2411: Add copyright notices to everything.
authorTom Clegg <tom@curoverse.com>
Wed, 28 Jun 2017 15:34:13 +0000 (11:34 -0400)
committerTom Clegg <tom@curoverse.com>
Wed, 28 Jun 2017 20:27:56 +0000 (16:27 -0400)
commit0f644e242ef37c911ad3dc25aca8135c339de349
tree0edca4c41d54a634097b17dc8676ee1799058c2d
parent7041d6b1812a107abe862b9e6194759474028b3e
2411: Add copyright notices to everything.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>
1833 files changed:
Makefile
README.md
apps/workbench/Gemfile
apps/workbench/README.textile
apps/workbench/Rakefile
apps/workbench/app/assets/javascripts/add_group.js
apps/workbench/app/assets/javascripts/add_repository.js
apps/workbench/app/assets/javascripts/ajax_error.js
apps/workbench/app/assets/javascripts/angular_shim.js
apps/workbench/app/assets/javascripts/application.js
apps/workbench/app/assets/javascripts/arvados_client.js
apps/workbench/app/assets/javascripts/bootstrap.js.coffee
apps/workbench/app/assets/javascripts/collections.js
apps/workbench/app/assets/javascripts/dates.js
apps/workbench/app/assets/javascripts/edit_collection.js
apps/workbench/app/assets/javascripts/edit_collection_tags.js
apps/workbench/app/assets/javascripts/editable.js
apps/workbench/app/assets/javascripts/event_log.js
apps/workbench/app/assets/javascripts/filterable.js
apps/workbench/app/assets/javascripts/infinite_scroll.js
apps/workbench/app/assets/javascripts/job_log_graph.js
apps/workbench/app/assets/javascripts/keep_disks.js.coffee
apps/workbench/app/assets/javascripts/link_to_remote.js
apps/workbench/app/assets/javascripts/log_viewer.js
apps/workbench/app/assets/javascripts/modal_pager.js
apps/workbench/app/assets/javascripts/permission_toggle.js
apps/workbench/app/assets/javascripts/pipeline_instances.js
apps/workbench/app/assets/javascripts/report_issue.js
apps/workbench/app/assets/javascripts/request_shell_access.js
apps/workbench/app/assets/javascripts/select_modal.js
apps/workbench/app/assets/javascripts/selection.js.erb
apps/workbench/app/assets/javascripts/sizing.js
apps/workbench/app/assets/javascripts/tab_panes.js
apps/workbench/app/assets/javascripts/upload_to_collection.js
apps/workbench/app/assets/javascripts/user_agreements.js
apps/workbench/app/assets/javascripts/users.js
apps/workbench/app/assets/javascripts/work_unit_component.js
apps/workbench/app/assets/javascripts/work_unit_log.js
apps/workbench/app/assets/stylesheets/api_client_authorizations.css.scss
apps/workbench/app/assets/stylesheets/application.css.scss
apps/workbench/app/assets/stylesheets/authorized_keys.css.scss
apps/workbench/app/assets/stylesheets/badges.css.scss
apps/workbench/app/assets/stylesheets/cards.css.scss
apps/workbench/app/assets/stylesheets/collections.css.scss
apps/workbench/app/assets/stylesheets/groups.css.scss
apps/workbench/app/assets/stylesheets/humans.css.scss
apps/workbench/app/assets/stylesheets/job_tasks.css.scss
apps/workbench/app/assets/stylesheets/jobs.css.scss
apps/workbench/app/assets/stylesheets/keep_disks.css.scss
apps/workbench/app/assets/stylesheets/links.css.scss
apps/workbench/app/assets/stylesheets/loading.css.scss.erb
apps/workbench/app/assets/stylesheets/log_viewer.scss
apps/workbench/app/assets/stylesheets/logs.css.scss
apps/workbench/app/assets/stylesheets/nodes.css.scss
apps/workbench/app/assets/stylesheets/pipeline_instances.css.scss
apps/workbench/app/assets/stylesheets/pipeline_templates.css.scss
apps/workbench/app/assets/stylesheets/projects.css.scss
apps/workbench/app/assets/stylesheets/repositories.css.scss
apps/workbench/app/assets/stylesheets/scaffolds.css.scss
apps/workbench/app/assets/stylesheets/select_modal.css.scss
apps/workbench/app/assets/stylesheets/sessions.css.scss
apps/workbench/app/assets/stylesheets/specimens.css.scss
apps/workbench/app/assets/stylesheets/traits.css.scss
apps/workbench/app/assets/stylesheets/user_agreements.css.scss
apps/workbench/app/assets/stylesheets/users.css.scss
apps/workbench/app/assets/stylesheets/virtual_machines.css.scss
apps/workbench/app/controllers/actions_controller.rb
apps/workbench/app/controllers/api_client_authorizations_controller.rb
apps/workbench/app/controllers/application_controller.rb
apps/workbench/app/controllers/authorized_keys_controller.rb
apps/workbench/app/controllers/collections_controller.rb
apps/workbench/app/controllers/container_requests_controller.rb
apps/workbench/app/controllers/containers_controller.rb
apps/workbench/app/controllers/groups_controller.rb
apps/workbench/app/controllers/humans_controller.rb
apps/workbench/app/controllers/job_tasks_controller.rb
apps/workbench/app/controllers/jobs_controller.rb
apps/workbench/app/controllers/keep_disks_controller.rb
apps/workbench/app/controllers/keep_services_controller.rb
apps/workbench/app/controllers/links_controller.rb
apps/workbench/app/controllers/logs_controller.rb
apps/workbench/app/controllers/nodes_controller.rb
apps/workbench/app/controllers/pipeline_instances_controller.rb
apps/workbench/app/controllers/pipeline_templates_controller.rb
apps/workbench/app/controllers/projects_controller.rb
apps/workbench/app/controllers/repositories_controller.rb
apps/workbench/app/controllers/search_controller.rb
apps/workbench/app/controllers/sessions_controller.rb
apps/workbench/app/controllers/specimens_controller.rb
apps/workbench/app/controllers/traits_controller.rb
apps/workbench/app/controllers/trash_items_controller.rb
apps/workbench/app/controllers/user_agreements_controller.rb
apps/workbench/app/controllers/users_controller.rb
apps/workbench/app/controllers/virtual_machines_controller.rb
apps/workbench/app/controllers/websocket_controller.rb
apps/workbench/app/controllers/work_unit_templates_controller.rb
apps/workbench/app/controllers/work_units_controller.rb
apps/workbench/app/controllers/workflows_controller.rb
apps/workbench/app/helpers/application_helper.rb
apps/workbench/app/helpers/arvados_api_client_helper.rb
apps/workbench/app/helpers/collections_helper.rb
apps/workbench/app/helpers/pipeline_components_helper.rb
apps/workbench/app/helpers/pipeline_instances_helper.rb
apps/workbench/app/helpers/provenance_helper.rb
apps/workbench/app/helpers/version_helper.rb
apps/workbench/app/mailers/issue_reporter.rb
apps/workbench/app/mailers/request_shell_access_reporter.rb
apps/workbench/app/models/api_client_authorization.rb
apps/workbench/app/models/arvados_api_client.rb
apps/workbench/app/models/arvados_base.rb
apps/workbench/app/models/arvados_resource_list.rb
apps/workbench/app/models/authorized_key.rb
apps/workbench/app/models/collection.rb
apps/workbench/app/models/container.rb
apps/workbench/app/models/container_request.rb
apps/workbench/app/models/container_work_unit.rb
apps/workbench/app/models/group.rb
apps/workbench/app/models/human.rb
apps/workbench/app/models/job.rb
apps/workbench/app/models/job_task.rb
apps/workbench/app/models/job_task_work_unit.rb
apps/workbench/app/models/job_work_unit.rb
apps/workbench/app/models/keep_disk.rb
apps/workbench/app/models/keep_service.rb
apps/workbench/app/models/link.rb
apps/workbench/app/models/log.rb
apps/workbench/app/models/node.rb
apps/workbench/app/models/pipeline_instance.rb
apps/workbench/app/models/pipeline_instance_work_unit.rb
apps/workbench/app/models/pipeline_template.rb
apps/workbench/app/models/proxy_work_unit.rb
apps/workbench/app/models/repository.rb
apps/workbench/app/models/specimen.rb
apps/workbench/app/models/trait.rb
apps/workbench/app/models/user.rb
apps/workbench/app/models/user_agreement.rb
apps/workbench/app/models/virtual_machine.rb
apps/workbench/app/models/work_unit.rb
apps/workbench/app/models/workflow.rb
apps/workbench/app/views/api_client_authorizations/_show_help.html.erb
apps/workbench/app/views/application/404.html.erb
apps/workbench/app/views/application/404.json.erb
apps/workbench/app/views/application/_arvados_attr_value.html.erb
apps/workbench/app/views/application/_arvados_object.html.erb
apps/workbench/app/views/application/_arvados_object_attr.html.erb
apps/workbench/app/views/application/_breadcrumb_page_name.html.erb
apps/workbench/app/views/application/_breadcrumbs.html.erb
apps/workbench/app/views/application/_browser_unsupported.html
apps/workbench/app/views/application/_choose.html.erb
apps/workbench/app/views/application/_choose.js.erb
apps/workbench/app/views/application/_choose_rows.html.erb
apps/workbench/app/views/application/_content.html.erb
apps/workbench/app/views/application/_content_layout.html.erb
apps/workbench/app/views/application/_create_new_object_button.html.erb
apps/workbench/app/views/application/_delete_object_button.html.erb
apps/workbench/app/views/application/_job_progress.html.erb
apps/workbench/app/views/application/_loading.html.erb
apps/workbench/app/views/application/_loading_modal.html.erb
apps/workbench/app/views/application/_name_and_description.html.erb
apps/workbench/app/views/application/_object_description.html.erb
apps/workbench/app/views/application/_object_name.html.erb
apps/workbench/app/views/application/_paging.html.erb
apps/workbench/app/views/application/_pipeline_progress.html.erb
apps/workbench/app/views/application/_pipeline_status_label.html.erb
apps/workbench/app/views/application/_projects_tree_menu.html.erb
apps/workbench/app/views/application/_report_error.html.erb
apps/workbench/app/views/application/_report_issue_popup.html.erb
apps/workbench/app/views/application/_selection_checkbox.html.erb
apps/workbench/app/views/application/_show_advanced.html.erb
apps/workbench/app/views/application/_show_advanced_api_response.html.erb
apps/workbench/app/views/application/_show_advanced_cli_example.html.erb
apps/workbench/app/views/application/_show_advanced_curl_example.html.erb
apps/workbench/app/views/application/_show_advanced_metadata.html.erb
apps/workbench/app/views/application/_show_advanced_python_example.html.erb
apps/workbench/app/views/application/_show_api.html.erb
apps/workbench/app/views/application/_show_attributes.html.erb
apps/workbench/app/views/application/_show_autoselect_text.html.erb
apps/workbench/app/views/application/_show_home_button.html.erb
apps/workbench/app/views/application/_show_object_button.html.erb
apps/workbench/app/views/application/_show_object_description_cell.html.erb
apps/workbench/app/views/application/_show_recent.html.erb
apps/workbench/app/views/application/_show_sharing.html.erb
apps/workbench/app/views/application/_show_star.html.erb
apps/workbench/app/views/application/_show_text_with_locators.html.erb
apps/workbench/app/views/application/_svg_div.html.erb
apps/workbench/app/views/application/_title_and_buttons.html.erb
apps/workbench/app/views/application/api_error.html.erb
apps/workbench/app/views/application/api_error.json.erb
apps/workbench/app/views/application/destroy.js.erb
apps/workbench/app/views/application/error.html.erb
apps/workbench/app/views/application/error.json.erb
apps/workbench/app/views/application/index.html.erb
apps/workbench/app/views/application/report_issue_popup.js.erb
apps/workbench/app/views/application/show.html.erb
apps/workbench/app/views/application/star.js.erb
