error handling compound names;smiles validation

6 files changed, 102 insertions, 45 deletions

diff --git a/application.rb b/application.rb
index 69cf031..54b2d10 100644
--- a/application.rb
+++ b/application.rb
@@ -8,10 +8,6 @@ require File.join(File.dirname(__FILE__),'helper.rb')
 require File.join(ENV["HOME"],".opentox","config","lazar-gui.rb")
 
 helpers do
-  def compound_uri(uri)
-    $logger.debug "\ncompound_uri: #{uri}\n"
-    @compound_uri = OpenTox::Compound.new uri
-  end
 end
 
 get '/?' do
@@ -20,50 +16,87 @@ end
 
 get '/predict/?' do
   @models = OpenTox::Model.all $model[:uri]
-
   haml :predict
 end
 
-post '/predict/?' do
-  # transfered input
-  @identifier = params[:identifier]
-  # get compound from SMILES
-  @compound = OpenTox::Compound.from_smiles $compound[:uri], @identifier.to_s
-  # init
-  @@prediction_models = []
-  @@predictions = []
-  # init lazar algorithm
-  lazar = OpenTox::Algorithm.new File.join($algorithm[:uri],"lazar")
-  # gather models from service and compare if selected
-  params[:selection].each do |model|
-    @mselected = model[0]
-    @mall = OpenTox::Model.all $model[:uri]
-    @mall.each do |m|
-      m.get
-      @@prediction_models << m if m.title =~ /#{@mselected}/
-    end
-    $logger.debug "@prediction_models: #{@@prediction_models.inspect}"
-  end
+get '/jme_help/?' do
+  File.read(File.join('views','jme_help.html'))
+end
 
-  # predict with selected models
-  # results in prediction variable
-  # store prediction in array for better handling
-  @@prediction_models.each do |m| 
-    @prediction_uri = m.run :compound_uri => "#{@compound.uri}"
-    prediction = OpenTox::Dataset.new @prediction_uri
-    pa = []
-    pa << prediction
-    @@predictions << pa
+# best way to get individual compound uri for details
+get '/prediction/:neighbour/details/?' do
+  @compound_uri = OpenTox::Compound.new params[:neighbour]
+  @smiles = @compound_uri.smiles
+  task = OpenTox::Task.create($task[:uri], @subjectid, RDF::DC.description => "look for names.") do
+    names = @compound_uri.names
   end
-
-  haml :prediction
+  sleep 1
+  task.get
+  case task[RDF::OT.hasStatus]
+  when "Error"
+    @names = "There are no names for this compound available."
+  when "Completed"
+    @names = @compound_uri.names
+  end
+  @inchi = @compound_uri.inchi.gsub("InChI=", "InChI: ")
+  haml :details, :layout => false
 end
 
+post '/predict/?' do
+  # validate identifier input
+  task = OpenTox::Task.create($task[:uri], @subjectid, RDF::DC.description => "#{params[:identifier] ? params[:identifier] : "no valid SMILES string."}: Validate SMILES string.") do
+    # transfered input
+    @identifier = params[:identifier]
+    # get compound from SMILES
+    @compound = OpenTox::Compound.from_smiles $compound[:uri], @identifier.to_s
+    # validate SMILES by converting to INCHI
+    inchi = @compound.inchi
+  end
+  # necessary to wait for task
+  sleep 1
+  task.get
+  $logger.debug "task uri: #{task.uri}"
+  $logger.debug "task status: #{task[RDF::OT.hasStatus]}"
+  # case task fails return message smiles invalid  
+  # case task completed go ahead
+  case task[RDF::OT.hasStatus]
+  when "Error"
+    @error_report = "Not a valid SMILES string."
+    haml :error
+  when "Completed"
+    @identifier = params[:identifier]
+    @compound = OpenTox::Compound.from_smiles $compound[:uri], @identifier.to_s
+    # init
+    @@prediction_models = []
+    @@predictions = []
+    # init lazar algorithm
+    lazar = OpenTox::Algorithm.new File.join($algorithm[:uri],"lazar")
+    # gather models from service and compare if selected
+    params[:selection].each do |model|
+      @mselected = model[0]
+      @mall = OpenTox::Model.all $model[:uri]
+      @mall.each do |m|
+        m.get
+        @@prediction_models << m if m.title =~ /#{@mselected}/
+      end
+      $logger.debug "@prediction_models: #{@@prediction_models.inspect}"
+    end
 
