params for task and qmrf jnlp

5 files changed, 98 insertions, 9 deletions

diff --git a/nightly/nightly.rb b/nightly/nightly.rb
index e3cf1bc..dca85d2 100644
--- a/nightly/nightly.rb
+++ b/nightly/nightly.rb
@@ -21,7 +21,7 @@ class Nightly
     validationExamples = ValidationExamples.select(select)
     return "please \"select\" validation examples:\n"+ValidationExamples.list if validationExamples.size==0
     
-    task_uri = OpenTox::Task.as_task("Build nightly", "nightly-validation-test-service") do
+    task_uri = OpenTox::Task.as_task("Build nightly", "nightly-validation-test-service", {:select => select, :dry_run => dry_run}) do
       LOGGER.info("Building nightly report")
       
       benchmarks = validationExamples.collect{ |e| ValidationBenchmark.new(e) }
diff --git a/reach_reports/reach_application.rb b/reach_reports/reach_application.rb
index 74a1006..87bfcbe 100644
--- a/reach_reports/reach_application.rb
+++ b/reach_reports/reach_application.rb
@@ -35,7 +35,7 @@ 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+"'"
+  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
@@ -75,6 +75,8 @@ post '/reach_report/:type/:id' do
   #f.puts rep.to_xml
 end
 
+
+
 #get '/reach_report/:type/:id/:section' do
 #  
 #  type = extract_type(params)
@@ -89,3 +91,90 @@ end
 #  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="qmrfedit2/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="qmrfedit2/OTLogo.png" />
+</information>
+<resources>
+<j2se version="1.6+" java-vm-args="-Xincgc"/>
+
+<jar href="qmrfedit2/OT_QMRFEditor.jar" download="eager" main="true"/>
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-applications.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-builder3d.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-charges.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-core.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-datadebug.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-data.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-experimental.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-extra.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-forcefield.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-interfaces.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-io.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-jchempaint.applet.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-jchempaint.application.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-jchempaint.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-libio-cml.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-libio-weka.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-nonotify.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-pdb-cml.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-pdb.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-qsar-cml.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-qsar.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/cdk-qsar-pdb.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/commons-cli-1.0.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/commons-io-1.1.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/commons-logging-1.0.4.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/fop.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/jai_codec.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/jai_core.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/jgrapht-0.6.0.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/jh.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/l2fprod-common-all.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/libfonts-0.1.4.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/log4j-1.2.8.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/log4j.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/mysql-connector-java-5.0.5-bin.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/naming-factory-dbcp.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/naming-factory.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/naming-resources.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/opsin-big-0.1.0.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/org.restlet.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/swing-layout-1.0.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/xmlgraphics-commons-1.1.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/xom-1.1b2.jar" download="lazy" />
+<jar href="qmrfedit2/OT_QMRFEditor_lib/xom-1.1.jar" download="lazy" />
+
+
+</resources>
+<application-desc main-class="ambit.applications.qmrf.QMRFEditor">
+<argument>-x http://opentox.informatik.uni-freiburg.de/validation/reach_report/QMRF/
+EOF
+  jnlp += params[:id].to_s
+
+  jnlp += <<EOF 
+</argument>
+<argument>-d http://opentox.informatik.uni-freiburg.de/qmrfedit2/qmrf.dtd</argument>
+<argument>-t http://opentox.informatik.uni-freiburg.de/qmrfedit2/verdana.ttf</argument>
+
+</application-desc> 
+<security>
+    <all-permissions/>
+</security>
+</jnlp>
+EOF
+  
+  content_type "application/x-java-jnlp-file"
+  jnlp
+end
+
diff --git a/report/report_application.rb b/report/report_application.rb
index 48787d3..12775cc 100644
--- a/report/report_application.rb
+++ b/report/report_application.rb
@@ -98,7 +98,7 @@ delete '/report/:type/:id' do
 end
 
