[ARVADOS] updated: fd696fac8234ff799aa6ac63819e5e6ac0a8a9d4
Git user
git at public.curoverse.com
Thu Apr 14 10:00:51 EDT 2016
Summary of changes:
.../pipeline_instances/_running_component.html.erb | 10 -
apps/workbench/test/test_helper.rb | 6 +-
build/run-build-docker-jobs-image.sh | 6 +-
build/run-build-packages-one-target.sh | 4 +-
build/run-build-packages-python-and-ruby.sh | 203 ++++++++++++
build/run-build-packages.sh | 50 +--
build/run-tests.sh | 9 +-
crunch_scripts/crunchrunner | 7 +-
crunch_scripts/cwl-runner | 92 ++++++
doc/api/schema/Job.html.textile.liquid | 1 +
doc/install/arvbox.html.textile.liquid | 11 +-
docker/build_tools/Makefile | 2 +-
docker/jobs/Dockerfile | 12 +-
docker/jobs/apt.arvados.org.list | 2 +-
sdk/cli/bin/crunch-job | 51 +--
sdk/cwl/arvados_cwl/__init__.py | 349 +++++++++++++++++----
sdk/cwl/setup.py | 4 +-
sdk/cwl/test_with_arvbox.sh | 7 +
sdk/cwl/tests/input/blorp.txt | 1 +
sdk/cwl/tests/submit_test_job.json | 6 +
sdk/cwl/tests/test_job.py | 167 +++++++---
sdk/cwl/tests/test_submit.py | 103 ++++++
sdk/cwl/tests/tool/blub.txt | 1 +
sdk/cwl/tests/tool/submit_tool.cwl | 19 ++
sdk/cwl/tests/wf/submit_wf.cwl | 16 +
sdk/go/arvadostest/fixtures.go | 2 +
sdk/go/crunchrunner/crunchrunner.go | 24 +-
sdk/python/arvados/commands/keepdocker.py | 12 +-
sdk/python/arvados/commands/run.py | 26 +-
sdk/python/arvados/events.py | 78 ++++-
sdk/python/setup.py | 1 +
sdk/python/tests/test_websockets.py | 109 ++++++-
.../v1/api_client_authorizations_controller.rb | 33 +-
.../app/controllers/arvados/v1/jobs_controller.rb | 5 +-
services/api/app/models/job.rb | 21 +-
.../20160324144017_add_components_to_job.rb | 11 +
services/api/db/structure.sql | 7 +-
services/api/test/fixtures/jobs.yml | 29 ++
.../api_client_authorizations_controller_test.rb | 40 ++-
.../arvados/v1/groups_controller_test.rb | 6 +-
.../functional/arvados/v1/jobs_controller_test.rb | 75 +++++
services/api/test/test_helper.rb | 6 +-
services/api/test/unit/job_test.rb | 1 -
services/dockercleaner/setup.py | 2 +-
services/fuse/arvados_fuse/fusedir.py | 5 +
services/fuse/tests/test_cache.py | 45 +++
services/keepstore/azure_blob_volume.go | 2 +-
.../arvnodeman/computenode/dispatch/__init__.py | 37 ++-
.../arvnodeman/computenode/dispatch/slurm.py | 72 +++--
.../arvnodeman/computenode/driver/__init__.py | 55 ++--
.../arvnodeman/computenode/driver/azure.py | 7 +-
.../arvnodeman/computenode/driver/ec2.py | 4 +-
.../arvnodeman/computenode/driver/gce.py | 7 +-
services/nodemanager/arvnodeman/daemon.py | 24 +-
.../nodemanager/tests/test_computenode_dispatch.py | 14 +-
.../tests/test_computenode_dispatch_slurm.py | 64 ++++
.../tests/test_computenode_driver_azure.py | 14 +
.../tests/test_computenode_driver_gce.py | 5 +
services/nodemanager/tests/test_daemon.py | 26 +-
services/nodemanager/tests/testutil.py | 39 +++
tools/arvbox/bin/arvbox | 47 +--
tools/arvbox/lib/arvbox/docker/Dockerfile.demo | 4 +
tools/arvbox/lib/arvbox/docker/common.sh | 8 +-
