gem 'uglifier', '>= 1.0.3'
end
+group :test do
+ gem 'rvm-capistrano'
+ gem 'selenium-webdriver'
+ gem 'capybara'
+ gem 'poltergeist'
+end
+
gem 'jquery-rails'
gem 'bootstrap-sass', '~> 3.1.0'
gem 'bootstrap-x-editable-rails'
# To use debugger
#gem 'byebug'
-gem 'rvm-capistrano', :group => :test
-
gem 'passenger', :group => :production
gem 'andand'
gem 'RedCloth'
net-sftp (>= 2.0.0)
net-ssh (>= 2.0.14)
net-ssh-gateway (>= 1.1.0)
+ capybara (2.2.1)
+ mime-types (>= 1.16)
+ nokogiri (>= 1.3.3)
+ rack (>= 1.0.0)
+ rack-test (>= 0.5.4)
+ xpath (~> 2.0)
+ childprocess (0.5.1)
+ ffi (~> 1.0, >= 1.0.11)
+ cliver (0.3.2)
coffee-rails (3.2.2)
coffee-script (>= 2.2.0)
railties (~> 3.2.0)
deep_merge (1.0.1)
erubis (2.7.0)
execjs (2.0.2)
+ ffi (1.9.3)
highline (1.6.20)
hike (1.2.3)
httpclient (2.3.4.1)
mime-types (~> 1.16)
treetop (~> 1.4.8)
mime-types (1.25)
+ mini_portile (0.5.2)
multi_json (1.8.2)
net-scp (1.1.2)
net-ssh (>= 2.6.5)
net-ssh (2.7.0)
net-ssh-gateway (1.2.0)
net-ssh (>= 2.6.5)
+ nokogiri (1.6.1)
+ mini_portile (~> 0.5.0)
oj (2.1.7)
passenger (4.0.23)
daemon_controller (>= 1.1.0)
actionpack
activesupport
rails (>= 3.0.0)
+ poltergeist (1.5.0)
+ capybara (~> 2.1)
+ cliver (~> 0.3.1)
+ multi_json (~> 1.0)
+ websocket-driver (>= 0.2.0)
polyglot (0.3.3)
rack (1.4.5)
rack-cache (1.2)
rdoc (3.12.2)
json (~> 1.4)
ref (1.0.5)
+ rubyzip (1.1.0)
rvm-capistrano (1.5.1)
capistrano (~> 2.15.4)
sass (3.2.12)
railties (~> 3.2.0)
sass (>= 3.1.10)
tilt (~> 1.3)
+ selenium-webdriver (2.40.0)
+ childprocess (>= 0.5.0)
+ multi_json (~> 1.0)
+ rubyzip (~> 1.0)
+ websocket (~> 1.0.4)
sprockets (2.2.2)
hike (~> 1.2)
multi_json (~> 1.0)
uglifier (2.3.1)
execjs (>= 0.3.0)
json (>= 1.8.0)
+ websocket (1.0.7)
+ websocket-driver (0.3.2)
+ xpath (2.0.0)
+ nokogiri (~> 1.3)
PLATFORMS
ruby
andand
bootstrap-sass (~> 3.1.0)
bootstrap-x-editable-rails
+ capybara
coffee-rails (~> 3.2.0)
deep_merge
httpclient
oj
passenger
piwik_analytics
+ poltergeist
rails (~> 3.2.0)
rvm-capistrano
sass
sass-rails (~> 3.2.0)
+ selenium-webdriver
sqlite3
themes_for_rails
therubyracer
+++ /dev/null
-== Welcome to Rails
-
-Rails is a web-application framework that includes everything needed to create
-database-backed web applications according to the Model-View-Control pattern.
-
-This pattern splits the view (also called the presentation) into "dumb"
-templates that are primarily responsible for inserting pre-built data in between
-HTML tags. The model contains the "smart" domain objects (such as Account,
-Product, Person, Post) that holds all the business logic and knows how to
-persist themselves to a database. The controller handles the incoming requests
-(such as Save New Account, Update Product, Show Post) by manipulating the model
-and directing data to the view.
-
-In Rails, the model is handled by what's called an object-relational mapping
-layer entitled Active Record. This layer allows you to present the data from
-database rows as objects and embellish these data objects with business logic
-methods. You can read more about Active Record in
-link:files/vendor/rails/activerecord/README.html.
-
-The controller and view are handled by the Action Pack, which handles both
-layers by its two parts: Action View and Action Controller. These two layers
-are bundled in a single package due to their heavy interdependence. This is
-unlike the relationship between the Active Record and Action Pack that is much
-more separate. Each of these packages can be used independently outside of
-Rails. You can read more about Action Pack in
-link:files/vendor/rails/actionpack/README.html.