-get '/prediction/:neighbour/details/?' do
-  @compound_uri = OpenTox::Compound.new params[:neighbour]
+    # predict with selected models
+    # results in prediction variable
+    # store prediction in array for better handling
+    @@prediction_models.each do |m| 
+      @prediction_uri = m.run :compound_uri => "#{@compound.uri}"
+      prediction = OpenTox::Dataset.new @prediction_uri
+      pa = []
+      pa << prediction
+      @@predictions << pa
+    end
+    
+    haml :prediction
+  end
+  
   
-  haml :details, :layout => false
 end
 
 get '/stylesheets/:name.css' do
diff --git a/public/stylesheets/screen.css b/public/stylesheets/screen.css
index 10ab093..d522e1d 100644
--- a/public/stylesheets/screen.css
+++ b/public/stylesheets/screen.css
@@ -1 +1 @@
-body{background-image:url("/images/gray_jean.png");background-color:#ccf;overflow:scroll;font-family:sans-serif;min-width:800px;min-heigth:600px}body a{text-decoration:none;font-weight:bold;color:#000}.logo img{float:left}.logo h1{margin-top:-2px;position:relative;top:-4px;left:20px}.content{background-image:url("/images/gray_jean.png")}.content h1{margin:0.3em;text-shadow:#fff 1px 1px 0;font-size:x-large;font-family:Verdana;display:inline}.content h2{text-shadow:#fff 1px 1px 0;font-size:x-large;color:#f55}.content .arrow{margin:5px 0px 5px 20px}.content .back{display:inline}.content .close{text-align:right}.content fieldset#top{border:0;margin-top:5em;padding:10px;background-color:#dbc87b;-moz-border-radius-topleft:25px;-webkit-border-top-left-radius:25px;border-top-left-radius:25px;-moz-border-radius-topright:25px;-webkit-border-top-right-radius:25px;border-top-right-radius:25px;-webkit-background-clip:border;-moz-background-clip:border;background-clip:border-box;-webkit-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset}.content fieldset#top draw{display:block}.content fieldset#middle{border:0;padding:10px;background-color:#dbc87b;-webkit-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset}.content fieldset#middle #model a{font-weight:normal}.content fieldset#bottom{border:0;background-color:#dbc87b;padding:10px;margin-bottom:5em;-webkit-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-border-radius-bottomleft:25px;-webkit-border-bottom-left-radius:25px;border-bottom-left-radius:25px;-moz-border-radius-bottomright:25px;-webkit-border-bottom-right-radius:25px;border-bottom-right-radius:25px;-webkit-background-clip:border;-moz-background-clip:border;background-clip:border-box}.content fieldset#bottom input#predict{margin-left:1em}.content .predictions{margin-top:5em;background-color:#dbc87b;padding:10px;text-align:justify;-webkit-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-border-radius-topleft:25px;-webkit-border-top-left-radius:25px;border-top-left-radius:25px;-moz-border-radius-bottomleft:25px;-webkit-border-bottom-left-radius:25px;border-bottom-left-radius:25px;-moz-border-radius-topright:25px;-webkit-border-top-right-radius:25px;border-top-right-radius:25px;-moz-border-radius-bottomright:25px;-webkit-border-bottom-right-radius:25px;border-bottom-right-radius:25px;-webkit-background-clip:border;-moz-background-clip:border;background-clip:border-box}.content .overview{background-image:url("/images/gray_jean.png");padding:12px;margin-top:1em;-webkit-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-border-radius-topleft:25px;-webkit-border-top-left-radius:25px;border-top-left-radius:25px;-moz-border-radius-topright:25px;-webkit-border-top-right-radius:25px;border-top-right-radius:25px;-webkit-background-clip:border;-moz-background-clip:border;background-clip:border-box}.content .overview caption{text-align:left}.content .overview #overview tr td{background-color:#fff;border:1px solid #dad9c7;padding-left:1em}.content .overview #overview tr td#compound{width:150px}.details{margin-bottom:2em;height:400px;scroll:auto;background-image:url("/images/gray_jean.png");-moz-border-radius-bottomleft:25px;-webkit-border-bottom-left-radius:25px;border-bottom-left-radius:25px;-moz-border-radius-bottomright:25px;-webkit-border-bottom-right-radius:25px;border-bottom-right-radius:25px;-webkit-background-clip:border;-moz-background-clip:border;background-clip:border-box}.results{background-image:url("/images/gray_jean.png");overflow:auto;margin-top:2em;margin-bottom:2em;-webkit-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset}.results .tablesorter{width:100%}.results .tablesorter thead{background-color:#fcfaf3}.results .tablesorter thead tr th.header{background-image:url("/images/bg.gif");background-repeat:no-repeat;background-position:center left;cursor:pointer;padding-left:20px;border:1px solid #dad9c7;margin-left:-1px}.results .tablesorter thead tr th.headerSortDown{background-image:url("/images/desc.gif");background-color:#e2d397}.results .tablesorter thead tr th.headerSortUp{background-image:url("/images/asc.gif");background-color:#e2d397}.results .tablesorter tbody tr.odd td{background-color:#f0f0f0}.results .tablesorter tbody tr.even td{background-color:ivory}input#predict{border:0px;background-color:#dbc87b;margin:0;padding:0}.footer{margin:20px 0 20px 0}
