├── .circleci ├── config.yml ├── heroku-app-name.sh ├── install_node.sh ├── report_coverage.rb └── required-config-var-names ├── .env ├── .gitignore ├── .rspec ├── .simplecov ├── Docker.README.md ├── Dockerfile ├── Gemfile ├── Gemfile.lock ├── GitlabCI.md ├── LICENSE.txt ├── Procfile ├── README.md ├── README.rdoc ├── Rakefile ├── api_design ├── DDS-1061-optimized_directory_structure_endpoint.md ├── DDS-1083-unique-project-slugs.md ├── DDS-1182-nonchucked_upload_api_design.md ├── DDS-826-reworking_search.md ├── DDS-829-trash_bin.md ├── DDS-872-eventual_consistency_status.md ├── DDS-919-modify_permissions_and_rules.md └── DDS-974-enforce_upload_chunk_size.md ├── api_docs ├── api_basics.apib ├── apiary.apib ├── authorization.apib ├── breaking_changes.apib ├── core_facility_workflow.apib ├── folders_files.apib ├── metadata.apib ├── projects.apib ├── provenance.apib ├── search.apib ├── trashbin.apib └── users_software_agents.apib ├── app ├── api │ ├── dds │ │ ├── base.rb │ │ └── v1 │ │ │ ├── activities_api.rb │ │ │ ├── app_api.rb │ │ │ ├── auth_providers_api.rb │ │ │ ├── auth_roles_api.rb │ │ │ ├── base.rb │ │ │ ├── children_api.rb │ │ │ ├── current_user_api.rb │ │ │ ├── file_versions_api.rb │ │ │ ├── files_api.rb │ │ │ ├── folders_api.rb │ │ │ ├── meta_templates_api.rb │ │ │ ├── project_affiliates_api.rb │ │ │ ├── project_permissions_api.rb │ │ │ ├── project_roles_api.rb │ │ │ ├── project_transfers_api.rb │ │ │ ├── projects_api.rb │ │ │ ├── properties_api.rb │ │ │ ├── relations_api.rb │ │ │ ├── search_api.rb │ │ │ ├── software_agents_api.rb │ │ │ ├── storage_providers_api.rb │ │ │ ├── system_permissions_api.rb │ │ │ ├── tags_api.rb │ │ │ ├── templates_api.rb │ │ │ ├── trashbin_api.rb │ │ │ ├── uploads_api.rb │ │ │ └── users_api.rb │ └── middleware │ │ └── audit_store_clean_up.rb ├── assets │ ├── images │ │ ├── .keep │ │ ├── explorer_icons.png │ │ ├── favicon-16x16.png │ │ ├── favicon-32x32.png │ │ ├── favicon.ico │ │ ├── logo_small.png │ │ ├── pet_store_api.png │ │ ├── throbber.gif │ │ └── wordnik_api.png │ ├── javascripts │ │ ├── application.js │ │ ├── bootstrap.min.js │ │ ├── html5.js │ │ ├── ie10-viewport-bug-workaround.js │ │ ├── respond.js │ │ ├── swaggerui.js │ │ └── swaggerui │ │ │ ├── backbone-min.js │ │ │ ├── handlebars-2.0.0.js │ │ │ ├── highlight.7.3.pack.js │ │ │ ├── jquery-1.11.3.min.js │ │ │ ├── jquery-migrate-1.0.0.js │ │ │ ├── jquery.ba-bbq.min.js │ │ │ ├── jquery.slideto.min.js │ │ │ ├── jquery.wiggle.min.js │ │ │ ├── marked.js │ │ │ ├── swagger-oauth.js │ │ │ ├── swagger-ui.min.js │ │ │ ├── underscore-min.js │ │ │ └── underscore-min.map │ └── stylesheets │ │ ├── application.css │ │ ├── bootstrap.min.css │ │ ├── layout_blue.css │ │ └── swaggerui │ │ ├── print.css │ │ ├── reset.css │ │ ├── screen.css.erb │ │ ├── style.css │ │ └── typography.css ├── controllers │ ├── application_controller.rb │ ├── concerns │ │ └── .keep │ └── swaggerui_controller.rb ├── helpers │ ├── application_helper.rb │ └── pagination_params.rb ├── jobs │ ├── application_job.rb │ ├── child_deletion_job.rb │ ├── child_purgation_job.rb │ ├── child_restoration_job.rb │ ├── elasticsearch_index_job.rb │ ├── graph_persistence_job.rb │ ├── project_container_elasticsearch_update_job.rb │ ├── project_storage_provider_initialization_job.rb │ ├── upload_completion_job.rb │ ├── upload_storage_provider_initialization_job.rb │ └── upload_storage_removal_job.rb ├── mailers │ └── .keep ├── models │ ├── .keep │ ├── activity.rb │ ├── affiliation.rb │ ├── api_key.rb │ ├── api_token.rb │ ├── application_audit.rb │ ├── application_record.rb │ ├── associated_with_prov_relation.rb │ ├── associated_with_software_agent_prov_relation.rb │ ├── associated_with_user_prov_relation.rb │ ├── attributed_to_prov_relation.rb │ ├── attributed_to_software_agent_prov_relation.rb │ ├── attributed_to_user_prov_relation.rb │ ├── auth_role.rb │ ├── authentication_service.rb │ ├── chunk.rb │ ├── chunked_upload.rb │ ├── concerns │ │ ├── .keep │ │ ├── child_minder.rb │ │ ├── graphed.rb │ │ ├── job_tracking.rb │ │ ├── job_transactionable.rb │ │ ├── project_updater.rb │ │ ├── purgable.rb │ │ ├── restorable.rb │ │ ├── searchable_model.rb │ │ └── un_restorable.rb │ ├── consistency_exception.rb │ ├── container.rb │ ├── data_file.rb │ ├── deprecated_elasticsearch_response.rb │ ├── derived_from_file_version_prov_relation.rb │ ├── duke_authentication_service.rb │ ├── file_version.rb │ ├── fingerprint.rb │ ├── folder.rb │ ├── folder_files_response.rb │ ├── generated_by_activity_prov_relation.rb │ ├── graph │ │ ├── activity.rb │ │ ├── agent.rb │ │ ├── file_version.rb │ │ ├── used.rb │ │ ├── was_associated_with.rb │ │ ├── was_attributed_to.rb │ │ ├── was_derived_from.rb │ │ ├── was_generated_by.rb │ │ └── was_invalidated_by.rb │ ├── identity_provider.rb │ ├── incompatible_parent_exception.rb │ ├── integrity_exception.rb │ ├── invalid_access_token_exception.rb │ ├── invalid_authentication_service_id_exception.rb │ ├── invalidated_by_activity_prov_relation.rb │ ├── job_transaction.rb │ ├── kinded.rb │ ├── kindness_factory.rb │ ├── ldap_identity_provider.rb │ ├── meta_property.rb │ ├── meta_template.rb │ ├── non_chunked_upload.rb │ ├── openid_authentication_service.rb │ ├── origin_provenance_graph.rb │ ├── project.rb │ ├── project_permission.rb │ ├── project_role.rb │ ├── project_storage_provider.rb │ ├── project_transfer.rb │ ├── project_transfer_user.rb │ ├── property.rb │ ├── prov_relation.rb │ ├── provenance_graph.rb │ ├── provenance_graph_node.rb │ ├── provenance_graph_relationship.rb │ ├── s3_storage_provider.rb │ ├── search_provenance_graph.rb │ ├── single_bucket_s3_storage_provider.rb │ ├── software_agent.rb │ ├── storage_provider.rb │ ├── storage_provider_exception.rb │ ├── swift_storage_provider.rb │ ├── system_permission.rb │ ├── tag.rb │ ├── tag_label.rb │ ├── template.rb │ ├── trashbin_parent_exception.rb │ ├── un_purgable_exception.rb │ ├── un_restorable_exception.rb │ ├── upload.rb │ ├── used_prov_relation.rb │ ├── user.rb │ ├── user_authentication_service.rb │ └── user_filter.rb ├── policies │ ├── activity_policy.rb │ ├── affiliation_policy.rb │ ├── api_key_policy.rb │ ├── application_policy.rb │ ├── associated_with_prov_relation_policy.rb │ ├── associated_with_software_agent_prov_relation_policy.rb │ ├── associated_with_user_prov_relation_policy.rb │ ├── attributed_to_prov_relation_policy.rb │ ├── attributed_to_software_agent_prov_relation_policy.rb │ ├── attributed_to_user_prov_relation_policy.rb │ ├── chunk_policy.rb │ ├── chunked_upload_policy.rb │ ├── container_policy.rb │ ├── data_file_policy.rb │ ├── derived_from_file_version_prov_relation_policy.rb │ ├── file_version_policy.rb │ ├── folder_policy.rb │ ├── generated_by_activity_prov_relation_policy.rb │ ├── invalidated_by_activity_prov_relation_policy.rb │ ├── meta_template_policy.rb │ ├── non_chunked_upload_policy.rb │ ├── project_permission_policy.rb │ ├── project_policy.rb │ ├── project_transfer_policy.rb │ ├── property_policy.rb │ ├── software_agent_policy.rb │ ├── system_permission_policy.rb │ ├── tag_policy.rb │ ├── template_policy.rb │ ├── upload_policy.rb │ ├── used_prov_relation_policy.rb │ └── user_policy.rb ├── serializers │ ├── activity_serializer.rb │ ├── affiliate_authentication_service_serializer.rb │ ├── affiliate_serializer.rb │ ├── affiliation_serializer.rb │ ├── ancestor_serializer.rb │ ├── api_key_serializer.rb │ ├── api_token_serializer.rb │ ├── associated_with_software_agent_prov_relation_serializer.rb │ ├── associated_with_user_prov_relation_serializer.rb │ ├── attributed_to_software_agent_prov_relation_serializer.rb │ ├── attributed_to_user_prov_relation_serializer.rb │ ├── audit_summary_serializer.rb │ ├── auth_role_preview_serializer.rb │ ├── auth_role_serializer.rb │ ├── authentication_service_preview_serializer.rb │ ├── authentication_service_serializer.rb │ ├── chunk_preview_serializer.rb │ ├── chunk_serializer.rb │ ├── chunked_upload_serializer.rb │ ├── data_file_preview_serializer.rb │ ├── data_file_serializer.rb │ ├── data_file_summary_serializer.rb │ ├── data_file_url_serializer.rb │ ├── deprecated_elasticsearch_response_serializer.rb │ ├── derived_from_file_version_prov_relation_serializer.rb │ ├── file_version_preview_serializer.rb │ ├── file_version_serializer.rb │ ├── file_version_url_serializer.rb │ ├── fingerprint_serializer.rb │ ├── folder_files_response_serializer.rb │ ├── folder_serializer.rb │ ├── generated_by_activity_prov_relation_serializer.rb │ ├── invalidated_by_activity_prov_relation_serializer.rb │ ├── meta_property_serializer.rb │ ├── meta_template_serializer.rb │ ├── non_chunked_upload_serializer.rb │ ├── project_permission_serializer.rb │ ├── project_preview_serializer.rb │ ├── project_role_preview_serializer.rb │ ├── project_role_serializer.rb │ ├── project_serializer.rb │ ├── project_transfer_serializer.rb │ ├── property_preview_serializer.rb │ ├── property_serializer.rb │ ├── prov_relation_serializer.rb │ ├── provenance_graph_node_serializer.rb │ ├── provenance_graph_relationship_serializer.rb │ ├── provenance_graph_serializer.rb │ ├── restricted_object_serializer.rb │ ├── search │ │ ├── data_file_serializer.rb │ │ ├── folder_serializer.rb │ │ ├── tag_summary_serializer.rb │ │ └── user_summary_serializer.rb │ ├── software_agent_preview_serializer.rb │ ├── software_agent_serializer.rb │ ├── storage_provider_preview_serializer.rb │ ├── storage_provider_serializer.rb │ ├── system_permission_serializer.rb │ ├── tag_label_serializer.rb │ ├── tag_serializer.rb │ ├── taggable_serializer.rb │ ├── templatable_serializer.rb │ ├── template_preview_serializer.rb │ ├── template_serializer.rb │ ├── upload_preview_serializer.rb │ ├── used_prov_relation_serializer.rb │ ├── user_authentication_service_serializer.rb │ ├── user_preview_serializer.rb │ ├── user_serializer.rb │ └── user_usage_serializer.rb ├── services │ ├── elasticsearch_handler.rb │ ├── jobs_runner.rb │ └── message_log_queue_handler.rb ├── validators │ └── immutable_validator.rb ├── views │ └── swaggerui │ │ └── index.html.erb └── workers │ └── message_log_worker.rb ├── application_info.yml ├── auth_service.env ├── auth_service.local.env ├── bin ├── apiary_section.js ├── bots │ └── sync_pr.rb ├── bundle ├── ci │ └── build ├── gen_apiary.sh ├── parse_apiary.js ├── rails ├── rake └── setup ├── circle ├── parallelize_test_suite.sh ├── run_dredd.circle.sh └── webapp.circle.env ├── config.ru ├── config ├── application.rb ├── boot.rb ├── database.yml ├── environment.rb ├── environments │ ├── development.rb │ ├── docker.rb │ ├── production.rb │ ├── test.rb │ └── ua_test.rb ├── initializers │ ├── active_model_serializers.rb │ ├── assets.rb │ ├── audited.rb │ ├── backtrace_silencers.rb │ ├── child_deletion_job.rb │ ├── cookies_serializer.rb │ ├── elasticsearch.rb │ ├── filter_parameter_logging.rb │ ├── inflections.rb │ ├── kaminari_config.rb │ ├── mime_types.rb │ ├── session_store.rb │ ├── sneakers.rb │ └── wrap_parameters.rb ├── locales │ └── en.yml ├── newrelic.yml ├── puma.rb ├── routes.rb └── secrets.yml ├── db.env ├── db.local.env ├── db ├── migrate │ ├── 20150616100000_enable_uuid_extension.rb │ ├── 20150616193850_create_users.rb │ ├── 20150616193938_create_authentication_services.rb │ ├── 20150616194039_create_user_authentication_services.rb │ ├── 20150624155037_create_auth_roles.rb │ ├── 20150630154305_create_projects.rb │ ├── 20150710203243_create_project_permissions.rb │ ├── 20150811175457_create_storage_providers.rb │ ├── 20150811180605_create_uploads.rb │ ├── 20150811181219_create_chunks.rb │ ├── 20150903160119_create_project_roles.rb │ ├── 20150903180944_create_affiliations.rb │ ├── 20150918202603_create_system_permissions.rb │ ├── 20150928151508_install_audited.rb │ ├── 20151029161136_create_containers.rb │ ├── 20151204171856_add_creator_id_to_uploads.rb │ ├── 20160111142052_change_upload_size.rb │ ├── 20160222200832_create_api_keys.rb │ ├── 20160223145153_create_software_agents.rb │ ├── 