source 'https://rubygems.org'
-gem 'rails', '~> 4.1.0'
+gem 'rails', '~> 4.1'
gem 'arvados', '>= 0.1.20150511150219'
gem 'activerecord-nulldb-adapter'
# in production environments by default.
group :assets do
gem 'sass-rails'
- gem 'uglifier', '>= 1.0.3'
+ gem 'uglifier', '~> 2.0'
# See https://github.com/sstephenson/execjs#readme for more supported runtimes
gem 'therubyracer', :platforms => :ruby
end
group :test, :diagnostics, :performance do
- gem 'minitest', '>= 5.0.0'
+ gem 'minitest', '~> 5.0'
gem 'selenium-webdriver'
gem 'capybara'
gem 'poltergeist'
deep_merge (1.0.1)
docile (1.1.5)
erubis (2.7.0)
- execjs (2.2.2)
+ execjs (2.7.0)
extlib (0.9.16)
faraday (0.9.2)
multipart-post (>= 1.2, < 3)
signet (~> 0.7)
headless (1.0.2)
highline (1.6.21)
- httpclient (2.6.0.1)
+ httpclient (2.8.2.4)
i18n (0.7.0)
jquery-rails (3.1.2)
railties (>= 3.0, < 5.0)
metaclass (~> 0.0.1)
morrisjs-rails (0.5.1)
railties (> 3.1, < 5)
- multi_json (1.12.0)
+ multi_json (1.12.1)
multipart-post (2.0.0)
net-scp (1.2.1)
net-ssh (>= 2.6.5)
tilt (1.4.1)
tzinfo (1.2.2)
thread_safe (~> 0.1)
- uglifier (2.7.0)
+ uglifier (2.7.2)
execjs (>= 0.3.0)
json (>= 1.8.0)
websocket (1.2.2)
less-rails
lograge
logstash-event
- minitest (>= 5.0.0)
+ minitest (~> 5.0)
mocha
morrisjs-rails
multi_json
piwik_analytics
poltergeist
rack-mini-profiler
- rails (~> 4.1.0)
+ rails (~> 4.1)
rails-perftest
raphael-rails
ruby-debug-passenger
sshkey
themes_for_rails!
therubyracer
- uglifier (>= 1.0.3)
+ uglifier (~> 2.0)
wiselinks
BUNDLED WITH
- 1.12.1
+ 1.13.2
# 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'}
["user1_with_load", 2, ["project_with_10_collections"], "project_with_2_pipelines_and_60_crs"],
["admin", 5, ["anonymously_accessible_project", "subproject_in_anonymous_accessible_project"], "aproject"],
].each do |user, page_size, tree_segment, unexpected|
+ # Note: this test is sensitive to database collation. It passes
+ # with en_US.UTF-8.
test "build my projects tree for #{user} user and verify #{unexpected} is omitted" do
use_token user
- ctrl = ProjectsController.new
-
- current_user = User.find(api_fixture('users')[user]['uuid'])
- my_tree = ctrl.send :my_wanted_projects_tree, current_user, page_size
+ tree, _, _ = @controller.send(:my_wanted_projects_tree,
+ User.current,
+ page_size)
tree_segment_at_depth_1 = api_fixture('groups')[tree_segment[0]]
tree_segment_at_depth_2 = api_fixture('groups')[tree_segment[1]] if tree_segment[1]
- tree_nodes = {}
- my_tree[0].each do |x|
- tree_nodes[x[:object]['uuid']] = x[:depth]
+ node_depth = {}
+ tree.each do |x|
+ node_depth[x[:object]['uuid']] = x[:depth]
end
- assert_equal(1, tree_nodes[tree_segment_at_depth_1['uuid']])
- assert_equal(2, tree_nodes[tree_segment_at_depth_2['uuid']]) if tree_segment[1]
+ assert_equal(1, node_depth[tree_segment_at_depth_1['uuid']])
+ assert_equal(2, node_depth[tree_segment_at_depth_2['uuid']]) if tree_segment[1]
unexpected_project = api_fixture('groups')[unexpected]
- assert_nil(tree_nodes[unexpected_project['uuid']])
+ assert_nil(node_depth[unexpected_project['uuid']], node_depth.inspect)
end
end
run-build-docker-images.sh Build arvbox Docker images.
-run-build-docker-jobs-image.sh Build arvados/jobs Docker image.
+run-build-docker-jobs-image.sh Build arvados/jobs Docker image
+ (uses published debian packages)
+
+build-dev-docker-jobs-image.sh Build developer arvados/jobs Docker image
+ (uses local git tree)
run-library.sh A library of functions shared by the
various scripts in this
--- /dev/null
+#!/bin/bash
+
+read -rd "\000" helpmessage <<EOF
+Build an arvados/jobs Docker image from local git tree.
+
+Intended for use by developers working on arvados-python-client or
+arvados-cwl-runner and need to run a crunch job with a custom package
+version. Also supports building custom cwltool if CWLTOOL is set.
+
+Syntax:
+ WORKSPACE=/path/to/arvados $(basename $0)
+
+WORKSPACE=path Path to the Arvados source tree to build packages from
+CWLTOOL=path (optional) Path to cwltool git repository.
+
+EOF
+
+set -e
+
+if [[ -z "$WORKSPACE" ]] ; then
+ echo "$helpmessage"
+ echo
+ echo "Must set WORKSPACE"
+ exit 1
+fi
+
+if [[ -z "$ARVADOS_API_HOST" || -z "$ARVADOS_API_TOKEN" ]] ; then
+ echo "$helpmessage"
+ echo
+ echo "Must set ARVADOS_API_HOST and ARVADOS_API_TOKEN"
+ exit 1
+fi
+
+cd "$WORKSPACE"
+
+(cd sdk/python && python setup.py sdist)
+sdk=$(cd sdk/python/dist && ls -t arvados-python-client-*.tar.gz | head -n1)
+
+(cd sdk/cwl && python setup.py sdist)
+runner=$(cd sdk/cwl/dist && ls -t arvados-cwl-runner-*.tar.gz | head -n1)
+
+rm -rf sdk/cwl/cwltool_dist
+mkdir -p sdk/cwl/cwltool_dist
+if [[ -n "$CWLTOOL" ]] ; then
+ (cd "$CWLTOOL" && python setup.py sdist)
+ cwltool=$(cd "$CWLTOOL/dist" && ls -t cwltool-*.tar.gz | head -n1)
+ cp "$CWLTOOL/dist/$cwltool" $WORKSPACE/sdk/cwl/cwltool_dist
+fi
+
+. build/run-library.sh
+
+python_sdk_ts=$(cd sdk/python && timestamp_from_git)
+cwl_runner_ts=$(cd sdk/cwl && timestamp_from_git)
+
+if [[ $python_sdk_ts -gt $cwl_runner_ts ]]; then
+ gittag=$(git log --first-parent --max-count=1 --format=format:%H sdk/python)
+else
+ gittag=$(git log --first-parent --max-count=1 --format=format:%H sdk/cwl)
+fi
+
+docker build --build-arg sdk=$sdk --build-arg runner=$runner --build-arg cwltool=$cwltool -f "$WORKSPACE/sdk/dev-jobs.dockerfile" -t arvados/jobs:$gittag "$WORKSPACE/sdk"
+echo arv-keepdocker arvados/jobs $gittag
+arv-keepdocker arvados/jobs $gittag
fpm_build cwltest "" "" python 1.0.20160907111242
# And for cwltool we have the same problem as for schema_salad. Ward, 2016-03-17
-fpm_build cwltool "" "" python 1.0.20161128202906
+cwltoolversion=$(cat "$WORKSPACE/sdk/cwl/setup.py" | grep cwltool== | sed "s/.*==\(1\.0\..*\)'.*/\1/")
+fpm_build cwltool "" "" python $cwltoolversion
# FPM eats the trailing .0 in the python-rdflib-jsonld package when built with 'rdflib-jsonld>=0.3.0'. Force the version. Ward, 2016-03-25
fpm_build rdflib-jsonld "" "" python 0.3.0
echo -n 'virtualenv: '
virtualenv --version \
|| fatal "No virtualenv. Try: apt-get install virtualenv (on ubuntu: python-virtualenv)"
+ echo -n 'ruby: '
+ ruby -v \
+ || fatal "No ruby. Install >=2.1.9 (using rbenv, rvm, or source)"
+ echo -n 'bundler: '
+ bundle version \
+ || fatal "No bundler. Try: gem install bundler"
echo -n 'go: '
go version \
|| fatal "No go binary. See http://golang.org/doc/install"
}, ensure_unique_name=True).execute(
num_retries=self.arvrunner.num_retries)
- done_outputs(self, record, tmpdir, outdir, keepdir)
+ return done_outputs(self, record, tmpdir, outdir, keepdir)
def done_outputs(self, record, tmpdir, outdir, keepdir):
self.builder.outdir = outdir
--- /dev/null
+# Dockerfile for building an arvados/jobs Docker image from local git tree.
