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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_create_paried_or_unpaired(history_id)

test_create_record(history_id)

test_record_requires_fields(history_id)

test_record_auto_fields(history_id)

test_record_field_validation(history_id)

test_sample_sheet_column_definition_problems(history_id)

test_sample_sheet_element_identifier_column_type(history_id)

test_sample_sheet_of_pairs_creation(history_id)

test_sample_sheet_validating_against_column_definition(history_id)

test_sample_sheet_requires_columns(history_id)

test_sample_sheet_map_over_preserves_columns(history_id)

Test that mapping cat1 over a sample sheet preserves columns metadata.

test_copy_sample_sheet_collection(history_id)

Test that copying a sample sheet collection preserves columns metadata.

test_workbook_download()

test_workbook_download_for_collection()

test_workbook_parse()

test_workbook_parse_for_collection()

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_upload_flat_sample_sheet()

test_upload_sample_sheet_paired()

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_dataset_collections.upload_flat_sample_sheet(dataset_populator: DatasetPopulator)

galaxy_test.api.test_dataset_collections.assert_one_collection_created_in_history(dataset_populator: DatasetPopulator, history_id: str)

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_extra_paths(history_id: str)

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_lddas()

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)

test_copy_dataset_from_history_with_copied_from_fields(history_id)

test_copy_dataset_from_library_with_copied_from_fields(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

dataset_populator: DatasetPopulator

setUp()

test_index()

test_reload_as_admin()

test_reload_with_some_ids()

test_reload_unknown_returns_as_failed()

test_reload_as_non_admin_returns_403()

test_create_link()

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_inheritance_chain_library_to_histories(history_id)

test_library_copy(history_id)

test_update(history_id)

test_rename_dataset(history_id)

test_rename_dataset_collection(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_job_build_for_rerun_switch_version(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_delete_job_with_message(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()

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_update()

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()

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_anon()

test_show_field()

test_download_field_file()

test_download_field_file_anon_raises_404()

test_download_field_file_anon_raises_403()

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_invalid_conditional_payload_handled()

test_show_multi_data()

test_show_output_collection()

test_tool_icon_endpoint_with_simple_id()

test_tool_icon_endpoint_with_toolshed_id()

test_data_source_build_request()

test_legacy_biotools_xref_injection()

test_tool_schemas()

test_data_source_ok_request()

test_data_source_sniff_fastqsanger()

test_data_sources_block_file_parameters()

test_model_attributes_sanitization()

test_fetch_workbook_generate()

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_with_error_in_mapping()

test_apply_rules_flatten_paired_unpaired()

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_apply_rules_create_paired_or_unpaired_list()

test_apply_rules_flatten_with_indices()

test_apply_rules_nested_list_from_sample_sheet()

test_apply_rules_nested_list_of_pairs_from_sample_sheet()

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_build_list()

test_run_cat_list_hdca_sort_order_respecrted_use_cached_job()

test_run_cat1_use_cached_job_from_public_history()

test_run_cat1_use_cached_job_renamed_input()

test_run_cat_list_use_cached_job_repeated_input()

test_run_collection_creates_list_use_cached_job()

test_run_collection_creates_list_use_cached_job_renamed_input()

test_run_identifier_single_map_over_nested_collection_use_cached_job()

test_run_identifier_single_use_cached_job_renamed_input()

test_run_collection_creates_dynamic_list_of_pairs_use_cached_job()

test_run_multi_output_assign_primary_ext_dbkey_use_cached_job()

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_dynamic_tool_shell_command()

test_collection_into_multiple_true()

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_can_map_over_dce_on_non_multiple_data_param()

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_input_dataset_tracking()

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_cached(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_geocsv_upload_auto()

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()

test_generate_tour_tool_not_found()

test_generate_tour_for_random_lines1()

galaxy_test.api.test_users module

class galaxy_test.api.test_users.TestUsersApi

Bases: ApiTestCase

test_index()

test_index_anon()

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)

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_workflow_download_instance()

test_workflow_run_input_extension_restriction_applied()

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_refactor_subworkflow_tool_state_upgrade()

test_update_no_tool_id()

test_update_missing_tool()

test_require_unique_step_uuids()

test_require_step_valid_v4_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_readme_metadata()

test_readme_too_large()

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_valid_url_hashes_cached()

run_workflow_with_valid_hashes(history_id: str, content_1: str, content_2: str, use_cached_job: bool = False)

test_run_workflow_with_invalid_url_hashes()

test_run_workflow_with_invalid_url()

test_run_workflow_with_url_collection()

test_run_workflow_with_url_invalid_hash_collection()

test_run_workflow_with_url_paired_collection()

test_run_workflow_from_url_with_implicit_conversion_on_collection()

test_run_workflow_from_urls_with_implicit_conversion_on_collection()

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_expression_tool_output_in_format_source()

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_subworkflow_missing_input_connection_error()

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_double_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_invocation_double_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_subworkflow_with_optional_parent_input_connected_but_not_provided()

Test subworkflow when parent’s optional input is connected but not provided.

This test verifies the fix for a bug where: 1. Parent workflow has an OPTIONAL input 2. That optional input IS CONNECTED to the subworkflow’s input 3. But NO DATA is provided for the parent’s optional input 4. Subworkflow has DELAYED SCHEDULING (via $link)

After the fix, the parent’s optional input outputs are pre-populated with NO_REPLACEMENT before the subworkflow executes, allowing it to properly handle the missing value.

This is different from the case where subworkflow inputs are completely unconnected, which was fixed in 2022.

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_skip_on_database_operation_collection_output()

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_data_meta_filter()

test_value_restriction_with_filter_param_value()

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_invalid_collection_input_rejected()

test_invalid_sample_sheet_definitions_rejected()

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_user_defined_workflow_update()

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)

class galaxy_test.api.test_workflows.TestCachedWorkflowsApi

Bases: BaseWorkflowsApiTestCase, ChangeDatatypeTests

dataset_populator: DatasetPopulator

test_run_workflow_use_cached_job_simple_conditional_step()

test_run_workflow_use_cached_job_format_source_pick_param()

test_run_workflow_use_cached_job_implicit_conversion_send_to_new_history()

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()

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()