[ARVADOS] updated: 49a6ced3c7a540a7da7155ab1c3120a5227c620c
git at public.curoverse.com
git at public.curoverse.com
Thu May 22 13:04:51 EDT 2014
Summary of changes:
apps/workbench/.gitignore | 4 +
apps/workbench/Gemfile | 18 +-
apps/workbench/Gemfile.lock | 147 ++--
.../api_client_authorizations.js.coffee | 3 -
.../assets/javascripts/authorized_keys.js.coffee | 3 -
.../app/assets/javascripts/collections.js | 1 -
.../app/assets/javascripts/folders.js.coffee | 3 -
.../app/assets/javascripts/groups.js.coffee | 3 -
.../app/assets/javascripts/humans.js.coffee | 3 -
.../app/assets/javascripts/job_tasks.js.coffee | 3 -
.../app/assets/javascripts/jobs.js.coffee | 3 -
.../app/assets/javascripts/keep_disks.js.coffee | 4 -
.../app/assets/javascripts/links.js.coffee | 3 -
.../app/assets/javascripts/logs.js.coffee | 3 -
.../app/assets/javascripts/nodes.js.coffee | 3 -
.../app/assets/javascripts/pipeline_instances.js | 1 -
.../javascripts/pipeline_templates.js.coffee | 3 -
.../app/assets/javascripts/repositories.js.coffee | 3 -
.../app/assets/javascripts/sessions.js.coffee | 3 -
.../app/assets/javascripts/specimens.js.coffee | 3 -
.../app/assets/javascripts/traits.js.coffee | 3 -
.../assets/javascripts/user_agreements.js.coffee | 3 -
.../app/assets/javascripts/users.js.coffee | 3 -
.../assets/javascripts/virtual_machines.js.coffee | 3 -
.../app/assets/stylesheets/collections.css.scss | 46 ++
.../app/assets/stylesheets/keep_disks.css.scss | 2 +-
.../app/controllers/actions_controller.rb | 2 +-
.../api_client_authorizations_controller.rb | 13 -
.../app/controllers/application_controller.rb | 42 +-
.../app/controllers/collections_controller.rb | 143 ++--
apps/workbench/app/controllers/jobs_controller.rb | 7 +-
.../app/controllers/keep_services_controller.rb | 2 +
.../controllers/pipeline_instances_controller.rb | 2 +-
.../app/controllers/sessions_controller.rb | 2 +-
apps/workbench/app/controllers/users_controller.rb | 10 +-
apps/workbench/app/helpers/application_helper.rb | 13 +
.../app/helpers/arvados_api_client_helper.rb | 13 +
apps/workbench/app/models/arvados_api_client.rb | 43 +-
apps/workbench/app/models/arvados_base.rb | 60 +-
apps/workbench/app/models/arvados_resource_list.rb | 7 +-
apps/workbench/app/models/collection.rb | 25 +-
apps/workbench/app/models/group.rb | 4 +-
apps/workbench/app/models/job.rb | 4 +
.../app/models/{keep_disk.rb => keep_service.rb} | 2 +-
apps/workbench/app/models/pipeline_instance.rb | 3 +-
apps/workbench/app/models/user.rb | 26 +-
apps/workbench/app/models/user_agreement.rb | 8 +-
.../application/_pipeline_status_label.html.erb | 6 +-
.../app/views/collections/_show_files.html.erb | 111 ++-
.../app/views/collections/_show_jobs.html.erb | 64 --
.../views/collections/_show_provenance.html.erb | 84 --
.../views/collections/_show_source_data.html.erb | 44 -
apps/workbench/app/views/collections/show.html.erb | 105 +++
.../app/views/collections/show_file_links.html.erb | 82 ++
apps/workbench/app/views/folders/show.html.erb | 60 +-
.../workbench/app/views/jobs/_show_recent.html.erb | 6 +-
.../app/views/layouts/application.html.erb | 13 +-
apps/workbench/app/views/links/_recent.html.erb | 2 +-
.../pipeline_instances/_show_components.html.erb | 25 +-
.../views/pipeline_instances/_show_recent.html.erb | 8 +-
.../app/views/pipeline_instances/show.js.erb | 6 +-
.../workbench/app/views/users/_show_admin.html.erb | 2 +-
apps/workbench/app/views/users/welcome.html.erb | 2 +-
apps/workbench/app/views/websocket/index.html.erb | 2 +-
apps/workbench/config/application.default.yml | 14 +-
apps/workbench/config/application.rb | 15 +-
.../config/environments/development.rb.example | 12 +-
.../config/environments/production.rb.example | 6 +-
apps/workbench/config/environments/test.rb.example | 6 -
.../config/initializers/zzz_arvados_api_client.rb | 8 -
.../zza_load_config.rb => load_config.rb} | 0