+body{background-image:url("/images/gray_jean.png");background-color:#ccf;overflow:scroll;font-family:sans-serif;min-width:800px;min-heigth:600px}body a{text-decoration:none;font-weight:bold;color:#000}.logo img{float:left}.logo h1{margin-top:-2px;position:relative;top:-4px;left:20px}.content{background-image:url("/images/gray_jean.png")}.content h1{margin:0.3em;text-shadow:#fff 1px 1px 0;font-size:x-large;font-family:Verdana;display:inline}.content h2{text-shadow:#fff 1px 1px 0;font-size:x-large;color:#f55}.content .arrow{margin:5px 0px 5px 20px}.content .back{display:inline}.content .close{text-align:right}.content fieldset#top{border:0;margin-top:5em;padding:10px;background-color:#dbc87b;-moz-border-radius-topleft:25px;-webkit-border-top-left-radius:25px;border-top-left-radius:25px;-moz-border-radius-topright:25px;-webkit-border-top-right-radius:25px;border-top-right-radius:25px;-webkit-background-clip:border;-moz-background-clip:border;background-clip:border-box;-webkit-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset}.content fieldset#top draw{display:block}.content fieldset#middle{border:0;padding:10px;background-color:#dbc87b;-webkit-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset}.content fieldset#middle #model a{font-weight:normal}.content fieldset#bottom{border:0;background-color:#dbc87b;padding:10px;margin-bottom:5em;-webkit-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-border-radius-bottomleft:25px;-webkit-border-bottom-left-radius:25px;border-bottom-left-radius:25px;-moz-border-radius-bottomright:25px;-webkit-border-bottom-right-radius:25px;border-bottom-right-radius:25px;-webkit-background-clip:border;-moz-background-clip:border;background-clip:border-box}.content fieldset#bottom input#predict{margin-left:1em}.content .predictions{margin-top:5em;background-color:#dbc87b;padding:10px;text-align:justify;-webkit-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-border-radius-topleft:25px;-webkit-border-top-left-radius:25px;border-top-left-radius:25px;-moz-border-radius-bottomleft:25px;-webkit-border-bottom-left-radius:25px;border-bottom-left-radius:25px;-moz-border-radius-topright:25px;-webkit-border-top-right-radius:25px;border-top-right-radius:25px;-moz-border-radius-bottomright:25px;-webkit-border-bottom-right-radius:25px;border-bottom-right-radius:25px;-webkit-background-clip:border;-moz-background-clip:border;background-clip:border-box}.content .overview{background-image:url("/images/gray_jean.png");padding:12px;margin-top:1em;-webkit-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-border-radius-topleft:25px;-webkit-border-top-left-radius:25px;border-top-left-radius:25px;-moz-border-radius-topright:25px;-webkit-border-top-right-radius:25px;border-top-right-radius:25px;-webkit-background-clip:border;-moz-background-clip:border;background-clip:border-box}.content .overview caption{text-align:left}.content .overview #overview tr td{background-color:#fff;border:1px solid #dad9c7;padding-left:1em}.content .overview #overview tr td#compound{width:150px}.content .error{margin-top:5em;background-color:#dbc87b;padding:10px;text-align:justify;-webkit-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-border-radius-topleft:25px;-webkit-border-top-left-radius:25px;border-top-left-radius:25px;-moz-border-radius-bottomleft:25px;-webkit-border-bottom-left-radius:25px;border-bottom-left-radius:25px;-moz-border-radius-topright:25px;-webkit-border-top-right-radius:25px;border-top-right-radius:25px;-moz-border-radius-bottomright:25px;-webkit-border-bottom-right-radius:25px;border-bottom-right-radius:25px;-webkit-background-clip:border;-moz-background-clip:border;background-clip:border-box}.content .error error{border:2px solid #f55;background-color:#fff;color:#f55}.details{margin-bottom:2em;height:400px;scroll:auto;background-image:url("/images/gray_jean.png");-moz-border-radius-bottomleft:25px;-webkit-border-bottom-left-radius:25px;border-bottom-left-radius:25px;-moz-border-radius-bottomright:25px;-webkit-border-bottom-right-radius:25px;border-bottom-right-radius:25px;-webkit-background-clip:border;-moz-background-clip:border;background-clip:border-box}.results{background-image:url("/images/gray_jean.png");overflow:auto;margin-top:2em;margin-bottom:2em;-webkit-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;-moz-box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset;box-shadow:1px 1px 1px #fff inset,-1px -1px 5px rgba(0,0,0,0.3) inset}.results .tablesorter{width:100%}.results .tablesorter thead{background-color:#fcfaf3}.results .tablesorter thead tr th.header{background-image:url("/images/bg.gif");background-repeat:no-repeat;background-position:center left;cursor:pointer;padding-left:20px;border:1px solid #dad9c7;margin-left:-1px}.results .tablesorter thead tr th.headerSortDown{background-image:url("/images/desc.gif");background-color:#e2d397}.results .tablesorter thead tr th.headerSortUp{background-image:url("/images/asc.gif");background-color:#e2d397}.results .tablesorter tbody tr.odd td{background-color:#f0f0f0}.results .tablesorter tbody tr.even td{background-color:ivory}input#predict{border:0px;background-color:#dbc87b;margin:0;padding:0}.footer{margin:20px 0 20px 0}
diff --git a/public/stylesheets/screen.sass b/public/stylesheets/screen.sass
index d521eb8..db6395d 100644
--- a/public/stylesheets/screen.sass
+++ b/public/stylesheets/screen.sass
@@ -121,6 +121,21 @@ body
       padding-left: 1em
     #overview tr td#compound
       width: 150px
+      
+  .error
+    margin-top: 5em
+    background-color: $ist-color
+    padding: 10px
+    text-align: justify
+    +box-shadow(1px 1px 1px rgba(white, 1) inset, -1px -1px 5px rgba(black, 0.3) inset)
+    +border-left-radius(25px)
+    +border-right-radius(25px)
+    +background-clip(border-box)
+    
+    error
+      border: 2px solid #FF5555
+      background-color: #FFFFFF
+      color: #FF5555
   
