[ARVADOS] updated: 974ad63fc24161cb228003f4ef4cc32d5da578ff

git at public.curoverse.com git at public.curoverse.com
Wed Nov 5 13:58:05 EST 2014


Summary of changes:
 .../app/assets/javascripts/application.js          |   4 +
 .../app/assets/javascripts/infinite_scroll.js      |  75 +++++
 .../app/assets/javascripts/select_modal.js         |  14 +-
 .../app/assets/stylesheets/application.css.scss    |   4 +
 .../app/controllers/application_controller.rb      |  22 +-
 apps/workbench/app/controllers/jobs_controller.rb  |  20 +-
 .../controllers/pipeline_instances_controller.rb   |  73 +++--
 .../app/controllers/projects_controller.rb         |   4 +-
 apps/workbench/app/helpers/application_helper.rb   |   6 +-
 apps/workbench/app/helpers/provenance_helper.rb    | 305 ++++++++++-----------
 apps/workbench/app/models/arvados_api_client.rb    |   2 +-
 .../app/views/collections/_show_files.html.erb     |   4 +-
 .../views/projects/_show_data_collections.html.erb |   3 +-
 .../projects/_show_jobs_and_pipelines.html.erb     |   5 +-
 .../views/projects/_show_other_objects.html.erb    |   3 +-
 .../projects/_show_pipeline_templates.html.erb     |   3 +-
 .../app/views/projects/_show_subprojects.html.erb  |   3 +-
 .../app/views/projects/_show_tab_contents.html.erb |  17 +-
 .../controllers/collections_controller_test.rb     |  69 +++++
 .../pipeline_instances_controller_test.rb          | 169 ++++++++++++
 .../test/integration/pipeline_instances_test.rb    |   6 +-
 apps/workbench/test/integration/projects_test.rb   | 204 +++++++-------
 apps/workbench/test/test_helper.rb                 |  15 +
 docker/arvdock                                     |   7 +-
 sdk/cli/bin/arv                                    |  14 +-
 sdk/cli/bin/arv-tag                                |   4 +-
 sdk/cli/bin/crunch-job                             |  99 ++++---
 sdk/python/arvados/collection.py                   | 208 ++++++++------
 sdk/python/arvados/commands/put.py                 |  49 ++--
 sdk/python/arvados/config.py                       |   2 +-
 sdk/python/arvados/keep.py                         |   2 +-
 sdk/python/arvados/stream.py                       |   4 +-
 sdk/python/arvados/util.py                         |  29 +-
 sdk/python/bin/arv-get                             |   2 +
 sdk/python/bin/arv-normalize                       |   1 +
 sdk/python/tests/run_test_server.py                |   8 +-
 sdk/python/tests/test_collections.py               | 162 ++++++++---
 sdk/ruby/lib/arvados.rb                            |   2 +-
 sdk/ruby/lib/arvados/keep.rb                       |   1 +
 sdk/ruby/test/test_keep_manifest.rb                |  22 +-
 .../arvados/v1/collections_controller.rb           |  53 +++-
 .../controllers/arvados/v1/groups_controller.rb    |  14 +-
 services/api/lib/load_param.rb                     |  16 +-
 services/api/test/fixtures/collections.yml         |  21 ++
 services/api/test/fixtures/jobs.yml                |  36 +++
 services/api/test/fixtures/pipeline_instances.yml  |  12 +-
 .../arvados/v1/groups_controller_test.rb           |  32 +++
 services/fuse/arvados_fuse/__init__.py             |   1 +
 services/fuse/setup.py                             |   2 +-
 49 files changed, 1292 insertions(+), 541 deletions(-)
 create mode 100644 apps/workbench/test/controllers/collections_controller_test.rb

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commit 974ad63fc24161cb228003f4ef4cc32d5da578ff
Merge: 87567c9 f91dff0
Author: radhika <radhika at curoverse.com>
Date:   Wed Nov 5 13:57:55 2014 -0500

