tests package

Submodules

tests.test_download module

tests.test_download_from_yaml module

tests.test_query module

Test for query functions.

class tests.test_query.TestQuery(methodName='runTest')

Bases: TestCase

Test query functions.

setUp() → None

Set up for query function tests.

test_parse_query_rq() → None

Test parsing a query in rq.

test_parse_query_rq_parameterized = None

test_parse_query_rq_parameterized_0_title() → None

Test parsing a query with parameters [with key=’title’, value=’some title’].

test_parse_query_rq_parameterized_1_description() → None

Test parsing a query with parameters [with key=’description’, value=’what is it’].

test_parse_query_rq_parameterized_2_endpoint() → None

Test parsing a query with parameters [with key=’endpoint’, value=’http://zombo.com’].

test_parse_query_rq_parameterized_3_query() → None

Test parsing a query with parameters [with key=’query’, value=’SELECT (COUNT(?v2) AS ?v1) ?v0...category> ?v0n} GROUP BY ?v0n’].

test_parse_query_rq_should_return_dict() → None

Test parsing a query in rq and returning a dict.

test_result_dict_to_tsv_makes_correct_file()

Test that result_dict converts a TSV, as expected.

test_result_dict_to_tsv_makes_file()

Test that result_dict converts to TSV.

tests.test_query.load_obj(name)

Load an object from a pickle.

tests.test_query.save_obj(obj, name)

Save an object as a pickle.

tests.test_run module

Tests for the run.py script defining the CLI.

class tests.test_run.TestRun(methodName='runTest')

Bases: TestCase

Tests the run.py script.

setUp() → None

Set up for the CLI script tests.

test_merge_missing_file_error()

Test case in which a file is missing.

test_transform()

Test the transformation command from the CLI.

tests.test_traits module

Test the traits transform.

class tests.test_traits.TestTraits(methodName='runTest')

Bases: TestCase

Test the traits transformation.

setUp() → None

Set up the transformation test.

test_edges_file(*args)

Test structure of the edges file.

test_nodes_are_not_repeated()

Test that nodes are not repeated.

test_nodes_file()

Test structure of the nodes file.

test_parse_traits_line = None

test_parse_traits_line_00_species_tax_id()

Test parsing traits line [with key=’species_tax_id’, value=’256826’].

test_parse_traits_line_01_data_source()

Test parsing traits line [with key=’data_source’, value=’methanogen’].

test_parse_traits_line_02_org_name()

Test parsing traits line [with key=’org_name’, value=’Methanobacterium aarhusense’].

test_parse_traits_line_03_species()

Test parsing traits line [with key=’species’, value=’Methanobacterium aarhusense’].

test_parse_traits_line_04_genus()

Test parsing traits line [with key=’genus’, value=’Methanobacterium’].

test_parse_traits_line_05_family()

Test parsing traits line [with key=’family’, value=’Methanobacteriaceae’].

test_parse_traits_line_06_order()

Test parsing traits line [with key=’order’, value=’Methanobacteriales’].

test_parse_traits_line_07_class()

Test parsing traits line [with key=’class’, value=’Methanobacteria’].

test_parse_traits_line_08_phylum()

Test parsing traits line [with key=’phylum’, value=’Euryarchaeota’].

test_parse_traits_line_09_superkingdom()

Test parsing traits line [with key=’superkingdom’, value=’Archaea’].

test_parse_traits_line_10_gram_stain()

Test parsing traits line [with key=’gram_stain’, value=’positive’].

test_parse_traits_line_11_metabolism()

Test parsing traits line [with key=’metabolism’, value=’anaerobic’].

test_parse_traits_line_12_pathways()

Test parsing traits line [with key=’pathways’, value=’methanogenesis’].

test_parse_traits_line_13_carbon_substrates()

Test parsing traits line [with key=’carbon_substrates’, value=’H2_CO2’].

test_parse_traits_line_14_sporulation()

Test parsing traits line [with key=’sporulation’, value=’NA’].

test_parse_traits_line_15_motility()

Test parsing traits line [with key=’motility’, value=’no’].

test_parse_traits_line_16_range_tmp()

Test parsing traits line [with key=’range_tmp’, value=’NA’].

test_parse_traits_line_17_range_salinity()

Test parsing traits line [with key=’range_salinity’, value=’NA’].

test_parse_traits_line_18_cell_shape()

Test parsing traits line [with key=’cell_shape’, value=’bacillus’].

test_parse_traits_line_19_isolation_source()

Test parsing traits line [with key=’isolation_source’, value=’NA’].

test_parse_traits_line_20_d1_lo()

Test parsing traits line [with key=’d1_lo’, value=’0.7’].

test_parse_traits_line_21_d1_up()

Test parsing traits line [with key=’d1_up’, value=’0.7’].

test_parse_traits_line_22_d2_lo()

Test parsing traits line [with key=’d2_lo’, value=’5’].

test_parse_traits_line_23_d2_up()

Test parsing traits line [with key=’d2_up’, value=’18’].

