first step towards new architecture (4store)

9 files changed, 45 insertions, 48 deletions

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']