rbbt-views 0.1.0

data/share/views/compass/main.sass

@@ -0,0 +1,161 @@
+@import "base"
+
+=subtle_link($color: $menu_color)
+  text-decoration: none
+  color: $color
+  &:link, &:active, &:visited, &:hover
+    color: $color
+  &:hover
+    text-decoration: underline
+
+=clean_list($inline: true)
+  margin: 0
+  padding: 0
+  li
+    margin: 0
+    padding: 0
+    list-style: none
+    @if $inline
+      +inline_block
+
+=inline_dl
+  dt, dd
+    +inline_block
+    float: left
+  dt
+    clear: both
+
+=inline_dt
+  +inline_block
+  float: left
+  clear: left
+  margin-right: 10px
+  &:after
+    content: ": "
+
+=hide()
+  :display none
+
+=tabs($inactive_color: grey, $active_color: white)
+  ul
+    +inline_block
+    width: 100%
+    border-bottom: 1px solid
+    margin: 12px 0 12px 0
+    padding: 0 10px 0 10px
+    li
+      +inline-block-list-item
+      a
+        +subtle_link(black)
+        +border-top-radius
+        text-decoration: none
+        background: none repeat scroll 0 0 $inactive_color
+        border: 1px solid black
+        border-bottom: 1px solid black
+        padding: 2px 5px 2px 5px
+        margin: 0
+      a:hover, a.active
+        text-decoration: none
+        background: none repeat scroll 0 0 $active_color
+      a.active
+        border-bottom: 1px solid $active_color
+
+
+=main_layout($logo_columns: 8, $logo_font: 4em, $nav_font: 2em)
+  +container
+  overflow: auto
+  margin-top: 10px
+  header
+    +column($blueprint_grid_columns)
+    +last
+
+    a
+      text-decoration: none
+    span.logo
+      +column($logo_columns)
+      font-size: $logo_font
+      a
+        &:active, &:visited, &:hover
+          color: $logo_color
+    nav
+      +column( $blueprint_grid_columns - $logo_columns - 1)
+      +inline_block
+      float: right
+      //margin-top: ($logo_font - $nav_font) / 2
+      margin-top: $logo_font - $nav_font
+      ul
+        +inline-block-list
+        li
+          +inline-block-list-item
+          font-size: $nav_font
+          display: inline
+          float: right
+          list-style-image: none
+          list-style-type: none
+          margin-left: 0
+          padding-left: 10px
+          padding-right: 10px
+          white-space: nowrap
+          a
+            &:active, &:visited, &:hover
+              color: $menu_color
+            &:hover
+              text-decoration: underline
+
+    margin-bottom: 20px
+    border-bottom: 1px solid black
+
+  footer
+    +column($blueprint_grid_columns)
+    +last
+    margin-top: 20px
+    border-top: 1px solid black
+
+    p#afiliacion
+      margin-top: 10px
+      span
+        +inline_block
+      text-align: right
+
+  .content
+    +column($blueprint_grid_columns)
+    +last
+    margin-left: $blueprint_grid_margin
+
+=main_form($form_size: $blueprint_grid_columns, $field_size: 8)
+  +column($form_size)
+  +container
+  +blueprint_form
+  fieldset
+    margin: 0
+    padding: 0
+    border: none
+  .field
+    +column($field_size)
+    margin-bottom: 30px
+    input, textarea
+      margin-left: $blueprint_grid_margin
+      width: 100%
+
+  label
+    margin-bottom: 10px
+    display: block
+
+  .text_or_file
+    textarea
+      display: block
+    .file label
+      margin-left: 30px
+
+  .submit
+    input
+      +button-button
+      margin-left: $blueprint_grid_margin
+
+=basic_table($header_color: black,$odd_color: white, $even_color: #e5ecf9)
+  +table-scaffolding
+  +inner-table-borders(1px, darken($odd_color, 40%))
+  +outer-table-borders(1px)
+  +alternating-rows-and-columns($odd_color, $even_color, 0, $header_color)
+
+

data/share/views/compass/screen.sass

@@ -0,0 +1,8 @@
+@import base
+
++blueprint-typography
++blueprint-utilities
++blueprint-grid
++blueprint-debug("/images/grid.png")
++blueprint-interaction
++blueprint-form

