.join(CONFIG[:services]["opentox-algorithm"],"fminer") +# WS_CLASS_ALG=File.join($algorithm[:uri],"lazar") +# WS_FEATURE_ALG=File.join($algorithm[:uri],"fminer") # # #WS_CLASS_ALG_2="local-ot:4008/algorithm" # #WS_FEATURE_ALG_2=nil diff --git a/report/statistical_test.rb b/report/statistical_test.rb index da46f6b..4b65f0a 100644 --- a/report/statistical_test.rb +++ b/report/statistical_test.rb @@ -1,5 +1,5 @@ -#require "rubygems" -#require "rinruby" +#require "./rubygems" +#require "./rinruby" module Reports diff --git a/report/validation_access.rb b/report/validation_access.rb index e2a3978..a14b397 100755 --- a/report/validation_access.rb +++ b/report/validation_access.rb @@ -1,4 +1,4 @@ -require "lib/validation_db.rb" +require "./lib/validation_db.rb" # = Reports::ValidationDB # @@ -187,8 +187,8 @@ class Reports::ValidationDB def get_predictions(validation, filter_params, subjectid, task) # we need compound info, cannot reuse stored prediction data data = Lib::PredictionData.create( validation.feature_type, validation.test_dataset_uri, - validation.test_target_dataset_uri, validation.prediction_feature, validation.prediction_dataset_uri, - validation.predicted_variable, validation.predicted_confidence, subjectid, OpenTox::SubTask.create(task, 0, 80 ) ) + validation.prediction_feature, validation.prediction_dataset_uri, validation.predicted_variable, + validation.predicted_confidence, subjectid, OpenTox::SubTask.create(task, 0, 80 ) ) data = Lib::PredictionData.filter_data( data.data, data.compounds, filter_params[:min_confidence], filter_params[:min_num_predictions], filter_params[:max_num_predictions] ) if filter_params!=nil task.progress(100) if task @@ -197,14 +197,13 @@ class Reports::ValidationDB def get_accept_values( validation, subjectid=nil ) # PENDING So far, one has to load the whole dataset to get the accept_value from ambit - test_target_datasets = validation.test_target_dataset_uri - test_target_datasets = validation.test_dataset_uri unless test_target_datasets + test_datasets = validation.test_dataset_uri res = nil - test_target_datasets.split(";").each do |test_target_dataset| - d = Lib::DatasetCache.find( test_target_dataset, subjectid ) - raise "cannot get test target dataset for accept values, dataset: "+test_target_dataset.to_s unless d + test_datasets.split(";").each do |test_dataset| + d = Lib::DatasetCache.find( test_dataset, subjectid ) + raise "cannot get test target dataset for accept values, dataset: "+test_dataset.to_s unless d accept_values = d.accept_values(validation.prediction_feature) - raise "cannot get accept values from dataset "+test_target_dataset.to_s+" for feature "+ + raise "cannot get accept values from dataset "+test_dataset.to_s+" for feature "+ validation.prediction_feature+":\n"+d.features[validation.prediction_feature].to_yaml unless accept_values!=nil raise "different accept values" if res && res!=accept_values res = accept_values diff --git a/report/xml_report.rb b/report/xml_report.rb index 5be5fdc..f610677 100755 --- a/report/xml_report.rb +++ b/report/xml_report.rb @@ -2,7 +2,7 @@ # require g #end -require "report/xml_report_util.rb" +require "./report/xml_report_util.rb" ENV['DOCBOOK_DIRECTORY'] = "docbook-xml-4.5" unless ENV['DOCBOOK_DIRECTORY'] ENV['REPORT_DTD'] = "docbookx.dtd" unless ENV['REPORT_DTD'] diff --git a/test/test_examples.rb b/test/test_examples.rb index 2b95cf2..813d0b0 100755 --- a/test/test_examples.rb +++ b/test/test_examples.rb @@ -1,5 +1,5 @@ -require 'test/test_examples_util.rb' +require './test/test_examples_util.rb' class Class def humanize @@ -26,8 +26,8 @@ module ValidationExamples class LazarIrisCrossvalidation < IrisCrossvalidation def initialize - @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer") + @algorithm_uri = File.join($algorithm[:uri],"lazar") + @algorithm_params = "feature_generation_uri="+File.join($algorithm[:uri],"fminer") super end end @@ -43,8 +43,8 @@ module ValidationExamples class LazarIrisSplit < IrisSplit def initialize - @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer") + @algorithm_uri = File.join($algorithm[:uri],"lazar") + @algorithm_params = "feature_generation_uri="+File.join($algorithm[:uri],"fminer") super end end @@ -68,8 +68,8 @@ module ValidationExamples class LazarEPAFHMSplit < EPAFHMSplit def initialize - @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") + @algorithm_uri = File.join($algorithm[:uri],"lazar") + @algorithm_params = "feature_generation_uri="+File.join($algorithm[:uri],"fminer/bbrc") super end end @@ -77,7 +77,7 @@ module ValidationExamples class LazarLastEPAFHMSplit < LazarEPAFHMSplit def initialize super - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/last") + @algorithm_params = "feature_generation_uri="+File.join($algorithm[:uri],"fminer/last") end end @@ -124,8 +124,8 @@ module ValidationExamples class LazarEPAFHMCrossvalidation < EPAFHMCrossvalidation def initialize - @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") + @algorithm_uri = File.join($algorithm[:uri],"lazar") + @algorithm_params = "feature_generation_uri="+File.join($algorithm[:uri],"fminer/bbrc") super end end @@ -144,8 +144,8 @@ module ValidationExamples class LazarHamsterSplit < HamsterSplit def initialize - @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") + @algorithm_uri = File.join($algorithm[:uri],"lazar") + @algorithm_params = "feature_generation_uri="+File.join($algorithm[:uri],"fminer/bbrc") super end end @@ -153,7 +153,7 @@ module ValidationExamples class LazarLastHamsterSplit < LazarHamsterSplit def initialize super - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/last") + @algorithm_params = "feature_generation_uri="+File.join($algorithm[:uri],"fminer/last") end end @@ -186,8 +186,8 @@ module ValidationExamples class LazarHamsterBootstrapping < HamsterBootstrapping def initialize - @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") + @algorithm_uri = File.join($algorithm[:uri],"lazar") + @algorithm_params = "feature_generation_uri="+File.join($algorithm[:uri],"fminer/bbrc") super end end @@ -203,11 +203,9 @@ module ValidationExamples class HamsterTrainingTest < TrainingTestValidation def initialize -# @test_target_dataset_file = File.new("data/hamster_carcinogenicity.yaml","r") # @training_dataset_file = File.new("data/hamster_carcinogenicity.train.yaml","r") # @test_dataset_file = File.new("data/hamster_carcinogenicity.test.yaml","r") - @test_target_dataset_file = File.new("data/hamster_carcinogenicity.csv","r") @training_dataset_file = File.new("data/hamster_carcinogenicity.train.csv","r") @test_dataset_file = File.new("data/hamster_carcinogenicity.test.csv","r") @@ -226,8 +224,8 @@ module ValidationExamples class LazarHamsterTrainingTest < HamsterTrainingTest def initialize - @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") + @algorithm_uri = File.join($algorithm[:uri],"lazar") + @algorithm_params = "feature_generation_uri="+File.join($algorithm[:uri],"fminer/bbrc") super end end @@ -261,8 +259,8 @@ module ValidationExamples class LazarHamsterCrossvalidation < HamsterCrossvalidation def initialize - @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") + @algorithm_uri = File.join($algorithm[:uri],"lazar") + @algorithm_params = "feature_generation_uri="+File.join($algorithm[:uri],"fminer/bbrc") super end end @@ -270,7 +268,7 @@ module ValidationExamples class LazarLastHamsterCrossvalidation < LazarHamsterCrossvalidation def initialize super - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/last") + @algorithm_params = "feature_generation_uri="+File.join($algorithm[:uri],"fminer/last") end end @@ -284,8 +282,8 @@ module ValidationExamples class LazarHamsterLooCrossvalidation < HamsterLooCrossvalidation def initialize - @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") + @algorithm_uri = File.join($algorithm[:uri],"lazar") + @algorithm_params = "feature_generation_uri="+File.join($algorithm[:uri],"fminer/bbrc") super end end @@ -294,8 +292,8 @@ module ValidationExamples class LazarHamsterMiniCrossvalidation < CrossValidation def initialize - @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") + @algorithm_uri = File.join($algorithm[:uri],"lazar") + @algorithm_params = "feature_generation_uri="+File.join($algorithm[:uri],"fminer/bbrc") @dataset_file = File.new("data/hamster_carcinogenicity.mini.csv","r") @num_folds = 2 end @@ -303,8 +301,8 @@ module ValidationExamples class ISSCANStratifiedCrossvalidation < CrossValidation def initialize - @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") + @algorithm_uri = File.join($algorithm[:uri],"lazar") + @algorithm_params = "feature_generation_uri="+File.join($algorithm[:uri],"fminer/bbrc") @dataset_file = File.new("data/ISSCAN_v3a_canc-red.csv","r") @stratified = true @num_folds = 10 @@ -313,8 +311,8 @@ module ValidationExamples class ISSCAN2StratifiedCrossvalidation < CrossValidation def initialize - @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") + @algorithm_uri = File.join($algorithm[:uri],"lazar") + @algorithm_params = "feature_generation_uri="+File.join($algorithm[:uri],"fminer/bbrc") @dataset_file = File.new("data/ISSCAN_v3a_sal.csv","r") @stratified = true @num_folds = 10 @@ -340,8 +338,8 @@ module ValidationExamples class LazarISTHamsterCrossvalidation < ISTHamsterCrossvalidation def initialize - @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer") + @algorithm_uri = File.join($algorithm[:uri],"lazar") + @algorithm_params = "feature_generation_uri="+File.join($algorithm[:uri],"fminer") super end end @@ -544,8 +542,8 @@ module ValidationExamples class LazarVsNtuaCrossvalidation < CrossValidation def initialize - @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") + @algorithm_uri = File.join($algorithm[:uri],"lazar") + @algorithm_params = "feature_generation_uri="+File.join($algorithm[:uri],"fminer/bbrc") @dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/R545" @prediction_feature="http://apps.ideaconsult.net:8080/ambit2/feature/22200" @num_folds=3 @@ -667,11 +665,9 @@ module ValidationExamples class HamsterTrainingTest < TrainingTestValidation def initialize -# @test_target_dataset_file = File.new("data/hamster_carcinogenicity.yaml","r") # @training_dataset_file = File.new("data/hamster_carcinogenicity.train.yaml","r") # @test_dataset_file = File.new("data/hamster_carcinogenicity.test.yaml","r") - @test_target_dataset_file = File.new("data/hamster_carcinogenicity.csv","r") @training_dataset_file = File.new("data/hamster_carcinogenicity.train.csv","r") @test_dataset_file = File.new("data/hamster_carcinogenicity.test.csv","r") @@ -698,8 +694,8 @@ module