[ARVADOS] updated: a6809bec920bdfdfc03c726d0808e696824289f5

git at public.curoverse.com git at public.curoverse.com
Fri Sep 19 08:38:32 EDT 2014


Summary of changes:
 apps/workbench/Gemfile                             |   2 +-
 apps/workbench/Gemfile.lock                        |   4 +-
 .../views/pipeline_templates/_show_recent.html.erb |   2 +-
 .../app/views/pipeline_templates/show.html.erb     |   2 +-
 .../app/views/projects/_show_dashboard.html.erb    |   2 +-
 apps/workbench/config/application.default.yml      |  26 +++++
 apps/workbench/config/database.yml                 |   7 ++
 apps/workbench/test/diagnostics/pipeline_test.rb   |  93 ++++++++++++++++++
 apps/workbench/test/diagnostics_test_helper.rb     |  29 ++++++
 .../test/integration/application_layout_test.rb    |   3 +-
 apps/workbench/test/integration/jobs_test.rb       |   3 +-
 apps/workbench/test/integration/logins_test.rb     |   2 +-
 .../test/integration/pipeline_instances_test.rb    |   6 +-
 .../test/integration/pipeline_templates_test.rb    |   3 +-
 apps/workbench/test/integration/projects_test.rb   |  60 +++++++-----
 .../test/integration/user_profile_test.rb          |   5 +-
 apps/workbench/test/test_helper.rb                 |   7 +-
 doc/_includes/_example_sdk_go.liquid               | 109 +++++++++++++++++++++
 doc/_includes/_example_sdk_go_imports.liquid       |   4 +
 doc/sdk/go/index.html.textile.liquid               |  52 ++--------
 ...nning-pipeline-command-line.html.textile.liquid |  12 ++-
 sdk/cli/bin/arv-run-pipeline-instance              |  97 +++++++++++-------
 sdk/cli/bin/crunch-job                             |  13 +--
 services/api/Gemfile                               |   4 +-
 services/api/Gemfile.lock                          |   8 +-
 .../app/controllers/arvados/v1/jobs_controller.rb  |   5 +-
 .../controllers/arvados/v1/schema_controller.rb    |   1 +
 services/api/app/models/collection.rb              |   3 +
 services/api/app/models/node.rb                    |  16 +--
 services/api/config/application.default.yml        |   3 +
 ...140918141529_change_user_owner_uuid_not_null.rb |  10 ++
 .../20140918153541_add_properties_to_node.rb       |   9 ++
 services/api/db/structure.sql                      |  14 ++-
 services/api/lib/tasks/config_check.rake           |   4 +
 services/api/test/fixtures/collections.yml         |  26 +++++
 services/api/test/fixtures/users.yml               |   1 +
 .../arvados/v1/collections_controller_test.rb      |  57 +++++++++++
 .../functional/arvados/v1/jobs_controller_test.rb  |  28 +++++-
 .../functional/arvados/v1/nodes_controller_test.rb |   7 +-
 .../arvados/v1/schema_controller_test.rb           |   7 ++
 services/api/test/unit/node_test.rb                |   8 +-
 services/fuse/tests/test_mount.py                  |   1 +
 42 files changed, 587 insertions(+), 168 deletions(-)
 create mode 100644 apps/workbench/test/diagnostics/pipeline_test.rb
 create mode 100644 apps/workbench/test/diagnostics_test_helper.rb
 create mode 100644 doc/_includes/_example_sdk_go.liquid
 create mode 100644 doc/_includes/_example_sdk_go_imports.liquid
 create mode 100644 services/api/db/migrate/20140918141529_change_user_owner_uuid_not_null.rb
 create mode 100644 services/api/db/migrate/20140918153541_add_properties_to_node.rb

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commit a6809bec920bdfdfc03c726d0808e696824289f5
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Fri Sep 19 08:38:25 2014 -0400

    3605: Workbench tests pass!

