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galaxy_test.api package

Subpackages

• galaxy_test.api.cwl package

Submodules

galaxy_test.api.sharable module

class galaxy_test.api.sharable.SharingApiTests

Bases: UsesApiTestCaseMixin

Includes some tests for the sharing functionality of a particular resource type.

api_name: str

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_sharing_get_status()

test_sharing_access()

test_sharing_publish()

test_sharing_without_user()

test_sharing_with_user_id()

test_sharing_with_user_email()

test_update_sharing_with_users()

test_sharing_with_invalid_user()

test_set_slug()

galaxy_test.api.test_authenticate module

class galaxy_test.api.test_authenticate.TestAuthenticateApi

Bases: ApiTestCase

test_auth()

test_tool_runner_session_cookie_handling()

test_anon_history_creation()

galaxy_test.api.test_configuration module

class galaxy_test.api.test_configuration.TestConfigurationApi

Bases: ApiTestCase

test_whoami()

test_normal_user_configuration()

test_admin_user_configuration()

test_normal_user_decode_id()

test_version()

galaxy_test.api.test_dataset_collections module

class galaxy_test.api.test_dataset_collections.TestDatasetCollectionsApi

Bases: ApiTestCase

dataset_populator: DatasetPopulator

setUp()

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_download_non_english_characters()

test_hda_security()

test_dataset_collection_element_security()

test_enforces_unique_names()

test_upload_collection()

test_upload_nested()

test_upload_collection_from_url()

test_upload_collection_deferred()

test_upload_collection_failed_expansion_url()

test_collection_contents_security(history_id)

test_published_collection_contents_accessible(history_id)

test_collection_contents_invalid_collection(history_id)

test_show_dataset_collection(history_id)

test_show_dataset_collection_contents(history_id)

test_collection_contents_limit_offset(history_id)

test_collection_contents_empty_root(history_id)

test_get_suitable_converters_single_datatype(history_id)

test_get_suitable_converters_different_datatypes_matches(history_id)

test_get_suitable_converters_different_datatypes_no_matches(history_id)

test_collection_tools_tag_propagation(history_id)

galaxy_test.api.test_datasets module

class galaxy_test.api.test_datasets.TestDatasetsApi

Bases: ApiTestCase

dataset_populator: DatasetPopulator

setUp()

test_index()

test_index_using_keys(history_id)

test_index_order_by_size()

test_search_datasets()

test_search_by_tag()

test_search_by_tag_case_insensitive()

test_search_by_tool_id()

test_search_by_extension()

test_invalid_search()

test_search_returns_only_accessible(history_id)

test_show(history_id)

test_show_permission_denied(history_id)

test_admin_can_update_permissions(history_id)

test_display(history_id)

test_display_error_handling(history_id)

test_get_content_as_text(history_id)

test_get_content_as_text_with_compressed_text_data(history_id)

test_anon_get_content_as_text(history_id)

test_anon_private_get_content_as_text(history_id)

test_dataprovider_chunk(history_id)

test_bam_chunking_through_display_endpoint(history_id)

test_tabular_chunking_through_display_endpoint(history_id)

test_connectivity_table_chunking_through_display_endpoint(history_id)

test_head(history_id)

test_byte_range_support(history_id)

test_tag_change(history_id)

test_anon_tag_permissions()

test_update_datatype(history_id)

test_delete_cancels_job(history_id)

test_delete_cancels_job_with_query_params(history_id)

test_purge_does_not_reset_file_size()

test_delete_batch()

test_delete_batch_error()

test_composite_datatype_download(history_id)

test_compute_md5_on_primary_dataset(history_id)

test_compute_sha1_on_composite_dataset(history_id)

test_duplicated_hash_requests_on_primary(history_id)

test_duplicated_hash_requests_on_extra_files(history_id)

assert_hash_value(dataset_details, expected_hash_value, hash_function, extra_files_path=None)

test_storage_show(history_id)

test_storage_show_on_discarded(history_id)

test_storage_show_on_deferred(history_id)

test_display_application_link(history_id)

test_cannot_update_datatype_on_immutable_history(history_id)

test_download_non_english_characters(history_id)

