[ARVADOS] updated: 660e8d8345bfe7f34dfc8db655eff6a0af8bd47f

git at public.curoverse.com git at public.curoverse.com
Fri Mar 28 11:49:15 EDT 2014


Summary of changes:
 apps/workbench/Gemfile                             |    9 +-
 apps/workbench/Gemfile.lock                        |   31 +
 apps/workbench/README.rdoc                         |  261 -------
 apps/workbench/README.textile                      |   19 +
 apps/workbench/app/assets/javascripts/editable.js  |    9 +
 .../api_client_authorizations_controller.rb        |    9 +-
 .../app/controllers/application_controller.rb      |   17 +-
 .../app/controllers/collections_controller.rb      |   14 +-
 .../controllers/pipeline_templates_controller.rb   |    5 +-
 apps/workbench/app/controllers/users_controller.rb |   73 ++-
 apps/workbench/app/helpers/application_helper.rb   |   14 +-
 apps/workbench/app/models/arvados_api_client.rb    |   26 +-
 apps/workbench/app/models/arvados_base.rb          |   31 +-
 apps/workbench/app/models/arvados_resource_list.rb |   26 +
 apps/workbench/app/models/user.rb                  |    7 +
 .../app/views/application/_paging.html.erb         |  126 ++++
 .../app/views/application/_show_recent.html.erb    |    4 +
 .../app/views/collections/_show_recent.html.erb    |    6 +-
 .../app/views/groups/_show_recent.html.erb         |    4 +
 .../app/views/layouts/application.html.erb         |    6 +-
 .../pipeline_instances/_show_components.html.erb   |   10 +
 .../views/pipeline_instances/_show_recent.html.erb |    4 +
 .../views/pipeline_templates/_show_recent.html.erb |    4 +
 .../app/views/users/_show_activity.html.erb        |    4 +
 .../workbench/app/views/users/_show_admin.html.erb |    6 +
 apps/workbench/app/views/users/_tables.html.erb    |   10 +-
 apps/workbench/app/views/users/activity.html.erb   |   72 ++
 apps/workbench/config/application.default.yml      |   12 +-
 .../config/environments/development.rb.example     |   20 -
 .../config/environments/production.rb.example      |   19 -
 apps/workbench/config/environments/test.rb.example |   19 -
 apps/workbench/config/routes.rb                    |    2 +
 apps/workbench/doc/README_FOR_APP                  |    2 -
 apps/workbench/lib/tasks/config_check.rake         |   13 +-
 apps/workbench/test/integration/logins_test.rb     |   14 +
 apps/workbench/test/integration/smoke_test.rb      |   39 +
 .../test/integration/virtual_machines_test.rb      |   17 +
 apps/workbench/test/integration_helper.rb          |   77 ++
 doc/README                                         |   28 -
 doc/README.textile                                 |   58 ++
 doc/_config.yml                                    |    7 +
 doc/_includes/_webring.liquid                      |    6 +-
 doc/api/schema/ApiClient.html.textile.liquid       |    4 +-
 .../ApiClientAuthorization.html.textile.liquid     |    2 +-
 doc/api/schema/AuthorizedKey.html.textile.liquid   |    5 +-
 doc/api/schema/Collection.html.textile.liquid      |    6 +-
 doc/api/schema/Commit.html.textile.liquid          |    4 +-
 doc/api/schema/CommitAncestor.html.textile.liquid  |    4 +-
 doc/api/schema/Group.html.textile.liquid           |    4 +-
 doc/api/schema/Human.html.textile.liquid           |    4 +-
 doc/api/schema/Job.html.textile.liquid             |    6 +-
 doc/api/schema/JobTask.html.textile.liquid         |    4 +-
 doc/api/schema/KeepDisk.html.textile.liquid        |    4 +-
 doc/api/schema/Link.html.textile.liquid            |    4 +-
 doc/api/schema/Log.html.textile.liquid             |    4 +-
 doc/api/schema/Node.html.textile.liquid            |    4 +-
 .../schema/PipelineInstance.html.textile.liquid    |    4 +-
 .../schema/PipelineTemplate.html.textile.liquid    |    4 +-
 doc/api/schema/Repository.html.textile.liquid      |    4 +-
 doc/api/schema/Specimen.html.textile.liquid        |    4 +-
 doc/api/schema/Trait.html.textile.liquid           |    4 +-
 doc/api/schema/User.html.textile.liquid            |    4 +-
 doc/api/schema/VirtualMachine.html.textile.liquid  |    4 +-
 doc/gen_api_schema_docs.py                         |    3 +-
 doc/images/dax-reading-book.png                    |  Bin 0 -> 211000 bytes
 doc/index.html.liquid                              |    4 +-
 .../install-workbench-app.html.textile.liquid      |    2 -
 doc/sdk/cli/index.html.textile.liquid              |   61 ++
 doc/sdk/index.html.textile.liquid                  |   10 +-
 doc/sdk/perl/index.html.textile.liquid             |   99 +++
 doc/sdk/ruby/index.html.textile.liquid             |  125 ++++
 doc/user/copying/agpl-3.0.html                     |    2 +-
 .../job-and-pipeline-reference.html.textile.liquid |  223 ++++++
 doc/user/topics/keep.html.textile.liquid           |    2 +-
 ...nning-pipeline-command-line.html.textile.liquid |    7 +-
 ...rial-gatk-variantfiltration.html.textile.liquid |    1 +
 doc/user/topics/tutorial-job1.html.textile.liquid  |   15 +-
 .../topics/tutorial-parallel.html.textile.liquid   |    3 +-
 .../running-external-program.html.textile.liquid   |    5 +-
 .../tutorial-firstscript.html.textile.liquid       |   10 +-
 .../tutorials/tutorial-keep.html.textile.liquid    |    2 +-
 .../tutorial-new-pipeline.html.textile.liquid      |    9 +-
 ...tutorial-pipeline-workbench.html.textile.liquid |    4 +-
 sdk/cli/bin/arv                                    |   21 +-
 sdk/cli/bin/arv-run-pipeline-instance              |  107 +---
 sdk/cli/bin/crunch-job                             |   67 ++-
 .../api/app/controllers/application_controller.rb  |   28 +-
 .../app/controllers/arvados/v1/jobs_controller.rb  |   76 ++-
 .../controllers/arvados/v1/schema_controller.rb    |   36 +-
 .../app/controllers/arvados/v1/users_controller.rb |   59 ++-
 services/api/app/models/commit.rb                  |  122 +++-
 services/api/app/models/job.rb                     |   16 +-
 services/api/app/models/user.rb                    |  194 +++++
 services/api/config/application.default.yml        |   12 +-
 services/api/config/application.yml.example        |    7 +-
 services/api/config/environment.rb                 |    6 +
 .../api/config/environments/development.rb.example |   39 -
 .../api/config/environments/production.rb.example  |   42 --
 services/api/config/environments/test.rb.example   |   40 -
 services/api/config/routes.rb                      |    5 +-
 ...317135600_add_nondeterministic_column_to_job.rb |    9 +
 ...0547_separate_repository_from_script_version.rb |   31 +
 .../20140321191343_add_repository_column_to_job.rb |    9 +
 services/api/db/schema.rb                          |   28 +-
 services/api/lib/tasks/config_check.rake           |   13 +-
 services/api/script/crunch-dispatch.rb             |   67 ++-
 services/api/script/rails                          |    8 +-
 services/api/script/setup-new-user.rb              |   66 ++
 services/api/test/fixtures/collections.yml         |    2 +-
 services/api/test/fixtures/jobs.yml                |   21 +
 services/api/test/fixtures/links.yml               |   23 +-
 services/api/test/fixtures/repositories.yml        |    4 +
 .../arvados/v1/collections_controller_test.rb      |   22 +
 .../arvados/v1/commits_controller_test.rb          |   86 +++
 .../api/test/functional/arvados/v1/git_setup.rb    |   27 +
 .../arvados/v1/job_reuse_controller_test.rb        |  167 +++++
 .../functional/arvados/v1/jobs_controller_test.rb  |    7 +
 .../arvados/v1/schema_controller_test.rb           |    2 +-
 .../functional/arvados/v1/users_controller_test.rb |  758 ++++++++++++++++++++
 .../api/test/integration/collections_api_test.rb   |   12 +
 services/api/test/integration/permissions_test.rb  |  244 +++++++
 services/api/test/test.git.tar                     |  Bin 0 -> 112640 bytes
 services/api/test/unit/user_test.rb                |  280 +++++++-
 services/keep/keep.go                              |  137 ++++
 services/keep/keep_test.go                         |  125 ++++
 125 files changed, 3979 insertions(+), 860 deletions(-)
 delete mode 100644 apps/workbench/README.rdoc
 create mode 100644 apps/workbench/README.textile
 create mode 100644 apps/workbench/app/views/application/_paging.html.erb
 create mode 100644 apps/workbench/app/views/users/_show_activity.html.erb
 create mode 100644 apps/workbench/app/views/users/activity.html.erb
 delete mode 100644 apps/workbench/doc/README_FOR_APP
 create mode 100644 apps/workbench/test/integration/logins_test.rb
 create mode 100644 apps/workbench/test/integration/smoke_test.rb
 create mode 100644 apps/workbench/test/integration/virtual_machines_test.rb
 create mode 100644 apps/workbench/test/integration_helper.rb
 delete mode 100644 doc/README
 create mode 100644 doc/README.textile
 create mode 100644 doc/images/dax-reading-book.png
 create mode 100644 doc/sdk/cli/index.html.textile.liquid
 create mode 100644 doc/sdk/perl/index.html.textile.liquid
 create mode 100644 doc/sdk/ruby/index.html.textile.liquid
 create mode 100644 doc/user/reference/job-and-pipeline-reference.html.textile.liquid
 create mode 100644 services/api/db/migrate/20140317135600_add_nondeterministic_column_to_job.rb
 create mode 100644 services/api/db/migrate/20140319160547_separate_repository_from_script_version.rb
 create mode 100644 services/api/db/migrate/20140321191343_add_repository_column_to_job.rb
 create mode 100755 services/api/script/setup-new-user.rb
 create mode 100644 services/api/test/fixtures/repositories.yml
 create mode 100644 services/api/test/functional/arvados/v1/commits_controller_test.rb
 create mode 100644 services/api/test/functional/arvados/v1/git_setup.rb
 create mode 100644 services/api/test/functional/arvados/v1/job_reuse_controller_test.rb
 create mode 100644 services/api/test/integration/permissions_test.rb
 create mode 100644 services/api/test/test.git.tar
 create mode 100644 services/keep/keep.go
 create mode 100644 services/keep/keep_test.go

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      from  ed65efe8ac537694369f46fb5130e4f3d47183d3 (commit)

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commit 660e8d8345bfe7f34dfc8db655eff6a0af8bd47f
Merge: ed65efe 736c7c6
Author: Tim Pierce <twp at curoverse.com>
Date:   Fri Mar 28 11:50:34 2014 -0400

    Merge branch 'master' into 2221-complete-docker
    
    Conflicts:
    	sdk/cli/bin/crunch-job

diff --cc sdk/cli/bin/crunch-job
index 2b31531,04f2b01..40b0033
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@@ -71,9 -77,10 +77,10 @@@ use POSIX ':sys_wait_h'
  use Fcntl qw(F_GETFL F_SETFL O_NONBLOCK);
  use Arvados;
  use Getopt::Long;
 -use Warehouse;
 -use Warehouse::Stream;
 -use IPC::System::Simple qw(capturex);
 +use IPC::Open2;
 +use IO::Select;
 +use File::Temp;
+ use Fcntl ':flock';
  
  $ENV{"TMPDIR"} ||= "/tmp";
  unless (defined $ENV{"CRUNCH_TMP"}) {

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