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galaxy_test.api package

Submodules

galaxy_test.api.test_api_batch module

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

Bases: galaxy_test.api._framework.ApiTestCase

test_simple_array()[source]
test_unallowed_route()[source]
test_404_route()[source]
test_errors()[source]
test_querystring_params()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_authenticate module

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

Bases: galaxy_test.api._framework.ApiTestCase

test_auth()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_configuration module

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

Bases: galaxy_test.api._framework.ApiTestCase

test_whoami()[source]
test_normal_user_configuration()[source]
test_admin_user_configuration()[source]
test_normal_user_decode_id()[source]
test_version()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_dataset_collections module

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

Bases: galaxy_test.api._framework.ApiTestCase

setUp()[source]

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

test_create_pair_from_history()[source]
test_create_list_from_history()[source]
test_create_list_of_existing_pairs()[source]
test_create_list_of_new_pairs()[source]
test_list_download()[source]
test_pair_download()[source]
test_list_pair_download()[source]
test_list_list_download()[source]
test_list_list_list_download()[source]
test_hda_security()[source]
test_enforces_unique_names()[source]
test_upload_collection()[source]
test_upload_nested()[source]
test_upload_collection_from_url()[source]
test_upload_collection_failed_expansion_url()[source]
test_collection_contents_security()[source]
test_collection_contents_invalid_collection()[source]
test_show_dataset_collection()[source]
test_show_dataset_collection_contents()[source]
test_collection_contents_limit_offset()[source]
test_get_suitable_converters_single_datatype()[source]
test_get_suitable_converters_different_datatypes_matches()[source]
test_get_suitable_converters_different_datatypes_no_matches()[source]
test_collection_tools_tag_propagation()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_datasets module

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

Bases: galaxy_test.api._framework.ApiTestCase

setUp()[source]

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

test_index()[source]
test_search_datasets()[source]
test_search_by_tag()[source]
test_search_by_tool_id()[source]
test_search_returns_only_accessible()[source]
test_show()[source]
test_show_permission_denied()[source]
test_admin_can_update_permissions()[source]
test_display()[source]
test_tag_change()[source]
test_update_datatype()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_datatypes module

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

Bases: galaxy_test.api._framework.ApiTestCase

test_index()[source]
test_index_upload_only()[source]
test_full_index()[source]
test_mapping()[source]
test_types_and_mapping()[source]
test_sniffers()[source]
test_converters()[source]
test_converter_present_after_toolbox_reload()[source]
test_edam_formats()[source]
test_edam_data()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_framework module

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

Bases: galaxy_test.api._framework.ApiTestCase

test_default_xframe_options()[source]
test_user_cannont_run_as()[source]
test_run_as_invalid_user()[source]
test_run_as_valid_user()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_galaxy_interactor module

galaxy_test.api.test_histories module

class galaxy_test.api.test_histories.BaseHistories[source]

Bases: object

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

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

setUp()[source]

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

test_create_history()[source]
test_show_history()[source]
test_show_most_recently_used()[source]
test_index_order()[source]
test_delete()[source]
test_purge()[source]
test_undelete()[source]
test_update()[source]
test_update_invalid_attribute()[source]
test_update_invalid_types()[source]
test_invalid_keys()[source]
test_create_anonymous_fails()[source]
test_create_without_session_fails()[source]
test_create_tag()[source]
test_copy_history()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver
class galaxy_test.api.test_histories.ImportExportHistoryTestCase(methodName='runTest')[source]

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

setUp()[source]

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

test_import_export()[source]
test_import_1901_histories()[source]
test_import_export_include_deleted()[source]
test_import_export_failed_job()[source]
test_import_metadata_regeneration()[source]
test_import_export_collection()[source]
test_import_export_nested_collection()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver
class galaxy_test.api.test_histories.SharingHistoryTestCase(methodName='runTest')[source]

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

Tests specific for the particularities of sharing Histories.

api_name: str = 'histories'
create(name: str)str[source]

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()[source]

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

test_sharing_with_private_datasets()[source]
test_sharing_without_manage_permissions()[source]
test_sharing_empty_not_allowed()[source]
test_sharing_with_duplicated_users()[source]
test_sharing_private_history_makes_datasets_public()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_history_contents module

