t2-web 0.0.5

data/public/scripts/jquery.tipsy.js

@@ -0,0 +1,104 @@
+(function($) {
+    $.fn.tipsy = function(options) {
+
+        options = $.extend({}, $.fn.tipsy.defaults, options);
+        
+        return this.each(function() {
+            
+            var opts = $.fn.tipsy.elementOptions(this, options);
+            
+            $(this).hover(function() {
+
+                $.data(this, 'cancel.tipsy', true);
+
+                var tip = $.data(this, 'active.tipsy');
+                if (!tip) {
+                    tip = $('<div class="tipsy"><div class="tipsy-inner"/></div>');
+                    tip.css({position: 'absolute', zIndex: 100000});
+                    $.data(this, 'active.tipsy', tip);
+                }
+
+                if ($(this).attr('title') || typeof($(this).attr('original-title')) != 'string') {
+                    $(this).attr('original-title', $(this).attr('title') || '').removeAttr('title');
+                }
+
+                var title;
+                if (typeof opts.title == 'string') {
+                    title = $(this).attr(opts.title == 'title' ? 'original-title' : opts.title);
+                } else if (typeof opts.title == 'function') {
+                    title = opts.title.call(this);
+                }
+
+                tip.find('.tipsy-inner')[opts.html ? 'html' : 'text'](title || opts.fallback);
+
+                var pos = $.extend({}, $(this).offset(), {width: this.offsetWidth, height: this.offsetHeight});
+                tip.get(0).className = 'tipsy'; // reset classname in case of dynamic gravity
+                tip.remove().css({top: 0, left: 0, visibility: 'hidden', display: 'block'}).appendTo(document.body);
+                var actualWidth = tip[0].offsetWidth, actualHeight = tip[0].offsetHeight;
+                var gravity = (typeof opts.gravity == 'function') ? opts.gravity.call(this) : opts.gravity;
+
+                switch (gravity.charAt(0)) {
+                    case 'n':
+                        tip.css({top: pos.top + pos.height, left: pos.left + pos.width / 2 - actualWidth / 2}).addClass('tipsy-north');
+                        break;
+                    case 's':
+                        tip.css({top: pos.top - actualHeight, left: pos.left + pos.width / 2 - actualWidth / 2}).addClass('tipsy-south');
+                        break;
+                    case 'e':
+                        tip.css({top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left - actualWidth}).addClass('tipsy-east');
+                        break;
+                    case 'w':
+                        tip.css({top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width}).addClass('tipsy-west');
+                        break;
+                }
+
+                if (opts.fade) {
+                    tip.css({opacity: 0, display: 'block', visibility: 'visible'}).animate({opacity: 0.8});
+                } else {
+                    tip.css({visibility: 'visible'});
+                }
+
+            }, function() {
+                $.data(this, 'cancel.tipsy', false);
+                var self = this;
+                setTimeout(function() {
+                    if ($.data(this, 'cancel.tipsy')) return;
+                    var tip = $.data(self, 'active.tipsy');
+                    if (opts.fade) {
+                        tip.stop().fadeOut(function() { $(this).remove(); });
+                    } else {
+                        tip.remove();
+                    }
+                }, 100);
+
+            });
+            
+        });
+        
+    };
+    
+    // Overwrite this method to provide options on a per-element basis.
+    // For example, you could store the gravity in a 'tipsy-gravity' attribute:
+    // return $.extend({}, options, {gravity: $(ele).attr('tipsy-gravity') || 'n' });
+    // (remember - do not modify 'options' in place!)
+    $.fn.tipsy.elementOptions = function(ele, options) {
+        return $.metadata ? $.extend({}, options, $(ele).metadata()) : options;
+    };
+    
+    $.fn.tipsy.defaults = {
+        fade: false,
+        fallback: '',
+        gravity: 'n',
+        html: false,
+        title: 'title'
+    };
+    
+    $.fn.tipsy.autoNS = function() {
+        return $(this).offset().top > ($(document).scrollTop() + $(window).height() / 2) ? 's' : 'n';
+    };
+    
+    $.fn.tipsy.autoWE = function() {
+        return $(this).offset().left > ($(document).scrollLeft() + $(window).width() / 2) ? 'e' : 'w';
+    };
+    
+})(jQuery);