+#
+# Intended for use by developers working on arvados-python-client or
+# arvados-cwl-runner and need to run a crunch job with a custom package
+# version.
+#
+# Use arvados/build/build-dev-docker-jobs-image.sh to build.
+#
+# (This dockerfile file must be located in the arvados/sdk/ directory because
+# of the docker build root.)
+
+FROM debian:jessie
+MAINTAINER Ward Vandewege <ward@curoverse.com>
+
+ENV DEBIAN_FRONTEND noninteractive
+
+RUN apt-get update -q && apt-get install -qy git python-pip python-virtualenv python-dev libcurl4-gnutls-dev libgnutls28-dev nodejs
+
+RUN pip install -U setuptools
+
+ARG sdk
+ARG runner
+ARG cwltool
+
+ADD python/dist/$sdk /tmp/
+ADD cwl/cwltool_dist/$cwltool /tmp/
+ADD cwl/dist/$runner /tmp/
+
+RUN cd /tmp/arvados-python-client-* && python setup.py install
+RUN if test -d /tmp/cwltool-* ; then cd /tmp/cwltool-* && python setup.py install ; fi
+RUN cd /tmp/arvados-cwl-runner-* && python setup.py install
+
+# Install dependencies and set up system.
+RUN /usr/sbin/adduser --disabled-password \
+ --gecos 'Crunch execution user' crunch && \
+ /usr/bin/install --directory --owner=crunch --group=crunch --mode=0700 /keep /tmp/crunch-src /tmp/crunch-job
+
+USER crunch
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 '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'
# 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)
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)
+ 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
andand
arvados (>= 0.1.20150615153458)
arvados-cli (>= 0.1.20161017193526)
- coffee-rails (~> 3.2.0)
+ coffee-rails (~> 3.2)
database_cleaner
factory_girl_rails
faye-websocket
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
+ 1.13.6
theme :select_theme
- attr_accessor :resource_attrs
+ attr_writer :resource_attrs
begin
rescue_from(Exception,
: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
def find_object_by_uuid
- if params[:id] and params[:id].match /\D/
+ if params[:id] and params[:id].match(/\D/)
params[:uuid] = params.delete :id
end
@where = { uuid: params[:uuid] }
}
end
end
- super *opts
+ super(*opts)
end
def select_theme
visited[uuid] = job.as_api_response
if direction == :search_up
# Follow upstream collections referenced in the script parameters
- find_collections(visited, job) do |hash, uuid|
+ find_collections(visited, job) do |hash, col_uuid|
search_edges(visited, hash, :search_up) if hash
- search_edges(visited, uuid, :search_up) if uuid
+ search_edges(visited, col_uuid, :search_up) if col_uuid
end
elsif direction == :search_down
# Follow downstream job output
if Rails.application.config.websocket_address
discovery[:websocketUrl] = Rails.application.config.websocket_address
elsif ENV['ARVADOS_WEBSOCKETS']
- discovery[:websocketUrl] = (root_url.sub /^http/, 'ws') + "websocket"
+ discovery[:websocketUrl] = root_url.sub(/^http/, 'ws') + "websocket"
end
ActiveRecord::Base.descendants.reject(&:abstract_class?).each do |k|
method = d_methods[action.to_sym]
end
if ctl_class.respond_to? "_#{action}_requires_parameters".to_sym
- ctl_class.send("_#{action}_requires_parameters".to_sym).each do |k, v|
+ ctl_class.send("_#{action}_requires_parameters".to_sym).each do |l, v|
if v.is_a? Hash
- method[:parameters][k] = v
+ method[:parameters][l] = v
else
- method[:parameters][k] = {}
+ method[:parameters][l] = {}
end
- if !method[:parameters][k][:default].nil?
+ if !method[:parameters][l][:default].nil?
# The JAVA SDK is sensitive to all values being strings
- method[:parameters][k][:default] = method[:parameters][k][:default].to_s
+ method[:parameters][l][:default] = method[:parameters][l][:default].to_s
end
- method[:parameters][k][:type] ||= 'string'
- method[:parameters][k][:description] ||= ''
- method[:parameters][k][:location] = (route.segment_keys.include?(k) ? 'path' : 'query')
- if method[:parameters][k][:required].nil?
- method[:parameters][k][:required] = v != false
+ method[:parameters][l][:type] ||= 'string'
+ method[:parameters][l][:description] ||= ''
+ method[:parameters][l][:location] = (route.segment_keys.include?(l) ? 'path' : 'query')
+ if method[:parameters][l][:required].nil?
+ method[:parameters][l][:required] = v != false
end
end
end
# use this installation.
@objects = []
else
- current_user_uuid = current_user.uuid
act_as_system_user do
uuids = Link.where("owner_uuid = ? and link_class = ? and name = ? and tail_uuid = ? and head_uuid like ?",
system_user_uuid,
'require',
system_user_uuid,
Collection.uuid_like_pattern).
- collect &:head_uuid
+ collect(&:head_uuid)
@objects = Collection.where('uuid in (?)', uuids)
end
end
end
def apply_filters(model_class=nil)
- return super if @read_users.any? &:is_admin
+ return super if @read_users.any?(&:is_admin)
if params[:uuid] != current_user.andand.uuid
# Non-admin index/show returns very basic information about readable users.
safe_attrs = ["uuid", "is_active", "email", "first_name", "last_name"]
@users = {}
User.eager_load(:authorized_keys).
where('users.uuid in (?)',
- @vms.map { |vm| vm.login_permissions.map &:tail_uuid }.flatten.uniq).
+ @vms.map { |vm| vm.login_permissions.map(&:tail_uuid) }.flatten.uniq).
each do |u|
@users[u.uuid] = u
end
# we can tell they're not valuable.
user_uuids = User.
where('email is null or email not like ?', '%@example.com').
- collect &:uuid
+ collect(&:uuid)
fixture_uuids =
YAML::load_file(File.expand_path('../../../test/fixtures/users.yml',
__FILE__)).
# Create a new ArvadosApiToken handler
# +app+ The next layer of the Rack stack.
def initialize(app = nil, options = nil)
- @app = app if app.respond_to?(:call)
+ @app = app.respond_to?(:call) ? app : nil
end
def call env
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
# Return value: true if the locator has a valid signature, false otherwise
# Arguments: signed_blob_locator, opts
#
- def self.verify_signature *args
+ def self.verify_signature(*args)
begin
- self.verify_signature! *args
+ self.verify_signature!(*args)
true
rescue Blob::InvalidSignatureError
false
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
@gitdirbase = Rails.configuration.git_repositories_dir
self.is = nil
Dir.foreach @gitdirbase do |repo|
- next if repo.match /^\./
+ next if repo.match(/^\./)
git_dir = repo.match(/\.git$/) ? repo : File.join(repo, '.git')
repo_name = repo.sub(/\.git$/, '')
ENV['GIT_DIR'] = File.join(@gitdirbase, git_dir)
- IO.foreach("|git rev-list --format=oneline '#{self.descendant.gsub /[^0-9a-f]/,""}'") do |line|
+ IO.foreach("|git rev-list --format=oneline '#{self.descendant.gsub(/[^0-9a-f]/,"")}'") do |line|
self.is = false
- sha1, message = line.strip.split(" ", 2)
+ sha1, _ = line.strip.split(" ", 2)
if sha1 == self.ancestor
self.is = true
break
(Complete = 'Complete'),
]
+ after_initialize do
+ @need_crunch_dispatch_trigger = false
+ end
+
def assert_finished
update_attributes(finished_at: finished_at || db_current_time,
success: success.nil? ? false : success,
assign_uuid
Commit.tag_in_internal_repository repository, script_version, uuid
rescue
- uuid = uuid_was
+ self.uuid = uuid_was
raise
end
end
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.
if self.script_parameters_changed?
