[ARVADOS] updated: d53ae1523e74c6edcc89e1cd6285d2fe829d92c8
Git user
git at public.curoverse.com
Thu Jun 29 15:45:53 EDT 2017
Summary of changes:
.licenseignore | 13 +++
Makefile | 4 +
README.md | 4 +
apps/workbench/Gemfile | 4 +
apps/workbench/README.textile | 4 +
apps/workbench/Rakefile | 4 +
apps/workbench/app/assets/javascripts/add_group.js | 4 +
.../app/assets/javascripts/add_repository.js | 4 +
.../workbench/app/assets/javascripts/ajax_error.js | 4 +
.../app/assets/javascripts/angular_shim.js | 4 +
.../app/assets/javascripts/application.js | 4 +
.../app/assets/javascripts/arvados_client.js | 4 +
.../app/assets/javascripts/bootstrap.js.coffee | 6 +-
.../app/assets/javascripts/collections.js | 4 +
apps/workbench/app/assets/javascripts/dates.js | 4 +
.../app/assets/javascripts/edit_collection.js | 4 +
.../app/assets/javascripts/edit_collection_tags.js | 72 +++++++++++++++
apps/workbench/app/assets/javascripts/editable.js | 4 +
apps/workbench/app/assets/javascripts/event_log.js | 4 +
.../workbench/app/assets/javascripts/filterable.js | 4 +
.../app/assets/javascripts/infinite_scroll.js | 4 +
.../app/assets/javascripts/job_log_graph.js | 4 +
.../app/assets/javascripts/keep_disks.js.coffee | 4 +
.../app/assets/javascripts/link_to_remote.js | 4 +
.../workbench/app/assets/javascripts/log_viewer.js | 4 +
.../app/assets/javascripts/modal_pager.js | 4 +
.../app/assets/javascripts/permission_toggle.js | 4 +
.../app/assets/javascripts/pipeline_instances.js | 4 +
.../app/assets/javascripts/report_issue.js | 4 +
.../app/assets/javascripts/request_shell_access.js | 4 +
.../app/assets/javascripts/select_modal.js | 4 +
.../app/assets/javascripts/selection.js.erb | 4 +
apps/workbench/app/assets/javascripts/sizing.js | 4 +
apps/workbench/app/assets/javascripts/tab_panes.js | 4 +
.../app/assets/javascripts/upload_to_collection.js | 4 +
.../app/assets/javascripts/user_agreements.js | 4 +
apps/workbench/app/assets/javascripts/users.js | 4 +
.../app/assets/javascripts/work_unit_component.js | 4 +
.../app/assets/javascripts/work_unit_log.js | 4 +
.../stylesheets/api_client_authorizations.css.scss | 4 +
.../app/assets/stylesheets/application.css.scss | 4 +
.../assets/stylesheets/authorized_keys.css.scss | 4 +
.../app/assets/stylesheets/badges.css.scss | 4 +
.../app/assets/stylesheets/cards.css.scss | 4 +
.../app/assets/stylesheets/collections.css.scss | 8 ++
.../app/assets/stylesheets/groups.css.scss | 4 +
.../app/assets/stylesheets/humans.css.scss | 4 +
.../app/assets/stylesheets/job_tasks.css.scss | 4 +
.../workbench/app/assets/stylesheets/jobs.css.scss | 4 +
.../app/assets/stylesheets/keep_disks.css.scss | 4 +
.../app/assets/stylesheets/links.css.scss | 4 +
.../app/assets/stylesheets/loading.css.scss.erb | 4 +
.../app/assets/stylesheets/log_viewer.scss | 4 +
.../workbench/app/assets/stylesheets/logs.css.scss | 4 +
.../app/assets/stylesheets/nodes.css.scss | 4 +
.../assets/stylesheets/pipeline_instances.css.scss | 4 +
.../assets/stylesheets/pipeline_templates.css.scss | 4 +
.../app/assets/stylesheets/projects.css.scss | 4 +
.../app/assets/stylesheets/repositories.css.scss | 4 +
.../app/assets/stylesheets/scaffolds.css.scss | 4 +
.../app/assets/stylesheets/select_modal.css.scss | 4 +
.../app/assets/stylesheets/sessions.css.scss | 4 +
.../app/assets/stylesheets/specimens.css.scss | 4 +
.../app/assets/stylesheets/traits.css.scss | 4 +
.../assets/stylesheets/user_agreements.css.scss | 4 +
.../app/assets/stylesheets/users.css.scss | 4 +
.../assets/stylesheets/virtual_machines.css.scss | 4 +
.../app/controllers/actions_controller.rb | 4 +
.../api_client_authorizations_controller.rb | 4 +
.../app/controllers/application_controller.rb | 4 +
.../app/controllers/authorized_keys_controller.rb | 4 +
.../app/controllers/collections_controller.rb | 30 ++++++-
.../controllers/container_requests_controller.rb | 4 +
.../app/controllers/containers_controller.rb | 4 +
.../workbench/app/controllers/groups_controller.rb | 4 +
.../workbench/app/controllers/humans_controller.rb | 4 +
.../app/controllers/job_tasks_controller.rb | 4 +
apps/workbench/app/controllers/jobs_controller.rb | 4 +
.../app/controllers/keep_disks_controller.rb | 4 +
.../app/controllers/keep_services_controller.rb | 4 +
apps/workbench/app/controllers/links_controller.rb | 4 +
apps/workbench/app/controllers/logs_controller.rb | 4 +
apps/workbench/app/controllers/nodes_controller.rb | 4 +
.../controllers/pipeline_instances_controller.rb | 4 +
.../controllers/pipeline_templates_controller.rb | 4 +
.../app/controllers/projects_controller.rb | 4 +
.../app/controllers/repositories_controller.rb | 4 +
.../workbench/app/controllers/search_controller.rb | 4 +
.../app/controllers/sessions_controller.rb | 4 +