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

Bases: galaxy_test.api._framework.ApiTestCase

setUp()[source]

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

test_index_hda_summary()[source]
test_make_private_and_public()[source]
test_set_permissions_add_admin_history_contents()[source]
test_set_permissions_add_admin_datasets()[source]
test_index_hda_all_details()[source]
test_index_hda_detail_by_id()[source]
test_show_hda()[source]
test_hda_copy()[source]
test_library_copy()[source]
test_update()[source]
test_update_batch()[source]
test_update_batch_collections()[source]
test_update_type_failures()[source]
test_delete()[source]
test_delete_anon()[source]
test_delete_permission_denied()[source]
test_purge()[source]
test_dataset_collection_creation_on_contents()[source]
test_dataset_collection_creation_on_typed_contents()[source]
test_dataset_collection_create_from_exisiting_datasets_with_new_tags()[source]
test_jobs_summary_simple_hdca()[source]
test_jobs_summary_implicit_hdca()[source]
test_dataset_collection_hide_originals()[source]
test_update_dataset_collection()[source]
test_update_batch_dataset_collection()[source]
test_hdca_copy()[source]
test_hdca_copy_with_new_dbkey()[source]
test_hdca_copy_and_elements()[source]
test_hdca_from_library_datasets()[source]
test_hdca_from_inaccessible_library_datasets()[source]
test_job_state_summary_field()[source]
test_history_contents_near_with_update_time()[source]
test_history_contents_near_with_since()[source]
test_history_contents_near_since_with_standard_iso8601_date()[source]
test_history_contents_near_with_update_time_implicit_collection()[source]
test_history_contents_near_with_update_time_explicit_collection()[source]
test_index_filter_by_type()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_history_contents_provenance module

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

Bases: galaxy_test.api._framework.ApiTestCase

setUp()[source]

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

test_show_prov()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_jobs module

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

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

setUp()[source]

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

test_index(history_id)[source]
test_system_details_admin_only(history_id)[source]
test_admin_job_list(history_id)[source]
test_index_state_filter(history_id)[source]
test_index_date_filter(history_id)[source]
test_index_history(history_id)[source]
test_index_workflow_and_invocation_filter(history_id)[source]
test_index_workflow_filter_implicit_jobs(history_id)[source]
test_index_limit_and_offset_filter(history_id)[source]
test_index_user_filter(history_id)[source]
test_index_multiple_states_filter(history_id)[source]
test_show(history_id)[source]
test_show_security(history_id)[source]
test_unhide_on_error()[source]
test_no_unhide_on_error_if_mapped_over()[source]
test_no_hide_on_rerun()[source]
test_common_problems()[source]
test_report_error()[source]
test_report_error_anon()[source]
test_report_error_bootstrap_admin()[source]
test_deleting_output_keep_running_until_all_deleted(history_id)[source]
test_purging_output_keep_running_until_all_purged(history_id)[source]
test_purging_output_cleaned_after_ok_run(history_id)[source]
test_resume_job(history_id)[source]
test_search_handle_identifiers(history_id)[source]
test_search_delete_outputs(history_id)[source]
test_search_with_hdca_list_input(history_id)[source]
test_search_delete_hdca_output(history_id)[source]
test_search_with_hdca_pair_input(history_id)[source]
test_search_with_hdca_list_pair_input(history_id)[source]
test_search_with_hdca_list_pair_collection_mapped_over_pair_input(history_id)[source]
test_job_build_for_rerun(history_id)[source]
test_dce_submission_security(history_id)[source]
test_job_build_for_rerun_list_list(history_id)[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_libraries module

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

Bases: galaxy_test.api._framework.ApiTestCase

setUp()[source]

