convert_models

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import os
import sys
from pathlib import Path
import shutil
import subprocess
import json


def load_genomes_file(filename):
    with open(filename, "r") as f:
        data = json.load(f)
    return data["models"]


ORIGINAL_MODEL_DIRECTORY = Path.cwd() / Path("original_models/")
CONVERTED_MODEL_DIRECTORY = Path.cwd() / Path("models/")
ENVIRONMENTS_DIRECTORY = Path.cwd() / Path("old_cobra_environments/")

ENVIRONMENTS = {
    "cobra_0.14.2": "cobra_0.14.2",
    "cobra_0.15.4": "cobra_0.15.4",
}

USER_ID = os.geteuid()
GROUP_ID = os.getegid()


def build_environments():
    envs = list(set(ENVIRONMENTS.values()))
    for env in envs:
        completed_process = subprocess.run(
            ["docker", "build", ".", "-f", f"Dockerfile.{env}", "-t", env],
            cwd=ENVIRONMENTS_DIRECTORY,
        )
        completed_process.check_returncode()


def main(filename):
    build_environments()
    model_genomes = load_genomes_file(filename)
    for model_data in model_genomes:
        model_filename = model_data["filename"]
        cobra_environment = model_data.get("cobra_env", "latest")
        original_filename = ORIGINAL_MODEL_DIRECTORY / model_filename
        converted_filename = CONVERTED_MODEL_DIRECTORY / model_filename
        if converted_filename.exists() and converted_filename.is_file():
            print(f"{model_filename}: Exists, skipping")
            continue
        if cobra_environment == "latest":
            print(f"{model_filename}: latest (copy file)")
            shutil.copy(original_filename, converted_filename)
        elif not (environment := ENVIRONMENTS.get(cobra_environment)) is None:
            print(f"{model_filename}: {cobra_environment}({environment})")
            completed_process = subprocess.run(
                [
                    "docker",
                    "run",
                    "--user",
                    f"{USER_ID}:{GROUP_ID}",
                    "-v",
                    f"{ORIGINAL_MODEL_DIRECTORY}:/models/",
                    "-v",
                    f"{CONVERTED_MODEL_DIRECTORY}:/converted_models",
                    environment,
                    Path("/models") / model_filename,
                    Path("/converted_models") / model_filename,
                ]
            )
            completed_process.check_returncode()
        else:
            print(f"{model_filename}: {cobra_environment}(ERROR)")
            raise ValueError(f"Unknown environment '{environment}'")


if __name__ == "__main__":
    main(sys.argv[1])