diff --git a/apps/workbench/app/views/projects/_show_dashboard.html.erb b/apps/workbench/app/views/projects/_show_dashboard.html.erb
index e7e8736..a197059 100644
--- a/apps/workbench/app/views/projects/_show_dashboard.html.erb
+++ b/apps/workbench/app/views/projects/_show_dashboard.html.erb
@@ -33,7 +33,7 @@
                     <% completed = [] %>
                     <% queued = [] %>
                     <% p.components.each do |k, v| %>
-                      <% if v[:job] %>
+                      <% if v.is_a? Hash and v[:job] %>
                         <% if Job::state(v[:job]) == "Running" %>
                           <% running << k %>
                         <% elsif Job::state(v[:job]) == "Failed" or Job::state(v[:job]) == "Canceled" %>
diff --git a/apps/workbench/test/integration/application_layout_test.rb b/apps/workbench/test/integration/application_layout_test.rb
index 6ec535b..69e346d 100644
--- a/apps/workbench/test/integration/application_layout_test.rb
+++ b/apps/workbench/test/integration/application_layout_test.rb
@@ -21,7 +21,8 @@ class ApplicationLayoutTest < ActionDispatch::IntegrationTest
       if profile_config && !has_profile
         assert page.has_text?('Save profile'), 'No text - Save profile'
       else
-        assert page.has_text?('My projects'), 'Not found text - My projects'
+        assert page.has_link?("Projects"), 'Not found link - Projects'
+        page.find("#projects-menu").click
         assert page.has_text?('Projects shared with me'), 'Not found text - Project shared with me'
       end
     elsif invited
diff --git a/apps/workbench/test/integration/jobs_test.rb b/apps/workbench/test/integration/jobs_test.rb
index b5fc56a..50616de 100644
--- a/apps/workbench/test/integration/jobs_test.rb
+++ b/apps/workbench/test/integration/jobs_test.rb
@@ -23,7 +23,6 @@ class JobsTest < ActionDispatch::IntegrationTest
     assert page.has_text? 'Textile description for job'
     assert page.has_link? 'Go to dashboard'
     click_link 'Go to dashboard'
-    assert page.has_text? 'My projects'
-    assert page.has_text? 'Projects shared with me'
+    assert page.has_text? 'Active pipelines'
   end
 end
diff --git a/apps/workbench/test/integration/logins_test.rb b/apps/workbench/test/integration/logins_test.rb
index 0317f16..9d4e04b 100644
--- a/apps/workbench/test/integration/logins_test.rb
+++ b/apps/workbench/test/integration/logins_test.rb
@@ -7,7 +7,7 @@ class LoginsTest < ActionDispatch::IntegrationTest
 
   test "login with api_token works after redirect" do
     visit page_with_token('active_trustedclient')
-    assert page.has_text?('Recent jobs'), "Missing 'Recent jobs' from page"
+    assert page.has_text?('Active pipelines'), "Missing 'Active pipelines' from page"
     assert_no_match(/\bapi_token=/, current_path)
   end
 
diff --git a/apps/workbench/test/integration/pipeline_instances_test.rb b/apps/workbench/test/integration/pipeline_instances_test.rb
index 0be483a..33e581a 100644
--- a/apps/workbench/test/integration/pipeline_instances_test.rb
+++ b/apps/workbench/test/integration/pipeline_instances_test.rb
@@ -38,7 +38,8 @@ class PipelineInstancesTest < ActionDispatch::IntegrationTest
 
     # Add this collection to the project
     visit '/projects'
-    find('.arv-project-list a,button', text: 'A Project').click
+    find("#projects-menu").click
+    find('.dropdown-menu a,button', text: 'A Project').click
     find('.btn', text: 'Add data').click
     within('.modal-dialog') do
       wait_for_ajax
@@ -100,7 +101,8 @@ class PipelineInstancesTest < ActionDispatch::IntegrationTest
 
