[ARVADOS] updated: 1.3.0-708-gb2addc888
Git user
git at public.curoverse.com
Mon Apr 8 14:14:39 UTC 2019
Summary of changes:
apps/workbench/.gitignore | 2 +
services/api/.gitignore | 3 +
services/api/Gemfile | 32 +-
services/api/Gemfile.lock | 264 +++++-----
services/api/Rakefile | 1 +
.../api/app/controllers/application_controller.rb | 54 +-
.../v1/api_client_authorizations_controller.rb | 8 +-
.../arvados/v1/api_clients_controller.rb | 2 +-
.../arvados/v1/containers_controller.rb | 4 +-
.../controllers/arvados/v1/groups_controller.rb | 4 +-
.../arvados/v1/healthcheck_controller.rb | 20 +-
.../app/controllers/arvados/v1/jobs_controller.rb | 4 +-
.../arvados/v1/keep_disks_controller.rb | 4 +-
.../arvados/v1/keep_services_controller.rb | 6 +-
.../app/controllers/arvados/v1/nodes_controller.rb | 6 +-
.../arvados/v1/repositories_controller.rb | 6 +-
.../controllers/arvados/v1/schema_controller.rb | 26 +-
.../arvados/v1/user_agreements_controller.rb | 6 +-
.../app/controllers/arvados/v1/users_controller.rb | 8 +-
.../arvados/v1/virtual_machines_controller.rb | 6 +-
.../api/app/controllers/database_controller.rb | 6 +-
services/api/app/controllers/static_controller.rb | 8 +-
.../app/controllers/user_sessions_controller.rb | 10 +-
.../api/app/models/application_record.rb | 5 +-
services/api/app/models/arvados_model.rb | 32 +-
services/api/app/models/collection.rb | 18 +-
services/api/app/models/container.rb | 8 +-
services/api/app/models/container_request.rb | 8 +-
services/api/app/models/group.rb | 5 +-
services/api/app/models/job.rb | 5 +-
services/api/app/models/jsonb_type.rb | 45 ++
services/api/app/models/link.rb | 7 +-
services/api/app/models/node.rb | 8 +-
services/api/app/models/pipeline_instance.rb | 6 +-
services/api/app/models/user.rb | 22 +-
services/api/{config/boot.rb => bin/bundle} | 8 +-
services/api/bin/rails | 9 +
.../api/bin/rake | 8 +-
services/api/bin/setup | 39 ++
services/api/bin/update | 34 ++
services/api/config/application.default.yml | 9 +-
services/api/config/application.rb | 16 +-
services/api/config/boot.rb | 6 +-
services/api/config/cable.yml | 13 +
services/api/config/environment.rb | 4 +-
.../api/config/environments/production.rb.example | 2 +-
services/api/config/environments/test.rb.example | 4 +-
...types.rb => application_controller_renderer.rb} | 9 +-
services/api/config/initializers/assets.rb | 15 +
.../api/config/initializers/cookies_serializer.rb | 9 +
services/api/config/initializers/custom_types.rb | 8 +
.../{mime_types.rb => filter_parameter_logging.rb} | 5 +-
.../config/initializers/new_framework_defaults.rb | 26 +
services/api/config/initializers/session_store.rb | 2 +-
services/api/config/puma.rb | 51 ++
services/api/config/secrets.yml | 26 +
services/api/config/spring.rb | 10 +
.../migrate/20121016005009_create_collections.rb | 2 +-
.../db/migrate/20130105203021_create_metadata.rb | 2 +-
.../20130105224358_rename_metadata_class.rb | 2 +-
...05224618_rename_collection_created_by_client.rb | 2 +-
.../20130107181109_add_uuid_to_collections.rb | 2 +-
.../api/db/migrate/20130107212832_create_nodes.rb | 2 +-
.../db/migrate/20130109175700_create_pipelines.rb | 2 +-
.../20130109220548_create_pipeline_invocations.rb | 2 +-
...214204_add_index_to_collections_and_metadata.rb | 2 +-
.../db/migrate/20130116024233_create_specimens.rb | 2 +-
.../db/migrate/20130116215213_create_projects.rb | 2 +-
.../20130118002239_rename_metadata_attributes.rb | 2 +-
.../api/db/migrate/20130122020042_create_users.rb | 2 +-
.../api/db/migrate/20130122201442_create_logs.rb | 2 +-
.../20130122221616_add_modified_at_to_logs.rb | 2 +-