.../app/controllers/specimens_controller.rb | 4 +
.../workbench/app/controllers/traits_controller.rb | 4 +
.../app/controllers/trash_items_controller.rb | 4 +
.../app/controllers/user_agreements_controller.rb | 4 +
apps/workbench/app/controllers/users_controller.rb | 34 +++----
.../app/controllers/virtual_machines_controller.rb | 4 +
.../app/controllers/websocket_controller.rb | 4 +
.../controllers/work_unit_templates_controller.rb | 4 +
.../app/controllers/work_units_controller.rb | 4 +
.../app/controllers/workflows_controller.rb | 4 +
apps/workbench/app/helpers/application_helper.rb | 4 +
.../app/helpers/arvados_api_client_helper.rb | 4 +
apps/workbench/app/helpers/collections_helper.rb | 4 +
.../app/helpers/pipeline_components_helper.rb | 4 +
.../app/helpers/pipeline_instances_helper.rb | 4 +
apps/workbench/app/helpers/provenance_helper.rb | 4 +
apps/workbench/app/helpers/version_helper.rb | 4 +
apps/workbench/app/mailers/issue_reporter.rb | 4 +
.../app/mailers/request_shell_access_reporter.rb | 4 +
.../app/models/api_client_authorization.rb | 4 +
apps/workbench/app/models/arvados_api_client.rb | 4 +
apps/workbench/app/models/arvados_base.rb | 4 +
apps/workbench/app/models/arvados_resource_list.rb | 4 +
apps/workbench/app/models/authorized_key.rb | 4 +
apps/workbench/app/models/collection.rb | 6 +-
apps/workbench/app/models/container.rb | 4 +
apps/workbench/app/models/container_request.rb | 4 +
apps/workbench/app/models/container_work_unit.rb | 4 +
apps/workbench/app/models/group.rb | 4 +
apps/workbench/app/models/human.rb | 4 +
apps/workbench/app/models/job.rb | 4 +
apps/workbench/app/models/job_task.rb | 4 +
apps/workbench/app/models/job_task_work_unit.rb | 4 +
apps/workbench/app/models/job_work_unit.rb | 4 +
apps/workbench/app/models/keep_disk.rb | 4 +
apps/workbench/app/models/keep_service.rb | 4 +
apps/workbench/app/models/link.rb | 4 +
apps/workbench/app/models/log.rb | 4 +
apps/workbench/app/models/node.rb | 4 +
apps/workbench/app/models/pipeline_instance.rb | 4 +
.../app/models/pipeline_instance_work_unit.rb | 4 +
apps/workbench/app/models/pipeline_template.rb | 4 +
apps/workbench/app/models/proxy_work_unit.rb | 4 +
apps/workbench/app/models/repository.rb | 4 +
apps/workbench/app/models/specimen.rb | 4 +
apps/workbench/app/models/trait.rb | 4 +
apps/workbench/app/models/user.rb | 4 +
apps/workbench/app/models/user_agreement.rb | 4 +
apps/workbench/app/models/virtual_machine.rb | 4 +
apps/workbench/app/models/work_unit.rb | 4 +
apps/workbench/app/models/workflow.rb | 4 +
.../api_client_authorizations/_show_help.html.erb | 4 +
apps/workbench/app/views/application/404.html.erb | 4 +
apps/workbench/app/views/application/404.json.erb | 4 +
.../views/application/_arvados_attr_value.html.erb | 4 +
.../app/views/application/_arvados_object.html.erb | 4 +
.../application/_arvados_object_attr.html.erb | 4 +
.../application/_breadcrumb_page_name.html.erb | 4 +
.../app/views/application/_breadcrumbs.html.erb | 4 +
.../views/application/_browser_unsupported.html | 4 +
.../app/views/application/_choose.html.erb | 4 +
.../workbench/app/views/application/_choose.js.erb | 4 +
.../app/views/application/_choose_rows.html.erb | 4 +
.../app/views/application/_content.html.erb | 4 +
.../app/views/application/_content_layout.html.erb | 4 +
.../application/_create_new_object_button.html.erb | 4 +
.../application/_delete_object_button.html.erb | 4 +
.../app/views/application/_job_progress.html.erb | 4 +
.../app/views/application/_loading.html.erb | 4 +
.../app/views/application/_loading_modal.html.erb | 4 +
.../application/_name_and_description.html.erb | 4 +
.../views/application/_object_description.html.erb | 4 +
.../app/views/application/_object_name.html.erb | 4 +
.../app/views/application/_paging.html.erb | 4 +
.../views/application/_pipeline_progress.html.erb | 4 +
.../application/_pipeline_status_label.html.erb | 4 +
.../views/application/_projects_tree_menu.html.erb | 4 +
.../app/views/application/_report_error.html.erb | 4 +
.../views/application/_report_issue_popup.html.erb | 4 +
.../views/application/_selection_checkbox.html.erb | 4 +
.../app/views/application/_show_advanced.html.erb | 4 +
.../_show_advanced_api_response.html.erb | 4 +
.../_show_advanced_cli_example.html.erb | 4 +
.../_show_advanced_curl_example.html.erb | 4 +
.../application/_show_advanced_metadata.html.erb | 4 +
.../_show_advanced_python_example.html.erb | 4 +
.../app/views/application/_show_api.html.erb | 4 +
.../views/application/_show_attributes.html.erb | 4 +
.../application/_show_autoselect_text.html.erb | 4 +
.../views/application/_show_home_button.html.erb | 4 +
.../views/application/_show_object_button.html.erb | 4 +
.../_show_object_description_cell.html.erb | 4 +
