GIT
remote: https://github.com/arvados/arvados.git
- revision: dd9f2403f43bcb93da5908ddde57d8c0491bb4c2
+ revision: c210114aa8c77ba0bb8e4d487fc1507b40f9560f
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
gpg --import --no-tty /tmp/pkuczynski.asc && \
curl -L https://get.rvm.io | bash -s stable && \
/usr/local/rvm/bin/rvm install 2.3 && \
- /usr/local/rvm/bin/rvm alias create default ruby-2.3
+ /usr/local/rvm/bin/rvm alias create default ruby-2.3 && \
+ /usr/local/rvm/bin/rvm-exec default gem install bundler --version 2.0.2
# Install Bash 4.4.12 // see https://dev.arvados.org/issues/15612
RUN cd /usr/local/src \
gpg --import --no-tty /tmp/pkuczynski.asc && \
curl -L https://get.rvm.io | bash -s stable && \
/usr/local/rvm/bin/rvm install 2.5 && \
- /usr/local/rvm/bin/rvm alias create default ruby-2.5
+ /usr/local/rvm/bin/rvm alias create default ruby-2.5 && \
+ /usr/local/rvm/bin/rvm-exec default gem install bundler --version 2.0.2
# udev daemon can't start in a container, so don't try.
RUN mkdir -p /etc/udev/disabled
gpg --import --no-tty /tmp/pkuczynski.asc && \
curl -L https://get.rvm.io | bash -s stable && \
/usr/local/rvm/bin/rvm install 2.5 && \
- /usr/local/rvm/bin/rvm alias create default ruby-2.5
+ /usr/local/rvm/bin/rvm alias create default ruby-2.5 && \
+ /usr/local/rvm/bin/rvm-exec default gem install bundler --version 2.0.2
# udev daemon can't start in a container, so don't try.
RUN mkdir -p /etc/udev/disabled
gpg --import --no-tty /tmp/pkuczynski.asc && \
curl -L https://get.rvm.io | bash -s stable && \
/usr/local/rvm/bin/rvm install 2.5 && \
- /usr/local/rvm/bin/rvm alias create default ruby-2.5
+ /usr/local/rvm/bin/rvm alias create default ruby-2.5 && \
+ /usr/local/rvm/bin/rvm-exec default gem install bundler --version 2.0.2
# udev daemon can't start in a container, so don't try.
RUN mkdir -p /etc/udev/disabled
gpg --import --no-tty /tmp/pkuczynski.asc && \
curl -L https://get.rvm.io | bash -s stable && \
/usr/local/rvm/bin/rvm install 2.5 && \
- /usr/local/rvm/bin/rvm alias create default ruby-2.5
+ /usr/local/rvm/bin/rvm alias create default ruby-2.5 && \
+ /usr/local/rvm/bin/rvm-exec default gem install bundler --version 2.0.2
# udev daemon can't start in a container, so don't try.
RUN mkdir -p /etc/udev/disabled
rm -rf "$WORKSPACE/cwltest"
fi
git clone https://github.com/common-workflow-language/cwltest.git
+# last release to support python 2.7
+(cd cwltest && git checkout 1.0.20190906212748)
# signal to our build script that we want a cwltest executable installed in /usr/bin/
mkdir cwltest/bin && touch cwltest/bin/cwltest
fpm_build_virtualenv "cwltest" "cwltest"