data/share/views/dependencies.haml

@@ -0,0 +1,7 @@
+%ul
+  - dependencies.each do |task, job|
+    %li
+      = task
+      \:
+      %a(href="#{File.join("/", workflow.to_s, task.to_s, job.sub(/.*\//, ''))}")= job.sub(/.*\//, '')
+

data/share/views/entity/Gene.haml

@@ -0,0 +1,6 @@
+%h2= entity.name
+
+%dl
+  %dt Description
+  %dd= entity.description
+

data/share/views/error.haml

@@ -0,0 +1,2 @@
+%span.error=step.messages.last
+

data/share/views/files.haml

@@ -0,0 +1,5 @@
+%ul
+  - files.each do |file|
+    %li
+      %a(href="#{File.join("/", workflow.to_s, task, jobname, "file", file)}")= file
+

data/share/views/form.haml

@@ -0,0 +1,66 @@
+- if (not task.nil?) and (not task.empty?)
+  %span.form_title
+    %span.workflow_name== [#{ workflow }]
+    %span.task_name= task
+
+- if (not description.nil?) and (not description.empty?)
+  %span.task_description= description
+
+- if authorized?
+  #other_task_jobs
+    %h3 Other jobs
+    %a.replace(href="/#{File.join(workflow.to_s, task, 'jobs')}") jobs
+
+%form.task(method="post" id=id enctype="multipart/form-data")
+  - if inputs.empty?
+    %input(type="hidden" name="noinputs" value="noinputs")
+
+  - inputs.each do |input|
+    - input_id = File.join(id, input.to_s)
+    - input_type = input_types[input]
+    %div.form_input(id="input_div_#{input_id}")
+      - value = params[input.to_s] || input_defaults[input]
+      - case input_type
+
+      - when :boolean
+        - not_value = ! value
+        %label(for=input_id)
+          %span.input_name= input
+          - if input_descriptions.include? input
+            \:
+            %span.input_description= input_descriptions[input]
+
+        %input(type='radio' id="input_#{input_id}_true" name=input value="true" checked=value)
+        %label.radio_option.radio_true(for="input_#{input_id}_true") true
+        %input(type='radio' id="input_#{input_id}_false" name=input value="false" checked=not_value)
+        %label.radio_option.radio_false(for="input_#{input_id}_false") false
+
+      - when :string, :float, :integer
+        %label(for=input_id)
+          %span.input_name= input
+          - if input_descriptions.include? input
+            \:
+            %span.input_description= input_descriptions[input]
+          - if input_defaults.include? input
+            == (Default: #{input_defaults[input]})
+        %input(class="#{ input } #{input_type}" name=input id="input_#{input_id}" value=value)
+
+      - when :tsv, :array, :text
+        %label(for=input_id)
+          %span.input_name= input
+          - if input_descriptions.include? input
+            \:
+            %span.input_description= input_descriptions[input]
+          %p
+            %input(class="param_file #{ input } #{input_type}" type="file" name="#{input}_param_file" id="input_#{input_id}_tsv_file")
+            %span.tsv_textarea_note.note (or use text area bellow)
+        %textarea(class="#{ input } #{input_type}" name=input id="input_#{input_id}")
+
+
+  %div.submit_job
+    - if not export == :exec
+      %span.jobname(id="jobname_#{id}")
+        Optional Job Name
+        %input(class="jobname" name="jobname" id="submit_#{id}")
+    %input(type="submit")
+

data/share/views/info.haml

@@ -0,0 +1,19 @@
+%dl
+  - info.each do |key, value|
+    %dt= key
+    %dd
+      - case
+      - when Hash === value
+        %dl
+          - value.each do |k,v|
+            %dt= k
+            %dd
+              - if Array === v
+                %pre= v * ", "
+              - else
+                %pre= v
+      - when Array === value
+        %pre= value * ", "
+      - else
+        %pre= value
+        

data/share/views/job_list.haml

@@ -0,0 +1,5 @@
+%ul
+  - job_list.sort.each do |jobname|
+    %li
+      %a(href="/#{File.join(workflow.to_s, task_name, jobname)}")= clean_jobname jobname
+      %a.DELETE(href="/#{File.join(workflow.to_s, task_name, jobname)}") delete

