[ARVADOS] updated: 90633a9dd56502566731991dd4084a57e0366064
Git user
git at public.curoverse.com
Tue Dec 27 10:18:22 EST 2016
Summary of changes:
.gitignore | 5 +
COPYING | 14 +-
README.md | 1 +
apps/workbench/Gemfile | 6 +-
apps/workbench/Gemfile.lock | 16 +-
.../app/assets/javascripts/work_unit_component.js | 16 +
.../app/controllers/application_controller.rb | 34 +-
.../app/controllers/collections_controller.rb | 13 +-
.../controllers/container_requests_controller.rb | 28 +
.../controllers/pipeline_instances_controller.rb | 2 +-
.../app/controllers/projects_controller.rb | 27 +-
.../controllers/work_unit_templates_controller.rb | 6 +-
.../app/controllers/work_units_controller.rb | 80 +-
apps/workbench/app/models/arvados_base.rb | 6 +-
apps/workbench/app/models/container.rb | 2 +-
apps/workbench/app/models/container_request.rb | 2 +-
apps/workbench/app/models/container_work_unit.rb | 19 +-
apps/workbench/app/models/job.rb | 2 +-
apps/workbench/app/models/job_task.rb | 2 +-
apps/workbench/app/models/pipeline_instance.rb | 2 +-
.../app/models/pipeline_instance_work_unit.rb | 4 +-
apps/workbench/app/models/proxy_work_unit.rb | 15 +-
apps/workbench/app/models/work_unit.rb | 4 +
.../application/_extra_tab_line_buttons.html.erb | 0
.../views/application/_title_and_buttons.html.erb | 3 +
.../_extra_tab_line_buttons.html.erb | 10 +
.../views/container_requests/_show_inputs.html.erb | 36 +-
.../pipeline_instances/_running_component.html.erb | 2 +-
.../pipeline_instances/_show_components.html.erb | 2 +-
.../_show_components_running.html.erb | 2 +-
.../app/views/projects/_show_dashboard.html.erb | 16 +-
.../app/views/projects/_show_processes.html.erb | 5 +
.../app/views/projects/_show_workflows.html.erb | 5 +
apps/workbench/app/views/projects/show.html.erb | 16 +-
.../views/work_units/_component_detail.html.erb | 28 +-
.../app/views/work_units/_show_child.html.erb | 29 +-
.../app/views/work_units/_show_component.html.erb | 47 +-
.../app/views/work_units/_show_status.html.erb | 2 +-
apps/workbench/config/application.default.yml | 5 +
apps/workbench/config/routes.rb | 5 +-
apps/workbench/lib/tasks/config_dump.rake | 6 +
.../container_requests_controller_test.rb | 27 +
.../test/controllers/disabled_api_test.rb | 66 ++
.../test/controllers/projects_controller_test.rb | 21 +-
.../test/controllers/work_units_controller_test.rb | 23 -
.../test/diagnostics/container_request_test.rb | 49 ++
apps/workbench/test/diagnostics/pipeline_test.rb | 45 +-
apps/workbench/test/diagnostics_test_helper.rb | 43 +
.../test/integration/application_layout_test.rb | 6 +-
.../test/integration/container_requests_test.rb | 13 +
apps/workbench/test/integration/jobs_test.rb | 2 +-
.../test/integration/pipeline_instances_test.rb | 15 +-
apps/workbench/test/integration/projects_test.rb | 2 +-
apps/workbench/test/integration/work_units_test.rb | 35 +-
apps/workbench/test/performance/browsing_test.rb | 2 +-
apps/workbench/test/unit/disabled_api_test.rb | 15 +
build/README | 6 +-
build/build-dev-docker-jobs-image.sh | 63 ++
build/go-python-package-scripts/postinst | 64 +-
build/go-python-package-scripts/prerm | 37 +-
build/libcloud-pin | 2 +-
.../test-package-python-arvados-cwl-runner.sh | 1 +
.../test-package-python-arvados-fuse.sh | 1 +
.../test-package-python-arvados-python-client.sh | 1 +
...t-package-python27-python-arvados-cwl-runner.sh | 6 +
...ackage-python27-python-arvados-python-client.sh | 2 +-
build/run-build-docker-images.sh | 2 +-
build/run-build-docker-jobs-image.sh | 69 +-
