[ARVADOS] updated: 9fbb2bbd4e2a0f1d15e1db3f3d606cdedae825a7
git at public.curoverse.com
git at public.curoverse.com
Wed Jul 8 01:37:19 EDT 2015
Summary of changes:
.../app/assets/javascripts/select_modal.js | 5 +-
apps/workbench/app/assets/javascripts/users.js | 2 +-
.../app/controllers/actions_controller.rb | 3 +-
.../app/controllers/projects_controller.rb | 20 +-
apps/workbench/app/controllers/users_controller.rb | 9 +-
.../app/views/application/_show_recent.html.erb | 16 +-
apps/workbench/app/views/layouts/body.html.erb | 4 +-
.../app/views/users/_setup_popup.html.erb | 7 +-
.../workbench/app/views/users/_show_admin.html.erb | 8 +-
apps/workbench/config/application.default.yml | 3 +
.../test/controllers/projects_controller_test.rb | 26 +++
apps/workbench/test/integration/search_box_test.rb | 13 +-
apps/workbench/test/integration/users_test.rb | 68 +++---
crunch_scripts/run-command | 9 +-
doc/_includes/_install_debian_key.liquid | 4 +
doc/_includes/_install_redhat_key.liquid | 6 +
doc/_includes/_note_python27_sc.liquid | 5 +
doc/install/install-api-server.html.textile.liquid | 255 +++++++++++++--------
.../install-arv-git-httpd.html.textile.liquid | 20 +-
.../install-compute-node.html.textile.liquid | 44 ++--
.../install-crunch-dispatch.html.textile.liquid | 34 +--
doc/install/install-keepproxy.html.textile.liquid | 18 +-
doc/install/install-keepstore.html.textile.liquid | 19 +-
...nstall-manual-prerequisites.html.textile.liquid | 52 ++++-
.../install-shell-server.html.textile.liquid | 38 ++-
.../install-workbench-app.html.textile.liquid | 165 ++++++++-----
doc/sdk/perl/index.html.textile.liquid | 40 +++-
doc/sdk/python/sdk-python.html.textile.liquid | 61 +++--
doc/user/topics/run-command.html.textile.liquid | 13 ++
docker/api/Dockerfile | 4 +-
docker/api/update-gitolite.rb | 11 +-
docker/base/Dockerfile | 14 +-
docker/compute/Dockerfile | 6 +-
docker/doc/Dockerfile | 4 +-
docker/java-bwa-samtools/Dockerfile | 4 +-
docker/keepproxy/Dockerfile | 4 +-
docker/passenger/Dockerfile | 4 +-
docker/postgresql/Dockerfile | 2 +-
docker/shell/Dockerfile | 4 +-
docker/slurm/Dockerfile | 4 +-
docker/workbench/Dockerfile | 4 +-
sdk/cli/bin/crunch-job | 4 +-
sdk/python/arvados/api.py | 6 +-
sdk/python/arvados/commands/put.py | 5 +-
sdk/python/arvados/events.py | 6 +-
sdk/python/arvados/util.py | 18 ++
sdk/python/tests/test_arv_put.py | 14 ++
services/api/Rakefile | 31 +++
.../app/controllers/user_sessions_controller.rb | 2 +-
services/api/app/mailers/user_notifier.rb | 2 +-
.../api/app/views/static/login_failure.html.erb | 2 +-
.../views/user_notifier/account_is_setup.text.erb | 7 +-
services/api/config/initializers/load_config.rb | 22 +-
services/api/config/initializers/omniauth_init.rb | 18 +-
services/api/db/structure.sql | 2 +-
.../functional/arvados/v1/users_controller_test.rb | 8 +-
services/api/test/unit/user_notifier_test.rb | 8 +-
57 files changed, 779 insertions(+), 408 deletions(-)
create mode 100644 doc/_includes/_install_debian_key.liquid
create mode 100644 doc/_includes/_install_redhat_key.liquid
create mode 100644 doc/_includes/_note_python27_sc.liquid
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commit 9fbb2bbd4e2a0f1d15e1db3f3d606cdedae825a7
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Jul 8 01:12:58 2015 -0400
6377: Fix crash if no asset pipeline.