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
after_update :maybe_invalidate_permissions_cache
after_create :maybe_invalidate_permissions_cache
after_destroy :maybe_invalidate_permissions_cache
- attr_accessor :head_kind, :tail_kind
validate :name_links_are_obsolete
api_accessible :user, extend: :common do |t|
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|
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
(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, UNUSED_NODE_IP)
prefix_match = Regexp.escape(owner.username + "/")
errmsg_start = "must be the owner's username, then '/', then"
end
- if not /^#{prefix_match}[A-Za-z][A-Za-z0-9]*$/.match(name)
+ if not (/^#{prefix_match}[A-Za-z][A-Za-z0-9]*$/.match(name))
errors.add(:name,
"#{errmsg_start} a letter followed by alphanumerics")
false
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],
# 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'])
# end
ActiveSupport::Inflector.inflections do |inflect|
- inflect.plural /^([Ss]pecimen)$/i, '\1s'
- inflect.singular /^([Ss]pecimen)s?/i, '\1'
- inflect.plural /^([Hh]uman)$/i, '\1s'
- inflect.singular /^([Hh]uman)s?/i, '\1'
+ inflect.plural(/^([Ss]pecimen)$/i, '\1s')
+ inflect.singular(/^([Ss]pecimen)s?/i, '\1')
+ inflect.plural(/^([Hh]uman)$/i, '\1s')
+ inflect.singular(/^([Hh]uman)s?/i, '\1')
end
# 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:
%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, deserialize_symbols: true)
# Ignore empty YAML file:
if Rails.env == 'development'
Dir.foreach("#{Rails.root}/app/models") do |model_file|
- require_dependency model_file if model_file.match /\.rb$/
+ require_dependency model_file if model_file.match(/\.rb$/)
end
end
@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
# into multiple rows with one hostname each.
`#{cmd} --noheader -o '%N:#{outfmt}'`.each_line do |line|
tokens = line.chomp.split(":", max_fields)
- if (re = tokens[0].match /^(.*?)\[([-,\d]+)\]$/)
+ if (re = tokens[0].match(/^(.*?)\[([-,\d]+)\]$/))
tokens.shift
re[2].split(",").each do |range|
range = range.split("-").collect(&:to_i)
end
def update_node_status
- return unless Server::Application.config.crunch_job_wrapper.to_s.match /^slurm/
+ return unless Server::Application.config.crunch_job_wrapper.to_s.match(/^slurm/)
slurm_status.each_pair do |hostname, slurmdata|
next if @node_state[hostname] == slurmdata
begin
end
usable_nodes << node
if usable_nodes.count >= min_node_count
- return usable_nodes.map { |node| node.hostname }
+ return usable_nodes.map { |n| n.hostname }
end
end
nil
def read_pipes
@running.each do |job_uuid, j|
- job = j[:job]
-
now = Time.now
if now > j[:log_throttle_reset_time]
# It has been more than throttle_period seconds since the last
+$system_user = nil
+$system_group = nil
+$all_users_group = nil
+$anonymous_user = nil
+$anonymous_group = nil
+$anonymous_group_read_permission = nil
+$empty_collection = nil
+
module CurrentApiClient
def current_user
Thread.current[:user]
User.all.collect(&:uuid).each do |user_uuid|
Link.create!(link_class: 'permission',
name: 'can_manage',
- tail_kind: 'arvados#group',
tail_uuid: system_group_uuid,
- head_kind: 'arvados#user',
head_uuid: user_uuid)
end
end
@connection_count = 0
end
+ def send_message(ws, obj)
+ ws.send(Oj.dump(obj, mode: :compat))
+ end
+
# Push out any pending events to the connection +ws+
# +notify_id+ the id of the most recent row in the log table, may be nil
#
logs.select('logs.id').find_each do |l|
if not ws.sent_ids.include?(l.id)
# only send if not a duplicate
- ws.send(Log.find(l.id).as_api_response.to_json)
+ send_message(ws, Log.find(l.id).as_api_response)
end
if not ws.last_log_id.nil?
# record ids only when sending "catchup" messages, not notifies
rescue ArgumentError => e
# There was some kind of user error.
Rails.logger.warn "Error publishing event: #{$!}"
- ws.send ({status: 500, message: $!}.to_json)
+ send_message(ws, {status: 500, message: $!})
ws.close
rescue => e
Rails.logger.warn "Error publishing event: #{$!}"
Rails.logger.warn "Backtrace:\n\t#{e.backtrace.join("\n\t")}"
- ws.send ({status: 500, message: $!}.to_json)
+ send_message(ws, {status: 500, message: $!})
ws.close
# These exceptions typically indicate serious server trouble:
# out of memory issues, database connection problems, etc. Go ahead and
p = (Oj.strict_load event.data).symbolize_keys
filter = Filter.new(p)
rescue Oj::Error => e
- ws.send ({status: 400, message: "malformed request"}.to_json)
+ send_message(ws, {status: 400, message: "malformed request"})
return
end
# Add a filter. This gets the :filters field which is the same
# format as used for regular index queries.
ws.filters << filter
- ws.send ({status: 200, message: 'subscribe ok', filter: p}.to_json)
+ send_message(ws, {status: 200, message: 'subscribe ok', filter: p})
# Send any pending events
push_events ws, nil
else
- ws.send ({status: 403, message: "maximum of #{Rails.configuration.websocket_max_filters} filters allowed per connection"}.to_json)
+ send_message(ws, {status: 403, message: "maximum of #{Rails.configuration.websocket_max_filters} filters allowed per connection"})
end
elsif p[:method] == 'unsubscribe'
len = ws.filters.length
ws.filters.select! { |f| not ((f.filters == p[:filters]) or (f.filters.empty? and p[:filters].nil?)) }
if ws.filters.length < len
- ws.send ({status: 200, message: 'unsubscribe ok'}.to_json)
+ send_message(ws, {status: 200, message: 'unsubscribe ok'})
else
- ws.send ({status: 404, message: 'filter not found'}.to_json)
+ send_message(ws, {status: 404, message: 'filter not found'})
end
else
- ws.send ({status: 400, message: "missing or unrecognized method"}.to_json)
+ send_message(ws, {status: 400, message: "missing or unrecognized method"})
end
rescue => e
Rails.logger.warn "Error handling message: #{$!}"
Rails.logger.warn "Backtrace:\n\t#{e.backtrace.join("\n\t")}"
- ws.send ({status: 500, message: 'error'}.to_json)
+ send_message(ws, {status: 500, message: 'error'})
ws.close
end
end
# Disconnect if no valid API token.
# current_user is included from CurrentApiClient
if not current_user
- ws.send ({status: 401, message: "Valid API token required"}.to_json)
- ws.close
+ send_message(ws, {status: 401, message: "Valid API token required"})
+ # Wait for the handshake to complete before closing the
+ # socket. Otherwise, nginx responds with HTTP 502 Bad gateway,
+ # and the client never sees our real error message.
