phenosentry 0.2.0

A tool and library for quality control and validation of GA4GH Phenopackets.

phenosentry

A Python package for ensuring data quality in phenopackets and collections of phenopackets.

Features

• Validate phenopacket with quality checks

Installation

Install with Poetry:

poetry add phenosentry

or with pip:

pip install phenosentry

Usage

command line interface (CLI):

phenosentry validate

or in Python code:

from phenosentry.model import AuditorLevel
from phenosentry.validation import get_phenopacket_auditor
from phenosentry.io import read_phenopacket
from pathlib import Path
import logging
# Single Phenopacket Validation
path = "path/to/phenopacket.json"
logger = logging.getLogger("phenosentry")
phenopacket = read_phenopacket(
        directory=Path(path),
        logger=logger
)
# Strict Validation
auditor = get_phenopacket_auditor(AuditorLevel.STRICT)
notepad = auditor.prepare_notepad(auditor.id())
auditor.audit(
    item=phenopacket,
    notepad=notepad,
)
if notepad.has_errors_or_warnings(include_subsections=True):
    return "Not Valid Phenopacket"
else:
    return "Valid Phenopacket"

Development

Run tests with:

poetry run pytest

Run lint with:

poetry run ruff check phenosentry

License

MIT License