[ARVADOS] updated: 1586823b65c7ec7656626e491a31f3f9516a4a56
Git user
git at public.curoverse.com
Wed May 3 14:15:20 EDT 2017
Summary of changes:
.../controllers/container_requests_controller.rb | 49 +-
apps/workbench/app/helpers/provenance_helper.rb | 48 ++
.../_extra_tab_line_buttons.html.erb | 49 +-
.../_show_provenance.html.erb | 4 +-
.../container_requests_controller_test.rb | 80 ++-
.../test/integration/container_requests_test.rb | 12 +
...nstall-manual-prerequisites.html.textile.liquid | 10 +-
doc/install/migrate-docker19.html.textile.liquid | 9 +-
sdk/cwl/arvados_cwl/arvcontainer.py | 86 ++-
sdk/cwl/arvados_cwl/arvjob.py | 8 +-
sdk/cwl/arvados_cwl/arvworkflow.py | 5 +-
sdk/cwl/arvados_cwl/crunch_script.py | 3 +-
sdk/cwl/arvados_cwl/pathmapper.py | 16 +
sdk/cwl/arvados_cwl/runner.py | 18 +-
sdk/cwl/tests/test_container.py | 106 ++-
sdk/go/arvados/container.go | 1 +
sdk/go/arvadosclient/arvadosclient_test.go | 7 +-
sdk/go/keepclient/discover.go | 15 +-
sdk/go/keepclient/keepclient.go | 22 +-
sdk/go/keepclient/keepclient_test.go | 20 +-
sdk/go/keepclient/support.go | 98 +--
sdk/python/arvados/commands/put.py | 55 +-
sdk/python/tests/run_test_server.py | 5 +-
sdk/python/tests/test_arv_put.py | 28 +
sdk/ruby/lib/arvados.rb | 23 +-
sdk/ruby/lib/arvados/keep.rb | 6 +-
services/api/.gitignore | 3 +-
services/api/Gemfile | 53 +-
services/api/Gemfile.lock | 279 ++++----
services/api/Rakefile | 6 -
.../api/app/controllers/application_controller.rb | 14 +-
.../app/controllers/arvados/v1/nodes_controller.rb | 6 +-
.../controllers/arvados/v1/schema_controller.rb | 7 +-
.../app/controllers/arvados/v1/users_controller.rb | 2 +-
.../api/app/controllers/database_controller.rb | 4 +-
.../app/controllers/user_sessions_controller.rb | 3 +-
.../api/app/models/api_client_authorization.rb | 8 +-
services/api/app/models/arvados_model.rb | 99 ++-
services/api/app/models/collection.rb | 2 +-
services/api/app/models/link.rb | 5 -
services/api/app/models/log.rb | 2 +-
services/api/app/models/user.rb | 8 +-
services/api/app/models/virtual_machine.rb | 6 +-
services/api/config/application.default.yml | 36 +-
services/api/config/application.rb | 31 +-
.../api/config/environments/development.rb.example | 3 -
.../api/config/environments/production.rb.example | 2 +-
services/api/config/environments/test.rb.example | 5 +-
services/api/config/initializers/eventbus.rb | 38 +-
services/api/config/initializers/load_config.rb | 1 +
.../api/config/initializers/noop_deep_munge.rb | 9 -
.../config/initializers/permit_all_parameters.rb | 1 +
services/api/config/initializers/time_format.rb | 2 +
services/api/config/routes.rb | 28 +-
...0170319063406_serialized_columns_accept_null.rb | 5 +
services/api/db/structure.sql | 9 +-
services/api/lib/can_be_an_owner.rb | 2 +-
services/api/lib/create_superuser_token.rb | 4 +-
services/api/lib/eventbus.rb | 358 ----------
services/api/lib/has_uuid.rb | 14 +-
services/api/lib/load_param.rb | 2 +-
services/api/lib/serializers.rb | 6 +
.../api/lib/tasks/delete_old_container_logs.rake | 2 +-
services/api/lib/tasks/delete_old_job_logs.rake | 2 +-
services/api/lib/whitelist_update.rb | 15 +-
services/api/log/.gitkeep | 0
services/api/test/fixtures/container_requests.yml | 2 +-
services/api/test/fixtures/containers.yml | 7 +
.../arvados/v1/collections_controller_test.rb | 6 +-
.../functional/arvados/v1/users_controller_test.rb | 1 +
.../arvados/v1/virtual_machines_controller_test.rb | 4 +-
.../test/functional/database_controller_test.rb | 2 +-
.../api_client_authorizations_scopes_test.rb | 6 +-
.../api/test/integration/crunch_dispatch_test.rb | 2 +-
.../api/test/integration/database_reset_test.rb | 2 -
services/api/test/integration/errors_test.rb | 2 +-
...{noop_deep_munge.rb => noop_deep_munge_test.rb} | 29 +-
services/api/test/integration/pipeline_test.rb | 2 +-
.../api/test/integration/reader_tokens_test.rb | 2 +-
services/api/test/integration/websocket_test.rb | 742 ---------------------
services/api/test/test_helper.rb | 26 +-
services/api/test/unit/arvados_model_test.rb | 76 ++-
.../api/test/unit/create_superuser_token_test.rb | 2 +-
services/api/test/unit/job_test.rb | 23 +-
services/api/test/unit/user_test.rb | 12 +-
services/api/test/unit/workflow_test.rb | 8 +-
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 14 +-
.../crunch-dispatch-slurm_test.go | 15 +-
services/crunch-run/crunchrun.go | 23 +-
services/crunch-run/crunchrun_test.go | 16 +
services/keep-web/handler.go | 4 +-
services/keepproxy/keepproxy.go | 118 ++--
services/keepproxy/keepproxy_test.go | 59 +-
services/keepproxy/proxy_client.go | 19 +
tools/keep-exercise/keep-exercise.go | 3 +-
95 files changed, 1337 insertions(+), 1755 deletions(-)
copy apps/workbench/app/views/{jobs => container_requests}/_show_provenance.html.erb (52%)
delete mode 100644 services/api/config/initializers/noop_deep_munge.rb
create mode 100644 services/api/config/initializers/permit_all_parameters.rb
create mode 100644 services/api/db/migrate/20170319063406_serialized_columns_accept_null.rb
delete mode 100644 services/api/lib/eventbus.rb
delete mode 100644 services/api/log/.gitkeep
rename services/api/test/integration/{noop_deep_munge.rb => noop_deep_munge_test.rb} (63%)
delete mode 100644 services/api/test/integration/websocket_test.rb
create mode 100644 services/keepproxy/proxy_client.go
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Those revisions listed above that are new to this repository have
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commit 1586823b65c7ec7656626e491a31f3f9516a4a56
Merge: ac3bafb c64d7e1
Author: radhika <radhika at curoverse.com>
Date: Wed May 3 14:15:05 2017 -0400
Merge branch 'master' into 10112-workflow-show
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