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

test_create()[source]
test_delete()[source]
test_nonadmin()[source]
test_update()[source]
test_create_private_library_legacy_permissions()[source]
test_create_private_library_permissions()[source]
test_get_library_current_permissions()[source]
test_get_library_available_permissions()[source]
test_get_library_available_permissions_with_query()[source]
test_create_library_dataset_bootstrap_user(library_name='private_dataset', wait=True)[source]
test_create_dataset_denied()[source]
test_create_dataset_bootstrap_admin_user()[source]
test_show_private_dataset_permissions()[source]
test_create_dataset()[source]
test_fetch_upload_to_folder()[source]
test_fetch_zip_to_folder()[source]
test_fetch_single_url_to_folder()[source]
test_fetch_single_url_with_invalid_datatype()[source]
test_legacy_upload_unknown_datatype()[source]
test_fetch_failed_validation()[source]
test_fetch_url_archive_to_folder()[source]
test_fetch_bagit_archive_to_folder()[source]
test_create_dataset_in_folder()[source]
test_create_dataset_in_subfolder()[source]
test_update_dataset_in_folder()[source]
test_update_dataset_tags()[source]
test_invalid_update_dataset_in_folder()[source]
test_detect_datatype_of_dataset_in_folder()[source]
test_ldda_collection_import_to_history()[source]
test_ldda_collection_import_to_history_hide_source()[source]
test_import_paired_collection()[source]
test_create_datasets_in_library_from_collection()[source]
test_create_datasets_in_folder_from_collection()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_licenses module

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

Bases: galaxy_test.api._framework.ApiTestCase

test_index()[source]
test_get_license()[source]
test_404_on_unknown_license()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_page_revisions module

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

Bases: galaxy_test.api.test_pages.BasePageApiTestCase

test_create()[source]
test_403_if_create_revision_on_unowned_page()[source]
test_revision_index()[source]
test_malformed_id_if_index_unknown_page()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_pages module

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

Bases: galaxy_test.api._framework.ApiTestCase

history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver
class galaxy_test.api.test_pages.PageApiTestCase(methodName='runTest')[source]

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

api_name: str = 'pages'
setUp()[source]

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

create(name: str)str[source]

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()[source]
test_create_from_report()[source]
test_index()[source]
test_index_does_not_show_unavailable_pages()[source]
test_cannot_create_pages_with_same_slug()[source]
test_cannot_create_pages_with_invalid_slug()[source]
test_cannot_create_page_with_invalid_content_format()[source]
test_page_requires_name()[source]
test_page_requires_slug()[source]
test_delete()[source]
test_400_on_delete_invalid_page_id()[source]
test_403_on_delete_unowned_page()[source]
test_400_on_invalid_id_encoding()[source]
test_400_on_invalid_id_encoding_markdown()[source]
test_400_on_invalid_embedded_content()[source]
test_400_on_invalid_markdown_call()[source]
test_show()[source]
test_403_on_unowner_show()[source]
test_501_on_download_pdf_when_service_unavailable()[source]
test_400_on_download_pdf_when_unsupported_content_format()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_roles module

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

Bases: galaxy_test.api._framework.ApiTestCase

setUp()[source]

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

test_list_and_show()[source]
test_create_invalid_params()[source]
test_create_valid()[source]
test_show_error_codes()[source]
test_create_only_admin()[source]
static check_role_dict(role_dict, assert_id=None)[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_tool_data module

Tests for the tool data API.

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

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

Bases: galaxy_test.api._framework.ApiTestCase

test_admin_only()[source]
test_list()[source]
test_show()[source]
test_show_field()[source]
test_download_field_file()[source]
test_reload()[source]
test_show_unknown_raises_404()[source]
test_show_unknown_field_raises_404()[source]
test_reload_unknown_raises_404()[source]
test_download_field_unknown_file_raises_404()[source]
test_delete_without_payload_raises_400()[source]
test_delete_without_values_raises_400()[source]
test_delete_with_wrong_values_raises_400()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_tools module

class galaxy_test.api.test_tools.TestsTools[source]

Bases: object

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

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

setUp()[source]