ValidationExamples class LazarRepdoseSplit < RepdoseSplit def initialize - @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") + @algorithm_uri = File.join($algorithm[:uri],"lazar") + @algorithm_params = "feature_generation_uri="+File.join($algorithm[:uri],"fminer/bbrc") super end end @@ -721,8 +717,8 @@ module ValidationExamples class LazarRepdoseCrossValidation < RepdoseCrossValidation def initialize - @algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"lazar") - @algorithm_params = "feature_generation_uri="+File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc") + @algorithm_uri = File.join($algorithm[:uri],"lazar") + @algorithm_params = "feature_generation_uri="+File.join($algorithm[:uri],"fminer/bbrc") super end end diff --git a/test/test_examples_util.rb b/test/test_examples_util.rb index 82c4c48..a323703 100755 --- a/test/test_examples_util.rb +++ b/test/test_examples_util.rb @@ -17,7 +17,7 @@ module ValidationExamples @@dataset_uris = {} @@prediction_features = {} - def self.upload_dataset(file, subjectid=nil, dataset_service=CONFIG[:services]["opentox-dataset"]) #, file_type="application/x-yaml") + def self.upload_dataset(file, subjectid=nil, dataset_service=$dataset[:uri]) #, file_type="application/x-yaml") raise "File not found: "+file.path.to_s unless File.exist?(file.path) if @@dataset_uris[file.path.to_s]==nil LOGGER.debug "uploading file: "+file.path.to_s @@ -26,7 +26,7 @@ module ValidationExamples #data_uri = OpenTox::RestClientWrapper.post(dataset_service,{:content_type => file_type},data).to_s.chomp #@@dataset_uris[file.path.to_s] = data_uri #LOGGER.debug "uploaded dataset: "+data_uri - d = OpenTox::Dataset.create(CONFIG[:services]["opentox-dataset"], subjectid) + d = OpenTox::Dataset.create($dataset[:uri], subjectid) d.load_yaml(data) d.save( subjectid ) @@dataset_uris[file.path.to_s] = d.uri @@ -36,7 +36,7 @@ module ValidationExamples @@prediction_features[file.path.to_s] = d.features.keys[0] @@dataset_uris[file.path.to_s] = d.uri elsif (file.path =~ /rdf$/) - d = OpenTox::Dataset.create(CONFIG[:services]["opentox-dataset"], subjectid) + d = OpenTox::Dataset.create($dataset[:uri], subjectid) d.load_rdfxml_file(file, subjectid) d.save(subjectid) @@dataset_uris[file.path.to_s] = d.uri @@ -77,7 +77,7 @@ module ValidationExamples $test_case.post uri,params return wait($test_case.last_response.body) else - return OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],uri),params,nil,waiting_task).to_s + return OpenTox::RestClientWrapper.post(File.join($validation[:uri],uri),params,nil,waiting_task).to_s end end @@ -90,7 +90,7 @@ module ValidationExamples return wait($test_case.last_response.body) else params[:accept] = accept_header - return OpenTox::RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"],uri),params) + return OpenTox::RestClientWrapper.get(File.join($validation[:uri],uri),params) end end @@ -100,7 +100,7 @@ module ValidationExamples $test_case.delete uri,{:subjectid => SUBJECTID},'HTTP_ACCEPT' => accept_header return wait($test_case.last_response.body) else - return OpenTox::RestClientWrapper.delete(File.join(CONFIG[:services]["opentox-validation"],uri),{:accept => accept_header,:subjectid => SUBJECTID}) + return OpenTox::RestClientWrapper.delete(File.join($validation[:uri],uri),{:accept => accept_header,:subjectid => SUBJECTID}) end end @@ -238,8 +238,6 @@ module ValidationExamples :model_uri, :test_dataset_uri, :test_dataset_file, - :test_target_dataset_uri, - :test_target_dataset_file, :training_dataset_uri, :training_dataset_file, :dataset_uri, @@ -258,7 +256,6 @@ module ValidationExamples def upload_files [[:test_dataset_uri, :test_dataset_file], - [:test_target_dataset_uri, :test_target_dataset_file], [:training_dataset_uri, :training_dataset_file], [:dataset_uri, :dataset_file]].each do |a| uri = a[0] @@ -438,7 +435,7 @@ module ValidationExamples end def opt_params - [ :prediction_feature, :test_target_dataset_uri ] + [ :prediction_feature ] end def validation_type @@ -452,7 +449,7 @@ module ValidationExamples end def opt_params - [ :algorithm_params, :test_target_dataset_uri ] + [ :algorithm_params ] end def validation_type diff --git a/validation.gemspec b/validation.gemspec new file mode 100644 index 0000000..2e12eed --- /dev/null +++ b/validation.gemspec @@ -0,0 +1,28 @@ +# -*- encoding: utf-8 -*- +$:.push File.expand_path("../lib", __FILE__) + +Gem::Specification.new do |s| + s.name = "opentox-validation" + s.version = File.read("./VERSION") + s.authors = ["Martin Gütlein"] + s.email = ["martin.guetlein@gmail.com"] + s.homepage = "http://github.com/OpenTox/validation" + s.summary = %q{opentox validation service} + s.description = %q{opentox validation service} + s.license = 'GPL-3' + #s.platform = Gem::Platform::CURRENT + + s.rubyforge_project = "validation" + + s.files = `git ls-files`.split("\n") + #s.test_files = `git ls-files -- {test,spec,features}/*`.split("\n") + #s.executables = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) } + #s.require_paths = ["lib"] + s.required_ruby_version = '>= 1.9.2' + + # specify any dependencies here; for example: + s.add_runtime_dependency "opentox-server" + s.post_install_message = "Please configure your service in ~/.opentox/config/validation.rb" +end + + diff --git a/validation/validation_application.rb