[ARVADOS] updated: 9849da2fdac89ec7f0b58dd9f1cfe466b6c7cdc1

Git user git at public.curoverse.com
Tue Jul 4 22:22:43 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 |   4 +
 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    |   4 +
 .../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      |   4 +
 .../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     |  74 +++++-
 .../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 |  26 +-
 .../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            |   4 +
 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     |   4 +
 .../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  |   4 +
 .../app/views/collections/_show_tags.html.erb      |   4 +
 .../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         |   4 +
 .../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   |   4 +
 .../_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     |  10 +-
 .../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 +
 .../_add_repository_modal.html.erb                 |   4 +
 .../repositories/_repository_breadcrumbs.html.erb  |   4 +
 .../app/views/repositories/_show_help.html.erb     |  12 +-
 .../views/repositories/_show_repositories.html.erb |  46 ++++
 .../repositories/_show_repositories_rows.html.erb  |  23 ++
 .../app/views/repositories/show_blob.html.erb      |   4 +
 .../app/views/repositories/show_commit.html.erb    |   4 +
 .../app/views/repositories/show_tree.html.erb      |   4 +
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 .../app/views/search/_choose_rows.html.erb         |   3 +
 apps/workbench/app/views/sessions/index.html.erb   |   4 +
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 .../app/views/users/_add_group_modal.html.erb      |   4 +
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 .../app/views/users/_choose_rows.html.erb          |   4 +
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 apps/workbench/app/views/users/_home.html.erb      |   4 +
 .../app/views/users/_repositories.html.erb         |  67 -----
 .../app/views/users/_setup_popup.html.erb          |   4 +
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 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 +
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 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 +
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 apps/workbench/app/views/users/welcome.html.erb    |   4 +
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 .../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 +
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 1839 files changed, 7944 insertions(+), 337 deletions(-)
 rename apps/workbench/app/views/{users => repositories}/_add_repository_modal.html.erb (95%)
 create mode 100644 apps/workbench/app/views/repositories/_show_repositories.html.erb
 create mode 100644 apps/workbench/app/views/repositories/_show_repositories_rows.html.erb
 delete mode 100644 apps/workbench/app/views/users/_repositories.html.erb
 delete mode 100644 apps/workbench/app/views/users/repositories.html.erb
 create mode 100644 sdk/cwl/tests/stdout.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
 create mode 100644 services/api/db/migrate/20170704160233_yaml_to_json.rb

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commit 9849da2fdac89ec7f0b58dd9f1cfe466b6c7cdc1
Author: Tom Clegg <tom at curoverse.com>
Date:   Tue Jul 4 22:14:23 2017 -0400

    11807: Migrate data from YAML to JSON.
    
    Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curoverse.com>

diff --git a/services/api/db/migrate/20170704160233_yaml_to_json.rb b/services/api/db/migrate/20170704160233_yaml_to_json.rb
new file mode 100644
index 0000000..dfa08db
--- /dev/null
+++ b/services/api/db/migrate/20170704160233_yaml_to_json.rb
@@ -0,0 +1,37 @@
+require 'migrate_yaml_to_json'
+
+class YamlToJson < ActiveRecord::Migration
+  def up
+    [
+      ['collections', 'properties'],
+      ['containers', 'environment'],
+      ['containers', 'mounts'],
+      ['containers', 'runtime_constraints'],
+      ['containers', 'command'],
+      ['containers', 'scheduling_parameters'],
+      ['container_requests', 'properties'],
+      ['container_requests', 'environment'],
+      ['container_requests', 'mounts'],
+      ['container_requests', 'runtime_constraints'],
+      ['container_requests', 'command'],
+      ['container_requests', 'scheduling_parameters'],
+      ['humans', 'properties'],
+      ['job_tasks', 'parameters'],
+      ['links', 'properties'],
+      ['nodes', 'info'],
+      ['nodes', 'properties'],
+      ['pipeline_instances', 'components'],
+      ['pipeline_instances', 'properties'],
+      ['pipeline_instances', 'components_summary'],
+      ['pipeline_templates', 'components'],
+      ['specimens', 'properties'],
+      ['traits', 'properties'],
+      ['users', 'prefs'],
+    ].each do |table, column|
+      MigrateYAMLToJSON.migrate(table, column)
+    end
+  end
+
+  def down
+  end
+end
diff --git a/services/api/db/structure.sql b/services/api/db/structure.sql
index 7e6bb1d..a10baab 100644
--- a/services/api/db/structure.sql
+++ b/services/api/db/structure.sql
@@ -2791,3 +2791,5 @@ INSERT INTO schema_migrations (version) VALUES ('20170419175801');
 
 INSERT INTO schema_migrations (version) VALUES ('20170628185847');
 
+INSERT INTO schema_migrations (version) VALUES ('20170704160233');
+

commit db9486508802d77d6e2baee897128cddc9079179
Author: Tom Clegg <tom at curoverse.com>
Date:   Tue Jul 4 22:13:36 2017 -0400

    2411: Fix regex usage.
    
    Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curoverse.com>

diff --git a/services/api/Rakefile b/services/api/Rakefile
index 3136cdd..fad803c 100644
--- a/services/api/Rakefile
+++ b/services/api/Rakefile
@@ -43,7 +43,7 @@ namespace :db do
         origfile = File.new origfnm
         origfile.each_line do |line|
           if !copyright_done
-            if !/Copyright .* Arvados/
+            if !/Copyright .* Arvados/.match(line)
                tmpfile.write "-- Copyright (C) The Arvados Authors. All rights reserved.\n--\n-- SPDX-License-Identifier: AGPL-3.0\n\n"
             end
             copyright_done = true

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