[ARVADOS] updated: fcfc87e95a90cbf869d4a66b5e3e87663ad03fe5
git at public.curoverse.com
git at public.curoverse.com
Fri Apr 4 10:55:53 EDT 2014
Summary of changes:
.gitignore | 7 +-
apps/workbench/Gemfile | 3 +-
apps/workbench/Gemfile.lock | 4 +
apps/workbench/app/controllers/users_controller.rb | 2 +-
apps/workbench/app/models/arvados_api_client.rb | 2 +-
.../config/initializers/arvados_api_client.rb | 1 -
.../{zz_load_config.rb => zza_load_config.rb} | 3 +
.../config/initializers/zzz_arvados_api_client.rb | 8 +
apps/workbench/test/integration/users_test.rb | 8 +-
doc/.gitignore | 1 -
doc/README.textile | 21 ++-
doc/Rakefile | 31 ++-
doc/api/permission-model.html.textile.liquid | 20 ++-
.../pipeline_templates/gatk-exome-fq-snp.json | 9 +-
doc/install/client.html.textile.liquid | 14 ++
.../getting_started/ssh-access.html.textile.liquid | 82 ++++----
doc/user/index.html.textile.liquid | 24 +-
doc/user/reference/api-tokens.html.textile.liquid | 25 +--
.../job-and-pipeline-reference.html.textile.liquid | 64 +++---
doc/user/topics/keep.html.textile.liquid | 8 +-
...nning-pipeline-command-line.html.textile.liquid | 42 ++--
.../topics/tutorial-job-debug.html.textile.liquid | 26 ++-
doc/user/topics/tutorial-job1.html.textile.liquid | 117 ++++++-----
.../topics/tutorial-parallel.html.textile.liquid | 10 +-
.../running-external-program.html.textile.liquid | 12 +-
.../tutorial-firstscript.html.textile.liquid | 38 ++--
.../tutorials/tutorial-keep.html.textile.liquid | 30 ++--
.../tutorial-new-pipeline.html.textile.liquid | 14 +-
...tutorial-pipeline-workbench.html.textile.liquid | 25 +--
docker/.gitignore | 2 +-
docker/api/Dockerfile | 6 +-
docker/api/production.rb.in | 2 +-
docker/arvdock | 4 +-
docker/base/Dockerfile | 19 +-
docker/build.sh | 44 +----
docker/{ => build_tools}/Makefile | 56 +++--
docker/build_tools/build.rb | 221 ++++++++++++++++++++
docker/{ => build_tools}/config.rb | 40 ++--
docker/doc/Dockerfile | 3 +-
docker/docker_build | 18 --
docker/install_sdk.sh | 13 ++
docker/workbench/Dockerfile | 15 +-
sdk/cli/bin/crunch-job | 140 +++++--------
sdk/perl/Makefile.PL | 10 +
.../api/app/controllers/application_controller.rb | 13 +-
services/api/app/models/arvados_model.rb | 9 +-
services/api/app/models/user.rb | 16 ++-
.../db/migrate/20140402001908_add_system_group.rb | 18 ++
services/api/db/schema.rb | 2 +-
services/api/db/seeds.rb | 14 +-
services/api/lib/current_api_client.rb | 29 +++
.../test/fixtures/api_client_authorizations.yml | 12 +
services/api/test/fixtures/groups.yml | 11 +
services/api/test/fixtures/links.yml | 80 +++++++
services/api/test/fixtures/specimens.yml | 11 +
services/api/test/fixtures/users.yml | 20 ++
.../arvados/v1/collections_controller_test.rb | 22 ++
.../functional/arvados/v1/jobs_controller_test.rb | 3 +-
.../functional/arvados/v1/users_controller_test.rb | 62 ++++--
services/api/test/integration/permissions_test.rb | 144 +++++++++----
60 files changed, 1137 insertions(+), 573 deletions(-)
delete mode 100644 apps/workbench/config/initializers/arvados_api_client.rb
rename apps/workbench/config/initializers/{zz_load_config.rb => zza_load_config.rb} (90%)
create mode 100644 apps/workbench/config/initializers/zzz_arvados_api_client.rb
delete mode 100644 doc/.gitignore
mode change 100644 => 100755 docker/build.sh
rename docker/{ => build_tools}/Makefile (79%)
create mode 100755 docker/build_tools/build.rb
rename docker/{ => build_tools}/config.rb (72%)
delete mode 100755 docker/docker_build
create mode 100755 docker/install_sdk.sh
create mode 100644 sdk/perl/Makefile.PL
create mode 100644 services/api/db/migrate/20140402001908_add_system_group.rb
create mode 100644 services/api/test/fixtures/specimens.yml
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commit fcfc87e95a90cbf869d4a66b5e3e87663ad03fe5
Merge: 2802e40 2c7e73f
Author: radhika chippada <radhika at radhika.curoverse>
Date: Fri Apr 4 10:47:05 2014 -0400
Merge branch 'master' into 2272-setup-user-in-workbench
commit 2802e403b8f07c023fae024fcac90a1272bbd4fe
Author: radhika chippada <radhika at radhika.curoverse>
Date: Fri Apr 4 10:45:14 2014 -0400
Use webkit driver for Capybara instead of selenium for tests that need dialog handling.