galaxy_test.api.test_datatypes module

class galaxy_test.api.test_datatypes.TestDatatypesApi

Bases: 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()

galaxy_test.api.test_display_applications module

class galaxy_test.api.test_display_applications.TestDisplayApplicationsApi

Bases: ApiTestCase

test_index()

test_reload_as_admin()

test_reload_with_some_ids()

test_reload_unknown_returns_as_failed()

test_reload_as_non_admin_returns_403()

galaxy_test.api.test_folder_contents module

class galaxy_test.api.test_folder_contents.TestFolderContentsApi

Bases: ApiTestCase

dataset_populator: DatasetPopulator

setUp()

test_create_hda_with_ldda_message(history_id)

test_create_hdca_with_ldda_message(history_id)

test_index(history_id)

test_index_include_deleted(history_id)

test_index_pagination(history_id)

test_index_search_text(history_id)

test_index_permissions(history_id)

test_index_permissions_include_deleted(history_id) → None

test_index_order_by(history_id)

galaxy_test.api.test_folders module

class galaxy_test.api.test_folders.TestFoldersApi

Bases: ApiTestCase

dataset_populator: DatasetPopulator

setUp()

test_create()

test_list_library()

test_create_without_name_raises_400()

test_permissions()

test_update()

test_delete()

test_undelete()

test_import_folder_to_history()

test_update_deleted_raise_403()

galaxy_test.api.test_framework module

class galaxy_test.api.test_framework.TestApiFramework

Bases: ApiTestCase

test_default_xframe_options()

test_user_cannont_run_as()

test_run_as_invalid_user()

test_run_as_valid_user()

galaxy_test.api.test_group_roles module

class galaxy_test.api.test_group_roles.TestGroupRolesApi

Bases: ApiTestCase

dataset_populator: DatasetPopulator

setUp()

test_index(group_name: str | None = None)

test_index_only_admin()

test_index_unknown_group_raises_400()

test_show()

test_show_only_admin()

test_show_unknown_raises_400()

test_update()

test_update_only_admin()

test_delete()

test_delete_only_admin()

test_delete_unknown_raises_400()

galaxy_test.api.test_group_users module

class galaxy_test.api.test_group_users.TestGroupUsersApi

Bases: ApiTestCase

dataset_populator: DatasetPopulator

setUp()

test_index(group_name: str | None = None)

test_index_only_admin()

test_index_unknown_group_raises_400()

test_show()

test_show_only_admin()

test_show_unknown_raises_400()

test_update()

test_update_only_admin()

test_delete()

test_delete_only_admin()

test_delete_unknown_raises_400()

galaxy_test.api.test_groups module

class galaxy_test.api.test_groups.TestGroupsApi

Bases: ApiTestCase

dataset_populator: DatasetPopulator

setUp()

test_create_valid(group_name: str | None = None)

test_create_only_admin()

test_create_invalid_params_raises_400()

test_create_duplicated_name_raises_409()

test_index()

test_index_only_admin()

test_show()

test_show_only_admin()

test_show_unknown_raises_400()

test_update()

test_update_only_admin()

test_update_duplicating_name_raises_409()

test_delete()

test_delete_duplicating_name_raises_409()

test_purge()

test_purge_can_reuse_name()

galaxy_test.api.test_histories module

class galaxy_test.api.test_histories.BaseHistories

Bases: object

class galaxy_test.api.test_histories.TestHistoriesApi

Bases: ApiTestCase, BaseHistories

setUp()

test_create_history()

test_create_history_json()

test_show_history()

test_show_history_returns_expected_urls()

test_show_respects_view()

test_show_most_recently_used()

test_index_order()

test_index_query()

test_index_views()

test_index_search_mode_views()

test_index_case_insensitive_contains_query()

test_index_advanced_filter()

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()

test_import_from_model_store_dict()

test_anonymous_can_import_published()

test_publish_non_alphanumeric()

test_immutable_history_update_fails()

test_immutable_history_cannot_add_datasets()

test_cannot_modify_tags_on_immutable_history()

test_histories_count()

class galaxy_test.api.test_histories.ImportExportTests

Bases: BaseHistories

task_based: ClassVar[bool]

