RubyGems - rbbt-rest - Versions diffs - 1.1.0 - Mend

rbbt-rest 1.1.0

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Files changed (590) hide show

data/share/views/form.haml ADDED Viewed

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+- id = [workflow.to_s, task.to_s] * "__"
+- action = to(File.join('/', workflow.to_s, task.to_s))
+- task_info = workflow.task_info(task)
+.workflow_task
+  .title
+    %h3
+      %span.workflow= workflow
+      %span.task= Misc.humanize task
+  .form
+    = partial_render('partials/form', :id => id, :action => action, :method => 'post', :enctype => "multipart/form-data", :info => task_info, :klass => 'workflow_task')

data/share/views/job_info.haml ADDED Viewed

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1	+ = hash2dl(info)

data/share/views/job_result.haml ADDED Viewed

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+- if job
+  .row
+    .twelve.column
+      = workflow_partial('job_result/job_control', workflow, task, locals)
+.row
+  .twelve.column
+    - case type
+    - when :tsv
+      = workflow_partial('job_result/tsv', workflow, task, locals)
+    - when :string
+      = workflow_partial('job_result/string', workflow, task, locals)
+    - when :array
+      = workflow_partial('job_result/array', workflow, task, locals)
+    - when :boolean
+      = workflow_partial('job_result/boolean', workflow, task, locals)
+    - when :binary
+      = workflow_partial('job_result/binary', workflow, task, locals)
+    - when :annotations
+      = workflow_partial('job_result/annotations', workflow, task, locals)
+    - when :yaml
+      = workflow_partial('job_result/yaml', workflow, task, locals)
+    - else
+      - raise "Unsupported result type: #{ type }"

data/share/views/job_result/annotations.haml ADDED Viewed

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+%ul.annotations
+  - result.each do |entity|
+    %li= entity.respond_to?(:link) ? entity.link : entity

data/share/views/job_result/array.haml ADDED Viewed

@@ -0,0 +1,4 @@
+%ul
+  - result.each do |elem|
+    %li= elem

data/share/views/job_result/binary.haml ADDED Viewed

	@@ -0,0 +1 @@
1	+ %a(href="#{@path}?_format=binary") Download

data/share/views/job_result/boolea.haml ADDED Viewed

	@@ -0,0 +1 @@
1	+ = result.to_s

data/share/views/job_result/boolean.haml ADDED Viewed

	@@ -0,0 +1 @@
1	+ %span.result_boolean= result.to_s

data/share/views/job_result/job_control.haml ADDED Viewed

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+%dl
+  %dt Job control
+  %dd.job_control
+    %ul
+      %li
+        %a(href="/#{[workflow, task, jobname] * "/"}?_update=clean") clean
+      %li
+        %a(href="/#{[workflow, task, jobname, "info"] * "/"}") info
+      %li
+        %a(href="/#{[workflow, task, jobname] * "/"}?_format=raw") raw
+  - if job.files.any?
+    %dt Files
+    %dd
+      %ul
+        - job.files.each do |file|
+          %li
+            %a(href="/#{[workflow, task, jobname, "file", file] * "/"}")= file

data/share/views/job_result/string.haml ADDED Viewed

	@@ -0,0 +1 @@
1	+ %span.result_string= result

data/share/views/job_result/tsv.haml ADDED Viewed

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+- table_id = [workflow.to_s, task, jobname] * "_"
+- table_class = 'workflow_tsv_result'
+- rows = tsv_rows(result)
+- header = result.all_fields
+= 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))