data/public/scripts/results.js

@@ -0,0 +1,25 @@
+function getSampleOutput(t2_server, uuid, output, wid, wkf_version) {
+  // t2 server REST call to sample output
+  var httpcall = "http://" + document.location.host + "/t2web/run/" + uuid + "/output/" + output +
+                 "?server=" + t2_server + "&wid=" + wid + "&wkf_version=" + wkf_version;
+  // ajax request
+  $.get(httpcall, function (result) {
+    window.frames['data-display'].document.documentElement.innerHTML = result;
+  });
+
+}
+
+function checkRunStatus(t2_server, uuid) {
+  // t2 server REST call to uuid's status
+  var httpcall = "http://" + document.location.host + "/runs/" + uuid + "/status?server=" + t2_server;
+
+  // ajax request
+  $.get(httpcall, function (result) {
+    if (result == 'Finished') {
+      window.frames['data-navigation'].document.documentElement.innerHTML = results_navigation;
+      clearInterval(runStatusIntervalId);
+    }
+  });
+
+}
+

data/views/form.haml

@@ -0,0 +1,173 @@
+!!!
+%html
+  %head
+    %title Workflow: #{@my_exp_wkf.title}
+    %link(rel="stylesheet" href="/css/form.css")
+    %link(rel="stylesheet" href="/css/tipsy.css")
+    %script{:type => "text/javascript", :src => "/scripts/jquery-1.6.1.js"}
+    %script{:type => "text/javascript", :src => "/scripts/jquery.tipsy.js"}
+    %script{:type => "text/javascript", :src => "/scripts/form.js"}
+
+  %body
+
+    = generate_header_table(@my_exp_wkf, @my_exp_usr)
+
+    -# TODO: should move coding to controller and not use haml's "-" for logic inside the template!!!
+    -#header
+      %table.header
+        %tr
+          %td
+            %img{:src => "/images/nbic_logo.gif", :alt => "NBIC logo"}
+          %td
+            %table.header-title
+              %tr
+                %td.header-title Workflow: #{@my_exp_wkf.title}
+              - if #{@my_exp_wkf.user.name}
+                %tr
+                  %td.right workflow by #{@my_exp_wkf.user.name}
+          %td
+            %img.right{:src => "/images/lumc_logo2.png", :alt => "LUMC logo"}
+
+    %br
+    #inputs
+      %form{:id => "workflow-form", :action => "/t2web/enact", :method => "post"}
+        %table.inputs
+          - if @my_exp_wkf.inputs.size >=1
+            %tr
+              %th.inputs
+                Configure Workflow Inputs
+          - @my_exp_wkf.inputs.each do |input|
+            %tr
+              %td.inputs
+                %div{:id => "#{input.name}-placeholder"}
+                Upload file?
+                %input{:id => "#{input.name}-checkbox", :type => "checkbox", :onclick => "toggleManualFileInput('#{input.name}')", :name => "upload-checkbox-#{input.name}", :value => "yes"}
+                %br
+                %br
+          %tr
+            %td.inputs
+              %input{:type => "hidden", :name => "wid", :value => "#{@wid}" }
+              %input{:type => "hidden", :name => "wkf_version", :value => "#{@wkf_version}" }
+              %input{:type => "hidden", :name => "server", :value => "#{@t2_server}" }
+              %input{:type => "submit", :value => "Execute", :class => "button"}
+      - if @my_exp_wkf.inputs.size >=1
+        - @my_exp_wkf.inputs.each do |input|
+          -# TODO: make helper create_input_tooltip(input) to return proper tooltip html string!!!
+          - if input.descriptions.size >=1
+            - input_label_tooltip = generate_label_tooltip(input)
+          - input_textarea_tooltip = ""
+          - if input.examples.size >=1
+            - input_textarea_tooltip = generate_textarea_tooltip(input)
+          %div{:id => "#{input.name}-upload-form-div"}
+            -#%form{:id => "#{input.name}-upload-form", :enctype => "multipart/form-data", :target => "hidden-iframe", :action => "/t2web/upload", :method => "post"}
+            %form{:id => "#{input.name}-upload-form", :enctype => "multipart/form-data"}
+              %label{:for => "#{input.name}-upload-label", :title => "#{input_label_tooltip}"} Select file for #{input.name}