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()

class galaxy_test.api.test_histories.TestImportExportHistory

Bases: ApiTestCase, ImportExportTests

task_based: ClassVar[bool] = False

setUp()

class galaxy_test.api.test_histories.TestSharingHistory

Bases: ApiTestCase, BaseHistories, 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()

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()

class galaxy_test.api.test_histories.TestArchivingHistoriesWithoutExportRecord

Bases: ApiTestCase, BaseHistories

setUp()

test_archive()

test_other_users_cannot_archive_history()

test_restore()

test_other_users_cannot_restore_history()

test_archived_histories_index()

test_archived_histories_filtering_and_sorting()

test_archiving_an_archived_history_conflicts()

test_archived_histories_are_not_listed_by_default()

galaxy_test.api.test_history_contents module

class galaxy_test.api.test_history_contents.TestHistoryContentsApi

Bases: ApiTestCase

dataset_populator: DatasetPopulator

setUp()

test_index_hda_summary(history_id)

test_make_private_and_public(history_id)

test_set_permissions_add_admin_history_contents(history_id)

test_set_permissions_add_admin_datasets(history_id)

test_index_hda_all_details(history_id)

test_index_hda_detail_by_id(history_id)

test_index_detail_parameter_error(history_id)

test_view_and_keys_parameters_for_datasets(history_id)

test_view_and_keys_parameters_for_collections(history_id)

test_show_hda(history_id)

test_hda_copy(history_id)

test_inheritance_chain(history_id)

test_library_copy(history_id)

test_update(history_id)

test_update_batch(history_id)

test_update_batch_collections(history_id)

test_update_type_failures(history_id)

test_delete(history_id)

test_delete_anon()

test_delete_permission_denied(history_id)

test_purge(history_id)

test_dataset_collection_creation_on_contents(history_id)

test_dataset_collection_creation_on_typed_contents(history_id)

test_dataset_collection_create_from_exisiting_datasets_with_new_tags()

test_jobs_summary_simple_hdca(history_id)

test_jobs_summary_implicit_hdca(history_id)

test_dataset_collection_hide_originals(history_id)

test_update_dataset_collection(history_id)

test_update_batch_dataset_collection(history_id)

test_hdca_copy(history_id)

test_hdca_copy_with_new_dbkey(history_id)

test_hdca_copy_and_elements(history_id)

test_hdca_from_library_datasets(history_id)

test_hdca_from_inaccessible_library_datasets(history_id)

test_job_state_summary_field(history_id)

test_index_filter_by_type(history_id)

test_index_filter_by_name_ignores_case(history_id)

test_index_filter_by_related_items(history_id)

test_elements_datatypes_field(history_id)

test_cannot_run_tools_on_immutable_histories(history_id)

test_cannot_update_dataset_collection_on_immutable_history(history_id)

test_cannot_update_dataset_on_immutable_history(history_id)

class galaxy_test.api.test_history_contents.TestHistoryContentsApiBulkOperation

Bases: ApiTestCase

Test the /api/histories/{history_id}/contents/bulk endpoint and the new count special view for /api/histories/{history_id}/contents?v=dev

setUp()

test_explicit_items_selection()

test_dynamic_query_selection()

test_bulk_operations()

test_purging_collection_should_purge_contents()

test_deleting_collection_should_delete_contents()

test_only_owner_can_apply_bulk_operations()

test_bulk_tag_changes()

test_bulk_dbkey_change()

test_bulk_dbkey_change_dataset_collection()

test_bulk_datatype_change()

test_bulk_datatype_change_collection()

test_bulk_datatype_change_should_skip_set_metadata_on_deferred_data()

test_bulk_datatype_change_errors()

test_bulk_datatype_change_auto()

test_index_returns_expected_total_matches()

test_index_with_stats_fails_with_non_orm_filters()

test_index_with_stats_has_extra_serialization()

galaxy_test.api.test_history_contents_provenance module

class galaxy_test.api.test_history_contents_provenance.TestProvenance

Bases: ApiTestCase

dataset_populator: DatasetPopulator

setUp()

test_get_prov()

galaxy_test.api.test_jobs module

class galaxy_test.api.test_jobs.TestJobsApi

Bases: ApiTestCase, TestsTools

dataset_populator: DatasetPopulator

setUp()

test_index(history_id)

test_system_details_admin_only(history_id)

test_admin_job_list(history_id)

test_job_list_collection_view(history_id)

test_job_list_default_view(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_search_filter_tool_id(history_id)

test_index_search_filter_email(history_id)

test_index_user_filter()

test_index_handler_runner_filters(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_rerun_exception_handling()

