[ARVADOS] updated: 2129d0fd84fa62a5498d9860f3307cd64dc2a704

git at public.curoverse.com git at public.curoverse.com
Mon Feb 3 17:58:00 EST 2014


Summary of changes:
 .../app/assets/javascripts/application.js          |    7 +
 .../app/assets/stylesheets/application.css         |    3 +
 apps/workbench/app/assets/stylesheets/loading.css  |  374 +++++++++++++++++
 .../app/controllers/application_controller.rb      |   15 +-
 .../controllers/pipeline_instances_controller.rb   |   84 ++++-
 apps/workbench/app/controllers/users_controller.rb |    6 +-
 apps/workbench/app/helpers/application_helper.rb   |    6 +-
 .../app/helpers/pipeline_instances_helper.rb       |   70 ++--
 apps/workbench/app/models/arvados_base.rb          |    4 +-
 apps/workbench/app/models/node.rb                  |    2 +-
 apps/workbench/app/models/pipeline_instance.rb     |    4 +
 apps/workbench/app/models/user.rb                  |    6 +-
 apps/workbench/app/models/virtual_machine.rb       |    2 +-
 .../views/application/_arvados_attr_value.html.erb |    3 +-
 .../app/views/application/_arvados_object.html.erb |    2 +-
 .../application/_arvados_object_attr.html.erb      |    5 +-
 .../application/_breadcrumb_page_name.html.erb     |    1 +
 .../app/views/application/_breadcrumbs.html.erb    |   20 +
 .../app/views/application/_index.html.erb          |    9 +-
 .../app/views/application/_loading.html.erb        |  190 +++++++++
 .../workbench/app/views/application/destroy.js.erb |    3 +
 apps/workbench/app/views/application/show.html.erb |    2 +-
 apps/workbench/app/views/jobs/index.html.erb       |    4 +-
 apps/workbench/app/views/jobs/show.html.erb        |    2 +-
 .../app/views/layouts/application.html.erb         |   11 +-
 .../app/views/links/_breadcrumb_page_name.html.erb |    8 +
 .../app/views/pipeline_instances/compare.html.erb  |   75 ++++
 .../app/views/pipeline_instances/index.html.erb    |   31 ++-
 .../app/views/pipeline_instances/show.html.erb     |  101 ++++--
 .../app/views/pipeline_instances/show.js.erb       |    3 +
 .../app/views/user_agreements/index.html.erb       |    2 +
 apps/workbench/app/views/users/_home.html.erb      |    3 +-
 apps/workbench/app/views/users/_tables.html.erb    |    9 +-
 apps/workbench/app/views/users/home.js.erb         |    3 +
 apps/workbench/app/views/users/index.html.erb      |   62 ---
 apps/workbench/app/views/users/welcome.html.erb    |    2 +
 apps/workbench/config/routes.rb                    |    4 +-
 doc/api/schema/Link.textile                        |    2 +-
 docker/build.sh                                    |   42 ++
 sdk/cli/Gemfile.lock                               |    2 +-
 sdk/cli/test/test_arv-tag.rb                       |   10 +-
 sdk/python/.gitignore                              |    1 +
 sdk/python/arvados/__init__.py                     |  428 +-------------------
 sdk/python/arvados/api.py                          |   91 +++++
 sdk/python/arvados/collection.py                   |    6 +-
 sdk/python/arvados/config.py                       |   34 ++
 sdk/python/arvados/errors.py                       |   14 +
 sdk/python/arvados/keep.py                         |   18 +-
 sdk/python/arvados/stream.py                       |    7 +-
 sdk/python/arvados/util.py                         |  306 ++++++++++++++
 sdk/python/bin/arv-mount                           |  158 +++++++
 sdk/python/requirements.txt                        |    1 +
 sdk/python/setup.py                                |    4 +
 sdk/python/test_util.py                            |   22 +
 services/api/test/fixtures/jobs.yml                |   22 +
 .../functional/arvados/v1/jobs_controller_test.rb  |   17 +
 56 files changed, 1719 insertions(+), 604 deletions(-)
 create mode 100644 apps/workbench/app/assets/stylesheets/loading.css
 create mode 100644 apps/workbench/app/views/application/_breadcrumb_page_name.html.erb
 create mode 100644 apps/workbench/app/views/application/_breadcrumbs.html.erb
 create mode 100644 apps/workbench/app/views/application/_loading.html.erb
 create mode 100644 apps/workbench/app/views/application/destroy.js.erb
 create mode 100644 apps/workbench/app/views/links/_breadcrumb_page_name.html.erb
 create mode 100644 apps/workbench/app/views/pipeline_instances/compare.html.erb
 create mode 100644 apps/workbench/app/views/pipeline_instances/show.js.erb
 create mode 100644 apps/workbench/app/views/users/home.js.erb
 delete mode 100644 apps/workbench/app/views/users/index.html.erb
 create mode 100644 docker/build.sh
 create mode 100644 sdk/python/arvados/api.py
 create mode 100644 sdk/python/arvados/config.py
 create mode 100644 sdk/python/arvados/errors.py
 create mode 100644 sdk/python/arvados/util.py
 create mode 100755 sdk/python/bin/arv-mount
 create mode 100644 sdk/python/test_util.py

