[ARVADOS] updated: 5a3d5ac75e3058698bad452bbd980a1e3cb9be2d
git at public.curoverse.com
git at public.curoverse.com
Tue Aug 12 16:00:29 EDT 2014
Summary of changes:
.../app/assets/javascripts/infinite_scroll.js | 3 +-
.../app/controllers/application_controller.rb | 30 ++++-
.../app/controllers/projects_controller.rb | 82 +++++++++---
.../app/views/application/_content.html.erb | 3 +-
.../app/views/application/_content_layout.html.erb | 15 +--
.../views/application/_tab_line_buttons.html.erb | 0
apps/workbench/app/views/application/show.html.erb | 1 -
.../app/views/collections/_show_files.html.erb | 5 -
.../app/views/collections/_show_recent.html.erb | 13 --
.../workbench/app/views/collections/index.html.erb | 14 ++
apps/workbench/app/views/collections/show.html.erb | 7 +-
.../app/views/keep_disks/_content_layout.html.erb | 4 +-
apps/workbench/app/views/layouts/body.html.erb | 2 +-
.../views/pipeline_instances/_show_recent.html.erb | 7 -
.../app/views/pipeline_instances/index.html.erb | 8 ++
.../pipeline_templates/_show_components.html.erb | 17 ---
.../{_show_components.html.erb => show.html.erb} | 2 +-
.../views/projects/_show_contents_rows.html.erb | 11 +-
.../views/projects/_show_data_collections.html.erb | 72 +----------
.../projects/_show_jobs_and_pipelines.html.erb | 11 +-
.../views/projects/_show_other_objects.html.erb | 11 +-
.../projects/_show_pipeline_templates.html.erb | 11 +-
.../app/views/projects/_show_sharing.html.erb | 10 +-
.../app/views/projects/_show_subprojects.html.erb | 11 +-
.../app/views/projects/_show_tab_contents.html.erb | 10 +-
...how_data_collections.html.erb => show.html.erb} | 9 +-
.../test/functional/projects_controller_test.rb | 72 ++++++++++-
.../test/integration/application_layout_test.rb | 51 ++------
apps/workbench/test/integration/projects_test.rb | 12 +-
apps/workbench/test/test_helper.rb | 3 +
crunch_scripts/collection-merge | 39 ++----
crunch_scripts/decompress-all.py | 62 +++++++++
crunch_scripts/run-command | 143 +++++++++++++++++----
crunch_scripts/split-fastq.py | 128 ++++++++++++++++++
crunch_scripts/subst.py | 6 +-
docker/jobs/Dockerfile | 4 +-
sdk/cli/bin/arv | 8 +-
sdk/cli/bin/arv-run-pipeline-instance | 14 +-
sdk/ruby/lib/arvados.rb | 20 ++-
.../app/controllers/arvados/v1/jobs_controller.rb | 18 +++
.../arvados/v1/repositories_controller.rb | 10 +-
.../controllers/arvados/v1/schema_controller.rb | 57 ++++----
.../app/controllers/arvados/v1/users_controller.rb | 16 ++-
services/api/app/models/job.rb | 2 +-
services/api/test/fixtures/jobs.yml | 11 ++
services/api/test/fixtures/pipeline_instances.yml | 5 +
46 files changed, 690 insertions(+), 360 deletions(-)
copy services/fuse/tests/__init__.py => apps/workbench/app/views/application/_tab_line_buttons.html.erb (100%)
create mode 100644 apps/workbench/app/views/collections/index.html.erb
create mode 100644 apps/workbench/app/views/pipeline_instances/index.html.erb
copy apps/workbench/app/views/pipeline_templates/{_show_components.html.erb => show.html.erb} (93%)
copy apps/workbench/app/views/projects/{_show_data_collections.html.erb => show.html.erb} (86%)
create mode 100755 crunch_scripts/decompress-all.py
create mode 100755 crunch_scripts/split-fastq.py
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commit 5a3d5ac75e3058698bad452bbd980a1e3cb9be2d
Author: radhika <radhika at curoverse.com>
Date: Tue Aug 12 15:49:21 2014 -0400
3296: fix tests
diff --git a/apps/workbench/app/views/layouts/body.html.erb b/apps/workbench/app/views/layouts/body.html.erb
index 9282acd..4c58dab 100644
--- a/apps/workbench/app/views/layouts/body.html.erb
+++ b/apps/workbench/app/views/layouts/body.html.erb
@@ -49,7 +49,7 @@
<% if current_user.is_active %>
<li role="presentation"><a href="/manage_account" role="menuitem"><i class="fa fa-key fa-fw"></i> Manage account</a></li>
<% if Rails.configuration.user_profile_form_fields %>
- <li role="presentation"><a href="/users/<%=current_user.uuid%>/profile" role="menuitem"><i class="fa fa-key fa-fw"></i> Manage my profile</a></li>
+ <li role="presentation"><a href="/users/<%=current_user.uuid%>/profile" role="menuitem"><i class="fa fa-key fa-fw"></i> Manage profile</a></li>
<% end %>
<li role="presentation" class="divider"></li>
<% end %>
