diff options
Diffstat (limited to 'reach_reports/reach_application.rb')
| -rwxr-xr-x | reach_reports/reach_application.rb | 242 |
1 files changed, 242 insertions, 0 deletions
diff --git a/reach_reports/reach_application.rb b/reach_reports/reach_application.rb new file mode 100755 index 0000000..cd0695c --- /dev/null +++ b/reach_reports/reach_application.rb @@ -0,0 +1,242 @@ + +[ 'rubygems', 'sinatra', 'sinatra/url_for', 'opentox-ruby' ].each do |lib| + require lib +end + +QMRF_EDITOR_URI = "http://ortona.informatik.uni-freiburg.de/qmrfedit2/OT_QMRFEditor.jnlp" + +require 'reach_reports/reach_persistance.rb' +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/ + 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" + 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_params = "" + 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"]]] + when /(?i)QPRF/ + #TODO + end + OpenTox.text_to_html ReachReports.list_reports(type),@subjectid,related_links,description,post_params + else + content_type "text/uri-list" + ReachReports.list_reports(type) + end +end + +post '/reach_report/:type' do + + type = extract_type(params) + content_type "text/uri-list" + + LOGGER.info "creating "+type+" report "+params.inspect + #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" + halt 400, "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 + 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\"." + 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 + halt 400, "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="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/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" /> + + +</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]) + + jnlp += <<EOF +</argument> +<argument>--subjectid= +EOF + jnlp.chomp! + jnlp += @subjectid.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 + |