From c74da4b41e6413d126ae8d6aa62874627cb14fca Mon Sep 17 00:00:00 2001 From: gebele Date: Tue, 9 Apr 2013 16:50:56 +0200 Subject: adjusted for services update --- application.rb | 21 +++++++++------------ public/stylesheets/screen.css | 2 +- public/stylesheets/screen.sass | 9 +++++++++ views/details.haml | 3 +-- views/layout.haml | 27 ++++++++++++++++++++++++++- views/neighbours.haml | 12 ++++++------ views/predict.haml | 2 +- views/prediction.haml | 11 ++++++----- 8 files changed, 59 insertions(+), 28 deletions(-) diff --git a/application.rb b/application.rb index 6dfc9b7..c04476d 100644 --- a/application.rb +++ b/application.rb @@ -27,14 +27,14 @@ end 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 + task = OpenTox::Task.run("look for names.") do names = @compound_uri.names end - sleep 1 - task.get + task.wait + $logger.debug "names task uri: #{task.uri}" case task[RDF::OT.hasStatus] when "Error" - @names = "There are no names for this compound available." + @names = "" when "Completed" @names = @compound_uri.names.join(",") end @@ -44,19 +44,16 @@ end post '/predict/?' do # validate identifier input - task = OpenTox::Task.create($task[:uri], @subjectid, RDF::DC.description => "#{params[:identifier] ? params[:identifier] : "no valid SMILES string."}: Validate SMILES string.") do + task = OpenTox::Task.run("Validate SMILES string.") do # transfered input @identifier = params[:identifier] # get compound from SMILES - @compound = OpenTox::Compound.from_smiles $compound[:uri], @identifier.to_s + @compound = OpenTox::Compound.from_smiles @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]}" + task.wait # case task fails return message smiles invalid # case task completed go ahead case task[RDF::OT.hasStatus] @@ -65,7 +62,7 @@ post '/predict/?' do haml :error when "Completed" @identifier = params[:identifier] - @compound = OpenTox::Compound.from_smiles $compound[:uri], @identifier.to_s + @compound = OpenTox::Compound.from_smiles @identifier.to_s # init @@prediction_models = [] @@predictions = [] @@ -76,7 +73,7 @@ post '/predict/?' do @mselected = model[0] @mall = OpenTox::Model.all $model[:uri] @mall.each do |m| - m.get + #m.get @@prediction_models << m if m.title =~ /#{@mselected}/ end $logger.debug "@prediction_models: #{@@prediction_models.inspect}" diff --git a/public/stylesheets/screen.css b/public/stylesheets/screen.css index 91bd649..b437053 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;display:inline;margin-right:1em}.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;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{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) 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-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 .error{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 td.false{text-align:center;background-color:#52ce00;-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 tbody tr td.true{text-align:center;background-color:#f80000;-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}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;display:inline;margin-right:1em}.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 #back-top{z-index:4;position:fixed;bottom:60px;margin-left:165px}.content #back-top a:hover{color:#bbb}.content fieldset#top{border:0;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{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 .overview #overview tr td.true{text-align:center;background-color:#f80000;-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 .overview #overview tr td.false{text-align:center;background-color:#52ce00;-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 .error{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 td.false{text-align:center;background-color:#52ce00;-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 tbody tr td.true{text-align:center;background-color:#f80000;-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}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 cc8878d..882749b 100644 --- a/public/stylesheets/screen.sass +++ b/public/stylesheets/screen.sass @@ -56,6 +56,15 @@ body .close text-align: right + #back-top + z-index: 4 + position: fixed + bottom: 60px + margin-left: 165px + + a:hover + color: #bbb + fieldset#top border: 0 //margin-top: 5em diff --git a/views/details.haml b/views/details.haml index 48d28bc..ff77783 100644 --- a/views/details.haml +++ b/views/details.haml @@ -4,14 +4,13 @@ .details %h2 Details: - %img{:src=>"#{@compound_uri.uri}/image", :alt=>@compound_uri.uri, :width=>"100px"} + %img{:src=>"#{@compound_uri.uri}/image", :alt=>"", :width=>"100px"} %br %b SMILES: %p= @smiles %br %b - // TODO handle OpenTox::ResourceNotFoundError Names: %p= @names %br diff --git a/views/layout.haml b/views/layout.haml index 7c05190..b6606a1 100644 --- a/views/layout.haml +++ b/views/layout.haml @@ -20,7 +20,32 @@ %h1 Lazar Toxicity Predictions %hr - .content + .content + :javascript + $(document).ready(function(){ + // hide #back-top first + $("#back-top").hide(); + // fade in #back-top + $(function () { + $(window).scroll(function () { + if ($(this).scrollTop() > 400) { + $('#back-top').fadeIn(); + } else { + $('#back-top').fadeOut(); + } + }); + // scroll body to 0px on click + $('#back-top a').click(function () { + $('body,html').animate({ + scrollTop: 0 + }, 500); + return false; + }); + }); + }); + #back-top + %a{:href => ""}^ top ^ + = yield .footer diff --git a/views/neighbours.haml b/views/neighbours.haml index a593e7b..7d99288 100644 --- a/views/neighbours.haml +++ b/views/neighbours.haml @@ -29,7 +29,7 @@ #results{:id=>"#{count_rs}"} - pa.each do |p| / get prediction OpenTox::Dataset - - p.get + -# p.get / prepare dataset for neighbours table ; / delete first array which contains input compound prediction ; / keep the following arrays they are the neighbour predictions ; @@ -64,12 +64,12 @@ - p.compounds.each do |neighbour_compound| %tr %td - %img{:src=>"#{neighbour_compound.uri}/image", :alt=>neighbour_compound.uri, :width=>"100px"} - %td{:class => p.data_entries[count][0]} - = p.data_entries[count][0] - %td{:class => p.data_entries[count][0]} + %img{:src=>"#{neighbour_compound.uri}/image", :alt=>"", :width=>"100px"} + %td{:class => p.data_entries[count][2]} + = p.data_entries[count][2] + %td{:class => p.data_entries[count][2]} = p.data_entries[count][3].round(3) - %td{:class => p.data_entries[count][0]} + %td{:class => p.data_entries[count][2]} %a{:href => to("/prediction/#{CGI.escape(neighbour_compound.uri)}/details"), :id=>"link#{count_rs}#{count}", :target=>"details"} %img{:src=>"/images/arrow_right_float.png", :alt=>"arrow"} :javascript diff --git a/views/predict.haml b/views/predict.haml index b53acb6..82f7bbc 100644 --- a/views/predict.haml +++ b/views/predict.haml @@ -1,4 +1,5 @@ :javascript + function getsmiles() { if (document.JME.smiles() != '') { document.form.identifier.value = document.JME.smiles() ; @@ -71,7 +72,6 @@ %p Please observe validation report for details. %br - @models.each do |model| - - model.get #model %input{:type => "checkbox", :name => "selection[#{model.title}]", :id => "selection[#{model.title}]", :value => true, :disabled => false} %label{:for => "selection[#{model.title}]"} diff --git a/views/prediction.haml b/views/prediction.haml index dd90847..02b3ab1 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -14,21 +14,22 @@ %tbody %tr %td{:id=>"compound"} - %img{:src=>"#{@compound.uri}/image", :alt=>@compound.uri, :width=>"100"} + %img{:src=>"#{@compound.uri}/image", :alt=>"image not available", :width=>"100"} - count=0 - @@predictions.each do |pa| - pa.each do |p| - - p.get - %td{:class => p.data_entries[0][1]} + -# p.get + %td{:class => p.data_entries[0][0]} %b{:class => "title"} = @@prediction_models[count].title %br + - $logger.debug "p.data_entries: #{p.data_entries}" %br = "Result:\n" - %b= p.data_entries[0][1] + %b= p.data_entries[0][0] %br = "Confidence:\n" - = p.data_entries[0][2].round(3) + = p.data_entries[0][1].round(3) %br %a{:href=> "#tabs", :id=>"link#{count}"} %img{:src=>"/images/arrow_down_float.png", :alt=>"arrow"} -- cgit v1.2.3