build/run-build-packages-one-target.sh | 12 +-
build/run-build-packages.sh | 60 +-
build/run-library.sh | 29 +-
build/run-tests.sh | 30 +-
doc/_config.yml | 99 ++-
.../_container_runtime_constraints.liquid | 2 +-
.../_container_scheduling_parameters.liquid | 7 +
doc/_includes/_crunch1only_begin.liquid | 2 +
doc/_includes/_crunch1only_end.liquid | 1 +
doc/_includes/_install_docker_cleaner.liquid | 35 +-
doc/_includes/_notebox_begin_warning.liquid | 2 +
doc/_includes/_pipeline_deprecation_notice.liquid | 2 +-
doc/_includes/_what_is_cwl.liquid | 1 +
doc/_layouts/default.html.liquid | 2 +-
doc/api/authentication.html.textile.liquid | 40 -
doc/api/crunch-scripts.html.textile.liquid | 5 +-
doc/api/execution.html.textile.liquid | 27 +
doc/api/index.html.textile.liquid | 44 +-
doc/api/methods.html.textile.liquid | 120 +--
.../api_client_authorizations.html.textile.liquid | 54 +-
doc/api/methods/api_clients.html.textile.liquid | 40 +-
.../methods/authorized_keys.html.textile.liquid | 43 +-
doc/api/methods/collections.html.textile.liquid | 55 +-
.../methods/container_requests.html.textile.liquid | 107 ++-
doc/api/methods/containers.html.textile.liquid | 81 +-
doc/api/methods/groups.html.textile.liquid | 47 +-
doc/api/methods/humans.html.textile.liquid | 39 +-
doc/api/methods/job_tasks.html.textile.liquid | 55 +-
doc/api/methods/jobs.html.textile.liquid | 101 ++-
doc/api/methods/keep_disks.html.textile.liquid | 52 +-
doc/api/methods/keep_services.html.textile.liquid | 52 +-
doc/api/methods/links.html.textile.liquid | 69 +-
doc/api/methods/logs.html.textile.liquid | 49 +-
doc/api/methods/nodes.html.textile.liquid | 50 +-
.../methods/pipeline_instances.html.textile.liquid | 44 +-
.../methods/pipeline_templates.html.textile.liquid | 182 ++++-
doc/api/methods/repositories.html.textile.liquid | 45 +-
doc/api/methods/specimens.html.textile.liquid | 41 +-
doc/api/methods/traits.html.textile.liquid | 40 +-
doc/api/methods/users.html.textile.liquid | 67 +-
.../methods/virtual_machines.html.textile.liquid | 52 +-
doc/api/methods/workflows.html.textile.liquid | 44 +-
doc/api/permission-model.html.textile.liquid | 143 ++--
doc/api/requests.html.textile.liquid | 349 ++++++++
doc/api/resources.html.textile.liquid | 46 +-
doc/api/schema/ApiClient.html.textile.liquid | 24 -
.../ApiClientAuthorization.html.textile.liquid | 29 -
doc/api/schema/AuthorizedKey.html.textile.liquid | 24 -
doc/api/schema/Collection.html.textile.liquid | 39 -
doc/api/schema/Container.html.textile.liquid | 59 --
.../schema/ContainerRequest.html.textile.liquid | 70 --
doc/api/schema/Group.html.textile.liquid | 25 -
doc/api/schema/Human.html.textile.liquid | 19 -
doc/api/schema/Job.html.textile.liquid | 69 --
doc/api/schema/JobTask.html.textile.liquid | 47 --
doc/api/schema/KeepDisk.html.textile.liquid | 31 -
doc/api/schema/KeepService.html.textile.liquid | 24 -
doc/api/schema/Link.html.textile.liquid | 83 --
doc/api/schema/Log.html.textile.liquid | 33 -
doc/api/schema/Node.html.textile.liquid | 28 -
.../schema/PipelineInstance.html.textile.liquid | 26 -
.../schema/PipelineTemplate.html.textile.liquid | 161 ----
doc/api/schema/Repository.html.textile.liquid | 25 -
doc/api/schema/Specimen.html.textile.liquid | 22 -
doc/api/schema/Trait.html.textile.liquid | 22 -
doc/api/schema/User.html.textile.liquid | 30 -
doc/api/schema/VirtualMachine.html.textile.liquid | 21 -
doc/api/schema/Workflow.html.textile.liquid | 23 -
doc/api/storage.html.textile.liquid | 170 ++++
doc/api/tokens.html.textile.liquid | 63 ++
