Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

galaxy_test.api package

Submodules

galaxy_test.api.test_api_batch module

class galaxy_test.api.test_api_batch.ApiBatchTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

test_simple_array()

test_unallowed_route()

test_404_route()

test_errors()

test_querystring_params()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_authenticate module

class galaxy_test.api.test_authenticate.AuthenticationApiTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

test_auth()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_configuration module

class galaxy_test.api.test_configuration.ConfigurationApiTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

test_whoami()

test_normal_user_configuration()

test_admin_user_configuration()

test_normal_user_decode_id()

test_version()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_dataset_collections module

class galaxy_test.api.test_dataset_collections.DatasetCollectionApiTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_create_pair_from_history()

test_create_list_from_history()

test_create_list_of_existing_pairs()

test_create_list_of_new_pairs()

test_list_download()

test_pair_download()

test_list_pair_download()

test_list_list_download()

test_list_list_list_download()

test_hda_security()

test_enforces_unique_names()

test_upload_collection()

test_upload_nested()

test_upload_collection_from_url()

test_upload_collection_failed_expansion_url()

test_collection_contents_security()

test_collection_contents_invalid_collection()

test_show_dataset_collection()

test_show_dataset_collection_contents()

test_collection_contents_limit_offset()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_datasets module

class galaxy_test.api.test_datasets.DatasetsApiTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_index()

test_search_datasets()

test_search_by_tag()

test_search_by_tool_id()

test_invalid_search()

test_search_returns_only_accessible()

test_show()

test_show_permission_denied()

test_admin_can_update_permissions()

test_display()

test_tag_change()

test_update_datatype()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_datatypes module

class galaxy_test.api.test_datatypes.DatatypesApiTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

test_index()

test_index_upload_only()

test_full_index()

test_mapping()

test_types_and_mapping()

test_sniffers()

test_converters()

test_converter_present_after_toolbox_reload()

test_edam_formats()

test_edam_data()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_framework module

class galaxy_test.api.test_framework.ApiFrameworkTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

test_default_xframe_options()

test_user_cannont_run_as()

test_run_as_invalid_user()

test_run_as_valid_user()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_galaxy_interactor module

class galaxy_test.api.test_galaxy_interactor.GalaxyInteractorBackwardCompatTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

test_local_test_data_download()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

class galaxy_test.api.test_galaxy_interactor.GalaxyInteractorTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

test_get_tool_tests()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_histories module

class galaxy_test.api.test_histories.BaseHistories

Bases: object

class galaxy_test.api.test_histories.HistoriesApiTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase, galaxy_test.api.test_histories.BaseHistories, galaxy_test.api.sharable.SharingApiTests

api_name: str = 'histories'

create(name: str) → str

Creates a shareable resource with the given name and returns it’s ID.

Parameters

name (str) – The name of the shareable resource to create.

Returns

The ID of the resource.

Return type

str

test_create_history()

test_show_history()

test_show_most_recently_used()

test_index_order()

test_delete()

test_purge()

test_undelete()

test_update()

test_update_invalid_attribute()

test_update_invalid_types()

test_invalid_keys()

test_create_anonymous_fails()

test_create_without_session_fails()

test_create_tag()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

class galaxy_test.api.test_histories.ImportExportHistoryTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase, galaxy_test.api.test_histories.BaseHistories

setUp()

Hook method for setting up the test fixture before exercising it.

test_import_export()

test_import_1901_histories()

test_import_export_include_deleted()

test_import_export_failed_job()

test_import_metadata_regeneration()

test_import_export_collection()

test_import_export_nested_collection()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_history_contents module

class galaxy_test.api.test_history_contents.HistoryContentsApiTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_index_hda_summary()

test_make_private_and_public()

test_set_permissions_add_admin_history_contents()

test_set_permissions_add_admin_datasets()

test_index_hda_all_details()

test_index_hda_detail_by_id()

test_show_hda()

test_hda_copy()

test_library_copy()

test_update()

test_update_batch()

test_update_type_failures()

test_delete()

test_purge()

test_dataset_collection_creation_on_contents()

test_dataset_collection_creation_on_typed_contents()