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_submission_on_collection_with_deleted_element(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_implicit_collection_jobs(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)

test_get_inputs_and_outputs(history_id)

test_delete_job(history_id)

test_destination_params(history_id)

test_job_metrics(history_id)

test_parameters_display(history_id)

galaxy_test.api.test_libraries module

class galaxy_test.api.test_libraries.TestLibrariesApi

Bases: ApiTestCase

dataset_populator: DatasetPopulator

setUp()

test_create()

test_create_from_store()

test_index()

test_delete()

test_nonadmin()

test_update()

test_update_non_admins_with_permission()

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()

galaxy_test.api.test_licenses module

class galaxy_test.api.test_licenses.TestLicensesApi

Bases: ApiTestCase

test_index()

test_get_license()

test_404_on_unknown_license()

galaxy_test.api.test_page_revisions module

class galaxy_test.api.test_page_revisions.TestPageRevisionsApi

Bases: BasePagesApiTestCase

test_create()

test_403_if_create_revision_on_unowned_page()

test_revision_index()

test_malformed_id_if_index_unknown_page()

dataset_populator: DatasetPopulator

galaxy_test.api.test_pages module

class galaxy_test.api.test_pages.BasePagesApiTestCase

Bases: ApiTestCase

dataset_populator: DatasetPopulator

setUp()

class galaxy_test.api.test_pages.TestPagesApi

Bases: BasePagesApiTestCase, SharingApiTests

api_name: str = 'pages'

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_400_on_index_deleted_shared()

test_index_deleted()

test_index_user_id_security()

test_index_user_published()

test_index_show_published()

test_index_show_shared_with_me()

test_index_show_shared_with_me_deleted()

test_index_owner()

test_index_ordering()

test_index_limit_offset()

test_index_search_slug()

test_index_search_title()

test_index_search_sharing_tags()

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_pdf_when_service_available()

test_400_on_download_pdf_when_unsupported_content_format()

dataset_populator: DatasetPopulator

host: str

port: str | None

url: str

keepOutdir: str

test_data_resolver: TestDataResolver

galaxy_test.api.test_roles module

class galaxy_test.api.test_roles.TestRolesApi

Bases: ApiTestCase

dataset_populator: DatasetPopulator

setUp()

test_list_and_show()

test_create_invalid_params()

test_create_valid()

test_show_error_codes()

test_create_only_admin()

test_delete()

test_delete_duplicating_name_raises_409()

test_purge()

test_purge_can_reuse_name()

static check_role_dict(role_dict: Dict[str, Any], assert_id: str | None = None) → None

galaxy_test.api.test_search module

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.TestToolDataApi

Bases: 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()

galaxy_test.api.test_tools module

class galaxy_test.api.test_tools.TestsTools

Bases: object

dataset_populator: DatasetPopulator

dataset_collection_populator: BaseDatasetCollectionPopulator

class galaxy_test.api.test_tools.TestToolsApi

Bases: ApiTestCase, TestsTools

dataset_populator: DatasetPopulator

setUp()

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()

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()

test_convert_dataset_implicit_history()

test_convert_hdca()

test_unzip_collection()

test_unzip_nested()

test_zip_inputs()

test_collection_operation_dataset_input_permissions()

test_collection_operation_collection_input_permissions()

test_zip_list_inputs()

test_database_operation_tool_with_pending_inputs()

test_extract_dataset_invalid_element_identifier()

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_dataset_hidden_after_job_finish()

test_drill_down_first_by_default()

test_data_column_defaults()

test_run_cat1()

test_run_cat1_use_cached_job()

test_run_cat1_use_cached_job_from_public_history()

test_run_cat1_listified_param()

test_run_by_versions()

test_test_by_versions()

test_show_with_wrong_tool_version_in_tool_id()

test_run_cat1_single_meta_wrapper()

test_guess_derived_permissions()

