Step 7: Edit populate.py

This file implements the function that serves as the "entry point" to the plugin's functionality.

Explanation

The populate.py file implements the populate function, which is the only function that will be directly exposed by the plugin to parsomics-core. This function instantiates the processor implemented in processor.py using the parameters set by the user in the configuration file.

Hands on

1. The template most likely generated the entire file correctly. All you need to do is remove the triple quotes and test the populate function for correctness.

2. Stage populate.py and commit it.

Result

populate.py

from typing import Sequence

from parsomics_core.globals.database import engine
from parsomics_core.populate import process_files
from timeit_decorator import timeit

from .processor import InterproOutputProcessor


@timeit()
def populate_interpro(
    run_info: dict, assembly_key: int, dereplicated_genomes: Sequence[str]
) -> None:
    def process_interpro_files(
        output_directory, assembly_key, run_key, tool_key, dereplicated_genomes
    ):
        interpro_output_processor = InterproOutputProcessor(
            output_directory=output_directory,
            assembly_key=assembly_key,
            run_key=run_key,
            tool_key=tool_key,
            dereplicated_genomes=dereplicated_genomes,
        )
        interpro_output_processor.process_interpro_tsv_files(engine)

    process_files(
        run_info, assembly_key, dereplicated_genomes, "interpro", process_interpro_files
    )