.../app/views/application/_show_recent.html.erb | 4 +
.../app/views/application/_show_sharing.html.erb | 4 +
.../app/views/application/_show_star.html.erb | 4 +
.../application/_show_text_with_locators.html.erb | 4 +
.../app/views/application/_svg_div.html.erb | 4 +
.../views/application/_title_and_buttons.html.erb | 4 +
.../app/views/application/api_error.html.erb | 4 +
.../app/views/application/api_error.json.erb | 4 +
.../workbench/app/views/application/destroy.js.erb | 4 +
.../workbench/app/views/application/error.html.erb | 4 +
.../workbench/app/views/application/error.json.erb | 4 +
.../workbench/app/views/application/index.html.erb | 4 +
.../views/application/report_issue_popup.js.erb | 4 +
apps/workbench/app/views/application/show.html.erb | 4 +
apps/workbench/app/views/application/star.js.erb | 4 +
.../app/views/authorized_keys/create.js.erb | 4 +
.../app/views/authorized_keys/edit.html.erb | 4 +
.../app/views/collections/_choose_rows.html.erb | 4 +
.../collections/_create_new_object_button.html.erb | 4 +
.../collections/_extra_tab_line_buttons.html.erb | 4 +
.../app/views/collections/_index_tbody.html.erb | 4 +
.../app/views/collections/_sharing_button.html.erb | 4 +
.../collections/_show_chooser_preview.html.erb | 4 +
.../app/views/collections/_show_files.html.erb | 6 +-
.../collections/_show_provenance_graph.html.erb | 4 +
.../app/views/collections/_show_recent.html.erb | 4 +
.../collections/_show_source_summary.html.erb | 4 +
.../app/views/collections/_show_tag_rows.html.erb | 35 ++++++++
.../app/views/collections/_show_tags.html.erb | 52 +++++++++++
.../app/views/collections/_show_upload.html.erb | 4 +
.../app/views/collections/_show_used_by.html.erb | 4 +
.../workbench/app/views/collections/graph.html.erb | 4 +
.../app/views/collections/hash_matches.html.erb | 4 +
.../workbench/app/views/collections/index.html.erb | 4 +
apps/workbench/app/views/collections/index.js.erb | 4 +
.../app/views/collections/save_tags.js.erb | 7 ++
.../app/views/collections/sharing_popup.js.erb | 4 +
apps/workbench/app/views/collections/show.html.erb | 4 +
.../app/views/collections/show_file_links.html.erb | 4 +
apps/workbench/app/views/collections/tags.js.erb | 5 ++
.../_extra_tab_line_buttons.html.erb | 4 +
.../_name_and_description.html.erb | 4 +
.../views/container_requests/_show_inputs.html.erb | 4 +
.../views/container_requests/_show_log.html.erb | 4 +
.../container_requests/_show_provenance.html.erb | 4 +
.../views/container_requests/_show_recent.html.erb | 4 +
.../container_requests/_show_recent_rows.html.erb | 4 +
.../views/container_requests/_show_status.html.erb | 4 +
.../app/views/container_requests/index.html.erb | 4 +
.../app/views/containers/_show_log.html.erb | 4 +
.../app/views/containers/_show_status.html.erb | 4 +
.../_getting_started_popup.html.erb | 4 +
.../app/views/groups/_choose_rows.html.erb | 4 +
.../app/views/groups/_show_recent.html.erb | 4 +
.../app/views/issue_reporter/send_report.text.erb | 4 +
.../views/jobs/_create_new_object_button.html.erb | 4 +
.../jobs/_rerun_job_with_options_popup.html.erb | 4 +
.../app/views/jobs/_show_details.html.erb | 4 +
.../app/views/jobs/_show_job_buttons.html.erb | 4 +
apps/workbench/app/views/jobs/_show_log.html.erb | 4 +
.../jobs/_show_object_description_cell.html.erb | 4 +
.../app/views/jobs/_show_provenance.html.erb | 4 +
.../workbench/app/views/jobs/_show_recent.html.erb | 4 +
.../workbench/app/views/jobs/_show_status.html.erb | 4 +
apps/workbench/app/views/jobs/show.html.erb | 4 +
.../app/views/keep_disks/_content_layout.html.erb | 4 +
.../app/views/layouts/application.html.erb | 4 +
apps/workbench/app/views/layouts/body.html.erb | 4 +
.../app/views/links/_breadcrumb_page_name.html.erb | 4 +
.../_collections_notification.html.erb | 4 +
.../notifications/_jobs_notification.html.erb | 4 +
.../notifications/_pipelines_notification.html.erb | 4 +
.../notifications/_ssh_key_notification.html.erb | 4 +
.../pipeline_instances/_component_labels.html.erb | 4 +
.../pipeline_instances/_running_component.html.erb | 4 +
.../pipeline_instances/_show_compare.html.erb | 4 +
.../pipeline_instances/_show_components.html.erb | 4 +
.../_show_components_editable.html.erb | 4 +
.../_show_components_json.html.erb | 4 +
.../_show_components_running.html.erb | 4 +
.../views/pipeline_instances/_show_graph.html.erb | 4 +
.../views/pipeline_instances/_show_inputs.html.erb | 4 +
.../views/pipeline_instances/_show_log.html.erb | 4 +
.../_show_object_description_cell.html.erb | 4 +
.../views/pipeline_instances/_show_recent.html.erb | 4 +
.../pipeline_instances/_show_recent_rows.html.erb | 4 +
.../pipeline_instances/_show_tab_buttons.html.erb | 4 +
.../app/views/pipeline_instances/compare.html.erb | 4 +
.../app/views/pipeline_instances/index.html.erb | 4 +
