rbbt-rest 1.1.4 → 1.1.5

data/share/views/help/workflow.haml

@@ -0,0 +1,77 @@
+.row.help
+  .column.small-12
+    :markdown
+
+      The Workflow subsystem
+      ===================
+
+      The workflow subsystem is used to package related functionalities and
+      offer a common, flexible, interface.  Each workflow is composed of a
+      number of tasks. Each task represents a step taken towards the completion
+      of a workflow, and thus, tasks may depend on other tasks, yet this is
+      often not the case and tasks are often stand-alone. 
+      
+      Tasks are design to be isolated or self-contained, meaning that executing
+      a particular task with the same values for the input parameters should
+      render the same identical result. This is not an imposition, but it is
+      encouraged, and almost all, if not all, tasks behave this way. The
+      consequence of this predictability is that results can be cached. 
+
+      ## Accessing workflow functionalities
+
+      You may access a workflow functionalities on three ways: using a
+      web-browser, remotely using web services, or locally. Local execution
+      requires the installation of the Rbbt framework and the workflow source
+      and it is out of the scope of this document.
+
+      ### Using the Browser
+
+      To use the web browser you just point your browser to the workflow page.
+      Check at the bottom of this page for a list of workflows available in
+      this server. The workflow page presents a description of the software
+      along with the tasks it includes and their descriptions (descriptions are
+      optional for workflow development and may be missing). Each task has its
+      own page, which contains the input form. Submitting the form takes you to
+      the results page. Form and result pages follow a general template, which
+      we shall review bellow. 
+      
+      Workflow and task pages, like any other page in this system, are subject
+      to being redefined; in this case by the workflow author. This makes it
+      possible to make both the input and the results page fit more closely the
+      user needs. This option, however, is rarely necessary, and most workflows 
+      use the default templates.
+
+      ### Using the Web Server
+
+      The browser interface follows the REST protocol (mostly) so that it can
+      be used as a web server. Any user familiar with 'curl' or 'wget' should
+      have little problems using it. The Rbbt all-purpose command 'rbbt' can
+      also be used to execute remote workflow. See the documentation on the
+      rbbt site (once it is available.)
+
+.row.help
+  .column.small-12
+    
+    %table
+      %caption Available workflows on this site
+      %thead
+        %tr
+          %th Workflow
+          %th Description
+      %tbody
+        - Sinatra::RbbtRESTWorkflow::WORKFLOWS.each do |workflow|
+          - next if workflow.asynchronous_exports.empty? and workflow.synchronous_exports.empty? and workflow.exec_exports.empty?
+          %tr
+            %th
+              %a(href="#{'/' << workflow.to_s}")= Misc.humanize(workflow.to_s)
+            %td
+              - description = workflow.workflow_description || ""
+
+              - case
+              - when description.empty?
+                No description
+              - else
+                = description.split("\n\n").first
+
+
+ 

data/share/views/job_result/tsv.haml

@@ -1,7 +1,8 @@
 - table_id = [workflow.to_s, task, jobname] * "_"
 - table_class = 'workflow_tsv_result'
-- rows = tsv_rows(result)
+- rows, total_size = tsv_rows(result)
 - header = result.all_fields
+- page = total_size > 50 ? "1" : nil
 
 = workflow_partial('partials/table', workflow, task, 
-  locals.merge(:table_id => table_id, :table_calss => table_class, :rows => rows, :header => result.all_fields, :row_ids => :use))
+  locals.merge(:table_id => table_id, :page => page, :table_class => table_class, :rows => rows, :total_size => total_size, :header => result.all_fields, :row_ids => :use, :table_url => File.join('/', workflow.to_s, task, jobname)))

data/share/views/layout.haml

@@ -15,12 +15,27 @@
 
   %link{:rel => "icon", :type => "image/gif", :href => "/favicon.gif"}/
 
-  %title= $title || "Genome Scout"
+  - title = $title.dup || "Genome Scout"
+  - case page_type.to_s
+  - when "entity"
+    - title << ": " << (entity.respond_to?(:name) ? entity.name || entity : entity)
+  - when "entity_list"
+    - title << ": " << list_id
+  - when "entity_map"
+    - title << ": " << map_id
+  - when "entity_action"
+    - title << ": " << "[#{page_action}]" # << (entity.respond_to?(:name) ? entity.name || entity : entity)
+  - when "entity_list_action"
+    - title << ": " << "[#{page_action}]" << list_id
+  - when "entity_map_action"
+    - title << ": " << "[#{page_action}]" << map_id
+
+
+  %title= title
   - record_css '/stylesheets/app'
 
   - record_css '/plugins/zurb-icons/foundation_icons_general/stylesheets/general_foundicons.css'
 
