removed suburi-prefix validation (to avoid name server/validation/validation)

print warning when R_HOME is missing instead of raising error

10 files changed, 68 insertions, 52 deletions

diff --git a/EXAMPLES b/EXAMPLES
index d984c96..cdf2b47 100644
--- a/EXAMPLES
+++ b/EXAMPLES
@@ -15,21 +15,21 @@ the examples listed below can be performed with the command line tool curl
 get list of available validations
 -------------------------------------------------------------------
 
->>> curl <validation_service>/validations
+>>> curl <validation_service>
 
 result example (accept-header: application/rdf-xml)			
 <<< not yet supported
 
 result example (accept-header: text/uri-list)
-<<< <validation_service>/validation/<validation_id>
-<<< <validation_service>/validation/validation_id_i
-<<< <validation_service>/validation/validation_id_j
+<<< <validation_service>/<validation_id>
+<<< <validation_service>/validation_id_i
+<<< <validation_service>/validation_id_j
 
 
 get validation
 -------------------------------------------------------------------
 
->>> curl <validation_service>/validation/<validation_id>
+>>> curl <validation_service>/<validation_id>
 
 supported accept-headers: "text/x-yaml" and "application/rdf-xml"			
 	
@@ -40,13 +40,13 @@ validate model on test-dateset
 >>> curl -X POST -d model_uri="<model_uri>" \
  -d test_dataset_uri="<test_dataset_uri>" \
  -d prediction_feature="<prediction_feature>" \
- <validation_service>/validation
+ <validation_service>
 	
 result example (accept-header: application/rdf-xml)			
 <<< not yet supported
 
 result example (accept-header: text/uri-list)
-<<< <validation_service>/validation/id_i
+<<< <validation_service>/id_i
 
 
 validate an algorithm on a training- and test-dataset
@@ -57,7 +57,7 @@ validate an algorithm on a training- and test-dataset
  -d test_dataset_uri="<test_dataset_uri>" \
  -d prediction_feature="<prediction_feature>" \
  -d algorithm_params="<algorithm_params>" \
- <validation_service>/validation
+ <validation_service>
 
 optional params:
 algorithm_params, default is empty
@@ -66,7 +66,7 @@ result example (accept-header: application/rdf-xml)
 <<< not yet supported
 
 result example (accept-header: text/uri-list)
-<<< <validation_service>/validation/id_i
+<<< <validation_service>/id_i
 
 
 validate an algorithm on a dataset via training-test-split
@@ -78,7 +78,7 @@ validate an algorithm on a dataset via training-test-split
  -d algorithm_params="<algorithm_params>" \
  -d split_ratio=0.9 \
  -d random_seed=2 \
- <validation_service>/validation/training_test_split
+ <validation_service>/training_test_split
 
 optional params:
 algorithm_params, default is empty
@@ -89,13 +89,13 @@ result example (accept-header: application/rdf-xml)
 <<< not yet supported
 
 result example (accept-header: text/uri-list)
-<<< <validation_service>/validation/id_i
+<<< <validation_service>/id_i
 
 
 get list of available crossvalidations
 -------------------------------------------------------------------
 
->>> curl <validation_service>/crossvalidations
+>>> curl <validation_service>/crossvalidation
 
 result example (accept-header: application/rdf-xml)			
 <<< not yet supported
@@ -115,6 +115,7 @@ 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>" \
diff --git a/application.rb b/application.rb
index feb19b1..82be7bb 100644
--- a/application.rb
+++ b/application.rb
@@ -1,6 +1,5 @@
 
-require "validation/validation_application.rb"
-require "report/report_application.rb"
+
 require "example.rb"
 
 [ 'rubygems', 'sinatra', 'sinatra/url_for' ].each do |lib|
@@ -17,5 +16,11 @@ get '/prepare_examples/?' do
   "done"
 end
 