data/share/views/job_result/yaml.haml ADDED Viewed

	@@ -0,0 +1 @@
1	+ %span.result= result.inspect

data/share/views/layout.haml ADDED Viewed

@@ -0,0 +1,89 @@
+/ paulirish.com/2008/conditional-stylesheets-vs-css-hacks-answer-neither/
+/[if lt IE 7 ] <html class=\"ie6\" lang=\"en\">
+/[if IE 7 ]    <html class=\"ie7\" lang=\"en\">
+/[if IE 8 ]    <html class=\"ie8\" lang=\"en\">
+/[if IE 9 ]    <html class=\"ie9\" lang=\"en\">
+/[if (gt IE 9)|!(IE)] <!--> <html lang=\"en\">
+- $zepto = false
+%head
+  %meta(name="viewport" content="width=device-width, initial-scale=1.0")
+  %link{:rel => "icon", :type => "image/gif", :href => "/favicon.gif"}/
+  %title= $title || "Genome Scout"
+  - 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'
+    = serve_js false
+  - else
+    - record_js '/js/deffer'
+    = serve_js
+    - %w(jquery-1.8.0.min jquery.cookie jquery.form).each do |jquery_file|
+      - record_js File.join('/plugins/jquery/js/', jquery_file)
+  -# %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 }"
+  - 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 app).each do |file|
+    - record_js "/js/#{ file }"
+  = serve_css
+%body
+  #header
+    = partial_render('layout/header')
+  #body
+    - $wait = false
+    = yield
+  %footer
+    CNIO
+  #coda
+    = serve_js
+    - if $wait
+      :javascript
+        var url = window.location.toString();
+        function reload(){
+          $.ajax({url: add_parameters(url, '_layout=false'), cache:false,
+          success: function(data, stat, req){
+            if (req.status == 202){
+              $('#body').html(data)
+              window.setTimeout(reload, 7000);
+            }else{
+              window.location = url;
+            }
+          },
+          error:function(jqXHR, status, thrownError){
+            if (undefined === jqXHR.responseText || jqXHR.responseText == ''){
+              $('#body').html('No response. Server down?')
+            }else{
+              $('#body').html(jqXHR.responseText)
+            }
+          }})
+        }
+        window.setTimeout(reload, 7000);
+  #modal1.reveal-modal
+  #modal2.reveal-modal

data/share/views/layout/favourites.haml ADDED Viewed

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+%li.divider
+%li#top-favourites.has-dropdown
+  %a(href="#") Fav. Entities
+  %ul.favourite_entities.dropdown
+    - favourite_entities.each do |type, entities|
+      %li.type.has-dropdown(entity_type=type)
+        %a(href="#")= type
+        %ul.dropdown
+          - entities.each do |entity|
+            %li
+              = entity.link
+%li.divider
+%li#top-favourite_lists.has-dropdown
+  %a(href="#") Fav. Entity Lists
+  %ul.favourite_entity_lists.dropdown
+    - favourite_entity_lists.each do |type, lists|
+      %li.type.has-dropdown(entity_type=type)
+        %a(href="#")= type
+        %ul.dropdown
+          - lists.each do |list_id|
+            %li
+              %a(href="#{Entity::REST.entity_list_url(list_id, type)}")= list_id
+%li#top-favourite_lists.has-dropdown
+  %a(href="#") New Entity List
+  %ul.new_entity_list.dropdown
+    - Entity::REST::REST_ENTITIES.each do |mod|
+      %li
+        %a.new_list(href="#" data-reveal-id='modal1')= mod.to_s

data/share/views/layout/header.haml ADDED Viewed

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+%nav.top-bar
+  %ul.title-area
+    %li.name
+      %h1
+        %a(href="/")= $title || "Genome Scout"
+    %li.toggle-topbar.menu-icon
+      %a(href="#")
+        %span
+          Menu
+  %section.top-bar-section
+    %ul.left
+      %li
+        %a#reload_page(href="#")
+          %i.general.foundicon-refresh.hide-for-small
+          %span.show-for-small
+            Reload page
+    %ul.left
+      - if user and self.respond_to? :favourite_entities
+        %li#top-add-favourite
+          %a#toggle_favourite.inactive
+            %i.general.foundicon-star.hide-for-small
+            %span.add.show-for-small
+              Add to Favourites
+            %span.remove.show-for-small
+              Remove from Favourites
+        = partial_render('layout/favourites')
+    %ul.right
+      - if settings.respond_to? :finder and not settings.finder.nil?
+        %li.search.has-form
+          %form.collapse(action='/find' method="POST")
+            %input(type="text" name="term")
+            %button.secondary.radius.button(type="submit") Search

data/share/views/main.haml ADDED Viewed

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1	+ - if user.nil?
2	+ - redirect to('/login')

data/share/views/partials/form.haml ADDED Viewed

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+- id      = nil unless defined? id
+- action  = nil unless defined? action
+- klass   = nil unless defined? klass
+- method  = 'post' unless defined? method
+- enctype = 'multipart/form-data' unless defined? enctype
+- info    = {} unless defined? info
+- klass = "#{klass} custom"
+%form(class=klass action=action method=method id=id enctype=enctype)
+  - inputs       = consume_parameter(:inputs, info) || []
+  - types        = consume_parameter(:input_types, info) || {}
+  - defaults     = consume_parameter(:input_defaults, info) || {}
+  - descriptions = consume_parameter(:input_descriptions, info) || {}
+  - options      = consume_parameter(:input_options, info) || {}
+  - values       = consume_parameter(:values, info) || {}
+  - inputs.each do |input|
+    - 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.submit
+    %input(type="submit")