20160315142313_create_file_versions.rb │ ├── 20160317152825_add_label_to_containers.rb │ ├── 20160322150600_add_chunk_hash_algorithm_to_storage_providers.rb │ ├── 20160329164550_rename_version_to_version_number_on_file_versions.rb │ ├── 20160418182708_create_tags.rb │ ├── 20160425143741_create_activities.rb │ ├── 20160425193145_remove_creator_id_from_containers.rb │ ├── 20160505163200_create_prov_relations.rb │ ├── 20160524195735_create_fingerprints.rb │ ├── 20160624181343_add_default_to_activities_is_deleted.rb │ ├── 20160825150213_create_templates.rb │ ├── 20160826200027_create_properties.rb │ ├── 20160913142157_create_meta_templates.rb │ ├── 20160913155812_create_meta_properties.rb │ ├── 20160915195014_recreate_meta_templates.rb │ ├── 20160915195034_recreate_meta_properties.rb │ ├── 20160927150304_create_project_transfers.rb │ ├── 20160927150424_create_project_transfer_users.rb │ ├── 20161107180243_add_type_to_authentication_service.rb │ ├── 20161108133010_change_project_transfer_status_to_integer.rb │ ├── 20161121165841_amend_authentication_services.rb │ ├── 20170125190412_create_identity_providers.rb │ ├── 20170125192343_add_identity_provider_id_to_authentication_service.rb │ ├── 20170320141138_create_job_transactions.rb │ ├── 20170516143208_create_job_transactions_with_uuid.rb │ ├── 20170608184211_add_eventual_consistency_support.rb │ ├── 20170622204323_remove_upload_id_from_containers.rb │ ├── 20170823195852_add_storage_container_to_upload.rb │ ├── 20170825182638_add_is_purged_to_containers_file_versions.rb │ ├── 20170911204850_add_chunk_max_number_chunk_max_size_bytes_to_storage_providers.rb │ ├── 20170912182841_change_chunk_size.rb │ ├── 20170926165229_index_foreign_keys.rb │ ├── 20180321142736_add_slug_to_projects.rb │ ├── 20180329165729_add_purged_on_to_upload.rb │ ├── 20180403120319_add_deleted_from_parent_to_containers.rb │ ├── 20181005183154_add_type_to_storage_provider.rb │ ├── 20181012171403_add_is_default_to_storage_provider.rb │ ├── 20181016134301_add_storage_provider_to_projects.rb │ ├── 20181210204037_add_multipart_upload_id_to_uploads.rb │ ├── 20190110235737_create_project_storage_providers.rb │ ├── 20190219200627_add_type_to_uploads.rb │ ├── 20190304211844_add_force_path_style_to_storage_providers.rb │ ├── 20190604184708_add_etag_to_containers.rb │ └── 20210810175654_add_bucket_name_to_storage_providers.rb ├── neo4j │ ├── migrate │ │ ├── 20180118225229_force_create_activity_uuid_constraint.rb │ │ ├── 20180118225250_force_create_agent_uuid_constraint.rb │ │ ├── 20180118225532_force_create_file_version_uuid_constraint.rb │ │ ├── 20180118225539_force_create_activity_is_deleted_index.rb │ │ ├── 20180118225548_force_create_activity_model_id_index.rb │ │ ├── 20180118225556_force_create_activity_model_kind_index.rb │ │ ├── 20180118225602_force_create_agent_model_id_index.rb │ │ ├── 20180118225611_force_create_agent_model_kind_index.rb │ │ ├── 20180118225620_force_create_file_version_is_deleted_index.rb │ │ ├── 20180118225628_force_create_file_version_model_id_index.rb │ │ └── 20180118225637_force_create_file_version_model_kind_index.rb │ └── schema.yml ├── schema.rb └── seeds.rb ├── docker-compose.dev.yml ├── docker-compose.swift.yml ├── docker-compose.yml ├── docker ├── builds │ ├── apiary │ │ └── Dockerfile │ ├── db │ │ ├── Dockerfile │ │ └── docker-entrypoint-initdb.d │ │ │ └── railsdbs.sh │ ├── dredd │ │ ├── Dockerfile │ │ └── dredd_scripts │ │ │ ├── .DS_Store │ │ │ ├── 01_auth_hooks.py │ │ │ ├── 02_software_agents.py │ │ │ ├── 03_current_users.py │ │ │ ├── 04_system_permission.py │ │ │ ├── 05_projects.py │ │ │ ├── 06_project_permissions.py │ │ │ ├── 07_project_roles.py │ │ │ ├── 08_affiliates.py │ │ │ ├── 09_storage_providers.py │ │ │ ├── 10_folders.py │ │ │ ├── 11_uploads.py │ │ │ ├── 12_files.py │ │ │ ├── 14_children_search.py │ │ │ ├── 15_provenance_activities.py │ │ │ ├── 16_provenance_relations.py │ │ │ ├── 17_tags.py │ │ │ ├── 18_metadata.py │ │ │ ├── apiary_changes.sh │ │ │ ├── apib_names.txt │ │ │ ├── dds-dredd.js │ │ │ └── utils.py │ └── swift │ │ ├── Dockerfile │ │ └── proxy-server.conf └── circle │ └── cache_dredd.sh ├── elastic.client.env ├── elastic.client.local.env ├── launch_application.sh ├── lib ├── assets │ └── .keep └── tasks │ ├── .keep │ ├── auth_service.rake │ ├── db_data_migrate.rake │ ├── elasticsearch.rake │ ├── graphdb.rake │ ├── identity_provider.rake │ ├── job_transaction.rake │ ├── queue.rake │ ├── storage_provider.rake │ └── workers.rake ├── log └── .keep ├── neo4j.client.env ├── neo4j.client.local.env ├── neo4j.server.env ├── neo4j.server.local.env ├── openshift ├── build-duke-data-service.template.yml ├── build_parameters ├── docker │ └── Dockerfile └── prepare-gitlab-ci-runner-environment.yml ├── public ├── 404.html ├── 422.html ├── 500.html ├── apidocs │ ├── api_basics.html │ ├── authorization.html │ ├── breaking_changes.html │ ├── core_facility_workflow.html │ ├── folders_files.html │ ├── index.html │ ├── metadata.html │ ├── projects.html │ ├── provenance.html │ ├── search.html │ ├── trashbin.html │ └── users_software_agents.html ├── apple-touch-icon-precomposed.png ├── apple-touch-icon.png ├── assets │ └── fonts │ │ ├── droid-sans-v6-latin-700.eot │ │ ├── droid-sans-v6-latin-700.svg │ │ ├── droid-sans-v6-latin-700.ttf │ │ ├── droid-sans-v6-latin-700.woff │ │ ├── droid-sans-v6-latin-700.woff2 │ │ ├── droid-sans-v6-latin-regular.eot │ │ ├── droid-sans-v6-latin-regular.svg │ │ ├── droid-sans-v6-latin-regular.ttf │ │ ├── droid-sans-v6-latin-regular.woff │ │ └── droid-sans-v6-latin-regular.woff2 ├── favicon.ico ├── images │ ├── dukeDSLogo.png │ ├── dukeDSVertical.png │ ├── fav.png │ └── mdl-icons │ │ ├── ic_folder_black_48dp_2x.png │ │ └── ic_search_black_24dp_1x.png └── robots.txt ├── rabbitmq.client.env ├── rabbitmq.client.local.env ├── spec ├── cassettes │ ├── DDS_V1_ProjectsAPI │ │ └── Project_collection │ │ │ └── POST │ │ │ └── with_inline_ActiveJob │ │ │ └── behaves_like_a_creatable_resource │ │ │ ├── should_be_persisted.yml │ │ │ ├── should_return_a_serialized_object.yml │ │ │ └── should_return_success.yml │ ├── DDS_V1_UploadsAPI │ │ └── Complete_the_chunked_file_upload │ │ │ ├── behaves_like_a_software_agent_accessible_resource │ │ │ ├── behaves_like_an_annotate_audits_endpoint │ │ │ │ ├── audit_should_include_other_expected_attributes.yml │ │ │ │ ├── audit_should_record_the_remote_address_uuid_endpoint_action.yml │ │ │ │ └── should_create_expected_audit_types.yml │ │ │ └── should_return_success.yml │ │ │ ├── behaves_like_a_storage_provider_backed_resource │ │ │ ├── should_return_a_500_error_and_JSON_error_when_a_StorageProviderException_is_experienced.yml │ │ │ ├── should_return_an_error_if_the_reported_chunk_hash_does_not_match_storage_provider_computed_size.yml │ │ │ └── should_return_an_error_if_the_reported_size_does_not_match_storage_provider_computed_size.yml │ │ │ ├── behaves_like_an_annotate_audits_endpoint │ │ │ ├── audit_should_include_other_expected_attributes.yml │ │ │ ├── audit_should_record_the_remote_address_uuid_endpoint_action.yml │ │ │ └── should_create_expected_audit_types.yml │ │ │ ├── behaves_like_an_authenticated_resource │ │ │ └── should_return_a_401_error_response.yml │ │ │ ├── behaves_like_an_authorized_resource │ │ │ └── should_return_a_403_error_response.yml │ │ │ ├── behaves_like_an_identified_resource │ │ │ └── should_return_404_with_error_when_resource_not_found_with_id.yml │ │ │ ├── behaves_like_an_updatable_resource │ │ │ ├── should_persist_changes_to_resource.yml │ │ │ ├── should_return_a_serialized_resource.yml │ │ │ └── should_return_success.yml │ │ │ ├── with_completed_upload │ │ │ └── behaves_like_a_validated_resource │ │ │ │ ├── returns_a_failed_response.yml │ │ │ │ └── returns_errors_as_a_JSON_payload.yml │ │ │ └── with_invalid_fingerprint_algorithm │ │ │ └── behaves_like_a_validated_resource │ │ │ ├── returns_a_failed_response.yml │ │ │ └── returns_errors_as_a_JSON_payload.yml │ └── SwiftStorageProvider │ │ └── methods_that_call_swift_api │ │ ├── _get_container_meta │ │ ├── before_container_exists │ │ │ └── should_return_null.yml │ │ └── when_container_exists │ │ │ └── should_return_null.yml │ │ ├── should_respond_to_auth_header.yml │ │ ├── should_respond_to_auth_token.yml │ │ ├── should_respond_to_delete_container.yml │ │ ├── should_respond_to_delete_object.yml │ │ ├── should_respond_to_delete_object_manifest.yml │ │ ├── should_respond_to_get_account_info.yml │ │ ├── should_respond_to_get_container_objects.yml │ │ ├── should_respond_to_get_containers.yml │ │ ├── should_respond_to_get_object_metadata.yml │ │ ├── should_respond_to_put_container.yml │ │ ├── should_respond_to_put_object.yml │ │ ├── should_respond_to_put_object_manifest.yml │ │ ├── should_respond_to_register_keys.yml │ │ ├── should_respond_to_storage_url.yml │ │ ├── should_set_X-Container-Meta-Access-Control-Allow-Origin.yml │ │ ├── should_store_both_the_content_type_and_filename_on_the_manifest_object.yml │ │ ├── should_store_the_content_type_on_the_manifest_object_as_the_content-type.yml │ │ ├── should_store_the_filename_on_the_manifest_object_in_the_content-disposition.yml │ │ └── with_invalid_auth │ │ └── 1_4_2_1.yml ├── controllers │ └── swaggerui_controller_spec.rb ├── factories │ ├── activities.rb │ ├── affiliations.rb │ ├── api_keys.rb │ ├── associated_with_software_agent_prov_relations.rb │ ├── associated_with_user_prov_relations.rb │ ├── attributed_to_software_agent_prov_relations.rb │ ├── attributed_to_user_prov_relations.rb │ ├── auth_roles.rb │ ├── chunked_uploads.rb │ ├── chunks.rb │ ├── data_files.rb │ ├── derived_from_file_version_prov_relation.rb │ ├── duke_authentication_services.rb │ ├── file_versions.rb │ ├── fingerprints.rb │ ├── folders.rb │ ├── generated_by_activity_prov_relation.rb │ ├── invalidated_by_activity_prov_relation.rb │ ├── job_transactions.rb │ ├── ldap_identity_providers.rb │ ├── meta_properties.rb │ ├── meta_templates.rb │ ├── non_chunked_uploads.rb │ ├── openid_authentication_services.rb │ ├── project_permissions.rb │ ├── project_roles.rb │ ├── project_storage_providers.rb │ ├── project_transfer_users.rb │ ├── project_transfers.rb │ ├── projects.rb │ ├── properties.rb │ ├── s3_storage_providers.rb │ ├── single_bucket_s3_storage_providers.rb │ ├── software_agents.rb │ ├── storage_providers.rb │ ├── swift_storage_providers.rb │ ├── system_permissions.rb │ ├── tags.rb │ ├── templates.rb │ ├── uploads.rb │ ├── used_prov_relations.rb │ ├── user_authentication_services.rb │ └── users.rb ├── jobs │ ├── application_job_spec.rb │ ├── child_deletion_job_spec.rb │ ├── child_purgation_job_spec.rb │ ├── child_restoration_job_spec.rb │ ├── elasticsearch_index_job_spec.rb │ ├── graph_persistence_job_spec.rb │ ├── job_tracking_spec.rb │ ├── project_container_elasticsearch_update_job_spec.rb │ ├── project_storage_provider_initialization_job_spec.rb │ ├── upload_completion_job_spec.rb │ ├── upload_storage_provider_initialization_job_spec.rb │ └── upload_storage_removal_job_spec.rb ├── lib │ └── tasks │ │ ├── auth_service_rake_spec.rb │ │ ├── db_data_migrate_rake_spec.rb │ │ ├── elasticsearch_rake_spec.rb │ │ ├── graphdb_rake_spec.rb │ │ ├── identity_provider_rake_spec.rb │ │ ├── job_transaction_rake_spec.rb │ │ ├── queue_rake_spec.rb │ │ ├── storage_provider_rake_spec.rb │ │ └── workers_rake_spec.rb ├── models │ ├── activity_spec.rb │ ├── affiliation_spec.rb │ ├── api_key_spec.rb │ ├── api_token_spec.rb │ ├── application_audit_spec.rb │ ├── associated_with_software_agent_prov_relation_spec.rb │ ├── associated_with_user_prov_relation_spec.rb │ ├── attributed_to_software_agent_prov_relation_spec.rb │ ├── attributed_to_user_prov_relation_spec.rb │ ├── auth_role_spec.rb │ ├── chunk_spec.rb │ ├── chunked_upload_spec.rb │ ├── data_file_spec.rb │ ├── deprecated_elasticsearch_response_spec.rb │ ├── derived_from_file_version_prov_relation_spec.rb │ ├── duke_authentication_service_spec.rb │ ├── file_version_spec.rb │ ├── fingerprint_spec.rb │ ├── folder_files_response_spec.rb │ ├── folder_spec.rb │ ├── generated_by_activity_prov_relation_spec.rb │ ├── graph_activity_spec.rb │ ├── graph_agent_spec.rb │ ├── graph_file_version_spec.rb │ ├── graph_used_spec.rb │ ├── graph_was_associated_with_spec.rb │ ├── graph_was_attributed_to_spec.rb │ ├── graph_was_derived_from_spec.rb │ ├── graph_was_generated_by_spec.rb │ ├── graph_was_invalidated_by_spec.rb │ ├── identity_provider_spec.rb │ ├── invalidated_by_activity_prov_relation_spec.rb │ ├── job_transaction_spec.rb │ ├── kindness_factory_spec.rb │ ├── ldap_identity_provider_spec.rb │ ├── meta_property_spec.rb │ ├── meta_template_spec.rb │ ├── non_chunked_upload_spec.rb │ ├── openid_authentication_service_spec.rb │ ├── origin_provenance_graph_spec.rb │ ├── project_permission_spec.rb │ ├── project_role_spec.rb │ ├── project_spec.rb │ ├── project_storage_provider_spec.rb │ ├── project_transfer_spec.rb │ ├── project_transfer_user_spec.rb │ ├── property_spec.rb │ ├── provenance_graph_node_spec.rb │ ├── provenance_graph_relationship_spec.rb │ ├── s3_storage_provider_spec.rb │ ├── search_provenance_graph_spec.rb │ ├── single_bucket_s3_storage_provider_spec.rb │ ├── software_agent_spec.rb │ ├── storage_provider_spec.rb │ ├── swift_storage_provider_spec.rb │ ├── system_permission_spec.rb │ ├── tag_label_spec.rb │ ├── tag_spec.rb │ ├── template_spec.rb │ ├── upload_spec.rb │ ├── used_prov_relation_spec.rb │ ├── user_authentication_service_spec.rb │ ├── user_filter_spec.rb │ └── user_spec.rb ├── policies │ ├── activity_policy_spec.rb │ ├── affiliation_policy_spec.rb │ ├── api_key_policy_spec.rb │ ├── application_policy_spec.rb │ ├── associated_with_prov_relation_policy_spec.rb │ ├── attributed_to_prov_relation_policy_spec.rb │ ├── chunk_policy_spec.rb │ ├── chunked_upload_policy_spec.rb │ ├── container_policy_spec.rb │ ├── data_file_policy_spec.rb │ ├── derived_from_file_version_prov_relation_policy_spec.rb │ ├── file_version_policy_spec.rb │ ├── folder_policy_spec.rb │ ├── generated_by_activity_prov_relation_policy_spec.rb │ ├── invalidated_by_activity_prov_relation_policy_spec.rb │ ├── meta_template_policy_spec.rb │ ├── non_chunked_upload_policy_spec.rb │ ├── project_permission_policy_spec.rb │ ├── project_policy_spec.rb │ ├── project_transfer_policy_spec.rb │ ├── property_policy_spec.rb │ ├── software_agent_policy_spec.rb │ ├── system_permission_policy_spec.rb │ ├── tag_policy_spec.rb │ ├── template_policy_spec.rb │ ├── upload_policy_spec.rb │ ├── used_prov_relation_policy_spec.rb │ └── user_policy_spec.rb ├── rails_helper.rb ├── requests │ ├── activities_api_spec.rb │ ├── app_api_spec.rb │ ├── auth_providers_api_spec.rb │ ├── auth_roles_api_spec.rb │ ├── base_spec.rb │ ├── children_api_spec.rb │ ├── current_user_api_spec.rb │ ├── file_versions_api_spec.rb │ ├── files_api_spec.rb │ ├── folders_api_spec.rb │ ├── meta_templates_api_spec.rb │ ├── project_affiliates_api_spec.rb │ ├── project_permissions_api_spec.rb │ ├── project_roles_api_spec.rb │ ├── project_transfers_api_spec.rb │ ├── projects_api_spec.rb │ ├── properties_api_spec.rb │ ├── relations_api_spec.rb │ ├── search_api_spec.rb │ ├── software_agents_api_spec.rb │ ├── storage_providers_api_spec.rb │ ├── swagger_doc_api_spec.rb │ ├── system_permissions_api_spec.rb │ ├── tags_api_spec.rb │ ├── templates_api_spec.rb │ ├── trashbin_api_spec.rb │ ├── uploads_api_spec.rb │ └── users_api_spec.rb ├── routing │ └── base_routing_spec.rb ├── serializers │ ├── activity_serializer_spec.rb │ ├── affiliate_authentication_service_serializer_spec.rb │ ├── affiliate_serializer_spec.rb │ ├── affiliation_serializer_spec.rb │ ├── ancestor_serializer_spec.rb │ ├── api_key_serializer_spec.rb │ ├── api_token_serializer_spec.rb │ ├── associated_with_software_agent_prov_relation_serializer_spec.rb │ ├── associated_with_user_prov_relation_serializer_spec.rb │ ├── attributed_to_software_agent_prov_relation_serializer_spec.rb │ ├── attributed_to_user_prov_relation_serializer_spec.rb │ ├── audit_summary_serializer_spec.rb │ ├── auth_role_preview_serializer_spec.rb │ ├── auth_role_serializer_spec.rb │ ├── authentication_service_preview_serializer_spec.rb │ ├── authentication_service_serializer_spec.rb │ ├── chunk_preview_serializer_spec.rb │ ├── chunk_serializer_spec.rb │ ├── chunked_upload_serializer_spec.rb │ ├── data_file_preview_serializer_spec.rb │ ├── data_file_serializer_spec.rb │ ├── data_file_summary_serializer_spec.rb │ ├── data_file_url_serializer_spec.rb │ ├── deprecated_elasticsearch_response_serializer_spec.rb │ ├── derived_from_agent_prov_relation_serializer_spec.rb │ ├── file_version_preview_serializer_spec.rb │ ├── file_version_serializer_spec.rb │ ├── file_version_url_serializer_spec.rb │ ├── fingerprint_serializer_spec.rb │ ├── folder_files_response_serializer_spec.rb │ ├── folder_serializer_spec.rb │ ├── generated_by_agent_prov_relation_serializer_spec.rb │ ├── invalidated_by_agent_prov_relation_serializer_spec.rb │ ├── meta_property_serializer_spec.rb │ ├── meta_template_serializer_spec.rb │ ├── non_chunked_upload_serializer_spec.rb │ ├── project_permission_serializer_spec.rb │ ├── project_preview_serializer_spec.rb │ ├── project_role_preview_serializer_spec.rb │ ├── project_role_serializer_spec.rb │ ├── project_serializer_spec.rb │ ├── project_transfer_serializer_spec.rb │ ├── property_preview_serializer_spec.rb │ ├── property_serializer_spec.rb │ ├── provenance_graph_node_serializer_spec.rb │ ├── provenance_graph_relationship_serializer_spec.rb │ ├── provenance_graph_serializer_spec.rb │ ├── restricted_object_serializer_spec.rb │ ├── search │ │ ├── data_file_serializer_spec.rb │ │ ├── folder_serializer_spec.rb │ │ ├── tag_summary_serializer_spec.rb │ │ └── user_summary_serializer_spec.rb │ ├── software_agent_preview_serializer_spec.rb │ ├── software_agent_serializer_spec.rb │ ├── storage_provider_preview_serializer_spec.rb │ ├── storage_provider_serializer_spec.rb │ ├── system_permission_serializer_spec.rb │ ├── tag_label_serializer_spec.rb │ ├── tag_serializer_spec.rb │ ├── taggable_serializer_spec.rb │ ├── templatable_serializer_spec.rb │ ├── template_preview_serializer_spec.rb │ ├── template_serializer_spec.rb │ ├── upload_preview_serializer_spec.rb │ ├── used_prov_relation_serializer_spec.rb │ ├── user_preview_serializer_spec.rb │ ├── user_serializer_spec.rb │ └── user_usage_serializer_spec.rb ├── services │ ├── elasticsearch_handler_spec.rb │ ├── jobs_runner_spec.rb │ └── message_log_queue_handler_spec.rb ├── spec_helper.rb ├── support │ ├── auditable_shared_examples.rb │ ├── authentication_service_shared_examples.rb │ ├── concerns │ │ ├── child_minder_shared_examples.rb │ │ ├── graphed_shared_examples.rb │ │ ├── job_tracking_shared_examples.rb │ │ ├── job_transactionable_shared_examples.rb │ │ ├── project_updater_shared_examples.rb │ │ ├── purgable_shared_examples.rb │ │ ├── restorable_shared_examples.rb │ │ ├── searchable_model_shared_examples.rb │ │ ├── storage_provider_shared_examples.rb │ │ └── un_restorable_shared_examples.rb │ ├── job_shared_examples.rb │ ├── ldap_shared_examples.rb │ ├── models_shared_examples.rb │ ├── policies_shared_examples.rb │ ├── rake_shared_context.rb │ ├── requests_shared_examples.rb │ ├── search_shared_examples.rb │ ├── serializers_shared_examples.rb │ └── utilities.rb └── workers │ └── message_log_worker_spec.rb ├── swift.circle.env ├── swift.empty.env ├── swift.env ├── swift.local.env ├── test_file.txt ├── vendor └── assets │ ├── javascripts │ └── .keep │ └── stylesheets │ └── .keep ├── webapp.env ├── webapp.local.env └── workflow ├── chunk1.txt ├── chunk2.txt ├── chunk3.txt ├── chunk4.txt ├── restlib.sh ├── software_agent_workflow.sh ├── upload.sh ├── upload_file.sh ├── upload_integrity ├── all_tests.md ├── bad_upload_md5_test.sh ├── chunks_out_of_order_test.sh ├── control_test.sh ├── data │ ├── chunk1.txt │ ├── chunk2.txt │ ├── chunk3.txt │ ├── 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