+# order is important, first add example methods, than validation 
+# (otherwise sinatra will try to locate a validation with name examples)
+
+require "validation/validation_application.rb"
+require "report/report_application.rb"
+
 
 
diff --git a/example.rb b/example.rb
index 80ae3b0..5ba4aa1 100644
--- a/example.rb
+++ b/example.rb
@@ -1,4 +1,8 @@
 
+[ 'opentox-ruby-api-wrapper' ].each do |lib|
+  require lib
+end
+
 class Example
   
   @@file=File.new("data/hamster_carcinogenicity.owl","r")
@@ -53,12 +57,12 @@ class Example
     
     Lib::Validation.auto_migrate!
     delete_all(@@config[:services]["opentox-model"])
-    vali_uri = RestClient.post File.join(@@config[:services]["opentox-validation"],'/validation/training_test_split'), { :dataset_uri => data_uri,
+    vali_uri = RestClient.post File.join(@@config[:services]["opentox-validation"],'/training_test_split'), { :dataset_uri => data_uri,
                                                          :algorithm_uri => @@alg,
                                                          :prediction_feature => @@feature,
                                                          :algorithm_params => @@alg_params }
     puts "created validation via training test split "+vali_uri
-    raise "failed to prepare demo" unless vali_uri==File.join(@@config[:services]["opentox-validation"],'/validation/1')
+    raise "failed to prepare demo" unless vali_uri==File.join(@@config[:services]["opentox-validation"],'/1')
     
     Lib::Crossvalidation.auto_migrate!
     cv_uri = RestClient.post File.join(@@config[:services]["opentox-validation"],'/crossvalidation'), { :dataset_uri => data_uri,
diff --git a/lib/predictions.rb b/lib/predictions.rb
index 88e8d6c..adc5882 100644
--- a/lib/predictions.rb
+++ b/lib/predictions.rb
@@ -1,6 +1,9 @@
 
-raise "Environment variable R_HOME missing" unless ENV['R_HOME']
-ENV['PATH'] = ENV['R_HOME']+":"+ENV['PATH'] unless ENV['PATH'].split(":").index(ENV['R_HOME'])
+if ENV['R_HOME']
+  ENV['PATH'] = ENV['R_HOME']+":"+ENV['PATH'] unless ENV['PATH'].split(":").index(ENV['R_HOME'])
+else
+  LOGGER.warn "Environment variable R_HOME not set"
+end
 require 'rinruby'
 
 module Lib
diff --git a/report/r_plot_factory.rb b/report/r_plot_factory.rb
index cff8e14..5c154b4 100644
--- a/report/r_plot_factory.rb
+++ b/report/r_plot_factory.rb
@@ -1,7 +1,10 @@
 
 # the r-path has to be added for the rinruby plugin
-raise "Environment variable R_HOME missing" unless ENV['R_HOME']
-ENV['PATH'] = ENV['R_HOME']+":"+ENV['PATH'] unless ENV['PATH'].split(":").index(ENV['R_HOME'])
+if ENV['R_HOME']
+  ENV['PATH'] = ENV['R_HOME']+":"+ENV['PATH'] unless ENV['PATH'].split(":").index(ENV['R_HOME'])
+else
+  LOGGER.warn "Environment variable R_HOME not set"
+end
 require "rinruby"
 
