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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()

test_tool_runner_session_cookie_handling()

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()

test_get_suitable_converters_single_datatype()

test_get_suitable_converters_different_datatypes_matches()

test_get_suitable_converters_different_datatypes_no_matches()

test_collection_tools_tag_propagation()

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

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

setUp()

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

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()

test_copy_history()

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

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

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

Tests specific for the particularities of sharing Histories.

api_name: str = 'histories'

create(name: str) → str

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

Parameters

name – The name of the shareable resource to create.

Returns

The ID of the resource.

setUp()

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

test_sharing_with_private_datasets()

test_sharing_without_manage_permissions()

test_sharing_empty_not_allowed()

test_sharing_with_duplicated_users()

test_sharing_private_history_makes_datasets_public()

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_batch_collections()

test_update_type_failures()

test_delete()

test_delete_anon()

test_delete_permission_denied()

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_update_batch_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_since()

test_history_contents_near_since_with_standard_iso8601_date()

test_history_contents_near_with_update_time_implicit_collection()

test_history_contents_near_with_update_time_explicit_collection()

test_index_filter_by_type()

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_no_hide_on_rerun()

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_legacy_permissions()

test_create_private_library_permissions()

test_get_library_current_permissions()

test_get_library_available_permissions()

test_get_library_available_permissions_with_query()

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'

setUp()

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

create(name: str) → str

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

Parameters

name – The name of the shareable resource to create.

Returns

The ID of the resource.

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_501_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_legacy_biotools_xref_injection()

test_data_source_ok_request()

test_data_source_sniff_fastqsanger()

test_data_sources_block_file_parameters()

test_model_attributes_sanitization(history_id)

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_convert_dataset_explicit_history(history_id)

test_convert_dataset_implicit_history(history_id)

test_convert_hdca(history_id)

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 – The name of the shareable resource to create.

Returns

The ID of the resource.

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_resume_with_mapped_over_collection_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_comma_separated_columns_with_trailing_newline()

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