Merge remote branch 'mguetlein/development' into development

9 files changed, 137 insertions, 74 deletions

diff --git a/lib/authorization.rb b/lib/authorization.rb
index 1942e95..eab20df 100644
--- a/lib/authorization.rb
+++ b/lib/authorization.rb
@@ -334,15 +334,15 @@ module OpenTox
         true
       elsif CONFIG[:authorization][:authenticate_request].include?(request_method)
         ret = OpenTox::Authorization.is_token_valid(subjectid)
-        #LOGGER.debug "authorized? >>#{ret}<< (token is in/valid), method: #{request_method}, URI: #{uri}, subjectid: #{subjectid}"
+        LOGGER.debug "authorized? >>#{ret}<< (token is in/valid), method: #{request_method}, URI: #{uri}, subjectid: #{subjectid}" unless ret
         ret
       elsif OpenTox::Authorization.authorize_exception?(uri, request_method)
         ret = OpenTox::Authorization.is_token_valid(subjectid)
-        #LOGGER.debug "authorized? >>#{ret}<< (uris is authorize exception, token is in/valid), method: #{request_method}, URI: #{uri}, subjectid: #{subjectid}"
+        LOGGER.debug "authorized? >>#{ret}<< (uris is authorize exception, token is in/valid), method: #{request_method}, URI: #{uri}, subjectid: #{subjectid}" unless ret
         ret
       elsif CONFIG[:authorization][:authorize_request].include?(request_method)
         ret = OpenTox::Authorization.authorize(uri, request_method, subjectid)
-        LOGGER.debug "authorized? >>#{ret}<< (uri (not) authorized), method: #{request_method}, URI: #{uri}, subjectid: #{subjectid}"
+        LOGGER.debug "authorized? >>#{ret}<< (uri (not) authorized), method: #{request_method}, URI: #{uri}, subjectid: #{subjectid}" unless ret
         ret
       else 
         LOGGER.error "invalid request/uri method: #{request_method}, URI: #{uri}, subjectid: #{subjectid}"
diff --git a/lib/dataset.rb b/lib/dataset.rb
index a843cea..2c47502 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -237,7 +237,7 @@ module OpenTox
       @features[feature] = {}  unless @features[feature]
       @data_entries[compound] = {} unless @data_entries[compound]
       @data_entries[compound][feature] = [] unless @data_entries[compound][feature]
-      @data_entries[compound][feature] << value
+      @data_entries[compound][feature] << value if value!=nil
     end
 
     # Add/modify metadata, existing entries will be overwritten
@@ -283,8 +283,12 @@ module OpenTox
       else
         compounds.each do |c|
           features.each do |f|
-            @data_entries[c][f].each do |v|
-              dataset.add(c,f,v)
+            unless @data_entries[c][f]
+              dataset.add(c,f,nil)
+            else
+              @data_entries[c][f].each do |v|
+                dataset.add(c,f,v)
+              end
             end
           end
         end
diff --git a/lib/feature.rb b/lib/feature.rb
index be063dd..c0729a7 100644
--- a/lib/feature.rb
+++ b/lib/feature.rb
@@ -16,8 +16,14 @@ module OpenTox
     # provides domain (possible target values) of classification feature 
     # @return [Array] list with possible target values
     def domain
-      #TODO derieve from metadata / ontology
-      return [true, false]
+      if metadata[OT.acceptValue]
+        raise "accept value found, remove hack and implement correctly"
+      else
+      if @uri=~/feature\/26221/ || @uri=~/feature\/221726/ 
+        return ["mutagen" , "nonmutagen"]
+      end
+        return [true, false]
+      end
     end
     
     # provides feature type, possible types are "regression" or "classification"
diff --git a/lib/helper.rb b/lib/helper.rb
index 191b932..b30908c 100644
--- a/lib/helper.rb
+++ b/lib/helper.rb
@@ -19,8 +19,6 @@ helpers do
 