doc/images/Arvados_Permissions.svg | 4 +
doc/images/Crunch_dispatch.svg | 4 +
doc/images/Keep_manifests.svg | 4 +
doc/images/Keep_reading_writing_block.svg | 4 +
doc/images/Keep_rendezvous_hashing.svg | 4 +
doc/images/Session_Establishment.svg | 4 +
doc/images/upload-using-workbench.png | Bin 49690 -> 23979 bytes
doc/images/workbench-dashboard.png | Bin 94257 -> 57930 bytes
doc/images/workbench-move-selected.png | Bin 47833 -> 15450 bytes
.../install-prerequisites.html.textile.liquid | 4 +-
doc/install/install-keep-web.html.textile.liquid | 2 +-
doc/install/install-keepproxy.html.textile.liquid | 2 +-
doc/install/install-ws.html.textile.liquid | 204 +++++
doc/sdk/cli/install.html.textile.liquid | 1 -
doc/sdk/go/example.html.textile.liquid | 76 ++
doc/sdk/go/index.html.textile.liquid | 15 +-
doc/sdk/index.html.textile.liquid | 13 +-
doc/sdk/java/example.html.textile.liquid | 78 ++
doc/sdk/java/index.html.textile.liquid | 11 +-
doc/sdk/perl/example.html.textile.liquid | 81 ++
doc/sdk/perl/index.html.textile.liquid | 59 +-
doc/sdk/python/events.html.textile.liquid | 2 +-
doc/sdk/python/example.html.textile.liquid | 51 ++
doc/sdk/python/sdk-python.html.textile.liquid | 3 +-
doc/sdk/ruby/example.html.textile.liquid | 75 ++
doc/sdk/ruby/index.html.textile.liquid | 74 +-
doc/user/cwl/cwl-extensions.html.textile.liquid | 56 ++
doc/user/cwl/cwl-run-options.html.textile.liquid | 94 +++
doc/user/cwl/cwl-runner.html.textile.liquid | 252 ++----
doc/user/cwl/cwl-style.html.textile.liquid | 2 +
.../examples/crunch-examples.html.textile.liquid | 2 +
.../getting_started/workbench.html.textile.liquid | 4 +-
.../reference/job-pipeline-ref.html.textile.liquid | 4 +-
doc/user/topics/arv-copy.html.textile.liquid | 3 +
doc/user/topics/arv-docker.html.textile.liquid | 12 +-
doc/user/topics/arv-run.html.textile.liquid | 4 +
doc/user/topics/run-command.html.textile.liquid | 2 +
...nning-pipeline-command-line.html.textile.liquid | 6 +-
.../running-external-program.html.textile.liquid | 6 +-
...tutorial-pipeline-workbench.html.textile.liquid | 31 -
.../tutorial-submit-job.html.textile.liquid | 6 +-
...tutorial-workflow-workbench.html.textile.liquid | 27 +
.../writing-cwl-workflow.html.textile.liquid | 196 +++++
docker/jobs/Dockerfile | 12 +-
sdk/cli/bin/arv-run-pipeline-instance | 2 +
sdk/cli/bin/crunch-job | 14 +-
sdk/cli/test/test_arv-keep-get.rb | 8 +
sdk/cli/test/test_arv-keep-put.rb | 8 +-
sdk/cwl/arvados_cwl/__init__.py | 271 +++++--
sdk/cwl/arvados_cwl/arvcontainer.py | 158 ++--
sdk/cwl/arvados_cwl/arvdocker.py | 45 +-
sdk/cwl/arvados_cwl/arvjob.py | 117 +--
sdk/cwl/arvados_cwl/arvworkflow.py | 23 +-
sdk/cwl/arvados_cwl/crunch_script.py | 34 +-
sdk/cwl/arvados_cwl/done.py | 3 +
sdk/cwl/arvados_cwl/fsaccess.py | 84 ++
sdk/cwl/arvados_cwl/pathmapper.py | 35 +-
sdk/cwl/arvados_cwl/runner.py | 69 +-
sdk/cwl/gittaggers.py | 38 +-
sdk/cwl/setup.py | 25 +-
sdk/cwl/test_with_arvbox.sh | 19 +-
sdk/cwl/tests/mock_discovery.py | 13 +
sdk/cwl/tests/test_container.py | 196 ++---
sdk/cwl/tests/test_job.py | 168 ++--
sdk/cwl/tests/test_make_output.py | 21 +-
sdk/cwl/tests/test_pathmapper.py | 3 +-
sdk/cwl/tests/test_submit.py | 713 +++++++++++++++--
sdk/cwl/tests/test_urljoin.py | 56 ++
sdk/cwl/tests/wf/expect_arvworkflow.cwl | 24 +
sdk/cwl/tests/wf/expect_packed.cwl | 2 +-
.../wf/{submit_wf.cwl => submit_keepref_wf.cwl} | 13 +-
sdk/dev-jobs.dockerfile | 38 +
sdk/go/arvados/client.go | 97 ++-
sdk/go/arvados/container.go | 39 +-
sdk/go/arvados/log.go | 25 +
sdk/go/arvadosclient/arvadosclient.go | 43 +-
