kg_microbe.transform_utils package

Subpackages

• kg_microbe.transform_utils.ontology package
  • Submodules
  • kg_microbe.transform_utils.ontology.ontology_transform module
    • OntologyTransform
      • OntologyTransform.parse()
      • OntologyTransform.run()
  • Module contents
    • OntologyTransform
      • OntologyTransform.parse()
      • OntologyTransform.run()
• kg_microbe.transform_utils.traits package
  • Submodules
  • kg_microbe.transform_utils.traits.traits module
    • TraitsTransform
      • TraitsTransform.run()
  • Module contents
    • TraitsTransform
      • TraitsTransform.run()

Submodules

kg_microbe.transform_utils.transform module

Defines the parent class for all transforms.

class kg_microbe.transform_utils.transform.Transform(source_name, input_dir: Optional[str] = None, output_dir: Optional[str] = None, nlp: bool = False)

Bases: object

Parent class for transforms to set up default file info.

DEFAULT_INPUT_DIR = 'data/raw'

DEFAULT_NLP_DIR = 'data/nlp'

DEFAULT_NLP_INPUT_DIR = 'data/nlp/input'

DEFAULT_NLP_OUTPUT_DIR = 'data/nlp/output'

DEFAULT_NLP_STOPWORDS_DIR = 'data/nlp/stopwords'

DEFAULT_NLP_TERMS_DIR = 'data/nlp/terms'

DEFAULT_OUTPUT_DIR = 'data/transformed'

DEFAULT_SCHEMA_DIR = 'schemas'

Module contents

Intialization of tranform utils.