GIT
remote: https://github.com/arvados/arvados.git
- revision: dd9f2403f43bcb93da5908ddde57d8c0491bb4c2
+ revision: 14d53b3386296eb9b4d25c91cd9d40a5dfb52b75
glob: sdk/ruby/arvados.gemspec
specs:
- arvados (1.4.2.20191019025325)
+ arvados (1.5.0.pre20200114202620)
activesupport (>= 3)
andand (~> 1.3, >= 1.3.3)
arvados-google-api-client (>= 0.7, < 0.8.9)
rails-dom-testing (>= 1, < 3)
railties (>= 4.2.0)
thor (>= 0.14, < 2.0)
- json (2.2.0)
+ json (2.3.0)
jwt (1.5.6)
launchy (2.4.3)
addressable (~> 2.3)
nokogiri (>= 1.5.9)
mail (2.7.1)
mini_mime (>= 0.1.1)
- memoist (0.16.0)
+ memoist (0.16.2)
metaclass (0.0.4)
method_source (0.9.2)
mime-types (3.2.2)
cliver (~> 0.3.1)
multi_json (~> 1.0)
websocket-driver (>= 0.2.0)
- public_suffix (4.0.1)
+ public_suffix (4.0.3)
rack (2.0.7)
rack-mini-profiler (1.0.2)
rack (>= 1.2.0)
thor (0.20.3)
thread_safe (0.3.6)
tilt (2.0.9)
- tzinfo (1.2.5)
+ tzinfo (1.2.6)
thread_safe (~> 0.1)
uglifier (2.7.2)
execjs (>= 0.3.0)
uglifier (~> 2.0)
BUNDLED WITH
- 1.17.3
+ 2.0.2
# x.y.(z+1).preTIMESTAMP, where x.y.z is the latest released ancestor of $commit
v=$(git describe --abbrev=0 --match "$versionglob" "$commit" | perl -pe 's/(\d+)$/$1+1/e')
fi
- ts=$(TZ=UTC git log -n1 --format=%cd --date="format-local:%Y%m%d%H%M%S" "$commit")
+ isodate=$(TZ=UTC git log -n1 --format=%cd --date=iso "$commit")
+ ts=$(TZ=UTC date --date="$isodate" "+%Y%m%d%H%M%S")
echo "$v.pre$ts"
fi
require "rubygems"
require "colorize"
+module Zenweb
+ class Site
+ @binary_files = %w[png jpg gif eot svg ttf woff2? ico pdf m4a t?gz xlsx]
+ end
+end
+
task :generate => [ :realclean, 'sdk/python/arvados/index.html', 'sdk/R/arvados/index.html', 'sdk/java-v2/javadoc/index.html' ] do
vars = ['baseurl', 'arvados_cluster_uuid', 'arvados_api_host', 'arvados_workbench_host']
vars.each do |v|
end
end
+file ["install/new_cluster_checklist_Azure.xlsx", "install/new_cluster_checklist_AWS.xlsx"] do |t|
+ cp(t, t)
+end
+
file "sdk/python/arvados/index.html" do |t|
if ENV['NO_SDK'] || File.exists?("no-sdk")
next
require "zenweb/tasks"
load "zenweb-textile.rb"
load "zenweb-liquid.rb"
+load "zenweb-fix-body.rb"
task :extra_wirings do
$website.pages["sdk/python/python.html.textile.liquid"].depends_on("sdk/python/arvados/index.html")
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-Before attempting installation, you should begin by reviewing supported platforms, choosing backends for identity, storage, and scheduling, and decide how you will distribute Arvados services onto machines. You should also choose an Arvados Cluster ID, choose your hostnames, and aquire TLS certificates. It may be helpful to make notes as you go along.