data/share/views/partials/table.haml ADDED Viewed

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+- table_options = {} unless defined? table_options and table_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
+- row_ids     = table_options[:row_ids]  unless defined? row_ids and row_ids
+- table_url   = table_options[:url]  unless defined? table_url and table_url
+- total_size  = table_options[:total_size]   unless defined? total_size and total_size
+- list_links  = table_options[:list_links]  unless defined? list_links and not list_links.nil?
+- page = @page unless defined? page and not page.nil?
+%table(id="#{Misc.snake_case(table_id)}" class=table_class attr-url=table_url attr-total_size=total_size attr-page=page)
+  - if table_id
+    %caption
+      %span.title= Misc.humanize table_id
+  - if header
+    %thead
+      %tr
+        - header.shift if row_ids == :consume
+        - header.each do |header|
+          %th= header
+  %tbody
+    - rows.each do |row|
+      - case row_ids
+      - when :consume
+        - row_id = row.shift
+      - when :use
+        - row_id = row.first
+      - else
+        - row_id = nil
+      %tr(id=row_id)
+        - 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)
+  -#{{{ 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="#") &laquo;
+            - 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 table_url
+          %ul.table_actions
+            %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/public/favicon.gif ADDED Viewed

Binary file

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

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+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"}
+function reload_time(object){
+  var tries = object.attr('reload-attempts');
+  if (undefined === tries){ tries = 0 };
+  if (typeof tries == 'string' || tries instanceof String){ tries = parseInt(tries) }
+  object.attr('reload-attempts', tries + 1);
+  return reload_seconds_for_try[tries];
+}
+function replace_object(object, href, embedd, complete){
+  if (embedd === undefined){ embedd = false; }
+  //if (complete === undefined){ complete = []; }
+  $.ajax({
+    url : href,
+    cache: false,
+    beforeSend: function(){ object.addClass("reloading"); object.find("span.error").remove() },
+    complete: complete,
+    error: function( req, text, error ) {
+      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);
+    },
+    success: function( data, stat, req ) {
+      object.removeClass('error');
+      if (req.status == 202){
+        object.addClass("reloading");
+        href = remove_parameter(href, '_update');
+        href = remove_parameter(href, '_');
+        var reload_seconds = reload_time(object);
+        if (reload_seconds == "STOP"){
+          object.removeClass("reloading").addClass("error").html("Maximum number or retries reached").attr('reload-attempts', 0);
+        }else{
+          window.setTimeout(function(){replace_object(object, href, embedd, complete)}, reload_seconds * 1000);
+        }
+      }else{
+        object.removeClass("reloading").attr('reload-attempts', 0);
+        if (embedd){
+          href = remove_parameter(href, '_update');
+          href = remove_parameter(href, '_');
+          object.html(data).addClass("embedded").attr('target-href', href);
+          capture_embedded_form(object);
+          update_rbbt();
+        }else{
+          object.replaceWith(data);
+          update_rbbt();
+        }
+      }
+    }
+  })
+}
+function replace_link(link){
+  var href = $(link).attr('href');
+  replace_object(link, href);
+}
+function update_embedded(object, reload){
+  var href = object.attr('target-href');
+  if (reload == true){
+      href = add_parameters(href, '_update=reload');
+      href = add_parameters(href, '_=' + Math.random().toString());
+  }
+  replace_object(object, href, true);
+}
+function capture_embedded_form(object){
+  object.find('form').submit(function(){
+    var form = $(this);
+    var embedded = object;
+    var params = "";
+    form.find('input').not('[type=submit]').not('[type=radio]').not('[type=checkbox]').each(function(){
+      var input = $(this)
+      if (params.length > 0){ params += '&'}
+      params += input.attr('name') + "=" + input.val();
+    })
+    form.find('input[type=checkbox]:checked').each(function(){
+      var input = $(this)
+      if (params.length > 0){ params += '&'}
+      params += input.attr('name') + "=" + input.val();
+    })
+    form.find('input[type=radio]:checked').each(function(){
+      var input = $(this)
+      if (params.length > 0){ params += '&'}
+      params += input.attr('name') + "=" + input.val();
+    })
+    form.find('select').not('[type=submit]').each(function(){
+      var select = $(this)
+      var option = select.find('option:selected');
+      if (params.length > 0){ params += '&'}
+      params += select.attr('name') + "=" + option.val();
+    })
+    form.find('textarea').each(function(){
+      var input = $(this)
+      if (params.length > 0){ params += '&'}
+      params += input.attr('name') + "=" + escape(input.val());
+    })
+    var url = embedded.attr('target-href');
+    if (url.indexOf('?') == -1){
+      url = url + '?' + params;
+    }else{
+      url = url.replace(/\?.*/, '?' + params);
+    }
+    embedded.attr('target-href', url)
+    update_embedded(embedded);
+    return false;
+  })
+}