diff options
| -rw-r--r-- | .gitignore | 2 | ||||
| -rw-r--r-- | aop.gemspec | 1 | ||||
| -rw-r--r-- | public/rect.png | bin | 0 -> 218 bytes | |||
| -rw-r--r-- | views/assays.haml | 12 | ||||
| -rw-r--r-- | views/layout.haml | 66 | ||||
| -rw-r--r-- | views/neighbors.haml | 65 | ||||
| -rw-r--r-- | views/predicted_assays.haml | 12 | ||||
| -rw-r--r-- | views/predicted_targets.haml | 6 | ||||
| -rw-r--r-- | views/style.scss | 11 | ||||
| -rw-r--r-- | views/targets.haml | 6 |
10 files changed, 135 insertions, 46 deletions
diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..49b161f --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +Gemfile.lock +.sass-cache/ diff --git a/aop.gemspec b/aop.gemspec index 51f4641..03e7a08 100644 --- a/aop.gemspec +++ b/aop.gemspec @@ -34,5 +34,6 @@ Gem::Specification.new do |s| # external requirements s.requirements << "memcached" s.post_install_message = "Please make sure you have memcached installed." + end diff --git a/public/rect.png b/public/rect.png Binary files differnew file mode 100644 index 0000000..e19845f --- /dev/null +++ b/public/rect.png diff --git a/views/assays.haml b/views/assays.haml index 510234d..5e7361f 100644 --- a/views/assays.haml +++ b/views/assays.haml @@ -1,7 +1,15 @@ %dl - @assays.sort{|a,b| a["Assay Name"] <=> b["Assay Name"]}.each do |assay| %dt - %a{:href => "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay["AID"]}"} #{assay['Assay Name']} + %a{:href => "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay["AID"]}", :rel => "_blank"} #{assay['Assay Name']} + :javascript + $('A[rel="_blank"]').each(function(){ + $(this).attr('target', '_blank'); + }); %dd Assay ID: - %a{:href => "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay["AID"]}"} #{assay['AID']} + %a{:href => "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay["AID"]}", :rel => "_blank"} #{assay['AID']} + :javascript + $('A[rel="_blank"]').each(function(){ + $(this).attr('target', '_blank'); + }); diff --git a/views/layout.haml b/views/layout.haml index 5160c31..b6b4c0e 100644 --- a/views/layout.haml +++ b/views/layout.haml @@ -6,7 +6,6 @@ %link{:rel=>'stylesheet', :href=>"#{'/style.css'}", :type => "text/css"} %script{:type => "text/javascript", :src => "/jquery-1.8.2.js"} :javascript - $(document).ready(function() { $.ajax({ url: "/cid/#{@cid}/experiments", cache: true }); }); function show(title,element,uri) { $(element).html("<h4>"+title+"</h4>"+"Retrieving data from PubChem. This may take some time, please be patient."+"<img src=\"/spinning-wait-icons/wait30trans.gif\" alt=\"Searching PubChem\">"); $.ajax({ @@ -45,14 +44,77 @@ } %body + %noscript + %div{ :style=>"width: 22em; position: absolute; left: 50%; margin-left: -11em; color: red; background-color: white; border: 1px solid red; padding: 4px; font-family: sans-serif"} + Your web browser must have JavaScript enabled in order for this application to display correctly. + %h1 PubChem read across + %button{:id=>"about", :style => "margin-left:80%;z-index:4;position:absolute; top:10px; right:0px;"} + About this service + :javascript + $("#about").click(function() { + $("info").toggle(); + }); + %info{:id=>"info", :style => "display:none;z-index:5;position:fixed; top:10px; left:25%; width: 50%; background-color:#F5F5F5;border:solid 1px black;"} + %button{:id => "x", :style => "position:absolute;right:0px;"} x + %div{:style => "align:justify;padding:1em;"} + %dt + (experimental) + %dd + Filtered experimental data from pubchem database. + %br + %dt + (read across) + %dd + Prediction results of processed pubchem data. + %br + %dt + Prediction relationship + %dd + Similar compounds, predicted assays and predicted targets are related considering relevant data. + :javascript + $("#x").click(function() { + $("info").toggle(); + }); %form{:name => "form", :action => '/search', :method => "GET"} %fieldset %label{:for => 'name'} Compound name: %input{:type => 'text', :name => 'name', :id => 'name'} %input{ :type => "submit", :value => "Search" } %em This is an experimental version. Loading data from PubChem can be slow. Please use the "Back" button and retry the offending operation if you have timeout problems. + + + = yield .footer - %a{:href => 'http://www.in-silico.ch', :rel => "external"} <i style="font-family: serife">in silico</i> toxicology gmbh 2013
\ No newline at end of file + © + %a{:href => 'http://www.in-silico.ch', :rel => "_blank"} <i style="font-family: serife">in silico</i> toxicology gmbh 2013 - 2014 + :javascript + $('A[rel="_blank"]').each(function(){ + $(this).attr('target', '_blank'); + }); + #back-top{:style => "z-index:100;position:fixed;bottom:0%;width:97%;"} + %hr{:style => "margin-bottom:0;"} + %a{:href => "", :style=>"text:decoration:none;color:#ccc;"} + %img{:src => "/rect.png", :alt => "top", :width => "100%", :height => "50px"} + %div{:style => "margin-top:-50px;font-size:x-small;text-align:center;z-index:101;"} + TOP + :javascript + $("#back-top").hide(); + $(function () { + $(window).scroll(function () { + if ($(this).scrollTop() > 600) { + $('#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; + }); + }); diff --git a/views/neighbors.haml