kg_microbe package

Subpackages

• kg_microbe.transform_utils package
  • Subpackages
    • kg_microbe.transform_utils.ontology package
      • Submodules
      • kg_microbe.transform_utils.ontology.ontology_transform module
      • Module contents
    • kg_microbe.transform_utils.traits package
      • Submodules
      • kg_microbe.transform_utils.traits.traits module
      • Module contents
  • Submodules
  • kg_microbe.transform_utils.transform module
    • Transform
      • Transform.DEFAULT_INPUT_DIR
      • Transform.DEFAULT_NLP_DIR
      • Transform.DEFAULT_NLP_INPUT_DIR
      • Transform.DEFAULT_NLP_OUTPUT_DIR
      • Transform.DEFAULT_NLP_STOPWORDS_DIR
      • Transform.DEFAULT_NLP_TERMS_DIR
      • Transform.DEFAULT_OUTPUT_DIR
      • Transform.DEFAULT_SCHEMA_DIR
  • Module contents
• kg_microbe.utils package
  • Submodules
  • kg_microbe.utils.biohub_converter module
    • parse()
    • parse_header()
    • write_line()
  • kg_microbe.utils.download_utils module
    • download_from_api()
    • download_from_yaml()
    • elastic_search_query()
  • kg_microbe.utils.nlp_utils module
    • assign_string_match_rating()
    • create_settings_file()
    • create_termlist()
    • prep_nlp_input()
    • process_oger_output()
    • run_oger()
  • kg_microbe.utils.robot_utils module
    • convert_to_json()
    • extract_convert_to_json()
    • initialize_robot()
  • kg_microbe.utils.transform_utils module
    • ItemInDictNotFoundError
    • TransformError
    • collapse_uniprot_curie()
    • data_to_dict()
    • get_header_items()
    • get_item_by_priority()
    • guess_bl_category()
    • multi_page_table_to_list()
    • parse_header()
    • parse_line()
    • ungzip_to_tempdir()
    • uniprot_make_name_to_id_mapping()
    • uniprot_name_to_id()
    • unzip_to_tempdir()
    • write_node_edge_item()
  • Module contents
    • download_from_yaml()
    • multi_page_table_to_list()
    • write_node_edge_item()

Submodules

kg_microbe.download module

Basic download function.

kg_microbe.download.download(yaml_file: str, output_dir: str, ignore_cache: bool = False) → None

Download data files from list of URLs into data directory.

Args:

yaml_file: A string pointing to the yaml file utilized to facilitate the downloading of data. output_dir: A string pointing to the location to download data to. ignore_cache: Ignore cache and download files even if they exist [false]

Returns:

None.

kg_microbe.query module

Functions for querying data.

kg_microbe.query.parse_query_rq(rq_file) → dict

Parse a SPARQL query file in grlc rq format.

Args:

rq_file: sparql query in grlc rq format

Returns: dict with parsed info about sparql query

kg_microbe.query.parse_query_yaml(yaml_file) → dict

Parse a yaml query.

kg_microbe.query.result_dict_to_tsv(result_dict: dict, outfile: str) → None

Convert a result_dict to a TSV for output.

kg_microbe.query.run_query(query: str, endpoint: str, return_format='json') → dict

Run a query.

kg_microbe.transform module

Top-level functions for transforming data.

kg_microbe.transform.transform(input_dir: str, output_dir: str, sources: Optional[List[str]] = None) → None

Call scripts in kg_microbe/transform/[source name]/ to transform data.

KGX can ingest each directly, in either TSV or JSON format. Args:

input_dir: A string pointing to the directory to import data from. output_dir: A string pointing to the directory to output data to. sources: A list of sources to transform.

Returns:

None.

Module contents

Initialize the KG-Microbe project.

kg_microbe.download(yaml_file: str, output_dir: str, ignore_cache: bool = False) → None

Download data files from list of URLs into data directory.

Args:

yaml_file: A string pointing to the yaml file utilized to facilitate the downloading of data. output_dir: A string pointing to the location to download data to. ignore_cache: Ignore cache and download files even if they exist [false]

Returns:

None.

kg_microbe.transform(input_dir: str, output_dir: str, sources: Optional[List[str]] = None) → None

Call scripts in kg_microbe/transform/[source name]/ to transform data.

KGX can ingest each directly, in either TSV or JSON format. Args:

input_dir: A string pointing to the directory to import data from. output_dir: A string pointing to the directory to output data to. sources: A list of sources to transform.

Returns:

None.