.../app/views/pipeline_instances/show.html.erb | 4 +
.../app/views/pipeline_instances/show.js.erb | 4 +
.../views/pipeline_templates/_choose_rows.html.erb | 4 +
.../pipeline_templates/_show_attributes.html.erb | 4 +
.../_show_chooser_preview.html.erb | 4 +
.../pipeline_templates/_show_components.html.erb | 4 +
.../pipeline_templates/_show_pipelines.html.erb | 4 +
.../views/pipeline_templates/_show_recent.html.erb | 4 +
.../app/views/pipeline_templates/show.html.erb | 4 +
apps/workbench/app/views/projects/_choose.html.erb | 4 +
.../views/projects/_compute_node_status.html.erb | 4 +
.../views/projects/_compute_node_summary.html.erb | 4 +
.../projects/_index_jobs_and_pipelines.html.erb | 4 +
.../app/views/projects/_index_projects.html.erb | 4 +
.../views/projects/_show_contents_rows.html.erb | 4 +
.../app/views/projects/_show_dashboard.html.erb | 4 +
.../views/projects/_show_data_collections.html.erb | 4 +
.../app/views/projects/_show_description.html.erb | 4 +
.../app/views/projects/_show_featured.html.erb | 4 +
.../views/projects/_show_other_objects.html.erb | 4 +
.../projects/_show_pipeline_templates.html.erb | 4 +
.../_show_pipelines_and_processes.html.erb | 4 +
.../app/views/projects/_show_processes.html.erb | 4 +
.../app/views/projects/_show_subprojects.html.erb | 4 +
.../app/views/projects/_show_tab_contents.html.erb | 4 +
.../app/views/projects/_show_workflows.html.erb | 4 +
apps/workbench/app/views/projects/index.html.erb | 4 +
apps/workbench/app/views/projects/public.html.erb | 4 +
.../app/views/projects/remove_items.js.erb | 4 +
apps/workbench/app/views/projects/show.html.erb | 4 +
.../workbench/app/views/projects/tab_counts.js.erb | 4 +
.../repositories/_repository_breadcrumbs.html.erb | 4 +
.../app/views/repositories/_show_help.html.erb | 4 +
.../app/views/repositories/show_blob.html.erb | 4 +
.../app/views/repositories/show_commit.html.erb | 4 +
.../app/views/repositories/show_tree.html.erb | 4 +
.../send_request.text.erb | 4 +
.../app/views/search/_choose_rows.html.erb | 3 +
apps/workbench/app/views/sessions/index.html.erb | 4 +
.../trash_items/_create_new_object_button.html.erb | 4 +
.../views/trash_items/_show_recent_trash.html.erb | 4 +
.../views/trash_items/_show_trash_rows.html.erb | 4 +
.../app/views/trash_items/_untrash_item.html.erb | 4 +
.../workbench/app/views/trash_items/index.html.erb | 4 +
.../app/views/trash_items/untrash_items.js.erb | 4 +
.../app/views/user_agreements/index.html.erb | 4 +
.../app/views/users/_add_group_modal.html.erb | 4 +
.../app/views/users/_add_repository_modal.html.erb | 4 +
.../app/views/users/_add_ssh_key_popup.html.erb | 4 +
.../app/views/users/_choose_rows.html.erb | 4 +
.../views/users/_create_new_object_button.html.erb | 4 +
.../app/views/users/_current_token.html.erb | 4 +
apps/workbench/app/views/users/_home.html.erb | 4 +
.../app/views/users/_repositories.html.erb | 100 +++++++++++----------
.../app/views/users/_setup_popup.html.erb | 4 +
.../app/views/users/_show_activity.html.erb | 4 +
.../workbench/app/views/users/_show_admin.html.erb | 4 +
apps/workbench/app/views/users/_ssh_keys.html.erb | 4 +
apps/workbench/app/views/users/_tables.html.erb | 4 +
.../app/views/users/_virtual_machines.html.erb | 4 +
apps/workbench/app/views/users/activity.html.erb | 4 +
apps/workbench/app/views/users/add_ssh_key.js.erb | 4 +
.../app/views/users/add_ssh_key_popup.js.erb | 4 +
.../app/views/users/current_token.html.erb | 4 +
apps/workbench/app/views/users/home.html.erb | 4 +
apps/workbench/app/views/users/home.js.erb | 4 +
apps/workbench/app/views/users/inactive.html.erb | 4 +
apps/workbench/app/views/users/profile.html.erb | 4 +
.../app/views/users/repositories.html.erb | 4 +
.../app/views/users/request_shell_access.js | 4 +
apps/workbench/app/views/users/setup.js.erb | 4 +
apps/workbench/app/views/users/setup_popup.js.erb | 4 +
apps/workbench/app/views/users/ssh_keys.html.erb | 4 +
apps/workbench/app/views/users/storage.html.erb | 4 +
.../app/views/users/virtual_machines.html.erb | 4 +
apps/workbench/app/views/users/welcome.html.erb | 4 +
.../app/views/virtual_machines/_show_help.html.erb | 4 +
.../app/views/virtual_machines/webshell.html.erb | 4 +
apps/workbench/app/views/websocket/index.html.erb | 4 +
.../views/work_units/_component_detail.html.erb | 4 +
.../app/views/work_units/_progress.html.erb | 4 +
.../views/work_units/_show_all_processes.html.erb | 4 +
.../work_units/_show_all_processes_rows.html.erb | 4 +
.../app/views/work_units/_show_child.html.erb | 4 +
.../app/views/work_units/_show_component.html.erb | 4 +
.../app/views/work_units/_show_log.html.erb | 4 +
.../app/views/work_units/_show_log_link.html.erb | 4 +
.../app/views/work_units/_show_output.html.erb | 4 +
