[ARVADOS] updated: b7f67c80916c2efa0c234ab5f4e92c24d47223c5
git at public.curoverse.com
git at public.curoverse.com
Thu Oct 16 11:32:08 EDT 2014
Summary of changes:
apps/workbench/Gemfile | 2 +
apps/workbench/Gemfile.lock | 7 +
.../app/assets/javascripts/application.js | 22 +
.../workbench/app/assets/javascripts/log_viewer.js | 2 +-
.../app/assets/stylesheets/application.css.scss | 4 +-
.../app/controllers/actions_controller.rb | 23 +-
.../app/controllers/application_controller.rb | 7 +
.../app/controllers/collections_controller.rb | 35 +-
.../controllers/pipeline_instances_controller.rb | 7 +
.../app/helpers/pipeline_instances_helper.rb | 8 +-
apps/workbench/app/helpers/provenance_helper.rb | 13 +-
.../app/views/application/_content.html.erb | 50 +-
.../app/views/application/_content_layout.html.erb | 2 +
.../app/views/application/_job_progress.html.erb | 88 +--
.../views/application/_job_status_label.html.erb | 10 -
.../app/views/application/_loading_modal.html.erb | 12 +
.../application/_pipeline_status_label.html.erb | 2 +-
.../views/application/_title_and_buttons.html.erb | 25 +-
.../app/views/collections/_show_files.html.erb | 4 +-
apps/workbench/app/views/jobs/_show_log.html.erb | 48 +-
.../workbench/app/views/jobs/_show_recent.html.erb | 6 -
apps/workbench/app/views/jobs/show.html.erb | 10 +-
.../pipeline_instances/_running_component.html.erb | 162 ++---
.../_show_components_running.html.erb | 16 +-
.../views/pipeline_instances/_show_recent.html.erb | 2 +-
.../pipeline_instances/_show_tab_buttons.html.erb | 9 +-
.../app/views/pipeline_templates/show.html.erb | 4 +-
.../app/views/projects/_show_dashboard.html.erb | 44 +-
.../app/views/projects/_show_tab_contents.html.erb | 2 +-
apps/workbench/app/views/projects/show.html.erb | 6 +-
apps/workbench/app/views/users/_tables.html.erb | 4 -
apps/workbench/config/application.default.yml | 3 +
.../test/functional/collections_controller_test.rb | 62 +-
.../workbench/test/integration/collections_test.rb | 60 +-
apps/workbench/test/integration/jobs_test.rb | 47 ++
.../test/integration/pipeline_instances_test.rb | 183 +++---
apps/workbench/test/integration/projects_test.rb | 56 +-
apps/workbench/test/integration/users_test.rb | 7 +-
apps/workbench/test/test_helper.rb | 10 +-
crunch_scripts/crunchutil/subst.py | 17 +-
crunch_scripts/run-command | 169 ++++--
doc/_config.yml | 1 +
doc/_includes/_run_command_foreach_example.liquid | 40 ++
doc/_includes/_run_command_simple_example.liquid | 30 +
.../_includes/_tutorial_submit_job.liquid | 11 +-
doc/install/install-keep.html.textile.liquid | 10 +-
doc/user/topics/run-command.html.textile.liquid | 212 +++++++
.../running-external-program.html.textile.liquid | 10 +-
.../tutorial-new-pipeline.html.textile.liquid | 27 -
.../tutorial-submit-job.html.textile.liquid | 38 +-
sdk/cli/bin/arv | 245 ++++++--
sdk/cli/bin/arv-run-pipeline-instance | 10 +-
sdk/cli/bin/crunch-job | 654 +++++++++++++--------
sdk/python/arvados/commands/keepdocker.py | 3 +-
sdk/python/arvados/commands/put.py | 6 +-
services/api/Gemfile | 2 +-
services/api/Gemfile.lock | 8 +-
.../app/controllers/arvados/v1/jobs_controller.rb | 7 +-
services/api/app/models/arvados_model.rb | 7 +-
services/api/app/models/job.rb | 54 +-
services/api/app/models/log.rb | 5 +
services/api/app/models/user.rb | 24 +
services/api/config/application.default.yml | 26 +-
services/api/config/initializers/eventbus.rb | 3 +
services/api/config/routes.rb | 1 +
services/api/lib/eventbus.rb | 33 +-
services/api/script/crunch-dispatch.rb | 204 ++++---
.../test/fixtures/api_client_authorizations.yml | 6 +
services/api/test/fixtures/collections.yml | 22 +
services/api/test/fixtures/groups.yml | 9 +
services/api/test/fixtures/jobs.yml | 61 ++
services/api/test/fixtures/links.yml | 47 ++
services/api/test/fixtures/users.yml | 22 +
.../functional/arvados/v1/jobs_controller_test.rb | 50 +-
.../functional/arvados/v1/links_controller_test.rb | 18 +
services/api/test/integration/jobs_api_test.rb | 2 +-
services/api/test/integration/websocket_test.rb | 36 ++
services/api/test/test_helper.rb | 2 +-
services/api/test/unit/job_test.rb | 76 ++-
services/crunchstat/crunchstat.go | 160 ++---
services/fuse/tests/test_mount.py | 3 +-
services/keepproxy/keepproxy.go | 25 +-
services/keepproxy/keepproxy_test.go | 31 +-
services/keepstore/handler_test.go | 113 ++--
services/keepstore/handlers.go | 17 +-
services/nodemanager/.gitignore | 5 +
services/nodemanager/README.rst | 39 ++
services/nodemanager/arvnodeman/__init__.py | 9 +
services/nodemanager/arvnodeman/clientactor.py | 96 +++