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

test_index()[source]
test_search_cat()[source]
test_search_trimmer()[source]
test_search_grep()[source]
test_no_panel_index()[source]
test_requirements()[source]
test_show_repeat()[source]
test_show_conditional()[source]
test_show_multi_data()[source]
test_show_output_collection()[source]
test_data_source_build_request()[source]
test_legacy_biotools_xref_injection()[source]
test_data_source_ok_request()[source]
test_data_source_sniff_fastqsanger()[source]
test_data_sources_block_file_parameters()[source]
test_model_attributes_sanitization(history_id)[source]
test_test_data_filepath_security()[source]
test_test_data_admin_security()[source]
test_data_table_requirement_annotated()[source]
test_test_data_composite_output()[source]
test_test_data_collection_two_paired()[source]
test_test_data_collection_nested()[source]
test_test_data_null_boolean_inputs()[source]
test_test_data_yaml_tools()[source]
test_test_data_download()[source]
test_test_data_downloads_security()[source]
test_test_data_download_composite()[source]
test_convert_dataset_explicit_history(history_id)[source]
test_convert_dataset_implicit_history(history_id)[source]
test_convert_hdca(history_id)[source]
test_unzip_collection()[source]
test_unzip_nested()[source]
test_zip_inputs()[source]
test_collection_operation_dataset_input_permissions(history_id)[source]
test_collection_operation_collection_input_permissions(history_id)[source]
test_zip_list_inputs()[source]
test_filter_failed_list()[source]
test_filter_failed_list_paired()[source]
test_apply_rules_1()[source]
test_apply_rules_2()[source]
test_apply_rules_3()[source]
test_apply_rules_4()[source]
test_apply_rules_5()[source]
test_apply_rules_6()[source]
test_multi_select_as_list()[source]
test_multi_select_optional()[source]
test_library_data_param()[source]
test_multidata_param()[source]
test_run_cat1(history_id)[source]
test_run_cat1_use_cached_job(history_id)[source]
test_run_cat1_listified_param(history_id)[source]
test_run_by_versions(history_id)[source]
test_test_by_versions(history_id)[source]
test_show_with_wrong_tool_version_in_tool_id(history_id)[source]
test_run_cat1_single_meta_wrapper(history_id)[source]
test_guess_derived_permissions(history_id)[source]
test_guess_derived_permissions_collections(history_id)[source]
test_validation(history_id)[source]
test_validation_empty_dataset(history_id)[source]
test_validation_in_repeat(history_id)[source]
test_collection_parameter(history_id)[source]
test_paired_collection_output(history_id)[source]
test_list_collection_output(history_id)[source]
test_list_collection_output_format_source(history_id)[source]
test_dynamic_list_output(history_id)[source]
test_dynamic_list_output_datasets_in_failed_state(history_id)[source]
test_nonadmin_users_cannot_create_tools()[source]
test_dynamic_tool_1()[source]
test_dynamic_tool_from_path()[source]
test_dynamic_tool_no_id()[source]
test_show_dynamic_tools()[source]
test_tool_deactivate()[source]
test_run_cat1_with_two_inputs(history_id)[source]
test_bam_state_regression(history_id)[source]
test_qc_messages(history_id)[source]
test_multirun_cat1(history_id)[source]
test_multirun_non_data_parameter(history_id)[source]
test_multirun_in_repeat()[source]
test_multirun_in_repeat_mismatch()[source]
test_multirun_on_multiple_inputs()[source]
test_multirun_on_multiple_inputs_unlinked()[source]
test_dynamic_parameter_error_handling()[source]
test_map_over_collection(history_id)[source]
test_map_over_empty_collection(history_id)[source]
test_map_over_with_output_format_actions(history_id)[source]
test_map_over_with_nested_paired_output_format_actions(history_id)[source]
test_map_over_with_output_filter_no_filtering(history_id)[source]
test_map_over_with_output_filter_on_optional_input(history_id)[source]
test_map_over_with_output_filter_one_filtered(history_id)[source]
test_map_over_with_complex_output_actions(history_id)[source]
test_map_over_with_discovered_output_collection_elements(history_id)[source]
test_identifier_in_map(history_id)[source]
test_identifier_outside_map(history_id)[source]
test_list_selectable_in_multidata_input(history_id)[source]
test_identifier_in_multiple_reduce(history_id)[source]
test_identifier_map_over_multiple_input_in_conditional(history_id)[source]
test_identifier_map_over_multiple_input_in_conditional_new_payload_form(history_id)[source]
test_identifier_multiple_reduce_in_repeat_new_payload_form(history_id)[source]
test_identifier_map_over_input_in_conditional(history_id)[source]
test_identifier_multiple_reduce_in_conditional(history_id)[source]
test_identifier_multiple_reduce_in_repeat(history_id)[source]
test_identifier_single_in_repeat(history_id)[source]
test_identifier_multiple_in_conditional(history_id)[source]
test_identifier_with_multiple_normal_datasets(history_id)[source]
test_identifier_with_data_collection(history_id)[source]
test_identifier_in_actions(history_id)[source]
test_map_over_nested_collections(history_id)[source]
test_paired_input_map_over_nested_collections(history_id)[source]
test_paired_input_conditional_map_over_nested_collections(history_id)[source]
test_map_over_two_collections(history_id)[source]
test_map_over_two_collections_unlinked(history_id)[source]
test_map_over_collected_and_individual_datasets(history_id)[source]
test_default_identifier_source_map_over()[source]
test_map_over_collection_output()[source]
test_cannot_map_over_incompatible_collections()[source]
test_map_over_collection_structured_like()[source]
test_map_over_collection_type_source()[source]
test_reduce_collections_legacy()[source]
test_reduce_collections()[source]
test_implicit_reduce_with_mapping()[source]
test_implicit_conversion_and_reduce()[source]
test_implicit_conversion_and_reduce_invalid_param()[source]
test_reduce_collections_in_repeat()[source]
test_reduce_collections_in_repeat_legacy()[source]
test_reduce_multiple_lists_on_multi_data()[source]
test_subcollection_mapping()[source]
test_combined_mapping_and_subcollection_mapping()[source]
test_group_tag_selection(history_id)[source]
test_group_tag_selection_multiple(history_id)[source]
test_galaxy_expression_tool_simplest()[source]
test_galaxy_expression_tool_simple()[source]
test_galaxy_expression_metadata()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver
galaxy_test.api.test_tools.dataset_to_param(dataset)[source]