.../app/views/work_units/_show_outputs.html.erb | 4 +
.../app/views/work_units/_show_status.html.erb | 4 +
.../app/views/work_units/_show_table_data.html.erb | 4 +
apps/workbench/app/views/work_units/index.html.erb | 4 +
.../views/workflows/_show_chooser_preview.html.erb | 4 +
.../app/views/workflows/_show_definition.html.erb | 4 +
.../app/views/workflows/_show_recent.html.erb | 4 +
apps/workbench/app/views/workflows/show.html.erb | 4 +
apps/workbench/config.ru | 4 +
apps/workbench/config/application.default.yml | 4 +
apps/workbench/config/application.rb | 4 +
apps/workbench/config/application.yml.example | 4 +
apps/workbench/config/boot.rb | 4 +
apps/workbench/config/database.yml | 4 +
apps/workbench/config/environment.rb | 4 +
.../config/environments/development.rb.example | 4 +
.../config/environments/production.rb.example | 4 +
apps/workbench/config/environments/test.rb.example | 4 +
.../config/initializers/backtrace_silencers.rb | 4 +
apps/workbench/config/initializers/inflections.rb | 4 +
apps/workbench/config/initializers/lograge.rb | 4 +
apps/workbench/config/initializers/mime_types.rb | 4 +
.../config/initializers/rack_mini_profile.rb | 4 +
apps/workbench/config/initializers/redcloth.rb | 4 +
.../config/initializers/secret_token.rb.example | 4 +
.../workbench/config/initializers/session_store.rb | 4 +
apps/workbench/config/initializers/time_format.rb | 4 +
.../config/initializers/wrap_parameters.rb | 4 +
apps/workbench/config/load_config.rb | 4 +
apps/workbench/config/locales/en.yml | 4 +
apps/workbench/config/piwik.yml.example | 4 +
apps/workbench/config/routes.rb | 6 ++
apps/workbench/db/schema.rb | 4 +
apps/workbench/db/seeds.rb | 4 +
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services/keep-web/handler.go | 4 +
services/keep-web/handler_test.go | 4 +
services/keep-web/keep-web.service | 4 +
services/keep-web/main.go | 4 +
services/keep-web/ranges_test.go | 4 +
services/keep-web/server.go | 4 +
services/keep-web/server_test.go | 4 +
services/keep-web/status_test.go | 4 +
services/keep-web/usage.go | 4 +
services/keep/tools/traffic_test.py | 3 +
services/keepproxy/keepproxy.go | 4 +
services/keepproxy/keepproxy.service | 4 +
services/keepproxy/keepproxy_test.go | 4 +
services/keepproxy/pkg-extras/etc/init.d/keepproxy | 4 +
services/keepproxy/proxy_client.go | 4 +
services/keepproxy/usage.go | 4 +
services/keepstore/azure_blob_volume.go | 4 +
services/keepstore/azure_blob_volume_test.go | 4 +
services/keepstore/bufferpool.go | 4 +
services/keepstore/bufferpool_test.go | 4 +
services/keepstore/collision.go | 4 +
services/keepstore/collision_test.go | 4 +
services/keepstore/config.go | 4 +
services/keepstore/config_test.go | 4 +
services/keepstore/count.go | 4 +
services/keepstore/deprecated.go | 4 +
services/keepstore/gocheck_test.go | 4 +
services/keepstore/handler_test.go | 4 +
services/keepstore/handlers.go | 4 +
.../keepstore/handlers_with_generic_volume_test.go | 4 +
services/keepstore/keepstore.go | 4 +
services/keepstore/keepstore.service | 4 +
services/keepstore/keepstore_test.go | 4 +
services/keepstore/logging_router.go | 4 +
services/keepstore/logging_router_test.go | 4 +
services/keepstore/mock_mutex_for_test.go | 4 +
services/keepstore/mounts_test.go | 4 +
services/keepstore/perms.go | 4 +
services/keepstore/perms_test.go | 4 +
services/keepstore/pipe_adapters.go | 4 +
services/keepstore/pull_worker.go | 4 +
services/keepstore/pull_worker_integration_test.go | 4 +
services/keepstore/pull_worker_test.go | 4 +
services/keepstore/s3_volume.go | 4 +
services/keepstore/s3_volume_test.go | 4 +
services/keepstore/stats_ticker.go | 4 +
services/keepstore/status_test.go | 4 +
services/keepstore/trash_worker.go | 4 +
services/keepstore/trash_worker_test.go | 4 +
services/keepstore/usage.go | 4 +
services/keepstore/volume.go | 4 +
services/keepstore/volume_generic_test.go | 4 +
services/keepstore/volume_test.go | 4 +
services/keepstore/volume_unix.go | 4 +
services/keepstore/volume_unix_test.go | 4 +
services/keepstore/work_queue.go | 4 +
services/keepstore/work_queue_test.go | 4 +
services/login-sync/Gemfile | 4 +
services/login-sync/Rakefile | 4 +
services/login-sync/arvados-login-sync.gemspec | 4 +
services/login-sync/bin/arvados-login-sync | 3 +
services/login-sync/test/binstub_new_user/useradd | 3 +
services/login-sync/test/stubs.rb | 4 +
services/login-sync/test/test_add_user.rb | 4 +
services/nodemanager/MANIFEST.in | 4 +
services/nodemanager/README.rst | 4 +
services/nodemanager/arvnodeman/__init__.py | 3 +
services/nodemanager/arvnodeman/_version.py | 4 +
services/nodemanager/arvnodeman/baseactor.py | 4 +
services/nodemanager/arvnodeman/clientactor.py | 3 +
.../nodemanager/arvnodeman/computenode/__init__.py | 3 +
