phenosentry 0.1.0

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phenosentry

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

Features

• Load phenopacket stores from the phenopacket-store or ZIP archives
• Load any phenopacket or phenopackets from a folder into a phenopacket store
• Validate phenopacket stores with quality checks

Installation

Install with Poetry:

poetry add phenosentry

or with pip:

pip install phenosentry

Usage

from phenosentry.model import DefaultPhenopacketStore
from phenosentry.validation import default_auditor

# Load a phenopacket store from a folder
store = DefaultPhenopacketStore.from_folder("path/to/phenopackets")

# Get the default auditor
auditor = default_auditor()

# Prepare a notepad for auditing
notepad = auditor.prepare_notepad("my-store")

# Audit the phenopacket store
auditor.audit(item=store, notepad=notepad)

if notepad.has_errors_or_warnings():
    print("Issues found in phenopacket store!")
else:
    print("Phenopacket store passed all checks.")

Development

Run tests with:

pytest

License

MIT License