test_parse_traits_line_24_doubling_h()

Test parsing traits line [with key=’doubling_h’, value=’NA’].

test_parse_traits_line_25_genome_size()

Test parsing traits line [with key=’genome_size’, value=’NA’].

test_parse_traits_line_26_gc_content()

Test parsing traits line [with key=’gc_content’, value=’NA’].

test_parse_traits_line_27_coding_genes()

Test parsing traits line [with key=’coding_genes’, value=’NA’].

test_parse_traits_line_28_optimum_tmp()

Test parsing traits line [with key=’optimum_tmp’, value=’45’].

test_parse_traits_line_29_optimum_ph()

Test parsing traits line [with key=’optimum_ph’, value=’7.75’].

test_parse_traits_line_30_growth_tmp()

Test parsing traits line [with key=’growth_tmp’, value=’NA’].

test_parse_traits_line_31_rRNA16S_genes()

Test parsing traits line [with key=’rRNA16S_genes’, value=’NA’].

test_parse_traits_line_32_tRNA_genes()

Test parsing traits line [with key=’tRNA_genes’, value=’NA’].

test_parse_traits_line_33_ref_id()

Test parsing traits line [with key=’ref_id’, value=’19751’].

test_run()

Test running the transformation.

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() → None

Set up the transform tests.

test_attributes = None

test_attributes_0_source_name()

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

test_attributes_1_node_header()

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

test_attributes_2_edge_header()

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

test_attributes_3_output_base_dir()

Test the attributes of a Transform instance [with attr=’output_base_dir’, default=’data/transformed’].

test_attributes_4_input_base_dir()

Test the attributes of a Transform instance [with attr=’input_base_dir’, default=’data/raw’].

test_attributes_5_output_dir()

Test the attributes of a Transform instance [with attr=’output_dir’, default=’data/transformed/test_transform’].

test_attributes_6_output_node_file()

Test the attributes of a Transform instance [with attr=’output_node_file’, default=’data/transformed/test_transform/nodes.tsv’].

test_attributes_7_output_edge_file()

Test the attributes of a Transform instance [with attr=’output_edge_file’, default=’data/transformed/test_transform/edges.tsv’].

test_attributes_8_output_json_file()

Test the attributes of a Transform instance [with attr=’output_json_file’, default=’data/transformed/test_transform/nodes_edges.json’].

test_default_dir = None

test_default_dir_0_DEFAULT_INPUT_DIR()

Test the default directory [with dir_var_name=’DEFAULT_INPUT_DIR’, dir_var_value=’data/raw’].

test_default_dir_1_DEFAULT_OUTPUT_DIR()

Test the default directory [with dir_var_name=’DEFAULT_OUTPUT_DIR’, dir_var_value=’data/transformed’].

test_reality()

Test the nature of reality.

test_transform_child_classes = None

test_transform_child_classes_0_ChebiTransform()

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

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_1_NCBITransform()

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

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_2_EnvoTransform()

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

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_3_GoTransform()

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

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_4_TraitsTransform()

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

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

Test the transformation utilities.

class tests.test_transform_utils.TestTransformUtils(methodName='runTest')

Bases: TestCase

Tests for running transform utilities.

test_collapse_uniprot_curie = None

test_collapse_uniprot_curie_0_foobar()

Test for collapsing a UniProtKB curie [with curie=’foobar’, collapsed_curie=’foobar’].

test_collapse_uniprot_curie_1_ENSEMBL_ENSG00000178607()

Test for collapsing a UniProtKB curie [with curie=’ENSEMBL:ENSG00000178607’, collapsed_curie=’ENSEMBL:ENSG00000178607’].

test_collapse_uniprot_curie_2_UniprotKB_P63151_1()

Test for collapsing a UniProtKB curie [with curie=’UniprotKB:P63151-1’, collapsed_curie=’UniprotKB:P63151’].

test_collapse_uniprot_curie_3_uniprotkb_P63151_1()

Test for collapsing a UniProtKB curie [with curie=’uniprotkb:P63151-1’, collapsed_curie=’uniprotkb:P63151’].

test_collapse_uniprot_curie_4_UniprotKB_P63151_2()

Test for collapsing a UniProtKB curie [with curie=’UniprotKB:P63151-2’, collapsed_curie=’UniprotKB:P63151’].

test_guess_bl_category = None

test_guess_bl_category_0_()

Test inference of Biolink categories for a CURIE [with curie=’’, category=’biolink:NamedThing’].

test_guess_bl_category_1_UniProtKB()

Test inference of Biolink categories for a CURIE [with curie=’UniProtKB’, category=’biolink:Protein’].

test_guess_bl_category_2_ComplexPortal()

Test inference of Biolink categories for a CURIE [with curie=’ComplexPortal’, category=’biolink:Protein’].

test_guess_bl_category_3_GO()

Test inference of Biolink categories for a CURIE [with curie=’GO’, category=’biolink:OntologyClass’].

tests.test_version module

Module contents

Initialize the tests.