data/share/views/js/app.js

@@ -0,0 +1,221 @@
+$.fn.getClassInList = function(list){
+  for(var i = 0; i < list.length; i++)
+  {
+    if($(this).hasClass(list[i]))
+    return list[i];
+  }
+  return "";
+}
+
+function add_parameters(url, parameters){
+  if (url.indexOf('?') == -1){
+    return url + '?' + parameters;
+  }else{
+    return url + '&' + parameters;
+  }
+}
+
+function show_details(){
+  var main_size = $(window).height() - $('#details').outerHeight() - $('#details_controls').outerHeight() - $('#header').outerHeight() - 45;
+  scroll(0,0);
+  $('#details').show();
+  $('#details_controls').show();
+  $('#main').css('height', main_size).addClass('contracted');
+  $('#menu').css('height', main_size + $('#details').outerHeight() + $('#details_controls').outerHeight()).addClass('contracted');
+  return false;
+}
+
+function hide_details(){
+  details_history = [];
+  $('#main').show();
+  $('#details').hide().removeClass('expanded');
+  $('#details').attr('href', null);
+  $('#details_controls').hide();
+  $('#main').css('height', '100%').removeClass('contracted');
+  $('#menu').css('height', '100%').removeClass('contracted');
+  return false;
+}
+
+function toggle_details(){
+  if ($('#details').is(":visible")){
+    hide_details;
+  }else{
+    show_details;
+  }
+  return false;
+}
+
+function toggle_expand_details(){
+  if ($('#details').hasClass('expanded')){
+    contract_details();
+  }else{
+    expand_details();
+  }
+  return false
+}
+
+function expand_details(){
+  var url =  $('#details').attr('url');
+  if (url == null) return false;
+
+  $.ajax(add_parameters(url, '_size=normal'), {
+    success: function(data){
+      $('#details').html(data).attr('url', url);
+      $('#main').hide()
+      $('#details').addClass("expanded")
+      show_details();
+      rbbt_link_setup();
+    },
+    error: function(){
+      $('#details').html("<span class='details_error'>Error loading " + href + "</span>");
+    }
+  })
+
+  return false
+}
+
+function contract_details(){
+  var url =  $('#details').attr('url');
+  if (url == null) return false;
+ 
+  $.ajax(add_parameters(url, '_size=small'), {
+    success: function(data){
+      $('#details').html(data).attr('url', url);
+      $('#main').show()
+      $('#details').removeClass("expanded")
+      show_details();
+      rbbt_link_setup();
+    },
+    error: function(){
+      $('#details').html("<span class='details_error'>Error loading " + href + "</span>");
+    }
+  })
+
+  return false
+}
+
+function replace_object(obj){
+  var href = obj.attr('href');
+  if (href == null || href == undefined || href == ""){href = obj.attr('target');}
+  if (href == null || href == undefined || href == ""){href = obj.attr('url');}
+
+  $.ajax(href,{
+    success: function( data, stat, req ) {
+      var html = '<div class="embedded" target="' + req.getResponseHeader("AJAX-URL")  + '">' + data + '</div>';
+      var embedded = $(html);
+      obj.replaceWith(embedded);
+      if (req.status == 202){
+        embedded.addClass("reloading");
+        window.setTimeout(function(){replace_object(embedded)}, 5000)
+      }else{
+        rbbt_link_setup();
+        rbbt_table_setup();
+      }
+    }
+    });
+}
+
+function back_details(){
+  var url = details_history.pop();
+  if (url != null && url != undefined ){
+
+    if ($('#details').hasClass("expanded")){
+      size = "normal";
+    }else{
+      size = "small";
+    }
+ 
+    $.ajax(add_parameters(url, '_size=' + size), {
+      success: function(data){
+        $('#details').html(data).attr('url', url);
+        rbbt_link_setup();
+      },
+      error: function(){
+        $('#details').html("<span class='details_error'>Error loading " + href + "</span>");
+      }
+    })
+  }
+  return false;
+}
+
+function rbbt_link_setup(){
+  $('a.entity').not('[class*=rbbt_link_setup]').click(function(){
+    var link = $(this);
+    var href = link.attr('href')
+
+    if ($('#details').hasClass("expanded")){
+      size = "normal";
+    }else{
+      size = "small";
+    }
+
+    $.ajax(add_parameters(href, '_size=' + size), {
+      success: function(data){
+        var old_url = $('#details').attr('url');
+        if (old_url != null && old_url != undefined ){
+          details_history.push(old_url);
+        }
+        $('#details').html(data).attr('url', href);
+        show_details();
+        rbbt_link_setup();
+      },
+      error: function(){
+        $('#details').html("<span class='details_error'>Error loading " + href + "</span>");
+      }
+    })
+
+    return false;
+  }).addClass('rbbt_link_setup');
+
+  $('.DELETE,.POST').not('[class*=rbbt_link_setup]').click(function() {
+    if(confirm('Are you sure?')) {
+      var link = $(this);
+      var href = link.attr('href')
+
+      $.ajax({url:href, data:{ _method: $(this).getClassInList(['POST', 'DELETE'])}, type:"post", asyn:false})
+    }
+    return false;
+  }).addClass('rbbt_link_setup');
+
+  $('form.replace').not('[class*=rbbt_link_setup]').each(function(){
+    var link = $(this);
+    var href = link.attr('href')
+    $.ajax(href,{
+      success: function( data, stat, req ) {
+        link.replaceWith('<div class="embedded" target="' + req.getResponseHeader("AJAX-URL")  + '">' + data + '</div>');
+        rbbt_link_setup();
+        rbbt_table_setup();
+      }
+    });
+  }).addClass('rbbt_link_setup');
+
+  $('a.replace').not('[class*=rbbt_link_setup]').each(function(){
+    replace_object($(this));
+  }).addClass('rbbt_link_setup');
+}
+
+function rbbt_table_setup(){
+  //$('table.sorted, table.results_tsv_table').not('[class*=table_sorted]').tablesorter({textExtraction:"complex", widgets: ['zebra']}).addClass('table_sorted');
+  $('table form.table_controls').each(function(){
+    var form = $(this);
+    var embedded_div = $(this).parents("div.embedded").first()
+    if (embedded_div.html() != null){
+      var href = embedded_div.attr('target')
+      form.find(".change_page").click(function(){ 
+        var pfield =  form.find(".pfield").first().val();
+        var pnum =  form.find(".pnum").first().val();
+        var psize =  form.find(".psize").first().val();
+        var change = $(this).val();
+        $.ajax({
+          url: add_parameters(href, "_pfield=" + pfield + "&_pnum=" + pnum + "&_psize=" + psize + "&_paginate=" + change),
+          success: function(data){
+            embedded_div.html(data);
+            rbbt_link_setup();
+            rbbt_table_setup();
+          }
+        })
+        return false;
+      })
+    }
+  })
+}