+              %input{:type => "file", :name => "file", :onchange => "uploadFile('#{input.name}')"} 
+          %div{:id => "#{input.name}-manual-group"}
+            %label{:for => "#{input.name}-label", :title => "#{input_label_tooltip}"} Enter #{input.name}:
+            %br
+            %textarea{:name => "#{input.name}-input", :rows => 3, :cols => 50, :title => "#{input_textarea_tooltip}"}
+              - if input.examples.size >= 1
+                = CGI::unescapeHTML(input.examples[0])
+        %iframe{:id => "hidden-iframe", :name => "hidden-iframe", :src => "#", :style => "width:0;height:0;border:0px solid #fff;"}
+
+    %br
+    #description
+      %table.inputs
+        %tr
+          %th.inputs
+            Workflow Description
+        %tr
+          %td.inputs
+            = @my_exp_wkf.description
+
+    -# %br
+    -# %br
+    -#inputs
+      - if @my_exp_wkf.inputs.size >=1
+        %table.inputs
+          %tr
+            %th.inputs
+              Input
+            %th.inputs
+              Description
+            %th.inputs
+              Examples
+          - @my_exp_wkf.inputs.each do |input|
+            %tr
+              %td.inputs
+                = input.name
+              %td.inputs
+                - if input.descriptions.size >=1
+                  - input.descriptions.each do |descr|
+                    = descr
+                    %br
+              %td.inputs
+                - if input.examples.size >=1
+                  - input.examples.each do |ex|
+                    = ex
+                    %br
+
+    %br
+    %br
+    #outputs
+      - if @my_exp_wkf.outputs.size >=1
+        %table.inputs
+          %tr
+            %th.inputs
+              Output
+            %th.inputs
+              Description
+            %th.inputs
+              Examples
+          - @my_exp_wkf.outputs.each do |output|
+            %tr
+              %td.inputs
+                = output.name
+              %td.inputs
+                - if output.descriptions.size >=1
+                  - output.descriptions.each do |descr|
+                    = descr
+                    %br
+              %td.inputs
+                - if output.examples.size >=1
+                  - if output.examples.size >=1
+                    - output.examples.each do |ex|
+                      = ex
+                      %br
+
+    %br
+    %br
+    #note
+      %table.inputs
+        %tr
+          %th.inputs
+          %th.inputs
+            Please Note
+          %th.inputs
+        %tr
+          %td.inputs
+            %img{:src => "/images/info.png", :alt => "Important!" }
+          %td.inputs
+            Some workflows are not up-to-date or have dependencies that cannot be met by the specific Taverna server that you specified during generation of this tool. You can make sure that the workflow is valid by running it in the Taverna Workbench first to confirm that it works before running it via the Web.
+        %tr
+          %td.inputs
+            %img{:src => "/images/info.png", :alt => "Important!" }
+          %td.inputs
+            There might be some repetitions in the workflow description in some of the generated workflows. This is due to a backwards compatibility issue on the myExperiment repository which keeps the old descriptions to make sure that no information is lost.
+        %tr
+          %td.inputs
+            %img{:src => "/images/info.png", :alt => "Important!" }
+          %td.inputs
+            For more information on this workflow please visit the
+            %a{ :href => "http://www.myExperiment.org/workflows/#{@wid}" } myExperiment website
+        - if #{@my_exp_wkf.user.email}
+          %tr
+            %td.inputs
+              %img{:src => "/images/info.png", :alt => "Important!" }
+            %td.inputs
+              For questions/comments you can also contact the workflow creator at:
+              %a{ :href => "mailto:#{@my_exp_usr.email}" } #{@my_exp_usr.email}
+
+    %br
+    %br

data/views/results.haml

@@ -0,0 +1,28 @@
+!!!
+%html
+  %head
+    %title Results:
+    %link(rel="stylesheet" href="/css/results.css")
+    %script{:type => "text/javascript", :src => "/scripts/jquery-1.6.1.js"}
+    %script{:type => "text/javascript"}
+      :plain
+        var runStatusIntervalId = 0;
+        var results_navigation = "";
+        $(document).ready(function() {
+          // calculate results_navigation here since helpers seem unavailable in results.js!?
+          results_navigation = "#{generate_data_navigation_frame(@my_exp_wkf, @run_uuid, @wid, @wkf_version, @t2_server, true)}";
+          window.frames['header'].document.write("#{generate_header_frame(@my_exp_wkf, @my_exp_usr).gsub!(/\n/, "")}");
+          window.frames['data-navigation'].document.write("#{generate_data_navigation_frame(@my_exp_wkf, @run_uuid, @wid, @wkf_version, @t2_server, false)}");
+          runStatusIntervalId = window.setInterval( "checkRunStatus('#{@t2_server}', '#{@run_uuid}')", 5000);
+        });
+    %script{:type => "text/javascript", :src => "/scripts/results.js"}
+
+  -# we use border for FF and framespacing for IE
+  %frameset{ :rows => "113px, *", :border => "1", :framespacing => "1" }
+    %noframes
+      To be viewed properly, this page requires frames.
+    %frame{ :name => "header", :id => "header" }
+    %frameset{ :cols => "250px, *", :border => "6", :framespacing => "6" }
+      %frame{ :name => "data-navigation", :id => "data-navigation" }
+      %frame{ :name => "data-display", :id => "data-display" }
+

metadata

@@ -0,0 +1,165 @@
+--- !ruby/object:Gem::Specification 
+name: t2-web
+version: !ruby/object:Gem::Version 
+  hash: 21
+  prerelease: 
+  segments: 
+  - 0
+  - 0
+  - 5
+  version: 0.0.5
+platform: ruby
+authors: 
+- Kostas Karasavvas
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2012-03-06 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: sinatra
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 19
+        segments: 
+        - 1
+        - 2
+        - 6
+        version: 1.2.6
+  type: :runtime
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: haml
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 7
+        segments: 
+        - 3
+        - 1
+        - 2
+        version: 3.1.2
+  type: :runtime
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: rest-client
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 9
+        segments: 
+        - 1
+        - 6
+        - 3
+        version: 1.6.3
+  type: :runtime
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: t2-server
+  prerelease: false
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 5
+        segments: 
+        - 0
+        - 6
+        - 1
+        version: 0.6.1
+  type: :runtime
+  version_requirements: *id004
+- !ruby/object:Gem::Dependency 
+  name: myexperiment-rest
+  prerelease: false
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 19
+        segments: 
+        - 0
+        - 3
+        - 0
+        version: 0.3.0
+  type: :runtime
+  version_requirements: *id005
+description: WS (with libs) that generates a Web UI form for a Taverna2 workflow and then enacts it to a T2 server.
+email: kostas.karasavvas@nbic.nl
+executables: 
+- t2_webapp.rb
+extensions: []
+
+extra_rdoc_files: 
+- README
+- LICENSE
+- CHANGES
+files: 
+- LICENSE
+- README
+- CHANGES
+- Rakefile
+- bin/t2_webapp.rb
+- public/scripts/results.js
+- public/scripts/form.js
+- public/scripts/jquery-1.6.1.js
+- public/scripts/jquery.tipsy.js
+- public/css/results_header.css
+- public/css/tipsy.css
+- public/css/form.css
+- public/css/results_navigation.css
+- public/images/nbic_logo.gif
+- public/images/snake_transparent.gif
+- public/images/tipsy.gif
+- public/images/info.png
+- public/images/lumc_logo2.png
+- views/results.haml
+- views/form.haml
+homepage: 
+licenses: []
+
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.7.2
+signing_key: 
+specification_version: 3
+summary: WS (with libs) that generates a Web UI form for a Taverna2 workflow and then enacts it to a T2 server.
+test_files: []
+