diff --git a/services/api/app/views/static/login_failure.html.erb b/services/api/app/views/static/login_failure.html.erb
index 830942c..35f4f10 100644
--- a/services/api/app/views/static/login_failure.html.erb
+++ b/services/api/app/views/static/login_failure.html.erb
@@ -6,7 +6,7 @@ $(function(){
<div id="intropage">
- <img class="curoverse-logo" src="<%= asset_path('logo.png') %>" style="display:block; margin:2em auto"/>
+ <img class="curoverse-logo" src="<%= asset_path('logo.png') rescue '/logo.png' %>" style="display:block; margin:2em auto"/>
<div style="width:30em; margin:2em auto 0 auto">
<h1>Error</h1>
commit e56ea5c6c9244d2baaef9a24efc5eaad5bdf290c
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Jul 7 16:45:16 2015 -0400
6377: Update ruby to 2.1.6. Remove bundler version pin (not needed since ca1d997).
diff --git a/doc/install/install-manual-prerequisites-ruby.html.textile.liquid b/doc/install/install-manual-prerequisites-ruby.html.textile.liquid
index a4f71ba..2142aca 100644
--- a/doc/install/install-manual-prerequisites-ruby.html.textile.liquid
+++ b/doc/install/install-manual-prerequisites-ruby.html.textile.liquid
@@ -4,14 +4,14 @@ navsection: installguide
title: Install Ruby and bundler
...
-We recommend Ruby >= 2.1. We currently require Bundler 1.9 (not 1.10 or above) because of a limitation in some of our gem dependencies.
+Currently, only Ruby 2.1 is supported.
h2(#rvm). Option 1: Install with rvm
<notextile>
<pre><code>~$ <span class="userinput">gpg --keyserver hkp://keys.gnupg.net --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3</span>
~$ <span class="userinput">\curl -sSL https://get.rvm.io | bash -s stable --ruby=2.1</span>
-~$ <span class="userinput">gem install -v 1.9.9 bundler
+~$ <span class="userinput">gem install bundler
</span></code></pre></notextile>
h2(#fromsource). Option 2: Install from source
@@ -19,12 +19,12 @@ h2(#fromsource). Option 2: Install from source
<notextile>
<pre><code><span class="userinput">mkdir -p ~/src
cd ~/src
-wget http://cache.ruby-lang.org/pub/ruby/2.1/ruby-2.1.5.tar.gz
-tar xzf ruby-2.1.5.tar.gz
-cd ruby-2.1.5
-./configure
+wget http://cache.ruby-lang.org/pub/ruby/2.1/ruby-2.1.6.tar.gz
+tar xzf ruby-2.1.6.tar.gz
+cd ruby-2.1.6
+./configure --no-rdoc --no-ri
make
sudo make install
-sudo gem install -v 1.9.9 bundler</span>
+sudo gem install bundler</span>
</code></pre></notextile>
commit 71ba12ca158c39c17187f15c26279ec00d461dc5
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Jun 30 22:47:50 2015 -0400
6377: Avoid "incompatible encoding" errors by using blank template0 instead of site-specific template1.
diff --git a/services/api/config/database.yml.sample b/services/api/config/database.yml.sample
index 6a27016..f58cc11 100644
--- a/services/api/config/database.yml.sample
+++ b/services/api/config/database.yml.sample
@@ -1,5 +1,6 @@
development:
adapter: postgresql
+ template: template0
encoding: utf8
database: arvados_development
username: arvados
@@ -8,6 +9,7 @@ development:
test:
adapter: postgresql
+ template: template0
encoding: utf8
database: arvados_test
username: arvados
@@ -16,6 +18,7 @@ test:
production:
adapter: postgresql
+ template: template0
encoding: utf8
database: arvados_production
username: arvados
commit 85de04ad9268e45bad459a606bfabfca4f6fad8c
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Jun 30 11:20:38 2015 -0400
6377: Fix reversed condition in "site application.yml is optional" fix.