b/views/neighbors.haml index 5563392..8435ac1 100644 --- a/views/neighbors.haml +++ b/views/neighbors.haml @@ -1,34 +1,41 @@ +- @neighbors = [] +- neighbors(@cid).each do |n| + - unless assays(n,"active").empty? and assays(n,"inactive").empty? + - @neighbors << n + %table %colgroup %col{:style => "width: 300px"} %col{:style => "width: 47%"} %col{:style => "width: 47%"} - - idx = 0 - - while idx < 10 - - neighbors(@cid).each do |n| - - unless assays(n,"active").empty? and assays(n,"inactive").empty? - %tr - %th{:style => "vertical-align:top;", :colspan => "3"} - = name n - ( - = similarity(@cid,n).round(3) - ) - %tr - %td{:style => "vertical-align:top;"} - %img{:src => image_uri(n), :alt => "#{name n}", :class => "compound"} - %td{:style => "vertical-align:top;"} - %p{:id => "targets#{n}", :class => "neighbors"} - :javascript - hide("Measured gene/protein targets","#targets#{n}", "/cid/#{n}/targets/active"); - %p{:id => "nontargets#{n}", :class => "neighbors"} - :javascript - hide("Measured gene/protein non-targets","#nontargets#{n}", "/cid/#{n}/targets/inactive"); - %td{:style => "vertical-align:top;"} - %p{:id => "assays#{n}", :class => "neighbors"} - :javascript - hide("Other active assays","#assays#{n}", "/cid/#{n}/assays/active"); - %p{:id => "inactive_assays#{n}", :class => "neighbors"} - :javascript - hide("Other inactive assays","#inactive_assays#{n}", "/cid/#{n}/assays/inactive"); - - - idx += 1 + + - unless @neighbors.empty? or @neighbors.nil? + - @neighbors.each do |n| + %tr + %th{:style => "vertical-align:top;", :colspan => "3"} + = name n + ( + = similarity(@cid,n).round(3) + ) + %tr + %td{:style => "vertical-align:top;"} + %img{:src => image_uri(n), :alt => "#{name n}", :class => "compound"} + %td{:style => "vertical-align:top;"} + %p{:id => "targets#{n}", :class => "neighbors"} + :javascript + hide("Measured gene/protein targets","#targets#{n}", "/cid/#{n}/targets/active"); + %p{:id => "nontargets#{n}", :class => "neighbors"} + :javascript + hide("Measured gene/protein non-targets","#nontargets#{n}", "/cid/#{n}/targets/inactive"); + %td{:style => "vertical-align:top;"} + %p{:id => "assays#{n}", :class => "neighbors"} + :javascript + hide("Other active assays","#assays#{n}", "/cid/#{n}/assays/active"); + %p{:id => "inactive_assays#{n}", :class => "neighbors"} + :javascript + hide("Other inactive assays","#inactive_assays#{n}", "/cid/#{n}/assays/inactive"); + - else + %tr + %td{ :colspan => "3"} + %em + Similar compounds depend on predicted assays and predicted targets. diff --git a/views/predicted_assays.haml b/views/predicted_assays.haml index 299abf4..6fca92b 100644 --- a/views/predicted_assays.haml +++ b/views/predicted_assays.haml @@ -1,10 +1,18 @@ %dl - @assays.sort{|a,b| [b["p_active"],b["p_inactive"]].max <=> [a["p_active"],a["p_inactive"]].max}.each do |assay| %dt - %a{:href => "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay["AID"]}"} #{assay['Assay Name']} + %a{:href => "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay["AID"]}", :rel => "_blank"} #{assay['Assay Name']} + :javascript + $('A[rel="_blank"]').each(function(){ + $(this).attr('target', '_blank'); + }); %dd Assay ID: - %a{:href => "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay["AID"]}"} #{assay['AID']} + %a{:href => "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay["AID"]}", :rel => "_blank"} #{assay['AID']} + :javascript + $('A[rel="_blank"]').each(function(){ + $(this).attr('target', '_blank'); + }); %dd p_active: = assay["p_active"].to_f.round(3) diff --git a/views/predicted_targets.haml b/views/predicted_targets.haml index 97c68c4..6abd4c1 100644 --- a/views/predicted_targets.haml +++ b/views/predicted_targets.haml @@ -6,7 +6,11 @@ = assay["Target GI"] %dd Assay ID: - %a{:href => "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay["AID"]}"} #{assay["AID"]} + %a{:href => "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay["AID"]}", :rel => "_blank"} #{assay["AID"]} + :javascript + $('A[rel="_blank"]').each(function(){ + $(this).attr('target', '_blank'); + }); %dd p_active: = assay["p_active"].to_f.round(3) diff --git a/views/style.scss b/views/style.scss index 225bee8..25833e7 100644 --- a/views/style.scss +++ b/views/style.scss @@ -103,21 +103,14 @@ img.compound { radius: 4px; } } + .footer { margin: 200px 0px 20px 4px; - width: 99%; text-align: right; } + .footer a { text-decoration: none; color: #000; &:hover { color: #900; } } -.tooltip { - background-color: #fff; - border: 2px solid #ccc; - font-size: 0.5em; - padding: 1em; - display: none; - z-index: 50; -}
\ No newline at end of file diff --git a/views/targets.haml b/views/targets.haml index 9622abd..09e6009 100644 --- a/views/targets.haml +++ b/views/targets.haml @@ -7,5 +7,9 @@ %dd Assay IDs: - @assays.select{|a| a["Target GI"] == target.last}.each do |assay| - %a{:href => "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay["AID"]}"} #{assay['AID']} + %a{:href => "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay["AID"]}", :rel => "_blank"} #{assay['AID']} + :javascript + $('A[rel="_blank"]').each(function(){ + $(this).attr('target', '_blank'); + }); |