test_dataset_collection_create_from_exisiting_datasets_with_new_tags()

test_jobs_summary_simple_hdca()

test_jobs_summary_implicit_hdca()

test_dataset_collection_hide_originals()

test_update_dataset_collection()

test_hdca_copy()

test_hdca_copy_with_new_dbkey()

test_hdca_copy_and_elements()

test_hdca_from_library_datasets()

test_hdca_from_inaccessible_library_datasets()

test_job_state_summary_field()

test_history_contents_near_with_update_time()

test_history_contents_near_with_update_time_implicit_collection()

test_history_contents_near_with_update_time_explicit_collection()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_history_contents_provenance module

class galaxy_test.api.test_history_contents_provenance.TestProvenance(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_show_prov()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_jobs module

class galaxy_test.api.test_jobs.JobsApiTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase, galaxy_test.api.test_tools.TestsTools

setUp()

Hook method for setting up the test fixture before exercising it.

test_index(history_id)

test_system_details_admin_only(history_id)

test_admin_job_list(history_id)

test_index_state_filter(history_id)

test_index_date_filter(history_id)

test_index_history(history_id)

test_index_workflow_and_invocation_filter(history_id)

test_index_workflow_filter_implicit_jobs(history_id)

test_index_limit_and_offset_filter(history_id)

test_index_user_filter(history_id)

test_index_multiple_states_filter(history_id)

test_show(history_id)

test_show_security(history_id)

test_unhide_on_error()

test_no_unhide_on_error_if_mapped_over()

test_common_problems()

test_report_error()

test_report_error_anon()

test_report_error_bootstrap_admin()

test_deleting_output_keep_running_until_all_deleted(history_id)

test_purging_output_keep_running_until_all_purged(history_id)

test_purging_output_cleaned_after_ok_run(history_id)

test_resume_job(history_id)

test_search(history_id)

test_search_handle_identifiers(history_id)

test_search_delete_outputs(history_id)

test_search_with_hdca_list_input(history_id)

test_search_delete_hdca_output(history_id)

test_search_with_hdca_pair_input(history_id)

test_search_with_hdca_list_pair_input(history_id)

test_search_with_hdca_list_pair_collection_mapped_over_pair_input(history_id)

test_job_build_for_rerun(history_id)

test_dce_submission_security(history_id)

test_job_build_for_rerun_list_list(history_id)

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_libraries module

class galaxy_test.api.test_libraries.LibrariesApiTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_create()

test_delete()

test_nonadmin()

test_update()

test_create_private_library_permissions()

test_create_library_dataset_bootstrap_user(library_name='private_dataset', wait=True)

test_create_dataset_denied()

test_create_dataset_bootstrap_admin_user()

test_show_private_dataset_permissions()

test_create_dataset()

test_fetch_upload_to_folder()

test_fetch_zip_to_folder()

test_fetch_single_url_to_folder()

test_fetch_single_url_with_invalid_datatype()

test_legacy_upload_unknown_datatype()

test_fetch_failed_validation()

test_fetch_url_archive_to_folder()

test_fetch_bagit_archive_to_folder()

test_create_dataset_in_folder()

test_create_dataset_in_subfolder()

test_update_dataset_in_folder()

test_update_dataset_tags()

test_invalid_update_dataset_in_folder()

test_detect_datatype_of_dataset_in_folder()

test_ldda_collection_import_to_history()

test_ldda_collection_import_to_history_hide_source()

test_import_paired_collection()

test_create_datasets_in_library_from_collection()

test_create_datasets_in_folder_from_collection()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_licenses module

class galaxy_test.api.test_licenses.LicensesApiTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

test_index()

test_get_license()

test_404_on_unknown_license()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_page_revisions module

class galaxy_test.api.test_page_revisions.PageRevisionsApiTestCase(methodName='runTest')

Bases: galaxy_test.api.test_pages.BasePageApiTestCase

test_create()

test_403_if_create_revision_on_unowned_page()

test_revision_index()

test_malformed_id_if_index_unknown_page()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_pages module

class galaxy_test.api.test_pages.BasePageApiTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

class galaxy_test.api.test_pages.PageApiTestCase(methodName='runTest')

Bases: galaxy_test.api.test_pages.BasePageApiTestCase, galaxy_test.api.sharable.SharingApiTests

api_name: str = 'pages'

create(name: str) → str

Creates a shareable resource with the given name and returns it’s ID.

