tests package

Submodules

tests.test_chembl module

class tests.test_chembl.TestChembl(methodName='runTest')

Bases: unittest.case.TestCase

Tests the ChEMBL transform

setUp() → None

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

classmethod setUpClass() → None

Hook method for setting up class fixture before running tests in the class.

test_parse_chembl_activity()

test_run() → None

test_source_name() → None

tests.test_download module

class tests.test_download.TestDownload(methodName='runTest')

Bases: unittest.case.TestCase

Tests kg_emerging_viruses.download

setUp() → None

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

test_api_download()

tests.test_download_from_yaml module

class tests.test_download_from_yaml.TestDownloadFromYaml(methodName='runTest')

Bases: unittest.case.TestCase

Tests download_yaml()

tests.test_drug_central module

class tests.test_drug_central.TestDrugCentral(methodName='runTest')

Bases: unittest.case.TestCase

setUp() → None

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

test_edges_file()

test_nodes_are_not_repeated()

test_nodes_file()

test_parse_drug_central_line = None

test_parse_drug_central_line_00_STRUCT_ID()

test_parse_drug_central_line_01_TARGET_NAME()

test_parse_drug_central_line_02_TARGET_CLASS()

test_parse_drug_central_line_03_ACCESSION()

test_parse_drug_central_line_04_GENE()

test_parse_drug_central_line_05_SWISSPROT()

test_parse_drug_central_line_06_ACT_VALUE()

test_parse_drug_central_line_07_ACT_UNIT()

test_parse_drug_central_line_08_ACT_TYPE()

test_parse_drug_central_line_09_ACT_COMMENT()

test_parse_drug_central_line_10_ACT_SOURCE()

test_parse_drug_central_line_11_RELATION()

test_parse_drug_central_line_12_MOA()

test_parse_drug_central_line_13_MOA_SOURCE()

test_parse_drug_central_line_14_ACT_SOURCE_URL()

test_parse_drug_central_line_15_MOA_SOURCE_URL()

test_parse_drug_central_line_16_ACTION_TYPE()

test_parse_drug_central_line_17_TDL()

test_parse_drug_central_line_18_ORGANISM()

test_run()

tests.test_gocams module

class tests.test_gocams.TestGOCams(methodName='runTest')

Bases: unittest.case.TestCase

setUp() → None

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

test_run()

test_run_exists()

tests.test_gpi_file module

class tests.test_gpi_file.TestGpiFile(methodName='runTest')

Bases: unittest.case.TestCase

setUp() → None

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

test_gpi_file_exists()

test_gpi_parsing()

tests.test_holdouts module

class tests.test_holdouts.TestEdges(methodName='runTest')

Bases: unittest.case.TestCase

setUp() → None

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

classmethod setUpClass() → None

Hook method for setting up class fixture before running tests in the class.

test_df_to_tsv()

test_make_edges_check_edge_output_files = None

test_make_edges_check_edge_output_files_0_pos_train_edges_tsv()

test_make_edges_check_edge_output_files_1_pos_test_edges_tsv()

test_make_edges_check_edge_output_files_2_pos_test_edges_tsv()

test_make_edges_check_edge_output_files_3_pos_valid_edges_tsv()

test_make_edges_check_edge_output_files_4_pos_valid_edges_tsv()

test_make_edges_check_edge_output_files_5_neg_train_edges_tsv()

test_make_edges_check_edge_output_files_6_neg_test_edges_tsv()

test_make_edges_check_edge_output_files_7_neg_test_edges_tsv()

test_make_edges_check_edge_output_files_8_neg_valid_edges_tsv()

test_make_edges_check_edge_output_files_9_neg_valid_edges_tsv()

test_make_edges_check_node_output_file()

test_make_edges_exists()

test_make_edges_pos_train_test_valid_edges_distinct = None

test_make_edges_pos_train_test_valid_edges_distinct_0_pos_train_edges_tsv()

test_make_edges_pos_train_test_valid_edges_distinct_1_neg_train_edges_tsv()

test_make_negative_edges_check_column_names()

test_make_negative_edges_check_edge_label_column()

test_make_negative_edges_check_instance_type()

test_make_negative_edges_check_neg_nodes()

test_make_negative_edges_check_num_edges_returned()

test_make_negative_edges_check_relation_column()

test_make_negative_edges_ensure_neg_edges_are_actually_negative()

test_make_negative_edges_no_reflexive_edges()

test_make_negative_edges_test_repeated_edges()