.../arvnodeman/computenode/dispatch/__init__.py | 3 +
.../arvnodeman/computenode/dispatch/slurm.py | 3 +
.../arvnodeman/computenode/dispatch/transitions.py | 4 +
.../arvnodeman/computenode/driver/__init__.py | 3 +
.../arvnodeman/computenode/driver/azure.py | 3 +
.../arvnodeman/computenode/driver/dummy.py | 3 +
.../arvnodeman/computenode/driver/ec2.py | 3 +
.../arvnodeman/computenode/driver/gce.py | 7 ++
services/nodemanager/arvnodeman/config.py | 3 +
services/nodemanager/arvnodeman/daemon.py | 3 +
services/nodemanager/arvnodeman/jobqueue.py | 5 ++
services/nodemanager/arvnodeman/launcher.py | 3 +
services/nodemanager/arvnodeman/nodelist.py | 5 +-
services/nodemanager/arvnodeman/status.py | 4 +
services/nodemanager/arvnodeman/test/__init__.py | 4 +
.../nodemanager/arvnodeman/test/fake_driver.py | 63 ++++++++++++-
services/nodemanager/arvnodeman/timedcallback.py | 3 +
services/nodemanager/bin/arvados-node-manager | 3 +
services/nodemanager/doc/azure.example.cfg | 4 +
services/nodemanager/doc/ec2.example.cfg | 4 +
services/nodemanager/doc/gce.example.cfg | 4 +
services/nodemanager/doc/local.example.cfg | 4 +
services/nodemanager/setup.py | 3 +
services/nodemanager/tests/__init__.py | 3 +
.../{fake.cfg.template => fake_azure.cfg.template} | 4 +
.../{fake.cfg.template => fake_ec2.cfg.template} | 48 +++-------
.../{fake.cfg.template => fake_gce.cfg.template} | 53 +++--------
services/nodemanager/tests/integration_test.py | 53 +++++++++--
services/nodemanager/tests/test_arguments.py | 3 +
services/nodemanager/tests/test_clientactor.py | 3 +
services/nodemanager/tests/test_computenode.py | 3 +
.../nodemanager/tests/test_computenode_dispatch.py | 3 +
.../tests/test_computenode_dispatch_slurm.py | 3 +
.../nodemanager/tests/test_computenode_driver.py | 3 +
.../tests/test_computenode_driver_azure.py | 3 +
.../tests/test_computenode_driver_ec2.py | 3 +
.../tests/test_computenode_driver_gce.py | 3 +
services/nodemanager/tests/test_config.py | 3 +
services/nodemanager/tests/test_daemon.py | 3 +
services/nodemanager/tests/test_failure.py | 3 +
services/nodemanager/tests/test_jobqueue.py | 3 +
services/nodemanager/tests/test_nodelist.py | 3 +
services/nodemanager/tests/test_status.py | 3 +
services/nodemanager/tests/test_timedcallback.py | 3 +
services/nodemanager/tests/testutil.py | 3 +
services/ws/arvados-ws.service | 4 +
services/ws/config.go | 6 ++
services/ws/doc.go | 4 +
services/ws/event.go | 5 ++
services/ws/event_source.go | 11 +++
services/ws/event_source_test.go | 6 ++
services/ws/event_test.go | 4 +
services/ws/gocheck_test.go | 4 +
services/ws/handler.go | 4 +
services/ws/main.go | 4 +
services/ws/permission.go | 4 +
services/ws/permission_test.go | 4 +
services/ws/router.go | 56 ++++++++++--
services/ws/server.go | 4 +
services/ws/server_test.go | 69 +++++++++++---
services/ws/session.go | 4 +
services/ws/session_v0.go | 5 ++
services/ws/session_v0_test.go | 14 ++-
services/ws/session_v1.go | 4 +
tools/arvbash/arvbash.sh | 4 +
tools/arvbox/bin/arvbox | 3 +
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 4 +
tools/arvbox/lib/arvbox/docker/Dockerfile.demo | 4 +
tools/arvbox/lib/arvbox/docker/Dockerfile.dev | 4 +
tools/arvbox/lib/arvbox/docker/api-setup.sh | 3 +
.../lib/arvbox/docker/application_yml_override.py | 3 +
tools/arvbox/lib/arvbox/docker/common.sh | 4 +
tools/arvbox/lib/arvbox/docker/createusers.sh | 3 +
tools/arvbox/lib/arvbox/docker/crunch-setup.sh | 3 +
tools/arvbox/lib/arvbox/docker/fuse.conf | 4 +
tools/arvbox/lib/arvbox/docker/gitolite.rc | 4 +
tools/arvbox/lib/arvbox/docker/keep-setup.sh | 3 +
tools/arvbox/lib/arvbox/docker/logger | 4 +
tools/arvbox/lib/arvbox/docker/runsu.sh | 3 +
.../lib/arvbox/docker/service/api/run-service | 3 +
.../docker/service/arv-git-httpd/run-service | 3 +
.../service/crunch-dispatch-local/run-service | 11 ++-
.../docker/service/crunch-dispatch0/run-service | 4 +
.../docker/service/crunch-dispatch1/run-service | 4 +
.../lib/arvbox/docker/service/doc/run-service | 3 +
tools/arvbox/lib/arvbox/docker/service/docker/run | 3 +
.../lib/arvbox/docker/service/gitolite/run-service | 3 +
.../lib/arvbox/docker/service/keep-web/run-service | 3 +
.../arvbox/docker/service/keepproxy/run-service | 3 +
.../arvbox/docker/service/keepstore0/run-service | 4 +
.../arvbox/docker/service/keepstore1/run-service | 4 +
.../arvbox/lib/arvbox/docker/service/postgres/run | 3 +
.../lib/arvbox/docker/service/postgres/run-service | 3 +
.../lib/arvbox/docker/service/ready/run-service | 3 +
tools/arvbox/lib/arvbox/docker/service/sdk/run | 4 +
.../lib/arvbox/docker/service/sdk/run-service | 5 ++
.../arvbox/lib/arvbox/docker/service/slurmctld/run | 3 +
tools/arvbox/lib/arvbox/docker/service/slurmd/run | 3 +
tools/arvbox/lib/arvbox/docker/service/ssh/run | 3 +
.../lib/arvbox/docker/service/sso/run-service | 3 +
tools/arvbox/lib/arvbox/docker/service/vm/run | 4 +
.../lib/arvbox/docker/service/vm/run-service | 3 +
.../arvbox/docker/service/websockets/run-service | 3 +
.../arvbox/lib/arvbox/docker/service/workbench/run | 4 +
.../arvbox/docker/service/workbench/run-service | 3 +
tools/arvbox/lib/arvbox/docker/waitforpostgres.sh | 4 +
tools/crunchstat-summary/MANIFEST.in | 4 +
tools/crunchstat-summary/bin/crunchstat-summary | 3 +
.../crunchstat_summary/__init__.py | 4 +
.../crunchstat_summary/chartjs.js | 4 +
.../crunchstat_summary/chartjs.py | 4 +
.../crunchstat_summary/command.py | 4 +
.../crunchstat_summary/reader.py | 4 +
.../crunchstat_summary/summarizer.py | 4 +
tools/crunchstat-summary/setup.py | 3 +
tools/crunchstat-summary/tests/test_examples.py | 4 +
tools/keep-block-check/keep-block-check.go | 4 +
tools/keep-block-check/keep-block-check_test.go | 4 +
tools/keep-exercise/keep-exercise.go | 4 +
tools/keep-rsync/keep-rsync.go | 4 +
tools/keep-rsync/keep-rsync_test.go | 4 +
1837 files changed, 8435 insertions(+), 409 deletions(-)
create mode 100644 apps/workbench/app/assets/javascripts/edit_collection_tags.js
create mode 100644 apps/workbench/app/views/collections/_show_tag_rows.html.erb
create mode 100644 apps/workbench/app/views/collections/_show_tags.html.erb
create mode 100644 apps/workbench/app/views/collections/save_tags.js.erb
create mode 100644 apps/workbench/app/views/collections/tags.js.erb
create mode 100644 apps/workbench/test/controllers/trash_items_controller_test.rb
create mode 100644 doc/images/trash-button-topnav.png
create mode 100644 doc/user/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid
create mode 100644 sdk/cwl/tests/noreuse.cwl
delete mode 100644 sdk/go/auth/basic_auth_go13.go
delete mode 100644 sdk/go/auth/basic_auth_go14.go
delete mode 100644 sdk/go/auth/basic_auth_test.go
copy services/nodemanager/tests/{fake.cfg.template => fake_azure.cfg.template} (98%)
copy services/nodemanager/tests/{fake.cfg.template => fake_ec2.cfg.template} (78%)
rename services/nodemanager/tests/{fake.cfg.template => fake_gce.cfg.template} (77%)
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Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit d53ae1523e74c6edcc89e1cd6285d2fe829d92c8
Author: Lucas Di Pentima <lucas at curoverse.com>
Date: Thu Jun 29 16:43:07 2017 -0300
11789: Added support for the corner case of needing to use a pathname
pattern that refers to a file or directory directoy beneath a given
input dir, the user should use './file-to-exclude.*' to do this.
Updated test to check for thi new behavior.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas at curoverse.com>
diff --git a/sdk/python/arvados/commands/put.py b/sdk/python/arvados/commands/put.py
index 9fcd27c..68f63b1 100644
--- a/sdk/python/arvados/commands/put.py
+++ b/sdk/python/arvados/commands/put.py
@@ -168,6 +168,8 @@ using a path-like pattern like 'subdir/*.txt', all text files inside 'subdir'
directory, relative to the provided input dirs will be excluded.
When using a filename pattern like '*.txt', any text file will be excluded
no matter where is placed.
+For the special case of needing to exclude only files or dirs directly below
+the given input directory, you can use a pattern like './exclude_this.gif'.
You can specify multiple patterns by using this argument more than once.
""")
@@ -920,7 +922,7 @@ _machine_format = "{} {}: {{}} written {{}} total\n".format(sys.argv[0],
def pathname_match(pathname, pattern):
name = pathname.split(os.sep)
# Fix patterns like 'some/subdir/' or 'some//subdir'
- pat = [x for x in pattern.split(os.sep) if x != '']
+ pat = [x for x in pattern.split(os.sep) if x != '' and x != '.']
if len(name) != len(pat):
return False
for i in range(len(name)):
@@ -1009,35 +1011,37 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr):
exclude_names = None
if len(args.exclude) > 0:
# We're supporting 2 kinds of exclusion patterns:
- # 1) --exclude '*.jpg' (file/dir name patterns, will only match
- # the name)
- # 2) --exclude 'foo/bar' (file/dir path patterns, will match the
+ # 1) --exclude '*.jpg' (file/dir name patterns, will only match
+ # the name, wherever the file is on the tree)
+ # 2.1) --exclude 'foo/bar' (file/dir path patterns, will match the
# entire path, and should be relative to
# any input dir argument)
+ # 2.2) --exclude './*.jpg' (Special case for excluding files/dirs
+ # placed directly underneath the input dir)
for p in args.exclude:
# Only relative paths patterns allowed
if p.startswith(os.sep):
logger.error("Cannot use absolute paths with --exclude")
sys.exit(1)
if os.path.dirname(p):
- # We don't support of path patterns with '.' or '..'
+ # We don't support of path patterns with '..'
p_parts = p.split(os.sep)
- if '.' in p_parts or '..' in p_parts:
+ if '..' in p_parts:
logger.error(
- "Cannot use path patterns that include '.' or '..'")
+ "Cannot use path patterns that include or '..'")
sys.exit(1)
# Path search pattern
exclude_paths.append(p)
else:
# Name-only search pattern
name_patterns.append(p)
- # For name only matching, we can combine all patterns into a single regexp,
- # for better performance.
+ # For name only matching, we can combine all patterns into a single
+ # regexp, for better performance.
exclude_names = re.compile('|'.join(
[fnmatch.translate(p) for p in name_patterns]
)) if len(name_patterns) > 0 else None
- # Show the user the patterns to be used, just in case they weren't specified inside
- # quotes and got changed by the shell expansion.
+ # Show the user the patterns to be used, just in case they weren't
+ # specified inside quotes and got changed by the shell expansion.
logger.info("Exclude patterns: {}".format(args.exclude))
# If this is used by a human, and there's at least one directory to be
diff --git a/sdk/python/tests/test_arv_put.py b/sdk/python/tests/test_arv_put.py
index 802dbdb..b8065ef 100644
--- a/sdk/python/tests/test_arv_put.py
+++ b/sdk/python/tests/test_arv_put.py
@@ -956,15 +956,17 @@ class ArvPutIntegrationTest(run_test_server.TestCaseWithServers,
f.write("This is %s" % fname)
col = self.run_and_find_collection("", ['--no-progress',
'--exclude', 'subdir/*2.txt',
+ '--exclude', './file1.*',
tmpdir])
self.assertNotEqual(None, col['uuid'])
c = arv_put.api_client.collections().get(uuid=col['uuid']).execute()
- # Only tmpdir/file2.txt should have been uploaded
- self.assertRegex(c['manifest_text'], r'^.*:file1.txt')
- self.assertRegex(c['manifest_text'],
- r'^\./%s.*:file2.txt' % os.path.basename(tmpdir))
+ # Only tmpdir/file1.txt & tmpdir/subdir/file2.txt should have been excluded
+ self.assertNotRegex(c['manifest_text'],
+ r'^\./%s.*:file1.txt' % os.path.basename(tmpdir))
self.assertNotRegex(c['manifest_text'],
r'^\./%s/subdir.*:file2.txt' % os.path.basename(tmpdir))
+ self.assertRegex(c['manifest_text'],
+ r'^\./%s.*:file2.txt' % os.path.basename(tmpdir))
self.assertRegex(c['manifest_text'], r'^.*:file3.txt')
commit 5936cf79d596af1c1e4075b9d3d63d341aa4995d
Author: Lucas Di Pentima <lucas at curoverse.com>
Date: Thu Jun 29 12:34:59 2017 -0300
11789: Replaced filter() with list comprehensions.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas at curoverse.com>
diff --git a/sdk/python/arvados/commands/put.py b/sdk/python/arvados/commands/put.py
index cd55914..9fcd27c 100644
--- a/sdk/python/arvados/commands/put.py
+++ b/sdk/python/arvados/commands/put.py
@@ -456,8 +456,8 @@ class ArvPutUploadJob(object):
"""
# If there aren't special files to be read, reset total bytes count to zero
# to start counting.
- if not any(filter(lambda p: not (os.path.isfile(p) or os.path.isdir(p)),
- self.paths)):
+ if not any([p for p in self.paths
+ if not (os.path.isfile(p) or os.path.isdir(p))]):
self.bytes_expected = 0
for path in self.paths:
@@ -490,22 +490,20 @@ class ArvPutUploadJob(object):
root_relpath = ''
# Exclude files/dirs by full path matching pattern
if self.exclude_paths:
- dirs[:] = list(filter(
- lambda d: not any(
- [pathname_match(os.path.join(root_relpath, d),
- pat)
- for pat in self.exclude_paths]),
- dirs))
- files = list(filter(
- lambda f: not any(
- [pathname_match(os.path.join(root_relpath, f),
- pat)
- for pat in self.exclude_paths]),
- files))
+ dirs[:] = [d for d in dirs
+ if not any(pathname_match(
+ os.path.join(root_relpath, d), pat)
+ for pat in self.exclude_paths)]
+ files = [f for f in files
+ if not any(pathname_match(
+ os.path.join(root_relpath, f), pat)
+ for pat in self.exclude_paths)]
# Exclude files/dirs by name matching pattern
if self.exclude_names is not None:
- dirs[:] = list(filter(lambda d: not self.exclude_names.match(d), dirs))
- files = list(filter(lambda f: not self.exclude_names.match(f), files))
+ dirs[:] = [d for d in dirs
+ if not self.exclude_names.match(d)]
+ files = [f for f in files
+ if not self.exclude_names.match(f)]
# Make os.walk()'s dir traversing order deterministic
dirs.sort()
files.sort()
commit 44c95f99098fa6c6acbfa82d4b6cbc6015eb6e39
Merge: 441ef97 060d38d
Author: Lucas Di Pentima <lucas at curoverse.com>
Date: Thu Jun 29 11:48:14 2017 -0300
11789: Merge branch 'master' into 11789-arvput-exclude-flag
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <lucas at curoverse.com>
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