   #Check Authorization for URI with method and subjectid. 
   def authorized?(subjectid)
-    # hack for reports, address problem as soon as subjectid is not longer allowed as param 
-    return true if request.env['REQUEST_URI'] =~ /validation\/report\/.*svg$/
     request_method = request.env['REQUEST_METHOD']
     uri = clean_uri("#{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']}")
     request_method = "GET" if request_method == "POST" &&  uri =~ /\/model\/\d+\/?$/
@@ -34,8 +32,9 @@ helpers do
     uri = uri[0,uri.index("InChI=")] if uri.index("InChI=") 
     
     out = URI.parse(uri)
-    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 
-    "#{out.scheme}:" + (out.port != 80 ? out.port : "") + "//#{out.host}#{out.path.chomp('/')}"
+    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
+    port = (out.scheme=="http" && out.port==80)||(out.scheme=="https" && out.port==443) ? "" : ":#{out.port.to_s}" 
+    "#{out.scheme}://#{out.host}#{port}#{out.path.chomp("/")}" #"
   end
 
   #unprotected uri for login
@@ -52,6 +51,7 @@ before do
       subjectid = session[:subjectid] if session[:subjectid]
       subjectid = params[:subjectid]  if params[:subjectid] and !subjectid
       subjectid = request.env['HTTP_SUBJECTID'] if request.env['HTTP_SUBJECTID'] and !subjectid
+      subjectid = request.cookies["subjectid"] unless subjectid
       # see http://rack.rubyforge.org/doc/SPEC.html
       subjectid = CGI.unescape(subjectid) if subjectid.include?("%23")
       @subjectid = subjectid
diff --git a/lib/model.rb b/lib/model.rb
index 9622d65..74408d8 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -38,24 +38,28 @@ module OpenTox
        # provides feature type, possible types are "regression" or "classification"
        # @return [String] feature type, "unknown" if type could not be estimated
       def feature_type(subjectid=nil)
+        return @feature_type if @feature_type
+        
         # dynamically perform restcalls if necessary
         load_metadata(subjectid) if @metadata==nil or @metadata.size==0 or (@metadata.size==1 && @metadata.values[0]==@uri)
-        
-        @algorithm = OpenTox::Algorithm::Generic.find(@metadata[OT.algorithm], subjectid) unless @algorithm
-        algorithm_title = @algorithm ? @algorithm.metadata[DC.title] : nil
-        algorithm_type = @algorithm ? @algorithm.metadata[OT.isA] : nil
-        @dependentVariable = OpenTox::Feature.find( @metadata[OT.dependentVariables],subjectid ) unless @dependentVariable
-        type_indicators = [@dependentVariable.feature_type, @metadata[OT.isA], @metadata[DC.title], 
+        algorithm = OpenTox::Algorithm::Generic.find(@metadata[OT.algorithm], subjectid)
+        algorithm_title = algorithm ? algorithm.metadata[DC.title] : nil
+        algorithm_type = algorithm ? algorithm.metadata[OT.isA] : nil
+        dependent_variable = OpenTox::Feature.find( @metadata[OT.dependentVariables],subjectid )
+        dependent_variable_type = dependent_variable ? dependent_variable.feature_type : nil
+        type_indicators = [dependent_variable_type, @metadata[OT.isA], @metadata[DC.title], 
           @uri, algorithm_type, algorithm_title] 
         type_indicators.each do |type|
           case type
           when /(?i)classification/
-            return "classification"
+            @feature_type =  "classification"
+            break
           when /(?i)regression/
-            return "regression"
+            @feature_type = "regression"
           end
         end
-        raise "unknown model "+type_indicators.inspect
+        raise "unknown model "+type_indicators.inspect unless @feature_type
+        @feature_type
       end
       
