Index

A

assign_string_match_rating() (in module kg_microbe.utils.nlp_utils)

C

collapse_uniprot_curie() (in module kg_microbe.utils.transform_utils) convert_to_json() (in module kg_microbe.utils.robot_utils)

create_settings_file() (in module kg_microbe.utils.nlp_utils) create_termlist() (in module kg_microbe.utils.nlp_utils)

D

data_to_dict() (in module kg_microbe.utils.transform_utils) DEFAULT_INPUT_DIR (kg_microbe.transform_utils.transform.Transform attribute) DEFAULT_NLP_DIR (kg_microbe.transform_utils.transform.Transform attribute) DEFAULT_NLP_INPUT_DIR (kg_microbe.transform_utils.transform.Transform attribute) DEFAULT_NLP_OUTPUT_DIR (kg_microbe.transform_utils.transform.Transform attribute) DEFAULT_NLP_STOPWORDS_DIR (kg_microbe.transform_utils.transform.Transform attribute) DEFAULT_NLP_TERMS_DIR (kg_microbe.transform_utils.transform.Transform attribute)

DEFAULT_OUTPUT_DIR (kg_microbe.transform_utils.transform.Transform attribute) DEFAULT_SCHEMA_DIR (kg_microbe.transform_utils.transform.Transform attribute) download() (in module kg_microbe) (in module kg_microbe.download) download_from_api() (in module kg_microbe.utils.download_utils) download_from_yaml() (in module kg_microbe.utils) (in module kg_microbe.utils.download_utils)

E

elastic_search_query() (in module kg_microbe.utils.download_utils)

extract_convert_to_json() (in module kg_microbe.utils.robot_utils)

G

get_header_items() (in module kg_microbe.utils.transform_utils)

get_item_by_priority() (in module kg_microbe.utils.transform_utils) guess_bl_category() (in module kg_microbe.utils.transform_utils)

I

initialize_robot() (in module kg_microbe.utils.robot_utils)

ItemInDictNotFoundError

K

kg_microbe module kg_microbe.download module kg_microbe.query module kg_microbe.transform module kg_microbe.transform_utils module kg_microbe.transform_utils.ontology module kg_microbe.transform_utils.ontology.ontology_transform module kg_microbe.transform_utils.traits module

kg_microbe.transform_utils.traits.traits module kg_microbe.transform_utils.transform module kg_microbe.utils module kg_microbe.utils.biohub_converter module kg_microbe.utils.download_utils module kg_microbe.utils.nlp_utils module kg_microbe.utils.robot_utils module kg_microbe.utils.transform_utils module

L

load_obj() (in module tests.test_query)

M

module kg_microbe kg_microbe.download kg_microbe.query kg_microbe.transform kg_microbe.transform_utils kg_microbe.transform_utils.ontology kg_microbe.transform_utils.ontology.ontology_transform kg_microbe.transform_utils.traits kg_microbe.transform_utils.traits.traits kg_microbe.transform_utils.transform kg_microbe.utils kg_microbe.utils.biohub_converter kg_microbe.utils.download_utils kg_microbe.utils.nlp_utils kg_microbe.utils.robot_utils kg_microbe.utils.transform_utils query_utils query_utils.query run tests tests.test_query tests.test_run tests.test_traits tests.test_transform_class tests.test_transform_utils

multi_page_table_to_list() (in module kg_microbe.utils) (in module kg_microbe.utils.transform_utils)

O

OntologyTransform (class in kg_microbe.transform_utils.ontology) (class in kg_microbe.transform_utils.ontology.ontology_transform)

P

parse() (in module kg_microbe.utils.biohub_converter) (kg_microbe.transform_utils.ontology.ontology_transform.OntologyTransform method) (kg_microbe.transform_utils.ontology.OntologyTransform method) parse_header() (in module kg_microbe.utils.biohub_converter) (in module kg_microbe.utils.transform_utils)

parse_line() (in module kg_microbe.utils.transform_utils) parse_query_rq() (in module kg_microbe.query) parse_query_yaml() (in module kg_microbe.query) prep_nlp_input() (in module kg_microbe.utils.nlp_utils) process_oger_output() (in module kg_microbe.utils.nlp_utils)

