[ARVADOS] updated: b1b8942ee0190343dd815b895f49d3894d7f2702
Git user
git at public.curoverse.com
Mon Sep 18 16:47:18 EDT 2017
Summary of changes:
.../assets/javascripts/components/collections.js | 7 +-
.../workbench/app/assets/javascripts/filterable.js | 7 +-
.../workbench/app/assets/javascripts/to_tsquery.js | 24 +++
.../views/trash_items/_show_recent_trash.html.erb | 12 +-
.../views/trash_items/_show_trash_rows.html.erb | 14 +-
apps/workbench/test/integration/trash_test.rb | 13 +-
build/libcloud-pin.sh | 2 +-
build/run-tests.sh | 3 +-
doc/_config.yml | 2 +
doc/sdk/go/example.html.textile.liquid | 28 ++--
doc/sdk/java/example.html.textile.liquid | 32 ++--
doc/sdk/perl/example.html.textile.liquid | 55 +++----
doc/sdk/python/cookbook.html.textile.liquid | 166 +++++++++++++++++++++
doc/sdk/python/example.html.textile.liquid | 28 ++--
doc/sdk/ruby/example.html.textile.liquid | 33 ++--
doc/user/reference/cookbook.html.textile.liquid | 12 ++
doc/zenweb-liquid.rb | 44 +++++-
sdk/cwl/arvados_cwl/arvcontainer.py | 8 +-
sdk/cwl/arvados_cwl/arvjob.py | 8 +-
sdk/cwl/arvados_cwl/arvworkflow.py | 8 +-
sdk/cwl/arvados_cwl/pathmapper.py | 10 +-
sdk/cwl/arvados_cwl/runner.py | 5 +
sdk/cwl/test_with_arvbox.sh | 2 +-
sdk/cwl/tests/test_job.py | 18 ++-
sdk/cwl/tests/test_submit.py | 12 +-
sdk/cwl/tests/wf/scatter2.cwl | 7 +
sdk/cwl/tests/wf/scatter2_subwf.cwl | 4 +
services/api/test/helpers/git_test_helper.rb | 13 +-
services/api/test/unit/commit_test.rb | 49 ++++++
services/nodemanager/setup.py | 4 +-
tools/arvbox/bin/arvbox | 5 +-
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 30 ++--
tools/arvbox/lib/arvbox/docker/Dockerfile.demo | 2 +-
tools/arvbox/lib/arvbox/docker/Dockerfile.dev | 2 +-
tools/arvbox/lib/arvbox/docker/api-setup.sh | 2 +-
tools/arvbox/lib/arvbox/docker/common.sh | 6 +-
tools/arvbox/lib/arvbox/docker/createusers.sh | 5 +-
.../arvbox/lib/arvbox/docker/service/postgres/run | 1 +
.../lib/arvbox/docker/service/postgres/run-service | 12 +-
.../arvbox/docker/service/workbench/run-service | 1 +
.../crunchstat_summary/reader.py | 31 +++-
.../crunchstat_summary/summarizer.py | 68 +++++++--
tools/crunchstat-summary/tests/test_examples.py | 81 +++++++++-
43 files changed, 679 insertions(+), 197 deletions(-)
create mode 100644 apps/workbench/app/assets/javascripts/to_tsquery.js
create mode 100644 doc/sdk/python/cookbook.html.textile.liquid
create mode 100644 doc/user/reference/cookbook.html.textile.liquid
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commit b1b8942ee0190343dd815b895f49d3894d7f2702
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date: Mon Sep 18 16:46:13 2017 -0400
12107: Test fetch-and-tag on unreferenced and non-tip commits.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>
diff --git a/services/api/test/unit/commit_test.rb b/services/api/test/unit/commit_test.rb
index ec7a0b9..6a8a5b4 100644
--- a/services/api/test/unit/commit_test.rb
+++ b/services/api/test/unit/commit_test.rb
@@ -26,6 +26,14 @@ class CommitTest < ActiveSupport::TestCase
end
end
+ def must_pipe(cmd)
+ begin
+ return IO.read("|#{cmd}")
+ ensure
+ assert $?.success?
+ end
+ end
+
[
'https://github.com/curoverse/arvados.git',
'http://github.com/curoverse/arvados.git',
@@ -79,6 +87,47 @@ class CommitTest < ActiveSupport::TestCase
assert $?.success?
end
+ def with_foo_repository
+ Dir.chdir("#{Rails.configuration.git_repositories_dir}/#{repositories(:foo).uuid}") do
+ must_pipe("git checkout master 2>&1")
+ yield
+ end
+ end
+
+ test 'tag_in_internal_repository, new non-tip sha1 in local repo' do
+ tag = "tag#{rand(10**10)}"
+ sha1 = nil
+ with_foo_repository do
+ must_pipe("git checkout -b branch-#{rand(10**10)} 2>&1")
+ must_pipe("echo -n #{tag.shellescape} >bar")
+ must_pipe("git add bar")
+ must_pipe("git commit -m -")
+ sha1 = must_pipe("git log -n1 --format=%H").strip
+ must_pipe("git rm bar")
+ must_pipe("git commit -m -")
+ end
+ Commit.tag_in_internal_repository 'active/foo', sha1, tag
+ gitint = "git --git-dir #{Rails.configuration.git_internal_dir.shellescape}"
+ assert_match(/^commit /, IO.read("|#{gitint} show #{tag.shellescape}"))
+ assert $?.success?
+ end
+
+ test 'tag_in_internal_repository, new unreferenced sha1 in local repo' do
+ tag = "tag#{rand(10**10)}"
+ sha1 = nil
+ with_foo_repository do
+ must_pipe("echo -n #{tag.shellescape} >bar")
+ must_pipe("git add bar")
+ must_pipe("git commit -m -")
+ sha1 = must_pipe("git log -n1 --format=%H").strip
+ must_pipe("git reset --hard HEAD^")
+ end
+ Commit.tag_in_internal_repository 'active/foo', sha1, tag
+ gitint = "git --git-dir #{Rails.configuration.git_internal_dir.shellescape}"
+ assert_match(/^commit /, IO.read("|#{gitint} show #{tag.shellescape}"))
+ assert $?.success?
+ end
+
# In active/shabranchnames, "7387838c69a21827834586cc42b467ff6c63293b" is
# both a commit hash, and the name of a branch that begins from that same
# commit.
commit 71ad589048fec9da45253ac4480085ac5b8f5048
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date: Mon Sep 18 16:41:31 2017 -0400
12107: Use a fresh internal.git repo for each test run.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>
diff --git a/services/api/test/helpers/git_test_helper.rb b/services/api/test/helpers/git_test_helper.rb
index 19639b3..673e0e2 100644
--- a/services/api/test/helpers/git_test_helper.rb
+++ b/services/api/test/helpers/git_test_helper.rb
@@ -27,12 +27,13 @@ module GitTestHelper
system("tar", "-xC", @tmpdir.to_s, "-f", "test/test.git.tar")
Rails.configuration.git_repositories_dir = "#{@tmpdir}/test"
- intdir = Rails.configuration.git_internal_dir
- if not File.exist? intdir
- FileUtils.mkdir_p intdir
- IO.read("|git --git-dir #{intdir.to_s.shellescape} init")
- assert $?.success?
- end
+ # Initialize an empty internal git repo.
+ intdir =
+ Rails.configuration.git_internal_dir =
+ Rails.root.join(@tmpdir, 'internal.git').to_s
+ FileUtils.mkdir_p intdir
+ IO.read("|git --git-dir #{intdir.shellescape} init")
+ assert $?.success?
end
base.teardown do
commit 3854e6bfcd5344bce5ee0388248cb115e3c5e902
Merge: bd5a371 a6d5c9b
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date: Mon Sep 18 14:33:36 2017 -0400
Merge branch 'master' into 12107-faster-git
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>
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