galaxy_test.api.test_tools_upload module

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

Bases: galaxy_test.api._framework.ApiTestCase

setUp()[source]

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

test_upload1_paste()[source]
test_upload1_paste_bad_datatype()[source]
test_upload_posix_newline_fixes_by_default()[source]
test_fetch_posix_unaltered()[source]
test_upload_disable_posix_fix()[source]
test_fetch_post_lines_option()[source]
test_post_lines_trailing()[source]
test_post_lines_trailing_off()[source]
test_fetch_post_lines_trailing_off_by_default()[source]
test_fetch_post_lines_trailing_if_to_posix()[source]
test_upload_tab_to_space_off_by_default()[source]
test_fetch_tab_to_space_off_by_default()[source]
test_upload_tab_to_space()[source]
test_fetch_tab_to_space()[source]
test_fetch_compressed_with_explicit_type()[source]
test_fetch_compressed_default()[source]
test_fetch_compressed_auto_decompress_target(history_id)[source]
test_upload_decompress_off_with_auto_by_default()[source]
test_upload_decompresses_if_uncompressed_type_selected()[source]
test_upload_decompress_off_if_compressed_type_selected()[source]
test_upload_auto_decompress_off()[source]
test_fetch_compressed_with_auto(history_id)[source]
test_rdata_not_decompressed()[source]
test_csv_upload()[source]
test_csv_upload_auto()[source]
test_csv_fetch()[source]
test_csv_sniff_fetch()[source]
test_image_upload_auto()[source]
test_newlines_stage_fetch(history_id)[source]
test_stage_object(history_id)[source]
test_stage_object_fetch(history_id)[source]
test_newlines_stage_fetch_configured(history_id)[source]
test_upload_multiple_mixed_success(history_id)[source]
test_fetch_bam_file_from_url_with_extension_set(history_id)[source]
test_fetch_html_from_url(history_id)[source]
test_composite_datatype()[source]
test_composite_datatype_fetch(history_id)[source]
test_composite_datatype_stage_fetch(history_id)[source]
test_composite_datatype_stage_upload1(history_id)[source]
test_composite_datatype_space_to_tab(history_id)[source]
test_composite_datatype_posix_lines()[source]
test_composite_datatype_isatab()[source]
test_upload_composite_as_tar(history_id)[source]
test_upload_composite_as_tar_fetch(history_id)[source]
test_upload_composite_from_bad_tar(history_id)[source]
test_upload_dbkey()[source]
test_fetch_bam_file(history_id)[source]
test_upload_bam_file()[source]
test_fetch_metadata()[source]
test_upload_multiple_files_1()[source]
test_upload_multiple_files_2()[source]
test_upload_multiple_files_3()[source]
test_upload_multiple_files_no_dbkey()[source]
test_upload_multiple_files_space_to_tab()[source]
test_multiple_files_posix_lines()[source]
test_upload_force_composite()[source]
test_upload_from_invalid_url()[source]
test_upload_from_404_url()[source]
test_upload_from_valid_url()[source]
test_upload_from_valid_url_spaces()[source]
test_upload_and_validate_invalid()[source]
test_upload_and_validate_valid()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_tours module