     # Add this collection to the project using collections menu from top nav
     visit '/projects'
-    find('.arv-project-list a,button', text: 'A Project').click
+    find("#projects-menu").click
+    find('.dropdown-menu a,button', text: 'A Project').click
     find('.btn', text: 'Add data').click
     within('.modal-dialog') do
       wait_for_ajax
diff --git a/apps/workbench/test/integration/pipeline_templates_test.rb b/apps/workbench/test/integration/pipeline_templates_test.rb
index 56d6f4a..b909ac0 100644
--- a/apps/workbench/test/integration/pipeline_templates_test.rb
+++ b/apps/workbench/test/integration/pipeline_templates_test.rb
@@ -35,8 +35,7 @@ class PipelineTemplatesTest < ActionDispatch::IntegrationTest
     assert page.has_text? 'Textile description for pipeline template'
     assert page.has_link? 'Go to dashboard'
     click_link 'Go to dashboard'
-    assert page.has_text? 'My projects'
-    assert page.has_text? 'Projects shared with me'
+    assert page.has_text? 'Active pipelines'
 
     # again visit recent templates page and verify edited description
     visit page_with_token("active", "/pipeline_templates")
diff --git a/apps/workbench/test/integration/projects_test.rb b/apps/workbench/test/integration/projects_test.rb
index 3b7f7a4..7c5f9a6 100644
--- a/apps/workbench/test/integration/projects_test.rb
+++ b/apps/workbench/test/integration/projects_test.rb
@@ -9,8 +9,8 @@ class ProjectsTest < ActionDispatch::IntegrationTest
 
   test 'Find a project and edit its description' do
     visit page_with_token 'active', '/'
-    find('.arv-project-list a,button', text: 'A Project').
-      click
+    find("#projects-menu").click
+    find(".dropdown-menu a", text: "A Project").click
     within('.container-fluid', text: api_fixture('groups')['aproject']['name']) do
       find('span', text: api_fixture('groups')['aproject']['name']).click
       within('.arv-description-as-subtitle') do
@@ -27,8 +27,8 @@ class ProjectsTest < ActionDispatch::IntegrationTest
 
   test 'Find a project and edit description to textile description' do
     visit page_with_token 'active', '/'
-    find('.arv-project-list a,button', text: 'A Project').
-      click
+    find("#projects-menu").click
+    find(".dropdown-menu a", text: "A Project").click
     within('.container-fluid', text: api_fixture('groups')['aproject']['name']) do
       find('span', text: api_fixture('groups')['aproject']['name']).click
       within('.arv-description-as-subtitle') do
@@ -52,17 +52,13 @@ class ProjectsTest < ActionDispatch::IntegrationTest
     click_link 'take me home'
 
     # now in dashboard
-    assert(page.has_text?('My projects'), 'My projects - not found on dashboard')
-    assert(page.has_text?('Projects shared with me'), 'Projects shared with me - not found on dashboard')
-    assert(page.has_text?('Textile description for A project'), "Project description not found")
-    assert(page.has_no_text?('*Textile description for A project*'), "Project description is not rendered properly in dashboard")
-    assert(page.has_no_text?('And a new paragraph in description'), "Project description is not truncated after first paragraph")
+    assert(page.has_text?('Active pipelines'), 'Active pipelines - not found on dashboard')
   end
 
   test 'Find a project and edit description to html description' do
     visit page_with_token 'active', '/'
-    find('.arv-project-list a,button', text: 'A Project').
-      click
+    find("#projects-menu").click
+    find(".dropdown-menu a", text: "A Project").click
     within('.container-fluid', text: api_fixture('groups')['aproject']['name']) do
       find('span', text: api_fixture('groups')['aproject']['name']).click
       within('.arv-description-as-subtitle') do
@@ -79,14 +75,13 @@ class ProjectsTest < ActionDispatch::IntegrationTest
            "Textile description is displayed with uninterpreted formatting characters")
     assert(page.has_link?("take me home"),"link not found in description")
     click_link 'take me home'
-    assert page.has_text?('My projects')
-    assert page.has_text?('Projects shared with me')
+    assert page.has_text?('Active pipelines')
   end
 