+Before attempting installation, you should begin by reviewing supported platforms, choosing backends for identity, storage, and scheduling, and decide how you will distribute Arvados services onto machines. You should also choose an Arvados Cluster ID, choose your hostnames, and aquire TLS certificates. It may be helpful to make notes as you go along using one of these worksheets: "New cluster checklist for AWS":new_cluster_checklist_AWS.xlsx - "New cluster checklist for Azure":new_cluster_checklist_Azure.xlsx - "New cluster checklist for on premise SLURM":new_cluster_checklist_slurm.xlsx
The Arvados storage subsystem is called "keep". The compute subsystem is called "crunch".
Choose how to allocate Arvados services to machines. We recommend that each machine start with a clean installation of a supported GNU/Linux distribution.
-For a production installation, this is a reasonable starting point:
+For a production installation, this is a reasonable starting point:
<div class="offset1">
table(table table-bordered table-condensed).
--- /dev/null
+require 'zenweb'
+
+module ZenwebTextile
+ VERSION = '0.0.1'
+end
+
+module Zenweb
+ class Page
+ alias_method :old_body, :body
+ def body
+ # Don't try to parse binary files as text
+ if /\.(?:#{Site.binary_files.join("|")})$/ =~ path
+ @body ||= File.binread path
+ else
+ @body ||= begin
+ _, body = Zenweb::Config.split path
+ body.strip
+ end
+ end
+ end
+ end
+end
exit
end
-version = `#{__dir__}/../../build/version-at-commit.sh HEAD`.encode('utf-8').strip
-git_timestamp, git_hash = `git log -n1 --first-parent --format=%ct:%H .`.chomp.split(":")
-git_timestamp = Time.at(git_timestamp.to_i).utc
+git_dir = ENV["GIT_DIR"]
+git_work = ENV["GIT_WORK_TREE"]
+begin
+ ENV["GIT_DIR"] = File.expand_path "#{__dir__}/../../.git"
+ ENV["GIT_WORK_TREE"] = File.expand_path "#{__dir__}/../.."
+ git_timestamp, git_hash = `git log -n1 --first-parent --format=%ct:%H #{__dir__}`.chomp.split(":")
+ version = `#{__dir__}/../../build/version-at-commit.sh #{git_hash}`.encode('utf-8').strip
+ git_timestamp = Time.at(git_timestamp.to_i).utc
+ensure
+ ENV["GIT_DIR"] = git_dir
+ ENV["GIT_WORK_TREE"] = git_work
+end
Gem::Specification.new do |s|
s.name = 'arvados-cli'
exit
end
-version = `#{__dir__}/../../build/version-at-commit.sh HEAD`.encode('utf-8').strip
-git_timestamp, git_hash = `git log -n1 --first-parent --format=%ct:%H .`.chomp.split(":")
-git_timestamp = Time.at(git_timestamp.to_i).utc
+git_dir = ENV["GIT_DIR"]
+git_work = ENV["GIT_WORK_TREE"]
+begin
+ ENV["GIT_DIR"] = File.expand_path "#{__dir__}/../../.git"
+ ENV["GIT_WORK_TREE"] = File.expand_path "#{__dir__}/../.."
+ git_timestamp, git_hash = `git log -n1 --first-parent --format=%ct:%H #{__dir__}`.chomp.split(":")
+ version = `#{__dir__}/../../build/version-at-commit.sh #{git_hash}`.encode('utf-8').strip
+ git_timestamp = Time.at(git_timestamp.to_i).utc
+ensure
+ ENV["GIT_DIR"] = git_dir
+ ENV["GIT_WORK_TREE"] = git_work
+end
Gem::Specification.new do |s|
s.name = 'arvados'
gem 'andand'
gem 'optimist'
-gem 'faye-websocket'
gem 'themes_for_rails', git: 'https://github.com/arvados/themes_for_rails'
-# We need arvados-cli because of crunchv1. Note: bundler can't handle
-# two gems with the same "git" url but different "glob" values, hence
-# the use of a wildcard here instead of literal paths
-# (sdk/cli/arvados-cli.gem and sdk/ruby/arvados.gem).
