[ARVADOS] updated: be4852ec32e5eeed1af9a62017cfc39ed66ac186
Git user
git at public.curoverse.com
Tue May 2 10:57:21 EDT 2017
Summary of changes:
.../controllers/container_requests_controller.rb | 27 +-
apps/workbench/app/helpers/provenance_helper.rb | 48 ++
.../_show_provenance.html.erb | 4 +-
.../container_requests_controller_test.rb | 21 +
.../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 | 62 +-
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 | 84 +++
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/_ranges.py | 2 +-
sdk/python/arvados/arvfile.py | 170 +++--
sdk/python/tests/run_test_server.py | 5 +-
sdk/python/tests/test_collections.py | 60 +-
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 | 29 +-
.../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 | 1 +
.../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
.../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 +-
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 +-
services/crunch-run/crunchrun.go | 6 +-
services/fuse/tests/test_tmp_collection.py | 13 +
services/keep-web/handler.go | 12 +-
services/keep-web/handler_test.go | 29 +
services/keepproxy/keepproxy.go | 118 ++--
services/keepproxy/keepproxy_test.go | 59 +-
services/keepproxy/proxy_client.go | 19 +
tools/keep-exercise/keep-exercise.go | 3 +-
90 files changed, 1257 insertions(+), 1747 deletions(-)
copy apps/workbench/app/views/{jobs => container_requests}/_show_provenance.html.erb (52%)
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
delete mode 100644 services/api/test/integration/websocket_test.rb
create mode 100644 services/keepproxy/proxy_client.go
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commit be4852ec32e5eeed1af9a62017cfc39ed66ac186
Merge: c6452ff ed37572
Author: Lucas Di Pentima <lucas at curoverse.com>
Date: Tue May 2 11:56:56 2017 -0300
11185: Merge branch 'master' into 11185-wb-disable-reuse
diff --cc apps/workbench/test/controllers/container_requests_controller_test.rb
index 01f740c,6f5a6da..bd2f6be
--- a/apps/workbench/test/controllers/container_requests_controller_test.rb
+++ b/apps/workbench/test/controllers/container_requests_controller_test.rb
@@@ -38,51 -38,43 +38,72 @@@ class ContainerRequestsControllerTest
get :show, {id: uuid}, session_for(:active)
assert_response :success
- assert_includes @response.body, "href=\"/container_requests/#{uuid}/copy\""
+ assert_includes @response.body, "action=\"/container_requests/#{uuid}/copy\""
end
- test "container request copy" do
- completed_cr = api_fixture('container_requests')['completed']
- post(:copy,
- {
- id: completed_cr['uuid']
- },
- session_for(:active))
- assert_response 302
- copied_cr = assigns(:object)
- assert_not_nil copied_cr
- assert_equal 'Uncommitted', copied_cr[:state]
- assert_equal "Copy of #{completed_cr['name']}", copied_cr['name']
- assert_equal completed_cr['cmd'], copied_cr['cmd']
- assert_equal completed_cr['runtime_constraints']['ram'], copied_cr['runtime_constraints'][:ram]
+ [
+ ['completed', false, false],
+ ['completed', true, false],
+ ['completed-older', false, true],
+ ['completed-older', true, true],
+ ].each do |cr_fixture, reuse_enabled, uses_acr|
+ test "container request #{uses_acr ? '' : 'not'} using arvados-cwl-runner copy #{reuse_enabled ? 'with' : 'without'} reuse enabled" do
+ completed_cr = api_fixture('container_requests')[cr_fixture]
+ # Set up post request params
+ copy_params = {id: completed_cr['uuid']}
+ if reuse_enabled
+ copy_params.merge!({use_existing: true})
+ end
+ post(:copy, copy_params, session_for(:active))
+ assert_response 302
+ copied_cr = assigns(:object)
+ assert_not_nil copied_cr
+ assert_equal 'Uncommitted', copied_cr[:state]
+ assert_equal "Copy of #{completed_cr['name']}", copied_cr['name']
+ assert_equal completed_cr['cmd'], copied_cr['cmd']
+ assert_equal completed_cr['runtime_constraints']['ram'], copied_cr['runtime_constraints'][:ram]
+ if reuse_enabled
+ assert copied_cr[:use_existing]
+ else
+ refute copied_cr[:use_existing]
+ end
+ # If the CR's command is arvados-cwl-runner, the appropriate flag should
+ # be passed to it
+ if uses_acr
+ if reuse_enabled
+ # arvados-cwl-runner's default behavior is to enable reuse
+ assert_includes copied_cr['command'], 'arvados-cwl-runner'
+ assert_not_includes copied_cr['command'], '--disable-reuse'
+ else
+ assert_includes copied_cr['command'], 'arvados-cwl-runner'
+ assert_includes copied_cr['command'], '--disable-reuse'
+ assert_not_includes copied_cr['command'], '--enable-reuse'
+ end
+ else
+ # If no arvados-cwl-runner is being used, the command should be left alone
+ assert_equal completed_cr['command'], copied_cr['command']
+ end
+ end
end
+
+ [
+ ['completed', true],
+ ['running', true],
+ ['queued', true],
+ ['uncommitted', false],
+ ].each do |cr_fixture, should_show|
+ test "provenance tab should #{should_show ? '' : 'not'} be shown on #{cr_fixture} container requests" do
+ cr = api_fixture('container_requests')[cr_fixture]
+ assert_not_nil cr
+ get(:show,
+ {id: cr['uuid']},
+ session_for(:active))
+ assert_response :success
+ if should_show
+ assert_includes @response.body, "href=\"#Provenance\""
+ else
+ assert_not_includes @response.body, "href=\"#Provenance\""
+ end
+ end
+ end
end
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