   test 'Find a project and edit description to textile description with link to object' do
     visit page_with_token 'active', '/'
-    find('.arv-project-list a,button', text: 'A Project').
-      click
+    find("#projects-menu").click
+    find(".dropdown-menu a", text: "A Project").click
     within('.container-fluid', text: api_fixture('groups')['aproject']['name']) do
       find('span', text: api_fixture('groups')['aproject']['name']).click
       within('.arv-description-as-subtitle') do
@@ -136,7 +131,9 @@ class ProjectsTest < ActionDispatch::IntegrationTest
 
   test 'Create a project and move it into a different project' do
     visit page_with_token 'active', '/projects'
-    find('.btn', text: "Add new project").click
+    find("#projects-menu").click
+    find(".dropdown-menu a", text: "Home").click
+    find('.btn', text: "Add a subproject").click
 
     # within('.editable', text: 'New project') do
     within('h2') do
@@ -147,7 +144,9 @@ class ProjectsTest < ActionDispatch::IntegrationTest
     wait_for_ajax
 
     visit '/projects'
-    find('.btn', text: "Add new project").click
+    find("#projects-menu").click
+    find(".dropdown-menu a", text: "Home").click
+    find('.btn', text: "Add a subproject").click
     within('h2') do
       find('.fa-pencil').click
       find('.editable-input input').set('Project 5678')
@@ -275,7 +274,8 @@ class ProjectsTest < ActionDispatch::IntegrationTest
       when 'Copy'
         assert page.has_text?(my_collection['name']), 'Collection not found in src project after copy'
         visit page_with_token 'active', '/'
-        find('.arv-project-list a,button', text: dest['name']).click
+        find("#projects-menu").click
+        find(".dropdown-menu a", text: dest['name']).click
         assert page.has_text?(my_collection['name']), 'Collection not found in dest project after copy'
 
         # now remove it from destination project to restore to original state
@@ -283,7 +283,8 @@ class ProjectsTest < ActionDispatch::IntegrationTest
       when 'Move'
         assert page.has_no_text?(my_collection['name']), 'Collection still found in src project after move'
         visit page_with_token 'active', '/'
-        find('.arv-project-list a,button', text: dest['name']).click
+        find("#projects-menu").click
+        find(".dropdown-menu a", text: dest['name']).click
         assert page.has_text?(my_collection['name']), 'Collection not found in dest project after move'
 
         # move it back to src project to restore to original state
@@ -291,7 +292,8 @@ class ProjectsTest < ActionDispatch::IntegrationTest
       when 'Remove'
         assert page.has_no_text?(my_collection['name']), 'Collection still found in src project after remove'
         visit page_with_token 'active', '/'
-        find('.arv-project-list a,button', text: 'Home').click
+        find("#projects-menu").click
+        find(".dropdown-menu a", text: "Home").click
         assert page.has_text?(my_collection['name']), 'Collection not found in home project after remove'
       end
     end
@@ -299,7 +301,8 @@ class ProjectsTest < ActionDispatch::IntegrationTest
 
   def perform_selection_action src, dest, item, action
     visit page_with_token 'active', '/'
-    find('.arv-project-list a,button', text: src['name']).click
+    find("#projects-menu").click
+    find(".dropdown-menu a", text: src['name']).click
     assert page.has_text?(item['name']), 'Collection not found in src project'
 
     within('tr', text: item['name']) do
@@ -335,7 +338,8 @@ class ProjectsTest < ActionDispatch::IntegrationTest
 
     # verify that selection options are disabled on the project until an item is selected
     visit page_with_token 'active', '/'
-    find('.arv-project-list a,button', text: my_project['name']).click
+    find("#projects-menu").click
+    find(".dropdown-menu a", text: my_project['name']).click
 
     click_button 'Selection...'
     within('.selection-action-container') do
@@ -348,7 +352,8 @@ class ProjectsTest < ActionDispatch::IntegrationTest
 
     # select collection and verify links are enabled
     visit page_with_token 'active', '/'
-    find('.arv-project-list a,button', text: my_project['name']).click
+    find("#projects-menu").click
+    find(".dropdown-menu a", text: my_project['name']).click
     assert page.has_text?(my_collection['name']), 'Collection not found in project'
 
     within('tr', text: my_collection['name']) do
@@ -370,7 +375,8 @@ class ProjectsTest < ActionDispatch::IntegrationTest
 