tools/arvbox/lib/arvbox/docker/crunch-setup.sh | 9 +-
tools/arvbox/lib/arvbox/docker/keep-setup.sh | 11 +-
.../docker/service/arv-git-httpd/run-service | 12 +-
.../service/crunch-dispatch-local/run-service | 8 +-
.../lib/arvbox/docker/service/keep-web/run-service | 12 +-
.../arvbox/docker/service/keepproxy/run-service | 12 +-
.../lib/arvbox/docker/service/sdk/run-service | 4 +-
.../crunchstat_summary/reader.py | 1 +
.../crunchstat_summary/summarizer.py | 1 +
tools/keep-block-check/.gitignore | 1 +
tools/keep-block-check/keep-block-check.go | 223 +++++++++++++
tools/keep-block-check/keep-block-check_test.go | 336 ++++++++++++++++++++
tools/keep-rsync/keep-rsync_test.go | 2 +-
76 files changed, 2375 insertions(+), 363 deletions(-)
create mode 100755 build/run-build-packages-python-and-ruby.sh
create mode 100755 crunch_scripts/cwl-runner
create mode 100644 sdk/cwl/tests/input/blorp.txt
create mode 100644 sdk/cwl/tests/submit_test_job.json
create mode 100644 sdk/cwl/tests/test_submit.py
create mode 100644 sdk/cwl/tests/tool/blub.txt
create mode 100644 sdk/cwl/tests/tool/submit_tool.cwl
create mode 100644 sdk/cwl/tests/wf/submit_wf.cwl
create mode 100644 services/api/db/migrate/20160324144017_add_components_to_job.rb
create mode 100644 services/fuse/tests/test_cache.py
create mode 100644 tools/keep-block-check/.gitignore
create mode 100644 tools/keep-block-check/keep-block-check.go
create mode 100644 tools/keep-block-check/keep-block-check_test.go
discards 915308ee58ef34d1fc86103b2d485212a72b5b98 (commit)
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commit fd696fac8234ff799aa6ac63819e5e6ac0a8a9d4
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Apr 13 10:57:09 2016 -0400
8697: Fix Locator.parse() (was failing on locators with hints).
diff --git a/sdk/ruby/lib/arvados/keep.rb b/sdk/ruby/lib/arvados/keep.rb
index 3c6b26b..489eeee 100644
--- a/sdk/ruby/lib/arvados/keep.rb
+++ b/sdk/ruby/lib/arvados/keep.rb
@@ -47,19 +47,19 @@ module Keep
raise ArgumentError.new "locator is nil or empty"
end
- m = LOCATOR_REGEXP.match(tok.strip)
+ m = LOCATOR_REGEXP.match(tok)
unless m
raise ArgumentError.new "not a valid locator #{tok}"
end
- tokhash, _, toksize, _, trailer = m[1..5]
+ tokhash, _, toksize, _, _, trailer = m[1..6]
tokhints = []
if trailer
trailer.split('+').each do |hint|
- if hint =~ /^[[:upper:]][[:alnum:]@_-]+$/
+ if hint =~ /^[[:upper:]][[:alnum:]@_-]*$/
tokhints.push(hint)
else
- raise ArgumentError.new "unknown hint #{hint}"
+ raise ArgumentError.new "invalid hint #{hint}"
end
end
end
diff --git a/sdk/ruby/test/test_keep_manifest.rb b/sdk/ruby/test/test_keep_manifest.rb
index 5ed9cfc..fa1dc3f 100644
--- a/sdk/ruby/test/test_keep_manifest.rb
+++ b/sdk/ruby/test/test_keep_manifest.rb
@@ -266,6 +266,8 @@ class ManifestTest < Minitest::Test
[true, 'd41d8cd98f00b204e9800998ecf8427e+0', '+0','0',nil],
[true, 'd41d8cd98f00b204e9800998ecf8427e+0+Fizz+Buzz','+0','0','+Fizz+Buzz'],
[true, 'd41d8cd98f00b204e9800998ecf8427e+Fizz+Buzz', nil,nil,'+Fizz+Buzz'],