# older packages.
LICENSE_PACKAGE_TS=20151208015500
+librarydir=`dirname "$(readlink -f "$0")"`
+
if [[ -z "$ARVADOS_BUILDING_VERSION" ]]; then
RAILS_PACKAGE_ITERATION=1
else
local git_ts git_hash
declare $(format_last_commit_here "git_ts=%ct git_hash=%h" "$subdir")
- ARVADOS_BUILDING_VERSION="$(git tag -l |sort -V -r |head -n1).$(date -ud "@$git_ts" +%Y%m%d%H%M%S)"
+ ARVADOS_BUILDING_VERSION="$($librarydir/version-at-commit.sh $git_hash)"
echo "$ARVADOS_BUILDING_VERSION"
}
set -e -o pipefail
commit="$1"
versionglob="[0-9].[0-9]*.[0-9]*"
+devsuffix=".dev"
if ! git describe --exact-match --match "$versionglob" "$commit" 2>/dev/null; then
if git merge-base --is-ancestor "$commit" origin/master; then
# 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" "$commit")
- echo "$v.pre$ts"
+ isodate=$(TZ=UTC git log -n1 --format=%cd --date=iso "$commit")
+ ts=$(TZ=UTC date --date="$isodate" "+%Y%m%d%H%M%S")
+ echo "${v}${devsuffix}${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 File.exists? "no-sdk"
+ if ENV['NO_SDK'] || File.exists?("no-sdk")
next
end
`which epydoc`
end
file "sdk/R/arvados/index.html" do |t|
- if File.exists? "no-sdk"
+ if ENV['NO_SDK'] || File.exists?("no-sdk")
next
end
`which R`
end
file "sdk/java-v2/javadoc/index.html" do |t|
- if File.exists? "no-sdk"
+ if ENV['NO_SDK'] || File.exists?("no-sdk")
next
end
`which java`
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")
- api/methods/container_requests.html.textile.liquid
- api/methods/containers.html.textile.liquid
- api/methods/workflows.html.textile.liquid
+ - Management (admin/system):
+ - api/dispatch.html.textile.liquid
- Jobs engine (legacy):
- api/crunch-scripts.html.textile.liquid
- api/methods/jobs.html.textile.liquid
--- /dev/null
+---
+layout: default
+navsection: api
+navmenu: API Methods
+title: "cloud dispatcher"
+
+...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+The cloud dispatcher provides several management/diagnostic APIs, intended to be used by a system administrator.
+
+These APIs are not normally exposed to external clients. To use them, connect directly to the dispatcher's internal URL (see Services.DispatchCloud.InternalURLs in the cluster config file). All requests must include the cluster's management token (@ManagementToken@ in the cluster config file).
+
+Example:
+
+<notextile><pre><code>curl -H "Authorization: Bearer $management_token" http://localhost:9006/arvados/v1/dispatch/containers</code></pre></notextile>
+
+These APIs are not available via @arv@ CLI tool.
+
+Note: the term "instance" here refers to a virtual machine provided by a cloud computing service. The alternate terms "cloud VM", "compute node", and "worker node" are sometimes used as well in config files, documentation, and log messages.
+
+h3. List containers
+
+@GET /arvados/v1/dispatch/containers@
+
+Return a list of containers that are either ready to dispatch, or being started/monitored by the dispatcher.
+
+Each entry in the returned list of @items@ includes:
+* an @instance_type@ entry with the name and attributes of the instance type that will be used to schedule the container (chosen from the @InstanceTypes@ section of your cluster config file); and
+* a @container@ entry with selected attributes of the container itself, including @uuid@, @priority@, @runtime_constraints@, and @state@. Other fields of the container records are not loaded by the dispatcher, and will have empty/zero values here (e.g., @{...,"created_at":"0001-01-01T00:00:00Z","command":[],...}@).
+
+Example response:
+
+<notextile><pre>{
+ "items": [
+ {
+ "container": {
+ "uuid": "zzzzz-dz642-xz68ptr62m49au7",
+ ...
+ "priority": 562948375092493200,
+ ...
+ "state": "Locked",
+ ...
+ },
+ "instance_type": {
+ "Name": "Standard_E2s_v3",
+ "ProviderType": "Standard_E2s_v3",
+ "VCPUs": 2,
+ "RAM": 17179869184,
+ "Scratch": 32000000000,
+ "IncludedScratch": 32000000000,
+ "AddedScratch": 0,
+ "Price": 0.146,
+ "Preemptible": false
+ }
+ },
+ ...
+ ]
+}</pre></notextile>
+
+h3. Terminate a container
+
+@POST /arvados/v1/dispatch/containers/kill?container_uuid={uuid}&reason={string}@
+
+Make a single attempt to terminate the indicated container on the relevant instance. (The caller can implement a delay-and-retry loop if needed.)
+
+A container terminated this way will end with state @Cancelled@ if its docker container had already started, or @Queued@ if it was terminated while setting up the runtime environment.
+
+The provided @reason@ string will appear in the dispatcher's log, but not in the user-visible container log.
+
+If the provided @container_uuid@ is not scheduled/running on an instance, the response status will be 404.
+
+h3. List instances
+
+@GET /arvados/v1/dispatch/instances@
+
+Return a list of cloud instances.
