tests package

Submodules

tests.test_download module

tests.test_download_from_yaml module

tests.test_query module

tests.test_run module

tests.test_traits module

tests.test_transform_class module

Test the parent Transform class.

class tests.test_transform_class.TestTransform(methodName='runTest')

Bases: TestCase

Tests for all transform child classes.

setUp()

Set up the transform tests, with the default output directory outside the checkout (#1592).

Return type:

None

test_attributes = None

test_attributes_0_source_name(**kw)

Test the attributes of a Transform instance [with attr=’source_name’, default=’test_transform’].

test_attributes_1_node_header(**kw)

Test the attributes of a Transform instance [with attr=’node_header’, default=[‘id’, ‘category’, ‘name’, ‘desc…nonym’, ‘deprecated’, ‘same_as’]].

test_attributes_2_edge_header(**kw)

Test the attributes of a Transform instance [with attr=’edge_header’, default=[‘subject’, ‘predicate’, ‘object…’knowledge_level’, ‘agent_type’]].

test_default_dirs_exist()

Test that default directories are set and are Path objects.

test_path_attributes()

Test that path attributes are set correctly.

test_reality()

Test the nature of reality.

test_transform_child_classes = None

test_transform_child_classes_00_mim_ingredients(**kw)

Test whether Transform child classes work as expected [with src_name=’mim_ingredients’].

Make sure Transform child classes: - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run() :param src_name: :return: None

test_transform_child_classes_01_ontologies(**kw)

Test whether Transform child classes work as expected [with src_name=’ontologies’].

Make sure Transform child classes: - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run() :param src_name: :return: None

test_transform_child_classes_02_ontologies_stubs(**kw)

Test whether Transform child classes work as expected [with src_name=’ontologies_stubs’].

Make sure Transform child classes: - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run() :param src_name: :return: None

test_transform_child_classes_03_bacdive(**kw)

Test whether Transform child classes work as expected [with src_name=’bacdive’].

Make sure Transform child classes: - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run() :param src_name: :return: None

test_transform_child_classes_04_bakta(**kw)

Test whether Transform child classes work as expected [with src_name=’bakta’].

Make sure Transform child classes: - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run() :param src_name: :return: None

test_transform_child_classes_05_cog(**kw)

Test whether Transform child classes work as expected [with src_name=’cog’].

Make sure Transform child classes: - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run() :param src_name: :return: None

test_transform_child_classes_06_gtdb(**kw)

Test whether Transform child classes work as expected [with src_name=’gtdb’].

Make sure Transform child classes: - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run() :param src_name: :return: None

test_transform_child_classes_07_kegg(**kw)

Test whether Transform child classes work as expected [with src_name=’kegg’].

Make sure Transform child classes: - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run() :param src_name: :return: None

test_transform_child_classes_08_lpsn(**kw)

Test whether Transform child classes work as expected [with src_name=’lpsn’].

Make sure Transform child classes: - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run() :param src_name: :return: None

test_transform_child_classes_09_lpsn_api(**kw)

Test whether Transform child classes work as expected [with src_name=’lpsn_api’].

Make sure Transform child classes: - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run() :param src_name: :return: None

test_transform_child_classes_10_mediadive(**kw)

Test whether Transform child classes work as expected [with src_name=’mediadive’].

Make sure Transform child classes: - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run() :param src_name: :return: None

test_transform_child_classes_11_madin_etal(**kw)

Test whether Transform child classes work as expected [with src_name=’madin_etal’].

Make sure Transform child classes: - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run() :param src_name: :return: None

test_transform_child_classes_12_metatraits(**kw)

Test whether Transform child classes work as expected [with src_name=’metatraits’].

Make sure Transform child classes: - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run() :param src_name: :return: None

test_transform_child_classes_13_metatraits_gtdb(**kw)

Test whether Transform child classes work as expected [with src_name=’metatraits_gtdb’].

Make sure Transform child classes: - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run() :param src_name: :return: None

test_transform_child_classes_14_rhea_mappings(**kw)

Test whether Transform child classes work as expected [with src_name=’rhea_mappings’].

Make sure Transform child classes: - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run() :param src_name: :return: None

test_transform_child_classes_15_bactotraits(**kw)

Test whether Transform child classes work as expected [with src_name=’bactotraits’].

Make sure Transform child classes: - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run() :param src_name: :return: None

test_transform_child_classes_16_gold(**kw)

Test whether Transform child classes work as expected [with src_name=’gold’].

Make sure Transform child classes: - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run() :param src_name: :return: None

test_transform_child_classes_17_microbedecoder(**kw)

Test whether Transform child classes work as expected [with src_name=’microbedecoder’].

Make sure Transform child classes: - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run() :param src_name: :return: None

test_transform_child_classes_18_prego(**kw)

Test whether Transform child classes work as expected [with src_name=’prego’].

Make sure Transform child classes: - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run() :param src_name: :return: None

class tests.test_transform_class.TransformChildClass

Bases: Transform

An example Transform class.

tests.test_transform_utils module

tests.test_version module

Module contents

Initialize the tests.