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commit 2129d0fd84fa62a5498d9860f3307cd64dc2a704
Author: Tom Clegg <tom at curoverse.com>
Date:   Mon Feb 3 14:52:10 2014 -0800

    Hide this/other/both legend if only one pipeline_instance is shown.

diff --git a/apps/workbench/app/controllers/pipeline_instances_controller.rb b/apps/workbench/app/controllers/pipeline_instances_controller.rb
index 1bb95e0..a42a734 100644
--- a/apps/workbench/app/controllers/pipeline_instances_controller.rb
+++ b/apps/workbench/app/controllers/pipeline_instances_controller.rb
@@ -4,11 +4,11 @@ class PipelineInstancesController < ApplicationController
   include PipelineInstancesHelper
 
   def show
-    pipelines = [@object]
+    @pipelines = [@object]
 
     if params[:compare]
       PipelineInstance.where(uuid: params[:compare]).each do |p|
-        pipelines << p
+        @pipelines << p
       end
     end
 
@@ -17,7 +17,7 @@ class PipelineInstancesController < ApplicationController
     pips = {}
     n = 1
 
-    pipelines.each do |p|
+    @pipelines.each do |p|
       collections = []
 
       p.components.each do |k, v|
diff --git a/apps/workbench/app/views/pipeline_instances/show.html.erb b/apps/workbench/app/views/pipeline_instances/show.html.erb
index 84c1e30..cf56b97 100644
--- a/apps/workbench/app/views/pipeline_instances/show.html.erb
+++ b/apps/workbench/app/views/pipeline_instances/show.html.erb
@@ -65,11 +65,13 @@ table.pipeline-components-table div.progress {
   </tfoot>
 </table>
 
-<div style="text-align: center">
-<span class="pipeline_color_legend" style="background: #88ff88">This pipeline</span> 
-<span class="pipeline_color_legend" style="background: #8888ff">Comparison pipeline</span>
-<span class="pipeline_color_legend" style="background: #88ffff">Shared by both pipelines</span>
-</div>
+<% if @pipelines.count > 1 %>
+  <div style="text-align: center">
+    <span class="pipeline_color_legend" style="background: #88ff88">This pipeline</span> 
+    <span class="pipeline_color_legend" style="background: #8888ff">Comparison pipeline</span>
+    <span class="pipeline_color_legend" style="background: #88ffff">Shared by both pipelines</span>
+  </div>
+<% end %>
 
    <%= render partial: 'application/svg_div', locals: {
          divId: "provenance_graph", 

commit d8c56aa6534d87105201372cd5f9f965a8246ea4
Merge: 6038a01 19552d4
Author: Tom Clegg <tom at curoverse.com>
Date:   Mon Feb 3 14:56:30 2014 -0800

    Merge branch '1976-pipeline-progress'
    
    Conflicts:
    	apps/workbench/app/views/pipeline_instances/show.html.erb

diff --cc apps/workbench/app/views/pipeline_instances/show.html.erb
index 96c32db,9000750..84c1e30
--- a/apps/workbench/app/views/pipeline_instances/show.html.erb
+++ b/apps/workbench/app/views/pipeline_instances/show.html.erb
@@@ -1,52 -1,72 +1,87 @@@
  <% content_for :css do %>
 +  .pipeline_color_legend {
 +    padding-left: 1em;
 +    padding-right: 1em;
 +  }
+ table.pipeline-components-table thead th {
+   text-align: bottom;
+ }
+ table.pipeline-components-table div.progress {
+   margin-bottom: 0;
+ }
  <% end %>
+ <br />
  