-gem 'arvados-cli', git: 'https://github.com/arvados/arvados.git', glob: 'sdk/*/*.gemspec'
-gem 'arvados', git: 'https://github.com/arvados/arvados.git', glob: 'sdk/*/*.gemspec'
+# Import arvados gem. Note: actual git commit is pinned via Gemfile.lock
+gem 'arvados', git: 'https://github.com/arvados/arvados.git', glob: 'sdk/ruby/arvados.gemspec'
gem 'httpclient'
gem 'sshkey'
GIT
remote: https://github.com/arvados/arvados.git
- revision: dd9f2403f43bcb93da5908ddde57d8c0491bb4c2
- glob: sdk/*/*.gemspec
+ revision: 6c033bdbc06d0929cec24ea16d4dfb7977e72f78
+ glob: sdk/ruby/arvados.gemspec
specs:
- arvados (1.4.2.20191019025325)
+ arvados (1.5.0.pre20200114202620)
activesupport (>= 3)
andand (~> 1.3, >= 1.3.3)
arvados-google-api-client (>= 0.7, < 0.8.9)
i18n (~> 0)
json (>= 1.7.7, < 3)
jwt (>= 0.1.5, < 2)
- arvados-cli (1.4.2.20191017145711)
- activesupport (>= 3.2.13, < 5.1)
- andand (~> 1.3, >= 1.3.3)
- arvados (>= 1.4.1.20190320201707)
- arvados-google-api-client (~> 0.6, >= 0.6.3, < 0.8.9)
- curb (~> 0.8)
- faraday (< 0.16)
- json (>= 1.7.7, < 3)
- oj (~> 3.0)
- optimist (~> 3.0)
GIT
remote: https://github.com/arvados/themes_for_rails
net-ssh-gateway (>= 1.1.0)
concurrent-ruby (1.1.5)
crass (1.0.4)
- curb (0.9.10)
database_cleaner (1.7.0)
erubis (2.7.0)
- eventmachine (1.2.7)
execjs (2.7.0)
extlib (0.9.16)
factory_bot (5.0.2)
railties (>= 4.2.0)
faraday (0.15.4)
multipart-post (>= 1.2, < 3)
- faye-websocket (0.10.7)
- eventmachine (>= 0.12.0)
- websocket-driver (>= 0.5.1)
ffi (1.9.25)
globalid (0.4.2)
activesupport (>= 4.2.0)
rails-dom-testing (>= 1, < 3)
railties (>= 4.2.0)
thor (>= 0.14, < 2.0)
- json (2.2.0)
+ json (2.3.0)
jwt (1.5.6)
launchy (2.4.3)
addressable (~> 2.3)
nokogiri (>= 1.5.9)
mail (2.7.1)
mini_mime (>= 0.1.1)
- memoist (0.16.0)
+ memoist (0.16.2)
metaclass (0.0.4)
method_source (0.9.2)
mini_mime (1.0.1)
rake (>= 0.8.1)
pg (1.1.4)
power_assert (1.1.4)
- public_suffix (4.0.1)
+ public_suffix (4.0.3)
rack (2.0.7)
rack-test (0.6.3)
rack (>= 1.0)
thor (0.20.3)
thread_safe (0.3.6)
tilt (2.0.8)
- tzinfo (1.2.5)
+ tzinfo (1.2.6)
thread_safe (~> 0.1)
uglifier (2.7.2)
execjs (>= 0.3.0)
acts_as_api
andand
arvados!
- arvados-cli!
byebug
database_cleaner
factory_bot_rails
- faye-websocket
httpclient
jquery-rails
lograge
uglifier (~> 2.0)
BUNDLED WITH
- 1.17.3
+ 2.0.2
+++ /dev/null
-# Copyright (C) The Arvados Authors. All rights reserved.
-#
-# SPDX-License-Identifier: AGPL-3.0
-
-require 'rack'
-require 'faye/websocket'
-require 'eventmachine'
-
-# A Rack middleware to handle inbound websocket connection requests and hand
-# them over to the faye websocket library.
-class RackSocket
-
- DEFAULT_ENDPOINT = '/websocket'
-
- # Stop EventMachine on signal, this should give it a chance to to unwind any
- # open connections.
- def die_gracefully_on_signal
- Signal.trap("INT") { EM.stop }
- Signal.trap("TERM") { EM.stop }
- end
-
- # Create a new RackSocket handler
- # +app+ The next layer of the Rack stack.
- #
- # Accepts options:
- # +:handler+ (Required) A class to handle new connections. #initialize will
- # call handler.new to create the actual handler instance object. When a new
- # websocket connection is established, #on_connect on the handler instance
- # object will be called with the new connection.
- #
- # +:mount+ The HTTP request path that will be recognized for websocket
- # connect requests, defaults to '/websocket'.
- #
- # +:websocket_only+ If true, the server will only handle websocket requests,
- # and all other requests will result in an error. If false, unhandled
- # non-websocket requests will be passed along on to 'app' in the usual Rack
- # way.
- def initialize(app = nil, options = nil)
- @app = app if app.respond_to?(:call)
- @options = [app, options].grep(Hash).first || {}
- @endpoint = @options[:mount] || DEFAULT_ENDPOINT
- @websocket_only = @options[:websocket_only] || false
-
- # from https://gist.github.com/eatenbyagrue/1338545#file-eventmachine-rb
- if defined?(PhusionPassenger)
- PhusionPassenger.on_event(:starting_worker_process) do |forked|
- # for passenger, we need to avoid orphaned threads
- if forked && EM.reactor_running?
- EM.stop
- end
- Thread.new do
- begin
- EM.run
- ensure
- ActiveRecord::Base.connection.close
- end
- end
- die_gracefully_on_signal
- end
- else
- # faciliates debugging
- Thread.abort_on_exception = true
- # just spawn a thread and start it up
- Thread.new do
- begin
- EM.run
- ensure
- ActiveRecord::Base.connection.close
- end
- end
- end
-
- # Create actual handler instance object from handler class.
- @handler = @options[:handler].new
- end
-
- # Handle websocket connection request, or pass on to the next middleware
- # supplied in +app+ initialize (unless +:websocket_only+ option is true, in
- # which case return an error response.)
- # +env+ the Rack environment with information about the request.
- def call env
- request = Rack::Request.new(env)
- if request.path_info == @endpoint and Faye::WebSocket.websocket?(env)
- if @handler.overloaded?
- return [503, {"Content-Type" => "text/plain"}, ["Too many connections, try again later."]]
- end
-
- ws = Faye::WebSocket.new(env, nil, :ping => 30)
-
- # Notify handler about new connection
- @handler.on_connect ws
-
- # Return async Rack response
- ws.rack_response
- elsif not @websocket_only
- @app.call env
- else
- [406, {"Content-Type" => "text/plain"}, ["Only websocket connections are permitted on this port."]]
- end
- end
-
-end
was_mounted = False
attempted = False
+ fusermount_output = b''
if timeout is None:
deadline = None
else:
return was_mounted
if attempted:
+ # Report buffered stderr from previous call to fusermount,
+ # now that we know it didn't succeed.
+ sys.stderr.write(fusermount_output)
+
delay = 1
if deadline:
delay = min(delay, deadline - time.time())
attempted = True
try:
- subprocess.check_call(["fusermount", "-u", "-z", path])
- except subprocess.CalledProcessError:
- pass
+ subprocess.check_output(
+ ["fusermount", "-u", "-z", path],
+ stderr=subprocess.STDOUT)
+ except subprocess.CalledProcessError as e:
+ fusermount_output = e.output
+ else:
+ fusermount_output = b''
PATH
remote: .
specs:
- arvados-login-sync (1.3.1.pre20191210204053)
+ arvados-login-sync (1.5.0.pre20200114204308)
arvados (~> 1.3.0, >= 1.3.0)
faraday (< 0.16)
+ signet (< 0.12)
GEM
remote: https://rubygems.org/
signet (~> 0.7)
i18n (0.9.5)
concurrent-ruby (~> 1.0)
- json (2.2.0)
+ json (2.3.0)
jwt (1.5.6)
launchy (2.4.3)
addressable (~> 2.3)
- memoist (0.16.0)
+ memoist (0.16.2)
metaclass (0.0.4)
minitest (5.11.3)
mocha (1.8.0)
multi_json (1.14.1)
multipart-post (2.1.1)
os (1.0.1)
- public_suffix (4.0.1)
+ public_suffix (4.0.3)
rake (12.3.2)
retriable (1.4.1)
signet (0.11.0)
jwt (>= 1.5, < 3.0)
multi_json (~> 1.10)
thread_safe (0.3.6)
- tzinfo (1.2.5)
+ tzinfo (1.2.6)
thread_safe (~> 0.1)
PLATFORMS
exit
end
-version = `#{__dir__}/../../build/version-at-commit.sh HEAD`.encode('utf-8').strip
-git_timestamp, git_hash = `git log -n1 --first-parent --format=%ct:%H .`.chomp.split(":")
-git_timestamp = Time.at(git_timestamp.to_i).utc
+git_dir = ENV["GIT_DIR"]
+git_work = ENV["GIT_WORK_TREE"]
+begin
+ ENV["GIT_DIR"] = File.expand_path "#{__dir__}/../../.git"
+ ENV["GIT_WORK_TREE"] = File.expand_path "#{__dir__}/../.."
+ git_timestamp, git_hash = `git log -n1 --first-parent --format=%ct:%H #{__dir__}`.chomp.split(":")
+ version = `#{__dir__}/../../build/version-at-commit.sh #{git_hash}`.encode('utf-8').strip
+ git_timestamp = Time.at(git_timestamp.to_i).utc
+ensure
+ ENV["GIT_DIR"] = git_dir
+ ENV["GIT_WORK_TREE"] = git_work
+end
Gem::Specification.new do |s|
s.name = 'arvados-login-sync'
s.description = "Creates and updates local login accounts for Arvados users. Built from git commit #{git_hash}"
s.authors = ["Arvados Authors"]
s.email = 'gem-dev@curoverse.com'
- s.licenses = ['GNU Affero General Public License, version 3.0']
+ s.licenses = ['AGPL-3.0']
s.files = ["bin/arvados-login-sync", "agpl-3.0.txt"]
s.executables << "arvados-login-sync"
s.required_ruby_version = '>= 2.1.0'
+++ /dev/null
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VOLUME /var/log/nginx
VOLUME /etc/ssl/private
-ADD 58118E89F3A912897C070ADBF76221572C52609D.asc /tmp/
-RUN apt-key add --no-tty /tmp/58118E89F3A912897C070ADBF76221572C52609D.asc && \
- rm -f /tmp/58118E89F3A912897C070ADBF76221572C52609D.asc
+ADD 8D81803C0EBFCD88.asc /tmp/
+RUN apt-key add --no-tty /tmp/8D81803C0EBFCD88.asc && \
+ rm -f /tmp/8D81803C0EBFCD88.asc
RUN mkdir -p /etc/apt/sources.list.d && \
- echo deb https://apt.dockerproject.org/repo debian-stretch main > /etc/apt/sources.list.d/docker.list && \
+ echo deb https://download.docker.com/linux/debian/ stretch stable > /etc/apt/sources.list.d/docker.list && \
apt-get update && \
- apt-get -yq --no-install-recommends install docker-engine=17.05.0~ce-0~debian-stretch && \
+ apt-get -yq --no-install-recommends install docker-ce=17.06.0~ce-0~debian && \
apt-get clean
RUN rm -rf /var/lib/postgresql && mkdir -p /var/lib/postgresql
git -C composer pull && \
git clone --no-checkout https://github.com/arvados/arvados-workbench2.git workbench2 && \
git -C workbench2 checkout ${workbench2_version} && \
- git -C workbench2 pull
+ git -C workbench2 pull && \
+ chown -R 1000:1000 /usr/src
ADD service/ /var/lib/arvbox/service
RUN ln -sf /var/lib/arvbox/service /etc
RUN echo "production" > /var/lib/arvados/sso_rails_env
RUN echo "production" > /var/lib/arvados/workbench_rails_env
-RUN chown -R 1000:1000 /usr/src && /usr/local/lib/arvbox/createusers.sh
+RUN /usr/local/lib/arvbox/createusers.sh
+RUN sudo -u arvbox /var/lib/arvbox/service/api/run-service --only-deps
RUN sudo -u arvbox /var/lib/arvbox/service/composer/run-service --only-deps
RUN sudo -u arvbox /var/lib/arvbox/service/workbench2/run-service --only-deps
RUN sudo -u arvbox /var/lib/arvbox/service/keep-web/run-service --only-deps
RUN sudo -u arvbox /var/lib/arvbox/service/sso/run-service --only-deps
-RUN sudo -u arvbox /var/lib/arvbox/service/api/run-service --only-deps
RUN sudo -u arvbox /var/lib/arvbox/service/workbench/run-service --only-deps
RUN sudo -u arvbox /var/lib/arvbox/service/doc/run-service --only-deps
RUN sudo -u arvbox /var/lib/arvbox/service/vm/run-service --only-deps
frozen=""
fi
if ! test -x /var/lib/gems/bin/bundler ; then
- bundlergem=$(ls -r $GEM_HOME/cache/bundler-*.gem 2>/dev/null | head -n1 || true)
+ bundleversion=2.0.2
+ bundlergem=$(ls -r $GEM_HOME/cache/bundler-${bundleversion}.gem 2>/dev/null | head -n1 || true)
if test -n "$bundlergem" ; then
- flock /var/lib/gems/gems.lock gem install --local --no-document $bundlergem
+ flock /var/lib/gems/gems.lock gem install --verbose --local --no-document $bundlergem
else
- flock /var/lib/gems/gems.lock gem install --no-document bundler
+ flock /var/lib/gems/gems.lock gem install --verbose --no-document bundler --version ${bundleversion}
fi
fi
- if ! flock /var/lib/gems/gems.lock bundler install --path $GEM_HOME --local --no-deployment $frozen "$@" ; then
- flock /var/lib/gems/gems.lock bundler install --path $GEM_HOME --no-deployment $frozen "$@"
+ if ! flock /var/lib/gems/gems.lock bundler install --verbose --path $GEM_HOME --local --no-deployment $frozen "$@" ; then
+ flock /var/lib/gems/gems.lock bundler install --verbose --path $GEM_HOME --no-deployment $frozen "$@"
fi
}
. /usr/local/lib/arvbox/common.sh
. /usr/local/lib/arvbox/go-setup.sh
-flock /var/lib/gopath/gopath.lock go install "git.arvados.org/arvados.git/services/crunch-run"
flock /var/lib/gopath/gopath.lock go install "git.arvados.org/arvados.git/services/crunch-dispatch-local"
-install $GOPATH/bin/crunch-run $GOPATH/bin/crunch-dispatch-local /usr/local/bin
+install $GOPATH/bin/crunch-dispatch-local /usr/local/bin
+ln -sf arvados-server /usr/local/bin/crunch-run
if test "$1" = "--only-deps" ; then
exit
export ARVADOS_VIRTUAL_MACHINE_UUID=$(cat /var/lib/arvados/vm-uuid)
while true ; do
- bundle exec arvados-login-sync
+ arvados-login-sync
sleep 120
done
. /usr/local/lib/arvbox/common.sh
cd /usr/src/arvados/services/login-sync
-run_bundler
+run_bundler --binstubs=$PWD/binstubs
+ln -sf /usr/src/arvados/services/login-sync/binstubs/arvados-login-sync /usr/local/bin/arvados-login-sync
if test "$1" = "--only-deps" ; then
exit
projects / arvados.git / commitdiff