data/share/views/layout.haml

@@ -0,0 +1,89 @@
+!!!
+!!! XML
+!!! Strict
+%html{ :xmlns => "http://www.w3.org/1999/xhtml", :lang => "en", 'xml:lang' => "en" }
+  %head
+    - if defined? @rbbt_refresh and Fixnum === @rbbt_refresh and @rbbt_refresh > 0
+      %meta(http-equiv="refresh" content=@rbbt_refresh)
+
+    - if defined? step and Step === step
+      - title = "#{step.task.name} [#{step.status}]"
+    - else
+      - title = "Workflow Explorer"
+    %title
+      = title
+
+
+    %meta{'http-equiv'=>"Content-Type", :content=>"text/html; charset=UTF-8"}/
+    %meta{'http-equiv'=>"Content-Language", :content=>"en-us"}/
+
+
+    %link{:href=>"/stylesheets/layout.css", :rel=>"stylesheet", :type=>"text/css"}/
+    %link{:href=>"/stylesheets/app.css", :rel=>"stylesheet", :type=>"text/css"}/
+
+    %script{:src => '/plugins/jquery/js/jquery-1.6.2.min.js', :type => 'text/javascript'}
+
+    -# %link{:href=>"/plugins/jquery-ui/css/custom-theme/jquery-ui-1.8.14.custom.css", :rel=>"stylesheet", :type=>"text/css"}/
+    -# %script{:src => '/plugins/jquery-ui/js/jquery-ui-1.8.14.custom.min.js', :type => 'text/javascript'}
+
+    %script{:src => '/js/app.js', :type => 'text/javascript'}
+  %body
+    #header
+      %h1
+        = title
+        %span.login
+          - if session[:user]
+            ==Logged in as: #{session[:user]}. 
+            %a(href="/logout") logout
+          - else
+            Not logged in
+            %a(href="/login") login
+ 
+    #menu
+      - if session.include?(:context) and Hash === session[:context] and session[:context].collect{|w,t| t.values}.flatten.any?
+        #context
+          %h2 Context Jobs
+          = workflow_partial(nil, nil, 'partials/_context_control', locals)
+
+        %h2 Workflows
+
+      - WorkflowREST.workflows.each do |workflow|
+        %h3.workflow_title(target=workflow)= workflow.to_s
+        %div.workflow_menu(id=workflow)
+          %a.replace(href="/#{workflow.to_s}")
+      #footer
+        %p Structural Computational Biology Group
+
+        %p Structural Biology and BioComputing Programme
+
+        %p Spanish National Cancer Research Centre (CNIO). C/ Melchor Fernández Almagro, 3, E-28029 Madrid Spain 
+    #content
+      #main
+        = yield
+      #details_controls
+        %ul
+          %li
+            %a(href="#" id="hide_details") [hide]
+          %li
+            %a(href="#" id="toggle_expand_details") [toggle]
+          %li
+            %a(href="#" id="back_details") [back]
+      #details
+
+:javascript        
+
+  $('h3.workflow_title').click(function(){
+    var target = $(this).attr('target');
+    $('div#' + target).toggle();
+  })
+
+  rbbt_link_setup();
+  rbbt_table_setup();
+
+  hide_details();
+ 
+  $('#hide_details').click(hide_details);
+  $('#toggle_expand_details').click(toggle_expand_details);
+  $('#back_details').click(back_details);
+
+  var details_history = [];