b/validation/validation_application.rb index 1bc55f6..37fea1e 100755 --- a/validation/validation_application.rb +++ b/validation/validation_application.rb @@ -1,10 +1,10 @@ -[ 'rubygems', 'sinatra', 'sinatra/url_for', 'opentox-ruby' ].each do |lib| +[ 'rubygems', 'sinatra', 'sinatra/url_for' ].each do |lib| require lib end -require 'lib/dataset_cache.rb' -require 'validation/validation_service.rb' +require './lib/dataset_cache.rb' +require './validation/validation_service.rb' helpers do def check_stratified(params) @@ -308,7 +308,6 @@ post '/test_set_validation' do 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], :prediction_feature => params[:prediction_feature] v.subjectid = @subjectid v.validate_model( task ) @@ -340,7 +339,6 @@ get '/test_set_validation' do post_command = OpenTox::PostCommand.new request.url,"Perform test-set-validation" post_command.attributes << OpenTox::PostAttribute.new("model_uri") post_command.attributes << OpenTox::PostAttribute.new("test_dataset_uri") - post_command.attributes << OpenTox::PostAttribute.new("test_target_dataset_uri",false,nil,"Specify if target endpoint values are not available in test dataset.") post_command.attributes << OpenTox::PostAttribute.new("prediction_feature",false,nil,"Default is 'dependentVariables' of the model.") content_type "text/html" OpenTox.text_to_html uri_list,@subjectid,related_links,description,post_command @@ -360,7 +358,6 @@ post '/training_test_validation/?' do :algorithm_params => params[:algorithm_params], :training_dataset_uri => params[:training_dataset_uri], :test_dataset_uri => params[:test_dataset_uri], - :test_target_dataset_uri => params[:test_target_dataset_uri], :prediction_feature => params[:prediction_feature] v.subjectid = @subjectid v.validate_algorithm( task ) @@ -392,7 +389,6 @@ get '/training_test_validation' do post_command.attributes << OpenTox::PostAttribute.new("algorithm_uri") post_command.attributes << OpenTox::PostAttribute.new("training_dataset_uri") post_command.attributes << OpenTox::PostAttribute.new("test_dataset_uri") - post_command.attributes << OpenTox::PostAttribute.new("test_target_dataset_uri",false,nil,"Specify if target endpoint values are not available in test dataset.") post_command.attributes << OpenTox::PostAttribute.new("prediction_feature") post_command.attributes << OpenTox::PostAttribute.new("algorithm_params",false,nil,"Params used for model building, separate with ';', example: param1=v1;param2=v2") content_type "text/html" @@ -414,7 +410,6 @@ post '/bootstrapping' do params[:random_seed], OpenTox::SubTask.create(task,0,33)) ) LOGGER.info "params after bootstrapping: "+params.inspect v = Validation::Validation.create :validation_type => "bootstrapping", - :test_target_dataset_uri => params[:dataset_uri], :prediction_feature => params[:prediction_feature], :algorithm_uri => params[:algorithm_uri], :algorithm_params => params[:algorithm_params], @@ -470,12 +465,11 @@ post '/training_test_split' do raise OpenTox::BadRequestError.new "prediction_feature missing" unless params[:prediction_feature].to_s.size>0 check_stratified(params) task = OpenTox::Task.create( "Perform training test split validation", url_for("/training_test_split", :full) ) do |task| #, params - params.merge!( Validation::Util.train_test_dataset_split(params[:dataset_uri], params[:prediction_feature], + params.merge!( Validation::Util.train_test_dataset_split(params[:dataset_uri], (params[:stratified].to_s=~/true/ ? params[:prediction_feature] : nil), @subjectid, params[:stratified], params[:split_ratio], params[:random_seed], OpenTox::SubTask.create(task,0,33))) 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], :prediction_feature => params[:prediction_feature], :algorithm_uri => params[:algorithm_uri], :algorithm_params => params[:algorithm_params] @@ -543,7 +537,6 @@ post '/cleanup_datasets/?' do end Validation::Validation.all.each do |val| used_datasets << val.training_dataset_uri - used_datasets << val.test_target_dataset_uri used_datasets << val.test_dataset_uri used_datasets << val.prediction_dataset_uri end @@ -595,7 +588,8 @@ post '/validate_datasets' do feature_type = "regression" if params.delete("regression")!=nil v = Validation::Validation.create params v.subjectid = @subjectid - v.compute_validation_stats(feature_type,predicted_variable,predicted_confidence,nil,nil,false,task) + v.compute_prediction_data(feature_type,predicted_variable,predicted_confidence,v.prediction_feature,nil,task) + v.compute_validation_stats()#feature_type,predicted_variable,predicted_confidence,nil,nil,false,task) end v.validation_uri end diff --git a/validation/validation_format.rb b/validation/validation_format.rb index 3c9a8ef..0594629 100755 --- a/validation/validation_format.rb +++ b/validation/validation_format.rb @@ -1,5 +1,5 @@ -require "lib/format_util.rb" +require "./lib/format_util.rb" module Validation diff --git a/validation/validation_service.rb b/validation/validation_service.rb index 8c8b11f..de583f6 100755 --- a/validation/validation_service.rb +++ b/validation/validation_service.rb @@ -1,9 +1,9 @@ -require "lib/validation_db.rb" -require "lib/ot_predictions.rb" +require "./lib/validation_db.rb" +require "./lib/ot_predictions.rb" -require "validation/validation_format.rb" +require "./validation/validation_format.rb" class Array @@ -64,20 +64,20 @@ module Validation # PENDING: model and referenced datasets are deleted as well, keep it that way? 