patch_child_json.py

#!/usr/bin/env python3
"""
This program inserts WP3-mapped data from a provided json file
into the postgres database used by the reference Beacon 2.0 implementation.
"""
import argparse
import csv
import json
import sys
import vcf

def vcf_samples(vcffile):
    """
    Samples from vcf file if present
    """
    try:
        vcf_reader = vcf.Reader(open(vcffile, 'r'))
        return vcf_reader.samples
    except Exception as error:
        print(f"Could not read vcffile {vcffile}: continuing without vcf data: {str(error)}")

    return []


def main():
    """
    Parse arguments, make database connection, read file, and start ingest
    """
    parser = argparse.ArgumentParser()
    parser.add_argument("datafile", help="Name of JSON file containing WP3-mapped metadata")
    parser.add_argument("csvfile", help="Corrected CSV file")
    parser.add_argument("vcffile", help="VCF file with samples")
    args = parser.parse_args()

    samples = vcf_samples(args.vcffile)

    with open(args.datafile, 'r') as infile:
        data = json.load(infile)

    if not data:
        print(f"Error reading data file {args.datafile}.", file=sys.stderr)
        return

    with open(args.csvfile, newline='') as csvfile:
        reader = csv.DictReader(csvfile)
        for idx, row in enumerate(reader):
            data[idx]["physiologicalMeasurements"]["anthropometry"]["weight"] = [str(float(row['birth_weight_g'])/1000.), row['sbjt_weight_kg']]
            data[idx]["physiologicalMeasurements"]["anthropometry"]["height"] = [row['height_cm'], row['sbjt_length_cm']]
            data[idx]["physiologicalMeasurements"]["circulationAndRespiration"]["bloodPressure"] = [row['sbjt_blood_pressure_systolic']]
            if len(samples) > idx:
                data[idx]["sample"] = samples[idx]

    print(json.dumps(data))


if __name__ == "__main__":
    main()