+ ws.on :open do |event|
+ ws.close
+ end
return
end
# forward them to the thread associated with the connection.
sub = @channel.subscribe do |msg|
if ws.queue.length > Rails.configuration.websocket_max_notify_backlog
- ws.send ({status: 500, message: 'Notify backlog too long'}.to_json)
+ send_message(ws, {status: 500, message: 'Notify backlog too long'})
ws.close
@channel.unsubscribe sub
ws.queue.clear
# has used set_table_name to use an alternate table name from the Rails standard.
# I could not find a perfect way to handle this well, but ActiveRecord::Base.send(:descendants)
# would be a place to start if this ever becomes necessary.
- if attr.match /^[a-z][_a-z0-9]+$/ and
+ if attr.match(/^[a-z][_a-z0-9]+$/) and
model_class.columns.collect(&:name).index(attr) and
['asc','desc'].index direction.downcase
@orders << "#{table_name}.#{attr} #{direction.downcase}"
- elsif attr.match /^([a-z][_a-z0-9]+)\.([a-z][_a-z0-9]+)$/ and
+ elsif attr.match(/^([a-z][_a-z0-9]+)\.([a-z][_a-z0-9]+)$/) and
['asc','desc'].index(direction.downcase) and
ActiveRecord::Base.connection.tables.include?($1) and
$1.classify.constantize.columns.collect(&:name).index($2)
def salvage_collection_locator_data manifest
locators = []
size = 0
- manifest.scan /(^|[^[:xdigit:]])([[:xdigit:]]{32})((\+\d+)(\+|\b))?/ do |_, hash, _, sizehint, _|
+ manifest.scan(/(^|[^[:xdigit:]])([[:xdigit:]]{32})((\+\d+)(\+|\b))?/) do |_, hash, _, sizehint, _|
if sizehint
locators << hash.downcase + sizehint
size += sizehint.to_i
# 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"
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}`
# 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"
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}`
FactoryGirl.define do
factory :user do
- ignore do
+ transient do
join_groups []
end
after :create do |user, evaluator|
get :index, search_params
assert_response :success
got_tokens = JSON.parse(@response.body)['items']
- .map { |auth| auth['api_token'] }
+ .map { |a| a['api_token'] }
assert_equal(expected_tokens.sort, got_tokens.sort,
"wrong results for #{search_params.inspect}")
end
[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'
filters: [['uuid', '@@', 'abcdef']],
}
assert_response 422
- assert_match /not supported/, json_response['errors'].join(' ')
+ assert_match(/not supported/, json_response['errors'].join(' '))
end
test 'difficult characters in full text search' do
filters: [['any', '@@', ['abc', 'def']]],
}
assert_response 422
- assert_match /not supported/, json_response['errors'].join(' ')
+ assert_match(/not supported/, json_response['errors'].join(' '))
end
test 'api responses provide timestamps with nanoseconds' do
%w(created_at modified_at).each do |attr|
# Pass fixtures with null timestamps.
next if item[attr].nil?
- assert_match /^\d{4}-\d\d-\d\dT\d\d:\d\d:\d\d.\d{9}Z$/, item[attr]
+ assert_match(/^\d{4}-\d\d-\d\dT\d\d:\d\d:\d\d.\d{9}Z$/, item[attr])
end
end
end
'server should correct bogus cancelled_at ' +
job['cancelled_at'])
assert_equal(true,
- File.exists?(Rails.configuration.crunch_refresh_trigger),
+ File.exist?(Rails.configuration.crunch_refresh_trigger),
'trigger file should be created when job is cancelled')
end
assert_response 404
end
- test "retrieve all permissions using generic links index api" do
- skip "(not implemented)"
+ # not implemented
+ skip "retrieve all permissions using generic links index api" do
# Links.readable_by() does not return the full set of permission
# links that are visible to a user (i.e., all permission links
# whose head_uuid references an object for which the user has
end
test "get_all_permissions takes into account is_active flag" do
- r = nil
act_as_user users(:active) do
- r = Repository.create! name: 'active/testrepo'
+ Repository.create! name: 'active/testrepo'
end
act_as_system_user do
u = users(:active)
u = User.find_by_uuid(user_uuid)
if perms['can_read']
assert u.can? read: repo['uuid']
- assert_match /R/, perms['gitolite_permissions']
+ assert_match(/R/, perms['gitolite_permissions'])
else
- refute_match /R/, perms['gitolite_permissions']
+ refute_match(/R/, perms['gitolite_permissions'])
end
if perms['can_write']
assert u.can? write: repo['uuid']
- assert_match /RW\+/, perms['gitolite_permissions']
+ assert_match(/RW\+/, perms['gitolite_permissions'])
else
- refute_match /W/, perms['gitolite_permissions']
+ refute_match(/W/, perms['gitolite_permissions'])
end
if perms['can_manage']
assert u.can? manage: repo['uuid']
- assert_match /RW\+/, perms['gitolite_permissions']
+ assert_match(/RW\+/, perms['gitolite_permissions'])
end
end
end
get :index
assert_response :success
discovery_doc = JSON.parse(@response.body)
- assert_match /^[0-9a-f]+(-modified)?$/, discovery_doc['source_version']
+ assert_match(/^[0-9a-f]+(-modified)?$/, discovery_doc['source_version'])
end
test "discovery document overrides source_version with config" do
active_user = User.find_by_uuid(users(:active).uuid)
readable_groups = active_user.groups_i_can(:read)
- all_users_group = Group.all.collect(&:uuid).select { |g| g.match /-f+$/ }
+ all_users_group = Group.all.collect(&:uuid).select { |g| g.match(/-f+$/) }
refute_includes(readable_groups, all_users_group,
"active user can read All Users group after being deactivated")
assert_equal(false, active_user.is_invited,
end
def verify_num_links (original_links, expected_additional_links)
- links_now = Link.all
assert_equal expected_additional_links, Link.all.size-original_links.size,
"Expected #{expected_additional_links.inspect} more links"
end
def find_obj_in_resp (response_items, object_type, head_kind=nil)
return_obj = nil
- response_items
response_items.each { |x|
if !x
next
test "groups is an empty list by default" do
get_logins_for(:testvm2)
active_login = find_login(:active)
- perm = links(:active_can_login_to_testvm2)
assert_equal([], active_login["groups"])
end
end
group = Group.where(name: 'All users').select do |g|
- g[:uuid].match /-f+$/
+ g[:uuid].match(/-f+$/)
end.first
group_read_perms = Link.where(tail_uuid: uuid,
head_uuid: group[:uuid],
:filters => ['uuid', '=', 'ad02e37b6a7f45bbe2ead3c29a109b8a+54'].to_json
}, auth(:active)
assert_response 422
- assert_match /nvalid element.*not an array/, json_response['errors'].join(' ')
+ assert_match(/nvalid element.*not an array/, json_response['errors'].join(' '))
end
test "get index with invalid filters (unsearchable column) responds 422" do
:filters => [['this_column_does_not_exist', '=', 'bogus']].to_json
}, auth(:active)
assert_response 422
- assert_match /nvalid attribute/, json_response['errors'].join(' ')
+ assert_match(/nvalid attribute/, json_response['errors'].join(' '))
end
test "get index with invalid filters (invalid operator) responds 422" do
:filters => [['uuid', ':-(', 'displeased']].to_json
}, auth(:active)
assert_response 422
- assert_match /nvalid operator/, json_response['errors'].join(' ')
+ assert_match(/nvalid operator/, json_response['errors'].join(' '))
end
test "get index with invalid filters (invalid operand type) responds 422" do
:filters => [['uuid', '=', {foo: 'bar'}]].to_json
}, auth(:active)
assert_response 422
- assert_match /nvalid operand type/, json_response['errors'].join(' ')
+ assert_match(/nvalid operand type/, json_response['errors'].join(' '))
end
test "get index with where= (empty string)" do
:select => ['bogus'].to_json
}, auth(:active)
assert_response 422
- assert_match /Invalid attribute.*bogus/, json_response['errors'].join(' ')
+ assert_match(/Invalid attribute.*bogus/, json_response['errors'].join(' '))
end
test "get index with select= (invalid attribute type) responds 422" do
:select => [['bogus']].to_json
}, auth(:active)
assert_response 422
- assert_match /Invalid attribute.*bogus/, json_response['errors'].join(' ')
+ assert_match(/Invalid attribute.*bogus/, json_response['errors'].join(' '))
end
test "controller 404 response is json" do
assert_response :success
assert_equal true, json_response['manifest_text'].include?('file4_in_subdir4.txt')
- created = json_response
-
# search using the filename
search_using_full_text_search 'subdir2', 0
search_using_full_text_search 'subdir2:*', 1
class CollectionsApiPerformanceTest < ActionDispatch::IntegrationTest
include ManifestExamples
- test "crud cycle for a collection with a big manifest" do
- slow_test
+ slow_test "crud cycle for a collection with a big manifest" do
bigmanifest = time_block 'make example' do
make_manifest(streams: 100,
files_per_stream: 100,
end
end
- test "memory usage" do
- slow_test
+ slow_test "memory usage" do
hugemanifest = make_manifest(streams: 1,
files_per_stream: 2000,
blocks_per_file: 200,
def assert_no_cors_headers
response.headers.keys.each do |h|
- assert_no_match /^Access-Control-/i, h
+ assert_no_match(/^Access-Control-/i, h)
end
end
end
class DatabaseResetTest < ActionDispatch::IntegrationTest
self.use_transactional_fixtures = false
- test "reset fails when Rails.env != 'test'" do
- slow_test
+ slow_test "reset fails when Rails.env != 'test'" do
rails_env_was = Rails.env
begin
Rails.env = 'production'
assert_response 403
end
- test "database reset doesn't break basic CRUD operations" do
- slow_test
+ slow_test "database reset doesn't break basic CRUD operations" do
active_auth = auth(:active)
admin_auth = auth(:admin)
assert_response 404
end
- test "roll back database change" do
- slow_test
+ slow_test "roll back database change" do
active_auth = auth(:active)
admin_auth = auth(:admin)
(repos.collect(&:name) +
vm_links.collect { |link| link.properties['username'] }
).each do |name|
- r = name.match /^(.{#{prefix.length}})(\d+)$/
+ r = name.match(/^(.{#{prefix.length}})(\d+)$/)
assert_not_nil r, "#{name.inspect} does not match {prefix}\\d+"
assert_equal(prefix, r[1],
"#{name.inspect} was not {#{prefix.inspect} plus digits}")
require 'test_helper'
-require 'websocket_runner'
require 'oj'
require 'database_cleaner'
DatabaseCleaner.clean
end
- def ws_helper (token = nil, timeout = true)
+ def self.startup
+ s = TCPServer.new('0.0.0.0', 0)
+ @@port = s.addr[1]
+ s.close
+ @@pidfile = "tmp/pids/passenger.#{@@port}.pid"
+ DatabaseCleaner.start
+ Dir.chdir(Rails.root) do |apidir|
+ # Only passenger seems to be able to run the websockets server
+ # successfully.