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 ] + to_delete = [:model_uri, :training_dataset_uri, :test_dataset_uri, :prediction_dataset_uri ] case self.validation_type when "test_set_validation" - to_delete -= [ :model_uri, :training_dataset_uri, :test_dataset_uri, :test_target_dataset_uri ] + to_delete -= [ :model_uri, :training_dataset_uri, :test_dataset_uri ] when "bootstrapping" - to_delete -= [ :test_target_dataset_uri ] + to_delete -= [] when "training_test_validation" - to_delete -= [ :training_dataset_uri, :test_dataset_uri, :test_target_dataset_uri ] + to_delete -= [ :training_dataset_uri, :test_dataset_uri ] when "training_test_split" - to_delete -= [ :test_target_dataset_uri ] + to_delete -= [] when "validate_datasets" to_delete = [] when "crossvalidation" - to_delete -= [ :test_target_dataset_uri ] + to_delete -= [] when "crossvalidation_statistics" to_delete = [] else @@ -189,12 +189,11 @@ module Validation models = cv_vals.collect{|v| OpenTox::Model::Generic.find(v.model_uri, subjectid)} feature_type = models.first.feature_type(subjectid) test_dataset_uris = cv_vals.collect{|v| v.test_dataset_uri} - test_target_dataset_uris = cv_vals.collect{|v| v.test_target_dataset_uri} prediction_feature = cv_vals.first.prediction_feature prediction_dataset_uris = cv_vals.collect{|v| v.prediction_dataset_uri} predicted_variables = models.collect{|m| m.predicted_variable(subjectid)} predicted_confidences = models.collect{|m| m.predicted_confidence(subjectid)} - p_data = Lib::PredictionData.create( feature_type, test_dataset_uris, test_target_dataset_uris, prediction_feature, + p_data = Lib::PredictionData.create( feature_type, test_dataset_uris, prediction_feature, prediction_dataset_uris, predicted_variables, predicted_confidences, subjectid, waiting_task ) self.prediction_data = p_data.data p_data.data @@ -225,7 +224,7 @@ module Validation LOGGER.debug "computing prediction stats" p_data = Lib::PredictionData.create( feature_type, - self.test_dataset_uri, self.test_target_dataset_uri, self.prediction_feature, + self.test_dataset_uri, self.prediction_feature, self.prediction_dataset_uri, predicted_variable, predicted_confidence, self.subjectid, OpenTox::SubTask.create(task, 0, 80) ) self.prediction_data = p_data.data @@ -418,7 +417,6 @@ module Validation tmp_val << { :validation_type => "crossvalidation", :training_dataset_uri => v.training_dataset_uri, :test_dataset_uri => v.test_dataset_uri, - :test_target_dataset_uri => self.dataset_uri, :crossvalidation_id => self.id, :crossvalidation_fold => v.crossvalidation_fold, :prediction_feature => prediction_feature, @@ -448,39 +446,38 @@ module Validation case stratified when "false" if self.loo=="true" - shuffled_compounds = orig_dataset.compounds + shuffled_compound_indices = (0..(orig_dataset.compounds.size-1)).to_a else - shuffled_compounds = orig_dataset.compounds.shuffle( self.random_seed ) + shuffled_compound_indices = (0..(orig_dataset.compounds.size-1)).to_a.shuffle( self.random_seed ) end - split_compounds = shuffled_compounds.chunk( self.num_folds.to_i ) - LOGGER.debug "cv: num instances for each fold: "+split_compounds.collect{|c| c.size}.join(", ") + split_compound_indices = shuffled_compound_indices.chunk( self.num_folds.to_i ) + LOGGER.debug "cv: num instances for each fold: "+split_compound_indices.collect{|c| c.size}.join(", ") self.num_folds.to_i.times do |n| - test_compounds = [] - train_compounds = [] + test_compound_indices = [] + train_compound_indices = [] self.num_folds.to_i.times do |nn| - compounds = split_compounds[nn] + compound_indices = split_compound_indices[nn] if n == nn - compounds.each{ |compound| test_compounds << compound} + compound_indices.each{ |compound| test_compound_indices << compound} else - compounds.each{ |compound| train_compounds << compound} + compound_indices.each{ |compound| train_compound_indices << compound} end end raise "internal error, num test compounds not correct,"+ - " is '#{test_compounds.size}', should be '#{(shuffled_compounds.size/self.num_folds.to_i)}'" 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 + " is '#{test_compound_indices.size}', should be '#{(shuffled_compound_indices.size/self.num_folds.to_i)}'" unless + (shuffled_compound_indices.size/self.num_folds.to_i - test_compound_indices.size).abs <= 1 + raise "internal error, num train compounds not correct, should be '"+(shuffled_compound_indices.size-test_compound_indices.size).to_s+ + "', is '"+train_compound_indices.size.to_s+"'" unless shuffled_compound_indices.size - test_compound_indices.size == train_compound_indices.size datasetname = 'dataset fold '+(n+1).to_s+' of '+self.num_folds.to_s meta[DC.title] = "training "+datasetname - LOGGER.debug "training set: "+datasetname+"_train, compounds: "+train_compounds.size.to_s - train_dataset_uri = orig_dataset.split( train_compounds, orig_dataset.features.keys, + LOGGER.debug "training set: "+datasetname+"_train, compounds: "+train_compound_indices.size.to_s + train_dataset_uri = orig_dataset.split( train_compound_indices, orig_dataset.features.keys, meta, self.subjectid ).uri train_dataset_uris << train_dataset_uri meta[DC.title] = "test "+datasetname - LOGGER.debug "test set: "+datasetname+"_test, compounds: "+test_compounds.size.to_s - test_features = orig_dataset.features.keys.dclone - [self.prediction_feature] - test_dataset_uri = orig_dataset.split( test_compounds, test_features, + LOGGER.debug "test set: "+datasetname+"_test, compounds: "+test_compound_indices.size.to_s + test_dataset_uri = orig_dataset.split( test_compound_indices, orig_dataset.features.keys, meta, self.subjectid ).uri test_dataset_uris << test_dataset_uri end @@ -505,7 +502,6 @@ module Validation tmp_validation = { :validation_type => "crossvalidation", :training_dataset_uri => train_dataset_uris[n], :test_dataset_uri => test_dataset_uris[n], - :test_target_dataset_uri => self.dataset_uri, :crossvalidation_id => self.id, :crossvalidation_fold => (n+1), :prediction_feature => self.prediction_feature, :algorithm_uri => self.algorithm_uri, @@ -537,25 +533,20 @@ module Validation LOGGER.warn "no prediciton feature given, all features included in test dataset" end - compounds = orig_dataset.compounds - raise OpenTox::NotFoundError.new "Cannot split datset, num compounds in dataset < 2 ("+compounds.size.to_s+")" if compounds.size<2 - - compounds.each do |c| - raise OpenTox::NotFoundError.new "Bootstrapping not yet implemented for duplicate compounds" if - orig_dataset.data_entries[c][prediction_feature].size > 1 - end + compound_indices = (0..(orig_dataset.compounds.size-1)).to_a + raise OpenTox::NotFoundError.new "Cannot split datset, num compounds in dataset < 2 ("+compound_indices.size.to_s+")" if compound_indices.size<2 srand random_seed.to_i while true - training_compounds = [] - compounds.size.times do - training_compounds << compounds[rand(compounds.size)] + training_compound_indices = [] + compound_indices.size.times do + training_compound_indices << compound_indices[rand(compound_indices.size)] end - test_compounds = [] - compounds.each do |c| - test_compounds << c unless training_compounds.include?(c) + test_compound_indices = [] + compound_indices.each do |idx| + test_compound_indices << idx unless training_compound_indices.include?(idx) end - if test_compounds.size > 0 + if test_compound_indices.size > 0 break else srand rand(10000) @@ -563,47 +554,26 @@ module Validation end LOGGER.debug "bootstrapping on dataset "+orig_dataset_uri+ - " into training ("+training_compounds.size.to_s+") and test ("+test_compounds.size.to_s+")"+ - ", duplicates in training dataset: "+test_compounds.size.to_s + " into training ("+training_compound_indices.size.to_s+") and test ("+test_compound_indices.size.to_s+")"+ + ", duplicates in training dataset: "+test_compound_indices.size.to_s task.progress(33) if task result = {} -# result[:training_dataset_uri] = orig_dataset.create_new_dataset( training_compounds, -# orig_dataset.features, -# "Bootstrapping training dataset of "+orig_dataset.title.to_s, -# $sinatra.url_for('/bootstrapping',:full) ) - result[:training_dataset_uri] = orig_dataset.split( training_compounds, + result[:training_dataset_uri] = orig_dataset.split( training_compound_indices, orig_dataset.features.keys, { DC.title => "Bootstrapping training dataset of "+orig_dataset.title.to_s, DC.creator => $url_provider.url_for('/bootstrapping',:full) }, subjectid ).uri task.progress(66) if task -# result[:test_dataset_uri] = orig_dataset.create_new_dataset( test_compounds, -# orig_dataset.features.dclone - [prediction_feature], -# "Bootstrapping test dataset of "+orig_dataset.title.to_s, -# $sinatra.url_for('/bootstrapping',:full) ) - result[:test_dataset_uri] = orig_dataset.split( test_compounds, - orig_dataset.features.keys.dclone - [prediction_feature], + result[:test_dataset_uri] = orig_dataset.split( test_compound_indices, + orig_dataset.features.keys, { DC.title => "Bootstrapping test dataset of "+orig_dataset.title.to_s, DC.creator => $url_provider.url_for('/bootstrapping',:full)} , subjectid ).uri task.progress(100) if task - if ENV['RACK_ENV'] =~ /test|debug/ - training_dataset = Lib::DatasetCache.find result[:training_dataset_uri],subjectid - raise OpenTox::NotFoundError.new "Training dataset not found: '"+result[:training_dataset_uri].to_s+"'" unless training_dataset - training_dataset.load_all - value_count = 0 - training_dataset.compounds.each do |c| - value_count += training_dataset.data_entries[c][prediction_feature].size - end - raise "training compounds error" unless value_count==training_compounds.size - raise OpenTox::NotFoundError.new "Test dataset not found: '"+result[:test_dataset_uri].to_s+"'" unless - Lib::DatasetCache.find result[:test_dataset_uri], subjectid - end LOGGER.debug "bootstrapping done, training dataset: '"+result[:training_dataset_uri].to_s+"', test dataset: '"+result[:test_dataset_uri].to_s+"'" - return result end @@ -620,12 +590,17 @@ module Validation orig_dataset = Lib::DatasetCache.find orig_dataset_uri, subjectid orig_dataset.load_all subjectid raise OpenTox::NotFoundError.new "Dataset not found: "+orig_dataset_uri.to_s unless orig_dataset + if prediction_feature - raise OpenTox::NotFoundError.new "Prediction feature '"+prediction_feature.to_s+ - "' not found in dataset, features are: \n"+ - orig_dataset.features.keys.inspect unless orig_dataset.features.include?(prediction_feature) - else - LOGGER.warn "no prediciton feature given, all features will be included in test dataset" + if stratified==/true/ + raise OpenTox::NotFoundError.new "Prediction feature '"+prediction_feature.to_s+ + "' not found in dataset, features are: \n"+orig_dataset.features.keys.inspect unless orig_dataset.features.include?(prediction_feature) + else + LOGGER.warn "prediction_feature argument is ignored for non-stratified splits" if prediction_feature + prediction_feature=nil + end + elsif stratified==/true/ + raise OpenTox::BadRequestError.new "prediction feature required for stratified splits" unless prediction_feature end meta = { DC.creator => $url_provider.url_for('/training_test_split',:full) } @@ -633,10 +608,8 @@ module Validation case stratified when /true|super/ if stratified=="true" - raise OpenTox::BadRequestError.new "prediction feature required for stratified splits" unless prediction_feature features = [prediction_feature] else - LOGGER.warn "prediction feature is ignored for super-stratified splits" if prediction_feature features = nil end r_util = OpenTox::RUtil.new @@ -644,39 +617,36 @@ module Validation r_util.quit_r result = {:training_dataset_uri => train.uri, :test_dataset_uri => test.uri} when "false" - compounds = orig_dataset.compounds - raise OpenTox::BadRequestError.new "Cannot split datset, num compounds in dataset < 2 ("+compounds.size.to_s+")" if compounds.size<2 - split = (compounds.size*split_ratio).to_i + compound_indices = (0..(orig_dataset.compounds.size-1)).to_a + raise OpenTox::BadRequestError.new "Cannot split datset, num compounds in dataset < 2 ("+compound_indices.size.to_s+")" if compound_indices.size<2 + split = (compound_indices.size*split_ratio).round split = [split,1].max - split = [split,compounds.size-2].min + split = [split,compound_indices.size-2].min LOGGER.debug "splitting dataset "+orig_dataset_uri+ - " into train:0-"+split.to_s+" and test:"+(split+1).to_s+"-"+(compounds.size-1).to_s+ + " into train:0-"+split.to_s+" and test:"+(split+1).to_s+"-"+(compound_indices.size-1).to_s+ " (shuffled with seed "+random_seed.to_s+")" - compounds.shuffle!( random_seed ) - training_compounds = compounds[0..split] - test_compounds = compounds[(split+1)..-1] + compound_indices.shuffle!( random_seed ) + training_compound_indices = compound_indices[0..(split-1)] + test_compound_indices = compound_indices[split..-1] task.progress(33) if task meta[DC.title] = "Training dataset split of "+orig_dataset.uri result = {} - result[:training_dataset_uri] = orig_dataset.split( training_compounds, - orig_dataset.features.keys, meta, subjectid ).uri + train_data = orig_dataset.split( training_compound_indices, + orig_dataset.features.keys, meta, subjectid ) + raise "Train dataset num coumpounds != "+(orig_dataset.compounds.size*split_ratio).round.to_s+", instead: "+train_data.compounds.size.to_s unless + train_data.compounds.size==(orig_dataset.compounds.size*split_ratio).round + result[:training_dataset_uri] = train_data.uri task.progress(66) if task meta[DC.title] = "Test dataset split of "+orig_dataset.uri - result[:test_dataset_uri] = orig_dataset.split( test_compounds, - orig_dataset.features.keys.dclone - [prediction_feature], meta, subjectid ).uri + test_data = orig_dataset.split( test_compound_indices, + orig_dataset.features.keys, meta, subjectid ) + raise "Test dataset num coumpounds != "+(orig_dataset.compounds.size*(1-split_ratio)).round.to_s+", instead: "+test_data.compounds.size.to_s unless + test_data.compounds.size==(orig_dataset.compounds.size*(1-split_ratio)).round + result[:test_dataset_uri] = test_data.uri task.progress(100) if task - if ENV['RACK_ENV'] =~ /test|debug/ - raise OpenTox::NotFoundError.new "Training dataset not found: '"+result[:training_dataset_uri].to_s+"'" unless - Lib::DatasetCache.find(result[:training_dataset_uri],subjectid) - test_data = Lib::DatasetCache.find result[:test_dataset_uri],subjectid - raise OpenTox::NotFoundError.new "Test dataset not found: '"+result[:test_dataset_uri].to_s+"'" unless test_data - test_data.load_compounds subjectid - raise "Test dataset num coumpounds != "+(compounds.size-split-1).to_s+", instead: "+ - test_data.compounds.size.to_s+"\n"+test_data.to_yaml unless test_data.compounds.size==(compounds.size-1-split) - end LOGGER.debug "split done, training dataset: '"+result[:training_dataset_uri].to_s+"', test dataset: '"+result[:test_dataset_uri].to_s+"'" else raise OpenTox::BadRequestError.new "stratified != false|true|super, is #{stratified}" diff --git a/validation/validation_test.rb b/validation/validation_test.rb index 70f3ca4..77a5415 100755 --- a/validation/validation_test.rb +++ b/validation/validation_test.rb @@ -9,11 +9,11 @@ before { require "uri" require "yaml" ENV['RACK_ENV'] = 'production' -require 'application.rb' +require './application.rb' require 'test/unit' require 'rack/test' -require 'lib/test_util.rb' -require 'test/test_examples.rb' +require './lib/test_util.rb' +require './test/test_examples.rb' LOGGER = OTLogger.new(STDOUT) LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S " @@ -59,6 +59,22 @@ class ValidationTest < Test::Unit::TestCase def test_it begin $test_case = self + + post '/validate_datasets',{:test_dataset_uri=>"http://local-ot/dataset/14111", + :prediction_dataset_uri=>"http://local-ot/dataset/14113", + :prediction_feature=>"http://local-ot/dataset/14109/feature/Hamster%20Carcinogenicity", + :predicted_variable=>"http://local-ot/model/21/predicted/value", + :predicted_confidence=>"http://local-ot/model/21/predicted/confidence", + :classification=>"true"} + +#D, [2012-11-07T12:38:11.291069 #31035] DEBUG -- : validation :: loading prediction -- test-dataset: ["http://local-ot/dataset/14099"] :: /validation_service.rb:227:in `compute_prediction_data' +# D, [2012-11-07T12:38:11.291174 #31035] DEBUG -- : validation :: loading prediction -- test-target-datset: ["http://local-ot/dataset/14097"] :: /validation_service.rb:227:in `compute_prediction_data' +# D, [2012-11-07T12:38:11.291281 #31035] DEBUG -- : validation :: loading prediction -- prediction-dataset: ["http://local-ot/dataset/14101"] :: /validation_service.rb:227:in `compute_prediction_data' +# D, [2012-11-07T12:38:11.291398 #31035] DEBUG -- : validation :: loading prediction -- predicted_variable: ["http://local-ot/model/19/predicted/value"] :: /validation_service.rb:227:in `compute_prediction_data' +# D, [2012-11-07T12:38:11.291506 #31035] DEBUG -- : validation :: loading prediction -- predicted_confidence: ["http://local-ot/model/19/predicted/confidence"] :: /validation_service.rb:227:in `compute_prediction_data' +# D, [2012-11-07T12:38:11.291611 #31035] DEBUG -- : validation :: loading prediction -- prediction_feature: http://local-ot/dataset/14097/feature/Hamster%20Carcinogenicity :: /validation_service.rb:227:in `compute_prediction_data' + + exit # dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/603206?pagesize=250&page=0" # test_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/603206?pagesize=250&page=1" @@ -117,7 +133,6 @@ class ValidationTest < Test::Unit::TestCase # post "/validate_datasets",{ # :test_dataset_uri=>"http://local-ot/dataset/6907", # :prediction_dataset_uri=>"http://local-ot/dataset/6909", -# :test_target_dataset_uri=>"http://local-ot/dataset/6905", # :prediction_feature=>"http://local-ot/dataset/6905/feature/Hamster%20Carcinogenicity", # #:model_uri=>"http://local-ot/model/1078", # :predicted_variable=>"http://local-ot/dataset/6909/feature/prediction/Hamster%20Carcinogenicity/value", @@ -351,7 +366,6 @@ end # post "/validate_datasets",{ # :test_dataset_uri=>"http://apps.deaconsult.net:8080/ambit2/dataset/R3924", # :prediction_dataset_uri=>"http://apps.ideaconsult.net:8080/ambit2/dataset/R3924?feature_uris[]=http%3A%2F%2Fapps.ideaconsult.net%3A8080%2Fambit2%2Fmodel%2F52%2Fpredicted", - # #:test_target_dataset_uri=>"http://local-ot/dataset/202", # :prediction_feature=>"http://apps.ideaconsult.net:8080/ambit2/feature/21715", # :predicted_feature=>"http://apps.ideaconsult.net:8080/ambit2/feature/28944", # :regression=>"true"} @@ -363,7 +377,6 @@ end #get "/crossvalidation/19/predictions",nil,'HTTP_ACCEPT' => "application/x-yaml" #/statistics" # post "",:model_uri=>"http://local-ot/model/1",:test_dataset_uri=>"http://local-ot/dataset/3", - # :test_target_dataset_uri=>"http://local-ot/dataset/1" # get "/crossvalidation/2",nil,'HTTP_ACCEPT' => "application/rdf+xml" #puts last_response.body @@ -384,7 +397,6 @@ end # post "/validate_datasets",{ # :test_dataset_uri=>"http://local-ot/dataset/204", # :prediction_dataset_uri=>"http://local-ot/dataset/206", - # :test_target_dataset_uri=>"http://local-ot/dataset/202", # :prediction_feature=>"http://ot-dev.in-silico.ch/toxcreate/feature#IRIS%20unit%20risk", # :predicted_feature=>"http://ot-dev.in-silico.ch/toxcreate/feature#IRIS%20unit%20risk_lazar_regression", # :regression=>"true"} @@ -394,7 +406,6 @@ end # post "/validate_datasets",{ # :test_dataset_uri=>"http://apps.ideaconsult.net:8080/ambit2/dataset/9?max=10", # :prediction_dataset_uri=>"http://apps.ideaconsult.net:8080/ambit2/dataset/9?max=10", -# #:test_target_dataset_uri=>"http://local-ot/dataset/202", # :prediction_feature=>"http://apps.ideaconsult.net:8080/ambit2/feature/21573", # :predicted_feature=>"http://apps.ideaconsult.net:8080/ambit2/feature/21573", # #:regression=>"true"} @@ -406,7 +417,6 @@ end # post "/validate_datasets",{ # :test_dataset_uri=>"http://local-ot/dataset/89", # :prediction_dataset_uri=>"http://local-ot/dataset/91", - # :test_target_dataset_uri=>"http://local-ot/dataset/87", # :prediction_feature=>"http://local-ot/dataset/1/feature/hamster_carcinogenicity", # :predicted_feature=>"", ## :regression=>"true"} @@ -419,7 +429,6 @@ end # post "/validate_datasets",{ # :test_dataset_uri=>"http://local-ot/dataset/390", # :prediction_dataset_uri=>"http://local-ot/dataset/392", -# :test_target_dataset_uri=>"http://local-ot/dataset/388", # :prediction_feature=>"http://local-ot/dataset/388/feature/repdose_classification", # :model_uri=>"http://local-ot/model/31"} # #:regression=>"true"} @@ -432,7 +441,6 @@ end # post "/validate_datasets",{ # :test_dataset_uri=>"http://opentox.informatik.uni-freiburg.de/dataset/409", # :prediction_dataset_uri=>"http://opentox.informatik.uni-freiburg.de/dataset/410", -# :test_target_dataset_uri=>"https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/R401560", # :prediction_feature=>"https://ambit.uni-plovdiv.bg:8443/ambit2/feature/22190", # :predicted_feature=>"https://ambit.uni-plovdiv.bg:8443/ambit2/feature/218304", # :regression=>"true", @@ -453,7 +461,6 @@ end # post "/validate_datasets",{ # :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", |