apps/workbench/app/views/authorized_keys/create.js.erb
apps/workbench/app/views/authorized_keys/edit.html.erb
apps/workbench/app/views/collections/_choose_rows.html.erb
apps/workbench/app/views/collections/_create_new_object_button.html.erb
apps/workbench/app/views/collections/_extra_tab_line_buttons.html.erb
apps/workbench/app/views/collections/_index_tbody.html.erb
apps/workbench/app/views/collections/_sharing_button.html.erb
apps/workbench/app/views/collections/_show_chooser_preview.html.erb
apps/workbench/app/views/collections/_show_files.html.erb
apps/workbench/app/views/collections/_show_provenance_graph.html.erb
apps/workbench/app/views/collections/_show_recent.html.erb
apps/workbench/app/views/collections/_show_source_summary.html.erb
apps/workbench/app/views/collections/_show_tag_rows.html.erb
apps/workbench/app/views/collections/_show_tags.html.erb
apps/workbench/app/views/collections/_show_upload.html.erb
apps/workbench/app/views/collections/_show_used_by.html.erb
apps/workbench/app/views/collections/graph.html.erb
apps/workbench/app/views/collections/hash_matches.html.erb
apps/workbench/app/views/collections/index.html.erb
apps/workbench/app/views/collections/index.js.erb
apps/workbench/app/views/collections/save_tags.js.erb
apps/workbench/app/views/collections/sharing_popup.js.erb
apps/workbench/app/views/collections/show.html.erb
apps/workbench/app/views/collections/show_file_links.html.erb
apps/workbench/app/views/collections/tags.js.erb
apps/workbench/app/views/container_requests/_extra_tab_line_buttons.html.erb
apps/workbench/app/views/container_requests/_name_and_description.html.erb
apps/workbench/app/views/container_requests/_show_inputs.html.erb
apps/workbench/app/views/container_requests/_show_log.html.erb
apps/workbench/app/views/container_requests/_show_provenance.html.erb
apps/workbench/app/views/container_requests/_show_recent.html.erb
apps/workbench/app/views/container_requests/_show_recent_rows.html.erb
apps/workbench/app/views/container_requests/_show_status.html.erb
apps/workbench/app/views/container_requests/index.html.erb
apps/workbench/app/views/containers/_show_log.html.erb
apps/workbench/app/views/containers/_show_status.html.erb
apps/workbench/app/views/getting_started/_getting_started_popup.html.erb
apps/workbench/app/views/groups/_choose_rows.html.erb
apps/workbench/app/views/groups/_show_recent.html.erb
apps/workbench/app/views/issue_reporter/send_report.text.erb
apps/workbench/app/views/jobs/_create_new_object_button.html.erb
apps/workbench/app/views/jobs/_rerun_job_with_options_popup.html.erb
apps/workbench/app/views/jobs/_show_details.html.erb
apps/workbench/app/views/jobs/_show_job_buttons.html.erb
apps/workbench/app/views/jobs/_show_log.html.erb
apps/workbench/app/views/jobs/_show_object_description_cell.html.erb
apps/workbench/app/views/jobs/_show_provenance.html.erb
apps/workbench/app/views/jobs/_show_recent.html.erb
apps/workbench/app/views/jobs/_show_status.html.erb
apps/workbench/app/views/jobs/show.html.erb
apps/workbench/app/views/keep_disks/_content_layout.html.erb
apps/workbench/app/views/layouts/application.html.erb
apps/workbench/app/views/layouts/body.html.erb
apps/workbench/app/views/links/_breadcrumb_page_name.html.erb
apps/workbench/app/views/notifications/_collections_notification.html.erb
apps/workbench/app/views/notifications/_jobs_notification.html.erb
apps/workbench/app/views/notifications/_pipelines_notification.html.erb
apps/workbench/app/views/notifications/_ssh_key_notification.html.erb
apps/workbench/app/views/pipeline_instances/_component_labels.html.erb
apps/workbench/app/views/pipeline_instances/_running_component.html.erb
apps/workbench/app/views/pipeline_instances/_show_compare.html.erb
apps/workbench/app/views/pipeline_instances/_show_components.html.erb
apps/workbench/app/views/pipeline_instances/_show_components_editable.html.erb
apps/workbench/app/views/pipeline_instances/_show_components_json.html.erb
apps/workbench/app/views/pipeline_instances/_show_components_running.html.erb
apps/workbench/app/views/pipeline_instances/_show_graph.html.erb
apps/workbench/app/views/pipeline_instances/_show_inputs.html.erb
apps/workbench/app/views/pipeline_instances/_show_log.html.erb
apps/workbench/app/views/pipeline_instances/_show_object_description_cell.html.erb
apps/workbench/app/views/pipeline_instances/_show_recent.html.erb
apps/workbench/app/views/pipeline_instances/_show_recent_rows.html.erb
apps/workbench/app/views/pipeline_instances/_show_tab_buttons.html.erb
apps/workbench/app/views/pipeline_instances/compare.html.erb
apps/workbench/app/views/pipeline_instances/index.html.erb
apps/workbench/app/views/pipeline_instances/show.html.erb
apps/workbench/app/views/pipeline_instances/show.js.erb
apps/workbench/app/views/pipeline_templates/_choose_rows.html.erb
apps/workbench/app/views/pipeline_templates/_show_attributes.html.erb
apps/workbench/app/views/pipeline_templates/_show_chooser_preview.html.erb
apps/workbench/app/views/pipeline_templates/_show_components.html.erb
apps/workbench/app/views/pipeline_templates/_show_pipelines.html.erb
apps/workbench/app/views/pipeline_templates/_show_recent.html.erb
apps/workbench/app/views/pipeline_templates/show.html.erb
apps/workbench/app/views/projects/_choose.html.erb
apps/workbench/app/views/projects/_compute_node_status.html.erb
apps/workbench/app/views/projects/_compute_node_summary.html.erb
apps/workbench/app/views/projects/_index_jobs_and_pipelines.html.erb
apps/workbench/app/views/projects/_index_projects.html.erb
apps/workbench/app/views/projects/_show_contents_rows.html.erb
apps/workbench/app/views/projects/_show_dashboard.html.erb
apps/workbench/app/views/projects/_show_data_collections.html.erb
apps/workbench/app/views/projects/_show_description.html.erb
apps/workbench/app/views/projects/_show_featured.html.erb
apps/workbench/app/views/projects/_show_other_objects.html.erb
apps/workbench/app/views/projects/_show_pipeline_templates.html.erb
apps/workbench/app/views/projects/_show_pipelines_and_processes.html.erb
apps/workbench/app/views/projects/_show_processes.html.erb
apps/workbench/app/views/projects/_show_subprojects.html.erb
apps/workbench/app/views/projects/_show_tab_contents.html.erb
apps/workbench/app/views/projects/_show_workflows.html.erb
apps/workbench/app/views/projects/index.html.erb
apps/workbench/app/views/projects/public.html.erb
apps/workbench/app/views/projects/remove_items.js.erb
apps/workbench/app/views/projects/show.html.erb
apps/workbench/app/views/projects/tab_counts.js.erb
apps/workbench/app/views/repositories/_repository_breadcrumbs.html.erb
apps/workbench/app/views/repositories/_show_help.html.erb
apps/workbench/app/views/repositories/show_blob.html.erb
apps/workbench/app/views/repositories/show_commit.html.erb
apps/workbench/app/views/repositories/show_tree.html.erb
apps/workbench/app/views/request_shell_access_reporter/send_request.text.erb
apps/workbench/app/views/search/_choose_rows.html.erb
apps/workbench/app/views/sessions/index.html.erb
apps/workbench/app/views/trash_items/_create_new_object_button.html.erb
apps/workbench/app/views/trash_items/_show_recent_trash.html.erb
apps/workbench/app/views/trash_items/_show_trash_rows.html.erb
apps/workbench/app/views/trash_items/_untrash_item.html.erb
apps/workbench/app/views/trash_items/index.html.erb
apps/workbench/app/views/trash_items/untrash_items.js.erb
apps/workbench/app/views/user_agreements/index.html.erb
apps/workbench/app/views/users/_add_group_modal.html.erb
apps/workbench/app/views/users/_add_repository_modal.html.erb
apps/workbench/app/views/users/_add_ssh_key_popup.html.erb
apps/workbench/app/views/users/_choose_rows.html.erb
apps/workbench/app/views/users/_create_new_object_button.html.erb
apps/workbench/app/views/users/_current_token.html.erb
apps/workbench/app/views/users/_home.html.erb
apps/workbench/app/views/users/_repositories.html.erb
apps/workbench/app/views/users/_setup_popup.html.erb
apps/workbench/app/views/users/_show_activity.html.erb
apps/workbench/app/views/users/_show_admin.html.erb
apps/workbench/app/views/users/_ssh_keys.html.erb
apps/workbench/app/views/users/_tables.html.erb
apps/workbench/app/views/users/_virtual_machines.html.erb
apps/workbench/app/views/users/activity.html.erb
apps/workbench/app/views/users/add_ssh_key.js.erb
apps/workbench/app/views/users/add_ssh_key_popup.js.erb
apps/workbench/app/views/users/current_token.html.erb
apps/workbench/app/views/users/home.html.erb
apps/workbench/app/views/users/home.js.erb
apps/workbench/app/views/users/inactive.html.erb
apps/workbench/app/views/users/profile.html.erb
apps/workbench/app/views/users/repositories.html.erb
apps/workbench/app/views/users/request_shell_access.js
apps/workbench/app/views/users/setup.js.erb
apps/workbench/app/views/users/setup_popup.js.erb
apps/workbench/app/views/users/ssh_keys.html.erb
apps/workbench/app/views/users/storage.html.erb
apps/workbench/app/views/users/virtual_machines.html.erb
apps/workbench/app/views/users/welcome.html.erb
apps/workbench/app/views/virtual_machines/_show_help.html.erb
apps/workbench/app/views/virtual_machines/webshell.html.erb
apps/workbench/app/views/websocket/index.html.erb
apps/workbench/app/views/work_units/_component_detail.html.erb
apps/workbench/app/views/work_units/_progress.html.erb
apps/workbench/app/views/work_units/_show_all_processes.html.erb
apps/workbench/app/views/work_units/_show_all_processes_rows.html.erb
apps/workbench/app/views/work_units/_show_child.html.erb
apps/workbench/app/views/work_units/_show_component.html.erb
apps/workbench/app/views/work_units/_show_log.html.erb
apps/workbench/app/views/work_units/_show_log_link.html.erb
apps/workbench/app/views/work_units/_show_output.html.erb
apps/workbench/app/views/work_units/_show_outputs.html.erb
apps/workbench/app/views/work_units/_show_status.html.erb
apps/workbench/app/views/work_units/_show_table_data.html.erb
apps/workbench/app/views/work_units/index.html.erb
apps/workbench/app/views/workflows/_show_chooser_preview.html.erb
apps/workbench/app/views/workflows/_show_definition.html.erb
apps/workbench/app/views/workflows/_show_recent.html.erb
apps/workbench/app/views/workflows/show.html.erb
apps/workbench/config.ru
apps/workbench/config/application.default.yml
apps/workbench/config/application.rb
apps/workbench/config/application.yml.example
apps/workbench/config/boot.rb
apps/workbench/config/database.yml
apps/workbench/config/environment.rb
apps/workbench/config/environments/development.rb.example
apps/workbench/config/environments/production.rb.example
apps/workbench/config/environments/test.rb.example
apps/workbench/config/initializers/backtrace_silencers.rb
apps/workbench/config/initializers/inflections.rb
apps/workbench/config/initializers/lograge.rb
apps/workbench/config/initializers/mime_types.rb
apps/workbench/config/initializers/rack_mini_profile.rb
apps/workbench/config/initializers/redcloth.rb
apps/workbench/config/initializers/secret_token.rb.example
apps/workbench/config/initializers/session_store.rb
apps/workbench/config/initializers/time_format.rb
apps/workbench/config/initializers/wrap_parameters.rb