test_make_positive_edges_check_nodes()

test_make_positive_edges_check_num_test_edges_returned()

test_make_positive_edges_check_num_train_edges_returned()

test_make_positive_edges_check_test_edge_label_column()

test_make_positive_edges_check_test_edge_relation_column()

test_make_positive_edges_check_test_edges_column_names()

test_make_positive_edges_check_train_edges_column_num()

test_make_positive_edges_check_train_edges_columns()

test_make_positive_edges_test_pos_edges_are_in_input_edge_df()

test_make_positive_edges_test_pos_edges_are_removed_from_train_edges()

test_make_positive_edges_test_repeated_edges()

test_make_positives_edges_check_new_edges_instance_type()

test_make_positives_edges_check_test_edge_instance_type()

test_tsv_to_df()

tests.test_intact module

class tests.test_intact.TestIntAct(methodName='runTest')

Bases: unittest.case.TestCase

setUp() → None

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

test_fix_for_chebi_id()

test_intact_instance()

test_nodes_parse_xml_to_nodes_edges = None

test_nodes_parse_xml_to_nodes_edges_0_tests_resources_intact_test_xml()

test_nodes_parse_xml_to_nodes_edges_1_tests_resources_intact_3_participants_xml()

test_parse_experiment_info = None

test_parse_experiment_info_0_tests_resources_intact_test_xml()

test_parse_experiment_info_1_tests_resources_intact_test_xml()

test_struct_parse_xml_to_nodes_edges()

tests.test_pharmgkb module

class tests.test_pharmgkb.TestPharmGKB(methodName='runTest')

Bases: unittest.case.TestCase

Tests the ttd transform

setUp() → None

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

test_make_id_mapping_file() → None

test_make_preferred_drug_id = None

test_make_preferred_drug_id_0_PA164712302() → None

test_make_preferred_drug_id_1_PA131887008() → None

test_parse_pharmgkb_line() → None

test_run() → None

tests.test_query module

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

Bases: unittest.case.TestCase

Tests query functions()

setUp() → None

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

test_parse_query_rq() → None

test_parse_query_rq_parameterized = None

test_parse_query_rq_parameterized_0_title() → None

test_parse_query_rq_parameterized_1_description() → None

test_parse_query_rq_parameterized_2_endpoint() → None

test_parse_query_rq_parameterized_3_query() → None

test_parse_query_rq_should_return_dict() → None

test_result_dict_to_tsv_makes_correct_file()

test_result_dict_to_tsv_makes_file()

tests.test_query.load_obj(name)

tests.test_query.save_obj(obj, name)

tests.test_run module

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

Bases: unittest.case.TestCase

Tests the run.py script.

setUp() → None

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

test_merge_missing_file_error()

test_transform()

tests.test_sars_cov_2_gene_annot module

class tests.test_sars_cov_2_gene_annot.TestSarsGeneAnnot(methodName='runTest')

Bases: unittest.case.TestCase

Tests the SARS-CoV-2 gene annotation transform

setUp() → None

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

test_gpa_to_edge_data()

test_gpi12iterator_instance = None

test_gpi12iterator_instance_0_DB()

test_gpi12iterator_instance_1_DB_Object_ID()

test_gpi12iterator_instance_2_DB_Object_Symbol()

test_gpi12iterator_instance_3_DB_Object_Name()

test_gpi12iterator_instance_4_DB_Object_Synonym()

test_gpi12iterator_instance_5_DB_Object_Type()

test_gpi12iterator_instance_6_DB_Xref()

test_gpi12iterator_instance_7_Taxon()

test_gpi_to_gene_node()

test_run() → None

tests.test_scibite_cord module

class tests.test_scibite_cord.TestScibiteCord(methodName='runTest')

Bases: unittest.case.TestCase

classmethod setUpClass() → None

Hook method for setting up class fixture before running tests in the class.

test_run()

tests.test_string module

class tests.test_string.TestString(methodName='runTest')

