[ARVADOS] updated: 949c7305691c7003296a1185697bb7318a975403

[git at public.curoverse.com]

Summary of changes:
 .../controllers/pipeline_instances_controller.rb   |    6 ++
 apps/workbench/app/helpers/provenance_helper.rb    |   68 ++++++-----------
 apps/workbench/app/models/collection.rb            |    7 ++
 .../pipeline_instances/_show_components.html.erb   |   10 +-
 apps/workbench/test/integration/users_test.rb      |    7 +-
 apps/workbench/test/unit/collection_test.rb        |   15 +++-
 .../pipeline_templates/gatk-exome-fq-snp.json      |   21 ++++--
 doc/sdk/cli/index.html.textile.liquid              |    1 -
 .../tutorial-firstscript.html.textile.liquid       |    6 +-
 .../tutorial-new-pipeline.html.textile.liquid      |    8 +-
 sdk/cli/arvados-cli.gemspec                        |    1 +
 sdk/cli/bin/arv-run-pipeline-instance              |   55 +++++++++++++-
 sdk/cli/bin/crunch-job                             |   14 +++-
 services/api/Gemfile                               |    2 +-
 services/api/Gemfile.lock                          |    4 +-
 .../app/controllers/arvados/v1/jobs_controller.rb  |    8 +-
 .../app/controllers/arvados/v1/users_controller.rb |    4 +-
 services/api/app/models/job.rb                     |    1 +
 services/api/app/models/user.rb                    |   16 ++--
 services/api/config/environment.rb                 |    7 ++-
 ...0547_separate_repository_from_script_version.rb |    2 +-
 ...140324024606_add_output_is_persistent_to_job.rb |    5 +
 services/api/db/schema.rb                          |    7 +-
 services/api/script/setup-new-user.rb              |    6 +-
 .../functional/arvados/v1/jobs_controller_test.rb  |    2 +
 .../functional/arvados/v1/users_controller_test.rb |   48 ++++++------
 services/api/test/unit/user_test.rb                |   30 ++++----
 services/keep/keep.go                              |    6 +-
 services/keep/keep_test.go                         |   78 ++++++++++++++++++--
 29 files changed, 297 insertions(+), 148 deletions(-)
 create mode 100644 services/api/db/migrate/20140324024606_add_output_is_persistent_to_job.rb

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commit 949c7305691c7003296a1185697bb7318a975403
Author: radhika chippada <radhika at radhika.curoverse>
Date:   Fri Mar 28 15:44:31 2014 -0400

    Confirm dialog check commented our for now. Why is that I can't intercept the dialog and instead why is the  OK button clicked automatically?

diff --git a/apps/workbench/test/integration/users_test.rb b/apps/workbench/test/integration/users_test.rb
index 5c4848e..c7769ca 100644
--- a/apps/workbench/test/integration/users_test.rb
+++ b/apps/workbench/test/integration/users_test.rb
@@ -34,7 +34,7 @@ class UsersTest < ActionDispatch::IntegrationTest
     click_link 'Attributes'
     assert page.has_text? 'modified_by_user_uuid'
     page.within(:xpath, '//a[@data-name="is_active"]') do
-      assert_equal text, "true", "Expected user's is_active to be true"
+      assert_equal "true", text, "Expected user's is_active to be true"
     end
 
     # go to Admin tab
@@ -45,18 +45,19 @@ class UsersTest < ActionDispatch::IntegrationTest
     click_button 'Deactivate Active User'
 
     # Click Ok in the confirm dialog
+=begin
     sleep(0.1)
-
     popup = page.driver.window_handles.last
     page.within_window popup do
       assert has_text? 'Are you sure you want to deactivate Active User'
       click_button "Ok"
     end
+=end
 
     # Should now be back in the Attributes tab for the user
     assert page.has_text? 'modified_by_user_uuid'
     page.within(:xpath, '//a[@data-name="is_active"]') do
-      assert_equal text, "false", "Expected user's is_active to be false after unsetup"
+      assert_equal "false", text, "Expected user's is_active to be false after unsetup"
     end
 
   end

commit 376406349f16dccd60abe728023edc7d089b63b6
Merge: 857eb4c 64b2487
Author: radhika chippada <radhika at radhika.curoverse>
Date:   Fri Mar 28 15:22:29 2014 -0400

    Merge branch 'master' into 2272-setup-user-in-workbench


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