[ARVADOS] updated: da2803a65e696bf85883e82a0bda6ef81dda5429

git at public.curoverse.com git at public.curoverse.com
Tue Feb 25 16:11:22 EST 2014


Summary of changes:
 .../app/assets/javascripts/application.js          |   55 ++++++++++++++++++++
 .../app/assets/stylesheets/application.css.scss    |   18 ++++++
 apps/workbench/app/assets/stylesheets/loading.css  |   29 +++++-----
 .../app/controllers/application_controller.rb      |    4 +-
 .../app/controllers/collections_controller.rb      |    4 +-
 .../app/views/collections/_index_tbody.html.erb    |   21 +++++--
 .../app/views/collections/_show_recent.html.erb    |    6 +-
 .../pipeline_instances/_show_components.html.erb   |   26 ++++++----
 .../install-crunch-dispatch.html.textile.liquid    |    8 ++--
 doc/sdk/python/sdk-python.html.textile.liquid      |    4 +-
 doc/user/reference/sdk-cli.html.textile.liquid     |    4 +-
 .../running-external-program.html.textile.liquid   |    4 +-
 ...rial-gatk-variantfiltration.html.textile.liquid |    2 +-
 .../tutorial-parallel.html.textile.liquid          |    4 +-
 docker/README.md                                   |   39 ++++++--------
 docker/api/passenger.conf                          |    6 +-
 docker/base/Dockerfile                             |    8 ++--
 docker/sso/passenger.conf                          |    6 +-
 docker/workbench/passenger.conf                    |    6 +-
 sdk/python/bin/arv-mount                           |   17 ++++--
 sdk/python/readme.llfuse                           |    2 +-
 services/api/app/models/collection.rb              |   10 ++--
 services/api/app/models/node.rb                    |   28 ++++++----
 services/api/script/crunch-dispatch.rb             |   26 +++++++++-
 .../arvados/v1/collections_controller_test.rb      |   39 ++++++++++++--
 25 files changed, 265 insertions(+), 111 deletions(-)

       via  da2803a65e696bf85883e82a0bda6ef81dda5429 (commit)
       via  ce3845c8ce108518832ea6ad9a10bb9b98a48174 (commit)
       via  be60b02bc5c56afaaec808d9e259eba51d951998 (commit)
       via  324dc9f33d95cdeacf23c0570607900be945d20f (commit)
       via  e76ee382d79d6726dcf6315dbae0e0f5aef09a86 (commit)
       via  c315a459778181e207034ae5385fdf34fec51fa7 (commit)
       via  b8ee617ec8af73120b427f7591744d0f4883a63f (commit)
       via  00af5ad16232b856ef1f3620a4f62f0946c681a7 (commit)
       via  e8f224e43292059d52f438995f30cb392da88262 (commit)
       via  60f6a0ade0f6ff2ed695c0d22fb4cfb8383014b4 (commit)
       via  75496f54ac81f6bb280aab3bd5b1cff72701acbb (commit)
       via  ba64c04f9340013d25138b40b92e51e4ad5bacd8 (commit)
       via  819757ca4018b20b4309d1d2d1b94d17cfee088c (commit)
       via  05e4ffd616ed333165532720ce3ec6819831d88f (commit)
       via  a82f7725c2a4c4c7f27d1219c8ffe51a22c52b16 (commit)
       via  e03fdab8240f07c5cb1e88b502c6d6b145e1e957 (commit)
       via  d0daa6d6968ecf1a3ec7e64f7747e842f20febad (commit)
       via  dd3a873512742870ef338028996ba36784f56bf8 (commit)
       via  6812b3350f48ed977ea2e3e788e49e1008a3b244 (commit)
       via  78a1683680177da480dc3ffaea2d4f2b79ab793d (commit)
       via  50567a15ccfdc5e73289227e343bfce946974ecd (commit)
       via  603517c58cb2a57961de70c7b67f9856206515da (commit)
       via  a23b909256ae2ee222036d91d6e46faccfe13542 (commit)
       via  3c6f8001fb5d63ef92da36e662ac58396f18a9d0 (commit)
       via  6ecd3b6f76a1dbb39a56fc81d306969dc0a3f6af (commit)
       via  7024cc159936593350aaf7939d700102f6510787 (commit)
       via  579300424ef50990ff9414f2eabf8f371f278d99 (commit)
      from  b354e03622eb2e47c055b6fcc38b24c22a59ab9f (commit)

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commit da2803a65e696bf85883e82a0bda6ef81dda5429
Merge: b354e03 ce3845c
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Feb 25 16:12:21 2014 -0500

    Merge remote-tracking branch 'origin/master' into 2049-run-job-from-workbench

diff --cc apps/workbench/app/controllers/application_controller.rb
index 162fd28,e94428e..2817735
--- a/apps/workbench/app/controllers/application_controller.rb
+++ b/apps/workbench/app/controllers/application_controller.rb
@@@ -107,10 -107,10 +107,11 @@@ class ApplicationController < ActionCon
    end
  
    def create
-     @object ||= model_class.new params[model_class.to_s.underscore.singularize.to_sym]
+     @object ||= model_class.new params[model_class.to_s.underscore.singularize]
      @object.save!
 +
      respond_to do |f|
+       f.json { render json: @object }
        f.html {
          redirect_to(params[:return_to] || @object)
        }
diff --cc apps/workbench/app/views/collections/_index_tbody.html.erb
index 57f6eeb,eb9c93f..96b7397
--- a/apps/workbench/app/views/collections/_index_tbody.html.erb
+++ b/apps/workbench/app/views/collections/_index_tbody.html.erb
@@@ -1,10 -1,7 +1,10 @@@
  <% @collections.each do |c| %>
  
