[ARVADOS] updated: 6122bbc7a1c48e8bded0ace61be5786ea398651f
Git user
git at public.curoverse.com
Mon Mar 14 15:34:30 EDT 2016
Summary of changes:
services/api/Rakefile | 34 ++++++++++++----------
.../arvados/v1/repositories_controller_test.rb | 1 -
2 files changed, 18 insertions(+), 17 deletions(-)
discards 802401710776e8efe1c7d7856b6e87d99fda178d (commit)
via 6122bbc7a1c48e8bded0ace61be5786ea398651f (commit)
via 0d4eeea43fdc67be95e5b45022db3a6234df5f40 (commit)
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commit 6122bbc7a1c48e8bded0ace61be5786ea398651f
Author: Tom Clegg <tom at curoverse.com>
Date: Mon Mar 14 15:34:07 2016 -0400
5737: Back out Rakefile stuff
diff --git a/services/api/Rakefile b/services/api/Rakefile
index fbbf53e..65cd4b3 100644
--- a/services/api/Rakefile
+++ b/services/api/Rakefile
@@ -12,23 +12,25 @@ end
Server::Application.load_tasks
-namespace :test do
- task(:run).clear
- # Copied from the definition in Rails 3.2.
- # This may need to be updated if we upgrade Rails.
- task :run do
- errors = %w(test:units test:functionals test:integration test:tasks).collect do |task|
- begin
- Rake::Task[task].invoke
- nil
- rescue => e
- { :task => task, :exception => e }
- end
- end.compact
+if false
+ namespace :test do
+ task(:run).clear
+ # Copied from the definition in Rails 3.2.
+ # This may need to be updated if we upgrade Rails.
+ task :run do
+ errors = %w(test:units test:functionals test:integration test:tasks).collect do |task|
+ begin
+ Rake::Task[task].invoke
+ nil
+ rescue => e
+ { :task => task, :exception => e }
+ end
+ end.compact
- if errors.any?
- puts errors.map { |e| "Errors running #{e[:task]}! #{e[:exception].inspect}" }.join("\n")
- abort
+ if errors.any?
+ puts errors.map { |e| "Errors running #{e[:task]}! #{e[:exception].inspect}" }.join("\n")
+ abort
+ end
end
end
end
commit 0d4eeea43fdc67be95e5b45022db3a6234df5f40
Author: Tom Clegg <tom at curoverse.com>
Date: Mon Mar 14 15:31:44 2016 -0400
5737: More Ruby 2.2 compat fixes
diff --git a/services/api/Gemfile b/services/api/Gemfile
index 43d0b67..efc0cad 100644
--- a/services/api/Gemfile
+++ b/services/api/Gemfile
@@ -9,7 +9,7 @@ group :test, :development do
gem 'factory_girl_rails'
gem 'database_cleaner'
gem 'ruby-prof'
- gem 'minitest', '~> 5.0'
+ gem 'test-unit', '~> 3.0'
# Note: "require: false" here tells bunder not to automatically
# 'require' the packages during application startup. Installation is
# still mandatory.
@@ -32,7 +32,7 @@ gem 'oj'
# Gems used only for assets and not required
# in production environments by default.
group :assets do
- gem 'sass-rails', '>= 3.2'
+ gem 'sass-rails', '~> 3.2'
gem 'coffee-rails', '~> 3.2'
# See https://github.com/sstephenson/execjs#readme for more supported runtimes
@@ -61,8 +61,8 @@ gem 'acts_as_api'
gem 'passenger'
-gem 'omniauth', '1.1.1'
-gem 'omniauth-oauth2', '1.1.1'
+gem 'omniauth', '~> 1.1.1'
+gem 'omniauth-oauth2', '~> 1.1.1'
gem 'andand'
diff --git a/services/api/Gemfile.lock b/services/api/Gemfile.lock
index 9854111..2599027 100644
--- a/services/api/Gemfile.lock
+++ b/services/api/Gemfile.lock
@@ -95,7 +95,7 @@ GEM
multi_json (>= 1.0.0)
signet (~> 0.4.5)
uuidtools (>= 2.1.0)
- hashie (1.2.0)
+ hashie (2.1.2)
highline (1.7.8)
hike (1.2.3)
httpauth (0.2.1)
@@ -115,7 +115,6 @@ GEM
treetop (~> 1.4.8)
metaclass (0.0.4)
mime-types (1.25.1)
- minitest (5.8.4)
mocha (1.1.0)
metaclass (~> 0.0.1)
multi_json (1.11.2)
@@ -134,8 +133,8 @@ GEM
multi_json (~> 1.0)
rack (~> 1.2)
oj (2.14.6)
- omniauth (1.1.1)
- hashie (~> 1.2)
+ omniauth (1.1.4)
+ hashie (>= 1.2, < 3)
rack
omniauth-oauth2 (1.1.1)
oauth2 (~> 0.8.0)
@@ -148,6 +147,7 @@ GEM
pg
rails (~> 3.1)
polyglot (0.3.5)
+ power_assert (0.2.7)
puma (3.1.0)
rack (1.4.7)
rack-cache (1.6.1)
@@ -171,7 +171,7 @@ GEM
rake (>= 0.8.7)
rdoc (~> 3.4)
thor (>= 0.14.6, < 2.0)
- rake (11.0.1)
+ rake (11.1.1)
rdoc (3.12.2)
json (~> 1.4)
ref (2.0.0)
@@ -200,6 +200,8 @@ GEM
rack (~> 1.0)
tilt (~> 1.1, != 1.3.0)
sshkey (1.8.0)
+ test-unit (3.1.7)
+ power_assert
test_after_commit (1.0.0)
activerecord (>= 3.2)
themes_for_rails (0.5.1)
@@ -236,12 +238,11 @@ DEPENDENCIES
faye-websocket
google-api-client (~> 0.6.3)
jquery-rails
- minitest (~> 5.0)
mocha
multi_json
oj
- omniauth (= 1.1.1)
- omniauth-oauth2 (= 1.1.1)
+ omniauth (~> 1.1.1)
+ omniauth-oauth2 (~> 1.1.1)
passenger
pg
pg_power
@@ -249,10 +250,11 @@ DEPENDENCIES
rails (~> 3.2)
ruby-prof
rvm-capistrano
- sass-rails (>= 3.2)
+ sass-rails (~> 3.2)
simplecov (~> 0.7.1)
simplecov-rcov
sshkey
+ test-unit (~> 3.0)
test_after_commit
themes_for_rails
therubyracer
diff --git a/services/api/app/models/collection.rb b/services/api/app/models/collection.rb
index f1e7b4f..cd2bd74 100644
--- a/services/api/app/models/collection.rb
+++ b/services/api/app/models/collection.rb
@@ -41,6 +41,11 @@ class Collection < ArvadosModel
)
end
+ def initialize *args
+ super
+ @signatures_checked = false
+ end
+
FILE_TOKEN = /^[[:digit:]]+:[[:digit:]]+:/
def check_signatures
return false if self.manifest_text.nil?
diff --git a/services/api/app/models/job.rb b/services/api/app/models/job.rb
index 6c24293..b65f70b 100644
--- a/services/api/app/models/job.rb
+++ b/services/api/app/models/job.rb
@@ -387,26 +387,8 @@ class Job < ArvadosModel
end
def ensure_no_collection_uuids_in_script_params
- # recursive_hash_search searches recursively through hashes and
- # arrays in 'thing' for string fields matching regular expression
- # 'pattern'. Returns true if pattern is found, false otherwise.
- def recursive_hash_search thing, pattern
- if thing.is_a? Hash
- thing.each do |k, v|
- return true if recursive_hash_search v, pattern
- end
- elsif thing.is_a? Array
- thing.each do |k|
- return true if recursive_hash_search k, pattern
- end
- elsif thing.is_a? String
- return true if thing.match pattern
- end
- false
- end
-
- # Fail validation if any script_parameters field includes a string containing a
- # collection uuid pattern.
+ # Fail validation if any script_parameters field includes a string
+ # containing a collection uuid pattern.
if self.script_parameters_changed?
if recursive_hash_search(self.script_parameters, Collection.uuid_regex)
self.errors.add :script_parameters, "must use portable_data_hash instead of collection uuid"
@@ -415,4 +397,22 @@ class Job < ArvadosModel
end
true
end
+
+ # recursive_hash_search searches recursively through hashes and
+ # arrays in 'thing' for string fields matching regular expression
+ # 'pattern'. Returns true if pattern is found, false otherwise.
+ def recursive_hash_search thing, pattern
+ if thing.is_a? Hash
+ thing.each do |k, v|
+ return true if recursive_hash_search v, pattern
+ end
+ elsif thing.is_a? Array
+ thing.each do |k|
+ return true if recursive_hash_search k, pattern
+ end
+ elsif thing.is_a? String
+ return true if thing.match pattern
+ end
+ false
+ end
end
diff --git a/services/api/app/models/node.rb b/services/api/app/models/node.rb
index abb46fd..0b84cdc 100644
--- a/services/api/app/models/node.rb
+++ b/services/api/app/models/node.rb
@@ -222,7 +222,7 @@ class Node < ArvadosModel
(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')
diff --git a/services/api/config/boot.rb b/services/api/config/boot.rb
index 4489e58..f2830ae 100644
--- a/services/api/config/boot.rb
+++ b/services/api/config/boot.rb
@@ -3,4 +3,4 @@ require 'rubygems'
# Set up gems listed in the Gemfile.
ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../../Gemfile', __FILE__)
-require 'bundler/setup' if File.exists?(ENV['BUNDLE_GEMFILE'])
+require 'bundler/setup' if File.exist?(ENV['BUNDLE_GEMFILE'])
diff --git a/services/api/config/initializers/load_config.rb b/services/api/config/initializers/load_config.rb
index de9770d..3a7f962 100644
--- a/services/api/config/initializers/load_config.rb
+++ b/services/api/config/initializers/load_config.rb
@@ -6,7 +6,7 @@ rescue LoadError
# configured by application.yml (i.e., here!) instead.
end
-if (File.exists?(File.expand_path '../omniauth.rb', __FILE__) and
+if (File.exist?(File.expand_path '../omniauth.rb', __FILE__) and
not defined? WARNED_OMNIAUTH_CONFIG)
Rails.logger.warn <<-EOS
DEPRECATED CONFIGURATION:
@@ -26,7 +26,7 @@ $application_config = {}
%w(application.default application).each do |cfgfile|
path = "#{::Rails.root.to_s}/config/#{cfgfile}.yml"
- if File.exists? path
+ if File.exist? path
yaml = ERB.new(IO.read path).result(binding)
confs = YAML.load(yaml)
# Ignore empty YAML file:
diff --git a/services/api/lib/crunch_dispatch.rb b/services/api/lib/crunch_dispatch.rb
index ce94f73..83cd1b9 100644
--- a/services/api/lib/crunch_dispatch.rb
+++ b/services/api/lib/crunch_dispatch.rb
@@ -27,7 +27,7 @@ class CrunchDispatch
@cgroup_root = ENV['CRUNCH_CGROUP_ROOT']
@arvados_internal = Rails.configuration.git_internal_dir
- if not File.exists? @arvados_internal
+ if not File.exist? @arvados_internal
$stderr.puts `mkdir -p #{@arvados_internal.shellescape} && git init --bare #{@arvados_internal.shellescape}`
raise "No internal git repository available" unless ($? == 0)
end
diff --git a/services/api/script/arvados-git-sync.rb b/services/api/script/arvados-git-sync.rb
index 3a8ed27..b785534 100755
--- a/services/api/script/arvados-git-sync.rb
+++ b/services/api/script/arvados-git-sync.rb
@@ -22,7 +22,7 @@ DEBUG = 1
# load and merge in the environment-specific application config info
# if present, overriding base config parameters as specified
path = File.absolute_path('../../config/arvados-clients.yml', __FILE__)
-if File.exists?(path) then
+if File.exist?(path) then
cp_config = YAML.load_file(path)[ENV['RAILS_ENV']]
else
puts "Please create a\n #{path}\n file"
@@ -214,7 +214,7 @@ end
begin
# Get our local gitolite-admin repo up to snuff
- if not File.exists?(gitolite_admin) then
+ if not File.exist?(gitolite_admin) then
ensure_directory(gitolite_tmpdir, 0700)
Dir.chdir(gitolite_tmpdir)
`git clone #{gitolite_url}`
diff --git a/services/api/script/migrate-gitolite-to-uuid-storage.rb b/services/api/script/migrate-gitolite-to-uuid-storage.rb
index 8db1a0e..169509f 100755
--- a/services/api/script/migrate-gitolite-to-uuid-storage.rb
+++ b/services/api/script/migrate-gitolite-to-uuid-storage.rb
@@ -35,7 +35,7 @@ DEBUG = 1
# load and merge in the environment-specific application config info
# if present, overriding base config parameters as specified
path = File.dirname(__FILE__) + '/config/arvados-clients.yml'
-if File.exists?(path) then
+if File.exist?(path) then
cp_config = YAML.load_file(path)[ENV['RAILS_ENV']]
else
puts "Please create a\n " + File.dirname(__FILE__) + "/config/arvados-clients.yml\n file"
@@ -186,7 +186,7 @@ end
begin
# Get our local gitolite-admin repo up to snuff
- if not File.exists?(gitolite_admin) then
+ if not File.exist?(gitolite_admin) then
ensure_directory(gitolite_tmpdir, 0700)
Dir.chdir(gitolite_tmpdir)
`git clone #{gitolite_url}`
diff --git a/services/api/test/functional/arvados/v1/collections_controller_test.rb b/services/api/test/functional/arvados/v1/collections_controller_test.rb
index a8583be..5aa96c8 100644
--- a/services/api/test/functional/arvados/v1/collections_controller_test.rb
+++ b/services/api/test/functional/arvados/v1/collections_controller_test.rb
@@ -753,7 +753,7 @@ EOS
].each do |description_size, expected_response|
test "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
+ omit "(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
diff --git a/services/api/test/functional/arvados/v1/jobs_controller_test.rb b/services/api/test/functional/arvados/v1/jobs_controller_test.rb
index 1e1425e..e66eb0d 100644
--- a/services/api/test/functional/arvados/v1/jobs_controller_test.rb
+++ b/services/api/test/functional/arvados/v1/jobs_controller_test.rb
@@ -97,7 +97,7 @@ class Arvados::V1::JobsControllerTest < ActionController::TestCase
'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
diff --git a/services/api/test/functional/arvados/v1/links_controller_test.rb b/services/api/test/functional/arvados/v1/links_controller_test.rb
index 1345701..af3cd3a 100644
--- a/services/api/test/functional/arvados/v1/links_controller_test.rb
+++ b/services/api/test/functional/arvados/v1/links_controller_test.rb
@@ -306,7 +306,7 @@ class Arvados::V1::LinksControllerTest < ActionController::TestCase
end
test "retrieve all permissions using generic links index api" do
- skip "(not implemented)"
+ omit "(not implemented)"
# Links.readable_by() does not return the full set of permission
# links that are visible to a user (i.e., all permission links
# whose head_uuid references an object for which the user has
diff --git a/services/api/test/functional/arvados/v1/repositories_controller_test.rb b/services/api/test/functional/arvados/v1/repositories_controller_test.rb
index c709d98..5a5ac4c 100644
--- a/services/api/test/functional/arvados/v1/repositories_controller_test.rb
+++ b/services/api/test/functional/arvados/v1/repositories_controller_test.rb
@@ -215,7 +215,6 @@ class Arvados::V1::RepositoriesControllerTest < ActionController::TestCase
refute_match expect[:refute], u
end
else
- assert_match expect[:match], u
assert((r['clone_urls'].any? do |u|
expect[:match].match u
end),
diff --git a/services/api/test/unit/app_version_test.rb b/services/api/test/unit/app_version_test.rb
index 3e9b167..4718ac2 100644
--- a/services/api/test/unit/app_version_test.rb
+++ b/services/api/test/unit/app_version_test.rb
@@ -29,7 +29,7 @@ class AppVersionTest < ActiveSupport::TestCase
test 'override with file' do
path = Rails.root.join 'git-commit.version'
- assert(!File.exists?(path),
+ assert(!File.exist?(path),
"Packaged version file found in source tree: #{path}")
begin
File.open(path, 'w') do |f|
diff --git a/services/api/test/unit/commit_test.rb b/services/api/test/unit/commit_test.rb
index b57c23b..301e071 100644
--- a/services/api/test/unit/commit_test.rb
+++ b/services/api/test/unit/commit_test.rb
@@ -183,34 +183,34 @@ class CommitTest < ActiveSupport::TestCase
Dir.mktmpdir do |touchdir|
# invalid input to maximum
a = Commit.find_commit_range('active/foo', nil, "31ce37fe365b3dc204300a3e4c396ad333ed0556 ; touch #{touchdir}/uh_oh", nil)
- assert !File.exists?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'maximum' parameter of find_commit_range is exploitable"
+ assert !File.exist?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'maximum' parameter of find_commit_range is exploitable"
assert_equal [], a
# invalid input to maximum
a = Commit.find_commit_range('active/foo', nil, "$(uname>#{touchdir}/uh_oh)", nil)
- assert !File.exists?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'maximum' parameter of find_commit_range is exploitable"
+ assert !File.exist?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'maximum' parameter of find_commit_range is exploitable"
assert_equal [], a
# invalid input to minimum
a = Commit.find_commit_range('active/foo', "31ce37fe365b3dc204300a3e4c396ad333ed0556 ; touch #{touchdir}/uh_oh", "31ce37fe365b3dc204300a3e4c396ad333ed0556", nil)
- assert !File.exists?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'minimum' parameter of find_commit_range is exploitable"
+ assert !File.exist?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'minimum' parameter of find_commit_range is exploitable"
assert_equal [], a
# invalid input to minimum
a = Commit.find_commit_range('active/foo', "$(uname>#{touchdir}/uh_oh)", "31ce37fe365b3dc204300a3e4c396ad333ed0556", nil)
- assert !File.exists?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'minimum' parameter of find_commit_range is exploitable"
+ assert !File.exist?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'minimum' parameter of find_commit_range is exploitable"
assert_equal [], a
# invalid input to 'excludes'
# complains "fatal: bad object 077ba2ad3ea24a929091a9e6ce545c93199b8e57"
a = Commit.find_commit_range('active/foo', "31ce37fe365b3dc204300a3e4c396ad333ed0556", "077ba2ad3ea24a929091a9e6ce545c93199b8e57", ["4fe459abe02d9b365932b8f5dc419439ab4e2577 ; touch #{touchdir}/uh_oh"])
- assert !File.exists?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'excludes' parameter of find_commit_range is exploitable"
+ assert !File.exist?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'excludes' parameter of find_commit_range is exploitable"
assert_equal [], a
# invalid input to 'excludes'
# complains "fatal: bad object 077ba2ad3ea24a929091a9e6ce545c93199b8e57"
a = Commit.find_commit_range('active/foo', "31ce37fe365b3dc204300a3e4c396ad333ed0556", "077ba2ad3ea24a929091a9e6ce545c93199b8e57", ["$(uname>#{touchdir}/uh_oh)"])
- assert !File.exists?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'excludes' parameter of find_commit_range is exploitable"
+ assert !File.exist?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'excludes' parameter of find_commit_range is exploitable"
assert_equal [], a
end
end
diff --git a/services/api/test/unit/permission_test.rb b/services/api/test/unit/permission_test.rb
index 4a6ddc6..bc60f3b 100644
--- a/services/api/test/unit/permission_test.rb
+++ b/services/api/test/unit/permission_test.rb
@@ -144,7 +144,7 @@ class PermissionTest < ActiveSupport::TestCase
# TODO(twp): fix bug #3091, which should fix this test.
test "can_manage permission on a non-group object" do
- skip
+ omit
set_user_from_auth :admin
ob = Specimen.create!
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