- <table class="table table-condensed table-hover topalign">
+ <table class="table pipeline-components-table">
+   <colgroup>
+     <col width="15%" />
+     <col width="15%" />
+     <col width="35%" />
+     <col width="35%" />
+   </colgroup>
    <thead>
+     <tr>
+       <th>
+         component
+       </th><th>
+         progress
+         <%= link_to '(refresh)', request.fullpath, class: 'refresh', remote: true, method: 'get' %>
+       </th><th>
+         script, version
+       </th><th>
+         output
+       </th>
+     </tr>
    </thead>
    <tbody>
-     <% @object.attributes_for_display.each do |attr, attrvalue| %>
-     <% if attr == 'components' and attrvalue.is_a? Hash %>
- 
-     <tr class="info"><td><%= attr %></td><td>
-         <table class="table">
-           <% render_pipeline_jobs.each do |pj| %>
-           <tr><% %w(index name result job_link script script_version progress_detail progress_bar output_link).each do |key| %>
-             <td>
-               <% if key == 'script_version' %>
-               <%= pj[key.to_sym][0..6] rescue '' %>
-               <% else %>
-               <%= pj[key.to_sym] %>
-               <% end %>
-             </td>
-             <% end %>
-           </tr>
-           <% end %>
-         </table>
-     </td></tr>
- 
-     <% else %>
-     <%= render partial: 'application/arvados_object_attr', locals: { attr: attr, attrvalue: attrvalue } %>
-     <% end %>
+     <% render_pipeline_jobs.each do |pj| %>
+     <tr>
+       <td>
+         <% if pj[:job].andand[:uuid] %>
+         <%= link_to pj[:name], job_url(id: pj[:job][:uuid]) %>
+         <% else %>
+         <%= pj[:name] %>
+         <% end %>
+       </td><td>
+         <%= pj[:progress_bar] %>
+         <% if pj[:job].andand[:cancelled_at] %>
+         <span class="pull-right label label-warning">cancelled</span>
+         <% elsif pj[:failed] %>
+         <span class="pull-right label label-warning">failed</span>
+         <% elsif pj[:result] == 'queued' %>
+         <span class="pull-right label">queued</span>
+         <% end %>
+       </td><td>
+         <%= pj[:script] %>
+         <br /><span class="deemphasize"><%= pj[:script_version] %></span>
+       </td><td>
+         <%= link_to_if_arvados_object pj[:output] %>
+       </td>
+     </tr>
      <% end %>
    </tbody>
+   <tfoot>
+     <tr><td colspan="4"></td></tr>
+   </tfoot>
  </table>
  
 +<div style="text-align: center">
 +<span class="pipeline_color_legend" style="background: #88ff88">This pipeline</span> 
 +<span class="pipeline_color_legend" style="background: #8888ff">Comparison pipeline</span>
 +<span class="pipeline_color_legend" style="background: #88ffff">Shared by both pipelines</span>
 +</div>
 +
 +   <%= render partial: 'application/svg_div', locals: {
 +         divId: "provenance_graph", 
 +         svgId: "provenance_svg", 
 +         svg: @prov_svg } %>
 +
- <pre>
- <%= JSON.pretty_generate(@object.attributes) rescue nil %>
- </pre>
+ <div style="height: 1em"></div>
+ 
+ <%= render partial: 'arvados_object' %>
+ 
+ <% if @object.active %>
+ <% content_for :js do %>
+ setInterval(function(){$('a.refresh').click()}, 30000);
+ <% end %>
+ <% end %>

commit 6038a018b758e1a4babc5669df50622cd470df2f
Merge: 5a016cb bfa69a7
Author: Tom Clegg <tom at curoverse.com>
Date:   Mon Feb 3 14:44:19 2014 -0800

    Merge branch 'master' into 1977-provenance-report
    
    Conflicts:
    	apps/workbench/app/controllers/pipeline_instances_controller.rb
    	apps/workbench/app/views/jobs/show.html.erb

diff --cc apps/workbench/app/controllers/pipeline_instances_controller.rb
index 55ee02b,d776941..1bb95e0
--- a/apps/workbench/app/controllers/pipeline_instances_controller.rb
+++ b/apps/workbench/app/controllers/pipeline_instances_controller.rb
@@@ -1,56 -1,77 +1,130 @@@
  class PipelineInstancesController < ApplicationController
+   skip_before_filter :find_object_by_uuid, only: :compare
+   before_filter :find_objects_by_uuid, only: :compare
+   include PipelineInstancesHelper
  