diff --git a/sdk/python/tests/test_arv_put.py b/sdk/python/tests/test_arv_put.py
index d337023..f4bd8b6 100644
--- a/sdk/python/tests/test_arv_put.py
+++ b/sdk/python/tests/test_arv_put.py
@@ -414,7 +414,7 @@ class ArvPutIntegrationTest(run_test_server.TestCaseWithServers,
ArvadosBaseTestCase):
def _getKeepServerConfig():
for config_file, mandatory in [
- ['application.yml', True], ['application.default.yml', False]]:
+ ['application.yml', False], ['application.default.yml', True]]:
path = os.path.join(run_test_server.SERVICES_SRC_DIR,
"api", "config", config_file)
if not mandatory and not os.path.exists(path):
commit 158b18f036fc5f3f5848390d7ef53c6493aeb5a9
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Jun 30 11:19:04 2015 -0400
6377: Use fork of themes_for_rails with fixed gemspec.
Allows installing with current bundler versions, which treat the invalid
gemspec as an error.
diff --git a/apps/workbench/Gemfile b/apps/workbench/Gemfile
index d4f5e6c..e35cc83 100644
--- a/apps/workbench/Gemfile
+++ b/apps/workbench/Gemfile
@@ -87,7 +87,7 @@ gem 'piwik_analytics'
gem 'httpclient', '~> 2.5'
# This fork has Rails 4 compatible routes
-gem 'themes_for_rails', git: 'https://github.com/holtkampw/themes_for_rails', ref: '1fd2d7897d75ae0d6375f4c390df87b8e91ad417'
+gem 'themes_for_rails', git: 'https://github.com/curoverse/themes_for_rails'
gem "deep_merge", :require => 'deep_merge/rails_compat'
diff --git a/apps/workbench/Gemfile.lock b/apps/workbench/Gemfile.lock
index 9fc7550..bc7ddaf 100644
--- a/apps/workbench/Gemfile.lock
+++ b/apps/workbench/Gemfile.lock
@@ -1,7 +1,6 @@
GIT
- remote: https://github.com/holtkampw/themes_for_rails
- revision: 1fd2d7897d75ae0d6375f4c390df87b8e91ad417
- ref: 1fd2d7897d75ae0d6375f4c390df87b8e91ad417
+ remote: https://github.com/curoverse/themes_for_rails
+ revision: 61154877047d2346890bda0b7be5827cf51a6a76
specs:
themes_for_rails (0.5.1)
rails (>= 3.0.0)
@@ -10,29 +9,29 @@ GEM
remote: https://rubygems.org/
specs:
RedCloth (4.2.9)
- actionmailer (4.1.9)
- actionpack (= 4.1.9)
- actionview (= 4.1.9)
+ actionmailer (4.1.12)
+ actionpack (= 4.1.12)
+ actionview (= 4.1.12)
mail (~> 2.5, >= 2.5.4)
- actionpack (4.1.9)
- actionview (= 4.1.9)
- activesupport (= 4.1.9)
+ actionpack (4.1.12)
+ actionview (= 4.1.12)
+ activesupport (= 4.1.12)
rack (~> 1.5.2)
rack-test (~> 0.6.2)
- actionview (4.1.9)
- activesupport (= 4.1.9)
+ actionview (4.1.12)
+ activesupport (= 4.1.12)
builder (~> 3.1)
erubis (~> 2.7.0)
- activemodel (4.1.9)
- activesupport (= 4.1.9)
+ activemodel (4.1.12)
+ activesupport (= 4.1.12)
builder (~> 3.1)