.../20130123174514_add_uuid_index_to_users.rb | 2 +-
.../migrate/20130123180224_create_api_clients.rb | 2 +-
...30123180228_create_api_client_authorizations.rb | 2 +-
.../20130125220425_rename_created_by_to_owner.rb | 2 +-
.../20130128202518_rename_metadata_to_links.rb | 2 +-
.../20130128231343_add_properties_to_specimen.rb | 2 +-
...130130205749_add_manifest_text_to_collection.rb | 2 +-
.../api/db/migrate/20130203104818_create_jobs.rb | 2 +-
.../db/migrate/20130203104824_create_job_steps.rb | 2 +-
.../migrate/20130203115329_add_priority_to_jobs.rb | 2 +-
.../20130207195855_add_index_on_timestamps.rb | 2 +-
...81504_add_properties_to_pipeline_invocations.rb | 2 +-
...130226170000_remove_native_target_from_links.rb | 2 +-
.../20130313175417_rename_projects_to_groups.rb | 2 +-
.../20130315155820_add_is_locked_by_to_jobs.rb | 2 +-
.../db/migrate/20130315183626_add_log_to_jobs.rb | 2 +-
.../20130315213205_add_tasks_summary_to_jobs.rb | 2 +-
.../20130318002138_add_resource_limits_to_jobs.rb | 2 +-
.../20130319165853_rename_job_command_to_script.rb | 2 +-
...ame_pipeline_invocation_to_pipeline_instance.rb | 2 +-
...94637_rename_pipelines_to_pipeline_templates.rb | 2 +-
...20130319201431_rename_job_steps_to_job_tasks.rb | 2 +-
.../20130319235957_add_default_owner_to_users.rb | 2 +-
...d_default_owner_to_api_client_authorizations.rb | 2 +-
.../db/migrate/20130326173804_create_commits.rb | 2 +-
.../20130326182917_create_commit_ancestors.rb | 2 +-
.../20130415020241_rename_orvos_to_arvados.rb | 2 +-
.../db/migrate/20130425024459_create_keep_disks.rb | 2 +-
...vice_port_and_service_ssl_flag_to_keep_disks.rb | 2 +-
...3060112_add_created_by_job_task_to_job_tasks.rb | 2 +-
.../20130523060213_add_qsequence_to_job_tasks.rb | 2 +-
.../20130524042319_fix_job_task_qsequence_type.rb | 2 +-
.../migrate/20130528134100_update_nodes_index.rb | 2 +-
.../20130606183519_create_authorized_keys.rb | 2 +-
.../20130608053730_create_virtual_machines.rb | 2 +-
.../migrate/20130610202538_create_repositories.rb | 2 +-
..._key_authorized_user_to_authorized_user_uuid.rb | 2 +-
...042554_add_name_unique_index_to_repositories.rb | 2 +-
...20130617150007_add_is_trusted_to_api_clients.rb | 2 +-
.../20130626002829_add_is_active_to_users.rb | 2 +-
.../migrate/20130626022810_activate_all_admins.rb | 2 +-
.../api/db/migrate/20130627154537_create_traits.rb | 2 +-
.../api/db/migrate/20130627184333_create_humans.rb | 2 +-
...0130708163414_rename_foreign_uuid_attributes.rb | 2 +-
...708182912_rename_job_foreign_uuid_attributes.rb | 2 +-
.../20130708185153_rename_user_default_owner.rb | 2 +-
...3034_add_scopes_to_api_client_authorizations.rb | 2 +-
...ename_resource_limits_to_runtime_constraints.rb | 2 +-
.../20140117231056_normalize_collection_uuid.rb | 2 +-
.../20140124222114_fix_link_kind_underscores.rb | 2 +-
...malize_collection_uuids_in_script_parameters.rb | 2 +-
...317135600_add_nondeterministic_column_to_job.rb | 2 +-
...0547_separate_repository_from_script_version.rb | 2 +-
.../20140321191343_add_repository_column_to_job.rb | 2 +-
...140324024606_add_output_is_persistent_to_job.rb | 2 +-
.../migrate/20140325175653_remove_kind_columns.rb | 2 +-
.../db/migrate/20140402001908_add_system_group.rb | 2 +-
...20140407184311_rename_log_info_to_properties.rb | 2 +-
.../20140421140924_add_group_class_to_groups.rb | 2 +-
.../20140421151939_rename_auth_keys_user_index.rb | 2 +-
.../migrate/20140421151940_timestamps_not_null.rb | 2 +-
.../20140422011506_pipeline_instance_state.rb | 2 +-
.../20140423132913_add_object_owner_to_logs.rb | 2 +-
.../db/migrate/20140423133559_new_scope_format.rb | 2 +-