sdk/go/config/load.go | 5 +
sdk/go/crunchrunner/crunchrunner.go | 20 -
sdk/go/ctxlog/log.go | 59 ++
sdk/go/httpserver/id_generator.go | 31 +
sdk/go/httpserver/request_limiter.go | 26 +-
sdk/go/keepclient/keepclient.go | 3 +-
sdk/go/logger/logger.go | 204 -----
sdk/go/logger/util.go | 20 -
sdk/go/stats/duration.go | 35 +
sdk/go/stats/duration_test.go | 23 +
sdk/go/util/util.go | 34 -
sdk/python/arvados/_version.py | 3 +
sdk/python/arvados/arvfile.py | 88 +-
sdk/python/arvados/collection.py | 13 +-
sdk/python/arvados/commands/arv_copy.py | 4 +
sdk/python/arvados/commands/keepdocker.py | 5 +
sdk/python/arvados/commands/ls.py | 6 +
sdk/python/arvados/commands/put.py | 710 +++++++++++++----
sdk/python/arvados/commands/run.py | 36 +-
sdk/python/arvados/commands/ws.py | 4 +
sdk/python/arvados/events.py | 77 +-
sdk/python/arvados/keep.py | 138 ++--
sdk/python/arvados/util.py | 2 +
sdk/python/bin/arv-get | 5 +
sdk/python/bin/arv-normalize | 14 +-
sdk/python/setup.py | 2 +-
sdk/python/tests/arvados_testutil.py | 13 +
sdk/python/tests/nginx.conf | 16 +
sdk/python/tests/run_test_server.py | 71 +-
sdk/python/tests/test_arv_copy.py | 29 +
sdk/python/tests/test_arv_keepdocker.py | 30 +
sdk/python/tests/test_arv_ls.py | 15 +-
sdk/python/tests/test_arv_normalize.py | 27 +
sdk/python/tests/test_arv_put.py | 319 ++++++--
sdk/python/tests/test_arv_run.py | 29 +
sdk/python/tests/test_arv_ws.py | 15 +
sdk/python/tests/test_arvfile.py | 21 +
sdk/python/tests/test_collections.py | 2 +
sdk/python/tests/test_events.py | 86 +-
sdk/python/tests/test_keep_client.py | 76 +-
services/api/Gemfile | 24 +-
services/api/Gemfile.lock | 239 +++---
.../api/app/controllers/application_controller.rb | 26 +-
.../arvados/v1/collections_controller.rb | 6 +-
.../arvados/v1/container_requests_controller.rb | 1 +
.../arvados/v1/containers_controller.rb | 18 +
.../controllers/arvados/v1/groups_controller.rb | 22 +-
.../controllers/arvados/v1/schema_controller.rb | 22 +-
.../arvados/v1/user_agreements_controller.rb | 3 +-
.../app/controllers/arvados/v1/users_controller.rb | 2 +-
.../arvados/v1/virtual_machines_controller.rb | 2 +-
.../api/app/controllers/database_controller.rb | 2 +-
services/api/app/middlewares/arvados_api_token.rb | 2 +-
services/api/app/models/arvados_model.rb | 18 +-
services/api/app/models/blob.rb | 4 +-
services/api/app/models/collection.rb | 15 +-
services/api/app/models/commit_ancestor.rb | 6 +-
services/api/app/models/container.rb | 59 +-
services/api/app/models/container_request.rb | 47 +-
services/api/app/models/job.rb | 46 +-
services/api/app/models/link.rb | 1 -
services/api/app/models/log.rb | 3 +-
services/api/app/models/node.rb | 36 +-
services/api/app/models/pipeline_instance.rb | 14 +
services/api/app/models/repository.rb | 2 +-
services/api/app/models/user.rb | 4 +-
services/api/config/application.default.yml | 9 +-
services/api/config/boot.rb | 2 +-
services/api/config/initializers/inflections.rb | 8 +-
services/api/config/initializers/load_config.rb | 4 +-
.../api/config/initializers/preload_all_models.rb | 2 +-
services/api/config/routes.rb | 1 +
...43147_add_scheduling_parameters_to_container.rb | 6 +
...add_output_and_log_uuid_to_container_request.rb | 22 +
..._log_uuids_to_container_request_search_index.rb | 21 +
.../20161213172944_full_text_search_indexes.rb | 33 +
services/api/db/structure.sql | 34 +-
services/api/lib/crunch_dispatch.rb | 10 +-
services/api/lib/current_api_client.rb | 10 +-
services/api/lib/eventbus.rb | 35 +-