- activerecord (4.1.9)
- activemodel (= 4.1.9)
- activesupport (= 4.1.9)
+ activerecord (4.1.12)
+ activemodel (= 4.1.12)
+ activesupport (= 4.1.12)
arel (~> 5.0.0)
activerecord-nulldb-adapter (0.3.1)
activerecord (>= 2.0.0)
- activesupport (4.1.9)
+ activesupport (4.1.12)
i18n (~> 0.6, >= 0.6.9)
json (~> 1.7, >= 1.7.7)
minitest (~> 5.1)
@@ -114,13 +113,12 @@ GEM
uuidtools (>= 2.1.0)
headless (1.0.2)
highline (1.6.21)
- hike (1.2.3)
httpclient (2.6.0.1)
i18n (0.7.0)
jquery-rails (3.1.2)
railties (>= 3.0, < 5.0)
thor (>= 0.14, < 2.0)
- json (1.8.2)
+ json (1.8.3)
jwt (0.1.13)
multi_json (>= 1.5)
launchy (2.4.3)
@@ -134,14 +132,14 @@ GEM
mail (2.6.3)
mime-types (>= 1.16, < 3)
metaclass (0.0.4)
- mime-types (2.4.3)
+ mime-types (2.6.1)
mini_portile (0.6.2)
- minitest (5.5.1)
+ minitest (5.7.0)
mocha (1.1.0)
metaclass (~> 0.0.1)
morrisjs-rails (0.5.1)
railties (> 3.1, < 5)
- multi_json (1.10.1)
+ multi_json (1.11.1)
multipart-post (1.2.0)
net-scp (1.2.1)
net-ssh (>= 2.6.5)
@@ -166,25 +164,25 @@ GEM
cliver (~> 0.3.1)
multi_json (~> 1.0)
websocket-driver (>= 0.2.0)
- rack (1.5.2)
+ rack (1.5.5)
rack-mini-profiler (0.9.2)
rack (>= 1.1.3)
rack-test (0.6.3)
rack (>= 1.0)
- rails (4.1.9)
- actionmailer (= 4.1.9)
- actionpack (= 4.1.9)
- actionview (= 4.1.9)
- activemodel (= 4.1.9)
- activerecord (= 4.1.9)
- activesupport (= 4.1.9)
+ rails (4.1.12)
+ actionmailer (= 4.1.12)
+ actionpack (= 4.1.12)
+ actionview (= 4.1.12)
+ activemodel (= 4.1.12)
+ activerecord (= 4.1.12)
+ activesupport (= 4.1.12)
bundler (>= 1.3.0, < 2.0)
- railties (= 4.1.9)
+ railties (= 4.1.12)
sprockets-rails (~> 2.0)
rails-perftest (0.0.5)
- railties (4.1.9)
- actionpack (= 4.1.9)
- activesupport (= 4.1.9)
+ railties (4.1.12)
+ actionpack (= 4.1.12)
+ activesupport (= 4.1.12)
rake (>= 0.8.7)
thor (>= 0.18.1, < 2.0)
rake (10.4.2)
@@ -222,12 +220,9 @@ GEM
simplecov-rcov (0.2.3)
simplecov (>= 0.4.1)
slop (3.6.0)
- sprockets (2.12.3)
- hike (~> 1.2)
- multi_json (~> 1.0)
+ sprockets (3.2.0)
rack (~> 1.0)
- tilt (~> 1.1, != 1.3.0)
- sprockets-rails (2.2.2)
+ sprockets-rails (2.3.2)
actionpack (>= 3.0)
activesupport (>= 3.0)
sprockets (>= 2.8, < 4.0)
@@ -236,7 +231,7 @@ GEM
libv8 (~> 3.16.14.0)
ref
thor (0.19.1)
- thread_safe (0.3.4)
+ thread_safe (0.3.5)
tilt (1.4.1)
tzinfo (1.2.2)
thread_safe (~> 0.1)
@@ -299,3 +294,6 @@ DEPENDENCIES
therubyracer
uglifier (>= 1.0.3)
wiselinks
+
+BUNDLED WITH
+ 1.10.5
commit acfbb64831047dcae895e57ceff3d0a834c91bf2
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Jun 30 11:07:24 2015 -0400
6377: Support loading omniauth config from application.yml.
