[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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