diff --git a/apps/workbench/test/integration/application_layout_test.rb b/apps/workbench/test/integration/application_layout_test.rb
index f231e4d..64eb2b2 100644
--- a/apps/workbench/test/integration/application_layout_test.rb
+++ b/apps/workbench/test/integration/application_layout_test.rb
@@ -45,19 +45,19 @@ class ApplicationLayoutTest < ActionDispatch::IntegrationTest
assert page.has_link? "#{user['email']}"
find('a', text: "#{user['email']}").click
within('.dropdown-menu') do
- if !invited
- page.has_no_link? ('Not active')
- else
- page.has_no_link? ('Sign agreements')
- page.has_link? ('Manage account')
+ if user['is_active']
+ assert page.has_no_link? ('Not active')
+ assert page.has_no_link? ('Sign agreements')
+
+ assert page.has_link? ('Manage account')
if profile_config
- page.has_link? ('Manage profile')
+ assert page.has_link? ('Manage profile')
else
- page.has_no_link? ('Manage profile')
+ assert page.has_no_link? ('Manage profile')
end
end
- page.has_link? ('Log out')
+ assert page.has_link? ('Log out')
end
end
end
@@ -261,7 +261,7 @@ class ApplicationLayoutTest < ActionDispatch::IntegrationTest
['active_no_prefs', api_fixture('users')['active_no_prefs'], true, false],
['active_no_prefs_profile', api_fixture('users')['active_no_prefs_profile'], true, false],
].each do |token, user, invited, has_profile|
- test "visit home page when profile is configured for user #{token}" do
+ test "visit home page when profile is configured for user #{token}" do
# Our test config enabled profile by default. So, no need to update config
if !token
visit ('/')
@@ -271,17 +271,7 @@ class ApplicationLayoutTest < ActionDispatch::IntegrationTest
verify_homepage_with_profile user, invited, has_profile
end
- end
- [
- [nil, nil, false, false],
- ['inactive', api_fixture('users')['inactive'], true, false],
- ['inactive_uninvited', api_fixture('users')['inactive_uninvited'], false, false],
- ['active', api_fixture('users')['active'], true, true],
- ['admin', api_fixture('users')['admin'], true, true],
- ['active_no_prefs', api_fixture('users')['active_no_prefs'], true, false],
- ['active_no_prefs_profile', api_fixture('users')['active_no_prefs_profile'], true, false],
- ].each do |token, user, invited, has_profile|
test "visit home page when profile not configured for user #{token}" do
Rails.configuration.user_profile_form_fields = false
@@ -293,20 +283,8 @@ class ApplicationLayoutTest < ActionDispatch::IntegrationTest
verify_homepage_with_profile user, invited, has_profile
end
- end
- [
- [nil, nil, false, false],
- ['inactive', api_fixture('users')['inactive'], true, false],
- ['inactive_uninvited', api_fixture('users')['inactive_uninvited'], false, false],
- ['active', api_fixture('users')['active'], true, true],
- ['admin', api_fixture('users')['admin'], true, true],
- ['active_no_prefs', api_fixture('users')['active_no_prefs'], true, false],
- ['active_no_prefs_profile', api_fixture('users')['active_no_prefs_profile'], true, false],
- ].each do |token, user, invited, has_profile|
test "check help for user #{token}" do
- Rails.configuration.user_profile_form_fields = false
-
if !token
visit ('/')
else
@@ -325,26 +303,15 @@ class ApplicationLayoutTest < ActionDispatch::IntegrationTest
visit page_with_token(token)
verify_system_menu user
end
- end
- [
- ['active', api_fixture('users')['active'], true, true],
- ['admin', api_fixture('users')['admin'], true, true],
- ].each do |token, user|
test "test manage account for user #{token}" do
visit page_with_token(token)
verify_manage_account user
end
- end
- [
- ['active', api_fixture('users')['active'], true, true],
- ['admin', api_fixture('users')['admin'], true, true],
- ].each do |token, user|
test "test search for user #{token}" do
visit page_with_token(token)
verify_search_box user
end
end
-
end
commit 32af86f5f4a2849b12c96e40ed20d33b7682ba55
Merge: 19e913d 71ed41b
Author: radhika <radhika at curoverse.com>
Date: Tue Aug 12 15:10:46 2014 -0400
Merge branch 'master' into 3296-user-profile
commit 19e913d3b754429be49c38505c249b7b2151a70f
Merge: 30a74a0 57ee969
Author: radhika <radhika at curoverse.com>
Date: Tue Aug 12 10:20:55 2014 -0400
Merge branch 'master' into 3296-user-profile
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