[ARVADOS] updated: bd86112ffba029e0f2c29c7d12ae6192e4097e18
git at public.curoverse.com
git at public.curoverse.com
Mon Sep 8 15:07:09 EDT 2014
Summary of changes:
apps/workbench/Gemfile | 2 +
apps/workbench/Gemfile.lock | 36 +++++
.../app/assets/javascripts/select_modal.js | 16 +-
apps/workbench/app/assets/javascripts/selection.js | 26 +--
.../app/controllers/actions_controller.rb | 38 +++--
.../app/controllers/application_controller.rb | 2 +
.../app/controllers/collections_controller.rb | 15 +-
.../app/controllers/projects_controller.rb | 29 +---
apps/workbench/app/helpers/application_helper.rb | 18 ++-
apps/workbench/app/helpers/collections_helper.rb | 22 ++-
apps/workbench/app/models/arvados_base.rb | 4 +-
apps/workbench/app/models/collection.rb | 32 ++--
.../app/views/application/_choose.html.erb | 24 +--
.../workbench/app/views/application/_choose.js.erb | 23 ++-
.../views/application/_report_issue_popup.html.erb | 2 +-
.../views/application/_selection_checkbox.html.erb | 2 +-
.../views/application/report_issue_popup.js.erb | 14 ++
.../app/views/collections/_show_files.html.erb | 2 +-
.../app/views/collections/show_file_links.html.erb | 7 +-
.../app/views/projects/_index_projects.html.erb | 2 +-
.../app/views/projects/_show_tab_contents.html.erb | 45 ++++--
apps/workbench/app/views/projects/show.html.erb | 2 +-
apps/workbench/config/routes.rb | 1 -
apps/workbench/test/integration/errors_test.rb | 6 +-
.../test/integration/pipeline_instances_test.rb | 45 +++++-
apps/workbench/test/integration/projects_test.rb | 177 ++++++++++++++++++++-
.../test/integration/report_issue_test.rb | 6 +-
apps/workbench/test/integration/search_box_test.rb | 6 +-
crunch_scripts/crunchutil/robust_put.py | 13 +-
crunch_scripts/crunchutil/subst.py | 39 +++--
crunch_scripts/run-command | 35 ++--
sdk/cli/Gemfile | 2 +-
sdk/cli/Gemfile.lock | 42 +++--
sdk/cli/bin/arv | 6 +-
sdk/cli/bin/arv-run-pipeline-instance | 36 +++--
sdk/cli/bin/crunch-job | 45 ++++--
sdk/python/arvados/commands/put.py | 8 +-
sdk/python/arvados/stream.py | 7 +-
sdk/python/tests/test_arv_put.py | 7 +-
sdk/python/tests/test_collections.py | 10 +-
sdk/ruby/arvados.gemspec | 2 +-
sdk/ruby/lib/arvados/keep.rb | 134 ++++++++++++++++
sdk/ruby/test/test_big_request.rb | 21 +--
sdk/ruby/test/test_keep_manifest.rb | 87 ++++++++++
services/api/.gitignore | 1 -
services/api/Gemfile | 3 +-
services/api/Gemfile.lock | 7 +-
.../api/app/assets/stylesheets/application.css | 2 +-
.../api/app/controllers/application_controller.rb | 42 ++++-
.../arvados/v1/collections_controller.rb | 14 +-
.../controllers/arvados/v1/schema_controller.rb | 28 ++--
services/api/app/models/collection.rb | 100 ++----------
services/api/app/models/locator.rb | 104 ------------
.../api/app/views/layouts/application.html.erb | 2 +-
services/api/app/views/static/intro.html.erb | 10 +-
.../api/app/views/static/login_failure.html.erb | 2 +-
services/api/db/structure.sql | 20 +--
services/api/test/fixtures/collections.yml | 12 ++
services/api/test/fixtures/pipeline_templates.yml | 21 +++
.../arvados/v1/collections_controller_test.rb | 70 +++-----
services/crunchstat/crunchstat.go | 11 +-
61 files changed, 1023 insertions(+), 524 deletions(-)
create mode 100644 sdk/ruby/lib/arvados/keep.rb
create mode 100644 sdk/ruby/test/test_keep_manifest.rb
delete mode 100644 services/api/app/models/locator.rb
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commit bd86112ffba029e0f2c29c7d12ae6192e4097e18
Merge: be4c2fe 90fc798
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Sep 8 15:07:05 2014 -0400
Merge branch 'master' into 3644-arv-mount-projects
diff --cc sdk/cli/bin/crunch-job
index 94865a1,0ba32b0..a2c5512
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@@ -656,8 -656,10 +656,10 @@@ for (my $todo_ptr = 0; $todo_ptr <= $#j
if ($build_script)
{
$build_script_to_send = $build_script;
+ $command .=
+ "&& perl -";
}
- $command .= "&& exec arv-mount --allow-other $ENV{TASK_KEEPMOUNT} --exec ";
+ $command .= "&& exec arv-mount --by-id --allow-other $ENV{TASK_KEEPMOUNT} --exec ";
if ($docker_hash)
{
$command .= "crunchstat -cgroup-root=/sys/fs/cgroup -cgroup-parent=docker -cgroup-cid=$ENV{TASK_WORK}/docker.cid -poll=10000 ";
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