Parameters

name (str) – The name of the shareable resource to create.

Returns

The ID of the resource.

Return type

str

test_create()

test_create_from_report()

test_index()

test_index_does_not_show_unavailable_pages()

test_cannot_create_pages_with_same_slug()

test_cannot_create_pages_with_invalid_slug()

test_cannot_create_page_with_invalid_content_format()

test_page_requires_name()

test_page_requires_slug()

test_delete()

test_400_on_delete_invalid_page_id()

test_403_on_delete_unowned_page()

test_400_on_invalid_id_encoding()

test_400_on_invalid_id_encoding_markdown()

test_400_on_invalid_embedded_content()

test_400_on_invalid_markdown_call()

test_show()

test_403_on_unowner_show()

test_400_on_download_pdf_when_service_unavailable()

test_400_on_download_pdf_when_unsupported_content_format()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_roles module

class galaxy_test.api.test_roles.RolesApiTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_list_and_show()

test_create_invalid_params()

test_create_valid()

test_show_error_codes()

test_create_only_admin()

static check_role_dict(role_dict, assert_id=None)

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_search module

class galaxy_test.api.test_search.SearchApiTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

test_search_workflows()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_tool_data module

Tests for the tool data API.

The tests for the DELETE endpoint can be found in the integration tests directory (tests/integration/test_tool_data_delete.py) since these tests can mutate the server config state.

class galaxy_test.api.test_tool_data.ToolDataApiTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

test_admin_only()

test_list()

test_show()

test_show_field()

test_download_field_file()

test_reload()

test_show_unknown_raises_404()

test_show_unknown_field_raises_404()

test_reload_unknown_raises_404()

test_download_field_unknown_file_raises_404()

test_delete_without_payload_raises_400()

test_delete_without_values_raises_400()

test_delete_with_wrong_values_raises_400()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_tools module

class galaxy_test.api.test_tools.TestsTools

Bases: object

class galaxy_test.api.test_tools.ToolsTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase, galaxy_test.api.test_tools.TestsTools

setUp()

Hook method for setting up the test fixture before exercising it.

test_index()

test_search_cat()

test_search_trimmer()

test_search_grep()

test_no_panel_index()

test_requirements()

test_show_repeat()

test_show_conditional()

test_show_multi_data()

test_show_output_collection()

test_data_source_build_request()

test_data_source_ok_request()

test_data_source_sniff_fastqsanger()

test_data_sources_block_file_parameters()

test_test_data_filepath_security()

test_test_data_admin_security()

test_data_table_requirement_annotated()

test_test_data_composite_output()

test_test_data_collection_two_paired()

test_test_data_collection_nested()

test_test_data_null_boolean_inputs()

test_test_data_yaml_tools()

test_test_data_download()

test_test_data_downloads_security()

test_test_data_download_composite()

test_unzip_collection()

test_unzip_nested()

test_zip_inputs()

test_collection_operation_dataset_input_permissions(history_id)

test_collection_operation_collection_input_permissions(history_id)

test_zip_list_inputs()

test_filter_failed_list()

test_filter_failed_list_paired()

test_apply_rules_1()

test_apply_rules_2()

test_apply_rules_3()

test_apply_rules_4()

test_apply_rules_5()

test_apply_rules_6()

test_multi_select_as_list()

test_multi_select_optional()

test_library_data_param()

test_multidata_param()

test_run_cat1(history_id)

test_run_cat1_use_cached_job(history_id)

test_run_cat1_listified_param(history_id)

test_run_by_versions(history_id)

test_test_by_versions(history_id)

test_show_with_wrong_tool_version_in_tool_id(history_id)

test_run_cat1_single_meta_wrapper(history_id)

test_guess_derived_permissions(history_id)

test_guess_derived_permissions_collections(history_id)

test_validation(history_id)

test_validation_empty_dataset(history_id)

test_validation_in_repeat(history_id)

test_select_legal_values(history_id)