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_show_tool_source_admin()

test_show_tool_source_denied()

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_dynamic_parameter_error_handling()

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_map_over_input_in_conditional(history_id)

test_identifier_multiple_reduce_in_conditional(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_multi_param_column_nested_list()

test_multi_param_column_nested_list_fails_on_invalid_column()

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_run_deferred_dataset(history_id)

test_run_deferred_dataset_with_metadata_options_filter(history_id)

test_metadata_validator_on_deferred_input(history_id)

test_metadata_validator_can_fail_on_deferred_input(history_id)

test_allow_uri_if_protocol_on_deferred_input(history_id)

test_allow_uri_if_protocol_on_collection_with_deferred(history_id)

test_run_deferred_mapping(history_id: str)

test_run_deferred_list_multi_data_reduction(history_id: str)

test_run_deferred_nested_list_input(history_id: str)

test_deferred_map_over_nested_collections(history_id)

galaxy_test.api.test_tools.dataset_to_param(dataset)

galaxy_test.api.test_tools_upload module

class galaxy_test.api.test_tools_upload.TestToolsUpload

Bases: ApiTestCase

dataset_populator: DatasetPopulator

setUp()

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_tab_to_space_doesnt_swap_newlines()

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: str) → None

test_stage_object(history_id: str) → None

test_stage_object_fetch(history_id: str) → None

test_newlines_stage_fetch_configured(history_id: str) → None

test_stage_fetch_decompress_true(history_id: str) → None

test_stage_fetch_decompress_false(history_id: str) → None

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_abort_fetch_job(history_id)

test_composite_datatype()

test_composite_datatype_fetch(history_id)

test_composite_datatype_stage_fetch(history_id: str) → None

test_composite_datatype_pbed_stage_fetch(history_id: str) → None

test_composite_datatype_stage_upload1(history_id: str) → None

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_tar_roundtrip(history_id)

test_upload_zip_roundtrip(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()

test_upload_and_validate_hash_valid()

test_upload_and_validate_hash_invalid()

test_upload_dataset_resumable()

test_upload_deferred(history_id)

galaxy_test.api.test_tours module

class galaxy_test.api.test_tours.TestToursApi

Bases: ApiTestCase

test_index()

test_show()

test_update()

galaxy_test.api.test_users module

class galaxy_test.api.test_users.TestUsersApi

Bases: 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_delete_user_cancel_all_jobs()

test_information()

test_manage_api_key()

test_only_admin_can_manage_other_users_api_key()

test_favorites()

test_search_favorites()

test_set_theme()

test_show_delete()

test_show_current()

test_manage_beacon_settings()

test_user_roles()

galaxy_test.api.test_visualizations module

class galaxy_test.api.test_visualizations.TestVisualizationsApi

Bases: ApiTestCase, 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_index_ordering()

test_index_filtering()

test_create()

test_create_fails_without_title()

test_create_fails_with_bad_slug()

test_create_fails_with_invalid_config()

test_sharing()

test_update_title()

galaxy_test.api.test_webhooks module

class galaxy_test.api.test_webhooks.TestWebhooksApi

Bases: ApiTestCase

setUp()

test_get_all()

test_get_data()

galaxy_test.api.test_workflow_extraction module

class galaxy_test.api.test_workflow_extraction.TestWorkflowExtractionApi

Bases: BaseWorkflowsApiTestCase

test_extract_from_history(history_id)

test_extract_with_copied_inputs(history_id)

test_extract_with_copied_inputs_reimported(history_id)

test_extract_mapping_workflow_from_history(history_id)

test_extract_copied_mapping_from_history(history_id)

test_extract_copied_mapping_from_history_reimported(history_id)

test_extract_reduction_from_history(history_id)

test_extract_workflows_with_dataset_collections(history_id)

test_empty_collection_map_over_extract_workflow()

test_subcollection_mapping(history_id)

test_subcollection_reduction(history_id)

test_extract_workflow_with_output_collections(history_id)