+ _system('passenger', 'start', '-d',
+ "-p#{@@port}",
+ "--log-file", "/dev/stderr",
+ "--pid-file", @@pidfile)
+ timeout = Time.now.tv_sec + 10
+ begin
+ sleep 0.2
+ begin
+ server_pid = IO.read(@@pidfile).to_i
+ good_pid = (server_pid > 0) and (Process.kill(0, pid) rescue false)
+ rescue Errno::ENOENT
+ good_pid = false
+ end
+ end while (not good_pid) and (Time.now.tv_sec < timeout)
+ if not good_pid
+ raise RuntimeError, "could not find API server Rails pid"
+ end
+ STDERR.puts "Started websocket server on port #{@@port} with pid #{server_pid}"
+ end
+ end
+
+ def self.shutdown
+ Dir.chdir(Rails.root) do
+ _system('passenger', 'stop', "-p#{@@port}",
+ "--pid-file", @@pidfile)
+ end
+ # DatabaseCleaner leaves the database empty. Prefer to leave it full.
+ dc = DatabaseController.new
+ dc.define_singleton_method :render do |*args| end
+ dc.reset
+ end
+
+ def self._system(*cmd)
+ Bundler.with_clean_env do
+ env = {
+ 'ARVADOS_WEBSOCKETS' => 'ws-only',
+ 'RAILS_ENV' => 'test',
+ }
+ if not system(env, *cmd)
+ raise RuntimeError, "Command exited #{$?}: #{cmd.inspect}"
+ end
+ end
+ end
+
+ def ws_helper(token: nil, timeout: 8)
opened = false
close_status = nil
too_long = false
- EM.run {
+ EM.run do
if token
- ws = Faye::WebSocket::Client.new("ws://localhost:#{WEBSOCKET_PORT}/websocket?api_token=#{api_client_authorizations(token).api_token}")
+ ws = Faye::WebSocket::Client.new("ws://localhost:#{@@port}/websocket?api_token=#{api_client_authorizations(token).api_token}")
else
- ws = Faye::WebSocket::Client.new("ws://localhost:#{WEBSOCKET_PORT}/websocket")
+ ws = Faye::WebSocket::Client.new("ws://localhost:#{@@port}/websocket")
end
ws.on :open do |event|
opened = true
if timeout
- EM::Timer.new 8 do
+ EM::Timer.new(timeout) do
too_long = true if close_status.nil?
EM.stop_event_loop
end
end
end
+ ws.on :error do |event|
+ STDERR.puts "websocket client error: #{event.inspect}"
+ end
+
ws.on :close do |event|
close_status = [:close, event.code, event.reason]
EM.stop_event_loop
end
yield ws
- }
+ end
assert opened, "Should have opened web socket"
assert (not too_long), "Test took too long"
assert_equal 401, status
end
-
test "connect, subscribe and get response" do
status = nil
- ws_helper :active do |ws|
+ ws_helper(token: :active) do |ws|
ws.on :open do |event|
ws.send ({method: 'subscribe'}.to_json)
end
authorize_with :active
- ws_helper :active do |ws|
+ ws_helper(token: :active) do |ws|
ws.on :open do |event|
ws.send ({method: 'subscribe'}.to_json)
end
authorize_with :active
- ws_helper :active do |ws|
+ ws_helper(token: :active) do |ws|
ws.on :open do |event|
ws.send ({method: 'subscribe'}.to_json)
end
authorize_with :active
- ws_helper :active do |ws|
+ ws_helper(token: :active) do |ws|
ws.on :open do |event|
ws.send ({method: 'subscribe', filters: [['object_uuid', 'is_a', 'arvados#human']]}.to_json)
end
authorize_with :active
- ws_helper :active do |ws|
+ ws_helper(token: :active) do |ws|
ws.on :open do |event|
ws.send ({method: 'subscribe', filters: [['object_uuid', 'is_a', 'arvados#human']]}.to_json)
ws.send ({method: 'subscribe', filters: [['object_uuid', 'is_a', 'arvados#specimen']]}.to_json)
authorize_with :active
- ws_helper :active do |ws|
+ ws_helper(token: :active) do |ws|
ws.on :open do |event|
ws.send ({method: 'subscribe', filters: [['object_uuid', 'is_a', 'arvados#trait'], ['event_type', '=', 'update']]}.to_json)
end
test "connect, subscribe, ask events starting at seq num" do
state = 1
- human = nil
- human_ev_uuid = nil
authorize_with :active
l1 = nil
l2 = nil
- ws_helper :active do |ws|
+ ws_helper(token: :active) do |ws|
ws.on :open do |event|
ws.send ({method: 'subscribe', last_log_id: lastid}.to_json)
end
assert_equal expect_next_logs[1].object_uuid, l2
end
- test "connect, subscribe, get event, unsubscribe" do
- slow_test
+ slow_test "connect, subscribe, get event, unsubscribe" do
state = 1
spec = nil
spec_ev_uuid = nil
- filter_id = nil
authorize_with :active
- ws_helper :active, false do |ws|
+ ws_helper(token: :active, timeout: false) do |ws|
ws.on :open do |event|
ws.send ({method: 'subscribe'}.to_json)
EM::Timer.new 3 do
assert_equal spec.uuid, spec_ev_uuid
end
- test "connect, subscribe, get event, unsubscribe with filter" do
- slow_test
+ slow_test "connect, subscribe, get event, unsubscribe with filter" do
state = 1
spec = nil
spec_ev_uuid = nil
authorize_with :active
- ws_helper :active, false do |ws|
+ ws_helper(token: :active, timeout: false) do |ws|
ws.on :open do |event|
ws.send ({method: 'subscribe', filters: [['object_uuid', 'is_a', 'arvados#human']]}.to_json)
EM::Timer.new 6 do
end
- test "connect, subscribe, get event, try to unsubscribe with bogus filter" do
- slow_test
+ slow_test "connect, subscribe, get event, try to unsubscribe with bogus filter" do
state = 1
spec = nil
spec_ev_uuid = nil
authorize_with :active
- ws_helper :active do |ws|
+ ws_helper(token: :active) do |ws|
ws.on :open do |event|
ws.send ({method: 'subscribe'}.to_json)
end
assert_equal human.uuid, human_ev_uuid
end
-
-
- test "connected, not subscribed, no event" do
- slow_test
+ slow_test "connected, not subscribed, no event" do
authorize_with :active
- ws_helper :active, false do |ws|
+ ws_helper(token: :active, timeout: false) do |ws|
ws.on :open do |event|
EM::Timer.new 1 do
Specimen.create
end
end
- test "connected, not authorized to see event" do
- slow_test
+ slow_test "connected, not authorized to see event" do
state = 1
authorize_with :admin
- ws_helper :active, false do |ws|
+ ws_helper(token: :active, timeout: false) do |ws|
ws.on :open do |event|
ws.send ({method: 'subscribe'}.to_json)
test "connect, try bogus method" do
status = nil
- ws_helper :active do |ws|
+ ws_helper(token: :active) do |ws|
ws.on :open do |event|
ws.send ({method: 'frobnabble'}.to_json)