test_column_legal_values(history_id)

test_collection_parameter(history_id)

test_paired_collection_output(history_id)

test_list_collection_output(history_id)

test_list_collection_output_format_source(history_id)

test_dynamic_list_output(history_id)

test_dynamic_list_output_datasets_in_failed_state(history_id)

test_nonadmin_users_cannot_create_tools()

test_dynamic_tool_1()

test_dynamic_tool_from_path()

test_dynamic_tool_no_id()

test_show_dynamic_tools()

test_tool_deactivate()

test_run_cat1_with_two_inputs(history_id)

test_bam_state_regression(history_id)

test_qc_messages(history_id)

test_multirun_cat1(history_id)

test_multirun_non_data_parameter(history_id)

test_multirun_in_repeat()

test_multirun_in_repeat_mismatch()

test_multirun_on_multiple_inputs()

test_multirun_on_multiple_inputs_unlinked()

test_dynamic_parameter_error_handling()

test_map_over_collection(history_id)

test_map_over_empty_collection(history_id)

test_map_over_with_output_format_actions(history_id)

test_map_over_with_nested_paired_output_format_actions(history_id)

test_map_over_with_output_filter_no_filtering(history_id)

test_map_over_with_output_filter_on_optional_input(history_id)

test_map_over_with_output_filter_one_filtered(history_id)

test_map_over_with_complex_output_actions(history_id)

test_map_over_with_discovered_output_collection_elements(history_id)

test_identifier_in_map(history_id)

test_identifier_outside_map(history_id)

test_list_selectable_in_multidata_input(history_id)

test_identifier_in_multiple_reduce(history_id)

test_identifier_map_over_multiple_input_in_conditional(history_id)

test_identifier_map_over_multiple_input_in_conditional_new_payload_form(history_id)

test_identifier_multiple_reduce_in_repeat_new_payload_form(history_id)

test_identifier_map_over_input_in_conditional(history_id)

test_identifier_multiple_reduce_in_conditional(history_id)

test_identifier_multiple_reduce_in_repeat(history_id)

test_identifier_single_in_repeat(history_id)

test_identifier_multiple_in_conditional(history_id)

test_identifier_with_multiple_normal_datasets(history_id)

test_identifier_with_data_collection(history_id)

test_identifier_in_actions(history_id)

test_map_over_nested_collections(history_id)

test_paired_input_map_over_nested_collections(history_id)

test_paired_input_conditional_map_over_nested_collections(history_id)

test_map_over_two_collections(history_id)

test_map_over_two_collections_unlinked(history_id)

test_map_over_collected_and_individual_datasets(history_id)

test_default_identifier_source_map_over()

test_map_over_collection_output()

test_cannot_map_over_incompatible_collections()

test_map_over_collection_structured_like()

test_map_over_collection_type_source()

test_reduce_collections_legacy()

test_reduce_collections()

test_implicit_reduce_with_mapping()

test_implicit_conversion_and_reduce()

test_implicit_conversion_and_reduce_invalid_param()

test_reduce_collections_in_repeat()

test_reduce_collections_in_repeat_legacy()

test_reduce_multiple_lists_on_multi_data()

test_subcollection_mapping()

test_combined_mapping_and_subcollection_mapping()

test_group_tag_selection(history_id)

test_group_tag_selection_multiple(history_id)

test_galaxy_expression_tool_simplest()

test_galaxy_expression_tool_simple()

test_galaxy_expression_metadata()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_tools.dataset_to_param(dataset)

galaxy_test.api.test_tools_upload module

class galaxy_test.api.test_tools_upload.ToolsUploadTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_upload1_paste()

test_upload1_paste_bad_datatype()

test_upload_posix_newline_fixes_by_default()

test_fetch_posix_unaltered()

test_upload_disable_posix_fix()

test_fetch_post_lines_option()

test_post_lines_trailing()

test_post_lines_trailing_off()

test_fetch_post_lines_trailing_off_by_default()

test_fetch_post_lines_trailing_if_to_posix()

test_upload_tab_to_space_off_by_default()

test_fetch_tab_to_space_off_by_default()

test_upload_tab_to_space()

test_fetch_tab_to_space()