...0140501165548_add_unique_name_index_to_links.rb | 2 +-
.../migrate/20140519205916_create_keep_services.rb | 2 +-
...152921_add_description_to_pipeline_templates.rb | 2 +-
.../20140530200539_add_supplied_script_version.rb | 2 +-
.../20140601022548_remove_name_from_collections.rb | 2 +-
...e_active_and_success_from_pipeline_instances.rb | 2 +-
.../20140607150616_rename_folder_to_project.rb | 2 +-
.../20140611173003_add_docker_locator_to_jobs.rb | 2 +-
.../db/migrate/20140627210837_anonymous_group.rb | 2 +-
.../20140709172343_job_task_serial_qsequence.rb | 2 +-
.../db/migrate/20140714184006_empty_collection.rb | 2 +-
.../20140811184643_collection_use_regular_uuids.rb | 2 +-
.../20140817035914_add_unique_name_constraints.rb | 2 +-
...125735_add_not_null_constraint_to_group_name.rb | 2 +-
...826180337_remove_output_is_persistent_column.rb | 2 +-
.../migrate/20140828141043_job_priority_fixup.rb | 2 +-
...add_start_finish_time_to_tasks_and_pipelines.rb | 2 +-
...d_description_to_pipeline_instances_and_jobs.rb | 2 +-
...140918141529_change_user_owner_uuid_not_null.rb | 2 +-
.../20140918153541_add_properties_to_node.rb | 2 +-
.../db/migrate/20140918153705_add_state_to_job.rb | 2 +-
.../20140924091559_add_job_uuid_to_nodes.rb | 2 +-
...141111133038_add_arvados_sdk_version_to_jobs.rb | 2 +-
.../db/migrate/20141208164553_owner_uuid_index.rb | 2 +-
.../20141208174553_descriptions_are_strings.rb | 2 +-
.../20141208174653_collection_file_names.rb | 2 +-
.../api/db/migrate/20141208185217_search_index.rb | 2 +-
...0150122175935_no_description_in_search_index.rb | 2 +-
.../db/migrate/20150123142953_full_text_search.rb | 2 +-
...203180223_set_group_class_on_anonymous_group.rb | 2 +-
...206210804_all_users_can_read_anonymous_group.rb | 2 +-
...20150206230342_rename_replication_attributes.rb | 2 +-
...ollection_name_owner_unique_only_non_expired.rb | 2 +-
...tion_portable_data_hash_with_hinted_manifest.rb | 2 +-
...136_change_collection_expires_at_to_datetime.rb | 2 +-
.../20150317132720_add_username_to_users.rb | 2 +-
...backward_compatibility_for_user_repositories.rb | 2 +-
...5759_no_filenames_in_collection_search_index.rb | 2 +-
.../20150512193020_read_only_on_keep_services.rb | 2 +-
...50526180251_leading_space_on_full_text_index.rb | 2 +-
...0151202151426_create_containers_and_requests.rb | 2 +-
.../migrate/20151215134304_fix_containers_index.rb | 2 +-
.../20151229214707_add_exit_code_to_containers.rb | 2 +-
...8210629_add_uuid_to_api_client_authorization.rb | 2 +-
...209155729_add_uuid_to_api_token_search_index.rb | 2 +-
.../20160324144017_add_components_to_job.rb | 2 +-
.../20160506175108_add_auths_to_container.rb | 2 +-
...9143250_add_auth_and_lock_to_container_index.rb | 2 +-
.../db/migrate/20160808151559_create_workflows.rb | 2 +-
...9195557_add_script_parameters_digest_to_jobs.rb | 2 +-
...0819195725_populate_script_parameters_digest.rb | 2 +-
...160901210110_repair_script_parameters_digest.rb | 2 +-
...20160909181442_rename_workflow_to_definition.rb | 6 +-
.../migrate/20160926194129_add_container_count.rb | 2 +-
...71346_add_use_existing_to_container_requests.rb | 2 +-
...43147_add_scheduling_parameters_to_container.rb | 2 +-
...add_output_and_log_uuid_to_container_request.rb | 2 +-
..._log_uuids_to_container_request_search_index.rb | 2 +-
.../20161213172944_full_text_search_indexes.rb | 2 +-
...61222153434_split_expiry_to_trash_and_delete.rb | 2 +-
...090712_add_output_name_to_container_requests.rb | 2 +-
...utput_name_to_container_request_search_index.rb | 2 +-
...170105160301_add_output_name_to_cr_fts_index.rb | 2 +-
...t_finished_at_on_finished_pipeline_instances.rb | 2 +-
...s_and_workflow_def_in_full_text_search_index.rb | 2 +-
.../20170301225558_no_downgrade_after_json.rb | 2 +-
...0170319063406_serialized_columns_accept_null.rb | 2 +-
..._add_portable_data_hash_index_to_collections.rb | 2 +-
...0012505_add_output_ttl_to_container_requests.rb | 2 +-
...1_add_created_by_job_task_index_to_job_tasks.rb | 2 +-
...0170419173712_add_object_owner_index_to_logs.rb | 2 +-
...esting_container_index_to_container_requests.rb | 2 +-
.../db/migrate/20170628185847_jobs_yaml_to_json.rb | 2 +-
.../api/db/migrate/20170704160233_yaml_to_json.rb | 2 +-
.../20170706141334_json_collection_properties.rb | 2 +-
.../db/migrate/20170824202826_trashable_groups.rb | 2 +-
.../20170906224040_materialized_permission_view.rb | 2 +-
.../20171027183824_add_index_to_containers.rb | 2 +-
.../20171208203841_fix_trash_flag_follow.rb | 2 +-
...53352_add_gin_index_to_collection_properties.rb | 2 +-
...216203422_add_storage_classes_to_collections.rb | 2 +-
...180228220311_add_secret_mounts_to_containers.rb | 2 +-
...80313180114_change_container_priority_bigint.rb | 2 +-
...501182859_add_redirect_to_user_uuid_to_users.rb | 2 +-
...20180514135529_add_container_auth_uuid_index.rb | 2 +-
.../migrate/20180607175050_properties_to_jsonb.rb | 2 +-
.../20180608123145_add_properties_to_groups.rb | 2 +-
.../migrate/20180806133039_index_all_filenames.rb | 2 +-
...30357_add_pdh_and_trash_index_to_collections.rb | 2 +-
.../20180820132617_add_lock_index_to_containers.rb | 2 +-
...180820135808_drop_pdh_index_from_collections.rb | 2 +-
.../20180824152014_add_md5_index_to_containers.rb | 2 +-
...20180824155207_add_queue_index_to_containers.rb | 2 +-
...80904110712_add_runtime_status_to_containers.rb | 2 +-
...180913175443_add_version_info_to_collections.rb | 2 +-
...5335_set_current_version_uuid_on_collections.rb | 2 +-
.../20180917200000_replace_full_text_indexes.rb | 2 +-
.../20180917205609_recompute_file_names_index.rb | 2 +-
...001158_recreate_collection_unique_name_index.rb | 2 +-
...01175023_add_preserve_version_to_collections.rb | 2 +-
...rent_version_uuid_to_collection_search_index.rb | 2 +-
.../20181005192222_add_container_runtime_token.rb | 6 +-
...0181011184200_add_runtime_token_to_container.rb | 6 +-
...20181213183234_add_expression_index_to_links.rb | 6 +-
.../20190214214814_add_container_lock_count.rb | 6 +-
.../20190322174136_add_file_info_to_collection.rb | 2 +-
services/api/db/structure.sql | 575 ++++++++-------------
services/api/lib/can_be_an_owner.rb | 1 +
services/api/lib/enable_jobs_api.rb | 4 +-
services/api/lib/has_uuid.rb | 4 +-
services/api/lib/load_param.rb | 4 +-
services/api/script/fail-jobs.rb | 4 +-
services/api/script/get_anonymous_user_token.rb | 4 +-
services/api/script/salvage_collection.rb | 4 +-
services/api/script/setup-new-user.rb | 6 +-
services/api/test/fixtures/nodes.yml | 5 +
.../test/functional/application_controller_test.rb | 12 +-
.../api_client_authorizations_controller_test.rb | 26 +-
.../arvados/v1/collections_controller_test.rb | 164 +++---
.../v1/container_requests_controller_test.rb | 10 +-
.../arvados/v1/containers_controller_test.rb | 23 +-
.../api/test/functional/arvados/v1/filters_test.rb | 37 +-
.../arvados/v1/groups_controller_test.rb | 153 ++----
.../arvados/v1/job_reuse_controller_test.rb | 262 +++++-----
.../functional/arvados/v1/jobs_controller_test.rb | 182 +++----
.../arvados/v1/keep_disks_controller_test.rb | 12 +-
.../arvados/v1/keep_services_controller_test.rb | 4 +-
.../functional/arvados/v1/links_controller_test.rb | 74 +--
.../functional/arvados/v1/logs_controller_test.rb | 8 +-
.../functional/arvados/v1/nodes_controller_test.rb | 38 +-
