# Methods that don't require login should
# skip_around_filter :require_thread_api_token
around_filter :require_thread_api_token, except: ERROR_ACTIONS
+ before_filter :ensure_arvados_api_exists, only: [:index, :show]
before_filter :set_cache_buster
before_filter :accept_uuid_as_id_param, except: ERROR_ACTIONS
before_filter :check_user_agreements, except: ERROR_ACTIONS
end
end
+ def ensure_arvados_api_exists
+ if model_class.is_a?(Class) && model_class < ArvadosBase && !model_class.api_exists?(params['action'].to_sym)
+ @errors = ["#{params['action']} method is not supported for #{params['controller']}"]
+ return render_error(status: 404)
+ end
+ end
+
def index
find_objects_for_index if !@objects
render_index
begin
if not model_class
@object = nil
+ elsif params[:uuid].nil? or params[:uuid].empty?
+ @object = nil
elsif not params[:uuid].is_a?(String)
@object = model_class.where(uuid: params[:uuid]).first
- elsif params[:uuid].empty?
- @object = nil
elsif (model_class != Link and
resource_class_for_uuid(params[:uuid]) == Link)
@name_link = Link.find(params[:uuid])
@object = model_class.find(@name_link.head_uuid)
else
@object = model_class.find(params[:uuid])
+ load_preloaded_objects [@object]
end
rescue ArvadosApiClient::NotFoundException, ArvadosApiClient::NotLoggedInException, RuntimeError => error
if error.is_a?(RuntimeError) and (error.message !~ /^argument to find\(/)
}
@@notification_tests.push lambda { |controller, current_user|
- PipelineInstance.limit(1).where(created_by: current_user.uuid).each do
+ if PipelineInstance.api_exists?(:index)
+ PipelineInstance.limit(1).where(created_by: current_user.uuid).each do
+ return nil
+ end
+ else
return nil
end
return lambda { |view|
def recent_processes lim
lim = 12 if lim.nil?
- cols = %w(uuid owner_uuid created_at modified_at pipeline_template_uuid name state started_at finished_at)
- pipelines = PipelineInstance.select(cols).limit(lim).order(["created_at desc"])
+ procs = {}
+ if PipelineInstance.api_exists?(:index)
+ cols = %w(uuid owner_uuid created_at modified_at pipeline_template_uuid name state started_at finished_at)
+ pipelines = PipelineInstance.select(cols).limit(lim).order(["created_at desc"])
+ pipelines.results.each { |pi| procs[pi] = pi.created_at }
+ end
crs = ContainerRequest.limit(lim).order(["created_at desc"]).filter([["requesting_container_uuid", "=", nil]])
- procs = {}
- pipelines.results.each { |pi| procs[pi] = pi.created_at }
crs.results.each { |c| procs[c] = c.created_at }
Hash[procs.sort_by {|key, value| value}].keys.reverse.first(lim)
# from the top three levels.
# That is: get toplevel projects under home, get subprojects of
# these projects, and so on until we hit the limit.
- def my_wanted_projects user, page_size=100
+ def my_wanted_projects(user, page_size=100)
return @my_wanted_projects if @my_wanted_projects
from_top = []
break if current_level.results.size == 0
@too_many_projects = true if current_level.items_available > current_level.results.size
from_top.concat current_level.results
- uuids = current_level.results.collect { |x| x.uuid }
+ uuids = current_level.results.collect(&:uuid)
depth += 1
if depth >= 3
@reached_level_limit = true
end
helper_method :my_wanted_projects_tree
- def my_wanted_projects_tree user, page_size=100
- build_my_wanted_projects_tree user, page_size
+ def my_wanted_projects_tree(user, page_size=100)
+ build_my_wanted_projects_tree(user, page_size)
[@my_wanted_projects_tree, @too_many_projects, @reached_level_limit]
end
- def build_my_wanted_projects_tree user, page_size=100
+ def build_my_wanted_projects_tree(user, page_size=100)
return @my_wanted_projects_tree if @my_wanted_projects_tree
parent_of = {user.uuid => 'me'}
# helper method to get object of a given dataclass and uuid
helper_method :object_for_dataclass
- def object_for_dataclass dataclass, uuid
+ def object_for_dataclass dataclass, uuid, by_attr=nil
raise ArgumentError, 'No input argument dataclass' unless (dataclass && uuid)
- preload_objects_for_dataclass(dataclass, [uuid])
+ preload_objects_for_dataclass(dataclass, [uuid], by_attr)
@objects_for[uuid]
end
# helper method to preload objects for given dataclass and uuids
helper_method :preload_objects_for_dataclass
- def preload_objects_for_dataclass dataclass, uuids
+ def preload_objects_for_dataclass dataclass, uuids, by_attr=nil
@objects_for ||= {}
raise ArgumentError, 'Argument is not a data class' unless dataclass.is_a? Class
uuids.each do |x|
@objects_for[x] = nil
end
- dataclass.where(uuid: uuids).each do |obj|
- @objects_for[obj.uuid] = obj
+ if by_attr and ![:uuid, :name].include?(by_attr)
+ raise ArgumentError, "Preloading only using lookups by uuid or name are supported: #{by_attr}"
+ elsif by_attr and by_attr == :name
+ dataclass.where(name: uuids).each do |obj|
+ @objects_for[obj.name] = obj
+ end
+ else
+ dataclass.where(uuid: uuids).each do |obj|
+ @objects_for[obj.uuid] = obj
+ end
end
@objects_for
end
+ # helper method to load objects that are already preloaded
+ helper_method :load_preloaded_objects
+ def load_preloaded_objects objs
+ @objects_for ||= {}
+ objs.each do |obj|
+ @objects_for[obj.uuid] = obj
+ end
+ end
+
def wiselinks_layout
'body'
end
sdk/go/crunchrunner
sdk/cwl
tools/crunchstat-summary
+ tools/keep-exercise
tools/keep-rsync
tools/keep-block-check
echo -n 'virtualenv: '
virtualenv --version \
|| fatal "No virtualenv. Try: apt-get install virtualenv (on ubuntu: python-virtualenv)"
+ echo -n 'ruby: '
+ ruby -v \
+ || fatal "No ruby. Install >=2.1.9 (using rbenv, rvm, or source)"
+ echo -n 'bundler: '
+ bundle version \
+ || fatal "No bundler. Try: gem install bundler"
echo -n 'go: '
go version \
|| fatal "No go binary. See http://golang.org/doc/install"
- [[ $(go version) =~ go1.([0-9]+) ]] && [[ ${BASH_REMATCH[1]} -ge 6 ]] \
- || fatal "Go >= 1.6 required. See http://golang.org/doc/install"
+ [[ $(go version) =~ go1.([0-9]+) ]] && [[ ${BASH_REMATCH[1]} -ge 7 ]] \
+ || fatal "Go >= 1.7 required. See http://golang.org/doc/install"
echo -n 'gcc: '
gcc --version | egrep ^gcc \
|| fatal "No gcc. Try: apt-get install build-essential"
services/crunch-dispatch-local
services/crunch-dispatch-slurm
services/crunch-run
- tools/keep-rsync
tools/keep-block-check
+ tools/keep-exercise
+ tools/keep-rsync
)
for g in "${gostuff[@]}"
do
source 'https://rubygems.org'
-gem 'rails', '~> 3.2.0'
+gem 'rails', '~> 3.2'
# Bundle edge Rails instead:
# gem 'rails', :git => 'git://github.com/rails/rails.git'
# Note: "require: false" here tells bunder not to automatically
# 'require' the packages during application startup. Installation is
# still mandatory.
+ gem 'test-unit', '~> 3.0', require: false
+ gem 'minitest-rails', require: false
+ gem 'minitest', '~> 4.0', require: false
gem 'simplecov', '~> 0.7.1', require: false
gem 'simplecov-rcov', require: false
gem 'mocha', require: false
end
-# This might not be needed in :test and :development, but we load it
-# anyway to make sure it always gets in Gemfile.lock and to help
-# reveal install problems sooner rather than later.
+# pg is the only supported database driver.
gem 'pg'
# Start using multi_json once we are on Rails 3.2;
# Gems used only for assets and not required
# in production environments by default.
group :assets do
- gem 'sass-rails', '>= 3.2.0'
- gem 'coffee-rails', '~> 3.2.0'
+ gem 'sass-rails', '~> 3.2'
+ gem 'coffee-rails', '~> 3.2'
# See https://github.com/sstephenson/execjs#readme for more supported runtimes
gem 'therubyracer'
- gem 'uglifier', '>= 1.0.3'
+ gem 'uglifier', '~> 2.0'
end
gem 'jquery-rails'
gem 'passenger'
-gem 'omniauth', '1.1.1'
-gem 'omniauth-oauth2', '1.1.1'
+gem 'omniauth', '~> 1.1'
+gem 'omniauth-oauth2', '~> 1.1'
gem 'andand'
gem 'themes_for_rails'
gem 'arvados', '>= 0.1.20150615153458'
- gem 'arvados-cli', '>= 0.1.20151207150126'
+ gem 'arvados-cli', '>= 0.1.20161017193526'
# pg_power lets us use partial indexes in schema.rb in Rails 3
gem 'pg_power'
-gem 'puma'
+gem 'puma', '~> 2.0'
gem 'sshkey'
gem 'safe_yaml'
gem 'lograge'
GEM
remote: https://rubygems.org/
specs:
- actionmailer (3.2.17)
- actionpack (= 3.2.17)
+ actionmailer (3.2.22.5)
+ actionpack (= 3.2.22.5)
mail (~> 2.5.4)
- actionpack (3.2.17)
- activemodel (= 3.2.17)
- activesupport (= 3.2.17)
+ actionpack (3.2.22.5)
+ activemodel (= 3.2.22.5)
+ activesupport (= 3.2.22.5)
builder (~> 3.0.0)
erubis (~> 2.7.0)
journey (~> 1.0.4)
rack-cache (~> 1.2)
rack-test (~> 0.6.1)
sprockets (~> 2.2.1)
- activemodel (3.2.17)
- activesupport (= 3.2.17)
+ activemodel (3.2.22.5)
+ activesupport (= 3.2.22.5)
builder (~> 3.0.0)
- activerecord (3.2.17)
- activemodel (= 3.2.17)
- activesupport (= 3.2.17)
+ activerecord (3.2.22.5)
+ activemodel (= 3.2.22.5)
+ activesupport (= 3.2.22.5)
arel (~> 3.0.2)
tzinfo (~> 0.3.29)
- activeresource (3.2.17)
- activemodel (= 3.2.17)
- activesupport (= 3.2.17)
- activesupport (3.2.17)
+ activeresource (3.2.22.5)
+ activemodel (= 3.2.22.5)
+ activesupport (= 3.2.22.5)
+ activesupport (3.2.22.5)
i18n (~> 0.6, >= 0.6.4)
multi_json (~> 1.0)
- acts_as_api (0.4.2)
+ acts_as_api (0.4.3)
activemodel (>= 3.0.0)
activesupport (>= 3.0.0)
rack (>= 1.1.0)
addressable (2.4.0)
andand (1.3.3)
arel (3.0.3)
- arvados (0.1.20160420143004)
+ arvados (0.1.20160513152536)
activesupport (>= 3, < 4.2.6)
andand (~> 1.3, >= 1.3.3)
- google-api-client (>= 0.7, < 0.9)
+ google-api-client (>= 0.7, < 0.8.9)
i18n (~> 0)
json (~> 1.7, >= 1.7.7)
jwt (>= 0.1.5, < 2)
- arvados-cli (0.1.20160913140509)
+ arvados-cli (0.1.20161017193526)
activesupport (~> 3.2, >= 3.2.13)
andand (~> 1.3, >= 1.3.3)
arvados (~> 0.1, >= 0.1.20150128223554)
extlib (>= 0.9.15)
multi_json (>= 1.0.0)
builder (3.0.4)
- capistrano (2.15.5)
+ capistrano (2.15.9)
highline
net-scp (>= 1.0.0)
net-sftp (>= 2.0.0)
net-ssh (>= 2.0.14)
net-ssh-gateway (>= 1.1.0)
- coffee-rails (3.2.1)
+ coffee-rails (3.2.2)
coffee-script (>= 2.2.0)
- railties (~> 3.2.0.beta)
- coffee-script (2.2.0)
+ railties (~> 3.2.0)
+ coffee-script (2.4.1)
coffee-script-source
execjs
- coffee-script-source (1.7.0)
+ coffee-script-source (1.10.0)
curb (0.9.3)
- daemon_controller (1.2.0)
- database_cleaner (1.2.0)
+ database_cleaner (1.5.3)
erubis (2.7.0)
- eventmachine (1.0.3)
- execjs (2.0.2)
+ eventmachine (1.2.0.1)
+ execjs (2.7.0)
extlib (0.9.16)
- factory_girl (4.4.0)
+ factory_girl (4.7.0)
activesupport (>= 3.0.0)
- factory_girl_rails (4.4.1)
- factory_girl (~> 4.4.0)
+ factory_girl_rails (4.7.0)
+ factory_girl (~> 4.7.0)
railties (>= 3.0.0)
faraday (0.9.2)
multipart-post (>= 1.2, < 3)
- faye-websocket (0.7.2)
+ faye-websocket (0.10.4)
eventmachine (>= 0.12.0)
- websocket-driver (>= 0.3.1)
- google-api-client (0.7.1)
- addressable (>= 2.3.2)
- autoparse (>= 0.3.3)
- extlib (>= 0.9.15)
- faraday (>= 0.9.0)
- jwt (>= 0.1.5)
- launchy (>= 2.1.1)
- multi_json (>= 1.0.0)
- retriable (>= 1.4)
- signet (>= 0.5.0)
- uuidtools (>= 2.1.0)
- hashie (1.2.0)
- highline (1.6.21)
+ websocket-driver (>= 0.5.1)
+ google-api-client (0.8.7)
+ activesupport (>= 3.2, < 5.0)
+ addressable (~> 2.3)
+ autoparse (~> 0.3)
+ extlib (~> 0.9)
+ faraday (~> 0.9)
+ googleauth (~> 0.3)
+ launchy (~> 2.4)
+ multi_json (~> 1.10)
+ retriable (~> 1.4)
+ signet (~> 0.6)
+ googleauth (0.5.1)
+ faraday (~> 0.9)
+ jwt (~> 1.4)
+ logging (~> 2.0)
+ memoist (~> 0.12)
+ multi_json (~> 1.11)
+ os (~> 0.9)
+ signet (~> 0.7)
+ hashie (3.4.6)
+ highline (1.7.8)
hike (1.2.3)
- httpauth (0.2.1)
i18n (0.7.0)
journey (1.0.4)
- jquery-rails (3.1.0)
+ jquery-rails (3.1.4)
railties (>= 3.0, < 5.0)
thor (>= 0.14, < 2.0)
json (1.8.3)
- jwt (0.1.13)
- multi_json (>= 1.5)
+ jwt (1.5.6)
launchy (2.4.3)
addressable (~> 2.3)
- libv8 (3.16.14.3)
+ libv8 (3.16.14.15)
+ little-plugger (1.1.4)
+ logging (2.1.0)
+ little-plugger (~> 1.1)
+ multi_json (~> 1.10)
lograge (0.3.6)
actionpack (>= 3)
activesupport (>= 3)
mail (2.5.4)
mime-types (~> 1.16)
treetop (~> 1.4.8)
+ memoist (0.15.0)
metaclass (0.0.4)
mime-types (1.25.1)
- mocha (1.1.0)
+ minitest (4.7.5)
+ minitest-rails (1.0.1)
+ minitest (~> 4.7)
+ minitest-test (~> 1.0)
+ railties (>= 3.0, < 4.1)
+ minitest-test (1.1.0)
+ minitest (~> 4.0)
+ mocha (1.2.0)
metaclass (~> 0.0.1)
- multi_json (1.12.0)
+ multi_json (1.12.1)
+ multi_xml (0.5.5)
multipart-post (2.0.0)
- net-scp (1.2.0)
+ net-scp (1.2.1)
net-ssh (>= 2.6.5)
net-sftp (2.1.2)
net-ssh (>= 2.6.5)
- net-ssh (2.8.0)
+ net-ssh (3.2.0)
net-ssh-gateway (1.2.0)
net-ssh (>= 2.6.5)
- oauth2 (0.8.1)
- faraday (~> 0.8)
- httpauth (~> 0.1)
- jwt (~> 0.1.4)
- multi_json (~> 1.0)
- rack (~> 1.2)
+ oauth2 (1.2.0)
+ faraday (>= 0.8, < 0.10)
+ jwt (~> 1.0)
+ multi_json (~> 1.3)
+ multi_xml (~> 0.5)
+ rack (>= 1.2, < 3)
oj (2.15.0)
- omniauth (1.1.1)
- hashie (~> 1.2)
- rack
- omniauth-oauth2 (1.1.1)
- oauth2 (~> 0.8.0)
- omniauth (~> 1.0)
- passenger (4.0.41)
- daemon_controller (>= 1.2.0)
+ omniauth (1.3.1)
+ hashie (>= 1.2, < 4)
+ rack (>= 1.0, < 3)
+ omniauth-oauth2 (1.4.0)
+ oauth2 (~> 1.0)
+ omniauth (~> 1.2)
+ os (0.9.6)
+ passenger (5.0.30)
rack
rake (>= 0.8.1)
- pg (0.17.1)
+ pg (0.19.0)
pg_power (1.6.4)
pg
rails (~> 3.1)
- polyglot (0.3.4)
- puma (2.8.2)
- rack (>= 1.1, < 2.0)
- rack (1.4.5)
- rack-cache (1.2)
+ polyglot (0.3.5)
+ power_assert (0.3.1)
+ puma (2.16.0)
+ rack (1.4.7)
+ rack-cache (1.6.1)
rack (>= 0.4)
rack-ssl (1.3.4)
rack
- rack-test (0.6.2)
+ rack-test (0.6.3)
rack (>= 1.0)
- rails (3.2.17)
- actionmailer (= 3.2.17)
- actionpack (= 3.2.17)
- activerecord (= 3.2.17)
- activeresource (= 3.2.17)
- activesupport (= 3.2.17)
+ rails (3.2.22.5)
+ actionmailer (= 3.2.22.5)
+ actionpack (= 3.2.22.5)
+ activerecord (= 3.2.22.5)
+ activeresource (= 3.2.22.5)
+ activesupport (= 3.2.22.5)
bundler (~> 1.0)
- railties (= 3.2.17)
- railties (3.2.17)
- actionpack (= 3.2.17)
- activesupport (= 3.2.17)
+ railties (= 3.2.22.5)
+ railties (3.2.22.5)
+ actionpack (= 3.2.22.5)
+ activesupport (= 3.2.22.5)
rack-ssl (~> 1.3.2)
rake (>= 0.8.7)
rdoc (~> 3.4)
thor (>= 0.14.6, < 2.0)
- rake (10.2.2)
+ rake (11.3.0)
rdoc (3.12.2)
json (~> 1.4)
- ref (1.0.5)
- retriable (2.1.0)
- ruby-prof (0.15.2)
- rvm-capistrano (1.5.1)
+ ref (2.0.0)
+ retriable (1.4.1)
+ ruby-prof (0.16.2)
+ rvm-capistrano (1.5.6)
capistrano (~> 2.15.4)
safe_yaml (1.0.4)
- sass (3.3.4)
+ sass (3.4.22)
sass-rails (3.2.6)
railties (~> 3.2.0)
sass (>= 3.1.10)
tilt (~> 1.3)
- signet (0.5.1)
- addressable (>= 2.2.3)
- faraday (>= 0.9.0.rc5)
- jwt (>= 0.1.5)
- multi_json (>= 1.0.0)
+ signet (0.7.3)
+ addressable (~> 2.3)
+ faraday (~> 0.9)
+ jwt (~> 1.5)
+ multi_json (~> 1.10)
simplecov (0.7.1)
multi_json (~> 1.0)
simplecov-html (~> 0.7.1)
simplecov-html (0.7.1)
simplecov-rcov (0.2.3)
simplecov (>= 0.4.1)
- sprockets (2.2.2)
+ sprockets (2.2.3)
hike (~> 1.2)
multi_json (~> 1.0)
rack (~> 1.0)
tilt (~> 1.1, != 1.3.0)
- sshkey (1.6.1)
- test_after_commit (0.2.3)
+ sshkey (1.8.0)
+ test-unit (3.2.1)
+ power_assert
+ test_after_commit (1.1.0)
+ activerecord (>= 3.2)
themes_for_rails (0.5.1)
rails (>= 3.0.0)
- therubyracer (0.12.1)
+ therubyracer (0.12.2)
libv8 (~> 3.16.14.0)
ref
thor (0.19.1)
polyglot
polyglot (>= 0.3.1)
trollop (2.1.2)
- tzinfo (0.3.39)
- uglifier (2.5.0)
+ tzinfo (0.3.51)
+ uglifier (2.7.2)
execjs (>= 0.3.0)
json (>= 1.8.0)
- uuidtools (2.1.5)
- websocket-driver (0.3.2)
+ websocket-driver (0.6.4)
+ websocket-extensions (>= 0.1.0)
+ websocket-extensions (0.1.2)
PLATFORMS
ruby
acts_as_api
andand
arvados (>= 0.1.20150615153458)
- arvados-cli (>= 0.1.20151207150126)
- coffee-rails (~> 3.2)
+ arvados-cli (>= 0.1.20161017193526)
+ coffee-rails (~> 3.2.0)
database_cleaner
factory_girl_rails
faye-websocket
jquery-rails
lograge
logstash-event
+ minitest (~> 4.0)
+ minitest-rails
mocha
multi_json
oj
- omniauth (= 1.1.1)
- omniauth-oauth2 (= 1.1.1)
+ omniauth (~> 1.1)
+ omniauth-oauth2 (~> 1.1)
passenger
pg
pg_power
- puma
- rails (~> 3.2.0)
+ puma (~> 2.0)
+ rails (~> 3.2)
ruby-prof
rvm-capistrano
safe_yaml
- sass-rails (>= 3.2.0)
+ sass-rails (~> 3.2)
simplecov (~> 0.7.1)
simplecov-rcov
sshkey
+ test-unit (~> 3.0)
test_after_commit
themes_for_rails
therubyracer
trollop
- uglifier (>= 1.0.3)
+ uglifier (~> 2.0)
+
+BUNDLED WITH
+ 1.13.2
ERROR_ACTIONS = [:render_error, :render_not_found]
+ before_filter :disable_api_methods
before_filter :set_cors_headers
before_filter :respond_with_json_by_default
before_filter :remote_ip
:with => :render_not_found)
end
+ def initialize *args
+ super
+ @object = nil
+ @objects = nil
+ @offset = nil
+ @limit = nil
+ @select = nil
+ @distinct = nil
+ @response_resource_name = nil
+ @attrs = nil
+ end
+
def default_url_options
if Rails.configuration.host
{:host => Rails.configuration.host}
end
end
+ def disable_api_methods
+ if Rails.configuration.disable_api_methods.
+ include?(controller_name + "." + action_name)
+ send_error("Disabled", status: 404)
+ end
+ end
+
def set_cors_headers
response.headers['Access-Control-Allow-Origin'] = '*'
response.headers['Access-Control-Allow-Methods'] = 'GET, HEAD, PUT, POST, DELETE'
end
def logged_attributes
- attributes.except *Rails.configuration.unlogged_attributes
+ attributes.except(*Rails.configuration.unlogged_attributes)
end
def self.full_text_searchable_columns
end
def foreign_key_attributes
- attributes.keys.select { |a| a.match /_uuid$/ }
+ attributes.keys.select { |a| a.match(/_uuid$/) }
end
def skip_uuid_read_permission_check
foreign_key_attributes.each do |attr|
attr_value = send attr
if attr_value.is_a? String and
- attr_value.match /^[0-9a-f]{32,}(\+[@\w]+)*$/
+ attr_value.match(/^[0-9a-f]{32,}(\+[@\w]+)*$/)
begin
send "#{attr}=", Collection.normalize_uuid(attr_value)
rescue
unless uuid.is_a? String
return nil
end
- resource_class = nil
uuid.match HasUuid::UUID_REGEX do |re|
return uuid_prefixes[re[1]] if uuid_prefixes[re[1]]
end
- if uuid.match /.+@.+/
+ if uuid.match(/.+@.+/)
return Email
end
end
def log_destroy
- log_change('destroy') do |log|
+ log_change('delete') do |log|
log.fill_properties('old', etag(@old_attributes), @old_logged_attributes)
log.update_to nil
end
t.add :expires_at
end
+ after_initialize do
+ @signatures_checked = false
+ @computed_pdh_for_manifest_text = false
+ end
+
def self.attributes_required_columns
super.merge(
# If we don't list manifest_text explicitly, the
# subsequent passes without checking any signatures. This is
# important because the signatures have probably been stripped off
# by the time we get to a second validation pass!
- return true if @signatures_checked and @signatures_checked == computed_pdh
+ if @signatures_checked && @signatures_checked == computed_pdh
+ return true
+ end
if self.manifest_text_changed?
# Check permissions on the collection manifest.
utf8 = manifest_text
utf8.force_encoding Encoding::UTF_8
if utf8.valid_encoding? and utf8 == manifest_text.encode(Encoding::UTF_8)
- manifest_text = utf8
+ self.manifest_text = utf8
return true
end
rescue
hash_part = nil
size_part = nil
uuid.split('+').each do |token|
- if token.match /^[0-9a-f]{32,}$/
+ if token.match(/^[0-9a-f]{32,}$/)
raise "uuid #{uuid} has multiple hash parts" if hash_part
hash_part = token
- elsif token.match /^\d+$/
+ elsif token.match(/^\d+$/)
raise "uuid #{uuid} has multiple size parts" if size_part
size_part = token
end
# looks like a saved Docker image.
manifest = Keep::Manifest.new(coll_match.manifest_text)
if manifest.exact_file_count?(1) and
- (manifest.files[0][1] =~ /^[0-9A-Fa-f]{64}\.tar$/)
+ (manifest.files[0][1] =~ /^(sha256:)?[0-9A-Fa-f]{64}\.tar$/)
return [coll_match]
end
end
include CommonApiTemplate
serialize :properties, Hash
before_validation :set_default_event_at
- attr_accessor :object, :object_kind
after_save :send_notify
api_accessible :user, extend: :common do |t|
self.event_at = thing.created_at
when "update"
self.event_at = thing.modified_at
- when "destroy"
+ when "delete"
self.event_at = db_current_time
end
self
belongs_to(:job, foreign_key: :job_uuid, primary_key: :uuid)
attr_accessor :job_readable
+ UNUSED_NODE_IP = '127.40.4.0'
+
api_accessible :user, :extend => :common do |t|
t.add :hostname
t.add :domain
t.add lambda { |x| Rails.configuration.compute_node_nameservers }, :as => :nameservers
end
+ after_initialize do
+ @bypass_arvados_authorization = false
+ end
+
def domain
super || Rails.configuration.compute_node_domain
end
end
def dns_server_update
- if self.hostname_changed? or self.ip_address_changed?
- if not self.ip_address.nil?
- stale_conflicting_nodes = Node.where('id != ? and ip_address = ? and last_ping_at < ?',self.id,self.ip_address,10.minutes.ago)
- if not stale_conflicting_nodes.empty?
- # One or more stale compute node records have the same IP address as the new node.
- # Clear the ip_address field on the stale nodes.
- stale_conflicting_nodes.each do |stale_node|
- stale_node.ip_address = nil
- stale_node.save!
- end
+ if hostname_changed? && hostname_was
+ self.class.dns_server_update(hostname_was, UNUSED_NODE_IP)
+ end
+ if hostname_changed? or ip_address_changed?
+ if ip_address
+ Node.where('id != ? and ip_address = ? and last_ping_at < ?',
+ id, ip_address, 10.minutes.ago).each do |stale_node|
+ # One or more stale compute node records have the same IP
+ # address as the new node. Clear the ip_address field on
+ # the stale nodes.
+ stale_node.ip_address = nil
+ stale_node.save!
end
end
- if self.hostname and self.ip_address
- self.class.dns_server_update(self.hostname, self.ip_address)
+ if hostname
+ self.class.dns_server_update(hostname, ip_address || UNUSED_NODE_IP)
end
end
end
(0..Rails.configuration.max_compute_nodes-1).each do |slot_number|
hostname = hostname_for_slot(slot_number)
hostfile = File.join Rails.configuration.dns_server_conf_dir, "#{hostname}.conf"
- if !File.exists? hostfile
+ if !File.exist? hostfile
n = Node.where(:slot_number => slot_number).first
if n.nil? or n.ip_address.nil?
- dns_server_update(hostname, '127.40.4.0')
+ dns_server_update(hostname, UNUSED_NODE_IP)
else
dns_server_update(hostname, n.ip_address)
end
def is_invited
!!(self.is_active ||
Rails.configuration.new_users_are_active ||
- self.groups_i_can(:read).select { |x| x.match /-f+$/ }.first)
+ self.groups_i_can(:read).select { |x| x.match(/-f+$/) }.first)
end
def groups_i_can(verb)
# delete "All users" group read permissions for this user
group = Group.where(name: 'All users').select do |g|
- g[:uuid].match /-f+$/
+ g[:uuid].match(/-f+$/)
end.first
Link.destroy_all(tail_uuid: self.uuid,
head_uuid: group[:uuid],
self.save!
end
+ def set_initial_username(requested: false)
+ if !requested.is_a?(String) || requested.empty?