apps/workbench/config/load_config.rb
apps/workbench/config/locales/en.yml
apps/workbench/config/piwik.yml.example
apps/workbench/config/routes.rb
apps/workbench/db/schema.rb
apps/workbench/db/seeds.rb
apps/workbench/fpm-info.sh
apps/workbench/lib/app_version.rb
apps/workbench/lib/tasks/config_check.rake
apps/workbench/lib/tasks/config_dump.rake
apps/workbench/public/404.html
apps/workbench/public/422.html
apps/workbench/public/500.html
apps/workbench/public/browser_unsupported.js
apps/workbench/public/graph-example.html
apps/workbench/test/controllers/actions_controller_test.rb
apps/workbench/test/controllers/api_client_authorizations_controller_test.rb
apps/workbench/test/controllers/application_controller_test.rb
apps/workbench/test/controllers/authorized_keys_controller_test.rb
apps/workbench/test/controllers/collections_controller_test.rb
apps/workbench/test/controllers/container_requests_controller_test.rb
apps/workbench/test/controllers/containers_controller_test.rb
apps/workbench/test/controllers/disabled_api_test.rb
apps/workbench/test/controllers/groups_controller_test.rb
apps/workbench/test/controllers/humans_controller_test.rb
apps/workbench/test/controllers/job_tasks_controller_test.rb
apps/workbench/test/controllers/jobs_controller_test.rb
apps/workbench/test/controllers/keep_disks_controller_test.rb
apps/workbench/test/controllers/links_controller_test.rb
apps/workbench/test/controllers/logs_controller_test.rb
apps/workbench/test/controllers/nodes_controller_test.rb
apps/workbench/test/controllers/pipeline_instances_controller_test.rb
apps/workbench/test/controllers/pipeline_templates_controller_test.rb
apps/workbench/test/controllers/projects_controller_test.rb
apps/workbench/test/controllers/repositories_controller_test.rb
apps/workbench/test/controllers/search_controller_test.rb
apps/workbench/test/controllers/sessions_controller_test.rb
apps/workbench/test/controllers/specimens_controller_test.rb
apps/workbench/test/controllers/traits_controller_test.rb
apps/workbench/test/controllers/trash_items_controller_test.rb
apps/workbench/test/controllers/user_agreements_controller_test.rb
apps/workbench/test/controllers/users_controller_test.rb
apps/workbench/test/controllers/virtual_machines_controller_test.rb
apps/workbench/test/controllers/work_units_controller_test.rb
apps/workbench/test/controllers/workflows_controller_test.rb
apps/workbench/test/diagnostics/container_request_test.rb
apps/workbench/test/diagnostics/pipeline_test.rb
apps/workbench/test/diagnostics_test_helper.rb
apps/workbench/test/helpers/collections_helper_test.rb
apps/workbench/test/helpers/download_helper.rb
apps/workbench/test/helpers/fake_websocket_helper.rb
apps/workbench/test/helpers/pipeline_instances_helper_test.rb
apps/workbench/test/helpers/repository_stub_helper.rb
apps/workbench/test/helpers/search_helper_test.rb
apps/workbench/test/helpers/share_object_helper.rb
apps/workbench/test/integration/ajax_errors_test.rb
apps/workbench/test/integration/anonymous_access_test.rb
apps/workbench/test/integration/application_layout_test.rb
apps/workbench/test/integration/browser_unsupported_test.rb
apps/workbench/test/integration/collection_upload_test.rb
apps/workbench/test/integration/collections_test.rb
apps/workbench/test/integration/container_requests_test.rb
apps/workbench/test/integration/download_test.rb
apps/workbench/test/integration/errors_test.rb
apps/workbench/test/integration/filterable_infinite_scroll_test.rb
apps/workbench/test/integration/integration_test_utils.rb
apps/workbench/test/integration/jobs_test.rb
apps/workbench/test/integration/logins_test.rb
apps/workbench/test/integration/pipeline_instances_test.rb
apps/workbench/test/integration/pipeline_templates_test.rb
apps/workbench/test/integration/projects_test.rb
apps/workbench/test/integration/report_issue_test.rb
apps/workbench/test/integration/repositories_browse_test.rb
apps/workbench/test/integration/repositories_test.rb
apps/workbench/test/integration/search_box_test.rb
apps/workbench/test/integration/smoke_test.rb
apps/workbench/test/integration/trash_test.rb
apps/workbench/test/integration/user_agreements_test.rb
apps/workbench/test/integration/user_profile_test.rb
apps/workbench/test/integration/user_settings_menu_test.rb
apps/workbench/test/integration/users_test.rb
apps/workbench/test/integration/virtual_machines_test.rb
apps/workbench/test/integration/websockets_test.rb
apps/workbench/test/integration/work_units_test.rb
apps/workbench/test/integration_helper.rb
apps/workbench/test/integration_performance/collection_unit_test.rb
apps/workbench/test/integration_performance/collections_controller_test.rb
apps/workbench/test/integration_performance/collections_perf_test.rb
apps/workbench/test/performance/browsing_test.rb
apps/workbench/test/performance_test_helper.rb
apps/workbench/test/support/fake_websocket.js
apps/workbench/test/support/remove_file_api.js
apps/workbench/test/test_helper.rb
apps/workbench/test/unit/arvados_api_client_test.rb
apps/workbench/test/unit/arvados_base_test.rb
apps/workbench/test/unit/arvados_resource_list_test.rb
apps/workbench/test/unit/collection_test.rb
apps/workbench/test/unit/disabled_api_test.rb
apps/workbench/test/unit/group_test.rb
apps/workbench/test/unit/helpers/api_client_authorizations_helper_test.rb
apps/workbench/test/unit/helpers/authorized_keys_helper_test.rb
apps/workbench/test/unit/helpers/collections_helper_test.rb
apps/workbench/test/unit/helpers/groups_helper_test.rb
apps/workbench/test/unit/helpers/humans_helper_test.rb
apps/workbench/test/unit/helpers/job_tasks_helper_test.rb
apps/workbench/test/unit/helpers/jobs_helper_test.rb
apps/workbench/test/unit/helpers/keep_disks_helper_test.rb
apps/workbench/test/unit/helpers/links_helper_test.rb
apps/workbench/test/unit/helpers/logs_helper_test.rb
apps/workbench/test/unit/helpers/nodes_helper_test.rb
apps/workbench/test/unit/helpers/pipeline_instances_helper_test.rb
apps/workbench/test/unit/helpers/pipeline_templates_helper_test.rb
apps/workbench/test/unit/helpers/projects_helper_test.rb
apps/workbench/test/unit/helpers/repositories_helper_test.rb
apps/workbench/test/unit/helpers/sessions_helper_test.rb
apps/workbench/test/unit/helpers/specimens_helper_test.rb
apps/workbench/test/unit/helpers/traits_helper_test.rb
apps/workbench/test/unit/helpers/user_agreements_helper_test.rb
apps/workbench/test/unit/helpers/users_helper_test.rb
apps/workbench/test/unit/helpers/virtual_machines_helper_test.rb
apps/workbench/test/unit/job_test.rb
apps/workbench/test/unit/link_test.rb
apps/workbench/test/unit/pipeline_instance_test.rb
apps/workbench/test/unit/repository_test.rb
apps/workbench/test/unit/user_test.rb
apps/workbench/test/unit/work_unit_test.rb
backports/deb-fuse/fpm-info.sh
backports/deb-libfuse-dev/fpm-info.sh
backports/python-apache-libcloud/fpm-info.sh
backports/python-ciso8601/fpm-info.sh
backports/python-llfuse/fpm-info.sh
backports/python-pycrypto/fpm-info.sh
backports/python-pycurl/fpm-info.sh
build/build-dev-docker-jobs-image.sh
build/build.list
build/create-plot-data-from-log.sh
build/go-python-package-scripts/postinst
build/go-python-package-scripts/prerm
build/libcloud-pin.sh
build/package-build-dockerfiles/Makefile
build/package-build-dockerfiles/build-all-build-containers.sh
build/package-build-dockerfiles/centos7/Dockerfile
build/package-build-dockerfiles/debian8/Dockerfile
build/package-build-dockerfiles/ubuntu1204/Dockerfile
build/package-build-dockerfiles/ubuntu1404/Dockerfile
build/package-build-dockerfiles/ubuntu1604/Dockerfile
build/package-test-dockerfiles/centos7/Dockerfile
build/package-test-dockerfiles/debian8/Dockerfile
build/package-test-dockerfiles/ubuntu1204/Dockerfile
build/package-test-dockerfiles/ubuntu1404/Dockerfile
build/package-test-dockerfiles/ubuntu1604/Dockerfile
build/package-testing/common-test-packages.sh
build/package-testing/common-test-rails-server-package.sh
build/package-testing/deb-common-test-packages.sh
build/package-testing/rpm-common-test-packages.sh
build/package-testing/test-package-arvados-node-manager.sh
build/package-testing/test-package-python27-python-arvados-cwl-runner.sh
build/package-testing/test-package-python27-python-arvados-fuse.sh
build/package-testing/test-package-python27-python-arvados-python-client.sh
build/rails-package-scripts/README.md
build/rails-package-scripts/arvados-api-server.sh
build/rails-package-scripts/arvados-sso-server.sh
build/rails-package-scripts/arvados-workbench.sh
build/rails-package-scripts/postinst.sh
build/rails-package-scripts/postrm.sh
build/rails-package-scripts/prerm.sh
build/rails-package-scripts/step2.sh
build/run-build-docker-images.sh
build/run-build-docker-jobs-image.sh
build/run-build-packages-all-targets.sh
build/run-build-packages-one-target.sh
build/run-build-packages-python-and-ruby.sh
build/run-build-packages-sso.sh
build/run-build-packages.sh
build/run-build-test-packages-one-target.sh
build/run-library.sh
build/run-tests.sh
crunch_scripts/GATK2-VariantFiltration
crunch_scripts/GATK2-bqsr
crunch_scripts/GATK2-merge-call
crunch_scripts/GATK2-realign
crunch_scripts/arvados-bcbio-nextgen.py
crunch_scripts/arvados_bwa.py
crunch_scripts/arvados_gatk2.py
crunch_scripts/arvados_ipc.py
crunch_scripts/arvados_picard.py
crunch_scripts/arvados_samtools.py
crunch_scripts/bwa-aln
crunch_scripts/bwa-index
crunch_scripts/collection-merge
crunch_scripts/crunchrunner
crunch_scripts/crunchutil/robust_put.py
crunch_scripts/crunchutil/subst.py
crunch_scripts/crunchutil/vwd.py
crunch_scripts/cwl-runner
crunch_scripts/decompress-all.py
crunch_scripts/file-select
crunch_scripts/grep
crunch_scripts/hash
crunch_scripts/pgp-survey-import
crunch_scripts/pgp-survey-parse
crunch_scripts/picard-gatk2-prep
crunch_scripts/pyrtg.py
crunch_scripts/rtg-fasta2sdf
crunch_scripts/rtg-fastq2sdf
crunch_scripts/rtg-map
crunch_scripts/rtg-snp
crunch_scripts/run-command
crunch_scripts/split-fastq.py
crunch_scripts/test/task_output_dir
doc/Gemfile
doc/README.textile
doc/Rakefile
doc/_config.yml
doc/_includes/_0_filter_py.liquid
doc/_includes/_alert-incomplete.liquid
doc/_includes/_alert_stub.liquid
doc/_includes/_arv_copy_expectations.liquid
doc/_includes/_arv_run_redirection.liquid
doc/_includes/_compute_ping_rb.liquid
doc/_includes/_concurrent_hash_script_py.liquid
doc/_includes/_container_runtime_constraints.liquid
doc/_includes/_container_scheduling_parameters.liquid
doc/_includes/_crunch1only_begin.liquid
doc/_includes/_crunch1only_end.liquid
doc/_includes/_events_py.liquid
doc/_includes/_example_docker.liquid
doc/_includes/_example_sdk_go.liquid
doc/_includes/_example_sdk_go_imports.liquid
doc/_includes/_install_compute_docker.liquid
doc/_includes/_install_compute_fuse.liquid
doc/_includes/_install_debian_key.liquid
doc/_includes/_install_docker_cleaner.liquid
doc/_includes/_install_git.liquid
doc/_includes/_install_git_curl.liquid
doc/_includes/_install_postgres_database.liquid
doc/_includes/_install_rails_command.liquid
doc/_includes/_install_rails_reconfigure.liquid
doc/_includes/_install_redhat_key.liquid
doc/_includes/_install_ruby_and_bundler.liquid
doc/_includes/_install_runit.liquid
doc/_includes/_mount_types.liquid
doc/_includes/_navbar_left.liquid
doc/_includes/_navbar_top.liquid
doc/_includes/_note_python_sc.liquid
doc/_includes/_notebox_begin.liquid
doc/_includes/_notebox_begin_warning.liquid
doc/_includes/_notebox_end.liquid
doc/_includes/_pipeline_deprecation_notice.liquid
doc/_includes/_run_command_foreach_example.liquid
doc/_includes/_run_command_simple_example.liquid
doc/_includes/_run_md5sum_py.liquid
doc/_includes/_skip_sso_server_install.liquid
doc/_includes/_ssh_addkey.liquid
doc/_includes/_ssh_intro.liquid
doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid
doc/_includes/_tutorial_cluster_name.liquid
doc/_includes/_tutorial_expectations.liquid
doc/_includes/_tutorial_expectations_workstation.liquid
doc/_includes/_tutorial_git_repo_expectations.liquid
doc/_includes/_tutorial_hash_script_py.liquid
doc/_includes/_tutorial_submit_job.liquid
doc/_includes/_webring.liquid
doc/_includes/_what_is_cwl.liquid
doc/_layouts/default.html.liquid
doc/api/crunch-scripts.html.textile.liquid
doc/api/execution.html.textile.liquid
doc/api/index.html.textile.liquid
doc/api/methods.html.textile.liquid
doc/api/methods/api_client_authorizations.html.textile.liquid
doc/api/methods/api_clients.html.textile.liquid
doc/api/methods/authorized_keys.html.textile.liquid
doc/api/methods/collections.html.textile.liquid
doc/api/methods/container_requests.html.textile.liquid
doc/api/methods/containers.html.textile.liquid
doc/api/methods/groups.html.textile.liquid
doc/api/methods/humans.html.textile.liquid
doc/api/methods/job_tasks.html.textile.liquid
doc/api/methods/jobs.html.textile.liquid
doc/api/methods/keep_disks.html.textile.liquid
doc/api/methods/keep_services.html.textile.liquid
doc/api/methods/links.html.textile.liquid
doc/api/methods/logs.html.textile.liquid
doc/api/methods/nodes.html.textile.liquid
doc/api/methods/pipeline_instances.html.textile.liquid
doc/api/methods/pipeline_templates.html.textile.liquid
doc/api/methods/repositories.html.textile.liquid
doc/api/methods/specimens.html.textile.liquid
doc/api/methods/traits.html.textile.liquid
doc/api/methods/users.html.textile.liquid
doc/api/methods/virtual_machines.html.textile.liquid
doc/api/methods/workflows.html.textile.liquid
doc/api/permission-model.html.textile.liquid
doc/api/requests.html.textile.liquid
doc/api/resources.html.textile.liquid
doc/api/storage.html.textile.liquid
doc/api/tokens.html.textile.liquid
doc/css/badges.css
doc/css/button-override.css
doc/css/carousel-override.css
doc/css/code.css
doc/css/nav-list.css
doc/examples/ruby/list-active-nodes.rb
doc/gen_api_method_docs.py
doc/gen_api_schema_docs.py
doc/images/Arvados_Permissions.svg
doc/images/Crunch_dispatch.svg
doc/images/Keep_manifests.svg
doc/images/Keep_reading_writing_block.svg
doc/images/Keep_rendezvous_hashing.svg
doc/images/Session_Establishment.svg
doc/index.html.liquid
doc/install/arvbox.html.textile.liquid
doc/install/cheat_sheet.html.textile.liquid
doc/install/client.html.textile.liquid
doc/install/configure-azure-blob-storage.html.textile.liquid
doc/install/copy_pipeline_from_curoverse.html.textile.liquid
doc/install/create-standard-objects.html.textile.liquid
doc/install/crunch2-slurm/install-compute-node.html.textile.liquid
doc/install/crunch2-slurm/install-dispatch.html.textile.liquid
doc/install/crunch2-slurm/install-prerequisites.html.textile.liquid
doc/install/crunch2-slurm/install-slurm.html.textile.liquid
doc/install/crunch2-slurm/install-test.html.textile.liquid
doc/install/index.html.textile.liquid
doc/install/install-api-server.html.textile.liquid
doc/install/install-arv-git-httpd.html.textile.liquid
doc/install/install-compute-node.html.textile.liquid
doc/install/install-compute-ping.html.textile.liquid
doc/install/install-crunch-dispatch.html.textile.liquid
doc/install/install-keep-balance.html.textile.liquid
doc/install/install-keep-web.html.textile.liquid
doc/install/install-keepproxy.html.textile.liquid
doc/install/install-keepstore.html.textile.liquid
doc/install/install-manual-overview.html.textile.liquid
doc/install/install-manual-prerequisites.html.textile.liquid
doc/install/install-nodemanager.html.textile.liquid
doc/install/install-postgresql.html.textile.liquid
doc/install/install-shell-server.html.textile.liquid
doc/install/install-sso.html.textile.liquid
doc/install/install-workbench-app.html.textile.liquid
doc/install/install-ws.html.textile.liquid
doc/install/migrate-docker19.html.textile.liquid
doc/install/pre-built-docker.html.textile.liquid
doc/sdk/cli/index.html.textile.liquid
doc/sdk/cli/install.html.textile.liquid
doc/sdk/cli/reference.html.textile.liquid
doc/sdk/cli/subcommands.html.textile.liquid
doc/sdk/go/example.html.textile.liquid
doc/sdk/go/index.html.textile.liquid
doc/sdk/index.html.textile.liquid
doc/sdk/java/example.html.textile.liquid
doc/sdk/java/index.html.textile.liquid
doc/sdk/perl/example.html.textile.liquid
doc/sdk/perl/index.html.textile.liquid
doc/sdk/python/crunch-utility-libraries.html.textile.liquid
doc/sdk/python/events.html.textile.liquid
doc/sdk/python/example.html.textile.liquid
doc/sdk/python/python.html.textile.liquid
doc/sdk/python/sdk-python.html.textile.liquid
doc/sdk/ruby/example.html.textile.liquid
doc/sdk/ruby/index.html.textile.liquid
doc/start/getting_started/firstpipeline.html.textile.liquid
doc/start/getting_started/nextsteps.html.textile.liquid
doc/start/getting_started/publicproject.html.textile.liquid
doc/start/getting_started/sharedata.html.textile.liquid
doc/start/index.html.textile.liquid
doc/user/copying/copying.html.textile.liquid
doc/user/cwl/bwa-mem/bwa-mem-input-local.yml
doc/user/cwl/bwa-mem/bwa-mem-input.yml
doc/user/cwl/bwa-mem/bwa-mem-template.yml
doc/user/cwl/bwa-mem/bwa-mem.cwl
doc/user/cwl/cwl-extensions.html.textile.liquid
doc/user/cwl/cwl-run-options.html.textile.liquid
doc/user/cwl/cwl-runner.html.textile.liquid
doc/user/cwl/cwl-style.html.textile.liquid
doc/user/examples/crunch-examples.html.textile.liquid
doc/user/getting_started/check-environment.html.textile.liquid
doc/user/getting_started/community.html.textile.liquid
doc/user/getting_started/ssh-access-unix.html.textile.liquid
doc/user/getting_started/ssh-access-windows.html.textile.liquid
doc/user/getting_started/vm-login-with-webshell.html.textile.liquid
doc/user/getting_started/workbench.html.textile.liquid
doc/user/index.html.textile.liquid
doc/user/reference/api-tokens.html.textile.liquid
doc/user/reference/job-pipeline-ref.html.textile.liquid
doc/user/topics/arv-copy.html.textile.liquid
doc/user/topics/arv-docker.html.textile.liquid
doc/user/topics/arv-run.html.textile.liquid
doc/user/topics/arv-web.html.textile.liquid
doc/user/topics/crunch-tools-overview.html.textile.liquid
doc/user/topics/keep.html.textile.liquid
doc/user/topics/run-command.html.textile.liquid
doc/user/topics/running-pipeline-command-line.html.textile.liquid
doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
doc/user/topics/tutorial-job1.html.textile.liquid
doc/user/topics/tutorial-parallel.html.textile.liquid
doc/user/topics/tutorial-trait-search.html.textile.liquid
doc/user/tutorials/add-new-repository.html.textile.liquid
doc/user/tutorials/git-arvados-guide.html.textile.liquid
doc/user/tutorials/intro-crunch.html.textile.liquid
doc/user/tutorials/running-external-program.html.textile.liquid
doc/user/tutorials/tutorial-firstscript.html.textile.liquid
doc/user/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid
doc/user/tutorials/tutorial-keep-get.html.textile.liquid
doc/user/tutorials/tutorial-keep-mount.html.textile.liquid
doc/user/tutorials/tutorial-keep.html.textile.liquid
doc/user/tutorials/tutorial-submit-job.html.textile.liquid
doc/user/tutorials/tutorial-workflow-workbench.html.textile.liquid
doc/user/tutorials/writing-cwl-workflow.html.textile.liquid
doc/zenweb-liquid.rb
doc/zenweb-textile.rb
docker/jobs/Dockerfile
docker/migrate-docker19/Dockerfile
docker/migrate-docker19/build.sh
docker/migrate-docker19/dnd.sh
docker/migrate-docker19/migrate.sh
lib/crunchstat/crunchstat.go
lib/crunchstat/crunchstat_test.go
sdk/cli/Gemfile
sdk/cli/Rakefile
sdk/cli/arvados-cli.gemspec
sdk/cli/bin/arv
sdk/cli/bin/arv-crunch-job
sdk/cli/bin/arv-run-pipeline-instance
sdk/cli/bin/arv-tag
sdk/cli/bin/crunch-job
sdk/cli/test/binstub_arv-mount/arv-mount
sdk/cli/test/binstub_clean_fail/arv-mount
sdk/cli/test/binstub_docker_noop/docker.io
sdk/cli/test/binstub_output_coll_owner/python
sdk/cli/test/binstub_sanity_check/docker.io
sdk/cli/test/binstub_sanity_check/true
sdk/cli/test/test_arv-collection-create.rb
sdk/cli/test/test_arv-get.rb
sdk/cli/test/test_arv-keep-get.rb
sdk/cli/test/test_arv-keep-put.rb
sdk/cli/test/test_arv-run-pipeline-instance.rb
sdk/cli/test/test_arv-tag.rb
sdk/cli/test/test_arv-ws.rb
sdk/cli/test/test_crunch-job.rb
sdk/cwl/MANIFEST.in
sdk/cwl/README.rst
sdk/cwl/arvados_cwl/__init__.py
sdk/cwl/arvados_cwl/arv-cwl-schema.yml
sdk/cwl/arvados_cwl/arvcontainer.py
sdk/cwl/arvados_cwl/arvdocker.py
sdk/cwl/arvados_cwl/arvjob.py
sdk/cwl/arvados_cwl/arvtool.py
sdk/cwl/arvados_cwl/arvworkflow.py
sdk/cwl/arvados_cwl/crunch_script.py
sdk/cwl/arvados_cwl/done.py
sdk/cwl/arvados_cwl/fsaccess.py
sdk/cwl/arvados_cwl/pathmapper.py
sdk/cwl/arvados_cwl/perf.py
sdk/cwl/arvados_cwl/runner.py
sdk/cwl/bin/arvados-cwl-runner
sdk/cwl/bin/cwl-runner
sdk/cwl/gittaggers.py
sdk/cwl/setup.py
sdk/cwl/test_with_arvbox.sh
sdk/cwl/tests/__init__.py
sdk/cwl/tests/arvados-tests.sh
sdk/cwl/tests/arvados-tests.yml
sdk/cwl/tests/cat.cwl
sdk/cwl/tests/collection_per_tool/collection_per_tool.cwl
sdk/cwl/tests/collection_per_tool/collection_per_tool_packed.cwl
sdk/cwl/tests/collection_per_tool/step1.cwl
sdk/cwl/tests/collection_per_tool/step2.cwl
sdk/cwl/tests/dir-job.yml
sdk/cwl/tests/dir-job2.yml
sdk/cwl/tests/hw.py
sdk/cwl/tests/keep-dir-test-input.cwl
sdk/cwl/tests/keep-dir-test-input2.cwl
sdk/cwl/tests/keep-dir-test-input3.cwl
sdk/cwl/tests/listing-job.yml
sdk/cwl/tests/matcher.py
sdk/cwl/tests/mock_discovery.py
sdk/cwl/tests/octo.yml
sdk/cwl/tests/runner.sh
sdk/cwl/tests/test_container.py
sdk/cwl/tests/test_fsaccess.py
sdk/cwl/tests/test_job.py
sdk/cwl/tests/test_make_output.py
sdk/cwl/tests/test_pathmapper.py
sdk/cwl/tests/test_submit.py
sdk/cwl/tests/test_urljoin.py
sdk/cwl/tests/tool/submit_tool.cwl
sdk/cwl/tests/wf/expect_arvworkflow.cwl
sdk/cwl/tests/wf/expect_packed.cwl
sdk/cwl/tests/wf/inputs_test.cwl
sdk/cwl/tests/wf/listing_deep.cwl
sdk/cwl/tests/wf/listing_none.cwl
sdk/cwl/tests/wf/listing_shallow.cwl
sdk/cwl/tests/wf/scatter2.cwl
sdk/cwl/tests/wf/scatter2_subwf.cwl
sdk/cwl/tests/wf/submit_keepref_wf.cwl
sdk/cwl/tests/wf/submit_wf.cwl
sdk/cwl/tests/wf/submit_wf_packed.cwl
sdk/dev-jobs.dockerfile
sdk/go/arvados/api_client_authorization.go
sdk/go/arvados/client.go
sdk/go/arvados/client_test.go
sdk/go/arvados/collection.go
sdk/go/arvados/collection_fs.go
sdk/go/arvados/collection_fs_test.go
sdk/go/arvados/container.go
sdk/go/arvados/doc.go
sdk/go/arvados/duration.go
sdk/go/arvados/error.go
sdk/go/arvados/keep_block.go
sdk/go/arvados/keep_service.go
sdk/go/arvados/log.go
sdk/go/arvados/resource_list.go
sdk/go/arvados/resource_list_test.go
sdk/go/arvados/user.go
sdk/go/arvados/workflow.go
sdk/go/arvadosclient/arvadosclient.go
sdk/go/arvadosclient/arvadosclient_test.go
sdk/go/arvadosclient/pool.go
sdk/go/arvadostest/fixtures.go
sdk/go/arvadostest/run_servers.go
sdk/go/arvadostest/stub.go
sdk/go/auth/auth.go
sdk/go/auth/basic_auth_go13.go
sdk/go/auth/basic_auth_go14.go
sdk/go/auth/basic_auth_test.go
sdk/go/blockdigest/blockdigest.go
sdk/go/blockdigest/blockdigest_test.go
sdk/go/blockdigest/testing.go
sdk/go/config/dump.go
sdk/go/config/load.go
sdk/go/crunchrunner/crunchrunner.go
sdk/go/crunchrunner/crunchrunner_test.go
sdk/go/crunchrunner/upload.go
sdk/go/crunchrunner/upload_test.go
sdk/go/ctxlog/log.go
sdk/go/dispatch/dispatch.go
sdk/go/dispatch/dispatch_test.go
sdk/go/dispatch/throttle.go
sdk/go/dispatch/throttle_test.go
sdk/go/httpserver/httpserver.go
sdk/go/httpserver/id_generator.go
sdk/go/httpserver/log.go
sdk/go/httpserver/request_limiter.go
sdk/go/httpserver/request_limiter_test.go
sdk/go/httpserver/responsewriter.go
sdk/go/keepclient/block_cache.go
sdk/go/keepclient/collectionreader.go
sdk/go/keepclient/collectionreader_test.go
sdk/go/keepclient/discover.go
sdk/go/keepclient/discover_test.go
sdk/go/keepclient/hashcheck.go
sdk/go/keepclient/hashcheck_test.go
sdk/go/keepclient/keepclient.go
sdk/go/keepclient/keepclient_test.go
sdk/go/keepclient/perms.go
sdk/go/keepclient/perms_test.go
sdk/go/keepclient/root_sorter.go
sdk/go/keepclient/root_sorter_test.go
sdk/go/keepclient/support.go
sdk/go/manifest/manifest.go
sdk/go/manifest/manifest_test.go
sdk/go/stats/duration.go
sdk/go/stats/duration_test.go
sdk/go/streamer/streamer.go
sdk/go/streamer/streamer_test.go
sdk/go/streamer/transfer.go
sdk/java/ArvadosSDKJavaExample.java
sdk/java/ArvadosSDKJavaExampleWithPrompt.java
sdk/java/src/main/java/org/arvados/sdk/Arvados.java
sdk/java/src/main/java/org/arvados/sdk/MethodDetails.java
sdk/java/src/test/java/org/arvados/sdk/java/ArvadosTest.java
sdk/pam/.dockerignore
sdk/pam/Dockerfile
sdk/pam/MANIFEST.in
sdk/pam/README.rst
sdk/pam/arvados_pam/__init__.py
sdk/pam/arvados_pam/auth_event.py
sdk/pam/fpm-info.sh
sdk/pam/integration_tests/test_pam.py
sdk/pam/lib/libpam_arvados.py
sdk/pam/setup.py
sdk/pam/tests/integration_test.pl
sdk/pam/tests/mocker.py
sdk/pam/tests/test_auth_event.py
sdk/pam/tests/test_pam_sm.py
sdk/perl/Makefile.PL
sdk/perl/lib/Arvados.pm
sdk/perl/lib/Arvados/Request.pm
sdk/perl/lib/Arvados/ResourceAccessor.pm
sdk/perl/lib/Arvados/ResourceMethod.pm
sdk/perl/lib/Arvados/ResourceProxy.pm
sdk/perl/lib/Arvados/ResourceProxyList.pm
sdk/python/MANIFEST.in
sdk/python/README.rst
sdk/python/arvados/__init__.py
sdk/python/arvados/_normalize_stream.py
sdk/python/arvados/_ranges.py
sdk/python/arvados/_version.py
sdk/python/arvados/api.py
sdk/python/arvados/arvfile.py
sdk/python/arvados/cache.py
sdk/python/arvados/collection.py
sdk/python/arvados/commands/_util.py
sdk/python/arvados/commands/arv_copy.py
sdk/python/arvados/commands/get.py
sdk/python/arvados/commands/keepdocker.py
sdk/python/arvados/commands/ls.py
sdk/python/arvados/commands/migrate19.py
sdk/python/arvados/commands/put.py
sdk/python/arvados/commands/run.py
sdk/python/arvados/commands/ws.py
sdk/python/arvados/config.py
sdk/python/arvados/crunch.py
sdk/python/arvados/errors.py
sdk/python/arvados/events.py
sdk/python/arvados/keep.py
sdk/python/arvados/retry.py
sdk/python/arvados/safeapi.py
sdk/python/arvados/stream.py
sdk/python/arvados/timer.py
sdk/python/arvados/util.py
sdk/python/bin/arv-copy
sdk/python/bin/arv-get
sdk/python/bin/arv-keepdocker
sdk/python/bin/arv-ls
sdk/python/bin/arv-migrate-docker19
sdk/python/bin/arv-normalize
sdk/python/bin/arv-put
sdk/python/bin/arv-run
sdk/python/bin/arv-ws
sdk/python/gittaggers.py
sdk/python/setup.py
sdk/python/tests/arvados_testutil.py
sdk/python/tests/keepstub.py
sdk/python/tests/manifest_examples.py
sdk/python/tests/nginx.conf
sdk/python/tests/performance/performance_profiler.py
sdk/python/tests/performance/test_a_sample.py
sdk/python/tests/run_test_server.py
sdk/python/tests/slow_test.py
sdk/python/tests/test_api.py
sdk/python/tests/test_arv_copy.py
sdk/python/tests/test_arv_get.py
sdk/python/tests/test_arv_keepdocker.py
sdk/python/tests/test_arv_ls.py
sdk/python/tests/test_arv_normalize.py
sdk/python/tests/test_arv_put.py
sdk/python/tests/test_arv_run.py
sdk/python/tests/test_arv_ws.py
sdk/python/tests/test_arvfile.py
sdk/python/tests/test_benchmark_collections.py
sdk/python/tests/test_cache.py
sdk/python/tests/test_collections.py
sdk/python/tests/test_crunch.py
sdk/python/tests/test_errors.py
sdk/python/tests/test_events.py
sdk/python/tests/test_keep_client.py
sdk/python/tests/test_keep_locator.py
sdk/python/tests/test_pipeline_template.py
sdk/python/tests/test_retry.py
sdk/python/tests/test_retry_job_helpers.py
sdk/python/tests/test_sdk.py
sdk/python/tests/test_stream.py
sdk/python/tests/test_util.py
sdk/ruby/Gemfile
sdk/ruby/Rakefile
sdk/ruby/arvados.gemspec
sdk/ruby/lib/arvados.rb
sdk/ruby/lib/arvados/collection.rb
sdk/ruby/lib/arvados/google_api_client.rb
sdk/ruby/lib/arvados/keep.rb
sdk/ruby/test/sdk_fixtures.rb
sdk/ruby/test/test_big_request.rb
sdk/ruby/test/test_collection.rb
sdk/ruby/test/test_keep_manifest.rb
services/api/Gemfile
services/api/Rakefile
services/api/app/assets/stylesheets/api_client_authorizations.css.scss
services/api/app/assets/stylesheets/api_clients.css.scss
services/api/app/assets/stylesheets/application.css
services/api/app/assets/stylesheets/authorized_keys.css.scss
services/api/app/assets/stylesheets/collections.css.scss
services/api/app/assets/stylesheets/commit_ancestors.css.scss
services/api/app/assets/stylesheets/commits.css.scss
services/api/app/assets/stylesheets/groups.css.scss
services/api/app/assets/stylesheets/humans.css.scss
services/api/app/assets/stylesheets/job_tasks.css.scss
services/api/app/assets/stylesheets/jobs.css.scss
services/api/app/assets/stylesheets/keep_disks.css.scss
services/api/app/assets/stylesheets/links.css.scss
services/api/app/assets/stylesheets/logs.css.scss
services/api/app/assets/stylesheets/nodes.css
services/api/app/assets/stylesheets/nodes.css.scss
services/api/app/assets/stylesheets/pipeline_instances.css.scss
services/api/app/assets/stylesheets/pipeline_templates.css.scss
services/api/app/assets/stylesheets/repositories.css.scss
services/api/app/assets/stylesheets/scaffolds.css.scss
services/api/app/assets/stylesheets/specimens.css.scss
services/api/app/assets/stylesheets/traits.css.scss
services/api/app/assets/stylesheets/virtual_machines.css.scss
services/api/app/controllers/application_controller.rb
services/api/app/controllers/arvados/v1/api_client_authorizations_controller.rb
services/api/app/controllers/arvados/v1/api_clients_controller.rb
services/api/app/controllers/arvados/v1/authorized_keys_controller.rb
services/api/app/controllers/arvados/v1/collections_controller.rb
services/api/app/controllers/arvados/v1/container_requests_controller.rb
services/api/app/controllers/arvados/v1/containers_controller.rb
services/api/app/controllers/arvados/v1/groups_controller.rb
services/api/app/controllers/arvados/v1/humans_controller.rb
services/api/app/controllers/arvados/v1/job_tasks_controller.rb
services/api/app/controllers/arvados/v1/jobs_controller.rb
services/api/app/controllers/arvados/v1/keep_disks_controller.rb
services/api/app/controllers/arvados/v1/keep_services_controller.rb
services/api/app/controllers/arvados/v1/links_controller.rb
services/api/app/controllers/arvados/v1/logs_controller.rb
services/api/app/controllers/arvados/v1/nodes_controller.rb
services/api/app/controllers/arvados/v1/pipeline_instances_controller.rb
services/api/app/controllers/arvados/v1/pipeline_templates_controller.rb
services/api/app/controllers/arvados/v1/repositories_controller.rb
services/api/app/controllers/arvados/v1/schema_controller.rb
services/api/app/controllers/arvados/v1/specimens_controller.rb
services/api/app/controllers/arvados/v1/traits_controller.rb
services/api/app/controllers/arvados/v1/user_agreements_controller.rb
services/api/app/controllers/arvados/v1/users_controller.rb
services/api/app/controllers/arvados/v1/virtual_machines_controller.rb
services/api/app/controllers/arvados/v1/workflows_controller.rb
services/api/app/controllers/database_controller.rb
services/api/app/controllers/static_controller.rb
services/api/app/controllers/user_sessions_controller.rb
services/api/app/helpers/api_client_authorizations_helper.rb
services/api/app/helpers/api_clients_helper.rb
services/api/app/helpers/application_helper.rb
services/api/app/helpers/authorized_keys_helper.rb
services/api/app/helpers/collections_helper.rb
services/api/app/helpers/commit_ancestors_helper.rb
services/api/app/helpers/commits_helper.rb
services/api/app/helpers/groups_helper.rb
services/api/app/helpers/humans_helper.rb
services/api/app/helpers/job_tasks_helper.rb
services/api/app/helpers/jobs_helper.rb
services/api/app/helpers/keep_disks_helper.rb
services/api/app/helpers/links_helper.rb
services/api/app/helpers/logs_helper.rb
services/api/app/helpers/nodes_helper.rb
services/api/app/helpers/pipeline_instances_helper.rb
services/api/app/helpers/pipeline_templates_helper.rb
services/api/app/helpers/repositories_helper.rb
services/api/app/helpers/specimens_helper.rb
services/api/app/helpers/traits_helper.rb
services/api/app/helpers/virtual_machines_helper.rb
services/api/app/mailers/admin_notifier.rb
services/api/app/mailers/profile_notifier.rb
services/api/app/mailers/user_notifier.rb
services/api/app/middlewares/arvados_api_token.rb
services/api/app/middlewares/rack_socket.rb
services/api/app/models/api_client.rb
services/api/app/models/api_client_authorization.rb
services/api/app/models/arvados_model.rb
services/api/app/models/authorized_key.rb
services/api/app/models/blob.rb
services/api/app/models/collection.rb
services/api/app/models/commit.rb
services/api/app/models/commit_ancestor.rb
services/api/app/models/container.rb
services/api/app/models/container_request.rb
services/api/app/models/database_seeds.rb
services/api/app/models/group.rb
services/api/app/models/human.rb
services/api/app/models/job.rb
services/api/app/models/job_task.rb
services/api/app/models/keep_disk.rb
services/api/app/models/keep_service.rb
services/api/app/models/link.rb
services/api/app/models/log.rb
services/api/app/models/node.rb
services/api/app/models/pipeline_instance.rb
services/api/app/models/pipeline_template.rb
services/api/app/models/repository.rb
services/api/app/models/specimen.rb
services/api/app/models/trait.rb
services/api/app/models/user.rb
services/api/app/models/user_agreement.rb
services/api/app/models/virtual_machine.rb
services/api/app/models/workflow.rb
services/api/app/views/admin_notifier/new_inactive_user.text.erb
services/api/app/views/admin_notifier/new_user.text.erb
services/api/app/views/layouts/application.html.erb
services/api/app/views/profile_notifier/profile_created.text.erb
services/api/app/views/static/intro.html.erb
services/api/app/views/static/login_failure.html.erb
services/api/app/views/user_notifier/account_is_setup.text.erb
services/api/app/views/user_sessions/failure.html.erb
services/api/config.ru
services/api/config/application.default.yml
services/api/config/application.rb
services/api/config/application.yml.example
services/api/config/boot.rb
services/api/config/database.yml.example
services/api/config/environment.rb
services/api/config/environments/development.rb.example
services/api/config/environments/production.rb.example
services/api/config/environments/test.rb.example
services/api/config/initializers/andand.rb
services/api/config/initializers/app_version.rb
services/api/config/initializers/authorization.rb
services/api/config/initializers/backtrace_silencers.rb
services/api/config/initializers/common_api_template.rb
services/api/config/initializers/current_api_client.rb
services/api/config/initializers/db_current_time.rb
services/api/config/initializers/eventbus.rb
services/api/config/initializers/fix_www_decode.rb
services/api/config/initializers/inflections.rb
services/api/config/initializers/kind_and_etag.rb
services/api/config/initializers/load_config.rb
services/api/config/initializers/lograge.rb
services/api/config/initializers/mime_types.rb
services/api/config/initializers/net_http.rb
services/api/config/initializers/omniauth_init.rb
services/api/config/initializers/permit_all_parameters.rb
services/api/config/initializers/preload_all_models.rb
services/api/config/initializers/schema_discovery_cache.rb
services/api/config/initializers/session_store.rb
services/api/config/initializers/time_format.rb
services/api/config/initializers/wrap_parameters.rb
services/api/config/locales/en.yml
services/api/config/routes.rb
services/api/db/migrate/20121016005009_create_collections.rb
services/api/db/migrate/20130105203021_create_metadata.rb
services/api/db/migrate/20130105224358_rename_metadata_class.rb
services/api/db/migrate/20130105224618_rename_collection_created_by_client.rb
services/api/db/migrate/20130107181109_add_uuid_to_collections.rb
services/api/db/migrate/20130107212832_create_nodes.rb
services/api/db/migrate/20130109175700_create_pipelines.rb
services/api/db/migrate/20130109220548_create_pipeline_invocations.rb
services/api/db/migrate/20130113214204_add_index_to_collections_and_metadata.rb
services/api/db/migrate/20130116024233_create_specimens.rb
services/api/db/migrate/20130116215213_create_projects.rb
services/api/db/migrate/20130118002239_rename_metadata_attributes.rb
services/api/db/migrate/20130122020042_create_users.rb
services/api/db/migrate/20130122201442_create_logs.rb
services/api/db/migrate/20130122221616_add_modified_at_to_logs.rb
services/api/db/migrate/20130123174514_add_uuid_index_to_users.rb
services/api/db/migrate/20130123180224_create_api_clients.rb
services/api/db/migrate/20130123180228_create_api_client_authorizations.rb
services/api/db/migrate/20130125220425_rename_created_by_to_owner.rb
services/api/db/migrate/20130128202518_rename_metadata_to_links.rb
services/api/db/migrate/20130128231343_add_properties_to_specimen.rb
services/api/db/migrate/20130130205749_add_manifest_text_to_collection.rb
services/api/db/migrate/20130203104818_create_jobs.rb
services/api/db/migrate/20130203104824_create_job_steps.rb
services/api/db/migrate/20130203115329_add_priority_to_jobs.rb
services/api/db/migrate/20130207195855_add_index_on_timestamps.rb
services/api/db/migrate/20130218181504_add_properties_to_pipeline_invocations.rb
services/api/db/migrate/20130226170000_remove_native_target_from_links.rb
services/api/db/migrate/20130313175417_rename_projects_to_groups.rb
services/api/db/migrate/20130315155820_add_is_locked_by_to_jobs.rb
services/api/db/migrate/20130315183626_add_log_to_jobs.rb
services/api/db/migrate/20130315213205_add_tasks_summary_to_jobs.rb
services/api/db/migrate/20130318002138_add_resource_limits_to_jobs.rb
services/api/db/migrate/20130319165853_rename_job_command_to_script.rb
services/api/db/migrate/20130319180730_rename_pipeline_invocation_to_pipeline_instance.rb
services/api/db/migrate/20130319194637_rename_pipelines_to_pipeline_templates.rb
services/api/db/migrate/20130319201431_rename_job_steps_to_job_tasks.rb
services/api/db/migrate/20130319235957_add_default_owner_to_users.rb
services/api/db/migrate/20130320000107_add_default_owner_to_api_client_authorizations.rb
services/api/db/migrate/20130326173804_create_commits.rb
services/api/db/migrate/20130326182917_create_commit_ancestors.rb
services/api/db/migrate/20130415020241_rename_orvos_to_arvados.rb
services/api/db/migrate/20130425024459_create_keep_disks.rb
services/api/db/migrate/20130425214427_add_service_host_and_service_port_and_service_ssl_flag_to_keep_disks.rb
services/api/db/migrate/20130523060112_add_created_by_job_task_to_job_tasks.rb
services/api/db/migrate/20130523060213_add_qsequence_to_job_tasks.rb
services/api/db/migrate/20130524042319_fix_job_task_qsequence_type.rb
services/api/db/migrate/20130528134100_update_nodes_index.rb
services/api/db/migrate/20130606183519_create_authorized_keys.rb
services/api/db/migrate/20130608053730_create_virtual_machines.rb
services/api/db/migrate/20130610202538_create_repositories.rb
services/api/db/migrate/20130611163736_rename_authorized_key_authorized_user_to_authorized_user_uuid.rb
services/api/db/migrate/20130612042554_add_name_unique_index_to_repositories.rb
services/api/db/migrate/20130617150007_add_is_trusted_to_api_clients.rb
services/api/db/migrate/20130626002829_add_is_active_to_users.rb
services/api/db/migrate/20130626022810_activate_all_admins.rb
services/api/db/migrate/20130627154537_create_traits.rb
services/api/db/migrate/20130627184333_create_humans.rb
services/api/db/migrate/20130708163414_rename_foreign_uuid_attributes.rb
services/api/db/migrate/20130708182912_rename_job_foreign_uuid_attributes.rb
services/api/db/migrate/20130708185153_rename_user_default_owner.rb
services/api/db/migrate/20130724153034_add_scopes_to_api_client_authorizations.rb
services/api/db/migrate/20131007180607_rename_resource_limits_to_runtime_constraints.rb
services/api/db/migrate/20140117231056_normalize_collection_uuid.rb
services/api/db/migrate/20140124222114_fix_link_kind_underscores.rb
services/api/db/migrate/20140129184311_normalize_collection_uuids_in_script_parameters.rb
services/api/db/migrate/20140317135600_add_nondeterministic_column_to_job.rb
services/api/db/migrate/20140319160547_separate_repository_from_script_version.rb
services/api/db/migrate/20140321191343_add_repository_column_to_job.rb
services/api/db/migrate/20140324024606_add_output_is_persistent_to_job.rb
services/api/db/migrate/20140325175653_remove_kind_columns.rb
services/api/db/migrate/20140402001908_add_system_group.rb
services/api/db/migrate/20140407184311_rename_log_info_to_properties.rb
services/api/db/migrate/20140421140924_add_group_class_to_groups.rb
services/api/db/migrate/20140421151939_rename_auth_keys_user_index.rb
services/api/db/migrate/20140421151940_timestamps_not_null.rb
services/api/db/migrate/20140422011506_pipeline_instance_state.rb
services/api/db/migrate/20140423132913_add_object_owner_to_logs.rb
services/api/db/migrate/20140423133559_new_scope_format.rb
services/api/db/migrate/20140501165548_add_unique_name_index_to_links.rb
services/api/db/migrate/20140519205916_create_keep_services.rb
services/api/db/migrate/20140527152921_add_description_to_pipeline_templates.rb
services/api/db/migrate/20140530200539_add_supplied_script_version.rb
services/api/db/migrate/20140601022548_remove_name_from_collections.rb
services/api/db/migrate/20140602143352_remove_active_and_success_from_pipeline_instances.rb
services/api/db/migrate/20140607150616_rename_folder_to_project.rb
services/api/db/migrate/20140611173003_add_docker_locator_to_jobs.rb
services/api/db/migrate/20140627210837_anonymous_group.rb
services/api/db/migrate/20140709172343_job_task_serial_qsequence.rb
services/api/db/migrate/20140714184006_empty_collection.rb
services/api/db/migrate/20140811184643_collection_use_regular_uuids.rb
services/api/db/migrate/20140817035914_add_unique_name_constraints.rb
services/api/db/migrate/20140818125735_add_not_null_constraint_to_group_name.rb
services/api/db/migrate/20140826180337_remove_output_is_persistent_column.rb
services/api/db/migrate/20140828141043_job_priority_fixup.rb
services/api/db/migrate/20140909183946_add_start_finish_time_to_tasks_and_pipelines.rb
services/api/db/migrate/20140911221252_add_description_to_pipeline_instances_and_jobs.rb
services/api/db/migrate/20140918141529_change_user_owner_uuid_not_null.rb
services/api/db/migrate/20140918153541_add_properties_to_node.rb
services/api/db/migrate/20140918153705_add_state_to_job.rb
services/api/db/migrate/20140924091559_add_job_uuid_to_nodes.rb
services/api/db/migrate/20141111133038_add_arvados_sdk_version_to_jobs.rb
services/api/db/migrate/20141208164553_owner_uuid_index.rb
services/api/db/migrate/20141208174553_descriptions_are_strings.rb
services/api/db/migrate/20141208174653_collection_file_names.rb
services/api/db/migrate/20141208185217_search_index.rb
services/api/db/migrate/20150122175935_no_description_in_search_index.rb
services/api/db/migrate/20150123142953_full_text_search.rb
services/api/db/migrate/20150203180223_set_group_class_on_anonymous_group.rb
services/api/db/migrate/20150206210804_all_users_can_read_anonymous_group.rb
services/api/db/migrate/20150206230342_rename_replication_attributes.rb
services/api/db/migrate/20150216193428_collection_name_owner_unique_only_non_expired.rb
services/api/db/migrate/20150303210106_fix_collection_portable_data_hash_with_hinted_manifest.rb
services/api/db/migrate/20150312151136_change_collection_expires_at_to_datetime.rb
services/api/db/migrate/20150317132720_add_username_to_users.rb
services/api/db/migrate/20150324152204_backward_compatibility_for_user_repositories.rb
services/api/db/migrate/20150423145759_no_filenames_in_collection_search_index.rb
services/api/db/migrate/20150512193020_read_only_on_keep_services.rb
services/api/db/migrate/20150526180251_leading_space_on_full_text_index.rb
services/api/db/migrate/20151202151426_create_containers_and_requests.rb
services/api/db/migrate/20151215134304_fix_containers_index.rb
services/api/db/migrate/20151229214707_add_exit_code_to_containers.rb
services/api/db/migrate/20160208210629_add_uuid_to_api_client_authorization.rb
services/api/db/migrate/20160209155729_add_uuid_to_api_token_search_index.rb
services/api/db/migrate/20160324144017_add_components_to_job.rb
services/api/db/migrate/20160506175108_add_auths_to_container.rb
services/api/db/migrate/20160509143250_add_auth_and_lock_to_container_index.rb
services/api/db/migrate/20160808151559_create_workflows.rb
services/api/db/migrate/20160819195557_add_script_parameters_digest_to_jobs.rb
services/api/db/migrate/20160819195725_populate_script_parameters_digest.rb
services/api/db/migrate/20160901210110_repair_script_parameters_digest.rb
services/api/db/migrate/20160909181442_rename_workflow_to_definition.rb
services/api/db/migrate/20160926194129_add_container_count.rb
services/api/db/migrate/20161019171346_add_use_existing_to_container_requests.rb
services/api/db/migrate/20161111143147_add_scheduling_parameters_to_container.rb
services/api/db/migrate/20161115171221_add_output_and_log_uuid_to_container_request.rb
services/api/db/migrate/20161115174218_add_output_and_log_uuids_to_container_request_search_index.rb
services/api/db/migrate/20161213172944_full_text_search_indexes.rb
services/api/db/migrate/20161222153434_split_expiry_to_trash_and_delete.rb
services/api/db/migrate/20161223090712_add_output_name_to_container_requests.rb
services/api/db/migrate/20170102153111_add_output_name_to_container_request_search_index.rb
services/api/db/migrate/20170105160301_add_output_name_to_cr_fts_index.rb
services/api/db/migrate/20170105160302_set_finished_at_on_finished_pipeline_instances.rb
services/api/db/migrate/20170216170823_no_cr_mounts_and_workflow_def_in_full_text_search_index.rb
services/api/db/migrate/20170301225558_no_downgrade_after_json.rb
services/api/db/migrate/20170319063406_serialized_columns_accept_null.rb
services/api/db/migrate/20170328215436_add_portable_data_hash_index_to_collections.rb
services/api/db/migrate/20170330012505_add_output_ttl_to_container_requests.rb
services/api/db/migrate/20170419173031_add_created_by_job_task_index_to_job_tasks.rb
services/api/db/migrate/20170419173712_add_object_owner_index_to_logs.rb
services/api/db/migrate/20170419175801_add_requesting_container_index_to_container_requests.rb
services/api/db/seeds.rb
services/api/db/structure.sql
services/api/fpm-info.sh
services/api/lib/app_version.rb
services/api/lib/audit_logs.rb
services/api/lib/can_be_an_owner.rb
services/api/lib/common_api_template.rb
services/api/lib/create_ancestor_view.sql
services/api/lib/create_permission_view.sql
services/api/lib/create_superuser_token.rb
services/api/lib/crunch_dispatch.rb
services/api/lib/current_api_client.rb
services/api/lib/db_current_time.rb
services/api/lib/has_uuid.rb
services/api/lib/josh_id.rb
services/api/lib/kind_and_etag.rb
services/api/lib/load_param.rb
services/api/lib/log_reuse_info.rb
services/api/lib/record_filters.rb
services/api/lib/safe_json.rb
services/api/lib/salvage_collection.rb
services/api/lib/serializers.rb
services/api/lib/simulate_job_log.rb
services/api/lib/sweep_trashed_collections.rb
services/api/lib/tasks/config_check.rake
services/api/lib/tasks/config_dump.rake
services/api/lib/tasks/delete_old_container_logs.rake
services/api/lib/tasks/delete_old_job_logs.rake
services/api/lib/tasks/replay_job_log.rake
services/api/lib/tasks/test_tasks.rake
services/api/lib/whitelist_update.rb
services/api/public/404.html
services/api/public/422.html
services/api/public/500.html
services/api/script/arvados-git-sync.rb
services/api/script/create_superuser_token.rb
services/api/script/crunch-dispatch.rb
services/api/script/crunch_failure_report.py
services/api/script/fail-jobs.rb
services/api/script/get_anonymous_user_token.rb
services/api/script/migrate-gitolite-to-uuid-storage.rb
services/api/script/permission-updater.rb
services/api/script/rake_test.sh
services/api/script/restart-dns-server
services/api/script/salvage_collection.rb
services/api/script/setup-new-user.rb
services/api/test/factories/api_client.rb
services/api/test/factories/api_client_authorization.rb
services/api/test/factories/group.rb
services/api/test/factories/link.rb
services/api/test/factories/user.rb
services/api/test/fixtures/api_client_authorizations.yml
services/api/test/fixtures/api_clients.yml
services/api/test/fixtures/authorized_keys.yml
services/api/test/fixtures/collections.yml
services/api/test/fixtures/container_requests.yml
services/api/test/fixtures/containers.yml
services/api/test/fixtures/groups.yml
services/api/test/fixtures/humans.yml
services/api/test/fixtures/job_tasks.yml
services/api/test/fixtures/jobs.yml
services/api/test/fixtures/keep_disks.yml
services/api/test/fixtures/keep_services.yml
services/api/test/fixtures/links.yml
services/api/test/fixtures/logs.yml
services/api/test/fixtures/nodes.yml
services/api/test/fixtures/pipeline_instances.yml
services/api/test/fixtures/pipeline_templates.yml
services/api/test/fixtures/repositories.yml
services/api/test/fixtures/specimens.yml
services/api/test/fixtures/traits.yml
services/api/test/fixtures/users.yml
services/api/test/fixtures/virtual_machines.yml
services/api/test/fixtures/workflows.yml
services/api/test/functional/application_controller_test.rb
services/api/test/functional/arvados/v1/api_client_authorizations_controller_test.rb
services/api/test/functional/arvados/v1/authorized_keys_controller_test.rb
services/api/test/functional/arvados/v1/collections_controller_test.rb
services/api/test/functional/arvados/v1/commits_controller_test.rb
services/api/test/functional/arvados/v1/container_requests_controller_test.rb
services/api/test/functional/arvados/v1/containers_controller_test.rb
services/api/test/functional/arvados/v1/filters_test.rb
services/api/test/functional/arvados/v1/groups_controller_test.rb
services/api/test/functional/arvados/v1/humans_controller_test.rb
services/api/test/functional/arvados/v1/job_reuse_controller_test.rb
services/api/test/functional/arvados/v1/job_tasks_controller_test.rb
services/api/test/functional/arvados/v1/jobs_controller_test.rb
services/api/test/functional/arvados/v1/keep_disks_controller_test.rb
services/api/test/functional/arvados/v1/keep_services_controller_test.rb
services/api/test/functional/arvados/v1/links_controller_test.rb
services/api/test/functional/arvados/v1/logs_controller_test.rb
services/api/test/functional/arvados/v1/nodes_controller_test.rb
services/api/test/functional/arvados/v1/pipeline_instances_controller_test.rb
services/api/test/functional/arvados/v1/pipeline_templates_controller_test.rb
services/api/test/functional/arvados/v1/query_test.rb
services/api/test/functional/arvados/v1/repositories_controller_test.rb
services/api/test/functional/arvados/v1/schema_controller_test.rb
services/api/test/functional/arvados/v1/specimens_controller_test.rb
services/api/test/functional/arvados/v1/traits_controller_test.rb
services/api/test/functional/arvados/v1/user_agreements_controller_test.rb
services/api/test/functional/arvados/v1/users_controller_test.rb
services/api/test/functional/arvados/v1/virtual_machines_controller_test.rb
services/api/test/functional/database_controller_test.rb
services/api/test/functional/user_sessions_controller_test.rb
services/api/test/helpers/docker_migration_helper.rb
services/api/test/helpers/git_test_helper.rb
services/api/test/helpers/manifest_examples.rb
services/api/test/helpers/time_block.rb
services/api/test/helpers/users_test_helper.rb
services/api/test/integration/api_client_authorizations_api_test.rb
services/api/test/integration/api_client_authorizations_scopes_test.rb
services/api/test/integration/collections_api_test.rb
services/api/test/integration/collections_performance_test.rb
services/api/test/integration/cross_origin_test.rb
services/api/test/integration/crunch_dispatch_test.rb
services/api/test/integration/database_reset_test.rb
services/api/test/integration/errors_test.rb
services/api/test/integration/groups_test.rb
services/api/test/integration/jobs_api_test.rb
services/api/test/integration/keep_proxy_test.rb
services/api/test/integration/login_workflow_test.rb
services/api/test/integration/noop_deep_munge_test.rb
services/api/test/integration/permissions_test.rb
services/api/test/integration/pipeline_test.rb
services/api/test/integration/reader_tokens_test.rb
services/api/test/integration/select_test.rb
services/api/test/integration/serialized_encoding_test.rb
services/api/test/integration/user_sessions_test.rb
services/api/test/integration/users_test.rb
services/api/test/integration/valid_links_test.rb
services/api/test/performance/links_index_test.rb
services/api/test/tasks/delete_old_container_logs_test.rb
services/api/test/tasks/delete_old_job_logs_test.rb
services/api/test/test_helper.rb
services/api/test/unit/api_client_authorization_test.rb
services/api/test/unit/api_client_test.rb
services/api/test/unit/app_version_test.rb
services/api/test/unit/application_test.rb
services/api/test/unit/arvados_model_test.rb
services/api/test/unit/authorized_key_test.rb
services/api/test/unit/blob_test.rb
services/api/test/unit/collection_performance_test.rb
services/api/test/unit/collection_test.rb
services/api/test/unit/commit_ancestor_test.rb
services/api/test/unit/commit_test.rb
services/api/test/unit/container_request_test.rb
services/api/test/unit/container_test.rb
services/api/test/unit/create_superuser_token_test.rb
services/api/test/unit/crunch_dispatch_test.rb
services/api/test/unit/fail_jobs_test.rb
services/api/test/unit/group_test.rb
services/api/test/unit/helpers/api_client_authorizations_helper_test.rb
services/api/test/unit/helpers/api_clients_helper_test.rb
services/api/test/unit/helpers/authorized_keys_helper_test.rb
services/api/test/unit/helpers/collections_helper_test.rb
services/api/test/unit/helpers/commit_ancestors_helper_test.rb
services/api/test/unit/helpers/commits_helper_test.rb
services/api/test/unit/helpers/groups_helper_test.rb
services/api/test/unit/helpers/humans_helper_test.rb
services/api/test/unit/helpers/job_tasks_helper_test.rb
services/api/test/unit/helpers/jobs_helper_test.rb
services/api/test/unit/helpers/keep_disks_helper_test.rb
services/api/test/unit/helpers/links_helper_test.rb
services/api/test/unit/helpers/logs_helper_test.rb
services/api/test/unit/helpers/nodes_helper_test.rb
services/api/test/unit/helpers/pipeline_instances_helper_test.rb
services/api/test/unit/helpers/pipeline_templates_helper_test.rb
services/api/test/unit/helpers/repositories_helper_test.rb
services/api/test/unit/helpers/specimens_helper_test.rb
services/api/test/unit/helpers/traits_helper_test.rb
services/api/test/unit/helpers/virtual_machines_helper_test.rb
services/api/test/unit/human_test.rb
services/api/test/unit/job_task_test.rb
services/api/test/unit/job_test.rb
services/api/test/unit/keep_disk_test.rb
services/api/test/unit/keep_service_test.rb
services/api/test/unit/link_test.rb
services/api/test/unit/log_test.rb
services/api/test/unit/node_test.rb
services/api/test/unit/owner_test.rb
services/api/test/unit/permission_test.rb
services/api/test/unit/pipeline_instance_test.rb
services/api/test/unit/pipeline_template_test.rb
services/api/test/unit/repository_test.rb
services/api/test/unit/salvage_collection_test.rb
services/api/test/unit/seralizer_test.rb
services/api/test/unit/specimen_test.rb
services/api/test/unit/trait_test.rb
services/api/test/unit/user_notifier_test.rb
services/api/test/unit/user_test.rb
services/api/test/unit/virtual_machine_test.rb
services/api/test/unit/workflow_test.rb
services/arv-git-httpd/arvados-git-httpd.service
services/arv-git-httpd/auth_handler.go
services/arv-git-httpd/git_handler.go
services/arv-git-httpd/git_handler_test.go
services/arv-git-httpd/gitolite_test.go
services/arv-git-httpd/integration_test.go
services/arv-git-httpd/main.go
services/arv-git-httpd/server.go
services/arv-git-httpd/server_test.go
services/arv-git-httpd/usage.go
services/arv-web/arv-web.py
services/arv-web/sample-rack-app/config.ru
services/arv-web/sample-static-page/public/index.html
services/arv-web/sample-wsgi-app/passenger_wsgi.py
services/crunch-dispatch-local/crunch-dispatch-local.go
services/crunch-dispatch-local/crunch-dispatch-local_test.go
services/crunch-dispatch-slurm/crunch-dispatch-slurm.go
services/crunch-dispatch-slurm/crunch-dispatch-slurm.service
services/crunch-dispatch-slurm/crunch-dispatch-slurm_test.go
services/crunch-dispatch-slurm/script.go
services/crunch-dispatch-slurm/script_test.go
services/crunch-dispatch-slurm/squeue.go
services/crunch-dispatch-slurm/usage.go
services/crunch-run/cgroup.go
services/crunch-run/cgroup_test.go
services/crunch-run/crunchrun.go
services/crunch-run/crunchrun_test.go
services/crunch-run/logging.go
services/crunch-run/logging_test.go
services/crunch-run/upload.go
services/crunch-run/upload_test.go
services/crunchstat/crunchstat.go
services/crunchstat/crunchstat_test.go
services/dockercleaner/MANIFEST.in
services/dockercleaner/arvados-docker-cleaner.service
services/dockercleaner/arvados_docker/cleaner.py
services/dockercleaner/setup.py
services/dockercleaner/tests/__init__.py
services/dockercleaner/tests/test_cleaner.py
services/fuse/MANIFEST.in
services/fuse/README.rst
services/fuse/arvados_fuse/__init__.py
services/fuse/arvados_fuse/_version.py
services/fuse/arvados_fuse/command.py
services/fuse/arvados_fuse/crunchstat.py
services/fuse/arvados_fuse/fresh.py
services/fuse/arvados_fuse/fusedir.py
services/fuse/arvados_fuse/fusefile.py
services/fuse/arvados_fuse/unmount.py
services/fuse/bin/arv-mount
services/fuse/fpm-info.sh
services/fuse/setup.py
services/fuse/tests/fstest.py
services/fuse/tests/integration_test.py
services/fuse/tests/mount_test_base.py
services/fuse/tests/performance/test_collection_performance.py
services/fuse/tests/prof.py
services/fuse/tests/test_cache.py
services/fuse/tests/test_command_args.py
services/fuse/tests/test_crunchstat.py
services/fuse/tests/test_exec.py
services/fuse/tests/test_inodes.py
services/fuse/tests/test_mount.py
services/fuse/tests/test_mount_type.py
services/fuse/tests/test_retry.py
services/fuse/tests/test_tmp_collection.py
services/fuse/tests/test_token_expiry.py
services/fuse/tests/test_unmount.py
services/keep-balance/balance.go
services/keep-balance/balance_run_test.go
services/keep-balance/balance_test.go
services/keep-balance/block_state.go
services/keep-balance/change_set.go
services/keep-balance/change_set_test.go
services/keep-balance/collection.go
services/keep-balance/collection_test.go
services/keep-balance/integration_test.go
services/keep-balance/keep-balance.service
services/keep-balance/keep_service.go
services/keep-balance/main.go
services/keep-balance/main_test.go
services/keep-balance/time_me.go
services/keep-balance/usage.go
services/keep-web/cache.go
services/keep-web/cache_test.go
services/keep-web/doc.go
services/keep-web/handler.go
services/keep-web/handler_test.go
services/keep-web/keep-web.service
services/keep-web/main.go
services/keep-web/ranges_test.go
services/keep-web/server.go
services/keep-web/server_test.go
services/keep-web/status_test.go
services/keep-web/usage.go
services/keep/tools/traffic_test.py
services/keepproxy/keepproxy.go
services/keepproxy/keepproxy.service
services/keepproxy/keepproxy_test.go
services/keepproxy/pkg-extras/etc/init.d/keepproxy
services/keepproxy/proxy_client.go
services/keepproxy/usage.go
services/keepstore/azure_blob_volume.go
services/keepstore/azure_blob_volume_test.go
services/keepstore/bufferpool.go
services/keepstore/bufferpool_test.go
services/keepstore/collision.go
services/keepstore/collision_test.go
services/keepstore/config.go
services/keepstore/config_test.go
services/keepstore/count.go
services/keepstore/deprecated.go
services/keepstore/gocheck_test.go
services/keepstore/handler_test.go
services/keepstore/handlers.go
services/keepstore/handlers_with_generic_volume_test.go
services/keepstore/keepstore.go
services/keepstore/keepstore.service
services/keepstore/keepstore_test.go
services/keepstore/logging_router.go
services/keepstore/logging_router_test.go
services/keepstore/mock_mutex_for_test.go
services/keepstore/mounts_test.go
services/keepstore/perms.go
services/keepstore/perms_test.go
services/keepstore/pipe_adapters.go
services/keepstore/pull_worker.go
services/keepstore/pull_worker_integration_test.go
services/keepstore/pull_worker_test.go
services/keepstore/s3_volume.go
services/keepstore/s3_volume_test.go
services/keepstore/stats_ticker.go
services/keepstore/status_test.go
services/keepstore/trash_worker.go
services/keepstore/trash_worker_test.go
services/keepstore/usage.go
services/keepstore/volume.go
services/keepstore/volume_generic_test.go
services/keepstore/volume_test.go
services/keepstore/volume_unix.go
services/keepstore/volume_unix_test.go
services/keepstore/work_queue.go
services/keepstore/work_queue_test.go
services/login-sync/Gemfile
services/login-sync/Rakefile
services/login-sync/arvados-login-sync.gemspec
services/login-sync/bin/arvados-login-sync
services/login-sync/test/binstub_new_user/useradd
services/login-sync/test/stubs.rb
services/login-sync/test/test_add_user.rb
services/nodemanager/MANIFEST.in
services/nodemanager/README.rst
services/nodemanager/arvnodeman/__init__.py
services/nodemanager/arvnodeman/_version.py
services/nodemanager/arvnodeman/baseactor.py
services/nodemanager/arvnodeman/clientactor.py
services/nodemanager/arvnodeman/computenode/__init__.py
services/nodemanager/arvnodeman/computenode/dispatch/__init__.py
services/nodemanager/arvnodeman/computenode/dispatch/slurm.py
services/nodemanager/arvnodeman/computenode/dispatch/transitions.py
services/nodemanager/arvnodeman/computenode/driver/__init__.py
services/nodemanager/arvnodeman/computenode/driver/azure.py
services/nodemanager/arvnodeman/computenode/driver/dummy.py
services/nodemanager/arvnodeman/computenode/driver/ec2.py
services/nodemanager/arvnodeman/computenode/driver/gce.py
services/nodemanager/arvnodeman/config.py
services/nodemanager/arvnodeman/daemon.py
services/nodemanager/arvnodeman/jobqueue.py
services/nodemanager/arvnodeman/launcher.py
services/nodemanager/arvnodeman/nodelist.py
services/nodemanager/arvnodeman/status.py
services/nodemanager/arvnodeman/test/__init__.py
services/nodemanager/arvnodeman/test/fake_driver.py
services/nodemanager/arvnodeman/timedcallback.py
services/nodemanager/bin/arvados-node-manager
services/nodemanager/doc/azure.example.cfg
services/nodemanager/doc/ec2.example.cfg
services/nodemanager/doc/gce.example.cfg
services/nodemanager/doc/local.example.cfg
services/nodemanager/setup.py
services/nodemanager/tests/__init__.py
services/nodemanager/tests/fake_azure.cfg.template
services/nodemanager/tests/fake_ec2.cfg.template
services/nodemanager/tests/fake_gce.cfg.template
services/nodemanager/tests/integration_test.py
services/nodemanager/tests/test_arguments.py
services/nodemanager/tests/test_clientactor.py
services/nodemanager/tests/test_computenode.py
services/nodemanager/tests/test_computenode_dispatch.py
services/nodemanager/tests/test_computenode_dispatch_slurm.py
services/nodemanager/tests/test_computenode_driver.py
services/nodemanager/tests/test_computenode_driver_azure.py
services/nodemanager/tests/test_computenode_driver_ec2.py
services/nodemanager/tests/test_computenode_driver_gce.py
services/nodemanager/tests/test_config.py
services/nodemanager/tests/test_daemon.py
services/nodemanager/tests/test_failure.py
services/nodemanager/tests/test_jobqueue.py
services/nodemanager/tests/test_nodelist.py
services/nodemanager/tests/test_status.py
services/nodemanager/tests/test_timedcallback.py
services/nodemanager/tests/testutil.py
services/ws/arvados-ws.service
services/ws/config.go
services/ws/doc.go
services/ws/event.go
services/ws/event_source.go
services/ws/event_source_test.go
services/ws/event_test.go
services/ws/gocheck_test.go
services/ws/handler.go
services/ws/main.go
services/ws/permission.go
services/ws/permission_test.go
services/ws/router.go
services/ws/server.go
services/ws/server_test.go
services/ws/session.go
services/ws/session_v0.go
services/ws/session_v0_test.go
services/ws/session_v1.go
tools/arvbash/arvbash.sh
tools/arvbox/bin/arvbox
tools/arvbox/lib/arvbox/docker/Dockerfile.base
tools/arvbox/lib/arvbox/docker/Dockerfile.demo
tools/arvbox/lib/arvbox/docker/Dockerfile.dev
tools/arvbox/lib/arvbox/docker/api-setup.sh
tools/arvbox/lib/arvbox/docker/application_yml_override.py
tools/arvbox/lib/arvbox/docker/common.sh
tools/arvbox/lib/arvbox/docker/createusers.sh
tools/arvbox/lib/arvbox/docker/crunch-setup.sh
tools/arvbox/lib/arvbox/docker/fuse.conf
tools/arvbox/lib/arvbox/docker/gitolite.rc
tools/arvbox/lib/arvbox/docker/keep-setup.sh
tools/arvbox/lib/arvbox/docker/logger
tools/arvbox/lib/arvbox/docker/runsu.sh
tools/arvbox/lib/arvbox/docker/service/api/run-service
tools/arvbox/lib/arvbox/docker/service/arv-git-httpd/run-service
tools/arvbox/lib/arvbox/docker/service/crunch-dispatch-local/run-service
tools/arvbox/lib/arvbox/docker/service/crunch-dispatch0/run-service
tools/arvbox/lib/arvbox/docker/service/crunch-dispatch1/run-service
tools/arvbox/lib/arvbox/docker/service/doc/run-service
tools/arvbox/lib/arvbox/docker/service/docker/run
tools/arvbox/lib/arvbox/docker/service/gitolite/run-service
tools/arvbox/lib/arvbox/docker/service/keep-web/run-service
tools/arvbox/lib/arvbox/docker/service/keepproxy/run-service
tools/arvbox/lib/arvbox/docker/service/keepstore0/run-service
tools/arvbox/lib/arvbox/docker/service/keepstore1/run-service
tools/arvbox/lib/arvbox/docker/service/postgres/run
tools/arvbox/lib/arvbox/docker/service/postgres/run-service
tools/arvbox/lib/arvbox/docker/service/ready/run-service
tools/arvbox/lib/arvbox/docker/service/sdk/run
tools/arvbox/lib/arvbox/docker/service/sdk/run-service
tools/arvbox/lib/arvbox/docker/service/slurmctld/run
tools/arvbox/lib/arvbox/docker/service/slurmd/run
tools/arvbox/lib/arvbox/docker/service/ssh/run
tools/arvbox/lib/arvbox/docker/service/sso/run-service
tools/arvbox/lib/arvbox/docker/service/vm/run
tools/arvbox/lib/arvbox/docker/service/vm/run-service
tools/arvbox/lib/arvbox/docker/service/websockets/run-service
tools/arvbox/lib/arvbox/docker/service/workbench/run
tools/arvbox/lib/arvbox/docker/service/workbench/run-service
tools/arvbox/lib/arvbox/docker/waitforpostgres.sh
tools/crunchstat-summary/MANIFEST.in
tools/crunchstat-summary/bin/crunchstat-summary
tools/crunchstat-summary/crunchstat_summary/__init__.py
tools/crunchstat-summary/crunchstat_summary/chartjs.js
tools/crunchstat-summary/crunchstat_summary/chartjs.py
tools/crunchstat-summary/crunchstat_summary/command.py
tools/crunchstat-summary/crunchstat_summary/reader.py
tools/crunchstat-summary/crunchstat_summary/summarizer.py
tools/crunchstat-summary/setup.py
tools/crunchstat-summary/tests/test_examples.py
tools/keep-block-check/keep-block-check.go
tools/keep-block-check/keep-block-check_test.go
tools/keep-exercise/keep-exercise.go
tools/keep-rsync/keep-rsync.go
tools/keep-rsync/keep-rsync_test.go