test_fetch_compressed_with_explicit_type()

test_fetch_compressed_default()

test_fetch_compressed_auto_decompress_target(history_id)

test_upload_decompress_off_with_auto_by_default()

test_upload_decompresses_if_uncompressed_type_selected()

test_upload_decompress_off_if_compressed_type_selected()

test_upload_auto_decompress_off()

test_fetch_compressed_with_auto(history_id)

test_rdata_not_decompressed()

test_csv_upload()

test_csv_upload_auto()

test_csv_fetch()

test_csv_sniff_fetch()

test_image_upload_auto()

test_newlines_stage_fetch(history_id)

test_stage_object(history_id)

test_stage_object_fetch(history_id)

test_newlines_stage_fetch_configured(history_id)

test_upload_multiple_mixed_success(history_id)

test_fetch_bam_file_from_url_with_extension_set(history_id)

test_fetch_html_from_url(history_id)

test_composite_datatype()

test_composite_datatype_fetch(history_id)

test_composite_datatype_stage_fetch(history_id)

test_composite_datatype_stage_upload1(history_id)

test_composite_datatype_space_to_tab(history_id)

test_composite_datatype_posix_lines()

test_composite_datatype_isatab()

test_upload_composite_as_tar(history_id)

test_upload_composite_as_tar_fetch(history_id)

test_upload_composite_from_bad_tar(history_id)

test_upload_dbkey()

test_fetch_bam_file(history_id)

test_upload_bam_file()

test_fetch_metadata()

test_upload_multiple_files_1()

test_upload_multiple_files_2()

test_upload_multiple_files_3()

test_upload_multiple_files_no_dbkey()

test_upload_multiple_files_space_to_tab()

test_multiple_files_posix_lines()

test_upload_force_composite()

test_upload_from_invalid_url()

test_upload_from_404_url()

test_upload_from_valid_url()

test_upload_from_valid_url_spaces()

test_upload_and_validate_invalid()

test_upload_and_validate_valid()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_tours module

class galaxy_test.api.test_tours.TourApiTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

test_index()

test_show()

test_update()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_users module

class galaxy_test.api.test_users.UsersApiTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

test_index()

test_index_only_self_for_nonadmins()

test_show()

test_update()

test_admin_update()

test_delete_user()

test_purge_user()

Delete user and then purge them.

test_undelete_user()

Delete user and then undelete them.

test_information()

test_create_api_key()

test_favorites()

test_search_favorites()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_visualizations module

class galaxy_test.api.test_visualizations.VisualizationsApiTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase, galaxy_test.api.sharable.SharingApiTests

api_name: str = 'visualizations'

create(_: str) → str

Creates a shareable resource with the given name and returns it’s ID.

Parameters

name (str) – The name of the shareable resource to create.

Returns

The ID of the resource.

Return type

str

test_index_and_show()

test_create()

test_create_fails_without_title()

test_create_fails_with_bad_slug()

test_create_fails_with_invalid_config()

test_sharing()

test_update_title()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_webhooks module

class galaxy_test.api.test_webhooks.WebhooksApiTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_get_all()

test_get_data()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_workflow_extraction module

class galaxy_test.api.test_workflow_extraction.WorkflowExtractionApiTestCase(methodName='runTest')

Bases: galaxy_test.api.test_workflows.BaseWorkflowsApiTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_extract_from_history()

test_extract_with_copied_inputs()

test_extract_with_copied_inputs_reimported()

test_extract_mapping_workflow_from_history()

test_extract_copied_mapping_from_history()

test_extract_copied_mapping_from_history_reimported()

test_extract_reduction_from_history()

test_extract_workflows_with_dataset_collections()

test_subcollection_mapping()

test_subcollection_reduction()

test_extract_workflow_with_output_collections()

test_extract_with_mapped_output_collections()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

class galaxy_test.api.test_workflow_extraction.RunJobsSummary(history_id, workflow_id, inputs, jobs)

Bases: tuple

property history_id

Alias for field number 0

property inputs

Alias for field number 2

property jobs

Alias for field number 3

property workflow_id

Alias for field number 1

galaxy_test.api.test_workflows module

class galaxy_test.api.test_workflows.BaseWorkflowsApiTestCase(methodName='runTest')