Bases: unittest.case.TestCase

Tests the string ingest

setUp() → None

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

test_edges_file()

test_input_dir()

test_instance_vars = None

test_instance_vars_0_ensembl2ncbi_map()

test_instance_vars_1_gene_info_map()

test_instance_vars_2_protein_gene_map()

test_nodes_file()

test_output_dir()

test_output_edge_file()

test_output_node_file()

test_run()

test_source_name()

tests.test_transform_class module

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

Bases: unittest.case.TestCase

setUp() → None

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

test_attributes = None

test_attributes_0_source_name()

test_attributes_1_node_header()

test_attributes_2_edge_header()

test_attributes_3_output_base_dir()

test_attributes_4_input_base_dir()

test_attributes_5_output_dir()

test_attributes_6_output_node_file()

test_attributes_7_output_edge_file()

test_attributes_8_output_json_file()

test_default_dir = None

test_default_dir_0_DEFAULT_INPUT_DIR()

test_default_dir_1_DEFAULT_OUTPUT_DIR()

test_reality()

test_transform_child_classes = None

test_transform_child_classes_00_ZhouTransform()

Make sure Transform child classes: [with src_name=’ZhouTransform’] - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run()

Parameters

src_name –

Returns

None

test_transform_child_classes_01_DrugCentralTransform()

Make sure Transform child classes: [with src_name=’DrugCentralTransform’] - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run()

Parameters

src_name –

Returns

None

test_transform_child_classes_02_TTDTransform()

Make sure Transform child classes: [with src_name=’TTDTransform’] - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run()

Parameters

src_name –

Returns

None

test_transform_child_classes_03_StringTransform()

Make sure Transform child classes: [with src_name=’StringTransform’] - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run()

Parameters

src_name –

Returns

None

test_transform_child_classes_04_ScibiteCordTransform()

Make sure Transform child classes: [with src_name=’ScibiteCordTransform’] - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run()

Parameters

src_name –

Returns

None

test_transform_child_classes_05_PharmGKB()

Make sure Transform child classes: [with src_name=’PharmGKB’] - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run()

Parameters

src_name –

Returns

None

test_transform_child_classes_06_SARSCoV2GeneAnnot()

Make sure Transform child classes: [with src_name=’SARSCoV2GeneAnnot’] - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run()

Parameters

src_name –

Returns

None

test_transform_child_classes_07_IntAct()

Make sure Transform child classes: [with src_name=’IntAct’] - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run()

Parameters

src_name –

Returns

None

test_transform_child_classes_08_GoTransform()

Make sure Transform child classes: [with src_name=’GoTransform’] - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run()

Parameters

src_name –

Returns

None

test_transform_child_classes_09_HpTransform()

Make sure Transform child classes: [with src_name=’HpTransform’] - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run()

Parameters

src_name –

Returns

None

test_transform_child_classes_10_MondoTransform()

Make sure Transform child classes: [with src_name=’MondoTransform’] - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run()

Parameters

src_name –

Returns

None

test_transform_child_classes_11_ChebiTransform()

Make sure Transform child classes: [with src_name=’ChebiTransform’] - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run()

Parameters

src_name –

Returns

None

test_transform_child_classes_12_GocamTransform()

Make sure Transform child classes: [with src_name=’GocamTransform’] - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run()

Parameters

src_name –

Returns

None

test_transform_child_classes_13_ChemblTransform()

Make sure Transform child classes: [with src_name=’ChemblTransform’] - properly set default input_dir and output_dir - properly pass and set input_dir and output from constructor - implement run()

Parameters

src_name –

Returns

None

class tests.test_transform_class.TransformChildClass

Bases: kg_covid_19.transform_utils.transform.Transform

tests.test_transform_utils module

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

Bases: unittest.case.TestCase

test_collapse_uniprot_curie = None

test_collapse_uniprot_curie_0_foobar()

test_collapse_uniprot_curie_1_ENSEMBL_ENSG00000178607()

test_collapse_uniprot_curie_2_UniprotKB_P63151_1()

test_collapse_uniprot_curie_3_uniprotkb_P63151_1()

test_collapse_uniprot_curie_4_UniprotKB_P63151_2()

test_guess_bl_category = None

test_guess_bl_category_0_()

test_guess_bl_category_1_UniProtKB()

test_guess_bl_category_2_ComplexPortal()

test_guess_bl_category_3_GO()

tests.test_ttd_transform module

class tests.test_ttd_transform.TestTTD(methodName='runTest')

Bases: unittest.case.TestCase

Tests the ttd transform

setUp() → None

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

test_parse_ttd_file_fxn() → None

test_parse_ttd_file_values = None

test_parse_ttd_file_values_0_T47101()

test_parse_ttd_file_values_1_T47101()

test_parse_ttd_file_values_2_T47101()

test_parse_ttd_file_values_3_T17514()

test_run() → None

tests.test_version module

tests.test_version.test_version()

Tests the package version.

Module contents