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require "report/environment.rb"
def perform
@@report_service = Reports::ReportService.instance( url_for("/report", :full) ) unless defined?@@report_service
yield( @@report_service )
end
def get_docbook_resource(filepath)
perform do |rs|
raise OpenTox::NotFoundError.new"not found: "+filepath unless File.exist?(filepath)
types = MIME::Types.type_for(filepath)
content_type(types[0].content_type) if types and types.size>0 and types[0]
result = body(File.new(filepath))
end
end
get '/'+ENV['DOCBOOK_DIRECTORY']+'/:subdir/:resource' do
path_array = request.env['REQUEST_URI'].split("/")
get_docbook_resource ENV['DOCBOOK_DIRECTORY']+"/"+path_array[-2]+"/"+path_array[-1]
end
get '/'+ENV['DOCBOOK_DIRECTORY']+'/:resource' do
get_docbook_resource ENV['DOCBOOK_DIRECTORY']+"/"+request.env['REQUEST_URI'].split("/")[-1]
end
get '/resources/:resource' do
get_docbook_resource "resources/"+request.env['REQUEST_URI'].split("/")[-1]
end
get '/report/:type/css_style_sheet/?' do
perform do |rs|
"@import \""+params[:css_style_sheet]+"\";"
end
end
get '/report/?' do
perform do |rs|
case request.env['HTTP_ACCEPT'].to_s
when /text\/html/
related_links =
"All validations: "+url_for("/",:full)
description =
"A list of all report types."
content_type "text/html"
OpenTox.text_to_html rs.get_report_types,@subjectid,related_links,description
else
content_type "text/uri-list"
rs.get_report_types
end
end
end
def wrap(s, width=78)
s.gsub(/(.{1,#{width}})(\s+|\Z)/, "\\1\n")
end
get '/report/:report_type' do
perform do |rs|
case request.env['HTTP_ACCEPT'].to_s
when /text\/html/
related_links =
"Available report types: "+url_for("/report",:full)+"\n"+
"Single validations: "+url_for("/",:full)+"\n"+
"Crossvalidations: "+url_for("/crossvalidation",:full)
description =
"A list of all "+params[:report_type]+" reports. To create a report, use the POST method."
if params[:report_type]=="algorithm_comparison"
description += "\n\nThis report can be used to compare the validation results of different algorithms that have been validated on the same dataset."
description += "\nThe following attributes can be compared with the t-test:"
description += "\n\n* All validation types:\n"+wrap((Validation::VAL_PROPS_SUM+Validation::VAL_PROPS_AVG).join(", "),120)
description += "\n* Classification validations:\n"+wrap(Validation::VAL_CLASS_PROPS.join(", "),120)
description += "\n* Regresssion validations:\n"+wrap(Validation::VAL_REGR_PROPS.join(", "),120)
end
post_params = [[:validation_uris]]
post_command = OpenTox::PostCommand.new request.url,"Create validation report"
val_uri_description = params[:report_type]=="algorithm_comparison" ? "Separate multiple uris with ','" : nil
# trick for easy report creation
# if searching for a report, ?validation="uri" or ?crossvalidaiton="uri" is given as search param
# use this (search param has equal name as report type) as default value for validation_uri
post_command.attributes << OpenTox::PostAttribute.new("validation_uris",true,params[params[:report_type]],val_uri_description)
if params[:report_type]=="algorithm_comparison"
post_command.attributes << OpenTox::PostAttribute.new("identifier",true,nil,"Specifiy one identifier for each uri, separated with ','")
post_command.attributes << OpenTox::PostAttribute.new("ttest_significance",false,"0.9","Significance level for t-tests (Set to '0' to disable t-test).")
post_command.attributes << OpenTox::PostAttribute.new("ttest_attributes",false,nil,"Attributes for t-test; default for classification: '"+
VAL_ATTR_TTEST_CLASS.join(",")+"', default for regression: '"+VAL_ATTR_TTEST_REGR.join(",")+"'")
end
content_type "text/html"
OpenTox.text_to_html rs.get_all_reports(params[:report_type], params),@subjectid,related_links,description,post_command
else
content_type "text/uri-list"
rs.get_all_reports(params[:report_type], params)
end
end
end
post '/report/:type/:id/format_html' do
perform do |rs|
rs.get_report(params[:type],params[:id],"text/html",true,params)
content_type "text/uri-list"
rs.get_uri(params[:type],params[:id])+"\n"
end
end
get '/report/:type/:id' do
perform do |rs|
accept_header = request.env['HTTP_ACCEPT']
report = rs.get_report(params[:type],params[:id],accept_header)
format = Reports::ReportFormat.get_format(accept_header)
content_type format
# default encoding is utf-8, html conversion produces iso-8859-1 encoding
content_type "text/html", 'charset' => 'ISO-8859-1' if format=="text/html"
#PENDING: get_report should return file or string, check for result.is_file instead of format
if format=="application/x-yaml" or format=="application/rdf+xml"
report
else
result = body(File.new(report))
end
end
end
#OpenTox::Authorization.whitelist( Regexp.new("/report/.*/[0-9]+/.*"),"GET")
get '/report/:type/:id/:resource' do
perform do |rs|
filepath = rs.get_report_resource(params[:type],params[:id],params[:resource])
types = MIME::Types.type_for(filepath)
content_type(types[0].content_type) if types and types.size>0 and types[0]
result = body(File.new(filepath))
end
end
delete '/report/:type/:id' do
perform do |rs|
content_type "text/plain"
rs.delete_report(params[:type],params[:id],@subjectid)
end
end
post '/report/:type' do
raise OpenTox::BadRequestError.new "validation_uris missing" unless params[:validation_uris].to_s.size>0
task = OpenTox::Task.create("Create report",url_for("/report/"+params[:type], :full)) do |task| #,params
perform do |rs|
rs.create_report(params[:type],params[:validation_uris]?params[:validation_uris].split(/\n|,/):nil,
params[:identifier]?params[:identifier].split(/\n|,/):nil,params,@subjectid,task)
end
end
return_task(task)
end
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