test_extract_with_mapped_output_collections(history_id)

dataset_populator: DatasetPopulator

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

Bases: tuple

history_id

Alias for field number 0

inputs

Alias for field number 2

jobs

Alias for field number 3

workflow_id

Alias for field number 1

galaxy_test.api.test_workflows module

class galaxy_test.api.test_workflows.RunsWorkflowFixtures

Bases: object

workflow_populator: WorkflowPopulator

class galaxy_test.api.test_workflows.BaseWorkflowsApiTestCase

Bases: ApiTestCase, RunsWorkflowFixtures

dataset_populator: DatasetPopulator

setUp()

import_workflow(workflow, **kwds)

class galaxy_test.api.test_workflows.ChangeDatatypeTests

Bases: object

dataset_populator: DatasetPopulator

workflow_populator: WorkflowPopulator

test_assign_column_pja()

class galaxy_test.api.test_workflows.TestWorkflowSharingApi

Bases: ApiTestCase, SharingApiTests

api_name: str = 'workflows'

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()

class galaxy_test.api.test_workflows.TestWorkflowsApi

Bases: BaseWorkflowsApiTestCase, ChangeDatatypeTests

dataset_populator: DatasetPopulator

test_show_valid()

test_show_subworkflow()

test_show_invalid_key_is_400()

test_cannot_show_private_workflow()

test_cannot_download_private_workflow()

test_anon_can_download_importable_workflow()

test_anon_can_download_public_workflow()

test_anon_can_see_workflow_preview()

test_delete()

test_other_cannot_delete()

test_undelete()

test_other_cannot_undelete()

test_index()

test_index_deleted()

test_index_hidden()

test_index_ordering()

test_index_sort_by()

test_index_limit_and_offset()

test_index_show_shared()

test_index_skip_step_counts()

test_index_search()

test_index_search_name()

test_index_search_name_exact_vs_inexact()

test_index_search_tags()

test_index_search_tags_multiple()

test_search_casing()

test_index_search_tags_exact()

test_index_published()

test_index_search_is_tags()

test_index_owner()

test_index_parameter_invalid_combinations()

test_index_total_matches()

test_upload()

test_upload_deprecated()

test_import_tools_requires_admin()

test_update()

test_update_tags()

test_update_name()

test_update_name_for_workflow_with_subworkflows()

test_update_name_empty()

test_workflow_run_form_with_broken_dataset()

test_refactor()

test_refactor_tool_state_upgrade()

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_url_import()

test_base64_import()

test_trs_import()

test_trs_import_from_dockstore_trs_url()

test_trs_import_from_workflowhub_trs_url()

test_anonymous_published()

test_import_published()

test_import_published_api()

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_workflow_by_deferred_url()

test_run_workflow_by_url()

test_run_workflow_with_valid_url_hashes()

test_run_workflow_with_invalid_url_hashes()

test_run_workflow_with_invalid_url()

test_workflow_run_output_collections() → None

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_workflow_input_tags()

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_workflow_pick_value_bam_pja()

test_run_workflow_simple_conditional_step()

test_run_workflow_simple_conditional_step_with_nested_tool_state()

test_run_workflow_invalid_when_expression()

test_run_workflow_fails_when_expression_not_boolean()

test_run_workflow_subworkflow_conditional_with_simple_mapping_step()

test_run_workflow_subworkflow_conditional_step()

test_run_nested_conditional_workflow_steps()

test_run_workflow_conditional_subworkflow_step_with_hdca_creation()

test_run_workflow_conditional_step_map_over_expression_tool()

test_run_workflow_conditional_subworkflow_step_map_over_expression_tool()

test_run_workflow_conditional_subworkflow_step_map_over_expression_tool_with_extra_nesting()

test_run_workflow_conditional_subworkflow_step_map_over_expression_tool_with_extra_nesting_skip_all()

test_run_workflow_conditional_step_map_over_expression_tool_pick_value()

test_run_subworkflow_simple() → None

test_run_subworkflow_runtime_parameters()

test_run_subworkflow_replacement_parameters()

test_run_runtime_parameters_after_pause()

test_run_subworkflow_auto_labels()

test_workflow_invocation_report_1()

test_workflow_invocation_report_custom()

test_export_invocation_bco()

test_export_invocation_ro_crate()

test_merge_collection_scheduling(history_id)

test_export_invocation_ro_crate_adv()

test_workflow_run_apply_rules()

test_filter_failed_mapping()

test_keep_success_mapping_error()

test_keep_success_mapping_paused()

test_workflow_request()

test_workflow_request_recover()

test_workflow_new_autocreated_history()

test_invocation_job_metrics_simple()

test_invocation_job_metrics_map_over()