-
   - if $zepto
     - record_js "/js/zepto"
     - record_js '/js/deffer'
@@ -32,6 +47,7 @@
       - record_js File.join('/plugins/jquery/js/', jquery_file)
 
 
+  - record_js "/plugins/underscore/js/underscore.js"
   -# %w(foundation foundation.alerts foundation.cookie foundation.forms foundation.reveal foundation.tooltips foundation.clearing foundation.dropdown foundation.joyride foundation.magellan foundation.placeholder foundation.section foundation.topbar custom.modernizr).each do |file|
   - %w(foundation foundation.cookie foundation.reveal foundation.dropdown foundation.section foundation.topbar custom.modernizr).each do |file|
     - record_js "/js/#{ file }"
@@ -39,7 +55,7 @@
   - record_js '/plugins/jquery.tablesorter/jquery.tablesorter'
   - record_js '/plugins/jquery.scrollTo/jquery.scrollTo'
 
-  - %w(_foundation _md5 _fix_tablesorter_science helpers _ajax_replace _dom_update _ellipsis entities favourites offcanvas actions lists tables tabs base workflow app).each do |file|
+  - %w(_ajax_replace _foundation _md5 _fix_tablesorter_science helpers _dom_update _ellipsis entities favourites offcanvas actions lists maps tables tabs reveal base workflow app).each do |file|
     - record_js "/js/#{ file }"
 
 
@@ -88,5 +104,19 @@
    
 
   #modal1.reveal-modal
+    .header
+      .title
+      .controls
+        %a(class='link-reveal-modal') 
+          %i.foundicon-right-arrow
+        %a(class='close-reveal-modal') x
+    .content
   #modal2.reveal-modal
+    .header
+      .title
+      .controls
+        %a(class='link-reveal-modal') 
+          %i.foundicon-right-arrow
+        %a(class='close-reveal-modal') x
+    .content
 

data/share/views/layout/favourites.haml

@@ -1,6 +1,4 @@
 
-%li.divider
-  
 %li#top-favourites.has-dropdown
   %a(href="#") Fav. Entities
  
@@ -13,8 +11,6 @@
             %li
               = entity.link
               
-%li.divider
-  
 %li#top-favourite_lists.has-dropdown
   %a(href="#") Fav. Entity Lists
  
@@ -26,6 +22,20 @@
           - lists.each do |list_id|
             %li
               %a(href="#{Entity::REST.entity_list_url(list_id, type)}")= list_id
+              
+%li#top-favourite_maps.has-dropdown
+  %a(href="#") Fav. Entity Maps
+ 
+  %ul.favourite_entity_maps.dropdown
+    - favourite_entity_maps.each do |type, columns|
+      - columns.each do |column, maps|
+        %li.type.has-dropdown(entity_type=type entity_column=column)
+          %a(href="#")= [type, column] * " - "
+          %ul.dropdown
+            - maps.each do |map_id|
+              %li
+                %a(href="#{Entity::REST.entity_map_url(map_id, type, column)}")= map_id
+
 
 %li#top-favourite_lists.has-dropdown
   %a(href="#") New Entity List

data/share/views/layout/header.haml

@@ -38,3 +38,7 @@
             %input(type="text" name="term")
             %button.secondary.radius.button(type="submit") Search
  
+      %li
+        %a(href="/help") Help
+      %li.ajax_counter
+        %a#ajax_processes 0

data/share/views/partials/form.haml

@@ -20,7 +20,9 @@
     - input_id = id.nil? ? nil : id + "__" << input.to_s
     - hide = (options[input] != nil and options[input][:hide])
     %div(class="input #{types[input]} #{input} #{hide ? 'hide' : ''}")
-      != form_input(input, types[input], defaults[input], values[input], descriptions[input], input_id, options[input])
+      - input_options = options[input]
+      - input_options = input_options.dup unless input_options.nil?
+      != form_input(input, types[input], defaults[input], values[input], descriptions[input], input_id, input_options)
 
   .input.submit
     %input(type="submit")

data/share/views/partials/table.haml

@@ -1,6 +1,6 @@
 - table_options = {} unless defined? table_options and table_options
+- entity_options = table_options[:tsv_entity_options] unless defined? entity_options and entity_options
 - headers = table_options[:headers]
-
 - table_id    = table_options[:table_id]  unless defined? table_id and table_id
 - table_class = table_options[:table_class]  unless defined? table_class and table_class
 - header      = table_options[:header]  unless defined? header and header
@@ -9,7 +9,7 @@
 - total_size  = table_options[:total_size]   unless defined? total_size and total_size
 - filters     = table_options[:filters]   unless defined? filters and filters
 
-- list_links  = table_options[:list_links]  unless defined? list_links and not list_links.nil?
+- list_links  = table_options[:list_links]   unless defined? list_links and list_links
 
 - page = @page unless defined? page and not page.nil?
 