 .details
   margin-bottom: 2em
diff --git a/views/details.haml b/views/details.haml
index 448e8a8..38d97fe 100644
--- a/views/details.haml
+++ b/views/details.haml
@@ -7,12 +7,12 @@
     %img{:src=>"#{@compound_uri.uri}/image", :alt=>@compound_uri.uri, :width=>"100px"}
     %p
       SMILES:
-      = @compound_uri.smiles if @compound_uri.smiles
+      = @smiles
 
     %p
       // TODO handle OpenTox::ResourceNotFoundError
       Names:
-      = @compound_uri.names if @compound_uri.names
+      = @names
 
     %p
-      = @compound_uri.inchi.gsub("InChI=", "InChI: ") if @compound_uri.inchi
+      = @inchi
diff --git a/views/error.haml b/views/error.haml
new file mode 100644
index 0000000..9aced43
--- /dev/null
+++ b/views/error.haml
@@ -0,0 +1,8 @@
+.error
+  .back
+    %h1
+      %img{:src=>"/images/arrow_left_float.png", :alt=>"arrow"}
+        %a{:href => to('/predict')} New Prediction
+  %error
+    = @error_report.to_s
+      
diff --git a/views/predict.haml b/views/predict.haml
index dbfab50..b53acb6 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -6,7 +6,7 @@
   };
   function checksmiles () {
     if (document.form.identifier.value == "") {
-      alert("Please insert a compound.")
+      alert("Please insert a compound.");
       document.form.identifier.focus();
       return false;
     };
@@ -20,7 +20,8 @@
     };
     return true;
   };
-  
+
+/ whole site content needs to be in one form. Input and checkboxes are checked by js functions. 
 %form{:name => "form", :action => to('/predict'), :method => "post", :enctype => "multipart/form-data", :onsubmit => "return  !!(checksmiles() & checkboxes())" }
   %fieldset#top
     %a{:href => "#insert", :id => "linkInsert"}