Q

Query (class in query_utils.query) query_utils module

query_utils.query module

R

result_dict_to_tsv() (in module kg_microbe.query) run module run() (kg_microbe.transform_utils.ontology.ontology_transform.OntologyTransform method) (kg_microbe.transform_utils.ontology.OntologyTransform method) (kg_microbe.transform_utils.traits.traits.TraitsTransform method) (kg_microbe.transform_utils.traits.TraitsTransform method) (query_utils.query.Query method)

run_oger() (in module kg_microbe.utils.nlp_utils) run_query() (in module kg_microbe.query)

S

save_obj() (in module tests.test_query) setUp() (tests.test_query.TestQuery method) (tests.test_run.TestRun method) (tests.test_traits.TestTraits method) (tests.test_transform_class.TestTransform method)

T

test_attributes (tests.test_transform_class.TestTransform attribute) test_attributes_0_source_name() (tests.test_transform_class.TestTransform method) test_attributes_1_node_header() (tests.test_transform_class.TestTransform method) test_attributes_2_edge_header() (tests.test_transform_class.TestTransform method) test_attributes_3_output_base_dir() (tests.test_transform_class.TestTransform method) test_attributes_4_input_base_dir() (tests.test_transform_class.TestTransform method) test_attributes_5_output_dir() (tests.test_transform_class.TestTransform method) test_attributes_6_output_node_file() (tests.test_transform_class.TestTransform method) test_attributes_7_output_edge_file() (tests.test_transform_class.TestTransform method) test_attributes_8_output_json_file() (tests.test_transform_class.TestTransform method) test_collapse_uniprot_curie (tests.test_transform_utils.TestTransformUtils attribute) test_collapse_uniprot_curie_0_foobar() (tests.test_transform_utils.TestTransformUtils method) test_collapse_uniprot_curie_1_ENSEMBL_ENSG00000178607() (tests.test_transform_utils.TestTransformUtils method) test_collapse_uniprot_curie_2_UniprotKB_P63151_1() (tests.test_transform_utils.TestTransformUtils method) test_collapse_uniprot_curie_3_uniprotkb_P63151_1() (tests.test_transform_utils.TestTransformUtils method) test_collapse_uniprot_curie_4_UniprotKB_P63151_2() (tests.test_transform_utils.TestTransformUtils method) test_default_dir (tests.test_transform_class.TestTransform attribute) test_default_dir_0_DEFAULT_INPUT_DIR() (tests.test_transform_class.TestTransform method) test_default_dir_1_DEFAULT_OUTPUT_DIR() (tests.test_transform_class.TestTransform method) test_edges_file() (tests.test_traits.TestTraits method) test_guess_bl_category (tests.test_transform_utils.TestTransformUtils attribute) test_guess_bl_category_0_() (tests.test_transform_utils.TestTransformUtils method) test_guess_bl_category_1_UniProtKB() (tests.test_transform_utils.TestTransformUtils method) test_guess_bl_category_2_ComplexPortal() (tests.test_transform_utils.TestTransformUtils method) test_guess_bl_category_3_GO() (tests.test_transform_utils.TestTransformUtils method) test_merge_missing_file_error() (tests.test_run.TestRun method) test_nodes_are_not_repeated() (tests.test_traits.TestTraits method) test_nodes_file() (tests.test_traits.TestTraits method) test_parse_query_rq() (tests.test_query.TestQuery method) test_parse_query_rq_parameterized (tests.test_query.TestQuery attribute) test_parse_query_rq_parameterized_0_title() (tests.test_query.TestQuery method) test_parse_query_rq_parameterized_1_description() (tests.test_query.TestQuery method) test_parse_query_rq_parameterized_2_endpoint() (tests.test_query.TestQuery method) test_parse_query_rq_parameterized_3_query() (tests.test_query.TestQuery method) test_parse_query_rq_should_return_dict() (tests.test_query.TestQuery method) test_parse_traits_line (tests.test_traits.TestTraits attribute) test_parse_traits_line_00_species_tax_id() (tests.test_traits.TestTraits method) test_parse_traits_line_01_data_source() (tests.test_traits.TestTraits method) test_parse_traits_line_02_org_name() (tests.test_traits.TestTraits method) test_parse_traits_line_03_species() (tests.test_traits.TestTraits method) test_parse_traits_line_04_genus() (tests.test_traits.TestTraits method) test_parse_traits_line_05_family() (tests.test_traits.TestTraits method) test_parse_traits_line_06_order() (tests.test_traits.TestTraits method) test_parse_traits_line_07_class() (tests.test_traits.TestTraits method) test_parse_traits_line_08_phylum() (tests.test_traits.TestTraits method) test_parse_traits_line_09_superkingdom() (tests.test_traits.TestTraits method) test_parse_traits_line_10_gram_stain() (tests.test_traits.TestTraits method) test_parse_traits_line_11_metabolism() (tests.test_traits.TestTraits method) test_parse_traits_line_12_pathways() (tests.test_traits.TestTraits method) test_parse_traits_line_13_carbon_substrates() (tests.test_traits.TestTraits method) test_parse_traits_line_14_sporulation() (tests.test_traits.TestTraits method) test_parse_traits_line_15_motility() (tests.test_traits.TestTraits method)