- <tr class="collection">
+ <tr class="collection" data-object-uuid="<%= c.uuid %>">
    <td>
 +    <%= render :partial => "selection_checkbox", :locals => {:object => c} %>
 +  </td>
 +  <td>
      <%= link_to_if_arvados_object c.uuid %>
    </td>
    <td>
diff --cc apps/workbench/app/views/collections/_show_recent.html.erb
index d94b169,3cedb57..a3b93d8
--- a/apps/workbench/app/views/collections/_show_recent.html.erb
+++ b/apps/workbench/app/views/collections/_show_recent.html.erb
@@@ -15,17 -15,14 +15,17 @@@
  
  <div style="padding-right: 1em">
  
 +<%= form_tag do |f| %>
 +
  <table id="collections-index" class="topalign table table-condensed table-fixedlayout table-fixed-header-row">
    <colgroup>
 +    <col width="4%" />
      <col width="10%" />
      <col width="36%" />
-     <col width="22%" />
+     <col width="15%" />
      <col width="8%" />
-     <col width="16%" />
      <col width="8%" />
+     <col width="23%" />
    </colgroup>
    <thead>
      <tr class="contain-align-left">
diff --cc apps/workbench/app/views/pipeline_instances/_show_components.html.erb
index 88bed69,9597964..1785f6a
--- a/apps/workbench/app/views/pipeline_instances/_show_components.html.erb
+++ b/apps/workbench/app/views/pipeline_instances/_show_components.html.erb
@@@ -3,27 -3,21 +3,33 @@@
      padding-left: 1em;
      padding-right: 1em;
    }
 +table.pipeline-components-table {
 +  width: 100%;
 +  table-layout: fixed;
++  overflow: hidden;
 +}
 +
  table.pipeline-components-table thead th {
    text-align: bottom;
  }
  table.pipeline-components-table div.progress {
    margin-bottom: 0;
  }
 +
++table.pipeline-components-table td {
++  overflow: hidden;
++  text-overflow: ellipsis;
++}
++
  <% end %>
 -<br />
  
 +<% if @object.active != nil %>
  <table class="table pipeline-components-table">
    <colgroup>
 -    <col width="15%" />
 -    <col width="15%" />
 -    <col width="35%" />
 -    <col width="35%" />
 +    <col style="width: 15%" />
-     <col style="width: 35%" />
-     <col style="width: 15%" />
-     <col style="width: 35%" />
++    <col style="width: 20%" />
++    <col style="width: 20%" />
++    <col style="width: 45%" />
    </colgroup>
    <thead>
      <tr>
@@@ -77,69 -71,4 +83,69 @@@ setInterval(function(){$('a.refresh').c
  <% end %>
  <% end %>
  
 -<pre><%= JSON.pretty_generate @object.attributes %></pre>
 +<% else %>
 +
 +  <%= form_tag @object, :method => :put do |f| %>
 +
 +  <%= hidden_field @object.class.to_s.underscore.singularize.to_sym, :active, :value => true %>
 +  <%= button_tag "Run pipeline", {class: 'btn btn-primary pull-right'} %>
 +  <% end %>
 +
 +<table class="table pipeline-components-table" style="margin-top: -.1em">
 +  <colgroup>
 +    <col style="width: 15%" />
-     <col style="width: 35%" />
-     <col style="width: 15%" />
-     <col style="width: 35%" />
++    <col style="width: 20%" />
++    <col style="width: 20%" />
++    <col style="width: 45%" />
 +  </colgroup>
 +
 +  <thead>
 +    <tr>
 +      <th>
 +        component
 +      </th><th>
 +        script, version
 +      </th><th>
 +        parameter
 +      </th><th>
 +        input
 +      </th>
 +    </tr>
 +  </thead>
 +  <tbody>
 +  <% @object.components.each do |k, v| %>
 +
 +    <% sp = v[:script_parameters].collect do |k, v| [k, v] end %>
 +
 +    <tr>
 +      <td><%= k %></td>
 +
 +      <td><%= v[:script] %>
 +        <br /><span class="deemphasize"> <%= v[:script_version] %></span>
 +      </td>
 +
 +      <td>
 +        <%= sp[0][0] %>
 +      </td>
 +
 +      <td>
 +        <%= sp[0][1] %>
 +      </td>
 +      </tr>
 +
 +    <% if sp.length > 1 %>
 +    <tr>
-       <td></td>
-       <td></td>
++      <td style="border-top: none"></td>
++      <td style="border-top: none"></td>
 +
 +      <% sp[1..-1].each do |p| %>
-         <%= p[0] %>
-         <%= p[1] %>
++        <td style="border-top: none"><%= p[0] %></td>
++        <td style="border-top: none"><%= p[1] %></td>
 +      <% end %>
 +    </tr>
 +  <% end %>
 +  <% end %>
 +  </tbody>
 +  </table>
 +  
 +<% end %>

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