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

Bases: galaxy_test.api._framework.ApiTestCase

test_index()[source]
test_show()[source]
test_update()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_users module

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

Bases: galaxy_test.api._framework.ApiTestCase

test_index()[source]
test_index_only_self_for_nonadmins()[source]
test_show()[source]
test_update()[source]
test_admin_update()[source]
test_delete_user()[source]
test_purge_user()[source]

Delete user and then purge them.

test_undelete_user()[source]

Delete user and then undelete them.

test_information()[source]
test_create_api_key()[source]
test_favorites()[source]
test_search_favorites()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_visualizations module

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

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

api_name: str = 'visualizations'
create(_: str)str[source]

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()[source]
test_create()[source]
test_create_fails_without_title()[source]
test_create_fails_with_bad_slug()[source]
test_create_fails_with_invalid_config()[source]
test_sharing()[source]
test_update_title()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_webhooks module

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

Bases: galaxy_test.api._framework.ApiTestCase

setUp()[source]

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

test_get_all()[source]
test_get_data()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_workflow_extraction module

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

Bases: galaxy_test.api.test_workflows.BaseWorkflowsApiTestCase

setUp()[source]

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

test_extract_from_history()[source]
test_extract_with_copied_inputs()[source]
test_extract_with_copied_inputs_reimported()[source]
test_extract_mapping_workflow_from_history()[source]
test_extract_copied_mapping_from_history()[source]
test_extract_copied_mapping_from_history_reimported()[source]
test_extract_reduction_from_history()[source]
test_extract_workflows_with_dataset_collections()[source]
test_subcollection_mapping()[source]
test_subcollection_reduction()[source]
test_extract_workflow_with_output_collections()[source]
test_extract_with_mapped_output_collections()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver
class galaxy_test.api.test_workflow_extraction.RunJobsSummary(history_id, workflow_id, inputs, jobs)

Bases: tuple

property history_id

Alias for field number 0

property inputs

Alias for field number 2

property jobs

Alias for field number 3

property workflow_id

Alias for field number 1

galaxy_test.api.test_workflows module

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

Bases: galaxy_test.api._framework.ApiTestCase

setUp()[source]

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

import_workflow(workflow, **kwds)[source]
wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id, assert_ok=True)[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver
class galaxy_test.api.test_workflows.ChangeDatatypeTestCase[source]

Bases: object

test_assign_column_pja()[source]
class galaxy_test.api.test_workflows.WorkflowsApiTestCase(methodName='runTest')[source]