-
-
-== Getting Started
-
-1. At the command prompt, create a new Rails application:
- <tt>rails new myapp</tt> (where <tt>myapp</tt> is the application name)
-
-2. Change directory to <tt>myapp</tt> and start the web server:
- <tt>cd myapp; rails server</tt> (run with --help for options)
-
-3. Go to http://localhost:3000/ and you'll see:
- "Welcome aboard: You're riding Ruby on Rails!"
-
-4. Follow the guidelines to start developing your application. You can find
-the following resources handy:
-
-* The Getting Started Guide: http://guides.rubyonrails.org/getting_started.html
-* Ruby on Rails Tutorial Book: http://www.railstutorial.org/
-
-
-== Debugging Rails
-
-Sometimes your application goes wrong. Fortunately there are a lot of tools that
-will help you debug it and get it back on the rails.
-
-First area to check is the application log files. Have "tail -f" commands
-running on the server.log and development.log. Rails will automatically display
-debugging and runtime information to these files. Debugging info will also be
-shown in the browser on requests from 127.0.0.1.
-
-You can also log your own messages directly into the log file from your code
-using the Ruby logger class from inside your controllers. Example:
-
- class WeblogController < ActionController::Base
- def destroy
- @weblog = Weblog.find(params[:id])
- @weblog.destroy
- logger.info("#{Time.now} Destroyed Weblog ID ##{@weblog.id}!")
- end
- end
-
-The result will be a message in your log file along the lines of:
-
- Mon Oct 08 14:22:29 +1000 2007 Destroyed Weblog ID #1!
-
-More information on how to use the logger is at http://www.ruby-doc.org/core/
-
-Also, Ruby documentation can be found at http://www.ruby-lang.org/. There are
-several books available online as well:
-
-* Programming Ruby: http://www.ruby-doc.org/docs/ProgrammingRuby/ (Pickaxe)
-* Learn to Program: http://pine.fm/LearnToProgram/ (a beginners guide)
-
-These two books will bring you up to speed on the Ruby language and also on
-programming in general.
-
-
-== Debugger
-
-Debugger support is available through the debugger command when you start your
-Mongrel or WEBrick server with --debugger. This means that you can break out of
-execution at any point in the code, investigate and change the model, and then,
-resume execution! You need to install ruby-debug to run the server in debugging
-mode. With gems, use <tt>sudo gem install ruby-debug</tt>. Example:
-
- class WeblogController < ActionController::Base
- def index
- @posts = Post.all
- debugger
- end
- end
-
-So the controller will accept the action, run the first line, then present you
-with a IRB prompt in the server window. Here you can do things like:
-
- >> @posts.inspect
- => "[#<Post:0x14a6be8
- @attributes={"title"=>nil, "body"=>nil, "id"=>"1"}>,
- #<Post:0x14a6620
- @attributes={"title"=>"Rails", "body"=>"Only ten..", "id"=>"2"}>]"
- >> @posts.first.title = "hello from a debugger"
- => "hello from a debugger"
-
-...and even better, you can examine how your runtime objects actually work:
-
- >> f = @posts.first
- => #<Post:0x13630c4 @attributes={"title"=>nil, "body"=>nil, "id"=>"1"}>
- >> f.
- Display all 152 possibilities? (y or n)
-
-Finally, when you're ready to resume execution, you can enter "cont".
-
-
-== Console
-
-The console is a Ruby shell, which allows you to interact with your
-application's domain model. Here you'll have all parts of the application
-configured, just like it is when the application is running. You can inspect
-domain models, change values, and save to the database. Starting the script
-without arguments will launch it in the development environment.
-
-To start the console, run <tt>rails console</tt> from the application
-directory.
-
-Options:
-
-* Passing the <tt>-s, --sandbox</tt> argument will rollback any modifications
- made to the database.
-* Passing an environment name as an argument will load the corresponding
- environment. Example: <tt>rails console production</tt>.
-
-To reload your controllers and models after launching the console run
-<tt>reload!</tt>
-
-More information about irb can be found at:
-link:http://www.rubycentral.org/pickaxe/irb.html
-
-
-== dbconsole
-
-You can go to the command line of your database directly through <tt>rails
-dbconsole</tt>. You would be connected to the database with the credentials
-defined in database.yml. Starting the script without arguments will connect you
-to the development database. Passing an argument will connect you to a different
-database, like <tt>rails dbconsole production</tt>. Currently works for MySQL,
-PostgreSQL and SQLite 3.
-
-== Description of Contents
-
-The default directory structure of a generated Ruby on Rails application:
-
- |-- app
- | |-- assets
- | |-- images
- | |-- javascripts
- | `-- stylesheets
- | |-- controllers
- | |-- helpers
- | |-- mailers
- | |-- models
- | `-- views
- | `-- layouts
- |-- config
- | |-- environments
- | |-- initializers
- | `-- locales
- |-- db
- |-- doc
- |-- lib
- | `-- tasks
- |-- log
- |-- public
- |-- script
- |-- test
- | |-- fixtures
- | |-- functional
- | |-- integration
- | |-- performance
- | `-- unit
- |-- tmp
- | |-- cache
- | |-- pids
- | |-- sessions
- | `-- sockets
- `-- vendor
- |-- assets
- `-- stylesheets
- `-- plugins
-
-app
- Holds all the code that's specific to this particular application.
-
-app/assets
- Contains subdirectories for images, stylesheets, and JavaScript files.
-
-app/controllers
- Holds controllers that should be named like weblogs_controller.rb for
- automated URL mapping. All controllers should descend from
- ApplicationController which itself descends from ActionController::Base.
-
-app/models
- Holds models that should be named like post.rb. Models descend from
- ActiveRecord::Base by default.
-
-app/views
- Holds the template files for the view that should be named like
- weblogs/index.html.erb for the WeblogsController#index action. All views use
- eRuby syntax by default.
-
-app/views/layouts
- Holds the template files for layouts to be used with views. This models the
- common header/footer method of wrapping views. In your views, define a layout
- using the <tt>layout :default</tt> and create a file named default.html.erb.
- Inside default.html.erb, call <% yield %> to render the view using this
- layout.
-
-app/helpers
- Holds view helpers that should be named like weblogs_helper.rb. These are
- generated for you automatically when using generators for controllers.
- Helpers can be used to wrap functionality for your views into methods.
-
-config
- Configuration files for the Rails environment, the routing map, the database,
- and other dependencies.
-
-db
- Contains the database schema in schema.rb. db/migrate contains all the
- sequence of Migrations for your schema.
-
-doc
- This directory is where your application documentation will be stored when
- generated using <tt>rake doc:app</tt>
-
-lib
- Application specific libraries. Basically, any kind of custom code that
- doesn't belong under controllers, models, or helpers. This directory is in
- the load path.
-
-public
- The directory available for the web server. Also contains the dispatchers and the
- default HTML files. This should be set as the DOCUMENT_ROOT of your web
- server.
-
-script
- Helper scripts for automation and generation.
-
-test
- Unit and functional tests along with fixtures. When using the rails generate
- command, template test files will be generated for you and placed in this
- directory.
-
-vendor
- External libraries that the application depends on. Also includes the plugins
- subdirectory. If the app has frozen rails, those gems also go here, under
- vendor/rails/. This directory is in the load path.
--- /dev/null
+h1. Developing Workbench
+
+This document includes information to help developers who would like to contribute to Workbench. If you just want to install it, please refer to our "Workbench installation guide":http://doc.arvados.org/install/install-workbench-app.html.
+
+h2. Running tests
+
+The Workbench application includes a series of integration tests. When you run these, it starts the API server in a test environment, with all of its fixtures loaded, then tests Workbench by starting that server and making requests against it.
+
+In addition to bundled gems, running the integration tests requires "PhantomJS":http://phantomjs.org/download.html to test JavaScript elements. The simplest way to get started is to download one of the binary builds provided, and install the executable into one of the directories in your @$PATH@.
+
+h2. Writing tests
+
+Integration tests are written with Capybara, which drives a fully-featured Web browser to interact with Workbench exactly as a user would.
+
+If your test requires JavaScript support, your test method should start with the line @Capybara.current_driver = Capybara.javascript_driver@. Otherwise, Capybara defaults to a simpler browser for speed.
+
+In most tests, you can directly call "Capybara's Session methods":http://rubydoc.info/github/jnicklas/capybara/Capybara/Session to drive the browser and check its state. If you need finer-grained control, refer to the "full Capybara documentation":http://rubydoc.info/github/jnicklas/capybara/Capybara.
return "Invalid selection";
}
}
+
+$.fn.editabletypes.text.defaults.tpl = '<input type="text" name="editable-text">'
+
+$.fn.editableform.buttons = '\
+<button type="submit" class="btn btn-primary btn-sm editable-submit" \
+ id="editable-submit"><i class="glyphicon glyphicon-ok"></i></button>\
+<button type="button" class="btn btn-default btn-sm editable-cancel" \
+ id="editable-cancel"><i class="glyphicon glyphicon-remove"></i></button>\
+'
class ApiClientAuthorizationsController < ApplicationController
def index
- @objects = model_class.all.to_ary.reject do |x|
+ m = model_class.all
+ items_available = m.items_available
+ offset = m.result_offset
+ limit = m.result_limit
+ filtered = m.to_ary.reject do |x|
x.api_client_id == 0 or (x.expires_at and x.expires_at < Time.now) rescue false
end
+ ArvadosApiClient::patch_paging_vars(filtered, items_available, offset, limit)
+ @objects = ArvadosResourceList.new(ApiClientAuthorization)
+ @objects.results= filtered
super
end
class PipelineTemplatesController < ApplicationController
def show
- @objects = []
- PipelineInstance.where(pipeline_template_uuid: @object.uuid).each do |pipeline|
- @objects.push(pipeline)
- end
+ @objects = PipelineInstance.where(pipeline_template_uuid: @object.uuid)
super
end
resp
end
+ def self.patch_paging_vars(ary, items_available, offset, limit)
+ if items_available
+ (class << ary; self; end).class_eval { attr_accessor :items_available }
+ ary.items_available = items_available
+ end
+ if offset
+ (class << ary; self; end).class_eval { attr_accessor :offset }
+ ary.offset = offset
+ end
+ if limit
+ (class << ary; self; end).class_eval { attr_accessor :limit }
+ ary.limit = limit
+ end
+ ary
+ end
+
def unpack_api_response(j, kind=nil)
if j.is_a? Hash and j[:items].is_a? Array and j[:kind].match(/(_list|List)$/)
ary = j[:items].collect { |x| unpack_api_response x, j[:kind] }
- if j[:items_available]
- (class << ary; self; end).class_eval { attr_accessor :items_available }
- ary.items_available = j[:items_available]
- end
- if j[:offset]
- (class << ary; self; end).class_eval { attr_accessor :offset }
- ary.offset = j[:offset]
- end
- if j[:limit]
- (class << ary; self; end).class_eval { attr_accessor :limit }
- ary.limit = j[:limit]
- end
- ary
+ ArvadosApiClient::patch_paging_vars(ary, j[:items_available], j[:offset], j[:limit])
elsif j.is_a? Hash and (kind || j[:kind])
oclass = self.kind_class(kind || j[:kind])
if oclass
Rails.configuration.arvados_v1_base
end
- def arvados_schema
- @arvados_schema ||= api 'schema', ''
- end
-
def discovery
@discovery ||= api '../../discovery/v1/apis/arvados/v1/rest', ''
end
return @columns unless @columns.nil?
@columns = []
@attribute_info ||= {}
- return @columns if $arvados_api_client.arvados_schema[self.to_s.to_sym].nil?
- $arvados_api_client.arvados_schema[self.to_s.to_sym].each do |coldef|
- k = coldef[:name].to_sym
- if coldef[:type] == coldef[:type].downcase
- @columns << column(k, coldef[:type].to_sym)
+ schema = $arvados_api_client.discovery[:schemas][self.to_s.to_sym]
+ return @columns if schema.nil?
+ schema[:properties].each do |k, coldef|
+ case k
+ when :etag, :kind
+ attr_reader k
else
- @columns << column(k, :text)
- serialize k, coldef[:type].constantize
+ if coldef[:type] == coldef[:type].downcase
+ # boolean, integer, etc.
+ @columns << column(k, coldef[:type].to_sym)
+ else
+ # Hash, Array
+ @columns << column(k, :text)
+ serialize k, coldef[:type].constantize
+ end
+ attr_accessible k
+ @attribute_info[k] = coldef
end
- attr_accessible k
- @attribute_info[k] = coldef
end
- attr_reader :etag
- attr_reader :kind
@columns
end
@results
end
+ def results=(r)
+ @results = r
+ end
+
def all
where({})
end
}
<% end %>
-<% if results.result_offset != nil and results.result_limit != nil and results.items_available != nil %>
+<% if results.respond_to? :result_offset and
+ results.respond_to? :result_limit and
+ results.respond_to? :items_available and
+ results.result_offset != nil and
+ results.result_limit != nil and
+ results.items_available != nil
+%>
<div class="index-paging">
Displaying <%= results.result_offset+1 %> –
<%= if results.result_offset + results.result_limit > results.items_available
<% end %>
<li class="dropdown">
- <a href="#" class="dropdown-toggle" data-toggle="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" id="user-menu">
<span class="glyphicon glyphicon-user"></span><span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
-# Do not use this file for site configuration. Create config.yml
+# Do not use this file for site configuration. Create application.yml
# instead (see application.yml.example).
development:
assets.compress: false
assets.debug: true
profiling_enabled: true
- site_name: Workbench:dev
+ site_name: Arvados Workbench (dev)
production:
force_ssl: true
profiling_enabled: false
secret_token: <%= rand(2**256).to_s(36) %>
+ # When you run the Workbench's integration tests, it starts the API
+ # server as a dependency. These settings should match the API
+ # server's Rails defaults. If you adjust those, change these
+ # settings in application.yml to match.
+ arvados_login_base: https://localhost:3001/login
+ arvados_v1_base: https://localhost:3001/arvados/v1
+ arvados_insecure_https: true
+
site_name: Workbench:test
common:
# Expands the lines which load the assets
config.assets.debug = true
- # Log timing data for API transactions
- config.profiling_enabled = true
-
- config.arvados_login_base = 'http://arvados.local/login'
- config.arvados_v1_base = 'http://arvados.local/arvados/v1'
- config.arvados_insecure_https = true # true = do not check server certificate
-
- config.data_import_dir = '/tmp/arvados-workbench-upload'
- config.data_export_dir = '/tmp/arvados-workbench-download'
-
- config.secret_token = File.read('config/.secret_token') if File.exist? 'config/.secret_token'
-
- config.site_name = 'Arvados Workbench (dev)'
- config.activation_contact_link = 'mailto:info@arvados.org'
-
- config.arvados_docsite = 'http://doc.arvados.org'
-
- config.arvados_theme = 'default'
-
- config.show_user_agreement_inline = false
end
# Log timing data for API transactions
config.profiling_enabled = false
- config.arvados_login_base = 'https://arvados.local/login'
- config.arvados_v1_base = 'https://arvados.local/arvados/v1'
- config.arvados_insecure_https = false # true = do not check server certificate
-
- config.data_import_dir = '/data/arvados-workbench-upload/data'
- config.data_export_dir = '/data/arvados-workbench-download/data'
-
- # Authentication stub: hard code pre-approved API tokens.
- # config.accept_api_token = { rand(2**256).to_s(36) => true }
- config.accept_api_token = {}
-
- config.site_name = 'Arvados Workbench'
- config.activation_contact_link = 'mailto:info@arvados.org'
-
- config.arvados_docsite = 'http://doc.arvados.org'
-
- config.arvados_theme = 'default'
-
- config.show_user_agreement_inline = false
end
# Log timing data for API transactions
config.profiling_enabled = false
- config.arvados_login_base = 'http://arvados.local/login'
- config.arvados_v1_base = 'https://arvados.local/arvados/v1'
- config.arvados_insecure_https = true # true = do not check server certificate
-
- config.data_import_dir = '/data/arvados-workbench-upload'
- config.data_export_dir = '/data/arvados-workbench-download'
-
- # Authentication stub: hard code pre-approved API tokens.
- # config.accept_api_token = { rand(2**256).to_s(36) => true }
- config.accept_api_token = {}
-
- config.site_name = 'Arvados Workbench (test)'
- config.activation_contact_link = 'mailto:info@arvados.org'
-
- config.arvados_docsite = 'http://doc.arvados.org'
-
- config.arvados_theme = 'default'
-
- config.show_user_agreement_inline = false
end
--- /dev/null
+require 'integration_helper'
+
+class ApiClientAuthorizationsTest < ActionDispatch::IntegrationTest
+ test "try loading Manage API tokens page" do
+ Capybara.current_driver = Capybara.javascript_driver
+ visit page_with_token('admin_trustedclient')
+ click_link 'user-menu'
+ click_link 'Manage API tokens'
+ assert_equal 200, status_code
+ end
+end
--- /dev/null
+require 'test_helper'
+
+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'
+ assert_no_match(/\bapi_token=/, current_path)
+ end
+
+ test "can't use expired token" do
+ visit page_with_token('expired_trustedclient')
+ assert page.has_text? 'Log in'
+ end
+end
--- /dev/null
+require 'integration_helper'
+
+class VirtualMachinesTest < ActionDispatch::IntegrationTest
+ test "make and name a new virtual machine" do
+ Capybara.current_driver = Capybara.javascript_driver
+ visit page_with_token('admin_trustedclient')
+ click_link 'Virtual machines'
+ assert page.has_text? 'testvm.shell'
+ click_on 'Add a new virtual machine'
+ assert page.has_text? 'none'
+ click_link 'none'
+ assert page.has_text? 'Update hostname'
+ fill_in 'editable-text', with: 'testname'
+ click_button 'editable-submit'
+ assert page.has_text? 'testname'
+ end
+end
--- /dev/null
+require 'test_helper'
+require 'capybara/rails'
+require 'capybara/poltergeist'
+require 'uri'
+require 'yaml'
+
+$ARV_API_SERVER_DIR = File.expand_path('../../../../services/api', __FILE__)
+SERVER_PID_PATH = 'tmp/pids/server.pid'
+
+class ActionDispatch::IntegrationTest
+ # Make the Capybara DSL available in all integration tests
+ include Capybara::DSL
+
+ def self.api_fixture(name)
+ # Returns the data structure from the named API server test fixture.
+ path = File.join($ARV_API_SERVER_DIR, 'test', 'fixtures', "#{name}.yml")
+ YAML.load(IO.read(path))
+ end
+
+ @@API_AUTHS = api_fixture('api_client_authorizations')
+
+ def page_with_token(token, path='/')
+ # Generate a page path with an embedded API token.
+ # Typical usage: visit page_with_token('token_name', page)
+ # The token can be specified by the name of an api_client_authorizations
+ # fixture, or passed as a raw string.
+ api_token = ((@@API_AUTHS.include? token) ?
+ @@API_AUTHS[token]['api_token'] : token)
+ sep = (path.include? '?') ? '&' : '?'
+ q_string = URI.encode_www_form('api_token' => api_token)
+ "#{path}#{sep}#{q_string}"
+ end
+end
+
+class IntegrationTestRunner < MiniTest::Unit
+ # Make a hash that unsets Bundle's environment variables.
+ # We'll use this environment when we launch Bundle commands in the API
+ # server. Otherwise, those commands will try to use Workbench's gems, etc.
+ @@APIENV = ENV.map { |(key, val)| (key =~ /^BUNDLE_/) ? [key, nil] : nil }.
+ compact.to_h
+
+ def _system(*cmd)
+ if not system(@@APIENV, *cmd)
+ raise RuntimeError, "#{cmd[0]} returned exit code #{$?.exitstatus}"
+ end
+ end
+
+ def _run(args=[])
+ Capybara.javascript_driver = :poltergeist
+ server_pid = Dir.chdir($ARV_API_SERVER_DIR) do |apidir|
+ _system('bundle', 'exec', 'rake', 'db:test:load')
+ _system('bundle', 'exec', 'rake', 'db:fixtures:load')
+ _system('bundle', 'exec', 'rails', 'server', '-d')
+ timeout = Time.now.tv_sec + 5
+ while (not File.exists? SERVER_PID_PATH) and (Time.now.tv_sec < timeout)
+ sleep 0.2
+ end
+ IO.read(SERVER_PID_PATH).to_i
+ end
+ begin
+ super(args)
+ ensure
+ Process.kill('TERM', server_pid)
+ end
+ end
+end
+
+MiniTest::Unit.runner = IntegrationTestRunner.new
irb(main):002:0> <span class="userinput">ApiClient.find(1234).update_attributes is_trusted: true</span>
</code></pre>
</notextile>
-
-
</code></pre>
</notextile>
-You can also download indvidual files:
+You can also download individual files:
<notextile>
<pre><code>/scratch/<b>you</b>$ <span class="userinput">arv keep get 887cd41e9c613463eab2f0d885c6dd96+83/alice.txt .</span>
Arvados API authorization token to use during the course of the job.
+=item --no-clear-tmp
+
+Do not clear per-job/task temporary directories during initial job
+setup. This can speed up development and debugging when running jobs
+locally.
+
=back
=head1 RUNNING JOBS LOCALLY
use Warehouse;
use Warehouse::Stream;
use IPC::System::Simple qw(capturex);
+use Fcntl ':flock';
$ENV{"TMPDIR"} ||= "/tmp";
unless (defined $ENV{"CRUNCH_TMP"}) {
my $git_dir;
my $jobspec;
my $job_api_token;
+my $no_clear_tmp;
my $resume_stash;
GetOptions('force-unlock' => \$force_unlock,
'git-dir=s' => \$git_dir,
'job=s' => \$jobspec,
'job-api-token=s' => \$job_api_token,
+ 'no-clear-tmp' => \$no_clear_tmp,
'resume-stash=s' => \$resume_stash,
);
}
+if (!$have_slurm)
+{
+ must_lock_now("$ENV{CRUNCH_TMP}/.lock", "a job is already running here.");
+}
+
+
my $build_script;
my $skip_install = ($local_job && $Job->{script_version} =~ m{^/});
if ($skip_install)
{
+ if (!defined $no_clear_tmp) {
+ my $clear_tmp_cmd = 'rm -rf $JOB_WORK $CRUNCH_TMP/opt $CRUNCH_TMP/src*';
+ system($clear_tmp_cmd) == 0
+ or croak ("`$clear_tmp_cmd` failed: ".($?>>8));
+ }
$ENV{"CRUNCH_SRC"} = $Job->{script_version};
for my $src_path ("$ENV{CRUNCH_SRC}/arvados/sdk/python") {
if (-d $src_path) {
Log (undef, "Install revision ".$Job->{script_version});
my $nodelist = join(",", @node);
- # Clean out crunch_tmp/work, crunch_tmp/opt, crunch_tmp/src*
+ if (!defined $no_clear_tmp) {
+ # Clean out crunch_tmp/work, crunch_tmp/opt, crunch_tmp/src*
- my $cleanpid = fork();
- if ($cleanpid == 0)
- {
- srun (["srun", "--nodelist=$nodelist", "-D", $ENV{'TMPDIR'}],
- ['bash', '-c', 'if mount | grep -q $JOB_WORK/; then sudo /bin/umount $JOB_WORK/* 2>/dev/null; fi; sleep 1; rm -rf $JOB_WORK $CRUNCH_TMP/opt $CRUNCH_TMP/src*']);
- exit (1);
- }
- while (1)
- {
- last if $cleanpid == waitpid (-1, WNOHANG);
- freeze_if_want_freeze ($cleanpid);
- select (undef, undef, undef, 0.1);
+ my $cleanpid = fork();
+ if ($cleanpid == 0)
+ {
+ srun (["srun", "--nodelist=$nodelist", "-D", $ENV{'TMPDIR'}],
+ ['bash', '-c', 'if mount | grep -q $JOB_WORK/; then sudo /bin/umount $JOB_WORK/* 2>/dev/null; fi; sleep 1; rm -rf $JOB_WORK $CRUNCH_TMP/opt $CRUNCH_TMP/src*']);
+ exit (1);
+ }
+ while (1)
+ {
+ last if $cleanpid == waitpid (-1, WNOHANG);
+ freeze_if_want_freeze ($cleanpid);
+ select (undef, undef, undef, 0.1);
+ }
+ Log (undef, "Clean-work-dir exited $?");
}
- Log (undef, "Clean-work-dir exited $?");
# Install requested code version
Log (undef, "Install exited $?");
}
+if (!$have_slurm)
+{
+ # Grab our lock again (we might have deleted and re-created CRUNCH_TMP above)
+ must_lock_now("$ENV{CRUNCH_TMP}/.lock", "a job is already running here.");
+}
+
foreach (qw (script script_version script_parameters runtime_constraints))
Log (undef, "backing off node " . $slot[$slotid]->{node}->{name} . " for 60 seconds");
}
+sub must_lock_now
+{
+ my ($lockfile, $error_message) = @_;
+ open L, ">", $lockfile or croak("$lockfile: $!");
+ if (!flock L, LOCK_EX|LOCK_NB) {
+ croak("Can't lock $lockfile: $error_message\n");
+ }
+}
+
__DATA__
#!/usr/bin/perl
jobrecord = Job.find_by_uuid(job_done.uuid)
jobrecord.running = false
- jobrecord.finished_at ||= Time.now,
+ jobrecord.finished_at ||= Time.now
# Don't set 'jobrecord.success = false' because if the job failed to run due to an
# issue with crunch-job or slurm, we want the job to stay in the queue.
jobrecord.save!
:config => File.expand_path("config.ru"),
:SSLEnable => true,
:SSLVerifyClient => OpenSSL::SSL::VERIFY_NONE,
- :SSLPrivateKey => OpenSSL::PKey::RSA.new(
- File.open("config/api.clinicalfuture.com.key.pem").read),
- :SSLCertificate => OpenSSL::X509::Certificate.new(
- File.open("config/api.clinicalfuture.com.crt.pem").read),
:SSLCertName => [["CN", WEBrick::Utils::getservername]]
})
end
--- /dev/null
+require 'test_helper'
+
+class PermissionsTest < ActionDispatch::IntegrationTest
+ fixtures :users, :groups, :api_client_authorizations, :collections
+
+ test "adding and removing direct can_read links" do
+ auth = {'HTTP_AUTHORIZATION' => "OAuth2 #{api_client_authorizations(:spectator).api_token}"}
+ admin_auth = {'HTTP_AUTHORIZATION' => "OAuth2 #{api_client_authorizations(:admin).api_token}"}
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth
+ assert_response 404
+
+ # try to add permission as spectator
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_kind: 'arvados#user',
+ tail_uuid: users(:spectator).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_kind: 'arvados#collection',
+ head_uuid: collections(:foo_file).uuid,
+ properties: {}
+ }
+ }, auth
+ assert_response 422
+
+ # add permission as admin
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_kind: 'arvados#user',
+ tail_uuid: users(:spectator).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_kind: 'arvados#collection',
+ head_uuid: collections(:foo_file).uuid,
+ properties: {}
+ }
+ }, admin_auth
+ u = jresponse['uuid']
+ assert_response :success
+
+ # read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth
+ assert_response :success
+
+ # try to delete permission as spectator
+ delete "/arvados/v1/links/#{u}", {:format => :json}, auth
+ assert_response 403
+
+ # delete permission as admin
+ delete "/arvados/v1/links/#{u}", {:format => :json}, admin_auth
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth
+ assert_response 404
+ end
+
+
+ test "adding can_read links from user to group, group to collection" do
+ auth = {'HTTP_AUTHORIZATION' => "OAuth2 #{api_client_authorizations(:spectator).api_token}"}
+ admin_auth = {'HTTP_AUTHORIZATION' => "OAuth2 #{api_client_authorizations(:admin).api_token}"}
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth
+ assert_response 404
+
+ # add permission for spectator to read group
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_kind: 'arvados#user',
+ tail_uuid: users(:spectator).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_kind: 'arvados#group',
+ head_uuid: groups(:private).uuid,
+ properties: {}
+ }
+ }, admin_auth
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth
+ assert_response 404
+
+ # add permission for group to read collection
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_kind: 'arvados#group',
+ tail_uuid: groups(:private).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_kind: 'arvados#collection',
+ head_uuid: collections(:foo_file).uuid,
+ properties: {}
+ }
+ }, admin_auth
+ u = jresponse['uuid']
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth
+ assert_response :success
+
+ # delete permission for group to read collection
+ delete "/arvados/v1/links/#{u}", {:format => :json}, admin_auth
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth
+ assert_response 404
+
+ end
+
+
+ test "adding can_read links from group to collection, user to group" do
+ auth = {'HTTP_AUTHORIZATION' => "OAuth2 #{api_client_authorizations(:spectator).api_token}"}
+ admin_auth = {'HTTP_AUTHORIZATION' => "OAuth2 #{api_client_authorizations(:admin).api_token}"}
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth
+ assert_response 404
+
+ # add permission for group to read collection
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_kind: 'arvados#group',
+ tail_uuid: groups(:private).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_kind: 'arvados#collection',
+ head_uuid: collections(:foo_file).uuid,
+ properties: {}
+ }
+ }, admin_auth
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth
+ assert_response 404
+
+ # add permission for spectator to read group
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_kind: 'arvados#user',
+ tail_uuid: users(:spectator).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_kind: 'arvados#group',
+ head_uuid: groups(:private).uuid,
+ properties: {}
+ }
+ }, admin_auth
+ u = jresponse['uuid']
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth
+ assert_response :success
+
+ # delete permission for spectator to read group
+ delete "/arvados/v1/links/#{u}", {:format => :json}, admin_auth
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth
+ assert_response 404
+
+ end
+
+ test "adding can_read links from user to group, group to group, group to collection" do
+ auth = {'HTTP_AUTHORIZATION' => "OAuth2 #{api_client_authorizations(:spectator).api_token}"}
+ admin_auth = {'HTTP_AUTHORIZATION' => "OAuth2 #{api_client_authorizations(:admin).api_token}"}
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth
+ assert_response 404
+
+ # add permission for user to read group
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_kind: 'arvados#user',
+ tail_uuid: users(:spectator).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_kind: 'arvados#group',
+ head_uuid: groups(:private).uuid,
+ properties: {}
+ }
+ }, admin_auth
+ assert_response :success
+
+ # add permission for group to read group
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_kind: 'arvados#group',
+ tail_uuid: groups(:private).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_kind: 'arvados#group',
+ head_uuid: groups(:empty_lonely_group).uuid,
+ properties: {}
+ }
+ }, admin_auth
+ assert_response :success
+
+ # add permission for group to read collection
+ post "/arvados/v1/links", {
+ :format => :json,
+ :link => {
+ tail_kind: 'arvados#group',
+ tail_uuid: groups(:empty_lonely_group).uuid,
+ link_class: 'permission',
+ name: 'can_read',
+ head_kind: 'arvados#collection',
+ head_uuid: collections(:foo_file).uuid,
+ properties: {}
+ }
+ }, admin_auth
+ u = jresponse['uuid']
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth
+ assert_response :success
+
+ # delete permission for group to read collection
+ delete "/arvados/v1/links/#{u}", {:format => :json}, admin_auth
+ assert_response :success
+
+ # try to read collection as spectator
+ get "/arvados/v1/collections/#{collections(:foo_file).uuid}", {:format => :json}, auth
+ assert_response 404
+ end
+end
projects / arvados.git / commitdiff