services/api/lib/load_param.rb | 4 +-
services/api/lib/salvage_collection.rb | 2 +-
services/api/lib/tasks/config_dump.rake | 6 +
services/api/script/arvados-git-sync.rb | 4 +-
.../api/script/migrate-gitolite-to-uuid-storage.rb | 4 +-
services/api/test/factories/user.rb | 2 +-
.../test/fixtures/api_client_authorizations.yml | 14 +
services/api/test/fixtures/collections.yml | 13 +
services/api/test/fixtures/container_requests.yml | 2 +
services/api/test/fixtures/containers.yml | 4 +-
services/api/test/fixtures/nodes.yml | 6 +-
services/api/test/fixtures/pipeline_templates.yml | 22 +
services/api/test/fixtures/workflows.yml | 19 +
.../api_client_authorizations_controller_test.rb | 2 +-
.../arvados/v1/collections_controller_test.rb | 51 +-
.../v1/container_requests_controller_test.rb | 22 +
.../arvados/v1/containers_controller_test.rb | 19 +
.../api/test/functional/arvados/v1/filters_test.rb | 6 +-
.../arvados/v1/groups_controller_test.rb | 19 +-
.../functional/arvados/v1/jobs_controller_test.rb | 15 +-
.../functional/arvados/v1/links_controller_test.rb | 4 +-
.../arvados/v1/repositories_controller_test.rb | 13 +-
.../arvados/v1/schema_controller_test.rb | 10 +-
.../functional/arvados/v1/users_controller_test.rb | 4 +-
.../arvados/v1/virtual_machines_controller_test.rb | 1 -
services/api/test/helpers/users_test_helper.rb | 2 +-
.../api/test/integration/collections_api_test.rb | 14 +-
.../integration/collections_performance_test.rb | 6 +-
services/api/test/integration/cross_origin_test.rb | 2 +-
.../api/test/integration/database_reset_test.rb | 9 +-
.../api/test/integration/user_sessions_test.rb | 2 +-
services/api/test/integration/websocket_test.rb | 136 ++--
services/api/test/test_helper.rb | 32 +-
services/api/test/unit/app_version_test.rb | 7 +-
services/api/test/unit/authorized_key_test.rb | 2 +-
.../api/test/unit/collection_performance_test.rb | 5 +-
services/api/test/unit/collection_test.rb | 16 +-
services/api/test/unit/commit_test.rb | 18 +-
services/api/test/unit/container_request_test.rb | 79 +-
services/api/test/unit/container_test.rb | 147 +++-
services/api/test/unit/fail_jobs_test.rb | 4 +-
services/api/test/unit/job_test.rb | 6 +-
services/api/test/unit/log_test.rb | 12 +-
services/api/test/unit/node_test.rb | 29 +-
services/api/test/unit/owner_test.rb | 3 +-
services/api/test/unit/permission_test.rb | 14 +-
services/api/test/unit/pipeline_instance_test.rb | 9 +-
services/api/test/unit/salvage_collection_test.rb | 12 +-
services/api/test/unit/user_test.rb | 1 -
services/api/test/websocket_runner.rb | 53 --
services/arv-git-httpd/main.go | 2 +-
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 20 +-
.../crunch-dispatch-slurm_test.go | 7 +-
services/crunch-dispatch-slurm/squeue.go | 42 +-
services/crunch-run/crunchrun.go | 48 +-
services/crunch-run/crunchrun_test.go | 105 ++-
services/crunchstat/crunchstat.go | 36 +
services/crunchstat/crunchstat_test.go | 150 ++++
services/datamanager/collection/collection.go | 408 ----------
services/datamanager/collection/collection_test.go | 202 -----
services/datamanager/collection/testing.go | 61 --
services/datamanager/datamanager.go | 220 -----
services/datamanager/datamanager_test.go | 732 -----------------
services/datamanager/experimental/datamanager.py | 887 ---------------------
.../datamanager/experimental/datamanager_test.py | 41 -
services/datamanager/keep/keep.go | 551 -------------
services/datamanager/keep/keep_test.go | 278 -------
services/datamanager/loggerutil/loggerutil.go | 52 --