     # select subproject and verify that copy action is disabled
     visit page_with_token 'active', '/'
-    find('.arv-project-list a,button', text: my_project['name']).click
+    find("#projects-menu").click
+    find(".dropdown-menu a", text: my_project['name']).click
 
     click_link 'Subprojects'
     assert page.has_text?(my_subproject['name']), 'Subproject not found in project'
@@ -392,7 +398,8 @@ class ProjectsTest < ActionDispatch::IntegrationTest
 
     # select subproject and a collection and verify that copy action is still disabled
     visit page_with_token 'active', '/'
-    find('.arv-project-list a,button', text: my_project['name']).click
+    find("#projects-menu").click
+    find(".dropdown-menu a", text: my_project['name']).click
 
     click_link 'Subprojects'
     assert page.has_text?(my_subproject['name']), 'Subproject not found in project'
@@ -425,7 +432,8 @@ class ProjectsTest < ActionDispatch::IntegrationTest
     my_collection = api_fixture('collections')['collection_to_move_around_in_aproject']
 
     visit page_with_token 'active', '/'
-    find('.arv-project-list a,button', text: my_project['name']).click
+    find("#projects-menu").click
+    find(".dropdown-menu a", text: my_project['name']).click
     assert page.has_text?(my_collection['name']), 'Collection not found in project'
 
     within('tr', text: my_collection['name']) do
diff --git a/apps/workbench/test/integration/user_profile_test.rb b/apps/workbench/test/integration/user_profile_test.rb
index ede67ff..6dbb90c 100644
--- a/apps/workbench/test/integration/user_profile_test.rb
+++ b/apps/workbench/test/integration/user_profile_test.rb
@@ -25,7 +25,7 @@ class UserProfileTest < ActionDispatch::IntegrationTest
         assert page.has_text?('Save profile'), 'No text - Save profile'
         add_profile user
       else
-        assert page.has_text?('My projects'), 'Not found text - My projects'
+        assert page.has_text?('Active pipelines'), 'Not found text - Active pipelines'
         assert page.has_no_text?('Save profile'), 'Found text - Save profile'
       end
     elsif invited
@@ -106,8 +106,7 @@ class UserProfileTest < ActionDispatch::IntegrationTest
     click_link 'Back to work!'
 
     # profile saved and in home page now
-    assert page.has_text?('My projects'), 'No text - My projects'
-    assert page.has_text?('Projects shared with me'), 'No text - Projects shared with me'
+    assert page.has_text?('Active pipelines'), 'No text - My projects'
   end
 
   [

commit b522f728ae1674c9b9bcee189885d919e91acccf
Merge: 5a3b04f 403d9f6
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Sep 18 13:51:13 2014 -0400

    Merge branch 'master' into 3605-improved-dashboard
    
    Conflicts:
    	services/api/app/controllers/arvados/v1/jobs_controller.rb

diff --cc services/api/app/controllers/arvados/v1/jobs_controller.rb
index 5a571d4,7b3b658..d8ceb85
--- a/services/api/app/controllers/arvados/v1/jobs_controller.rb
+++ b/services/api/app/controllers/arvados/v1/jobs_controller.rb
@@@ -163,7 -163,9 +163,10 @@@ class Arvados::V1::JobsController < App
    end
  
    def queue_size
-           render :json => {:queue_size => Job.queue.size}
+     # Users may not be allowed to see all the jobs in the queue, so provide a
 -    # method to get the actual queue length.
++    # method to get just the queue size in order to get a gist of how busy the
++    # cluster is.
+     render :json => {:queue_size => Job.queue.size}
    end
  
    def self._create_requires_parameters

commit 5a3b04f7177afe202ab4f8776b5ca2567b4fdabe
Merge: c51634c a9f3e9c
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Sep 18 09:30:27 2014 -0400

    Merge remote-tracking branch 'origin/master' into 3605-improved-dashboard


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