apps/workbench/config/routes.rb | 12 +-
apps/workbench/public/robots.txt | 2 -
.../test/functional/collections_controller_test.rb | 80 +-
.../workbench/test/integration/collections_test.rb | 27 +-
apps/workbench/test/integration/users_test.rb | 7 +-
apps/workbench/test/integration_helper.rb | 5 +
apps/workbench/test/test_helper.rb | 79 +-
apps/workbench/test/unit/collection_test.rb | 27 +
.../test/unit/helpers/collections_helper_test.rb | 8 +
doc/_config.yml | 2 +
doc/api/methods/keep_services.html.textile.liquid | 75 ++
doc/api/schema/KeepDisk.html.textile.liquid | 4 +-
doc/api/schema/KeepService.html.textile.liquid | 24 +
.../install-workbench-app.html.textile.liquid | 11 +
sdk/cli/arvados-cli.gemspec | 1 +
sdk/cli/bin/arv | 11 +-
sdk/cli/bin/arv-run-pipeline-instance | 62 +-
sdk/cli/bin/crunch-job | 12 +-
sdk/perl/lib/Arvados.pm | 2 +-
sdk/perl/lib/Arvados/Request.pm | 9 +-
sdk/python/run_test_server.py | 9 +-
sdk/ruby/arvados.gemspec | 1 +
sdk/ruby/lib/arvados.rb | 7 +-
services/api/.gitignore | 4 +
services/api/Gemfile.lock | 10 +-
.../arvados/v1/collections_controller.rb | 62 +-
.../arvados/v1/keep_services_controller.rb | 21 +
services/api/app/models/api_client.rb | 2 +-
.../api/app/models/api_client_authorization.rb | 2 +-
services/api/app/models/arvados_model.rb | 10 +-
services/api/app/models/authorized_key.rb | 2 +-
services/api/app/models/collection.rb | 2 +-
services/api/app/models/group.rb | 5 +-
services/api/app/models/human.rb | 2 +-
services/api/app/models/job.rb | 2 +-
services/api/app/models/job_task.rb | 2 +-
services/api/app/models/keep_disk.rb | 20 +-
services/api/app/models/keep_service.rb | 15 +
services/api/app/models/link.rb | 2 +-
services/api/app/models/locator.rb | 84 ++
services/api/app/models/log.rb | 2 +-
services/api/app/models/node.rb | 2 +-
services/api/app/models/pipeline_instance.rb | 8 +-
services/api/app/models/pipeline_template.rb | 2 +-
services/api/app/models/repository.rb | 2 +-
services/api/app/models/specimen.rb | 2 +-
services/api/app/models/trait.rb | 2 +-
services/api/app/models/user.rb | 6 +-
services/api/app/models/virtual_machine.rb | 2 +-
services/api/config/application.default.yml | 5 +
services/api/config/application.yml.example | 13 +
services/api/config/initializers/assign_uuid.rb | 1 -
services/api/config/initializers/secret_token.rb | 7 -
services/api/config/routes.rb | 3 +
.../20140422011506_pipeline_instance_state.rb | 2 +
.../migrate/20140519205916_create_keep_services.rb | 51 ++
services/api/db/schema.rb | 23 +-
services/api/lib/assign_uuid.rb | 31 -
services/api/lib/can_be_an_owner.rb | 47 ++
services/api/lib/has_uuid.rb | 42 +
services/api/lib/record_filters.rb | 4 +
services/api/script/crunch-dispatch.rb | 20 +-
.../test/fixtures/api_client_authorizations.yml | 7 +
services/api/test/fixtures/collections.yml | 21 +
services/api/test/fixtures/jobs.yml | 2 +-
services/api/test/fixtures/keep_disks.yml | 12 +-
services/api/test/fixtures/keep_services.yml | 23 +
services/api/test/fixtures/links.yml | 14 +
services/api/test/fixtures/logs.yml | 5 +
.../arvados/v1/collections_controller_test.rb | 216 +++++
.../api/test/functional/arvados/v1/filters_test.rb | 16 +
.../arvados/v1/keep_disks_controller_test.rb | 34 +-
.../arvados/v1/keep_services_controller_test.rb | 23 +
services/api/test/integration/keep_proxy_test.rb | 25 +
services/api/test/unit/arvados_model_test.rb | 34 +
.../api/test/unit/keep_service_test.rb | 2 +-
services/api/test/unit/link_test.rb | 14 +-
services/api/test/unit/owner_test.rb | 126 +++
services/datamanager/experimental/datamanager.py | 887 +++++++++++++++++++++
.../datamanager/experimental/datamanager_test.py | 41 +
services/fuse/arvados_fuse/__init__.py | 27 +-
services/fuse/bin/arv-mount | 4 +-
services/keep/src/keep/handler_test.go | 438 ++++++++++
services/keep/src/keep/keep.go | 304 +++++--