 
diff --git a/report/report_test.rb b/report/report_test.rb
index 6ac8810..279e968 100644
--- a/report/report_test.rb
+++ b/report/report_test.rb
@@ -31,26 +31,26 @@ require "'lib/test_util.rb"
 #    get '/osterhase'
 #    assert last_response.not_found?
 #
-#    post '/validation', :uri_list => "validation_uri_1\nvalidation_uri_2"  
+#    post '', :uri_list => "validation_uri_1\nvalidation_uri_2"  
 #    assert last_response.status == 400
 # 
-#    post '/validation', :uri_list => "validation_uri_1"
+#    post '', :uri_list => "validation_uri_1"
 #    assert last_response.ok?
 #    report_uri = last_response.body 
 #    type = $rep.parse_type(report_uri)
 #    assert type == "validation"
 #    id = $rep.parse_id(report_uri)
 #    
-#    get '/validation/'+id.to_s, {}, {"HTTP_ACCEPT" => "weihnachtsmann"}
+#    get '/'+id.to_s, {}, {"HTTP_ACCEPT" => "weihnachtsmann"}
 #    assert last_response.status == 400
-#    get '/validation/'+id.to_s, {}, {"HTTP_ACCEPT" => "text/xml"}
+#    get '/'+id.to_s, {}, {"HTTP_ACCEPT" => "text/xml"}
 #    assert last_response.ok?
-#    get '/validation/'+id.to_s, {}, {"HTTP_ACCEPT" => "text/html"}
+#    get '/'+id.to_s, {}, {"HTTP_ACCEPT" => "text/html"}
 #    assert last_response.ok?
 #    
-#    delete '/validation/43984398'
+#    delete '/43984398'
 #    assert last_response.not_found?
-#    delete '/validation/'+id.to_s
+#    delete '/'+id.to_s
 #    assert last_response.ok?
 #    
 #    map = {"crossvalidation"=>"validation_uri_1\nvalidation_uri_2\nvalidation_uri_3\nvalidation_uri_4\nvalidation_uri_5",
diff --git a/report/validation_access.rb b/report/validation_access.rb
index 2526e01..2187f46 100644
--- a/report/validation_access.rb
+++ b/report/validation_access.rb
@@ -48,7 +48,7 @@ class Reports::ValidationDB < Reports::ValidationAccess
   
   def init_validation(validation, uri)
   
-    raise Reports::BadRequest.new "not a validation uri: "+uri.to_s unless uri =~ /.*\/validation\/[0-9]+/
+    raise Reports::BadRequest.new "not a validation uri: "+uri.to_s unless uri =~ /.*\/[0-9]+/
     validation_id = uri.split("/")[-1]
     v = Lib::Validation.get(validation_id)
     raise Reports::BadRequest.new "no validation found with id "+validation_id.to_s unless v
diff --git a/validation/validation_application.rb b/validation/validation_application.rb
index 05909c5..5921907 100644
--- a/validation/validation_application.rb
+++ b/validation/validation_application.rb
@@ -23,7 +23,7 @@ class Sinatra::Base
 end
 
 ## REST API
-get '/crossvalidations/?' do
+get '/crossvalidation/?' do
   LOGGER.info "list all crossvalidations"
   Crossvalidation.all.collect{ |d| url_for("/crossvalidation/", :full) + d.id.to_s }.join("\n")
 end
@@ -71,12 +71,12 @@ post '/crossvalidation/?' do
   cv.uri
 end
 
-get '/validations/?' do
+get '/?' do
   LOGGER.info "list all validations"
-  Validation.all.collect{ |d| url_for("/validation/", :full) + d.id.to_s }.join("\n")
+  Validation.all.collect{ |d| url_for("/", :full) + d.id.to_s }.join("\n")
 end
 
-get '/validation/:id' do
+get '/:id' do
   LOGGER.info "get validation with id "+params[:id].to_s+" '"+request.env['HTTP_ACCEPT'].to_s+"'"
   halt 404, "Validation '#{params[:id]}' not found." unless validation = Validation.get(params[:id])
   
@@ -93,7 +93,7 @@ get '/validation/:id' do
   result
 end
 
-post '/validation/?' do
+post '/?' do
   LOGGER.info "creating validation "+params.inspect
   if params[:model_uri] and params[:test_dataset_uri] and !params[:training_dataset_uri] and !params[:algorithm_uri] and params[:prediction_feature]
     v = Validation.new :model_uri => params[:model_uri], 
@@ -115,7 +115,7 @@ post '/validation/?' do
   v.uri
 end
 
