run

autocorpus.run

Module to run the autocorpus pipeline.

Functions

run_autocorpus(config, structure, key, output_format)

Run the autocorpus pipeline on a given file.

Parameters:

Name	Type	Description	Default
config		The configuration file to use.	required
structure		The structure of the input files.	required
key		The key in the structure dict for the current file.	required
output_format		The output format to use (JSON or XML).	required

Source code in autocorpus/run.py

def run_autocorpus(config, structure, key, output_format):
    """Run the autocorpus pipeline on a given file.

    Args:
        config: The configuration file to use.
        structure: The structure of the input files.
        key: The key in the structure dict for the current file.
        output_format: The output format to use (JSON or XML).
    """
    ac = process_file(
        config=config,
        file_path=Path(structure[key]["main_text"]),
        linked_tables=sorted(Path(lt) for lt in structure[key]["linked_tables"]),
    )

    out_dir = Path(structure[key]["out_dir"])
    if structure[key]["main_text"]:
        key = key.replace("\\", "/")
        if output_format.lower() == "json":
            with open(
                out_dir / f"{Path(key).name}_bioc.json",
                "w",
                encoding="utf-8",
            ) as outfp:
                outfp.write(ac.main_text_to_bioc_json())
        else:
            with open(
                out_dir / f"{Path(key).name}_bioc.xml",
                "w",
                encoding="utf-8",
            ) as outfp:
                outfp.write(ac.main_text_to_bioc_xml())
        with open(
            out_dir / f"{Path(key).name}_abbreviations.json",
            "w",
            encoding="utf-8",
        ) as outfp:
            outfp.write(ac.abbreviations_to_bioc_json())

        ## TODO: Uncomment when SI conversion is supported
        # out_filename = str(file_path).replace(".pdf", ".pdf_bioc.json")
        # with open(out_filename, "w", encoding="utf-8") as f:
        #     BioCJSON.dump(bioc_text, f, indent=4)

        # out_table_filename = str(file_path).replace(".pdf", ".pdf_tables.json")
        # with open(out_table_filename, "w", encoding="utf-8") as f:
        #     BioCTableJSON.dump(bioc_tables, f, indent=4)

    # AC does not support the conversion of tables or abbreviations to XML
    if ac.has_tables:
        with open(
            out_dir / f"{Path(key).name}_tables.json", "w", encoding="utf-8"
        ) as outfp:
            outfp.write(ac.tables_to_bioc_json())