[ARVADOS] updated: 4f0e07d462b7860bb10686c27fac16970220377f

Git user git at public.curoverse.com
Mon Feb 20 15:46:42 EST 2017


Summary of changes:
 .../app/views/work_units/_show_child.html.erb      |   4 +-
 build/package-build-dockerfiles/Makefile           |   2 +-
 build/package-build-dockerfiles/centos7/Dockerfile |   6 +-
 build/package-build-dockerfiles/debian8/Dockerfile |   6 +-
 .../ubuntu1204/Dockerfile                          |   6 +-
 .../ubuntu1404/Dockerfile                          |   6 +-
 .../ubuntu1604/Dockerfile                          |   6 +-
 doc/_includes/_install_ruby_and_bundler.liquid     |   8 +-
 sdk/cli/arvados-cli.gemspec                        |   4 +-
 sdk/cli/bin/crunch-job                             |   5 +-
 sdk/cli/test/binstub_output_coll_owner/python      |   4 +
 sdk/cli/test/test_crunch-job.rb                    |   9 +
 sdk/cwl/arvados_cwl/__init__.py                    |   7 +-
 sdk/cwl/arvados_cwl/arvcontainer.py                |  61 +++-
 sdk/cwl/arvados_cwl/arvjob.py                      |  11 +-
 sdk/cwl/arvados_cwl/done.py                        |   2 +-
 sdk/cwl/arvados_cwl/fsaccess.py                    |   9 +-
 sdk/cwl/arvados_cwl/pathmapper.py                  |   4 +-
 sdk/cwl/setup.py                                   |   2 +-
 sdk/cwl/test_with_arvbox.sh                        |   2 +
 sdk/cwl/tests/test_container.py                    | 123 ++++++++
 sdk/cwl/tests/test_submit.py                       |   2 +-
 sdk/go/dispatch/dispatch.go                        | 340 ++++++++++-----------
 sdk/python/arvados/commands/keepdocker.py          |  63 ++++
 sdk/python/bin/arv-migrate-docker19                |   4 +
 sdk/python/setup.py                                |   1 +
 sdk/python/tests/test_arv_keepdocker.py            |  17 ++
 sdk/ruby/arvados.gemspec                           |   4 +-
 services/api/app/models/arvados_model.rb           |   6 +-
 services/api/app/models/collection.rb              |  18 ++
 services/api/app/models/container_request.rb       |   8 +-
 services/api/app/models/job.rb                     |  18 +-
 services/api/app/models/node.rb                    |   4 +-
 services/api/app/models/workflow.rb                |   4 +
 ..._and_workflow_def_in_full_text_search_index.rb} |  17 +-
 services/api/db/structure.sql                      |   8 +-
 services/api/lib/crunch_dispatch.rb                |   2 +-
 services/api/lib/has_uuid.rb                       |   4 +-
 services/api/lib/sweep_trashed_collections.rb      |   3 +
 services/api/test/fixtures/collections.yml         |   2 +-
 services/api/test/fixtures/links.yml               |  56 ++++
 .../api/test/helpers/docker_migration_helper.rb    |  13 +
 services/api/test/unit/collection_test.rb          |  16 +
 services/api/test/unit/container_request_test.rb   |  19 ++
 services/api/test/unit/container_test.rb           |  12 +-
 services/api/test/unit/job_test.rb                 |  56 ++++
 services/api/test/unit/link_test.rb                |  24 +-
 .../crunch-dispatch-local/crunch-dispatch-local.go |  18 +-
 .../crunch-dispatch-local_test.go                  |  42 +--
 .../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 170 +++++------
 .../crunch-dispatch-slurm_test.go                  |  77 +++--
 services/crunch-run/crunchrun.go                   |  14 +-
 .../arvnodeman/computenode/dispatch/__init__.py    |   2 +
 .../arvnodeman/computenode/dispatch/slurm.py       |  18 +-
 services/nodemanager/arvnodeman/daemon.py          |   6 +-
 services/nodemanager/arvnodeman/jobqueue.py        |  20 +-
 services/nodemanager/arvnodeman/launcher.py        |   2 +-
 services/nodemanager/arvnodeman/nodelist.py        |  42 ++-
 .../nodemanager/tests/test_computenode_dispatch.py |   8 +-
 .../tests/test_computenode_dispatch_slurm.py       |  15 +-
 services/nodemanager/tests/test_jobqueue.py        |  19 +-
 services/nodemanager/tests/test_nodelist.py        |  45 ++-
 tools/arvbox/lib/arvbox/docker/Dockerfile.base     |  23 +-
 tools/arvbox/lib/arvbox/docker/api-setup.sh        |   4 +-
 tools/arvbox/lib/arvbox/docker/createusers.sh      |  15 +-
 65 files changed, 1067 insertions(+), 481 deletions(-)
 create mode 100755 sdk/cli/test/binstub_output_coll_owner/python
 create mode 100755 sdk/python/bin/arv-migrate-docker19
 copy services/api/db/migrate/{20161213172944_full_text_search_indexes.rb => 20170216170823_no_cr_mounts_and_workflow_def_in_full_text_search_index.rb} (55%)
 create mode 100644 services/api/test/helpers/docker_migration_helper.rb

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commit 4f0e07d462b7860bb10686c27fac16970220377f
Author: Tom Clegg <tom at curoverse.com>
Date:   Mon Feb 20 15:45:40 2017 -0500

    11097: Update test to match new behavior.

diff --git a/services/api/test/unit/container_test.rb b/services/api/test/unit/container_test.rb
index a175533..03944d6 100644
--- a/services/api/test/unit/container_test.rb
+++ b/services/api/test/unit/container_test.rb
@@ -140,7 +140,7 @@ class ContainerTest < ActiveSupport::TestCase
     assert_equal reused.uuid, c_older.uuid
   end
 
-  test "find_reusable method should not select completed container when inconsistent outputs exist" do
+  test "find_reusable method should select oldest completed container when inconsistent outputs exist" do
     set_user_from_auth :active
     common_attrs = REUSABLE_COMMON_ATTRS.merge({environment: {"var" => "complete"}, priority: 1})
     completed_attrs = {
@@ -165,16 +165,20 @@ class ContainerTest < ActiveSupport::TestCase
     cr.container_uuid = c_output2.uuid
     cr.save!
 
+    out1 = '1f4b0bc7583c2a7f9102c395f4ffc5e3+45'
+    log1 = collections(:real_log_collection).portable_data_hash
     c_output1.update_attributes!({state: Container::Locked})
     c_output1.update_attributes!({state: Container::Running})
-    c_output1.update_attributes!(completed_attrs.merge({output: '1f4b0bc7583c2a7f9102c395f4ffc5e3+45'}))
+    c_output1.update_attributes!(completed_attrs.merge({log: log1, output: out1}))
 
+    out2 = 'fa7aeb5140e2848d39b416daeef4ffc5+45'
     c_output2.update_attributes!({state: Container::Locked})
     c_output2.update_attributes!({state: Container::Running})
-    c_output2.update_attributes!(completed_attrs.merge({output: 'fa7aeb5140e2848d39b416daeef4ffc5+45'}))
+    c_output2.update_attributes!(completed_attrs.merge({log: log1, output: out2}))
 
     reused = Container.find_reusable(common_attrs)
-    assert_nil reused
+    assert_not_nil reused
+    assert_equal reused.uuid, c_output1.uuid
   end
 
   test "find_reusable method should select running container by start date" do

commit 4cd89bd1767bece226c412ae7c9ea37669e8706b
Merge: 264ffa3 d069de0
Author: Tom Clegg <tom at curoverse.com>
Date:   Mon Feb 20 15:34:15 2017 -0500

    11097: Merge branch 'master' into 11097-reuse-impure


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