services/keep/src/keep/keep_test.go | 5 +-
services/keep/src/keep/perms.go | 11 +-
157 files changed, 3697 insertions(+), 986 deletions(-)
delete mode 100644 apps/workbench/app/assets/javascripts/api_client_authorizations.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/authorized_keys.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/folders.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/groups.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/humans.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/job_tasks.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/jobs.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/links.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/logs.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/nodes.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/pipeline_templates.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/repositories.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/sessions.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/specimens.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/traits.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/user_agreements.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/users.js.coffee
delete mode 100644 apps/workbench/app/assets/javascripts/virtual_machines.js.coffee
create mode 100644 apps/workbench/app/controllers/keep_services_controller.rb
create mode 100644 apps/workbench/app/helpers/arvados_api_client_helper.rb
copy apps/workbench/app/models/{keep_disk.rb => keep_service.rb} (70%)
delete mode 100644 apps/workbench/app/views/collections/_show_jobs.html.erb
delete mode 100644 apps/workbench/app/views/collections/_show_provenance.html.erb
delete mode 100644 apps/workbench/app/views/collections/_show_source_data.html.erb
create mode 100644 apps/workbench/app/views/collections/show.html.erb
create mode 100644 apps/workbench/app/views/collections/show_file_links.html.erb
delete mode 100644 apps/workbench/config/initializers/zzz_arvados_api_client.rb
rename apps/workbench/config/{initializers/zza_load_config.rb => load_config.rb} (100%)
create mode 100644 doc/api/methods/keep_services.html.textile.liquid
create mode 100644 doc/api/schema/KeepService.html.textile.liquid
create mode 100644 services/api/app/controllers/arvados/v1/keep_services_controller.rb
create mode 100644 services/api/app/models/keep_service.rb
create mode 100644 services/api/app/models/locator.rb
delete mode 100644 services/api/config/initializers/assign_uuid.rb
delete mode 100644 services/api/config/initializers/secret_token.rb
create mode 100644 services/api/db/migrate/20140519205916_create_keep_services.rb
delete mode 100644 services/api/lib/assign_uuid.rb
create mode 100644 services/api/lib/can_be_an_owner.rb
create mode 100644 services/api/lib/has_uuid.rb
create mode 100644 services/api/test/fixtures/keep_services.yml
create mode 100644 services/api/test/functional/arvados/v1/filters_test.rb
create mode 100644 services/api/test/functional/arvados/v1/keep_services_controller_test.rb
create mode 100644 services/api/test/integration/keep_proxy_test.rb
create mode 100644 services/api/test/unit/arvados_model_test.rb
copy apps/workbench/test/unit/job_task_test.rb => services/api/test/unit/keep_service_test.rb (61%)
create mode 100644 services/api/test/unit/owner_test.rb
create mode 100755 services/datamanager/experimental/datamanager.py
create mode 100755 services/datamanager/experimental/datamanager_test.py
create mode 100644 services/keep/src/keep/handler_test.go
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commit 49a6ced3c7a540a7da7155ab1c3120a5227c620c
Merge: 465b105 c2e70e0
Author: radhika <radhika at curoverse.com>
Date: Thu May 22 11:21:53 2014 -0400
Merge branch 'master' into 2767-doc-updates
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