diff --git a/apps/workbench/Gemfile b/apps/workbench/Gemfile
index b273d91..1e43d1c 100644
--- a/apps/workbench/Gemfile
+++ b/apps/workbench/Gemfile
@@ -28,6 +28,7 @@ group :test do
gem 'selenium-webdriver'
gem 'capybara'
gem 'poltergeist'
+ gem 'capybara-webkit'
end
gem 'jquery-rails'
@@ -59,4 +60,4 @@ gem 'RedCloth'
gem 'piwik_analytics'
gem 'httpclient'
gem 'themes_for_rails'
-gem "deep_merge", :require => 'deep_merge/rails_compat'
\ No newline at end of file
+gem "deep_merge", :require => 'deep_merge/rails_compat'
diff --git a/apps/workbench/Gemfile.lock b/apps/workbench/Gemfile.lock
index 0c65ca8..0795f75 100644
--- a/apps/workbench/Gemfile.lock
+++ b/apps/workbench/Gemfile.lock
@@ -48,6 +48,9 @@ GEM
rack (>= 1.0.0)
rack-test (>= 0.5.4)
xpath (~> 2.0)
+ capybara-webkit (1.1.0)
+ capybara (~> 2.0, >= 2.0.2)
+ json
childprocess (0.5.1)
ffi (~> 1.0, >= 1.0.11)
cliver (0.3.2)
@@ -182,6 +185,7 @@ DEPENDENCIES
bootstrap-sass (~> 3.1.0)
bootstrap-x-editable-rails
capybara
+ capybara-webkit
coffee-rails (~> 3.2.0)
deep_merge
httpclient
diff --git a/apps/workbench/test/integration/users_test.rb b/apps/workbench/test/integration/users_test.rb
index 7555e3a..2472ec8 100644
--- a/apps/workbench/test/integration/users_test.rb
+++ b/apps/workbench/test/integration/users_test.rb
@@ -1,5 +1,4 @@
require 'integration_helper'
-require "selenium-webdriver"
class UsersTest < ActionDispatch::IntegrationTest
test "login as active user but not admin" do
@@ -39,7 +38,7 @@ class UsersTest < ActionDispatch::IntegrationTest
end
test "create a new user" do
- Capybara.current_driver = :selenium
+ Capybara.current_driver = :webkit
visit page_with_token('admin_trustedclient')
click_link 'Users'
@@ -81,7 +80,7 @@ class UsersTest < ActionDispatch::IntegrationTest
end
test "setup the active user" do
- Capybara.current_driver = :selenium
+ Capybara.current_driver = :webkit
visit page_with_token('admin_trustedclient')
click_link 'Users'
@@ -133,7 +132,7 @@ class UsersTest < ActionDispatch::IntegrationTest
end
test "unsetup active user" do
- Capybara.current_driver = :selenium
+ Capybara.current_driver = :webkit
visit page_with_token('admin_trustedclient')
@@ -158,7 +157,6 @@ class UsersTest < ActionDispatch::IntegrationTest
# unsetup user and verify all the above links are deleted
click_link 'Admin'
click_button 'Deactivate Active User'
- page.driver.browser.switch_to.alert.accept
sleep(0.1)
# Should now be back in the Attributes tab for the user
commit 771a7b4e46f0f8369feea88570c944794978563f
Merge: 203958b 39717c4
Author: radhika chippada <radhika at radhika.curoverse>
Date: Thu Apr 3 22:44:18 2014 -0400
Merge branch 'master' into 2272-setup-user-in-workbench
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