data/share/views/partials/_context_control.haml

@@ -0,0 +1,14 @@
+%dl
+- session[:context].each do |workflow, tasks|
+  - next unless tasks.any?
+
+  %dt=workflow.to_s
+  %dd
+    - tasks.each do |task, job|
+      = task 
+      \:
+      %ul.context_control
+        %li
+          %a(href="/#{[workflow.to_s, task, job] * "/"}")= clean_jobname job
+        %li
+          %a.DELETE(href="/context/#{[workflow.to_s, task] * "/"}") delete

data/share/views/partials/_job_control.haml

@@ -0,0 +1,17 @@
+%ul.job_control
+  %li
+    %a(href="/#{[workflow, task_name, jobname] * "/"}")= clean_jobname jobname
+  %li
+    %a.POST(href="/context/#{[workflow, task_name, jobname] * "/"}") context
+  %li
+    %a(href="/#{[workflow, task_name, jobname] * "/"}?_format=raw") raw
+  %li
+    %a(href="/#{[workflow, task_name, jobname] * "/"}?_format=json") json
+  %li
+    %a(href="/#{[workflow, task_name, jobname] * "/"}/info") info
+  %li
+    %a(href="/#{[workflow, task_name, jobname] * "/"}/files") files
+  %li
+    %a(href="/#{[workflow, task_name, jobname] * "/"}/dependencies") dependencies
+  %li
+    %a.DELETE(href="/#{[workflow, task_name, jobname] * "/"}") delete

data/share/views/partials/_result_table.haml

@@ -0,0 +1,43 @@
+%table(class="results_tsv_table" id="result_tsv_table_#{task_name}")
+
+  -# HEAD
+  %thead
+    - if result.key_field == "ID"
+      - fields = result.fields
+    - else
+      - fields = result.all_fields
+    - fields.each do |field|
+      %th(class=field)= field
+
+
+  -# BODY
+  %tbody
+    - rows, total = process_result(result, locals)
+
+    - rows.each do |key, values|
+      - values = [values] if not Array === values
+      - if result.key_field != "ID"
+        - values = [key] + values
+        - id = ""
+        - NamedArray.setup(values, result.all_fields) if result.fields
+      - else
+        - id = key
+        - NamedArray.setup(values, result.fields) if result.fields
+      %tr(id=id)
+        - values.each do |value|
+          - value = value.link if value.respond_to? :link
+          - type = value.respond_to?(:format)? value.format : ""
+          - if Array === value
+            %td(class=type)= value * ", "
+          - else
+            %td(class=type)= value
+            
+  -# FOOT
+  %tfoot
+    -# paginate
+    - if locals.include? :step
+      %tr
+        %th(colspan="#{fields.length}") 
+          = workflow_partial(workflow, task_name, 'partials/_result_table_controls', locals.merge(:fields => fields, :total => total))         
+         
+