diff options
Diffstat (limited to 'reach_reports/reach_application.rb')
| -rwxr-xr-x | reach_reports/reach_application.rb | 128 |
1 files changed, 67 insertions, 61 deletions
diff --git a/reach_reports/reach_application.rb b/reach_reports/reach_application.rb index 9b45e8b..e35df7b 100755 --- a/reach_reports/reach_application.rb +++ b/reach_reports/reach_application.rb @@ -3,7 +3,7 @@ require lib end -QMRF_EDITOR_URI = "http://ortona.informatik.uni-freiburg.de/qmrfedit2/OT_QMRFEditor.jnlp" +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 ) @@ -25,7 +25,7 @@ require 'reach_reports/reach_service.rb' require "lib/format_util.rb" def extract_type(params) - halt 400, "illegal type, neither QMRF nor QPRF: "+params[:type] unless params[:type] && params[:type] =~ /(?i)Q(M|P)RF/ + 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 @@ -54,18 +54,19 @@ get '/reach_report/:type' do "All REACH reporting types: "+url_for("/reach_report",:full) description = "A list of "+type+" reports." - post_params = "" + 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_params = [[[:model_uri]],[["Existing QMRF report, content-type application/qmrf-xml"]]] + 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 ReachReports.list_reports(type),@subjectid,related_links,description,post_params + OpenTox.text_to_html ReachReports.list_reports(type),@subjectid,related_links,description,post_command else content_type "text/uri-list" ReachReports.list_reports(type) @@ -78,6 +79,9 @@ post '/reach_report/:type' do 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"]) @@ -96,7 +100,7 @@ get '/reach_report/:type/:id' do case request.env['HTTP_ACCEPT'].to_s when "application/rdf+xml" - halt 400, "application/rdf+xml not yet supported" + 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 @@ -117,7 +121,7 @@ get '/reach_report/:type/:id' do content_type "application/x-yaml" rep.to_yaml else - halt 400, "MIME type '"+request.env['HTTP_ACCEPT'].to_s+"' not supported, valid Accept-Headers are \"application/rdf+xml\", \"application/x-yaml\", \"application/qmrf-xml\"." + 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 @@ -128,7 +132,7 @@ post '/reach_report/:type/:id' do rep = ReachReports.get_report(type, params[:id]) input = request.env["rack.input"].read - halt 400, "no xml data specified" unless input && input.to_s.size>0 + 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) @@ -165,63 +169,63 @@ get '/reach_report/:type/:id/editor' do 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" > +<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="qmrfedit2/OTLogo.png" /> +<icon href="qmrfedit/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/commons-codec-1.3.jar" download="eager" /> -<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" /> +<jar href="qmrfedit/OT_QMRFEditor.jar" download="eager" main="true"/> +<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> @@ -231,17 +235,19 @@ EOF jnlp.chomp! jnlp += File.join(url_for("/reach_report/QMRF",:full),params[:id]) - jnlp += <<EOF + if @subjectid.to_s.size>0 + jnlp += <<EOF </argument> <argument>--subjectid= EOF - jnlp.chomp! - jnlp += @subjectid.to_s + jnlp.chomp! + jnlp += @subjectid.to_s + end 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> +<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> |