diff --git a/services/api/app/controllers/user_sessions_controller.rb b/services/api/app/controllers/user_sessions_controller.rb
index 256a67b..795b114 100644
--- a/services/api/app/controllers/user_sessions_controller.rb
+++ b/services/api/app/controllers/user_sessions_controller.rb
@@ -15,7 +15,7 @@ class UserSessionsController < ApplicationController
unless identity_url_ok
# Whoa. This should never happen.
logger.error "UserSessionsController.create: omniauth object missing/invalid"
- logger.error "omniauth.pretty_inspect():\n\n#{omniauth.pretty_inspect()}"
+ logger.error "omniauth: "+omniauth.pretty_inspect
return redirect_to login_failure_url
end
@@ -93,7 +93,7 @@ class UserSessionsController < ApplicationController
flash[:notice] = 'You have logged off'
return_to = params[:return_to] || root_url
- redirect_to "#{CUSTOM_PROVIDER_URL}/users/sign_out?redirect_uri=#{CGI.escape return_to}"
+ redirect_to "#{Rails.configuration.sso_provider_url}/users/sign_out?redirect_uri=#{CGI.escape return_to}"
end
# login - Just bounce to /auth/joshid. The only purpose of this function is
diff --git a/services/api/config/application.default.yml b/services/api/config/application.default.yml
index 9b758e6..409dea6 100644
--- a/services/api/config/application.default.yml
+++ b/services/api/config/application.default.yml
@@ -41,6 +41,9 @@ test:
active_support.deprecation: :stderr
active_record.mass_assignment_sanitizer: :strict
uuid_prefix: zzzzz
+ sso_app_id: arvados-server
+ sso_app_secret: <%= rand(2**512).to_s(36) %>
+ sso_provider_url: http://localhost:3002
secret_token: <%= rand(2**512).to_s(36) %>
blob_signing_key: zfhgfenhffzltr9dixws36j1yhksjoll2grmku38mi7yxd66h5j4q9w4jzanezacp8s6q0ro3hxakfye02152hncy6zml2ed0uc
user_profile_notification_address: arvados at example.com
@@ -291,6 +294,12 @@ common:
# server is using a self-signed cert.
sso_insecure: false
+ # These settings are provided by your OAuth2 provider (e.g.,
+ # sso-provider).
+ sso_app_id: ~
+ sso_app_secret: ~
+ sso_provider_url: ~
+
# Default replication level for collections. This is used when a
# collection's replication_desired attribute is nil.
default_collection_replication: 2
diff --git a/services/api/config/application.yml.example b/services/api/config/application.yml.example
index c3e599f..ee14c0e 100644
--- a/services/api/config/application.yml.example
+++ b/services/api/config/application.yml.example
@@ -23,6 +23,9 @@ production:
blob_signing_key: ~
uuid_prefix: bogus
workbench_address: https://workbench.bogus.arvadosapi.com
+ sso_app_id: arvados-server
+ sso_app_secret: ~
+ sso_provider_url: https://login.bogus.arvadosapi.com
test:
# Tests should be able to run without further configuration, but if you do
diff --git a/services/api/config/initializers/load_config.rb b/services/api/config/initializers/load_config.rb
index 3b516da..de9770d 100644
--- a/services/api/config/initializers/load_config.rb
+++ b/services/api/config/initializers/load_config.rb
@@ -6,6 +6,22 @@ rescue LoadError
# configured by application.yml (i.e., here!) instead.
end
+if (File.exists?(File.expand_path '../omniauth.rb', __FILE__) and
+ not defined? WARNED_OMNIAUTH_CONFIG)
+ Rails.logger.warn <<-EOS
+DEPRECATED CONFIGURATION:
+ Please move your SSO provider config into config/application.yml
+ and delete config/initializers/omniauth.rb.
