[ARVADOS] updated: 12d990a6590e5f23a5998d29a2d8efdb0f733688

git at public.curoverse.com git at public.curoverse.com
Fri Sep 19 11:34:55 EDT 2014


Summary of changes:
 apps/workbench/Gemfile                             |   2 +-
 apps/workbench/Gemfile.lock                        |   4 +-
 .../javascripts/{selection.js => selection.js.erb} |  17 ++-
 apps/workbench/app/assets/javascripts/tab_panes.js |   8 ++
 .../app/controllers/actions_controller.rb          |   8 +-
 .../app/controllers/projects_controller.rb         |  75 ++++++++--
 .../app/controllers/user_agreements_controller.rb  |   2 +-
 apps/workbench/app/models/arvados_base.rb          |   6 +
 apps/workbench/app/models/collection.rb            |   4 +
 apps/workbench/app/models/group.rb                 |   4 +
 apps/workbench/app/models/job.rb                   |  10 +-
 apps/workbench/app/models/pipeline_instance.rb     |   6 +-
 apps/workbench/app/models/pipeline_template.rb     |   4 +
 .../views/application/_arvados_attr_value.html.erb |   2 +-
 .../app/views/application/_content.html.erb        |  58 ++++----
 .../application/_name_and_description.html.erb     |  12 ++
 .../workbench/app/views/application/destroy.js.erb |   1 +
 apps/workbench/app/views/application/show.html.erb |  42 ++++++
 .../app/views/collections/_show_files.html.erb     |  45 ++++--
 .../app/views/collections/_show_recent.html.erb    |  21 +++
 .../collections/_show_source_summary.html.erb      |   5 +-
 apps/workbench/app/views/collections/show.html.erb |  21 +--
 .../app/views/pipeline_instances/show.html.erb     |  22 +--
 .../views/pipeline_templates/_show_recent.html.erb |   3 +-
 .../app/views/pipeline_templates/show.html.erb     |   3 +-
 .../app/views/projects/_show_tab_contents.html.erb |  12 +-
 .../app/views/projects/remove_items.js.erb         |   7 +-
 apps/workbench/app/views/projects/show.html.erb    |  28 +---
 .../workbench/app/views/projects/tab_counts.js.erb |   3 +
 apps/workbench/config/application.default.yml      |  29 ++++
 apps/workbench/config/database.yml                 |   7 +
 apps/workbench/config/routes.rb                    |   2 +
 apps/workbench/test/diagnostics/pipeline_test.rb   |  93 ++++++++++++
 apps/workbench/test/diagnostics_test_helper.rb     |  29 ++++
 .../test/functional/actions_controller_test.rb     |  30 ++++
 .../workbench/test/integration/collections_test.rb |  89 +++++++++++-
 apps/workbench/test/integration/jobs_test.rb       |  29 ++++
 .../test/integration/pipeline_instances_test.rb    |  22 ++-
 .../test/integration/pipeline_templates_test.rb    |  31 ++++
 apps/workbench/test/integration/projects_test.rb   |  36 ++++-
 apps/workbench/test/integration_helper.rb          |   6 +-
 apps/workbench/test/test_helper.rb                 |   7 +-
 crunch_scripts/split-fastq.py                      |   7 +-
 doc/_includes/_example_sdk_go.liquid               | 109 ++++++++++++++
 doc/_includes/_example_sdk_go_imports.liquid       |   4 +
 doc/sdk/go/index.html.textile.liquid               |  52 +------
 ...nning-pipeline-command-line.html.textile.liquid |  12 +-
 docker/java-bwa-samtools/Dockerfile                |   5 +-
 sdk/cli/bin/arv-run-pipeline-instance              | 115 ++++++++++-----
 sdk/cli/bin/crunch-job                             |  41 ++++--
 sdk/python/arvados/collection.py                   | 154 ++++++++++++--------
 sdk/python/arvados/commands/_util.py               |  12 ++
 sdk/python/arvados/commands/keepdocker.py          |  55 ++++---
 sdk/python/arvados/commands/put.py                 |  45 +++---
 sdk/python/arvados/keep.py                         | 156 +++++++++++---------
 sdk/python/arvados/retry.py                        |  18 +++
 sdk/python/arvados/stream.py                       |  68 +++++----
 sdk/python/arvados/util.py                         |   4 +-
 sdk/python/bin/arv-get                             |  46 +++---
 sdk/python/bin/arv-ls                              |  21 +--
 sdk/python/setup.py                                |   2 +-
 sdk/python/tests/arvados_testutil.py               |  11 ++
 sdk/python/tests/test_arv_put.py                   |   8 +-
 sdk/python/tests/test_collections.py               | 143 +++++++++++++++++-
 sdk/python/tests/test_keep_client.py               |  69 ++++-----
 sdk/python/tests/test_retry.py                     |  27 ++++
 sdk/python/tests/test_stream.py                    | 117 +++++++++++++++
 services/api/Gemfile                               |   4 +-
 services/api/Gemfile.lock                          |   8 +-
 .../app/controllers/arvados/v1/jobs_controller.rb  |  10 +-
 .../controllers/arvados/v1/schema_controller.rb    |   1 +
 services/api/app/models/collection.rb              |   3 +
 services/api/app/models/job.rb                     |  12 ++
 services/api/app/models/job_task.rb                |   2 +
 services/api/app/models/node.rb                    |  11 +-
 services/api/app/models/pipeline_instance.rb       |   3 +
 services/api/config/application.default.yml        |   3 +
 services/api/config/routes.rb                      |   1 +
 ...add_start_finish_time_to_tasks_and_pipelines.rb |  15 ++
 ...d_description_to_pipeline_instances_and_jobs.rb |  11 ++
 ...140918141529_change_user_owner_uuid_not_null.rb |  12 ++
 .../20140918153541_add_properties_to_node.rb       |   9 ++
 services/api/db/structure.sql                      |  24 +++-
 services/api/lib/tasks/config_check.rake           |   4 +
 services/api/script/crunch-dispatch.rb             |  82 ++++++-----
 services/api/test/fixtures/collections.yml         |  26 ++++
 services/api/test/fixtures/users.yml               |   1 +
 .../arvados/v1/collections_controller_test.rb      |  57 ++++++++
 .../functional/arvados/v1/jobs_controller_test.rb  |  28 +++-
 .../functional/arvados/v1/nodes_controller_test.rb |   8 +-
 .../arvados/v1/schema_controller_test.rb           |   7 +
 services/api/test/unit/node_test.rb                |   8 +-
 services/fuse/arvados_fuse/__init__.py             | 122 ++++++++++------
 services/fuse/bin/arv-mount                        |  66 +++++----
 services/fuse/setup.py                             |   2 +-
 services/fuse/tests/test_mount.py                  |  13 +-
 services/keepstore/block_work_list.go              | 160 +++++++++++++++++++++
 services/keepstore/block_work_list_test.go         | 149 +++++++++++++++++++
 services/keepstore/handler_test.go                 |  13 +-
 services/keepstore/handlers.go                     |  24 +++-
 services/keepstore/keepstore.go                    |   3 +-
 services/keepstore/pull_list/pull_list.go          |  81 -----------
 102 files changed, 2376 insertions(+), 753 deletions(-)
 rename apps/workbench/app/assets/javascripts/{selection.js => selection.js.erb} (93%)
 create mode 100644 apps/workbench/app/views/application/_name_and_description.html.erb
 create mode 100644 apps/workbench/app/views/projects/tab_counts.js.erb
 create mode 100644 apps/workbench/test/diagnostics/pipeline_test.rb
 create mode 100644 apps/workbench/test/diagnostics_test_helper.rb
 create mode 100644 apps/workbench/test/integration/jobs_test.rb
 create mode 100644 doc/_includes/_example_sdk_go.liquid
 create mode 100644 doc/_includes/_example_sdk_go_imports.liquid
 create mode 100644 sdk/python/tests/test_stream.py
 create mode 100644 services/api/db/migrate/20140909183946_add_start_finish_time_to_tasks_and_pipelines.rb
 create mode 100644 services/api/db/migrate/20140911221252_add_description_to_pipeline_instances_and_jobs.rb
 create mode 100644 services/api/db/migrate/20140918141529_change_user_owner_uuid_not_null.rb
 create mode 100644 services/api/db/migrate/20140918153541_add_properties_to_node.rb
 create mode 100644 services/keepstore/block_work_list.go
 create mode 100644 services/keepstore/block_work_list_test.go
 delete mode 100644 services/keepstore/pull_list/pull_list.go

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       via  34081b99f265f9baaabcd791f7c520c3f5b37f19 (commit)
       via  a6a9e10686e3ffc8c56b0aad61633524be7e5cc4 (commit)
       via  9564076de96d8c0084cf00f47348c41d6abfe673 (commit)
       via  74ac5edcb6ecff4003ec70cf904c900392a31814 (commit)
       via  8c4233dae52c96ceb629d2be1be73b518118863a (commit)
       via  e322205a65bdc3a0565997eb68c86e74cd191762 (commit)
       via  fd910ade561ddec093ec29a79a216259e53bef90 (commit)
       via  c90d8145634022d2d0c66b36bfb99e4c21248fed (commit)
       via  498f3130928f58e830be3abe74b20d06904af3cd (commit)
       via  33710e325a775d8f52ce89ce365b4a5153a68b18 (commit)
       via  72af8e487f399fd726b8985a346a37f2e2160ca6 (commit)
       via  8a4691d711947a83e9155599e96c4173e655a8f3 (commit)
      from  ab7c97818a088e7205d4d01db1e8a0c0709b9aa0 (commit)

Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.


commit 12d990a6590e5f23a5998d29a2d8efdb0f733688
Merge: ab7c978 5bb258b
Author: Tim Pierce <twp at curoverse.com>
Date:   Fri Sep 19 11:34:46 2014 -0400

    Merge branch 'master' into 3699-arv-copy


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