 post '/report/:type' do
-  task_uri = OpenTox::Task.as_task("Create report",url_for("/report/"+params[:type], :full)) do
+  task_uri = OpenTox::Task.as_task("Create report",url_for("/report/"+params[:type], :full), params) do
     perform do |rs|
       content_type "text/uri-list"
       rs.create_report(params[:type],params[:validation_uris]?params[:validation_uris].split(/\n|,/):nil)
diff --git a/test/test_application.rb b/test/test_application.rb
index 94022da..48cced7 100644
--- a/test/test_application.rb
+++ b/test/test_application.rb
@@ -2,7 +2,7 @@
 post '/test_validation/?' do
   validationExamples = ValidationExamples.select(params[:select])
   return "please \"select\" a single validation example:\n"+ValidationExamples.list if validationExamples.size!=1 or validationExamples[0].size!=1
-  OpenTox::Task.as_task("Test validation",url_for("/test_validation",:full)) do
+  OpenTox::Task.as_task("Test validation",url_for("/test_validation",:full), params) do
     v = validationExamples[0][0]
     ex = v.new
     ex.upload_files
diff --git a/validation/validation_application.rb b/validation/validation_application.rb
index ff6cc4c..ecaab4f 100644
--- a/validation/validation_application.rb
+++ b/validation/validation_application.rb
@@ -117,7 +117,7 @@ end
 
 post '/crossvalidation/?' do
   content_type "text/uri-list"
-  task_uri = OpenTox::Task.as_task( "Perform crossvalidation", url_for("/crossvalidation", :full) ) do
+  task_uri = OpenTox::Task.as_task( "Perform crossvalidation", url_for("/crossvalidation", :full), params ) do
     LOGGER.info "creating crossvalidation "+params.inspect
     halt 400, "dataset_uri missing" unless params[:dataset_uri]
     halt 400, "algorithm_uri missing" unless params[:algorithm_uri]
@@ -177,7 +177,7 @@ end
 
 post '/?' do
   content_type "text/uri-list"
-  task_uri = OpenTox::Task.as_task( "Perform validation", url_for("/", :full) ) do |task|
+  task_uri = OpenTox::Task.as_task( "Perform validation", url_for("/", :full), params ) do |task|
     LOGGER.info "creating validation "+params.inspect
     if params[:model_uri] and params[:test_dataset_uri] and !params[:training_dataset_uri] and !params[:algorithm_uri]
       v = Validation::Validation.new :model_uri => params[:model_uri], 
@@ -206,7 +206,7 @@ end
 
 post '/training_test_split' do
   content_type "text/uri-list"
-  task_uri = OpenTox::Task.as_task( "Perform training test split validation", url_for("/training_test_split", :full) ) do
+  task_uri = OpenTox::Task.as_task( "Perform training test split validation", url_for("/training_test_split", :full), params ) 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]
@@ -228,7 +228,7 @@ end
 
 post '/bootstrapping' do
   content_type "text/uri-list"
-  task_uri = OpenTox::Task.as_task( "Perform bootstrapping validation", url_for("/bootstrapping", :full) ) do
+  task_uri = OpenTox::Task.as_task( "Perform bootstrapping validation", url_for("/bootstrapping", :full), params ) do
     LOGGER.info "performing bootstrapping validation "+params.inspect
     halt 400, "dataset_uri missing" unless params[:dataset_uri]
     halt 400, "algorithm_uri missing" unless params[:algorithm_uri]
@@ -259,7 +259,7 @@ end
 
 post '/validate_datasets' do
   content_type "text/uri-list"
-  task_uri = OpenTox::Task.as_task( "Perform dataset validation", url_for("/validate_datasets", :full) ) do
+  task_uri = OpenTox::Task.as_task( "Perform dataset validation", url_for("/validate_datasets", :full), params ) do
     LOGGER.info "validating values "+params.inspect
     halt 400, "test_dataset_uri missing" unless params[:test_dataset_uri]
     halt 400, "prediction_datset_uri missing" unless params[:prediction_dataset_uri]