[ARVADOS] updated: 7a537556b3503bf957ad3da2bf27885518a33230

[git at public.curoverse.com]

Summary of changes:
 .../pipeline_instances/_show_components.html.erb   |   10 +
 apps/workbench/app/views/users/_tables.html.erb    |   10 +-
 apps/workbench/doc/README_FOR_APP                  |    2 -
 apps/workbench/test/integration/logins_test.rb     |    2 +-
 doc/_config.yml                                    |    1 +
 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/index.html.liquid                              |    2 +-
 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 +-
 .../tutorial-new-pipeline.html.textile.liquid      |    9 +-
 ...tutorial-pipeline-workbench.html.textile.liquid |    4 +-
 sdk/cli/bin/arv-run-pipeline-instance              |  102 ++-------
 .../app/controllers/arvados/v1/jobs_controller.rb  |   74 ++++---
 .../controllers/arvados/v1/schema_controller.rb    |    2 +-
 services/api/app/models/commit.rb                  |  121 +++++++++---
 services/api/app/models/job.rb                     |    8 +-
 services/api/config/environment.rb                 |    1 +
 ...317135600_add_nondeterministic_column_to_job.rb |    9 +
 ...0547_separate_repository_from_script_version.rb |   31 +++
 services/api/db/schema.rb                          |   27 ++--
 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/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 +
 services/api/test/test.git.tar                     |  Bin 0 -> 112640 bytes
 58 files changed, 877 insertions(+), 239 deletions(-)
 delete mode 100644 apps/workbench/doc/README_FOR_APP
 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/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/test.git.tar

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commit 7a537556b3503bf957ad3da2bf27885518a33230
Merge: 1013c7c c54e3ca
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Mar 27 08:37:33 2014 -0400

    Merge branch '2051-nondeterministic-jobs'


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