.../v1/pipeline_instances_controller_test.rb | 6 +-
.../api/test/functional/arvados/v1/query_test.rb | 16 +-
.../arvados/v1/repositories_controller_test.rb | 4 +-
.../functional/arvados/v1/users_controller_test.rb | 102 ++--
.../arvados/v1/virtual_machines_controller_test.rb | 4 +-
.../functional/user_sessions_controller_test.rb | 6 +-
.../api_client_authorizations_api_test.rb | 52 +-
.../api_client_authorizations_scopes_test.rb | 22 +-
.../api/test/integration/collections_api_test.rb | 226 ++++----
.../integration/collections_performance_test.rb | 20 +-
.../api/test/integration/container_auth_test.rb | 46 +-
services/api/test/integration/cross_origin_test.rb | 12 +-
.../api/test/integration/crunch_dispatch_test.rb | 23 +-
.../api/test/integration/database_reset_test.rb | 29 +-
services/api/test/integration/errors_test.rb | 2 +-
services/api/test/integration/groups_test.rb | 149 ++++--
services/api/test/integration/jobs_api_test.rb | 55 +-
services/api/test/integration/keep_proxy_test.rb | 8 +-
.../api/test/integration/login_workflow_test.rb | 15 +-
.../api/test/integration/noop_deep_munge_test.rb | 35 +-
services/api/test/integration/permissions_test.rb | 430 ++++++++-------
services/api/test/integration/pipeline_test.rb | 10 +-
.../api/test/integration/reader_tokens_test.rb | 10 +-
services/api/test/integration/remote_user_test.rb | 116 +++--
services/api/test/integration/select_test.rb | 34 +-
.../test/integration/serialized_encoding_test.rb | 3 +-
.../api/test/integration/user_sessions_test.rb | 4 +-
services/api/test/integration/users_test.rb | 158 +++---
services/api/test/integration/valid_links_test.rb | 48 +-
services/api/test/performance/links_index_test.rb | 24 +-
services/api/test/performance/permission_test.rb | 5 +-
services/api/test/test_helper.rb | 14 +
services/api/test/unit/arvados_model_test.rb | 6 +-
services/api/test/unit/container_test.rb | 2 +
services/api/test/unit/crunch_dispatch_test.rb | 11 -
services/api/test/unit/job_test.rb | 5 +-
302 files changed, 2610 insertions(+), 2080 deletions(-)
copy apps/workbench/app/controllers/keep_services_controller.rb => services/api/app/models/application_record.rb (55%)
create mode 100644 services/api/app/models/jsonb_type.rb
copy services/api/{config/boot.rb => bin/bundle} (58%)
mode change 100644 => 100755
create mode 100755 services/api/bin/rails
copy apps/workbench/config/initializers/validate_wb2_url_config.rb => services/api/bin/rake (52%)
mode change 100644 => 100755
create mode 100755 services/api/bin/setup
create mode 100755 services/api/bin/update
create mode 100644 services/api/config/cable.yml
copy services/api/config/initializers/{mime_types.rb => application_controller_renderer.rb} (50%)
create mode 100644 services/api/config/initializers/assets.rb
create mode 100644 services/api/config/initializers/cookies_serializer.rb
create mode 100644 services/api/config/initializers/custom_types.rb
copy services/api/config/initializers/{mime_types.rb => filter_parameter_logging.rb} (52%)
create mode 100644 services/api/config/initializers/new_framework_defaults.rb
create mode 100644 services/api/config/puma.rb
create mode 100644 services/api/config/secrets.yml
create mode 100644 services/api/config/spring.rb
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commit b2addc8887d200219b44121c87a7a44bf4566e42
Merge: 4ec3bf28a 7e1bf9eba
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date: Mon Apr 8 11:14:15 2019 -0300
Merge branch '14873-api-rails5-upgrade'
Closes #14873
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>
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