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

test_show_valid()[source]
test_show_invalid_key_is_400()[source]
test_cannot_show_private_workflow()[source]
test_cannot_download_private_workflow()[source]
test_anon_can_download_public_workflow()[source]
test_delete()[source]
test_other_cannot_delete()[source]
test_index()[source]
test_index_deleted()[source]
test_index_hidden()[source]
test_upload()[source]
test_upload_deprecated()[source]
test_import_tools_requires_admin()[source]
test_get_tool_predictions()[source]
test_update()[source]
test_update_tags()[source]
test_update_name()[source]
test_refactor()[source]
test_update_no_tool_id()[source]
test_update_missing_tool()[source]
test_require_unique_step_uuids()[source]
test_require_unique_step_labels()[source]
test_import_deprecated()[source]
test_import_export_dynamic()[source]
test_import_annotations()[source]
test_import_subworkflows()[source]
test_subworkflow_inputs_optional_editor()[source]
test_not_importable_prevents_import()[source]
test_anonymous_published()[source]
test_import_published()[source]
test_export()[source]
test_export_format2()[source]
test_export_editor()[source]
test_export_editor_filtered_outputs()[source]
test_export_editor_filtered_outputs_exception_handling()[source]
test_export_editor_collection_type_source()[source]
test_export_editor_subworkflow_collection_type_source()[source]
test_import_missing_tool()[source]
test_import_no_tool_id()[source]
test_import_export_with_runtime_inputs()[source]
test_run_workflow_by_index()[source]
test_run_workflow_by_uuid()[source]
test_run_workflow_by_uuid_implicitly()[source]
test_run_workflow_by_name()[source]
test_run_workflow()[source]
test_run_versioned_tools()[source]
test_run_workflow_with_missing_tool()[source]
test_workflow_run_output_collections()[source]
test_workflow_resume_from_failed_step()[source]
test_workflow_resume_from_failed_step_with_hdca_input()[source]
test_workflow_resume_with_mapped_over_input()[source]
test_workflow_resume_with_mapped_over_collection_input()[source]
test_workflow_list_list_multi_data_map_over()[source]
test_workflow_run_output_collection_mapping()[source]
test_workflow_run_dynamic_output_collections()[source]
test_workflow_run_dynamic_output_collections_2()[source]
test_workflow_run_dynamic_output_collections_3()[source]
test_empty_file_data_column_specified()[source]
test_comma_separated_columns()[source]
test_runtime_data_column_parameter()[source]
test_workflow_metadata_validation_0()[source]
test_run_subworkflow_simple()[source]
test_run_subworkflow_runtime_parameters()[source]
test_run_subworkflow_replacement_parameters()[source]
test_placements_from_text_inputs()[source]
test_run_runtime_parameters_after_pause()[source]
test_run_subworkflow_auto_labels()[source]
test_workflow_run_zip_collections()[source]
test_workflow_flatten()[source]
test_workflow_flatten_with_mapped_over_execution()[source]
test_workflow_invocation_report_1()[source]
test_workflow_invocation_report_custom()[source]
test_export_invocation_bco()[source]
test_workflow_run_apply_rules()[source]
test_filter_failed_mapping()[source]
test_workflow_request()[source]
test_workflow_output_dataset()[source]
test_workflow_output_dataset_collection()[source]
test_workflow_input_as_output()[source]
test_subworkflow_output_as_output()[source]
test_workflow_input_mapping()[source]
test_workflow_run_input_mapping_with_output_collections()[source]
test_workflow_run_input_mapping_with_subworkflows()[source]
test_subworkflow_recover_mapping_1()[source]
test_subworkflow_recover_mapping_2()[source]
test_recover_mapping_in_subworkflow()[source]
test_empty_list_mapping()[source]
test_change_datatype_collection_map_over()[source]
test_mapping_and_subcollection_mapping()[source]
test_empty_list_reduction()[source]
test_cancel_new_workflow_when_history_deleted()[source]
test_cancel_ready_workflow_when_history_deleted()[source]
test_workflow_pause()[source]
test_workflow_pause_cancel()[source]
test_workflow_map_reduce_pause()[source]
test_cancel_workflow_invocation()[source]
test_pause_outputs_with_deleted_inputs()[source]
test_error_outputs_with_purged_inputs()[source]
test_run_with_implicit_connection()[source]
test_run_with_optional_data_specified_to_multi_data()[source]
test_run_with_optional_data_unspecified_to_multi_data()[source]
test_run_with_non_optional_data_unspecified_fails_invocation()[source]
test_run_with_optional_collection_specified()[source]
test_run_with_optional_collection_unspecified()[source]
test_run_with_non_optional_collection_unspecified_fails_invocation()[source]