end
test "connect, missing method" do
status = nil
- ws_helper :active do |ws|
+ ws_helper(token: :active) do |ws|
ws.on :open do |event|
ws.send ({fizzbuzz: 'frobnabble'}.to_json)
end
test "connect, send malformed request" do
status = nil
- ws_helper :active do |ws|
+ ws_helper(token: :active) do |ws|
ws.on :open do |event|
ws.send '<XML4EVER></XML4EVER>'
end
authorize_with :active
- ws_helper :active do |ws|
+ ws_helper(token: :active) do |ws|
ws.on :open do |event|
(1..17).each do |i|
ws.send ({method: 'subscribe', filters: [['object_uuid', '=', i]]}.to_json)
end
- test "connect, subscribe, lots of events" do
- slow_test
+ slow_test "connect, subscribe, lots of events" do
state = 1
event_count = 0
log_start = Log.order(:id).last.id
authorize_with :active
- ws_helper :active, false do |ws|
+ ws_helper(token: :active, timeout: false) do |ws|
EM::Timer.new 45 do
# Needs a longer timeout than the default
ws.close
assert_equal 200, d["status"]
ActiveRecord::Base.transaction do
(1..202).each do
- spec = Specimen.create
+ Specimen.create
end
end
state = 2
test "connect, subscribe with invalid filter" do
state = 1
- human = nil
- human_ev_uuid = nil
authorize_with :active
- ws_helper :active do |ws|
+ ws_helper(token: :active) do |ws|
ws.on :open do |event|
# test that #6451 is fixed (invalid filter crashes websockets)
ws.send ({method: 'subscribe', filters: [['object_blarg', 'is_a', 'arvados#human']]}.to_json)
when 1
assert_equal 200, d["status"]
Specimen.create
- human = Human.create
+ Human.create
state = 2
when 2
assert_equal 500, d["status"]
require File.expand_path('../../config/environment', __FILE__)
require 'rails/test_help'
-require 'mocha/mini_test'
+require 'mocha'
module ArvadosTestSupport
def json_response
def restore_configuration
# Restore configuration settings changed during tests
$application_config.each do |k,v|
- if k.match /^[^.]*$/
+ if k.match(/^[^.]*$/)
Rails.configuration.send (k + '='), v
end
end
"HTTP_AUTHORIZATION" => "OAuth2 #{t}")
end
- def slow_test
- skip "RAILS_TEST_SHORT is set" unless (ENV['RAILS_TEST_SHORT'] || '').empty?
+ def self.skip_slow_tests?
+ !(ENV['RAILS_TEST_SHORT'] || '').empty?
end
+
+ def self.skip(*args, &block)
+ end
+
+ def self.slow_test(name, &block)
+ define_method(name, block) unless skip_slow_tests?
+ end
+
+ alias_method :skip, :omit
end
class ActionController::TestCase
super action, *args
end
end
+
+ def self.suite
+ s = super
+ def s.run(*args)
+ @test_case.startup()
+ begin
+ super
+ ensure
+ @test_case.shutdown()
+ end
+ end
+ s
+ end
+ def self.startup; end
+ def self.shutdown; end
end
class ActionDispatch::IntegrationTest
end
end
- test 'override with configuration' do
+ test 'override with configuration "foobar"' do
Rails.configuration.source_version = 'foobar'
assert_equal 'foobar', AppVersion.hash
+ end
+
+ test 'override with configuration false' do
Rails.configuration.source_version = false
assert_not_equal 'foobar', AppVersion.hash
end
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|
ak2 = AuthorizedKey.new(name: "bar", public_key: TEST_KEY, authorized_user_uuid: u2.uuid)
refute ak2.valid?
refute ak2.save
- assert_match /already exists/, ak2.errors.full_messages.to_s
+ assert_match(/already exists/, ak2.errors.full_messages.to_s)
end
end
end
# "crrud" == "create read render update delete", not a typo
- test "crrud cycle for a collection with a big manifest)" do
- slow_test
+ slow_test "crrud cycle for a collection with a big manifest)" do
bigmanifest = time_block 'make example' do
make_manifest(streams: 100,
files_per_stream: 100,
c.signed_manifest_text
end
time_block 'sign + render' do
- resp = c.as_api_response(nil)
+ c.as_api_response(nil)
end
loc = Blob.sign_locator(Digest::MD5.hexdigest('foo') + '+3',
api_token: api_token(:active))
c = create_collection "f\xc8o", Encoding::UTF_8
assert !c.valid?
assert_equal [:manifest_text], c.errors.messages.keys
- assert_match /UTF-8/, c.errors.messages[:manifest_text].first
+ assert_match(/UTF-8/, c.errors.messages[:manifest_text].first)
end
end
c = create_collection "f\xc8o", Encoding::ASCII_8BIT
assert !c.valid?
assert_equal [:manifest_text], c.errors.messages.keys
- assert_match /UTF-8/, c.errors.messages[:manifest_text].first
+ assert_match(/UTF-8/, c.errors.messages[:manifest_text].first)
end
end
assert c.valid?
created_file_names = c.file_names
assert created_file_names
- assert_match /foo.txt/, c.file_names
+ assert_match(/foo.txt/, c.file_names)
c.update_attribute 'manifest_text', ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:foo2.txt\n"
assert_not_equal created_file_names, c.file_names
- assert_match /foo2.txt/, c.file_names
+ assert_match(/foo2.txt/, c.file_names)
end
end
assert c.valid?
assert c.file_names
- assert_match /veryverylongfilename0000000000001.txt/, c.file_names
- assert_match /veryverylongfilename0000000000002.txt/, c.file_names
+ assert_match(/veryverylongfilename0000000000001.txt/, c.file_names)
+ assert_match(/veryverylongfilename0000000000002.txt/, c.file_names)
if not allow_truncate
- assert_match /veryverylastfilename/, c.file_names
- assert_match /laststreamname/, c.file_names
+ assert_match(/veryverylastfilename/, c.file_names)
+ assert_match(/laststreamname/, c.file_names)
end
end
end
test 'find_commit_range does not bypass permissions' do
authorize_with :inactive
assert_raises ArgumentError do
- c = Commit.find_commit_range 'foo', nil, 'master', []
+ Commit.find_commit_range 'foo', nil, 'master', []
end
end
authorize_with :active
gitint = "git --git-dir #{Rails.configuration.git_internal_dir}"
IO.read("|#{gitint} tag -d testtag 2>/dev/null") # "no such tag", fine
- assert_match /^fatal: /, IO.read("|#{gitint} show testtag 2>&1")
+ assert_match(/^fatal: /, IO.read("|#{gitint} show testtag 2>&1"))
refute $?.success?