    Merge branch 'master' into 3177-collection-choose-files


commit 87567c9440a65a42fdde62e513b40dc5a8585fdf
Author: radhika <radhika at curoverse.com>
Date:   Wed Nov 5 13:57:14 2014 -0500

    3177: look for checked persistent selections on submit.

diff --git a/apps/workbench/app/assets/javascripts/select_modal.js b/apps/workbench/app/assets/javascripts/select_modal.js
index ba106d1..596cb70 100644
--- a/apps/workbench/app/assets/javascripts/select_modal.js
+++ b/apps/workbench/app/assets/javascripts/select_modal.js
@@ -40,10 +40,20 @@ $(document).on('click', '.selectable', function() {
     var action_data_from_params = $(this).data('action-data-from-params');
     var selection_param = action_data.selection_param;
     $modal.find('.modal-error').removeClass('hide').hide();
-    $modal.find('.selectable.active[data-object-uuid]').each(function() {
+
+    $checked_selections = $modal.find('.persistent-selection:checked');
+    if ($checked_selections) {
+      $checked_selections.each(function() {
+          data.push({name: selection_param, value: $(this).attr('value')});
+      });
+    }
+
+    if (data.length == 0) {   // no checked persistent selection
+      $modal.find('.selectable.active[data-object-uuid]').each(function() {
         var val = $(this).attr('data-object-uuid');
         data.push({name: selection_param, value: val});
-    });
+      });
+    }
     $.each($.extend({}, action_data, action_data_from_params),
            function(key, value) {
                if (value instanceof Array && key[-1] != ']') {
diff --git a/apps/workbench/app/helpers/application_helper.rb b/apps/workbench/app/helpers/application_helper.rb
index cfe7f19..165f062 100644
--- a/apps/workbench/app/helpers/application_helper.rb
+++ b/apps/workbench/app/helpers/application_helper.rb
@@ -261,7 +261,7 @@ module ApplicationHelper
       dn += '[value]'
     end
 
-    if dataclass == Collection
+    if (dataclass == Collection) or (dataclass == File)
       selection_param = object.class.to_s.underscore + dn
       display_value = attrvalue
       if value_info.is_a?(Hash)
@@ -274,9 +274,9 @@ module ApplicationHelper
         end
       end
       if (attr == :components) and (subattr.size > 2)
-        chooser_title = "Choose a dataset for #{object.component_input_title(subattr[0], subattr[2])}:"
+        chooser_title = "Choose a #{dataclass == Collection ? 'dataset' : 'file'} for #{object.component_input_title(subattr[0], subattr[2])}:"
       else
-        chooser_title = "Choose a dataset:"
+        chooser_title = "Choose a #{dataclass == Collection ? 'dataset' : 'file'}:"
       end
       modal_path = choose_collections_path \
       ({ title: chooser_title,
diff --git a/apps/workbench/app/views/collections/_show_files.html.erb b/apps/workbench/app/views/collections/_show_files.html.erb
index 9cd77b0..adbf480 100644
--- a/apps/workbench/app/views/collections/_show_files.html.erb
+++ b/apps/workbench/app/views/collections/_show_files.html.erb
@@ -86,7 +86,7 @@
         </div>
 
         <div class="collection_files_name">
-          <% if !defined? no_checkboxes or !no_checkboxes %>
+          <%# if !defined? no_checkboxes or !no_checkboxes %>
           <%= check_box_tag 'uuids[]', "#{@object.uuid}/#{file_path}", false, {
                 :class => 'persistent-selection',
                 :friendly_type => "File",
@@ -96,7 +96,7 @@
                 :title => "Include #{file_path} in your selections",
               } %>
           <span> </span>
-          <% end %>
+          <%# end %>
       <% if CollectionsHelper::is_image(filename) %>
           <i class="fa fa-fw fa-bar-chart-o"></i> <%= filename %></div>
        </div>

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