test_run_with_validated_parameter_connection_optional()[source]
test_run_with_int_parameter()[source]
test_run_with_int_parameter_nested()[source]
test_run_with_validated_parameter_connection_default_values()[source]
test_run_with_validated_parameter_connection_invalid()[source]
test_run_with_text_input_connection()[source]
test_run_with_numeric_input_connection()[source]
test_expression_tool_map_over()[source]
test_workflow_optional_input_text_parameter_reevaluation()[source]
test_workflow_rerun_with_use_cached_job()[source]
test_nested_workflow_rerun_with_use_cached_job()[source]
test_cannot_run_inaccessible_workflow()[source]
test_400_on_invalid_workflow_id()[source]
test_cannot_run_against_other_users_history()[source]
test_cannot_run_bootstrap_admin_workflow()[source]
test_workflow_run_with_matching_lists()[source]
test_workflow_stability()[source]
test_empty_create()[source]
test_invalid_create_multiple_types()[source]
test_run_with_pja()[source]
test_hidden_param_in_workflow()[source]
test_optional_workflow_output()[source]
test_workflow_optional_input_filtering()[source]
test_run_rename_on_mapped_over_collection()[source]
test_run_rename_based_on_inputs_on_mapped_over_collection()[source]
test_run_rename_collection_output()[source]
test_run_build_list_hide_collection_output()[source]
test_run_build_list_delete_intermediate_collection_output()[source]
test_run_build_list_change_datatype_collection_output()[source]
test_run_build_list_rename_collection_output()[source]
test_run_rename_multiple_outputs()[source]
test_run_rename_based_on_input()[source]
test_run_rename_when_resuming_jobs()[source]
test_run_rename_based_on_input_recursive()[source]
test_run_rename_based_on_input_repeat()[source]
test_run_rename_based_on_input_conditional()[source]
test_run_rename_based_on_input_collection()[source]
test_run_hide_on_collection_output()[source]
test_run_hide_on_mapped_over_collection()[source]
test_tag_auto_propagation()[source]
test_run_add_tag_on_collection_output()[source]
test_run_add_tag_on_mapped_over_collection()[source]
test_run_remove_tag_on_collection_output()[source]
test_run_with_runtime_pja()[source]
test_run_with_delayed_runtime_pja()[source]
test_delete_intermediate_datasets_pja_1()[source]
test_validated_post_job_action_validated()[source]
test_validated_post_job_action_unvalidated_default()[source]
test_validated_post_job_action_invalid()[source]
test_value_restriction_with_select_and_text_param()[source]
test_run_replace_params_by_tool()[source]
test_run_replace_params_by_uuid()[source]
test_run_batch()[source]
test_run_batch_inputs()[source]
test_parameter_substitution_sanitization()[source]
test_parameter_substitution_validation_value_errors_0()[source]
test_parameter_substitution_validation_value_errors_1()[source]
test_workflow_import_state_validation_1()[source]
test_run_replace_params_by_steps()[source]
test_run_replace_params_nested()[source]
test_run_replace_params_nested_normalized()[source]
test_run_replace_params_over_default()[source]
test_defaults_editor()[source]
test_run_replace_params_over_default_delayed()[source]
test_pja_import_export()[source]
test_only_own_invocations_indexed_and_accessible()[source]
test_invocation_usage()[source]
test_invocation_with_collection_mapping()[source]
test_invocations_accessible_imported_workflow()[source]
test_invocations_accessible_published_workflow()[source]
test_invocations_not_accessible_by_different_user_for_published_workflow()[source]
test_workflow_publishing()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver
class galaxy_test.api.test_workflows.AdminWorkflowsApiTestCase(methodName='runTest')[source]

Bases: galaxy_test.api.test_workflows.BaseWorkflowsApiTestCase

require_admin_user = True
test_import_export_dynamic_tools()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

galaxy_test.api.test_workflows_from_yaml module

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

Bases: galaxy_test.api.test_workflows.BaseWorkflowsApiTestCase

setUp()[source]

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

test_simple_upload()[source]
test_simple_output_actions()[source]
test_inputs_to_steps()[source]
test_outputs()[source]
test_runtime_inputs()[source]
test_subworkflow_simple()[source]
test_subworkflow_duplicate()[source]
test_pause()[source]
test_implicit_connections()[source]
test_conditional_ints(history_id)[source]
test_workflow_embed_tool()[source]
test_workflow_import_tool()[source]
test_parameter_default_rep()[source]
history_id: Optional[str]
host: str
port: Optional[str]
url: str
keepOutdir: str
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver