[ARVADOS] updated: a86762d9a654aa820b534207dc0b126e1b055340

git at public.curoverse.com git at public.curoverse.com
Mon Jan 26 13:35:32 EST 2015


Summary of changes:
 apps/workbench/Gemfile                             |  31 +-
 apps/workbench/Gemfile.lock                        | 126 ++++----
 .../app/assets/javascripts/angular_shim.js         |  13 +-
 .../workbench/app/assets/javascripts/filterable.js |  14 +-
 .../app/assets/javascripts/infinite_scroll.js      |   8 +-
 .../app/assets/javascripts/select_modal.js         |  11 +-
 .../app/assets/javascripts/selection.js.erb        |  50 ++--
 .../app/controllers/application_controller.rb      |  79 +++--
 .../controllers/pipeline_instances_controller.rb   |  20 +-
 .../app/controllers/projects_controller.rb         |  46 ---
 .../app/controllers/repositories_controller.rb     |  12 +
 apps/workbench/app/controllers/users_controller.rb |   1 -
 .../app/controllers/virtual_machines_controller.rb |   3 -
 .../helpers/api_client_authorizations_helper.rb    |   2 -
 apps/workbench/app/helpers/application_helper.rb   |   6 +-
 .../app/helpers/authorized_keys_helper.rb          |   2 -
 apps/workbench/app/helpers/groups_helper.rb        |   2 -
 apps/workbench/app/helpers/humans_helper.rb        |   2 -
 apps/workbench/app/helpers/job_tasks_helper.rb     |   2 -
 apps/workbench/app/helpers/keep_disks_helper.rb    |   2 -
 apps/workbench/app/helpers/links_helper.rb         |   2 -
 apps/workbench/app/helpers/logs_helper.rb          |   2 -
 apps/workbench/app/helpers/nodes_helper.rb         |   2 -
 .../app/helpers/pipeline_instances_helper.rb       |   2 +-
 apps/workbench/app/helpers/projects_helper.rb      |   2 -
 apps/workbench/app/helpers/repositories_helper.rb  |   2 -
 apps/workbench/app/helpers/sessions_helper.rb      |   2 -
 apps/workbench/app/helpers/specimens_helper.rb     |   2 -
 apps/workbench/app/helpers/traits_helper.rb        |   2 -
 .../app/helpers/user_agreements_helper.rb          |   2 -
 apps/workbench/app/helpers/users_helper.rb         |   2 -
 apps/workbench/app/helpers/vcf_pipeline_helper.rb  | 234 ---------------
 .../app/helpers/virtual_machines_helper.rb         |   2 -
 apps/workbench/app/models/arvados_api_client.rb    |   1 +
 .../app/views/application/_show_recent.html.erb    |   4 +-
 .../_show_sharing.html.erb                         |  12 +-
 .../app/views/authorized_keys/_show_help.html.erb  |  10 -
 apps/workbench/app/views/layouts/body.html.erb     |  11 +-
 .../views/projects/_show_contents_rows.html.erb    |   2 +-
 .../app/views/projects/_show_tab_contents.html.erb |  11 +-
 apps/workbench/app/views/users/profile.html.erb    |   6 +-
 apps/workbench/app/views/users/welcome.html.erb    |  27 +-
 .../config/initializers/rack_mini_profile.rb       |   5 +
 apps/workbench/config/routes.rb                    |   4 +-
 .../test/controllers/projects_controller_test.rb   |  27 +-
 .../controllers/repositories_controller_test.rb    |  44 +++
 apps/workbench/test/diagnostics/pipeline_test.rb   |  17 +-
 apps/workbench/test/diagnostics_test_helper.rb     |   7 +-
 apps/workbench/test/helpers/share_object_helper.rb |  78 +++++
 .../test/integration/application_layout_test.rb    |   6 +-
 .../test/integration/collection_upload_test.rb     |  14 +-
 .../workbench/test/integration/collections_test.rb |  34 +--
 apps/workbench/test/integration/errors_test.rb     |   6 +-
 .../integration/filterable_infinite_scroll_test.rb |   4 +-
 apps/workbench/test/integration/jobs_test.rb       |   6 +-
 apps/workbench/test/integration/logins_test.rb     |   2 +-
 .../test/integration/pipeline_instances_test.rb    |  63 ++--
 .../test/integration/pipeline_templates_test.rb    |   4 +-
 apps/workbench/test/integration/projects_test.rb   |  98 ++-----
 .../test/integration/report_issue_test.rb          |  21 +-
 .../test/integration/repositories_test.rb          |  43 +++
 apps/workbench/test/integration/search_box_test.rb |   6 +-
 apps/workbench/test/integration/smoke_test.rb      |   2 +-
 .../test/integration/user_agreements_test.rb       |   4 +-
 .../test/integration/user_manage_account_test.rb   |   6 +-
 .../test/integration/user_profile_test.rb          |  17 +-
 apps/workbench/test/integration/users_test.rb      |  73 +++--
 .../test/integration/virtual_machines_test.rb      |   2 +-
 apps/workbench/test/integration/websockets_test.rb |   7 +-
 apps/workbench/test/integration_helper.rb          |  72 ++++-
 apps/workbench/test/performance/browsing_test.rb   |  20 +-
 apps/workbench/test/performance_test_helper.rb     |  16 +-
 apps/workbench/test/test_helper.rb                 |  13 +-
 .../test/unit/api_client_authorization_test.rb     |   7 -
 apps/workbench/test/unit/authorized_key_test.rb    |   7 -
 apps/workbench/test/unit/human_test.rb             |   7 -
 apps/workbench/test/unit/job_task_test.rb          |   7 -
 apps/workbench/test/unit/keep_disk_test.rb         |   4 -
 apps/workbench/test/unit/log_test.rb               |   7 -
 apps/workbench/test/unit/node_test.rb              |   7 -
 apps/workbench/test/unit/pipeline_template_test.rb |   7 -
 apps/workbench/test/unit/repository_test.rb        |   7 -
 apps/workbench/test/unit/specimen_test.rb          |   7 -
 apps/workbench/test/unit/trait_test.rb             |   7 -
 apps/workbench/test/unit/user_agreement_test.rb    |   7 -
 apps/workbench/test/unit/virtual_machine_test.rb   |   7 -
 doc/_config.yml                                    |   8 +
 doc/_includes/_navbar_top.liquid                   |   1 +
 doc/_layouts/default.html.liquid                   |   1 +
 doc/css/carousel-override.css                      |  25 ++
 doc/images/download-shared-collection.png          | Bin 0 -> 39610 bytes
 doc/images/files-uploaded.png                      | Bin 0 -> 53926 bytes
 doc/images/keyfeatures/chooseinputs.png            | Bin 0 -> 76641 bytes
 doc/images/keyfeatures/collectionpage.png          | Bin 0 -> 84533 bytes
 doc/images/keyfeatures/dashboard2.png              | Bin 0 -> 44396 bytes
 doc/images/keyfeatures/graph.png                   | Bin 0 -> 49127 bytes
 doc/images/keyfeatures/log.png                     | Bin 0 -> 135214 bytes
 doc/images/keyfeatures/provenance.png              | Bin 0 -> 67060 bytes
 doc/images/keyfeatures/rerun.png                   | Bin 0 -> 73314 bytes
 doc/images/keyfeatures/running2.png                | Bin 0 -> 56959 bytes
 doc/images/keyfeatures/shared.png                  | Bin 0 -> 62395 bytes
 doc/images/keyfeatures/webupload.png               | Bin 0 -> 88061 bytes
 doc/images/quickstart/1.png                        | Bin 0 -> 47239 bytes
 doc/images/quickstart/2.png                        | Bin 0 -> 74431 bytes
 doc/images/quickstart/3.png                        | Bin 0 -> 80668 bytes
 doc/images/quickstart/4.png                        | Bin 0 -> 66686 bytes
 doc/images/quickstart/5.png                        | Bin 0 -> 83038 bytes
 doc/images/quickstart/6.png                        | Bin 0 -> 98604 bytes
 doc/images/quickstart/7.png                        | Bin 0 -> 77820 bytes
 doc/images/shared-collection.png                   | Bin 0 -> 31833 bytes
 doc/images/upload-tab-in-new-collection.png        | Bin 0 -> 77537 bytes
 doc/images/upload-using-workbench.png              | Bin 0 -> 49690 bytes
 doc/images/uses/choosefiles.png                    | Bin 0 -> 75434 bytes
 doc/images/uses/gotohome.png                       | Bin 0 -> 76218 bytes
 doc/images/uses/rename.png                         | Bin 0 -> 77738 bytes
 doc/images/uses/share.png                          | Bin 0 -> 85695 bytes
 doc/images/uses/shared.png                         | Bin 0 -> 57235 bytes
 doc/images/uses/sharedsubdirs.png                  | Bin 0 -> 67642 bytes
 doc/images/uses/uploaddata.png                     | Bin 0 -> 85535 bytes
 doc/images/uses/uploading.png                      | Bin 0 -> 74365 bytes
 doc/index.html.liquid                              |  12 +-
 doc/install/install-api-server.html.textile.liquid |  24 +-
 doc/install/install-sso.html.textile.liquid        |  58 +++-
 .../firstpipeline.html.textile.liquid              |  89 ++++++
 .../getting_started/sharedata.html.textile.liquid  |  97 +++++++
 doc/start/index.html.textile.liquid                | 128 +++++++++
 doc/start/index.html.textile.liquid.bkup           |  50 ++++
 ...rial-gatk-variantfiltration.html.textile.liquid |   7 +-
 doc/user/topics/tutorial-job1.html.textile.liquid  |  10 +-
 .../tutorial-keep-get.html.textile.liquid          |  36 ++-
 .../tutorials/tutorial-keep.html.textile.liquid    |  33 ++-
 docker/base/Dockerfile                             |   2 +-
 sdk/cli/bin/arv                                    | 318 ++++++++++-----------
 sdk/cli/bin/crunch-job                             |  22 +-
 sdk/cli/test/test_arv-get.rb                       |   2 +
 sdk/go/arvadosclient/arvadosclient.go              |  53 ++--
 sdk/go/arvadosclient/arvadosclient_test.go         |  28 ++
 sdk/go/keepclient/keepclient.go                    |  22 +-
 sdk/go/keepclient/keepclient_test.go               |  91 +++---
 sdk/go/keepclient/support.go                       | 119 ++++++--
 sdk/python/arvados/errors.py                       |  47 ++-
 sdk/python/arvados/events.py                       |   4 +-
 sdk/python/arvados/keep.py                         |  40 ++-
 sdk/python/bin/arv-get                             |   2 +-
 sdk/python/setup.py                                |   2 +-
 sdk/python/tests/test_errors.py                    |  68 +++++
 sdk/python/tests/test_keep_client.py               |  65 +++++
 sdk/ruby/lib/arvados/keep.rb                       |  73 +++--
 services/api/Gemfile                               |   3 +-
 services/api/Gemfile.lock                          |   6 +-
 .../api/app/controllers/application_controller.rb  |  15 +-
 .../arvados/v1/collections_controller.rb           |   6 +-
 .../controllers/arvados/v1/groups_controller.rb    |   2 +-
 .../arvados/v1/keep_disks_controller.rb            |   2 +-
 .../app/controllers/arvados/v1/nodes_controller.rb |   2 +-
 .../arvados/v1/repositories_controller.rb          |   8 +-
 .../controllers/arvados/v1/schema_controller.rb    |   2 +-
 .../app/controllers/arvados/v1/users_controller.rb |   2 +-
 .../arvados/v1/virtual_machines_controller.rb      |   2 +-
 .../api/app/controllers/database_controller.rb     |   2 +-
 .../app/controllers/user_sessions_controller.rb    |   6 +-
 services/api/app/models/arvados_model.rb           |  10 +-
 services/api/app/models/collection.rb              |  31 ++
 services/api/app/models/job.rb                     |   1 -
 services/api/app/models/node.rb                    |  18 +-
 services/api/app/models/pipeline_instance.rb       |   6 -
 services/api/config/application.default.yml        |   7 +-
 .../20140422011506_pipeline_instance_state.rb      |   9 +-
 .../db/migrate/20141208164553_owner_uuid_index.rb  |  26 ++
 .../20141208174553_descriptions_are_strings.rb     |  21 ++
 .../20141208174653_collection_file_names.rb        |  20 ++
 .../api/db/migrate/20141208185217_search_index.rb  |  32 +++
 services/api/db/structure.sql                      | 298 ++++++++++++++++++-
 services/api/lib/josh_id.rb                        |  14 +-
 services/api/lib/kind_and_etag.rb                  |   4 +-
 services/api/script/crunch_failure_report.py       | 219 ++++++++++++++
 .../arvados/v1/collections_controller_test.rb      |  34 +++
 .../api/test/integration/collections_api_test.rb   |  70 +++++
 services/api/test/performance/browsing_test.rb     |  12 -
 services/api/test/performance/links_index_test.rb  |  14 +
 services/api/test/test_helper.rb                   |   2 +-
 services/api/test/unit/arvados_model_test.rb       |  59 ++++
 services/api/test/unit/collection_test.rb          |  43 +++
 services/api/test/unit/log_test.rb                 |  14 +
 services/crunchstat/crunchstat.go                  |  13 +-
 services/crunchstat/crunchstat_test.go             |  29 ++
 services/fuse/arvados_fuse/__init__.py             |   4 +
 services/fuse/bin/arv-mount                        |   2 +
 services/fuse/setup.py                             |   4 +-
 services/keepproxy/keepproxy.go                    |  42 ++-
 services/keepproxy/keepproxy_test.go               |  29 +-
 services/keepstore/handler_test.go                 |  18 +-
 services/keepstore/handlers.go                     |   2 +-
 services/keepstore/logging_router.go               |  14 +-
 services/nodemanager/arvnodeman/daemon.py          |  11 +-
 services/nodemanager/arvnodeman/jobqueue.py        |  13 +-
 services/nodemanager/arvnodeman/launcher.py        |  21 +-
 services/nodemanager/setup.py                      |   4 +-
 services/nodemanager/tests/test_daemon.py          |  55 ++--
 services/nodemanager/tests/test_jobqueue.py        |  22 +-
 200 files changed, 3015 insertions(+), 1410 deletions(-)
 delete mode 100644 apps/workbench/app/helpers/api_client_authorizations_helper.rb
 delete mode 100644 apps/workbench/app/helpers/authorized_keys_helper.rb
 delete mode 100644 apps/workbench/app/helpers/groups_helper.rb
 delete mode 100644 apps/workbench/app/helpers/humans_helper.rb
 delete mode 100644 apps/workbench/app/helpers/job_tasks_helper.rb
 delete mode 100644 apps/workbench/app/helpers/keep_disks_helper.rb
 delete mode 100644 apps/workbench/app/helpers/links_helper.rb
 delete mode 100644 apps/workbench/app/helpers/logs_helper.rb
 delete mode 100644 apps/workbench/app/helpers/nodes_helper.rb
 delete mode 100644 apps/workbench/app/helpers/projects_helper.rb
 delete mode 100644 apps/workbench/app/helpers/repositories_helper.rb
 delete mode 100644 apps/workbench/app/helpers/sessions_helper.rb
 delete mode 100644 apps/workbench/app/helpers/specimens_helper.rb
 delete mode 100644 apps/workbench/app/helpers/traits_helper.rb
 delete mode 100644 apps/workbench/app/helpers/user_agreements_helper.rb
 delete mode 100644 apps/workbench/app/helpers/users_helper.rb
 delete mode 100644 apps/workbench/app/helpers/vcf_pipeline_helper.rb
 delete mode 100644 apps/workbench/app/helpers/virtual_machines_helper.rb
 rename apps/workbench/app/views/{projects => application}/_show_sharing.html.erb (88%)
 delete mode 100644 apps/workbench/app/views/authorized_keys/_show_help.html.erb
 create mode 100644 apps/workbench/config/initializers/rack_mini_profile.rb
 create mode 100644 apps/workbench/test/helpers/share_object_helper.rb
 create mode 100644 apps/workbench/test/integration/repositories_test.rb
 delete mode 100644 apps/workbench/test/unit/api_client_authorization_test.rb
 delete mode 100644 apps/workbench/test/unit/authorized_key_test.rb
 delete mode 100644 apps/workbench/test/unit/human_test.rb
 delete mode 100644 apps/workbench/test/unit/job_task_test.rb
 delete mode 100644 apps/workbench/test/unit/keep_disk_test.rb
 delete mode 100644 apps/workbench/test/unit/log_test.rb
 delete mode 100644 apps/workbench/test/unit/node_test.rb
 delete mode 100644 apps/workbench/test/unit/pipeline_template_test.rb
 delete mode 100644 apps/workbench/test/unit/repository_test.rb
 delete mode 100644 apps/workbench/test/unit/specimen_test.rb
 delete mode 100644 apps/workbench/test/unit/trait_test.rb
 delete mode 100644 apps/workbench/test/unit/user_agreement_test.rb
 delete mode 100644 apps/workbench/test/unit/virtual_machine_test.rb
 create mode 100644 doc/css/carousel-override.css
 create mode 100644 doc/images/download-shared-collection.png
 create mode 100644 doc/images/files-uploaded.png
 create mode 100644 doc/images/keyfeatures/chooseinputs.png
 create mode 100644 doc/images/keyfeatures/collectionpage.png
 create mode 100644 doc/images/keyfeatures/dashboard2.png
 create mode 100644 doc/images/keyfeatures/graph.png
 create mode 100644 doc/images/keyfeatures/log.png
 create mode 100644 doc/images/keyfeatures/provenance.png
 create mode 100644 doc/images/keyfeatures/rerun.png
 create mode 100644 doc/images/keyfeatures/running2.png
 create mode 100644 doc/images/keyfeatures/shared.png
 create mode 100644 doc/images/keyfeatures/webupload.png
 create mode 100644 doc/images/quickstart/1.png
 create mode 100644 doc/images/quickstart/2.png
 create mode 100644 doc/images/quickstart/3.png
 create mode 100644 doc/images/quickstart/4.png
 create mode 100644 doc/images/quickstart/5.png
 create mode 100644 doc/images/quickstart/6.png
 create mode 100644 doc/images/quickstart/7.png
 create mode 100644 doc/images/shared-collection.png
 create mode 100644 doc/images/upload-tab-in-new-collection.png
 create mode 100644 doc/images/upload-using-workbench.png
 create mode 100644 doc/images/uses/choosefiles.png
 create mode 100644 doc/images/uses/gotohome.png
 create mode 100644 doc/images/uses/rename.png
 create mode 100644 doc/images/uses/share.png
 create mode 100644 doc/images/uses/shared.png
 create mode 100644 doc/images/uses/sharedsubdirs.png
 create mode 100644 doc/images/uses/uploaddata.png
 create mode 100644 doc/images/uses/uploading.png
 create mode 100644 doc/start/getting_started/firstpipeline.html.textile.liquid
 create mode 100644 doc/start/getting_started/sharedata.html.textile.liquid
 create mode 100644 doc/start/index.html.textile.liquid
 create mode 100644 doc/start/index.html.textile.liquid.bkup
 create mode 100644 sdk/python/tests/test_errors.py
 create mode 100644 services/api/db/migrate/20141208164553_owner_uuid_index.rb
 create mode 100644 services/api/db/migrate/20141208174553_descriptions_are_strings.rb
 create mode 100644 services/api/db/migrate/20141208174653_collection_file_names.rb
 create mode 100644 services/api/db/migrate/20141208185217_search_index.rb
 create mode 100755 services/api/script/crunch_failure_report.py
 delete mode 100644 services/api/test/performance/browsing_test.rb
 create mode 100644 services/api/test/performance/links_index_test.rb

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commit a86762d9a654aa820b534207dc0b126e1b055340
Author: Phil Hodgson <bitbucket at philhodgson.net>
Date:   Mon Jan 26 17:47:08 2015 +0100

    4232: remove "dependencies" entries from examples in the tutorials if the API is no longer going to be returning them

commit 9ac2a7d67db543a0356bdcc7c3ca37920086eae1
Author: Phil Hodgson <bitbucket at philhodgson.net>
Date:   Mon Jan 26 17:03:50 2015 +0100

    4232: remove uselessness (commented out code and other wastes of spacetime)

commit f8af0c6c331d5b52deab50abf7afa8c7881cddfb
Merge: 2fc8f46 0dfab8a
Author: Phil Hodgson <bitbucket at philhodgson.net>
Date:   Mon Jan 26 16:08:47 2015 +0100

    Merge branch 'master' into 4232-slow-pipes-n-jobs

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