+EOS
+ # Real values will be copied from globals by omniauth_init.rb. For
+ # now, assign some strings so the generic *.yml config loader
+ # doesn't overwrite them or complain that they're missing.
+ Rails.configuration.sso_app_id = 'xxx'
+ Rails.configuration.sso_app_secret = 'xxx'
+ Rails.configuration.sso_provider_url = '//xxx'
+ WARNED_OMNIAUTH_CONFIG = true
+end
+
$application_config = {}
%w(application.default application).each do |cfgfile|
diff --git a/services/api/config/initializers/omniauth.rb.example b/services/api/config/initializers/omniauth.rb.example
deleted file mode 100644
index aefcf56..0000000
--- a/services/api/config/initializers/omniauth.rb.example
+++ /dev/null
@@ -1,13 +0,0 @@
-# Change this omniauth configuration to point to your registered provider
-# Since this is a registered application, add the app id and secret here
-APP_ID = 'arvados-server'
-APP_SECRET = rand(2**512).to_s(36) # CHANGE ME!
-
-# Update your custom Omniauth provider URL here
-CUSTOM_PROVIDER_URL = 'http://localhost:3002'
-
-Rails.application.config.middleware.use OmniAuth::Builder do
- provider :josh_id, APP_ID, APP_SECRET, CUSTOM_PROVIDER_URL
-end
-
-OmniAuth.config.on_failure = StaticController.action(:login_failure)
diff --git a/services/api/config/initializers/omniauth_init.rb b/services/api/config/initializers/omniauth_init.rb
new file mode 100644
index 0000000..3277c2b
--- /dev/null
+++ b/services/api/config/initializers/omniauth_init.rb
@@ -0,0 +1,19 @@
+# This file is called omniauth_init.rb instead of omniauth.rb because
+# older versions had site configuration in omniauth.rb.
+#
+# It must come after omniauth.rb in (lexical) load order.
+
+if defined? CUSTOM_PROVIDER_URL
+ Rails.logger.warn "Copying omniauth from globals in legacy config file."
+ Rails.configuration.sso_app_id = APP_ID
+ Rails.configuration.sso_app_secret = APP_SECRET
+ Rails.configuration.sso_provider_url = CUSTOM_PROVIDER_URL
+else
+ Rails.application.config.middleware.use OmniAuth::Builder do
+ provider(:josh_id,
+ Rails.configuration.sso_app_id,
+ Rails.configuration.sso_app_secret,
+ Rails.configuration.sso_provider_url)
+ end
+ OmniAuth.config.on_failure = StaticController.action(:login_failure)
+end
commit 734a66939892064fe9c663fd746cb7371c7d84e4
Author: Tom Clegg <tom at curoverse.com>
Date: Fri Jun 26 11:19:54 2015 -0400
6377: Missing application.yml is not an error.
diff --git a/sdk/python/tests/run_test_server.py b/sdk/python/tests/run_test_server.py
index b25bf62..02f65e6 100644
--- a/sdk/python/tests/run_test_server.py
+++ b/sdk/python/tests/run_test_server.py
@@ -453,10 +453,13 @@ def _getport(program):
def _apiconfig(key):
if _cached_config:
return _cached_config[key]
- def _load(f):
- return yaml.load(os.path.join(SERVICES_SRC_DIR, 'api', 'config', f))
+ def _load(f, required=True):
+ fullpath = os.path.join(SERVICES_SRC_DIR, 'api', 'config', f)
+ if not required and not os.path.exists(fullpath):
+ return {}
+ return yaml.load(fullpath)
cdefault = _load('application.default.yml')
- csite = _load('application.yml')
+ csite = _load('application.yml', required=False)
_cached_config = {}
for section in [cdefault.get('common',{}), cdefault.get('test',{}),
csite.get('common',{}), csite.get('test',{})]:
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