     end
diff --git a/lib/overwrite.rb b/lib/overwrite.rb
index 7b53122..b5c3942 100644
--- a/lib/overwrite.rb
+++ b/lib/overwrite.rb
@@ -29,7 +29,7 @@ error Exception do
     halt error.http_code,rep.to_rdfxml
   when /html/
     content_type 'text/html'
-    halt error.http_code,(OpenTox.text_to_html rep.to_yaml)
+    halt error.http_code,(OpenTox.text_to_html rep.to_yaml, @subjectid)
   else
     content_type 'application/x-yaml'
     halt error.http_code,rep.to_yaml
@@ -45,11 +45,11 @@ class Sinatra::Base
       response['Content-Type'] = "application/rdf+xml"
       halt code,task.to_rdfxml
     when /yaml/
-      response['Content-Type'] = "application/rdf+xml"
+      response['Content-Type'] = "application/x-yaml"
       halt code,task.to_yaml # PENDING differs from task-webservice
     when /html/
       response['Content-Type'] = "text/html"
-      halt code,OpenTox.text_to_html(task.to_yaml)
+      halt code,OpenTox.text_to_html(task.to_yaml, @subjectid)
     else # default /uri-list/
       response['Content-Type'] = "text/uri-list"
       halt code,task.uri+"\n"
diff --git a/lib/parser.rb b/lib/parser.rb
index d2beeac..f33017d 100644
--- a/lib/parser.rb
+++ b/lib/parser.rb
@@ -39,7 +39,14 @@ module OpenTox
           file = File.new(@uri)
         else
           file = Tempfile.new("ot-rdfxml")
-          uri = @dataset ? File.join(@uri,"metadata") : @uri
+          if @dataset
+            # do not concat /metadata to uri string, this would not work for dataset/R401577?max=3 
+            uri = URI::parse(@uri)
+            uri.path = File.join(uri.path,"metadata")
+            uri = uri.to_s
+          else
+            uri = @uri
+          end
           file.puts OpenTox::RestClientWrapper.get uri,{:subjectid => subjectid,:accept => "application/rdf+xml"},nil,false
           file.close
           to_delete = file.path
@@ -163,26 +170,35 @@ module OpenTox
               data[triple[0]] = {:compound => "", :values => []} unless data[triple[0]]
               data[triple[0]][:compound] = triple[2]  
             when /#{OT.feature}/i
-              feature[triple[0]] = triple[2] 
+              feature[triple[0]] = triple[2]
+            when /#{RDF.type}/i
+              if triple[2]=~/#{OT.Compound}/i and !data[triple[0]]
+                data[triple[0]] = {:compound => triple[0], :values => []} 
+              end
             else 
             end
           end
           File.delete(to_delete) if to_delete
           data.each do |id,entry|
-            entry[:values].each do |value_id|
-              split = feature_values[value_id].split(/\^\^/)
-              case split[-1]
-              when XSD.double, XSD.float 
-                value = split.first.to_f
-              when XSD.boolean
-                value = split.first=~/(?i)true/ ? true : false                
-              else
-                value = split.first
+            if entry[:values].size==0
+              # no feature values add plain compounds
+              @dataset.add_compound(entry[:compound])
+            else
+              entry[:values].each do |value_id|
+                split = feature_values[value_id].split(/\^\^/)
+                case split[-1]
+                when XSD.double, XSD.float 
+                  value = split.first.to_f
+                when XSD.boolean
+                  value = split.first=~/(?i)true/ ? true : false                
+                else
+                  value = split.first
+                end
+                @dataset.add entry[:compound],feature[value_id],value
               end
-              @dataset.add entry[:compound],feature[value_id],value
             end
           end
-          load_features
+          load_features subjectid
           @dataset.metadata = load_metadata(subjectid)
           @dataset
         end
@@ -194,7 +210,10 @@ module OpenTox
             file = File.new(@uri)
           else
             file = Tempfile.new("ot-rdfxml")
-            uri = File.join(@uri,"features")
+            # do not concat /features to uri string, this would not work for dataset/R401577?max=3 
+            uri = URI::parse(@uri)
+            uri.path = File.join(uri.path,"features")
+            uri = uri.to_s
             file.puts OpenTox::RestClientWrapper.get uri,{:subjectid => subjectid,:accept => "application/rdf+xml"},nil,false
             file.close
             to_delete = file.path
diff --git a/lib/rest_client_wrapper.rb b/lib/rest_client_wrapper.rb
index d3136c7..dac24dc 100644
--- a/lib/rest_client_wrapper.rb
+++ b/lib/rest_client_wrapper.rb
@@ -76,7 +76,8 @@ module OpenTox
         else
           result = resource.send(rest_call, headers)
         end
-        
+        #LOGGER.debug "result body size: #{result.body.size}"
+
         # PENDING NTUA does return errors with 200
         raise RestClient::ExceptionWithResponse.new(result) if uri=~/ntua/ and result.body =~ /about.*http:\/\/anonymous.org\/error/
         
diff --git a/lib/to-html.rb b/lib/to-html.rb
index 4de5ee6..1f30ca1 100755
--- a/lib/to-html.rb
+++ b/lib/to-html.rb
@@ -1,7 +1,6 @@
 
 OT_LOGO = "http://opentox.informatik.uni-freiburg.de/ot-logo.png"
 
-
 class String
   
   # encloses URI in text with with link tag
@@ -25,29 +24,30 @@ module OpenTox
   # @param [optional,String] description general info
   # @param [optional,Array] post_params, array of arrays containing info on POST operation, see example
   # @return [String] html page
-  def self.text_to_html( text, related_links=nil, description=nil, post_params=nil )
+  def self.text_to_html( text, subjectid=nil, related_links=nil, description=nil, post_params=nil  )
     