Bases: galaxy_test.api._framework.ApiTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

import_workflow(workflow, **kwds)

wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id, assert_ok=True)

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

class galaxy_test.api.test_workflows.ChangeDatatypeTestCase

Bases: object

test_assign_column_pja()

class galaxy_test.api.test_workflows.WorkflowsApiTestCase(methodName='runTest')

Bases: galaxy_test.api.test_workflows.BaseWorkflowsApiTestCase, galaxy_test.api.test_workflows.ChangeDatatypeTestCase

test_show_valid()

test_show_invalid_key_is_400()

test_cannot_show_private_workflow()

test_cannot_download_private_workflow()

test_anon_can_download_public_workflow()

test_delete()

test_other_cannot_delete()

test_index()

test_index_deleted()

test_index_hidden()

test_upload()

test_upload_deprecated()

test_import_tools_requires_admin()

test_get_tool_predictions()

test_update()

test_update_tags()

test_update_name()

test_refactor()

test_update_no_tool_id()

test_update_missing_tool()

test_require_unique_step_uuids()

test_require_unique_step_labels()

test_import_deprecated()

test_import_export_dynamic()

test_import_annotations()

test_import_subworkflows()

test_subworkflow_inputs_optional_editor()

test_not_importable_prevents_import()

test_anonymous_published()

test_import_published()

test_export()

test_export_format2()

test_export_editor()

test_export_editor_filtered_outputs()

test_export_editor_filtered_outputs_exception_handling()

test_export_editor_collection_type_source()

test_export_editor_subworkflow_collection_type_source()

test_import_missing_tool()

test_import_no_tool_id()

test_import_export_with_runtime_inputs()

test_run_workflow_by_index()

test_run_workflow_by_uuid()

test_run_workflow_by_uuid_implicitly()

test_run_workflow_by_name()

test_run_workflow()

test_run_versioned_tools()

test_run_workflow_with_missing_tool()

test_workflow_run_output_collections()

test_workflow_resume_from_failed_step()

test_workflow_resume_from_failed_step_with_hdca_input()

test_workflow_resume_with_mapped_over_input()

test_workflow_list_list_multi_data_map_over()

test_workflow_run_output_collection_mapping()

test_workflow_run_dynamic_output_collections()

test_workflow_run_dynamic_output_collections_2()

test_workflow_run_dynamic_output_collections_3()

test_empty_file_data_column_specified()

test_comma_separated_columns()

test_runtime_data_column_parameter()

test_workflow_metadata_validation_0()

test_run_subworkflow_simple()

test_run_subworkflow_runtime_parameters()

test_run_subworkflow_replacement_parameters()

test_placements_from_text_inputs()

test_run_runtime_parameters_after_pause()

test_run_subworkflow_auto_labels()

test_workflow_run_zip_collections()

test_workflow_flatten()

test_workflow_flatten_with_mapped_over_execution()

test_workflow_invocation_report_1()

test_workflow_invocation_report_custom()

test_export_invocation_bco()

test_workflow_run_apply_rules()

test_filter_failed_mapping()

test_workflow_request()

test_workflow_output_dataset()

test_workflow_output_dataset_collection()

test_workflow_input_as_output()

test_subworkflow_output_as_output()

test_workflow_input_mapping()

test_workflow_run_input_mapping_with_output_collections()

test_workflow_run_input_mapping_with_subworkflows()

test_subworkflow_recover_mapping_1()

test_subworkflow_recover_mapping_2()

test_recover_mapping_in_subworkflow()

test_empty_list_mapping()

test_change_datatype_collection_map_over()

test_mapping_and_subcollection_mapping()

test_empty_list_reduction()

test_cancel_new_workflow_when_history_deleted()

test_cancel_ready_workflow_when_history_deleted()

test_workflow_pause()

test_workflow_pause_cancel()

test_workflow_map_reduce_pause()

test_cancel_workflow_invocation()

test_pause_outputs_with_deleted_inputs()

test_error_outputs_with_purged_inputs()

test_run_with_implicit_connection()

test_run_with_optional_data_specified_to_multi_data()