+ email_parts = email.partition("@")
+ local_parts = email_parts.first.partition("+")
+ if email_parts.any?(&:empty?)
+ return
+ elsif not local_parts.first.empty?
+ requested = local_parts.first
+ else
+ requested = email_parts.first
+ end
+ end
+ requested.sub!(/^[^A-Za-z]+/, "")
+ requested.gsub!(/[^A-Za-z0-9]/, "")
+ unless requested.empty?
+ self.username = find_usable_username_from(requested)
+ end
+ end
+
protected
def ensure_ownership_path_leads_to_user
nil
end
- def set_initial_username
- email_parts = email.partition("@")
- local_parts = email_parts.first.partition("+")
- if email_parts.any?(&:empty?)
- return
- elsif not local_parts.first.empty?
- base_username = local_parts.first
- else
- base_username = email_parts.first
- end
- base_username.sub!(/^[^A-Za-z]+/, "")
- base_username.gsub!(/[^A-Za-z0-9]/, "")
- unless base_username.empty?
- self.username = find_usable_username_from(base_username)
- end
- end
-
def prevent_privilege_escalation
if current_user.andand.is_admin
return true
end
end
+ test 'index without select returns everything except manifest' do
+ authorize_with :active
+ get :index
+ assert_response :success
+ assert json_response['items'].any?
+ json_response['items'].each do |coll|
+ assert_includes(coll.keys, 'uuid')
+ assert_includes(coll.keys, 'name')
+ assert_includes(coll.keys, 'created_at')
+ refute_includes(coll.keys, 'manifest_text')
+ end
+ end
+
+ ['', nil, false, 'null'].each do |select|
+ test "index with select=#{select.inspect} returns everything except manifest" do
+ authorize_with :active
+ get :index, select: select
+ assert_response :success
+ assert json_response['items'].any?
+ json_response['items'].each do |coll|
+ assert_includes(coll.keys, 'uuid')
+ assert_includes(coll.keys, 'name')
+ assert_includes(coll.keys, 'created_at')
+ refute_includes(coll.keys, 'manifest_text')
+ end
+ end
+ end
+
+ [["uuid"],
+ ["uuid", "manifest_text"],
+ '["uuid"]',
+ '["uuid", "manifest_text"]'].each do |select|
+ test "index with select=#{select.inspect} returns no name" do
+ authorize_with :active
+ get :index, select: select
+ assert_response :success
+ assert json_response['items'].any?
+ json_response['items'].each do |coll|
+ refute_includes(coll.keys, 'name')
+ end
+ end
+ end
+
[0,1,2].each do |limit|
test "get index with limit=#{limit}" do
authorize_with :active
[2**8, :success],
[2**18, 422],
].each do |description_size, expected_response|
- test "create collection with description size #{description_size}
+ # Descriptions are not part of search indexes. Skip until
+ # full-text search is implemented, at which point replace with a
+ # search in description.
+ skip "create collection with description size #{description_size}
and expect response #{expected_response}" do
- skip "(Descriptions are not part of search indexes. Skip until full-text search
- is implemented, at which point replace with a search in description.)"
-
authorize_with :active
description = 'here is a collection with a very large description'
'server should correct bogus cancelled_at ' +
job['cancelled_at'])
assert_equal(true,
- File.exists?(Rails.configuration.crunch_refresh_trigger),
+ File.exist?(Rails.configuration.crunch_refresh_trigger),
'trigger file should be created when job is cancelled')
end
assert_not_nil json_response["components"]
assert_equal [], json_response["components"].keys
end
+
+ test 'jobs.create disabled in config' do
+ Rails.configuration.disable_api_methods = ["jobs.create",
+ "pipeline_instances.create"]
+ authorize_with :active
+ post :create, job: {
+ script: "hash",
+ script_version: "master",
+ repository: "active/foo",
+ script_parameters: {}
+ }
+ assert_response 404
+ end
end
projects / arvados.git / commitdiff