.../nodemanager/arvnodeman/computenode/__init__.py | 383 ++++++++++++
.../nodemanager/arvnodeman/computenode/dummy.py | 52 ++
services/nodemanager/arvnodeman/computenode/ec2.py | 101 ++++
services/nodemanager/arvnodeman/config.py | 108 ++++
services/nodemanager/arvnodeman/daemon.py | 294 +++++++++
services/nodemanager/arvnodeman/jobqueue.py | 96 +++
services/nodemanager/arvnodeman/launcher.py | 130 ++++
services/nodemanager/arvnodeman/nodelist.py | 39 ++
services/nodemanager/arvnodeman/timedcallback.py | 41 ++
services/nodemanager/bin/arvados-node-manager | 6 +
services/nodemanager/doc/ec2.example.cfg | 121 ++++
services/nodemanager/doc/local.example.cfg | 41 ++
services/{fuse => nodemanager}/setup.py | 27 +-
services/nodemanager/tests/__init__.py | 15 +
services/nodemanager/tests/test_clientactor.py | 124 ++++
services/nodemanager/tests/test_computenode.py | 280 +++++++++
services/nodemanager/tests/test_computenode_ec2.py | 89 +++
services/nodemanager/tests/test_config.py | 65 ++
services/nodemanager/tests/test_daemon.py | 161 +++++
services/nodemanager/tests/test_jobqueue.py | 74 +++
services/nodemanager/tests/test_nodelist.py | 57 ++
services/nodemanager/tests/test_timedcallback.py | 61 ++
services/nodemanager/tests/testutil.py | 91 +++
112 files changed, 5100 insertions(+), 1126 deletions(-)
delete mode 100644 apps/workbench/app/views/application/_job_status_label.html.erb
create mode 100644 apps/workbench/app/views/application/_loading_modal.html.erb
create mode 100644 doc/_includes/_run_command_foreach_example.liquid
create mode 100644 doc/_includes/_run_command_simple_example.liquid
copy sdk/java/src/test/resources/first_pipeline.json => doc/_includes/_tutorial_submit_job.liquid (61%)
create mode 100644 doc/user/topics/run-command.html.textile.liquid
delete mode 100644 doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
create mode 100644 services/nodemanager/.gitignore
create mode 100644 services/nodemanager/README.rst
create mode 100644 services/nodemanager/arvnodeman/__init__.py
create mode 100644 services/nodemanager/arvnodeman/clientactor.py
create mode 100644 services/nodemanager/arvnodeman/computenode/__init__.py
create mode 100644 services/nodemanager/arvnodeman/computenode/dummy.py
create mode 100644 services/nodemanager/arvnodeman/computenode/ec2.py
create mode 100644 services/nodemanager/arvnodeman/config.py
create mode 100644 services/nodemanager/arvnodeman/daemon.py
create mode 100644 services/nodemanager/arvnodeman/jobqueue.py
create mode 100644 services/nodemanager/arvnodeman/launcher.py
create mode 100644 services/nodemanager/arvnodeman/nodelist.py
create mode 100644 services/nodemanager/arvnodeman/timedcallback.py
create mode 100644 services/nodemanager/bin/arvados-node-manager
create mode 100644 services/nodemanager/doc/ec2.example.cfg
create mode 100644 services/nodemanager/doc/local.example.cfg
copy services/{fuse => nodemanager}/setup.py (63%)
create mode 100644 services/nodemanager/tests/__init__.py
create mode 100644 services/nodemanager/tests/test_clientactor.py
create mode 100644 services/nodemanager/tests/test_computenode.py
create mode 100644 services/nodemanager/tests/test_computenode_ec2.py
create mode 100644 services/nodemanager/tests/test_config.py
create mode 100644 services/nodemanager/tests/test_daemon.py
create mode 100644 services/nodemanager/tests/test_jobqueue.py
create mode 100644 services/nodemanager/tests/test_nodelist.py
create mode 100644 services/nodemanager/tests/test_timedcallback.py
create mode 100644 services/nodemanager/tests/testutil.py
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commit b7f67c80916c2efa0c234ab5f4e92c24d47223c5
Merge: d0b0a2b 69441aa
Author: Tim Pierce <twp at curoverse.com>
Date: Thu Oct 16 11:31:59 2014 -0400
Merge branch 'master' into 3699-arv-copy
diff --cc sdk/cli/bin/arv
index ec3d806,481cd9e..3489f8e
--- a/sdk/cli/bin/arv
+++ b/sdk/cli/bin/arv
@@@ -116,9 -117,13 +117,13 @@@ subcommands = %w(create edit keep pipel
def check_subcommands client, arvados, subcommand, global_opts, remaining_opts
case subcommand
+ when 'create'
+ arv_create client, arvados, global_opts, remaining_opts
+ when 'edit'
+ arv_edit client, arvados, global_opts, remaining_opts
when 'keep'
@sub = remaining_opts.shift
- if ['get', 'put', 'ls', 'normalize'].index @sub then
+ if ['get', 'put', 'ls', 'normalize', 'copy'].index @sub then
# Native Arvados
exec `which arv-#{@sub}`.strip, *remaining_opts
elsif ['less', 'check'].index @sub then
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