test_parse_traits_line_16_range_tmp() (tests.test_traits.TestTraits method) test_parse_traits_line_17_range_salinity() (tests.test_traits.TestTraits method) test_parse_traits_line_18_cell_shape() (tests.test_traits.TestTraits method) test_parse_traits_line_19_isolation_source() (tests.test_traits.TestTraits method) test_parse_traits_line_20_d1_lo() (tests.test_traits.TestTraits method) test_parse_traits_line_21_d1_up() (tests.test_traits.TestTraits method) test_parse_traits_line_22_d2_lo() (tests.test_traits.TestTraits method) test_parse_traits_line_23_d2_up() (tests.test_traits.TestTraits method) test_parse_traits_line_24_doubling_h() (tests.test_traits.TestTraits method) test_parse_traits_line_25_genome_size() (tests.test_traits.TestTraits method) test_parse_traits_line_26_gc_content() (tests.test_traits.TestTraits method) test_parse_traits_line_27_coding_genes() (tests.test_traits.TestTraits method) test_parse_traits_line_28_optimum_tmp() (tests.test_traits.TestTraits method) test_parse_traits_line_29_optimum_ph() (tests.test_traits.TestTraits method) test_parse_traits_line_30_growth_tmp() (tests.test_traits.TestTraits method) test_parse_traits_line_31_rRNA16S_genes() (tests.test_traits.TestTraits method) test_parse_traits_line_32_tRNA_genes() (tests.test_traits.TestTraits method) test_parse_traits_line_33_ref_id() (tests.test_traits.TestTraits method) test_reality() (tests.test_transform_class.TestTransform method) test_result_dict_to_tsv_makes_correct_file() (tests.test_query.TestQuery method) test_result_dict_to_tsv_makes_file() (tests.test_query.TestQuery method) test_run() (tests.test_traits.TestTraits method) test_transform() (tests.test_run.TestRun method) test_transform_child_classes (tests.test_transform_class.TestTransform attribute) test_transform_child_classes_0_ChebiTransform() (tests.test_transform_class.TestTransform method) test_transform_child_classes_1_NCBITransform() (tests.test_transform_class.TestTransform method) test_transform_child_classes_2_EnvoTransform() (tests.test_transform_class.TestTransform method) test_transform_child_classes_3_GoTransform() (tests.test_transform_class.TestTransform method) test_transform_child_classes_4_TraitsTransform() (tests.test_transform_class.TestTransform method) TestQuery (class in tests.test_query) TestRun (class in tests.test_run) tests module tests.test_query module tests.test_run module tests.test_traits module tests.test_transform_class module tests.test_transform_utils module TestTraits (class in tests.test_traits) TestTransform (class in tests.test_transform_class) TestTransformUtils (class in tests.test_transform_utils) TraitsTransform (class in kg_microbe.transform_utils.traits) (class in kg_microbe.transform_utils.traits.traits) Transform (class in kg_microbe.transform_utils.transform) transform() (in module kg_microbe) (in module kg_microbe.transform) TransformChildClass (class in tests.test_transform_class) TransformError

U

ungzip_to_tempdir() (in module kg_microbe.utils.transform_utils) uniprot_make_name_to_id_mapping() (in module kg_microbe.utils.transform_utils)

uniprot_name_to_id() (in module kg_microbe.utils.transform_utils) unzip_to_tempdir() (in module kg_microbe.utils.transform_utils)

W

write_line() (in module kg_microbe.utils.biohub_converter)

write_node_edge_item() (in module kg_microbe.utils) (in module kg_microbe.utils.transform_utils)