opentox-server 0.0.1pre → 0.0.2pre
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/lib/authorization-helper.rb +131 -0
- data/lib/file-store.rb +37 -0
- data/lib/opentox-server.rb +3 -0
- data/lib/opentox.rb +23 -20
- data/opentox-server.gemspec +1 -1
- metadata +20 -18
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@@ -0,0 +1,131 @@
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module OpenTox
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# Base class for OpenTox services
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class Application < Service
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helpers do
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# Login to get session for browser application(e.G.: ToxCreate)
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#
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# @param [String, String] username,password
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# @return [String] subjectid from session or nil
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def login(username, password)
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logout
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session[:subjectid] = OpenTox::Authorization.authenticate(username, password)
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$logger.debug "ToxCreate login user #{username} with subjectid: " + session[:subjectid].to_s
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if session[:subjectid] != nil
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session[:username] = username
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return session[:subjectid]
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else
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session[:username] = ""
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return nil
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end
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end
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# Logout to reset session
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#
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# @return [Boolean] true/false
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def logout
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if session[:subjectid] != nil
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session[:subjectid] = nil
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session[:username] = ""
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return true
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end
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return false
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end
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# Checks session and valid subjectid token.
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# @return [Boolean] true/false
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def logged_in()
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return true if !$aa[:uri]
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if session[:subjectid] != nil
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return OpenTox::Authorization.is_token_valid(session[:subjectid])
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end
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return false
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end
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# Authorization for a browser/webservice request
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# webapplication: redirects with flash[:notice] if unauthorized
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# webservice: raises error if unauthorized
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# @param [String]subjectid
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def protected!(subjectid)
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if env["session"]
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unless authorized?(subjectid)
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flash[:notice] = "You don't have access to this section: "
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redirect back
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end
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elsif !env["session"] && subjectid
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unless authorized?(subjectid)
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$logger.debug "URI not authorized: clean: " + clean_uri("#{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']}").sub("http://","https://").to_s + " full: #{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']} with request: #{request.env['REQUEST_METHOD']}"
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raise OpenTox::NotAuthorizedError.new "Not authorized"
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end
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else
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raise OpenTox::NotAuthorizedError.new "Not authorized" unless authorized?(subjectid)
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end
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end
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# Check Authorization for URI with method and subjectid.
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# @param [String]subjectid
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def authorized?(subjectid)
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request_method = request.env['REQUEST_METHOD']
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uri = clean_uri("#{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']}").sub("http://","https://")
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request_method = "GET" if request_method == "POST" && uri =~ /\/model\/\d+\/?$/
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return OpenTox::Authorization.authorized?(uri, request_method, subjectid)
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end
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# Cleans URI from querystring and file-extension. Sets port 80 to emptystring
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# @param [String] uri
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def clean_uri(uri)
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uri = uri.sub(" ", "%20") #dirty hacks => to fix
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uri = uri[0,uri.index("InChI=")] if uri.index("InChI=")
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out = URI.parse(uri)
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out.path = out.path[0, out.path.length - (out.path.reverse.rindex(/\/{1}\d+\/{1}/))] if out.path.index(/\/{1}\d+\/{1}/) #cuts after /id/ for a&a
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out.path = out.path.split('.').first #cut extension
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port = (out.scheme=="http" && out.port==80)||(out.scheme=="https" && out.port==443) ? "" : ":#{out.port.to_s}"
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"#{out.scheme}://#{out.host}#{port}#{out.path.chomp("/")}" #"
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end
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# Unprotected uri for login
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def login_request?
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return env['REQUEST_URI'] =~ /\/login$/
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end
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# Check if URI returns code 200 //used in model/lazar.rb
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# @param [String]URLString
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# @return [Boolean] true/false
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def uri_available?(urlStr)
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url = URI.parse(urlStr)
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subjectidstr = @subjectid ? "?subjectid=#{CGI.escape @subjectid}" : ""
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http = Net::HTTP.new(url.host, url.port)
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if url.is_a?(URI::HTTPS)
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http.use_ssl = true
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http.verify_mode = OpenSSL::SSL::VERIFY_NONE
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end
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return http.head("#{url.request_uri}#{subjectidstr}").code == "200"
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end
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# Get subjectid out of session, params or rack-environment and unescape it if necessary
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# @return [String] subjectid
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def get_subjectid
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begin
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subjectid = nil
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subjectid = session[:subjectid] if session[:subjectid]
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subjectid = params[:subjectid] if params[:subjectid] and !subjectid
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subjectid = request.env['HTTP_SUBJECTID'] if request.env['HTTP_SUBJECTID'] and !subjectid
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# see http://rack.rubyforge.org/doc/SPEC.html
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subjectid = CGI.unescape(subjectid) if subjectid.include?("%23")
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@subjectid = subjectid
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rescue
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@subjectid = nil
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end
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end
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end
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before do
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get_subjectid()
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unless !$aa[:uri] or login_request? or $aa[:free_request].include?(env['REQUEST_METHOD'].to_sym)
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protected!(@subjectid)
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end
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end
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end
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end
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data/lib/file-store.rb
ADDED
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@@ -0,0 +1,37 @@
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FileUtils.mkdir_p File.join(File.dirname(__FILE__),"private")
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module OpenTox
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# Base class for OpenTox services
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class FileStore < Service
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helpers do
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def next_id
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id = Dir["./private/*.nt"].collect{|f| File.basename(f,"nt").to_i}.sort.last
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id = 0 if id.nil?
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id + 1
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end
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def file id
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File.join File.dirname(File.expand_path __FILE__), "private", "#{id.to_s}.nt"
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end
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def uri_list
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Dir["./private/*.nt"].collect{|f| url_for File.basename(f,".nt")}.join("\n")
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end
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end
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get '/?' do
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uri_list
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end
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post '/?' do
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File.open(file(next_id),"w+"){|f| f.puts request.env["rack.input"].read}
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end
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get '/:id/?' do
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send_file file(params[:id])
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end
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end
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end
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data/lib/opentox-server.rb
CHANGED
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@@ -3,5 +3,8 @@ require 'rack'
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require 'rack/contrib'
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require 'sinatra'
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require 'sinatra/url_for'
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require 'roo'
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require File.join(File.dirname(__FILE__),"environment.rb")
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require File.join(File.dirname(__FILE__),"opentox.rb")
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require File.join(File.dirname(__FILE__),"file-store.rb")
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require File.join(File.dirname(__FILE__),"authorization-helper.rb")
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data/lib/opentox.rb
CHANGED
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@@ -2,9 +2,8 @@ require 'sinatra/base'
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require "sinatra/reloader"
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module OpenTox
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# Base class for OpenTox services
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# Errors are formated according to acccept-header
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# Non OpenTox::Errors (defined in error.rb) are handled as internal error (500), stacktrace is logged
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class Service < Sinatra::Base
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helpers Sinatra::UrlForHelper
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@@ -17,39 +16,43 @@ module OpenTox
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register Sinatra::Reloader
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end
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helpers do
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def uri
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params[:id] ? url_for("/#{params[:id]}", :full) : "#{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}"
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end
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end
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before do
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@accept = request.env['HTTP_ACCEPT']
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response['Content-Type'] = @accept
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# TODO: A+A
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end
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error do
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# TODO:
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# TODO: convert to OpenTox::Error and set URI
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error = request.env['sinatra.error']
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#error.
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case request.env['HTTP_ACCEPT']
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when 'application/rdf+xml'
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content_type 'application/rdf+xml'
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when /html/
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content_type 'text/html'
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when "text/n3"
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content_type "text/n3"
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else
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content_type "text/turtle"
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end
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#error.uri = uri
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if error.respond_to? :report
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-
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# Errors are formated according to acccept-header
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case @accept
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when 'application/rdf+xml'
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body = error.report.to_rdfxml
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when /html/
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-
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# TODO
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# body = error.report.to_html
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body = error.report.to_turtle
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when "text/n3"
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body = error.report.to_ntriples
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else
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body = error.report.to_turtle
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end
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else
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-
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response['Content-Type'] = "text/plain"
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body = error.message
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body += "\n#{error.backtrace}"
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end
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code = error.http_code
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code
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halt code, error.report.to_turtle
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error.respond_to?(:http_code) ? code = error.http_code : code = 500
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halt code, body
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end
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end
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end
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data/opentox-server.gemspec
CHANGED
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@@ -3,7 +3,7 @@ $:.push File.expand_path("../lib", __FILE__)
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Gem::Specification.new do |s|
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s.name = "opentox-server"
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s.version = "0.0.
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s.version = "0.0.2pre"
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s.authors = ["Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler"]
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s.email = ["helma@in-silico.ch"]
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s.homepage = "http://github.com/opentox/opentox-server"
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metadata
CHANGED
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--- !ruby/object:Gem::Specification
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name: opentox-server
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version: !ruby/object:Gem::Version
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version: 0.0.
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version: 0.0.2pre
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prerelease: 5
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platform: ruby
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authors:
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@@ -9,11 +9,11 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2012-
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date: 2012-04-02 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: opentox-client
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requirement: &
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requirement: &84856440 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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@@ -21,10 +21,10 @@ dependencies:
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version: '0'
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type: :runtime
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prerelease: false
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version_requirements: *
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version_requirements: *84856440
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- !ruby/object:Gem::Dependency
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name: rack
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requirement: &
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requirement: &84855790 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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@@ -32,10 +32,10 @@ dependencies:
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version: '0'
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type: :runtime
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prerelease: false
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version_requirements: *
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version_requirements: *84855790
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- !ruby/object:Gem::Dependency
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name: rack-contrib
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requirement: &
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requirement: &84855290 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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@@ -43,10 +43,10 @@ dependencies:
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version: '0'
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type: :runtime
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prerelease: false
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version_requirements: *
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version_requirements: *84855290
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- !ruby/object:Gem::Dependency
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name: sinatra
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requirement: &
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requirement: &84854680 !ruby/object:Gem::Requirement
|
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none: false
|
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|
requirements:
|
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|
- - ! '>='
|
|
@@ -54,10 +54,10 @@ dependencies:
|
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|
version: '0'
|
|
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|
type: :runtime
|
|
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|
prerelease: false
|
|
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|
-
version_requirements: *
|
|
57
|
+
version_requirements: *84854680
|
|
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|
- !ruby/object:Gem::Dependency
|
|
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|
name: sinatra-contrib
|
|
60
|
-
requirement: &
|
|
60
|
+
requirement: &84853820 !ruby/object:Gem::Requirement
|
|
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none: false
|
|
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|
requirements:
|
|
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|
- - ! '>='
|
|
@@ -65,10 +65,10 @@ dependencies:
|
|
|
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|
version: '0'
|
|
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|
type: :runtime
|
|
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|
prerelease: false
|
|
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|
-
version_requirements: *
|
|
68
|
+
version_requirements: *84853820
|
|
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69
|
- !ruby/object:Gem::Dependency
|
|
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|
name: emk-sinatra-url-for
|
|
71
|
-
requirement: &
|
|
71
|
+
requirement: &84852960 !ruby/object:Gem::Requirement
|
|
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|
none: false
|
|
73
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|
requirements:
|
|
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|
- - ! '>='
|
|
@@ -76,10 +76,10 @@ dependencies:
|
|
|
76
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|
version: '0'
|
|
77
77
|
type: :runtime
|
|
78
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|
prerelease: false
|
|
79
|
-
version_requirements: *
|
|
79
|
+
version_requirements: *84852960
|
|
80
80
|
- !ruby/object:Gem::Dependency
|
|
81
81
|
name: roo
|
|
82
|
-
requirement: &
|
|
82
|
+
requirement: &84851990 !ruby/object:Gem::Requirement
|
|
83
83
|
none: false
|
|
84
84
|
requirements:
|
|
85
85
|
- - ! '>='
|
|
@@ -87,10 +87,10 @@ dependencies:
|
|
|
87
87
|
version: '0'
|
|
88
88
|
type: :runtime
|
|
89
89
|
prerelease: false
|
|
90
|
-
version_requirements: *
|
|
90
|
+
version_requirements: *84851990
|
|
91
91
|
- !ruby/object:Gem::Dependency
|
|
92
92
|
name: unicorn
|
|
93
|
-
requirement: &
|
|
93
|
+
requirement: &84851710 !ruby/object:Gem::Requirement
|
|
94
94
|
none: false
|
|
95
95
|
requirements:
|
|
96
96
|
- - ! '>='
|
|
@@ -98,7 +98,7 @@ dependencies:
|
|
|
98
98
|
version: '0'
|
|
99
99
|
type: :runtime
|
|
100
100
|
prerelease: false
|
|
101
|
-
version_requirements: *
|
|
101
|
+
version_requirements: *84851710
|
|
102
102
|
description: Ruby library for opentox services
|
|
103
103
|
email:
|
|
104
104
|
- helma@in-silico.ch
|
|
@@ -111,7 +111,9 @@ files:
|
|
|
111
111
|
- LICENSE
|
|
112
112
|
- README
|
|
113
113
|
- Rakefile
|
|
114
|
+
- lib/authorization-helper.rb
|
|
114
115
|
- lib/environment.rb
|
|
116
|
+
- lib/file-store.rb
|
|
115
117
|
- lib/opentox-server.rb
|
|
116
118
|
- lib/opentox.rb
|
|
117
119
|
- opentox-server.gemspec
|