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_subworkflow_map_over_data_column()

test_run_with_implicit_collection_map_over()

test_change_datatype_collection_map_over()

test_change_datatype_discovered_outputs()

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_cancel_workflow_invocation_deletes_jobs()

test_workflow_failed_output_not_found(history_id)

test_workflow_warning_workflow_output_not_found(history_id)

test_workflow_failed_input_not_ok(history_id)

test_workflow_failed_with_message_exception(history_id)

test_invocation_map_over(history_id)

test_invocation_map_over_inner_collection(history_id)

test_invocation_map_over_inner_collection_with_tool_collection_input(history_id)

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_optional_data_unspecified_survives_delayed_step()

test_run_subworkflow_with_optional_data_unspecified()

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_default_file_dataset_input()

test_run_with_default_file_dataset_input_and_explicit_input()

test_run_with_default_file_in_step_inline()

test_conditional_flat_crossproduct_subworkflow()

test_run_with_validated_parameter_connection_invalid()

test_run_with_text_input_connection()

test_run_with_numeric_input_connection(history_id)

test_workflow_optional_input_text_parameter_reevaluation()

test_workflow_rerun_with_use_cached_job()

test_workflow_rerun_with_cached_job_consumes_implicit_hdca(history_id: str)

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_workflow_as_anon()

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_change_datatype_new_metadata_file_parameter()

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_conditional_legacy_pja_reference()

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_add_tag_on_database_operation_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_value_restriction_with_select_from_subworkflow_input()

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_run_map_over_with_step_parameter_dict()

test_parameter_substitution_validation_value_errors_1()

test_workflow_import_state_validation_1()

test_subworkflow_import_order_maintained(history_id)

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_invocation_filtering()

test_only_own_invocations_indexed_and_accessible()

test_invocation_usage()

test_invocation_with_collection_mapping()

test_data_input_recovery_on_delayed_input()

test_subworkflow_output_not_found_fails()

test_invocations_accessible_imported_workflow()

test_invocations_accessible_published_workflow()

test_invocations_not_accessible_by_different_user_for_published_workflow()

test_invocation_filtering_exclude_subworkflow()

test_workflow_publishing()

test_workflow_from_path_requires_admin()

test_cannot_run_workflow_on_immutable_history() → None

test_subworkflow_tags()

test_upload_malformated_yaml()

class galaxy_test.api.test_workflows.TestAdminWorkflowsApi

Bases: BaseWorkflowsApiTestCase

require_admin_user = True

test_import_export_dynamic_tools(history_id)

dataset_populator: DatasetPopulator

host: str

port: str | None

url: str

keepOutdir: str

test_data_resolver: TestDataResolver

workflow_populator: WorkflowPopulator

galaxy_test.api.test_workflows_cwl module

Test CWL workflow functionality.

class galaxy_test.api.test_workflows_cwl.BaseCwlWorkflowsApiTestCase

Bases: BaseWorkflowsApiTestCase

allow_path_paste = True

require_admin_user = True

setUp()

dataset_populator: DatasetPopulator

host: str

port: str | None

url: str

keepOutdir: str

test_data_resolver: TestDataResolver

workflow_populator: WorkflowPopulator

galaxy_test.api.test_workflows_from_yaml module

class galaxy_test.api.test_workflows_from_yaml.TestWorkflowsFromYamlApi

Bases: BaseWorkflowsApiTestCase

setUp()

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()

dataset_populator: DatasetPopulator

host: str

port: str | None

url: str

keepOutdir: str

test_data_resolver: TestDataResolver

workflow_populator: WorkflowPopulator