test_run_with_optional_data_unspecified_to_multi_data()

test_run_with_non_optional_data_unspecified_fails_invocation()

test_run_with_optional_collection_specified()

test_run_with_optional_collection_unspecified()

test_run_with_non_optional_collection_unspecified_fails_invocation()

test_run_with_validated_parameter_connection_optional()

test_run_with_int_parameter()

test_run_with_int_parameter_nested()

test_run_with_validated_parameter_connection_default_values()

test_run_with_validated_parameter_connection_invalid()

test_run_with_text_input_connection()

test_run_with_numeric_input_connection()

test_expression_tool_map_over()

test_workflow_optional_input_text_parameter_reevaluation()

test_workflow_rerun_with_use_cached_job()

test_nested_workflow_rerun_with_use_cached_job()

test_cannot_run_inaccessible_workflow()

test_400_on_invalid_workflow_id()

test_cannot_run_against_other_users_history()

test_cannot_run_bootstrap_admin_workflow()

test_workflow_run_with_matching_lists()

test_workflow_stability()

test_empty_create()

test_invalid_create_multiple_types()

test_run_with_pja()

test_hidden_param_in_workflow()

test_optional_workflow_output()

test_workflow_optional_input_filtering()

test_run_rename_on_mapped_over_collection()

test_run_rename_based_on_inputs_on_mapped_over_collection()

test_run_rename_collection_output()

test_run_build_list_hide_collection_output()

test_run_build_list_delete_intermediate_collection_output()

test_run_build_list_change_datatype_collection_output()

test_run_build_list_rename_collection_output()

test_run_rename_multiple_outputs()

test_run_rename_based_on_input()

test_run_rename_when_resuming_jobs()

test_run_rename_based_on_input_recursive()

test_run_rename_based_on_input_repeat()

test_run_rename_based_on_input_conditional()

test_run_rename_based_on_input_collection()

test_run_hide_on_collection_output()

test_run_hide_on_mapped_over_collection()

test_tag_auto_propagation()

test_run_add_tag_on_collection_output()

test_run_add_tag_on_mapped_over_collection()

test_run_remove_tag_on_collection_output()

test_run_with_runtime_pja()

test_run_with_delayed_runtime_pja()

test_delete_intermediate_datasets_pja_1()

test_validated_post_job_action_validated()

test_validated_post_job_action_unvalidated_default()

test_validated_post_job_action_invalid()

test_value_restriction_with_select_and_text_param()

test_run_replace_params_by_tool()

test_run_replace_params_by_uuid()

test_run_batch()

test_run_batch_inputs()

test_parameter_substitution_sanitization()

test_parameter_substitution_validation_value_errors_0()

test_parameter_substitution_validation_value_errors_1()

test_workflow_import_state_validation_1()

test_run_replace_params_by_steps()

test_run_replace_params_nested()

test_run_replace_params_nested_normalized()

test_run_replace_params_over_default()

test_defaults_editor()

test_run_replace_params_over_default_delayed()

test_pja_import_export()

test_only_own_invocations_indexed_and_accessible()

test_invocation_usage()

test_invocation_with_collection_mapping()

test_invocations_accessible_imported_workflow()

test_invocations_accessible_published_workflow()

test_invocations_not_accessible_by_different_user_for_published_workflow()

test_workflow_publishing()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

class galaxy_test.api.test_workflows.AdminWorkflowsApiTestCase(methodName='runTest')

Bases: galaxy_test.api.test_workflows.BaseWorkflowsApiTestCase

require_admin_user = True

test_import_export_dynamic_tools()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_workflows_from_yaml module

class galaxy_test.api.test_workflows_from_yaml.WorkflowsFromYamlApiTestCase(methodName='runTest')

Bases: galaxy_test.api.test_workflows.BaseWorkflowsApiTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_simple_upload()

test_simple_output_actions()

test_inputs_to_steps()

test_outputs()

test_runtime_inputs()

test_subworkflow_simple()

test_subworkflow_duplicate()

test_pause()

test_implicit_connections()

test_conditional_ints(history_id)

test_workflow_embed_tool()

test_workflow_import_tool()

test_parameter_default_rep()

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver