kg_bacdive.transform_utils package

Subpackages

• kg_bacdive.transform_utils.bacdive package
  • Submodules
  • kg_bacdive.transform_utils.bacdive.bacdive module
    • BacDiveTransform
      • BacDiveTransform.run()
  • Module contents
    • BacDiveTransform
      • BacDiveTransform.run()
• kg_bacdive.transform_utils.example_transform package
  • Submodules
  • kg_bacdive.transform_utils.example_transform.example_transform module
  • Module contents
• kg_bacdive.transform_utils.mediadive package
  • Submodules
  • kg_bacdive.transform_utils.mediadive.mediadive module
    • MediaDiveTransform
      • MediaDiveTransform.download_yaml_and_get_json()
      • MediaDiveTransform.get_compounds_of_solution()
      • MediaDiveTransform.run()
      • MediaDiveTransform.standardize_compound_id()
  • Module contents
    • MediaDiveTransform
      • MediaDiveTransform.download_yaml_and_get_json()
      • MediaDiveTransform.get_compounds_of_solution()
      • MediaDiveTransform.run()
      • MediaDiveTransform.standardize_compound_id()
• kg_bacdive.transform_utils.ontology package
  • Submodules
  • kg_bacdive.transform_utils.ontology.ontology_transform module
    • OntologyTransform
      • OntologyTransform.decompress()
      • OntologyTransform.parse()
      • OntologyTransform.run()
  • Module contents
    • OntologyTransform
      • OntologyTransform.decompress()
      • OntologyTransform.parse()
      • OntologyTransform.run()
• kg_bacdive.transform_utils.traits package
  • Submodules
  • kg_bacdive.transform_utils.traits.traits module
    • TraitsTransform
      • TraitsTransform.run()
  • Module contents
    • TraitsTransform
      • TraitsTransform.run()

Submodules

kg_bacdive.transform_utils.constants module

Constants for transform_utilities.

kg_bacdive.transform_utils.transform module

Transform utility module.

class kg_bacdive.transform_utils.transform.Transform(source_name, input_dir=None, output_dir=None, nlp=False)

Bases: object

Parent class for transforms, that sets up a lot of default file info.

DATA_DIR = PosixPath('/home/runner/work/kg-bacdive/kg-bacdive/kg_bacdive/transform_utils/data')

DEFAULT_INPUT_DIR = PosixPath('/home/runner/work/kg-bacdive/kg-bacdive/kg_bacdive/transform_utils/data/raw')

DEFAULT_OUTPUT_DIR = PosixPath('/home/runner/work/kg-bacdive/kg-bacdive/kg_bacdive/transform_utils/data/transformed')

pass_through(nodes_file, edges_file)

Copy nodes and edges files to output directory.

Parameters:

• nodes_file (str) – nodes files to take from raw directory and put in transform directory

• edges_file (str) – edges files to take from raw directory and put in transform directory

Return type:

None

run(data_file=None)

Run the transform.

Parameters:

data_file (Union[Path, None, str]) – Input data file, defaults to None

Module contents

Transform utilities module.