@@ -40,64 +40,28 @@
         - row.each_with_index do |value, i|
           - list_id = "#{ Misc.humanize(table_id) }: #{header[i]} for #{row.first}" if list_links and table_id and header and AnnotatedArray === value
           - field = header ? header[i] : nil
-          -# if headers and headers.include? field
-            - value = Misc.prepare_entity(value.to_s, headers[field].first, headers[field].last)
-          %td= table_value(value, field, :list_id => list_id)
+          - val = table_value(value, field, :list_id => list_id, :unnamed => table_options[:unnamed], :entity_options => entity_options)
+          %td= Float === val ? "%.5g" % val : val.to_s
 
 
   -#{{{ TFOOT
   %tfoot
     %tr
       %th(colspan="#{header ? header.length : 100}")
-        - if page
-          - num, size, field = parse_page(page)
-          - num = num.to_i
-          - total_nums = total_size.to_i / size.to_i
-          - total_nums += 1 if total_size.to_i % size.to_i > 0
-          - start = [1, num - 2].max
-          - eend = [total_nums, num + 2].min
-          %ul.table_pagination.pagination
-            %li(class="arrow") 
-              %a.prev(href="#") «
-
-            - if num - 2 > 1
-              %li(class="num") 
-                %a(href="#") 1
-
-            - if num - 2 > 2
-              %li(class="inactive") 
-                %a(href="#") ...
-
-            - (start..eend).each do |p|
-              %li(class="num#{p.to_s == num.to_s ? " active" : "" }") 
-                %a(href="#")= p
-
-            - if num + 3 < total_nums
-              %li(class="inactive") 
-                %a(href="#") ...
-
-            - if num + 2 < total_nums
-              %li(class="num") 
-                %a(href="#")= total_nums
-
-            %li(class="arrow") 
-              %a.next(href="#") &raquo;
-
-            %li(class="all") 
-              %a.all(href="#") all 
 
+        - if page
+          = partial_render('partials/table/page', :page => page, :total_size => total_size) 
 
         - if table_url
           %ul.table_actions
-            - if filters and filters.any?
-              %li.filter()
-                %a(href="#" data-reveal-id="modal1") filter
-                .filters(id="filter-#{(rand * 1000).to_i}")
-                  = action_parameters nil, :class => 'filter_controls' do
-                    - filters.each do |field, attrs|
-                      - input field, :string, "Field value"
-            %li.tsv
-              %a(href="#{add_GET_param(table_url, "_format", "tsv")}") tsv
-            %li.excel
-              %a(href="#{add_GET_param(table_url, "_format", "excel")}") excel
+
+            = partial_render('partials/table/filters', :table_url => table_url, :header => header, :id => "rbbt_reveal_" << Misc.digest(table_url)) 
+              
+            = partial_render('partials/table/column', :table_url => table_url, :header => header) 
+
+            = partial_render('partials/table/files', :table_url => table_url) 
+            
+            
+            
+            
 

data/share/views/partials/table/column.haml

@@ -0,0 +1,10 @@
+- table_columns_id = "rbbt_table_columns_" << (rand * 1000).to_i.to_s
+%li.table_column
+  = reveal :column do
+    %ul.table_column_selector.clean_list
+      - header.each do |field|
+        %li
+          %span.field= field
+          %a.save_column_map(href="#") save map
+          - if Entity.formats.include? field and Entity.formats[field].include? Entity::REST 
+            %a.save_column_list(href="#") save list

data/share/views/partials/table/files.haml

@@ -0,0 +1,4 @@
+%li.tsv
+  %a(href="#{add_GET_param(table_url, "_format", "tsv")}") tsv
+%li.excel
+  %a(href="#{add_GET_param(table_url, "_format", "excel")}") excel

data/share/views/partials/table/filters.haml

@@ -0,0 +1,11 @@
+%li.filter
+  = reveal :filter, id do
+    - if @filter
+      - filter_values = Hash[*@filter.split(";;").collect{|f| f.split("~")}.flatten]
+    - else
+      - filter_values = {}
+
+    .filters()
+      = action_parameters nil, :class => 'filter_controls' do
+        - header.each do |field|
+          - input field, :string, "Filter for #{ field }", filter_values[field]

