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Update the s3_upload module to run as script #24

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merged 2 commits into from
Jul 26, 2023
Merged

Update the s3_upload module to run as script #24

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68f4a0d
update s3_upload to run as the main program
dontseyit Jul 26, 2023
00c8679
bump version number
dontseyit Jul 26, 2023
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2 changes: 1 addition & 1 deletion ghga_datasteward_kit/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,4 +15,4 @@

"""A utils package for GHGA data stewards."""

__version__ = "0.4.6"
__version__ = "0.4.7"
12 changes: 11 additions & 1 deletion ghga_datasteward_kit/s3_upload.py
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Expand Up @@ -37,6 +37,7 @@
import crypt4gh.keys # type: ignore
import crypt4gh.lib # type: ignore
import httpx
import typer
from hexkit.providers.s3 import S3Config, S3ObjectStorage # type: ignore
from nacl.bindings import crypto_aead_chacha20poly1305_ietf_encrypt
from pydantic import BaseSettings, Field, SecretStr, validator
Expand Down Expand Up @@ -612,11 +613,20 @@ async def async_main(input_path: Path, alias: str, config: Config):
metadata.serialize(output_path)


def main(input_path, alias: str, config_path: Path):
def main(
input_path: Path = typer.Option(..., help="Local path of the input file"),
alias: str = typer.Option(..., help="A human readable file alias"),
config_path: Path = typer.Option(..., help="Path to a config YAML."),
):
"""
Custom script to encrypt data using Crypt4GH and directly uploading it to S3
objectstorage.
"""

config = load_config_yaml(config_path, Config)
asyncio.run(async_main(input_path=input_path, alias=alias, config=config))


if __name__ == "__main__":
logging.basicConfig(level=logging.INFO)
typer.run(main)