-post '/validation/training_test_split' do
+post '/training_test_split' do
   LOGGER.info "creating training test split "+params.inspect
   halt 400, "dataset_uri missing" unless params[:dataset_uri]
   halt 400, "algorithm_uri missing" unless params[:algorithm_uri]
@@ -129,7 +129,7 @@ post '/validation/training_test_split' do
   v.uri
 end
 
-get '/validation/:id/:attribute' do
+get '/:id/:attribute' do
   LOGGER.info "access validation attribute "+params.inspect
   halt 404, "Validation #{params[:id]} not found." unless validation = Validation.get(params[:id])
   begin
@@ -140,7 +140,7 @@ get '/validation/:id/:attribute' do
   return validation.send(params[:attribute])
 end
 
-delete '/validation/:id' do
+delete '/:id' do
   LOGGER.info "delete validation with id "+params[:id].to_s
   halt 404, "Validation #{params[:id]} not found." unless validation = Validation.get(params[:id])
   validation.delete
diff --git a/validation/validation_service.rb b/validation/validation_service.rb
index 4f738fb..88ac28f 100644
--- a/validation/validation_service.rb
+++ b/validation/validation_service.rb
@@ -41,7 +41,7 @@ class Validation < Lib::Validation
     super params
     save unless attribute_dirty?("id")
     raise "internal error, id not set "+to_yaml unless @id
-    update :uri => $sinatra.url_for("/validation/"+@id.to_s, :full)
+    update :uri => $sinatra.url_for("/"+@id.to_s, :full)
   end
   
   # deletes a validation
@@ -240,7 +240,7 @@ class Crossvalidation < Lib::Crossvalidation
              '_f'+n.to_s+'of'+@num_folds.to_s+
              '_r'+@random_seed.to_s+
              '_s'+@stratified.to_s 
-      source = $sinatra.url_for('/validation/crossvalidation',:full)
+      source = $sinatra.url_for('/crossvalidation',:full)
       
       test_compounds = []
       train_compounds = []
@@ -345,7 +345,7 @@ module ValidationUtil
       else
         title = "Test dataset split of "+orig_dataset.title.to_s
       end
-      source = $sinatra.url_for('/validation/training_test_split',:full)
+      source = $sinatra.url_for('/training_test_split',:full)
       result[sym] = create_new_dataset( data, compound_array, title, source )
     end
     
diff --git a/validation/validation_test.rb b/validation/validation_test.rb
index 350e973..680e459 100644
--- a/validation/validation_test.rb
+++ b/validation/validation_test.rb
@@ -42,7 +42,7 @@ class ValidationTest < Test::Unit::TestCase
   end
 