+ [true, 'd41d8cd98f00b204e9800998ecf8427e+0+Ad41d8cd98f00b204e9800998ecf8427e00000000+Foo', '+0','0','+Ad41d8cd98f00b204e9800998ecf8427e00000000+Foo'],
+ [true, 'd41d8cd98f00b204e9800998ecf8427e+Ad41d8cd98f00b204e9800998ecf8427e00000000+Foo', nil,nil,'+Ad41d8cd98f00b204e9800998ecf8427e00000000+Foo'],
[true, 'd41d8cd98f00b204e9800998ecf8427e+0+Z', '+0','0','+Z'],
[true, 'd41d8cd98f00b204e9800998ecf8427e+Z', nil,nil,'+Z'],
].each do |ok, locator, match2, match3, match4|
@@ -278,6 +280,18 @@ class ManifestTest < Minitest::Test
assert_equal match4, match[4]
end
end
+ define_method "test_parse_method_on_#{locator.inspect}" do
+ loc = Keep::Locator.parse locator
+ if !ok
+ assert_nil loc
+ else
+ refute_nil loc
+ assert loc.is_a?(Keep::Locator)
+ #assert loc.hash
+ #assert loc.size
+ #assert loc.hints.is_a?(Array)
+ end
+ end
end
[
@@ -301,6 +315,7 @@ class ManifestTest < Minitest::Test
[true, ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:\\040\n"],
[true, ". 00000000000000000000000000000000+0 0:0:0\n"],
[true, ". 00000000000000000000000000000000+0 0:0:d41d8cd98f00b204e9800998ecf8427e+0+Ad41d8cd98f00b204e9800998ecf8427e00000000 at ffffffff\n"],
+ [true, ". d41d8cd98f00b204e9800998ecf8427e+0+Ad41d8cd98f00b204e9800998ecf8427e00000000 at ffffffff 0:0:empty.txt\n"],
[false, '. d41d8cd98f00b204e9800998ecf8427e 0:0:abc.txt',
"Invalid manifest: does not end with newline"],
[false, "abc d41d8cd98f00b204e9800998ecf8427e 0:0:abc.txt\n",
commit 3a31612fdc5e1ccdfa91d04ff5a089d6e06c0f60
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Apr 13 10:24:14 2016 -0400
8697: ruby 1.8.7 compatibility in arvados/collection.
diff --git a/sdk/ruby/lib/arvados/collection.rb b/sdk/ruby/lib/arvados/collection.rb
index 07b7519..474241d 100644
--- a/sdk/ruby/lib/arvados/collection.rb
+++ b/sdk/ruby/lib/arvados/collection.rb
@@ -44,7 +44,7 @@ module Arv
end
def cp_r(source, target, source_collection=nil)
- opts = {descend_target: !source.end_with?("/")}
+ opts = {:descend_target => !source.end_with?("/")}
copy(:merge, source.chomp("/"), target, source_collection, opts)
end
@@ -70,7 +70,7 @@ module Arv
end
def rm_r(source)
- remove(source, recursive: true)
+ remove(source, :recursive => true)
end
protected
@@ -155,7 +155,7 @@ module Arv
modified
end
- LocatorSegment = Struct.new(:locators, :start_pos, :length)
+ Struct.new("LocatorSegment", :locators, :start_pos, :length)
class LocatorRange < Range
attr_reader :locator
@@ -187,9 +187,9 @@ module Arv
end_index = search_for_byte(start_pos + length - 1, start_index)
end
seg_ranges = @ranges[start_index..end_index]
- LocatorSegment.new(seg_ranges.map(&:locator),
- start_pos - seg_ranges.first.begin,
- length)
+ Struct::LocatorSegment.new(seg_ranges.map(&:locator),
+ start_pos - seg_ranges.first.begin,
+ length)
end
private
commit 065cefa6e87c8b668af5a4abc065514b84db83b5
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Mar 22 17:29:29 2016 -0400
8697: Move error messages from stdout to stderr.