     # TODO add title as parameter
     title = nil #$sinatra.url_for($sinatra.request.env['PATH_INFO'], :full) if $sinatra
-    
-    html = <<EOF
-<html>
-EOF
-    html.chomp!
+    html = "<html>"
     html += "<title>"+title+"</title>" if title
-    html += <<EOF 
-<img src="
-EOF
-    html.chomp!
-    html += OT_LOGO
-    html += <<EOF 
-">
-<body>
-EOF
-   html.chomp!
-   html += "<h3>Description</h3><pre><p>"+description.link_urls+"</p></pre>" if description
-   html += "<h3>Related links</h3><pre><p>"+related_links.link_urls+"</p></pre>" if related_links
-   if post_params
+    html += "<img src="+OT_LOGO+"><body>"
+      
+    if AA_SERVER
+      user = OpenTox::Authorization.get_user(subjectid) if subjectid
+      html +=  "<pre><p align=\"right\">"
+      unless user
+        html += "You are currently not logged in to "+$url_provider.url_for("",:full)+
+          ", <a href="+$url_provider.url_for("/login",:full)+">login</a>"
+      else
+        html += "You are logged in as '#{user}' to "+$url_provider.url_for("",:full)+
+          ", <a href="+$url_provider.url_for("/logout",:full)+">logout</a>"
+      end
+      html += "  </p></pre>"
+    end 
+   
+    html += "<h3>Description</h3><pre><p>"+description.link_urls+"</p></pre>" if description
+    html += "<h3>Related links</h3><pre><p>"+related_links.link_urls+"</p></pre>" if related_links
+    if post_params
       html += "<h3>POST parameters</h3>"
       count = 0
       post_params.each do |p|
@@ -59,23 +59,52 @@ EOF
         html += "</table></p></pre>"
         count += 1
       end
-   end
-   html += "<h3>Content</h3>" if description || related_links
-   html += <<EOF
-<pre>
-<p style="padding:15px; border:10px solid #5D308A">
-EOF
-   html.chomp!
-   html += text.link_urls
-   html += <<EOF
-</p>
-</pre>
-</body>
-<html>
-EOF
+    end
+    html += "<h3>Content</h3>" if description || related_links
+    html += "<pre><p style=\"padding:15px; border:10px solid \#5D308A\">"
+    html += text.link_urls
+    html += "</p></pre></body><html>"
     html
   end
   
+  def self.login( msg=nil )
+    html = "<html><title>Login</title><img src="+OT_LOGO+"><body>"
+    html += "<form method='POST' action='"+$url_provider.url_for("/login",:full)+"'>"
+    html += "<pre><p style=\"padding:15px; border:10px solid \#5D308A\">"
+    html += msg+"\n\n" if msg
+    html += "Please login to "+$url_provider.url_for("",:full)+"\n\n"
+    html += "<table border=0>"
+    html += "<tr><td>user:</td><td><input type='text' name='user' size='15' /></td></tr>"+
+          "<tr><td>password:</td><td><input type='password' name='password' size='15' /></td></tr>"+
+          #"<input type=hidden name=back_to value="+back_to.to_s+">"+
+          "<tr><td><input type='submit' value='Login' /></td></tr>"
+    html += "</table></p></pre></form></body><html>"
+    html
+  end
+end
+
+get '/logout/?' do
+  response.set_cookie("subjectid",{:value=>nil})
+  content_type "text/html"
+  content = "Sucessfully logged out from "+$url_provider.url_for("",:full)
+  OpenTox.text_to_html(content)
+end
+
+get '/login/?' do
+  content_type "text/html"
+  OpenTox.login
+end
+
+post '/login/?' do
+  subjectid = OpenTox::Authorization.authenticate(params[:user], params[:password])
+  if (subjectid)
+    response.set_cookie("subjectid",{:value=>subjectid})
+    content_type "text/html"
+    content = "Sucessfully logged in as '"+params[:user]+"' to "+$url_provider.url_for("",:full)
+    OpenTox.text_to_html(content,subjectid)    
+  else
+    content_type "text/html"
+    OpenTox.login("Login failed, please try again")
+  end
 end
 
-#puts OpenTox.text_to_html("bla")
\ No newline at end of file