Commit.tag_in_internal_repository 'active/foo', '31ce37fe365b3dc204300a3e4c396ad333ed0556', 'testtag'
- assert_match /^commit 31ce37f/, IO.read("|#{gitint} show testtag")
+ assert_match(/^commit 31ce37f/, IO.read("|#{gitint} show testtag"))
assert $?.success?
end
Dir.mktmpdir do |touchdir|
# invalid input to maximum
a = Commit.find_commit_range('active/foo', nil, "31ce37fe365b3dc204300a3e4c396ad333ed0556 ; touch #{touchdir}/uh_oh", nil)
- assert !File.exists?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'maximum' parameter of find_commit_range is exploitable"
+ assert !File.exist?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'maximum' parameter of find_commit_range is exploitable"
assert_equal [], a
# invalid input to maximum
a = Commit.find_commit_range('active/foo', nil, "$(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
test "find_reusable method should select higher priority queued container" do
set_user_from_auth :active
common_attrs = REUSABLE_COMMON_ATTRS.merge({environment:{"var" => "queued"}})
- c_low_priority, _ = minimal_new(common_attrs.merge({priority:1}))
- c_high_priority, _ = minimal_new(common_attrs.merge({priority:2}))
+ c_low_priority, _ = minimal_new(common_attrs.merge({use_existing:false, priority:1}))
+ c_high_priority, _ = minimal_new(common_attrs.merge({use_existing:false, priority:2}))
+ assert_not_equal c_low_priority.uuid, c_high_priority.uuid
assert_equal Container::Queued, c_low_priority.state
assert_equal Container::Queued, c_high_priority.state
reused = Container.find_reusable(common_attrs)
output: '1f4b0bc7583c2a7f9102c395f4ffc5e3+45'
}
- c_older, _ = minimal_new(common_attrs)
- c_recent, _ = minimal_new(common_attrs)
+ c_older, _ = minimal_new(common_attrs.merge({use_existing: false}))
+ c_recent, _ = minimal_new(common_attrs.merge({use_existing: false}))
+ assert_not_equal c_older.uuid, c_recent.uuid
set_user_from_auth :dispatch1
c_older.update_attributes!({state: Container::Locked})
c_output1 = Container.create common_attrs
c_output2 = Container.create common_attrs
+ assert_not_equal c_output1.uuid, c_output2.uuid
cr = ContainerRequest.new common_attrs
cr.state = ContainerRequest::Committed
test "find_reusable method should select running container by start date" do
set_user_from_auth :active
common_attrs = REUSABLE_COMMON_ATTRS.merge({environment: {"var" => "running"}})
- c_slower, _ = minimal_new(common_attrs)
- c_faster_started_first, _ = minimal_new(common_attrs)
- c_faster_started_second, _ = minimal_new(common_attrs)
+ c_slower, _ = minimal_new(common_attrs.merge({use_existing: false}))
+ c_faster_started_first, _ = minimal_new(common_attrs.merge({use_existing: false}))
+ c_faster_started_second, _ = minimal_new(common_attrs.merge({use_existing: false}))
+ # Confirm the 3 container UUIDs are different.
+ assert_equal 3, [c_slower.uuid, c_faster_started_first.uuid, c_faster_started_second.uuid].uniq.length
set_user_from_auth :dispatch1
c_slower.update_attributes!({state: Container::Locked})
c_slower.update_attributes!({state: Container::Running,
test "find_reusable method should select running container by progress" do
set_user_from_auth :active
common_attrs = REUSABLE_COMMON_ATTRS.merge({environment: {"var" => "running2"}})
- c_slower, _ = minimal_new(common_attrs)
- c_faster_started_first, _ = minimal_new(common_attrs)
- c_faster_started_second, _ = minimal_new(common_attrs)
+ c_slower, _ = minimal_new(common_attrs.merge({use_existing: false}))
+ c_faster_started_first, _ = minimal_new(common_attrs.merge({use_existing: false}))
+ c_faster_started_second, _ = minimal_new(common_attrs.merge({use_existing: false}))
+ # Confirm the 3 container UUIDs are different.
+ assert_equal 3, [c_slower.uuid, c_faster_started_first.uuid, c_faster_started_second.uuid].uniq.length
set_user_from_auth :dispatch1
c_slower.update_attributes!({state: Container::Locked})
c_slower.update_attributes!({state: Container::Running,
test "find_reusable method should select locked container most likely to start sooner" do
set_user_from_auth :active
common_attrs = REUSABLE_COMMON_ATTRS.merge({environment: {"var" => "locked"}})
- c_low_priority, _ = minimal_new(common_attrs)
- c_high_priority_older, _ = minimal_new(common_attrs)
- c_high_priority_newer, _ = minimal_new(common_attrs)
+ c_low_priority, _ = minimal_new(common_attrs.merge({use_existing: false}))
+ c_high_priority_older, _ = minimal_new(common_attrs.merge({use_existing: false}))
+ c_high_priority_newer, _ = minimal_new(common_attrs.merge({use_existing: false}))
+ # Confirm the 3 container UUIDs are different.
+ assert_equal 3, [c_low_priority.uuid, c_high_priority_older.uuid, c_high_priority_newer.uuid].uniq.length
set_user_from_auth :dispatch1
c_low_priority.update_attributes!({state: Container::Locked,
priority: 1})
test "find_reusable method should select running over failed container" do
set_user_from_auth :active
common_attrs = REUSABLE_COMMON_ATTRS.merge({environment: {"var" => "failed_vs_running"}})
- c_failed, _ = minimal_new(common_attrs)
- c_running, _ = minimal_new(common_attrs)
+ c_failed, _ = minimal_new(common_attrs.merge({use_existing: false}))
+ c_running, _ = minimal_new(common_attrs.merge({use_existing: false}))
+ assert_not_equal c_failed.uuid, c_running.uuid
set_user_from_auth :dispatch1
c_failed.update_attributes!({state: Container::Locked})
c_failed.update_attributes!({state: Container::Running})
test "find_reusable method should select complete over running container" do
set_user_from_auth :active
common_attrs = REUSABLE_COMMON_ATTRS.merge({environment: {"var" => "completed_vs_running"}})
- c_completed, _ = minimal_new(common_attrs)
- c_running, _ = minimal_new(common_attrs)
+ c_completed, _ = minimal_new(common_attrs.merge({use_existing: false}))
+ c_running, _ = minimal_new(common_attrs.merge({use_existing: false}))
+ assert_not_equal c_completed.uuid, c_running.uuid
set_user_from_auth :dispatch1
c_completed.update_attributes!({state: Container::Locked})
c_completed.update_attributes!({state: Container::Running})
test "find_reusable method should select running over locked container" do
set_user_from_auth :active
common_attrs = REUSABLE_COMMON_ATTRS.merge({environment: {"var" => "running_vs_locked"}})
- c_locked, _ = minimal_new(common_attrs)
- c_running, _ = minimal_new(common_attrs)
+ c_locked, _ = minimal_new(common_attrs.merge({use_existing: false}))
+ c_running, _ = minimal_new(common_attrs.merge({use_existing: false}))
+ assert_not_equal c_running.uuid, c_locked.uuid
set_user_from_auth :dispatch1
c_locked.update_attributes!({state: Container::Locked})
c_running.update_attributes!({state: Container::Locked})
test "find_reusable method should select locked over queued container" do
set_user_from_auth :active
common_attrs = REUSABLE_COMMON_ATTRS.merge({environment: {"var" => "running_vs_locked"}})
- c_locked, _ = minimal_new(common_attrs)
- c_queued, _ = minimal_new(common_attrs)
+ c_locked, _ = minimal_new(common_attrs.merge({use_existing: false}))
+ c_queued, _ = minimal_new(common_attrs.merge({use_existing: false}))
+ assert_not_equal c_queued.uuid, c_locked.uuid
set_user_from_auth :dispatch1
c_locked.update_attributes!({state: Container::Locked})
reused = Container.find_reusable(common_attrs)
test 'command line help' do
cmd = Rails.root.join('script/fail-jobs.rb').to_s
- assert_match /Options:.*--before=/m, File.popen([cmd, '--help']).read
+ assert_match(/Options:.*--before=/m, File.popen([cmd, '--help']).read)
end
protected
def assert_end_states
- @job.values.map &:reload
+ @job.values.map(&:reload)
