[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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