[ARVADOS] updated: 0d5be4fa36006459e1579f087b695904e4f32ee3
Git user
git at public.curoverse.com
Mon Apr 10 13:13:39 EDT 2017
Summary of changes:
.../app/controllers/actions_controller.rb | 37 +--
.../app/controllers/application_controller.rb | 43 ++++
.../app/controllers/collections_controller.rb | 52 ++++
apps/workbench/app/helpers/application_helper.rb | 4 +-
apps/workbench/app/models/collection.rb | 2 +-
.../app/views/collections/_show_files.html.erb | 30 ++-
apps/workbench/config/routes.rb | 1 +
.../controllers/collections_controller_test.rb | 132 +++++++++-
.../workbench/test/integration/collections_test.rb | 59 +++++
build/build.list | 10 +-
.../package-test-dockerfiles/ubuntu1204/Dockerfile | 2 +-
build/rails-package-scripts/postinst.sh | 4 +-
build/run-tests.sh | 3 +
.../methods/container_requests.html.textile.liquid | 2 +
sdk/cli/arvados-cli.gemspec | 2 +-
sdk/cli/test/test_arv-keep-get.rb | 4 +-
sdk/cwl/arvados_cwl/__init__.py | 3 +
sdk/cwl/arvados_cwl/arvcontainer.py | 3 +-
sdk/cwl/arvados_cwl/fsaccess.py | 7 +-
sdk/cwl/arvados_cwl/pathmapper.py | 13 +-
sdk/cwl/arvados_cwl/runner.py | 3 -
sdk/cwl/setup.py | 5 +-
sdk/cwl/tests/arvados-tests.sh | 2 +-
sdk/cwl/tests/arvados-tests.yml | 38 +++
sdk/cwl/tests/cat.cwl | 8 +
sdk/cwl/tests/dir-job2.yml | 3 +
...dir-test-input.cwl => keep-dir-test-input2.cwl} | 3 +
...dir-test-input.cwl => keep-dir-test-input3.cwl} | 3 +
sdk/cwl/tests/octo.yml | 3 +
.../cwl/tests/octothorpe/item #1.txt | 0
sdk/cwl/tests/test_submit.py | 16 +-
sdk/go/keepclient/support.go | 10 +
sdk/python/arvados/__init__.py | 1 -
sdk/python/arvados/api.py | 10 +-
sdk/python/arvados/commands/get.py | 276 +++++++++++++++++++++
sdk/python/arvados/commands/ls.py | 57 ++++-
sdk/python/arvados/commands/run.py | 88 ++++---
sdk/python/arvados/keep.py | 19 +-
sdk/python/bin/arv-get | 235 +-----------------
sdk/python/setup.py | 10 +-
sdk/python/tests/test_arv_get.py | 108 ++++++++
sdk/python/tests/test_arv_ls.py | 11 +-
sdk/python/tests/test_cache.py | 15 +-
sdk/ruby/arvados.gemspec | 2 +-
.../api/app/controllers/application_controller.rb | 4 +-
.../app/controllers/arvados/v1/nodes_controller.rb | 2 +-
services/api/app/models/arvados_model.rb | 53 ++--
services/api/app/models/collection.rb | 42 +++-
services/api/app/models/container_request.rb | 85 ++++---
..._add_portable_data_hash_index_to_collections.rb | 5 +
...0012505_add_output_ttl_to_container_requests.rb | 5 +
services/api/db/structure.sql | 13 +-
services/api/lib/crunch_dispatch.rb | 7 +-
services/api/test/fixtures/collections.yml | 16 +-
.../functional/arvados/v1/nodes_controller_test.rb | 10 +-
services/api/test/unit/collection_test.rb | 23 +-
services/api/test/unit/container_request_test.rb | 115 +++++++--
services/crunch-run/crunchrun.go | 151 +++++++----
services/crunch-run/crunchrun_test.go | 161 ++++++------
services/fuse/arvados_fuse/command.py | 42 ++--
services/fuse/arvados_fuse/unmount.py | 108 ++++++++
services/fuse/tests/test_crunchstat.py | 13 +
services/fuse/tests/test_mount.py | 17 +-
services/fuse/tests/test_unmount.py | 87 +++++++
.../arvnodeman/computenode/dispatch/__init__.py | 10 +-
.../arvnodeman/computenode/driver/__init__.py | 17 ++
.../arvnodeman/computenode/driver/gce.py | 12 +-
services/nodemanager/arvnodeman/daemon.py | 2 +-
.../tests/test_computenode_driver_gce.py | 13 +-
services/nodemanager/tests/test_failure.py | 2 +-
70 files changed, 1686 insertions(+), 668 deletions(-)
create mode 100644 sdk/cwl/tests/cat.cwl
create mode 100644 sdk/cwl/tests/dir-job2.yml
copy sdk/cwl/tests/{keep-dir-test-input.cwl => keep-dir-test-input2.cwl} (77%)
copy sdk/cwl/tests/{keep-dir-test-input.cwl => keep-dir-test-input3.cwl} (76%)
create mode 100644 sdk/cwl/tests/octo.yml
copy tools/crunchstat-summary/tests/__init__.py => sdk/cwl/tests/octothorpe/item #1.txt (100%)
create mode 100755 sdk/python/arvados/commands/get.py
create mode 100644 sdk/python/tests/test_arv_get.py
create mode 100644 services/api/db/migrate/20170328215436_add_portable_data_hash_index_to_collections.rb
create mode 100644 services/api/db/migrate/20170330012505_add_output_ttl_to_container_requests.rb
create mode 100644 services/fuse/arvados_fuse/unmount.py
create mode 100644 services/fuse/tests/test_crunchstat.py
create mode 100644 services/fuse/tests/test_unmount.py
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commit 0d5be4fa36006459e1579f087b695904e4f32ee3
Author: Tom Clegg <tom at curoverse.com>
Date: Mon Apr 10 13:07:07 2017 -0400
7709: Fix ActiveRecord::ImmutableRelation.
diff --git a/services/api/app/controllers/application_controller.rb b/services/api/app/controllers/application_controller.rb
index 6ba334f..831bcce 100644
--- a/services/api/app/controllers/application_controller.rb
+++ b/services/api/app/controllers/application_controller.rb
@@ -83,7 +83,9 @@ class ApplicationController < ActionController::Base
end
def index
- @objects.uniq!(&:id) if @select.nil? or @select.include? "id"
+ if @select.nil? || @select.include?("id")
+ @objects = @objects.uniq(&:id)
+ end
if params[:eager] and params[:eager] != '0' and params[:eager] != 0 and params[:eager] != ''
@objects.each(&:eager_load_associations)
end
commit 77d9c05d89dabc9e9e9a15f46cd12c8ad61ed64e
Merge: e1e0584 909313b
Author: Tom Clegg <tom at curoverse.com>
Date: Mon Apr 10 12:37:42 2017 -0400
7709: Merge branch 'master' into 7709-api-rails4
Conflicts:
services/api/app/controllers/arvados/v1/nodes_controller.rb
services/api/app/models/container_request.rb
services/api/db/structure.sql
diff --cc services/api/db/structure.sql
index 015db6f,e25a2a9..5c592a2
--- a/services/api/db/structure.sql
+++ b/services/api/db/structure.sql
@@@ -2744,5 -2754,6 +2752,8 @@@ INSERT INTO schema_migrations (version
INSERT INTO schema_migrations (version) VALUES ('20170301225558');
+INSERT INTO schema_migrations (version) VALUES ('20170319063406');
+
+ INSERT INTO schema_migrations (version) VALUES ('20170328215436');
+
-INSERT INTO schema_migrations (version) VALUES ('20170330012505');
++INSERT INTO schema_migrations (version) VALUES ('20170330012505');
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