[ARVADOS] updated: 1.3.0-723-gef9ad9c47

Git user git at public.curoverse.com
Tue Apr 16 13:55:17 UTC 2019


Summary of changes:
 apps/workbench/.gitignore                          |   2 +
 build/run-tests.sh                                 |  93 +++-
 doc/_config.yml                                    |   2 +
 doc/api/methods/collections.html.textile.liquid    |   2 +
 doc/install/arvbox.html.textile.liquid             |  37 +-
 .../install-dispatch-cloud.html.textile.liquid     | 200 +++++++
 .../install-nodemanager.html.textile.liquid        |   2 +-
 doc/sdk/java-v2/index.html.textile.liquid          |   5 +-
 lib/cloud/azure/azure.go                           |  17 +-
 lib/crunchstat/crunchstat.go                       |   9 +-
 lib/dispatchcloud/container/queue.go               |  14 +-
 lib/dispatchcloud/container/queue_test.go          |  10 +
 sdk/cwl/setup.py                                   |   1 +
 sdk/cwl/tests/federation/framework/check-exist.cwl |   5 +-
 sdk/cwl/tests/federation/framework/prepare.cwl     |   5 +-
 sdk/go/arvados/client.go                           |   2 +-
 sdk/python/tests/nginx.conf                        |   4 +
 sdk/python/tests/run_test_server.py                |   7 +-
 sdk/python/tests/test_arv_put.py                   |   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              |  35 +-
 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/database.yml.example           |   4 +-
 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  |  63 +++
 services/api/db/structure.sql                      | 577 ++++++++-------------
 services/api/lib/can_be_an_owner.rb                |   1 +
 services/api/lib/enable_jobs_api.rb                |   4 +-
 services/api/lib/group_pdhs.rb                     |  39 ++
 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/collections.yml         |  16 +
 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      | 237 ++++++---
 .../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/collection_test.rb          |  50 ++
 services/api/test/unit/container_test.rb           |   2 +
 services/api/test/unit/crunch_dispatch_test.rb     |  11 -
 services/api/test/unit/group_pdhs_test.rb          |  27 +
 services/api/test/unit/job_test.rb                 |   5 +-
 services/arv-git-httpd/gitolite_test.go            |   2 +-
 services/arv-git-httpd/integration_test.go         |   2 +-
 .../crunch-dispatch-local/crunch-dispatch-local.go |  40 +-
 .../crunch-dispatch-local_test.go                  |  22 +-
 services/crunch-run/crunchrun.go                   |   4 +-
 services/keep-web/server_test.go                   |  11 +-
 services/keepproxy/keepproxy.go                    |   4 +-
 services/login-sync/Gemfile                        |   2 +-
 services/login-sync/arvados-login-sync.gemspec     |   2 +-
 services/login-sync/bin/arvados-login-sync         |   6 +-
 services/login-sync/test/stubs.rb                  |  19 +-
 services/login-sync/test/test_add_user.rb          |   7 +-
 tools/arvbox/bin/arvbox                            |  57 +-
 tools/arvbox/lib/arvbox/docker/Dockerfile.base     |   4 +-
 tools/arvbox/lib/arvbox/docker/Dockerfile.dev      |   4 +-
 tools/arvbox/lib/arvbox/docker/api-setup.sh        |   3 -
 .../docker/service/slurmctld/log/main/.gitstub     |   0
 .../lib/arvbox/docker/service/slurmctld/log/run    |   1 -
 .../arvbox/lib/arvbox/docker/service/slurmctld/run |  34 --
 .../arvbox/docker/service/slurmd/log/main/.gitstub |   0
 .../lib/arvbox/docker/service/slurmd/log/run       |   1 -
 tools/arvbox/lib/arvbox/docker/service/slurmd/run  |   9 -
 .../lib/arvbox/docker/service/sso/run-service      |   6 +-
 tools/arvbox/lib/arvbox/docker/waitforpostgres.sh  |   8 +-
 349 files changed, 3396 insertions(+), 2248 deletions(-)
 create mode 100644 doc/install/install-dispatch-cloud.html.textile.liquid
 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
 create mode 100755 services/api/db/migrate/20190322174136_add_file_info_to_collection.rb
 create mode 100644 services/api/lib/group_pdhs.rb
 create mode 100644 services/api/test/unit/group_pdhs_test.rb
 delete mode 100644 tools/arvbox/lib/arvbox/docker/service/slurmctld/log/main/.gitstub
 delete mode 120000 tools/arvbox/lib/arvbox/docker/service/slurmctld/log/run
 delete mode 100755 tools/arvbox/lib/arvbox/docker/service/slurmctld/run
 delete mode 100644 tools/arvbox/lib/arvbox/docker/service/slurmd/log/main/.gitstub
 delete mode 120000 tools/arvbox/lib/arvbox/docker/service/slurmd/log/run
 delete mode 100755 tools/arvbox/lib/arvbox/docker/service/slurmd/run

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commit ef9ad9c4771dbcd90d884fdb2c55344434d59bd9
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Tue Apr 16 09:50:46 2019 -0400

    14670: Fix jdk and gradle links
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/doc/sdk/java-v2/index.html.textile.liquid b/doc/sdk/java-v2/index.html.textile.liquid
index 90e8cfe00..2693b6956 100644
--- a/doc/sdk/java-v2/index.html.textile.liquid
+++ b/doc/sdk/java-v2/index.html.textile.liquid
@@ -111,8 +111,8 @@ See "Javadoc":javadoc.html
 h2. Building the Arvados SDK
 
 Dependencies:
-* JDK for Java 8 or later https://www.oracle.com/technetwork/java/javase/downloads/index.html
-* Gradle https://gradle.org/install/
+* JDK for Java 8 or later "https://www.oracle.com/technetwork/java/javase/downloads/index.html":https://www.oracle.com/technetwork/java/javase/downloads/index.html
+* Gradle "https://gradle.org/install/":https://gradle.org/install/
 
 
 <notextile>
@@ -124,4 +124,3 @@ $ <code class="userinput">gradle jar</code>
 </pre>
 This will build the SDK and run all unit tests, then generate an Arvados Java sdk jar file in build/libs/arvados-java-2.0.0.jar
 </notextile>
-

commit 96fefe6c6fc2e3bd7e4efbb0b6a7dedb9221aff7
Merge: d66aa1521 a7c078164
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Fri Apr 12 10:56:24 2019 -0400

    Merge branch 'master' into 14670-new-java-sdk-docs
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>


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