diff --git a/sdk/cli/bin/arv-run-pipeline-instance b/sdk/cli/bin/arv-run-pipeline-instance
index 70e2f42..6dc82c5 100755
--- a/sdk/cli/bin/arv-run-pipeline-instance
+++ b/sdk/cli/bin/arv-run-pipeline-instance
@@ -17,7 +17,7 @@ begin
require 'trollop'
require 'google/api_client'
rescue LoadError => l
- puts $:
+ $stderr.puts $:
abort <<-EOS
#{$0}: fatal: #{l.message}
Some runtime dependencies may be missing.
@@ -132,7 +132,7 @@ if $options[:instance]
abort "#{$0}: syntax error: --instance cannot be combined with --template or --submit."
end
elsif not $options[:template]
- puts "error: you must supply a --template or --instance."
+ $stderr.puts "error: you must supply a --template or --instance."
p.educate
abort
end
commit 40ad5fb3f699c348222c90692b9ae27a8f716af9
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Mar 22 17:28:39 2016 -0400
8697: Relax version constraints so gem can be used in ruby187/ree projects.
diff --git a/sdk/ruby/arvados.gemspec b/sdk/ruby/arvados.gemspec
index 3d090f4..355ed5d 100644
--- a/sdk/ruby/arvados.gemspec
+++ b/sdk/ruby/arvados.gemspec
@@ -18,13 +18,15 @@ Gem::Specification.new do |s|
s.files = ["lib/arvados.rb", "lib/arvados/google_api_client.rb",
"lib/arvados/collection.rb", "lib/arvados/keep.rb",
"README", "LICENSE-2.0.txt"]
- s.required_ruby_version = '>= 2.1.0'
+ s.required_ruby_version = '>= 1.8.7'
# activesupport <4.2.6 only because https://dev.arvados.org/issues/8222
- s.add_dependency('activesupport', '>= 3.2.13', '< 4.2.6')
+ s.add_dependency('activesupport', '>= 3', '< 4.2.6')
s.add_dependency('andand', '~> 1.3', '>= 1.3.3')
- s.add_dependency('google-api-client', '~> 0.6.3', '>= 0.6.3')
+ s.add_dependency('google-api-client', '>= 0.7', '< 0.9')
+ # work around undeclared dependency on i18n in some activesupport 3.x.x:
+ s.add_dependency('i18n', '~> 0')
s.add_dependency('json', '~> 1.7', '>= 1.7.7')
- s.add_runtime_dependency('jwt', '>= 0.1.5', '< 1.0.0')
+ s.add_runtime_dependency('jwt', '<2', '>= 0.1.5')
s.homepage =
'https://arvados.org'
end
diff --git a/sdk/ruby/lib/arvados.rb b/sdk/ruby/lib/arvados.rb
index 753c518..7a3f4b4 100644
--- a/sdk/ruby/lib/arvados.rb
+++ b/sdk/ruby/lib/arvados.rb
@@ -209,7 +209,7 @@ class Arvados
:parameters => parameters,
:body_object => body,
:headers => {
- authorization: 'OAuth2 '+arvados.config['ARVADOS_API_TOKEN']
+ :authorization => 'OAuth2 '+arvados.config['ARVADOS_API_TOKEN']
})
resp = JSON.parse result.body, :symbolize_names => true
if resp[:errors]
@@ -217,7 +217,7 @@ class Arvados
elsif resp[:uuid] and resp[:etag]
self.new(resp)
elsif resp[:items].is_a? Array
- resp.merge(items: resp[:items].collect do |i|
+ resp.merge(:items => resp[:items].collect do |i|
self.new(i)
end)
else
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