data/share/views/partials/table/page.haml

@@ -0,0 +1,37 @@
+- num, size, field = parse_page(page)
+- num = num.to_i
+- total_nums = total_size.to_i / size.to_i
+- total_nums += 1 if total_size.to_i % size.to_i > 0
+- start = [1, num - 2].max
+- eend = [total_nums, num + 2].min
+%ul.table_pagination.pagination
+  %li(class="arrow") 
+    %a.prev(href="#") «
+
+  - if num - 2 > 1
+    %li(class="num") 
+      %a(href="#") 1
+
+  - if num - 2 > 2
+    %li(class="inactive") 
+      %a(href="#") ...
+
+  - (start..eend).each do |p|
+    %li(class="num#{p.to_s == num.to_s ? " active" : "" }") 
+      %a(href="#")= p
+
+  - if num + 3 < total_nums
+    %li(class="inactive") 
+      %a(href="#") ...
+
+  - if num + 2 < total_nums
+    %li(class="num") 
+      %a(href="#")= total_nums
+
+  %li(class="arrow") 
+    %a.next(href="#") &raquo;
+
+  %li(class="all") 
+    %a.all(href="#") all 
+
+

data/share/views/public/js/_ajax_replace.js

@@ -1,5 +1,38 @@
 var reload_seconds_for_try = {0: 1, 1: 1, 2: 2, 3: 2, 4: 3, 5: 7, 6: 7, 7: 7, 8: 7, 9: 7, 10: 30, 11: 30, 12: 60, 13: 120, 14: 120, 15: 120, 16: "STOP"}
 
+var ajax_processes = []
+function update_ajax_counter(){
+  $('#ajax_processes').html(ajax_processes.length)
+}
+function add_ajax(url){
+  ajax_processes.push(url)
+  update_ajax_counter();
+}
+
+function remove_ajax(url){
+  ajax_processes.splice( $.inArray(url, ajax_processes), 1 );
+  update_ajax_counter();
+}
+
+$.old_ajax = $.ajax;
+$.ajax = function(url, options){
+  if (typeof url == 'string'){
+    options['url'] = url;
+  }else{
+    options = url;
+    url = options['url'];
+  }
+
+  add_ajax(url);
+
+  complete = options['complete'];
+  if (undefined === complete){ options['complete'] = function(){ remove_ajax(url)} }
+  if (typeof complete == 'function'){ options['complete'] = [complete, function(){ remove_ajax(url)}] }
+  if (typeof complete == 'array'){ options['complete'].push(function(){ remove_ajax(url)}) }
+
+  return $.old_ajax(options);
+}
+
 function reload_time(object){
   var tries = object.attr('reload-attempts');
   if (undefined === tries){ tries = 0 };
@@ -11,9 +44,42 @@ function reload_time(object){
   return reload_seconds_for_try[tries];
 }
 
+function get_ajax(options, complete){
+  options.success = function( data, stat, req ) {
+    if (req.status == 202){
+      href = options.url
+      href = remove_parameter(href, '_update');
+      href = remove_parameter(href, '_');
+      options.url = href
+      window.setTimeout(function(){ get_ajax(options, complete)}, 3 * 1000);
+    }else{
+      if (undefined !== complete){
+        return complete(data)
+      }else{
+        return(data)
+      }
+    }
+  }
+
+  console.log(options.data)
+  response = $.ajax(options)
+  if (undefined !== response.responseText){
+    if (response.status == 202){
+      href = options.url
+      href = remove_parameter(href, '_update');
+      href = remove_parameter(href, '_');
+      options.url = href
+      return get_ajax(options, complete);
+    }else{
+      return response.responseText;
+    }
+  }else{
+    return response;
+  }
+}
+
 function replace_object(object, href, embedd, complete){
   if (embedd === undefined){ embedd = false; }
-  //if (complete === undefined){ complete = []; }
 
   $.ajax({
     url : href,
@@ -24,7 +90,9 @@ function replace_object(object, href, embedd, complete){
       href = remove_parameter(href, '_update');
       href = remove_parameter(href, '_');
       error_span = $('<span>').html(error).addClass('error')
-      object.removeClass("reloading").addClass("error").css('height', 0).html(error_span).css('height', 'auto').attr('target-href', href);
+      error_message = $(req.responseText).find('span.error_message')
+      error = $('<div>').append(error_span).append(error_message)
+      object.removeClass("reloading").addClass("error").css('height', 0).html(error).css('height', 'auto').attr('target-href', href);
     },
     success: function( data, stat, req ) {
       object.removeClass('error');
@@ -42,8 +110,12 @@ function replace_object(object, href, embedd, complete){
       }else{
         object.removeClass("reloading").attr('reload-attempts', 0);
         if (embedd){
-          href = remove_parameter(href, '_update');
-          href = remove_parameter(href, '_');
+          if (undefined !== req.getResponseHeader("URI")){
+            href = req.getResponseHeader("URI")
+          }else{
+            href = remove_parameter(href, '_update');
+            href = remove_parameter(href, '_');
+          }
           object.html(data).addClass("embedded").attr('target-href', href);
           capture_embedded_form(object);
           update_rbbt();