[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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