+
+Example response:
+
+<notextile><pre>{
+ "items": [
+ {
+ "instance": "/subscriptions/abcdefab-abcd-abcd-abcd-abcdefabcdef/resourceGroups/zzzzz/providers/Microsoft.Compute/virtualMachines/compute-abcdef0123456789abcdef0123456789-abcdefghijklmno",
+ "address": "10.23.45.67",
+ "price": 0.073,
+ "arvados_instance_type": "Standard_DS1_v2",
+ "provider_instance_type": "Standard_DS1_v2",
+ "last_container_uuid": "zzzzz-dz642-vp7scm21telkadq",
+ "last_busy": "2020-01-13T15:20:21.775019617Z",
+ "worker_state": "running",
+ "idle_behavior": "run"
+ },
+ ...
+}</pre></notextile>
+
+The @instance@ value is the instance's identifier, assigned by the cloud provider. It can be used with the instance APIs below.
+
+The @worker_state@ value indicates the instance's capability to run containers.
+* @unknown@: instance was not created by this dispatcher, and a boot probe has not yet succeeded (this state typically appears briefly after the dispatcher restarts).
+* @booting@: cloud provider says the instance exists, but a boot probe has not yet succeeded.
+* @idle@: instance is idle and ready to run a container.
+* @running@: instance is running a container.
+* @shutdown@: cloud provider has been instructed to terminate the instance.
+
+The @idle_behavior@ value determines what the dispatcher will do with the instance when it is idle; see hold/drain/run APIs below.
+
+h3. Hold an instance
+
+@POST /arvados/v1/dispatch/instances/hold?instance_id={instance}@
+
+Set the indicated instance's idle behavior to @hold@. The instance will not be shut down automatically. If a container is currently running, it will be allowed to continue, but no new containers will be scheduled.
+
+h3. Drain an instance
+
+@POST /arvados/v1/dispatch/instances/drain?instance_id={instance}@
+
+Set the indicated instance's idle behavior to @drain@. If a container is currently running, it will be allowed to continue, but when the instance becomes idle, it will be shut down.
+
+h3. Resume an instance
+
+@POST /arvados/v1/dispatch/instances/run?instance_id={instance}@
+
+Set the indicated instance's idle behavior to @run@ (the normal behavior). When it becomes idle, it will be eligible to run new containers. It will be shut down automatically when the configured idle threshold is reached.
+
+h3. Shut down an instance
+
+@POST /arvados/v1/dispatch/instances/kill?instance_id={instance}&reason={string}@
+
+Terminate the indicated instance.
+
+If a container is running on the instance, it will be killed too; no effort is made to wait for it to end gracefully.
+
+The provided @reason@ string will appear in the dispatcher's log.
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
} else {
mux := httprouter.New()
mux.HandlerFunc("GET", "/arvados/v1/dispatch/containers", disp.apiContainers)
- mux.HandlerFunc("POST", "/arvados/v1/dispatch/containers/kill", disp.apiInstanceKill)
+ mux.HandlerFunc("POST", "/arvados/v1/dispatch/containers/kill", disp.apiContainerKill)
mux.HandlerFunc("GET", "/arvados/v1/dispatch/instances", disp.apiInstances)
mux.HandlerFunc("POST", "/arvados/v1/dispatch/instances/hold", disp.apiInstanceHold)
mux.HandlerFunc("POST", "/arvados/v1/dispatch/instances/drain", disp.apiInstanceDrain)
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'
import os
import re
-SETUP_DIR = os.path.dirname(__file__) or '.'
-
-def git_latest_tag():
- gittags = subprocess.check_output(['git', 'tag', '-l']).split()
- gittags.sort(key=lambda s: [int(u) for u in s.split(b'.')],reverse=True)
- return str(next(iter(gittags)).decode('utf-8'))
-
-def choose_version_from():
- sdk_ts = subprocess.check_output(
- ['git', 'log', '--first-parent', '--max-count=1',
- '--format=format:%ct', os.path.join(SETUP_DIR, "../python")]).strip()
- cwl_ts = subprocess.check_output(
- ['git', 'log', '--first-parent', '--max-count=1',
- '--format=format:%ct', SETUP_DIR]).strip()
- if int(sdk_ts) > int(cwl_ts):
- getver = os.path.join(SETUP_DIR, "../python")
- else:
- getver = SETUP_DIR
- return getver
-
-def git_timestamp_tag():
- gitinfo = subprocess.check_output(
- ['git', 'log', '--first-parent', '--max-count=1',
- '--format=format:%ct', choose_version_from()]).strip()
- return str(time.strftime('.%Y%m%d%H%M%S', time.gmtime(int(gitinfo))))
+def git_version_at_commit():
+ curdir = os.path.dirname(os.path.abspath(__file__))
+ myhash = subprocess.check_output(['git', 'log', '-n1', '--first-parent',
+ '--format=%H', curdir]).strip()
+ myversion = subprocess.check_output([curdir+'/../../build/version-at-commit.sh', myhash]).strip().decode()
+ return myversion
def save_version(setup_dir, module, v):
- with open(os.path.join(setup_dir, module, "_version.py"), 'w') as fp:
+ with open(os.path.join(setup_dir, module, "_version.py"), 'wt') as fp:
return fp.write("__version__ = '%s'\n" % v)
def read_version(setup_dir, module):
- with open(os.path.join(setup_dir, module, "_version.py"), 'r') as fp:
+ with open(os.path.join(setup_dir, module, "_version.py"), 'rt') as fp:
return re.match("__version__ = '(.*)'$", fp.read()).groups()[0]
def get_version(setup_dir, module):
save_version(setup_dir, module, env_version)
else:
try:
- save_version(setup_dir, module, git_latest_tag() + git_timestamp_tag())
+ save_version(setup_dir, module, git_version_at_commit())
except (subprocess.CalledProcessError, OSError):
pass
import os
import re
-def git_latest_tag():
- gittags = subprocess.check_output(['git', 'tag', '-l']).split()
- gittags.sort(key=lambda s: [int(u) for u in s.split(b'.')],reverse=True)
- return str(next(iter(gittags)).decode('utf-8'))
-
-def git_timestamp_tag():
- gitinfo = subprocess.check_output(
- ['git', 'log', '--first-parent', '--max-count=1',
- '--format=format:%ct', '.']).strip()
- return str(time.strftime('.%Y%m%d%H%M%S', time.gmtime(int(gitinfo))))
+def git_version_at_commit():
+ curdir = os.path.dirname(os.path.abspath(__file__))
+ myhash = subprocess.check_output(['git', 'log', '-n1', '--first-parent',
+ '--format=%H', curdir]).strip()
+ myversion = subprocess.check_output([curdir+'/../../build/version-at-commit.sh', myhash]).strip().decode()
+ return myversion
def save_version(setup_dir, module, v):
- with open(os.path.join(setup_dir, module, "_version.py"), 'w') as fp:
+ with open(os.path.join(setup_dir, module, "_version.py"), 'wt') as fp:
return fp.write("__version__ = '%s'\n" % v)
def read_version(setup_dir, module):
- with open(os.path.join(setup_dir, module, "_version.py"), 'r') as fp:
+ with open(os.path.join(setup_dir, module, "_version.py"), 'rt') as fp:
return re.match("__version__ = '(.*)'$", fp.read()).groups()[0]
def get_version(setup_dir, module):
save_version(setup_dir, module, env_version)
else:
try:
- save_version(setup_dir, module, git_latest_tag() + git_timestamp_tag())
- except subprocess.CalledProcessError:
+ save_version(setup_dir, module, git_version_at_commit())
+ except (subprocess.CalledProcessError, OSError):
pass
return read_version(setup_dir, module)
import os
import re
-def git_latest_tag():
- gittags = subprocess.check_output(['git', 'tag', '-l']).split()
- gittags.sort(key=lambda s: [int(u) for u in s.split(b'.')],reverse=True)
- return str(next(iter(gittags)).decode('utf-8'))
-
-def git_timestamp_tag():
- gitinfo = subprocess.check_output(
- ['git', 'log', '--first-parent', '--max-count=1',
- '--format=format:%ct', '.']).strip()
- return str(time.strftime('.%Y%m%d%H%M%S', time.gmtime(int(gitinfo))))
+def git_version_at_commit():
+ curdir = os.path.dirname(os.path.abspath(__file__))
+ myhash = subprocess.check_output(['git', 'log', '-n1', '--first-parent',
+ '--format=%H', curdir]).strip()
+ myversion = subprocess.check_output([curdir+'/../../build/version-at-commit.sh', myhash]).strip().decode()
+ return myversion
def save_version(setup_dir, module, v):
- with open(os.path.join(setup_dir, module, "_version.py"), 'w') as fp:
+ with open(os.path.join(setup_dir, module, "_version.py"), 'wt') as fp:
return fp.write("__version__ = '%s'\n" % v)
def read_version(setup_dir, module):
- with open(os.path.join(setup_dir, module, "_version.py"), 'r') as fp:
+ with open(os.path.join(setup_dir, module, "_version.py"), 'rt') as fp:
return re.match("__version__ = '(.*)'$", fp.read()).groups()[0]
def get_version(setup_dir, module):
save_version(setup_dir, module, env_version)
else:
try:
- save_version(setup_dir, module, git_latest_tag() + git_timestamp_tag())
+ save_version(setup_dir, module, git_version_at_commit())
except (subprocess.CalledProcessError, OSError):
pass
# Python 2 writes version info on stderr.
self.assertEqual(out.getvalue(), '')
v = err.getvalue()
- self.assertRegex(v, r"[0-9]+\.[0-9]+\.[0-9]+$\n")
+ self.assertRegex(v, r"[0-9]+\.[0-9]+\.[0-9]+(\.dev[0-9]+)?$\n")
class FakeCurl(object):
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: 81725af5d5d2e6cd18ba7099ba5fb1fc520f4f8c
+ 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
import os
import re
-def git_latest_tag():
- gittags = subprocess.check_output(['git', 'tag', '-l']).split()
- gittags.sort(key=lambda s: [int(u) for u in s.split(b'.')],reverse=True)
- return str(next(iter(gittags)).decode('utf-8'))
-
-def git_timestamp_tag():
- gitinfo = subprocess.check_output(
- ['git', 'log', '--first-parent', '--max-count=1',
- '--format=format:%ct', '.']).strip()
- return str(time.strftime('.%Y%m%d%H%M%S', time.gmtime(int(gitinfo))))
+def git_version_at_commit():
+ curdir = os.path.dirname(os.path.abspath(__file__))
+ myhash = subprocess.check_output(['git', 'log', '-n1', '--first-parent',
+ '--format=%H', curdir]).strip()
+ myversion = subprocess.check_output([curdir+'/../../build/version-at-commit.sh', myhash]).strip().decode()
+ return myversion
def save_version(setup_dir, module, v):
- with open(os.path.join(setup_dir, module, "_version.py"), 'w') as fp:
+ with open(os.path.join(setup_dir, module, "_version.py"), 'wt') as fp:
return fp.write("__version__ = '%s'\n" % v)
def read_version(setup_dir, module):
- with open(os.path.join(setup_dir, module, "_version.py"), 'r') as fp:
+ with open(os.path.join(setup_dir, module, "_version.py"), 'rt') as fp:
return re.match("__version__ = '(.*)'$", fp.read()).groups()[0]
def get_version(setup_dir, module):
save_version(setup_dir, module, env_version)
else:
try:
- save_version(setup_dir, module, git_latest_tag() + git_timestamp_tag())
- except subprocess.CalledProcessError:
+ save_version(setup_dir, module, git_version_at_commit())
+ except (subprocess.CalledProcessError, OSError):
pass
return read_version(setup_dir, module)
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''
import os
import re
-def git_latest_tag():
- gittags = subprocess.check_output(['git', 'tag', '-l']).split()
- gittags.sort(key=lambda s: [int(u) for u in s.split(b'.')],reverse=True)
- return str(next(iter(gittags)).decode('utf-8'))
-
-def git_timestamp_tag():
- gitinfo = subprocess.check_output(
- ['git', 'log', '--first-parent', '--max-count=1',
- '--format=format:%ct', '.']).strip()
- return str(time.strftime('.%Y%m%d%H%M%S', time.gmtime(int(gitinfo))))
+def git_version_at_commit():
+ curdir = os.path.dirname(os.path.abspath(__file__))
+ myhash = subprocess.check_output(['git', 'log', '-n1', '--first-parent',
+ '--format=%H', curdir]).strip()
+ myversion = subprocess.check_output([curdir+'/../../build/version-at-commit.sh', myhash]).strip().decode()
+ return myversion
def save_version(setup_dir, module, v):
- with open(os.path.join(setup_dir, module, "_version.py"), 'w') as fp:
+ with open(os.path.join(setup_dir, module, "_version.py"), 'wt') as fp:
return fp.write("__version__ = '%s'\n" % v)
def read_version(setup_dir, module):
- with open(os.path.join(setup_dir, module, "_version.py"), 'r') as fp:
+ with open(os.path.join(setup_dir, module, "_version.py"), 'rt') as fp:
return re.match("__version__ = '(.*)'$", fp.read()).groups()[0]
def get_version(setup_dir, module):
save_version(setup_dir, module, env_version)
else:
try:
- save_version(setup_dir, module, git_latest_tag() + git_timestamp_tag())
- except subprocess.CalledProcessError:
+ save_version(setup_dir, module, git_version_at_commit())
+ except (subprocess.CalledProcessError, OSError):
pass
return read_version(setup_dir, module)
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'
import os
import re
-def git_latest_tag():
- gittags = subprocess.check_output(['git', 'tag', '-l']).split()
- gittags.sort(key=lambda s: [int(u) for u in s.split(b'.')],reverse=True)
- return str(next(iter(gittags)).decode('utf-8'))
-
-def git_timestamp_tag():
- gitinfo = subprocess.check_output(
- ['git', 'log', '--first-parent', '--max-count=1',
- '--format=format:%ct', '.']).strip()
- return str(time.strftime('.%Y%m%d%H%M%S', time.gmtime(int(gitinfo))))
+def git_version_at_commit():
+ curdir = os.path.dirname(os.path.abspath(__file__))
+ myhash = subprocess.check_output(['git', 'log', '-n1', '--first-parent',
+ '--format=%H', curdir]).strip()
+ myversion = subprocess.check_output([curdir+'/../../build/version-at-commit.sh', myhash]).strip().decode()
+ return myversion
def save_version(setup_dir, module, v):
- with open(os.path.join(setup_dir, module, "_version.py"), 'w') as fp:
+ with open(os.path.join(setup_dir, module, "_version.py"), 'wt') as fp:
return fp.write("__version__ = '%s'\n" % v)
def read_version(setup_dir, module):
- with open(os.path.join(setup_dir, module, "_version.py"), 'r') as fp:
+ with open(os.path.join(setup_dir, module, "_version.py"), 'rt') as fp:
return re.match("__version__ = '(.*)'$", fp.read()).groups()[0]
def get_version(setup_dir, module):
save_version(setup_dir, module, env_version)
else:
try:
- save_version(setup_dir, module, git_latest_tag() + git_timestamp_tag())
- except subprocess.CalledProcessError:
+ save_version(setup_dir, module, git_version_at_commit())
+ except (subprocess.CalledProcessError, OSError):
pass
return read_version(setup_dir, module)
+++ /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 "$1" = "--only-deps" ; then
exit
import os
import re
-def git_latest_tag():
- gittags = subprocess.check_output(['git', 'tag', '-l']).split()
- gittags.sort(key=lambda s: [int(u) for u in s.split(b'.')],reverse=True)
- return str(next(iter(gittags)).decode('utf-8'))
-
-def git_timestamp_tag():
- gitinfo = subprocess.check_output(
- ['git', 'log', '--first-parent', '--max-count=1',
- '--format=format:%ct', '.']).strip()
- return str(time.strftime('.%Y%m%d%H%M%S', time.gmtime(int(gitinfo))))
+def git_version_at_commit():
+ curdir = os.path.dirname(os.path.abspath(__file__))
+ myhash = subprocess.check_output(['git', 'log', '-n1', '--first-parent',
+ '--format=%H', curdir]).strip()
+ myversion = subprocess.check_output([curdir+'/../../build/version-at-commit.sh', myhash]).strip().decode()
+ return myversion
def save_version(setup_dir, module, v):
- with open(os.path.join(setup_dir, module, "_version.py"), 'w') as fp:
+ with open(os.path.join(setup_dir, module, "_version.py"), 'wt') as fp:
return fp.write("__version__ = '%s'\n" % v)
def read_version(setup_dir, module):
- with open(os.path.join(setup_dir, module, "_version.py"), 'r') as fp:
+ with open(os.path.join(setup_dir, module, "_version.py"), 'rt') as fp:
return re.match("__version__ = '(.*)'$", fp.read()).groups()[0]
def get_version(setup_dir, module):
save_version(setup_dir, module, env_version)
else:
try:
- save_version(setup_dir, module, git_latest_tag() + git_timestamp_tag())
- except subprocess.CalledProcessError:
+ save_version(setup_dir, module, git_version_at_commit())
+ except (subprocess.CalledProcessError, OSError):
pass
return read_version(setup_dir, module)
projects / arvados.git / commitdiff