 #  def test_all_validations
-#    get '/validations'
+#    get '/'
 #    assert last_response.ok?
 #    puts "all validations:\n"+last_response.body
 #    validations = last_response.body.split("\n")
@@ -101,11 +101,11 @@ class ValidationTest < Test::Unit::TestCase
 ##          # assert that both cross validaitons use the same datasets
 ##          first_validation2 = last_response.body.split("\n")[0].split("/")[-1]
 ##          
-##          get '/validation/'+first_validation+'/test_dataset_uri'
+##          get '/'+first_validation+'/test_dataset_uri'
 ##          assert last_response.ok?
 ##          first_val_test_data = last_response.body
 ##
-##          get '/validation/'+first_validation2+'/test_dataset_uri'
+##          get '/'+first_validation2+'/test_dataset_uri'
 ##          assert last_response.ok?
 ##          first_val2_test_data = last_response.body
 ##          assert first_val_test_data==first_val2_test_data
@@ -137,7 +137,7 @@ class ValidationTest < Test::Unit::TestCase
 #      model_uri = "http://ot.model.de/45" #trained with training split from hamster
 #      data_uri_test = "http://ot.dataset.de/367" #hamster test split
 #      
-#      post '/validation', {:test_dataset_uri => data_uri_test, :model_uri => model_uri, :prediction_feature => FEATURE_URI}
+#      post '', {:test_dataset_uri => data_uri_test, :model_uri => model_uri, :prediction_feature => FEATURE_URI}
 #      verify_validation
 #    ensure
 #      #delete_resources
@@ -147,13 +147,13 @@ class ValidationTest < Test::Unit::TestCase
 #  def test_validate_algorithm
 #    begin
 #      
-#      #get '/validation/41',nil,'HTTP_ACCEPT' => "application/rdf+xml" #"text/x-yaml"
+#      #get '/41',nil,'HTTP_ACCEPT' => "application/rdf+xml" #"text/x-yaml"
 #      #puts last_response.body
 #      data_uri_train = upload_data(WS_DATA, FILE_TRAIN)
 #      data_uri_test = upload_data(WS_DATA, FILE_TEST)
 #      #data_uri_train = WS_DATA+"/"+DATA_TRAIN
 #      #data_uri_test = WS_DATA+"/"+DATA_TEST
-#      post '/validation', { :training_dataset_uri => data_uri_train, :test_dataset_uri => data_uri_test,
+#      post '', { :training_dataset_uri => data_uri_train, :test_dataset_uri => data_uri_test,
 #        :algorithm_uri => WS_CLASS_ALG, :prediction_feature => FEATURE_URI, :feature_generation_uri => WS_FEATURE_ALG}
 #      verify_validation
 #    ensure
@@ -168,7 +168,7 @@ class ValidationTest < Test::Unit::TestCase
 #      #data_uri = "http://ot.dataset.de/67" #hamster
 #      
 #      #data_uri=WS_DATA+"/"+DATA
-#      post '/validation/training_test_split', { :dataset_uri => data_uri, :algorithm_uri => WS_CLASS_ALG, :prediction_feature => FEATURE_URI,
+#      post '/training_test_split', { :dataset_uri => data_uri, :algorithm_uri => WS_CLASS_ALG, :prediction_feature => FEATURE_URI,
 #        :algorithm_params => "feature_generation_uri="+WS_FEATURE_ALG, :split_ratio=>0.8, :random_seed=>5}
 #      verify_validation
 #    ensure
@@ -182,8 +182,8 @@ class ValidationTest < Test::Unit::TestCase
     
     get '/examples'
 
-    #get '/validation/350',nil,'HTTP_ACCEPT' => "application/rdf+xml"
-    #get '/validation/350',nil,'HTTP_ACCEPT' => "text/x-yaml"
+    #get '/350',nil,'HTTP_ACCEPT' => "application/rdf+xml"
+    #get '/350',nil,'HTTP_ACCEPT' => "text/x-yaml"
     
     #get '/crossvalidation/1',nil,'HTTP_ACCEPT' => "application/rdf+xml"
     #get '/crossvalidation/1',nil,'HTTP_ACCEPT' => "text/x-yaml"
@@ -200,15 +200,15 @@ class ValidationTest < Test::Unit::TestCase
 
     puts "uri: "+last_response.body
     puts "id:"+validation_id
-    add_resource("/validation/"+validation_id) if delete
+    add_resource("/"+validation_id) if delete
 
-    #get '/validation/'+validation_id,nil,'HTTP_ACCEPT' => "application/rdf+xml"
-    get '/validation/'+validation_id,nil,'HTTP_ACCEPT' => "text/x-yaml"
+    #get '/'+validation_id,nil,'HTTP_ACCEPT' => "application/rdf+xml"
+    get '/'+validation_id,nil,'HTTP_ACCEPT' => "text/x-yaml"
     puts last_response.body
     assert last_response.ok? || last_response.status==202
 
 #    ["test_dataset_uri", "model_uri", "prediction_dataset_uri"].each do |t|
-#      get '/validation/'+validation_id+'/'+t
+#      get '/'+validation_id+'/'+t
 #      puts ""+t+": "+last_response.body
 #      assert last_response.ok?
 #