 +  def show
 +    pipelines = [@object]
 +
 +    if params[:compare]
-       PipelineInstance.where(uuid: params[:compare]).each do |p| pipelines << p end
++      PipelineInstance.where(uuid: params[:compare]).each do |p|
++        pipelines << p
++      end
 +    end
 +
 +    count = {}    
 +    provenance = {}
 +    pips = {}
 +    n = 1
 +
 +    pipelines.each do |p|
 +      collections = []
 +
 +      p.components.each do |k, v|
 +        j = v[:job]
 +
 +        uuid = j[:uuid].intern
 +        provenance[uuid] = j
 +        pips[uuid] = 0 unless pips[uuid] != nil
 +        pips[uuid] |= n
 +
 +        collections << j[:output]
 +        ProvenanceHelper::find_collections(j[:script_parameters]).each do |k|
 +          collections << k
 +        end
 +
 +        uuid = j[:script_version].intern
 +        provenance[uuid] = {:uuid => uuid}
 +        pips[uuid] = 0 unless pips[uuid] != nil
 +        pips[uuid] |= n
 +      end
 +
 +      Collection.where(uuid: collections).each do |c|
 +        uuid = c.uuid.intern
 +        provenance[uuid] = c
 +        pips[uuid] = 0 unless pips[uuid] != nil
 +        pips[uuid] |= n
 +      end
 +      
 +      n = n << 1
 +    end
 +
-     #puts pips
- 
 +    @prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
 +      :all_script_parameters => true, 
 +      :combine_jobs => :script_and_version,
 +      :script_version_nodes => true,
 +      :pips => pips }
 +  end
 +
+   def compare
+     @breadcrumb_page_name = 'compare'
+ 
+     @rows = []          # each is {name: S, components: [...]}
+ 
+     # Build a table: x=pipeline y=component
+     @objects.each_with_index do |pi, pi_index|
+       pipeline_jobs(pi).each do |component|
+         # Find a cell with the same name as this component but no
+         # entry for this pipeline
+         target_row = nil
+         @rows.each_with_index do |row, row_index|
+           if row[:name] == component[:name] and !row[:components][pi_index]
+             target_row = row
+           end
+         end
+         if !target_row
+           target_row = {name: component[:name], components: []}
+           @rows << target_row
+         end
+         target_row[:components][pi_index] = component
+       end
+     end
+ 
+     @rows.each do |row|
+       # Build a "normal" pseudo-component for this row by picking the
+       # most common value for each attribute. If all values are
+       # equally common, there is no "normal".
+       normal = {}              # attr => most common value
+       highscore = {}           # attr => how common "normal" is
+       score = {}               # attr => { value => how common }
+       row[:components].each do |pj|
+         pj.each do |k,v|
+           vstr = for_comparison v
+           score[k] ||= {}
+           score[k][vstr] = (score[k][vstr.to_s] || 0) + 1
+           highscore[k] ||= 0
+           if score[k][vstr] == highscore[k]
+             # tie for first place = no "normal"
+             normal.delete k
+           elsif score[k][vstr] == highscore[k] + 1
+             # more pipelines have v than anything else
+             highscore[k] = score[k][vstr]
+             normal[k] = vstr
+           end
+         end
+       end
+ 
+       # Add a hash in component[:is_normal]: { attr => is_the_value_normal? }
+       row[:components].each do |pj|
+         pj[:is_normal] = {}
+         pj.each do |k,v|
+           pj[:is_normal][k] = (normal.has_key?(k) && normal[k] == for_comparison(v))
+         end
+       end
+     end
+   end
+ 
+   protected
+   def for_comparison v
+     if v.is_a? Hash or v.is_a? Array
+       v.to_json
+     else
+       v.to_s
+     end
+   end
+ 
+   def find_objects_by_uuid
+     @objects = model_class.where(uuid: params[:uuids])
+   end
+ 
  end
diff --cc apps/workbench/app/views/jobs/show.html.erb
index 5022b8b,0000000..2bc74ca
mode 100644,000000..100644
--- a/apps/workbench/app/views/jobs/show.html.erb
+++ b/apps/workbench/app/views/jobs/show.html.erb
@@@ -1,6 -1,0 +1,6 @@@
- <%= render :partial => 'application/arvados_object' %>
++<%= render partial: 'arvados_object' %>
 +
 +<%= render partial: 'application/svg_div', locals: {
 +      divId: "provenance_graph", 
 +      svgId: "provenance_svg", 
 +      svg: @svg } %>

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