assert_equal 'Failed', @job[:before_reboot].state
assert_equal false, @job[:before_reboot].running
assert_equal false, @job[:before_reboot].success
# Ensure valid_attrs doesn't produce errors -- otherwise we will
# not know whether errors reported below are actually caused by
# invalid_attrs.
- dummy = Job.create! job_attrs
+ Job.create! job_attrs
job = Job.create job_attrs(invalid_attrs)
assert_raises(ActiveRecord::RecordInvalid, ArgumentError,
parameters.each do |parameter|
expectations = parameter[2]
- if parameter[1] == 'use_current_user_uuid'
+ if 'use_current_user_uuid' == parameter[1]
parameter[1] = Thread.current[:user].uuid
end
}
assert_raises(ActiveRecord::RecordInvalid,
"created job with a collection uuid in script_parameters") do
- job = Job.create!(job_attrs(bad_params))
+ Job.create!(job_attrs(bad_params))
end
end
# appear too, but only if they are _not_ listed in known_logs
# (i.e., we do not make any assertions about logs not mentioned in
# either "known" or "expected".)
- result_ids = result.collect &:id
+ result_ids = result.collect(&:id)
expected_logs.each do |want|
assert_includes result_ids, logs(want).id
end
conffile = Rails.root.join 'tmp', 'compute65535.conf'
File.unlink conffile rescue nil
assert Node.dns_server_update 'compute65535', '127.0.0.1'
- assert_match /\"1\.0\.0\.127\.in-addr\.arpa\. IN PTR compute65535\.zzzzz\.arvadosapi\.com\"/, IO.read(conffile)
+ assert_match(/\"1\.0\.0\.127\.in-addr\.arpa\. IN PTR compute65535\.zzzzz\.arvadosapi\.com\"/, IO.read(conffile))
File.unlink conffile
end
test "create object with non-existent #{o_class} owner" do
assert_raises(ActiveRecord::RecordInvalid,
"create should fail with random owner_uuid") do
- i = Specimen.create!(owner_uuid: o_class.generate_uuid)
+ Specimen.create!(owner_uuid: o_class.generate_uuid)
end
i = Specimen.create(owner_uuid: o_class.generate_uuid)
o = eval ofixt
assert_equal(true, Specimen.where(owner_uuid: o.uuid).any?,
"need something to be owned by #{o.uuid} for this test")
- old_uuid = o.uuid
new_uuid = o.uuid.sub(/..........$/, rand(2**256).to_s(36)[0..9])
assert(!o.update_attributes(uuid: new_uuid),
"should not change uuid of #{ofixt} that owns objects")
sp_grp = Group.create!
sp = Specimen.create!(owner_uuid: sp_grp.uuid)
- manage_perm = Link.create!(link_class: 'permission',
- name: 'can_manage',
- tail_uuid: owner_grp.uuid,
- head_uuid: sp_grp.uuid)
+ Link.create!(link_class: 'permission',
+ name: 'can_manage',
+ tail_uuid: owner_grp.uuid,
+ head_uuid: sp_grp.uuid)
# active user owns owner_grp, which has can_manage permission on sp_grp
# user should be able to add permissions on sp.
head_uuid: sp.uuid,
link_class: 'permission',
name: 'can_write')
- test_uuid = test_perm.uuid
assert test_perm.save, "could not save new permission on target object"
assert test_perm.destroy, "could not delete new permission on target object"
end
- # TODO(twp): fix bug #3091, which should fix this test.
- test "can_manage permission on a non-group object" do
- skip
+ # bug #3091
+ skip "can_manage permission on a non-group object" do
set_user_from_auth :admin
ob = Specimen.create!
component2 = {'script_parameters' => {"something_else" => "xxxad4b39ca5a924e481008009d94e32+210", "input_missing" => {"required" => true}}}
pi.components['first'] = component1
pi.components['second'] = component2
- components = pi.components
Thread.current[:user] = users(:admin)
pi.update_attribute 'components', pi.components
updated_name = updated_src_collection.name
assert_equal true, updated_name.include?(src_collection.name)
- match = updated_name.match /^test collection.*salvaged data at (.*)\)$/
+ match = updated_name.match(/^test collection.*salvaged data at (.*)\)$/)
assert_not_nil match
assert_not_nil match[1]
assert_empty updated_src_collection.manifest_text
# match[1] is the uuid of the new collection created from src_collection's salvaged data
# use this to get the new collection and verify
new_collection = Collection.find_by_uuid match[1]
- match = new_collection.name.match /^salvaged from (.*),.*/
+ match = new_collection.name.match(/^salvaged from (.*),.*/)
assert_not_nil match
assert_equal src_collection.uuid, match[1]
end
test "salvage collection with no uuid required argument" do
- e = assert_raises RuntimeError do
+ assert_raises RuntimeError do
salvage_collection nil
end
end
e = assert_raises RuntimeError do
salvage_collection collections('user_agreement').uuid
end
- assert_match /Error during arv-put: pid \d+ exit \d+ \(cmd was \"arv-put .*\"\)/, e.message
+ assert_match(/Error during arv-put: pid \d+ exit \d+ \(cmd was \"arv-put .*\"\)/, e.message)
end
# This test uses BAD_MANIFEST, which has the following flaws:
updated_name = updated_src_collection.name
assert_equal true, updated_name.include?(src_collection.name)
- match = updated_name.match /^test collection.*salvaged data at (.*)\)$/
+ match = updated_name.match(/^test collection.*salvaged data at (.*)\)$/)
assert_not_nil match
assert_not_nil match[1]
assert_empty updated_src_collection.manifest_text
# match[1] is the uuid of the new collection created from src_collection's salvaged data
# use this to get the new collection and verify
new_collection = Collection.find_by_uuid match[1]
- match = new_collection.name.match /^salvaged from (.*),.*/
+ match = new_collection.name.match(/^salvaged from (.*),.*/)
assert_not_nil match
assert_equal src_collection.uuid, match[1]
# verify the new collection's manifest includes the bad locators
test "admin can't clear username when user owns repositories" do
set_user_from_auth :admin
user = users(:active)
- start_username = user.username
user.username = nil
assert_not_allowed { user.save }
refute_empty(user.errors[:username])
+++ /dev/null
-require 'bundler'
-require 'socket'
-
-$ARV_API_SERVER_DIR = File.expand_path('../..', __FILE__)
-
-s = TCPServer.new('0.0.0.0', 0)
-WEBSOCKET_PORT = s.addr[1]
-s.close
-SERVER_PID_PATH = "tmp/pids/passenger.#{WEBSOCKET_PORT}.pid"
-
-class WebsocketTestRunner < MiniTest::Unit
- def _system(*cmd)
- Bundler.with_clean_env do
- if not system({'ARVADOS_WEBSOCKETS' => 'ws-only', 'RAILS_ENV' => 'test'}, *cmd)
- raise RuntimeError, "Command failed with exit status #{$?}: #{cmd.inspect}"
- end
- end
- end
-
- def _run(args=[])
- server_pid = Dir.chdir($ARV_API_SERVER_DIR) do |apidir|
- # Only passenger seems to be able to run the websockets server successfully.
- _system('passenger', 'start', '-d', "-p#{WEBSOCKET_PORT}")
- timeout = Time.now.tv_sec + 10
- begin
- sleep 0.2
- begin
- server_pid = IO.read(SERVER_PID_PATH).to_i
- good_pid = (server_pid > 0) and (Process.kill(0, pid) rescue false)
- rescue Errno::ENOENT
- good_pid = false
- end
- end while (not good_pid) and (Time.now.tv_sec < timeout)
- if not good_pid
- raise RuntimeError, "could not find API server Rails pid"
- end
- server_pid
- end
- begin
- super(args)
- ensure
- Dir.chdir($ARV_API_SERVER_DIR) do
- _system('passenger', 'stop', "-p#{WEBSOCKET_PORT}")
- end
- # DatabaseCleaner leaves the database empty. Prefer to leave it full.
- dc = DatabaseController.new
- dc.define_singleton_method :render do |*args| end
- dc.reset
- end
- end
-end
-
-MiniTest::Unit.runner = WebsocketTestRunner.new
export RAILS_ENV=development
run_bundler --without=development
-bundle exec passenger start --runtime-check-only --runtime-dir=/var/lib/passenger
+bundle exec passenger-config build-native-support
+bundle exec passenger-config install-standalone-runtime
if test "$1" = "--only-deps" ; then
exit
fi
exec bundle exec passenger start --port=${services[api]} \
- --runtime-dir=/var/lib/passenger \
--ssl --ssl-certificate=/var/lib/arvados/self-signed.pem \
--ssl-certificate-key=/var/lib/arvados/self-signed.key
projects / arvados.git / commitdiff