services/datamanager/summary/canonical_string.go | 30 -
services/datamanager/summary/file.go | 115 ---
services/datamanager/summary/pull_list.go | 215 -----
services/datamanager/summary/pull_list_test.go | 272 -------
services/datamanager/summary/summary.go | 277 -------
services/datamanager/summary/summary_test.go | 220 -----
services/datamanager/summary/trash_list.go | 62 --
services/datamanager/summary/trash_list_test.go | 76 --
.../dockercleaner/arvados-docker-cleaner.service | 7 +-
services/dockercleaner/arvados_docker/cleaner.py | 21 +-
services/dockercleaner/setup.py | 1 +
services/dockercleaner/tests/test_cleaner.py | 6 +
services/fuse/arvados_fuse/__init__.py | 51 +-
services/fuse/arvados_fuse/_version.py | 3 +
services/fuse/arvados_fuse/command.py | 6 +
services/fuse/setup.py | 3 +-
services/fuse/tests/integration_test.py | 1 -
services/fuse/tests/mount_test_base.py | 2 +
services/fuse/tests/test_command_args.py | 16 +
services/fuse/tests/test_mount.py | 34 -
services/fuse/tests/test_retry.py | 2 +-
services/fuse/tests/test_token_expiry.py | 68 ++
services/keep-balance/balance.go | 2 +-
services/keep-web/main.go | 2 +-
services/keepproxy/keepproxy.go | 2 +-
services/keepstore/azure_blob_volume.go | 149 +++-
services/keepstore/azure_blob_volume_test.go | 77 +-
services/keepstore/bufferpool.go | 3 +-
services/keepstore/collision.go | 16 +-
services/keepstore/config.go | 31 +-
services/keepstore/config_test.go | 9 +
services/keepstore/count.go | 44 +
services/keepstore/handler_test.go | 27 +-
services/keepstore/handlers.go | 178 +++--
.../keepstore/handlers_with_generic_volume_test.go | 15 +-
services/keepstore/keepstore.go | 15 +-
services/keepstore/keepstore_test.go | 49 +-
services/keepstore/logging_router.go | 46 +-
services/keepstore/pull_worker.go | 6 +-
services/keepstore/s3_volume.go | 299 +++++--
services/keepstore/s3_volume_test.go | 158 +++-
services/keepstore/trash_worker.go | 2 +-
services/keepstore/trash_worker_test.go | 19 +-
services/keepstore/usage.go | 4 +
services/keepstore/volume.go | 52 +-
services/keepstore/volume_generic_test.go | 87 +-
services/keepstore/volume_test.go | 7 +-
services/keepstore/volume_unix.go | 33 +-
services/keepstore/volume_unix_test.go | 37 +-
services/login-sync/bin/arvados-login-sync | 56 +-
services/login-sync/test/test_add_user.rb | 2 +-
services/nodemanager/arvnodeman/_version.py | 3 +
.../arvnodeman/computenode/driver/gce.py | 3 +-
services/nodemanager/arvnodeman/launcher.py | 10 +-
services/nodemanager/setup.py | 1 +
services/nodemanager/tests/test_arguments.py | 27 +
services/nodemanager/tests/testutil.py | 17 +-
.../keepproxy.service => ws/arvados-ws.service} | 6 +-
services/ws/config.go | 40 +
services/ws/doc.go | 55 ++
services/ws/event.go | 65 ++
services/ws/event_source.go | 216 +++++
services/ws/handler.go | 235 ++++++
services/ws/main.go | 67 ++
services/ws/permission.go | 94 +++
services/ws/router.go | 140 ++++
services/ws/session.go | 33 +
services/ws/session_v0.go | 295 +++++++
services/ws/session_v1.go | 14 +
tools/arvbash/arvbash.sh | 124 +++
tools/arvbox/bin/arvbox | 28 +-
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 60 +-
tools/arvbox/lib/arvbox/docker/Dockerfile.demo | 2 +-
tools/arvbox/lib/arvbox/docker/Dockerfile.dev | 11 +-
tools/arvbox/lib/arvbox/docker/common.sh | 17 +-
tools/arvbox/lib/arvbox/docker/crunch-setup.sh | 1 +
.../lib/arvbox/docker/service/api/run-service | 4 +-
.../lib/arvbox/docker/service/ready/run-service | 4 +-
.../lib/arvbox/docker/service/sdk/run-service | 8 +-
tools/keep-exercise/keep-exercise.go | 19 +-
442 files changed, 11624 insertions(+), 9432 deletions(-)
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create mode 120000 build/package-testing/test-package-python-arvados-cwl-runner.sh
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create mode 100755 build/package-testing/test-package-python27-python-arvados-cwl-runner.sh
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copy services/{keepproxy/keepproxy.service => ws/arvados-ws.service} (55%)
create mode 100644 services/ws/config.go
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create mode 100755 tools/arvbash/arvbash.sh
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commit 90633a9dd56502566731991dd4084a57e0366064
Author: Tom Clegg <tom at curoverse.com>
Date: Thu Oct 20 11:26:23 2016 -0400
10273: Check scope=[all] when looking for an existing superuser token.
diff --git a/services/api/lib/create_superuser_token.rb b/services/api/lib/create_superuser_token.rb
index 54faa9a..72b1ae7 100755
--- a/services/api/lib/create_superuser_token.rb
+++ b/services/api/lib/create_superuser_token.rb
@@ -14,8 +14,12 @@ module CreateSuperUserToken
api_client_auth = ApiClientAuthorization.
where(api_token: supplied_token).
first
- if api_client_auth && !api_client_auth.user.uuid.match(/-000000000000000$/)
- raise "Token already exists but is not a superuser token."
+ if !api_client_auth
+ # fall through to create a token
+ elsif !api_client_auth.user.uuid.match(/-000000000000000$/)
+ raise "Token exists but is not a superuser token."
+ elsif api_client_auth.scopes != ['all']
+ raise "Token exists but has limited scope #{api_client_auth.scopes.inspect}."
end
end
@@ -26,10 +30,11 @@ module CreateSuperUserToken
# Check if there is an unexpired superuser token corresponding to this api client
api_client_auth = ApiClientAuthorization.where(
- 'user_id = (?) AND
- api_client_id = (?) AND
+ 'user_id = ? AND
+ api_client_id = ? AND
+ scopes = ? AND
(expires_at IS NULL OR expires_at > CURRENT_TIMESTAMP)',
- system_user.id, apiClient.id).first
+ system_user.id, apiClient.id, ['all'].to_yaml).first
# none exist; create one with the supplied token
if !api_client_auth
diff --git a/services/api/test/unit/create_superuser_token_test.rb b/services/api/test/unit/create_superuser_token_test.rb
index d5ca3f9..ba81360 100644
--- a/services/api/test/unit/create_superuser_token_test.rb
+++ b/services/api/test/unit/create_superuser_token_test.rb
@@ -73,6 +73,25 @@ class CreateSuperUserTokenTest < ActiveSupport::TestCase
create_superuser_token active_user_token
end
assert_not_nil e
- assert_equal "Token already exists but is not a superuser token.", e.message
+ assert_equal "Token exists but is not a superuser token.", e.message
+ end
+
+ test "specified token has limited scope" do
+ active_user_token = api_client_authorizations("data_manager").api_token
+ e = assert_raises RuntimeError do
+ create_superuser_token active_user_token
+ end
+ assert_not_nil e
+ assert_match /^Token exists but has limited scope/, e.message
+ end
+
+ test "existing token has limited scope" do
+ active_user_token = api_client_authorizations("admin_vm").api_token
+ ApiClientAuthorization.
+ where(user_id: system_user.id).
+ update_all(scopes: ["GET /"])
+ fixture_tokens = ApiClientAuthorization.all.collect(&:api_token)
+ new_token = create_superuser_token
+ refute_includes(fixture_tokens, new_token)
end
end
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