How one might create compliant metadata without directly writing to iRODS

make_metadata_json_from_npg_irods_python.py

#!/usr/bin/env python

# Find sample in warehouse, also find a study row
# Feed to npg_irods.metadata.lims.make_sample_metadata()
# Extract AVU objects and convert to JSON. They'll be turned back into AVUs later... but that's batching for you.

import json
import sqlalchemy
from npg.conf import IniData
from npg_irods.db import Config
from npg_irods.metadata.lims import make_sample_metadata, make_study_metadata
from npg_irods.db.mlwh import (
    find_study_by_study_id,
    find_sample_by_sample_id,
    session_context,
)

dbconfig = IniData(Config).from_file(
    ini_file="/Users/kt19/.npg/mlwh_ro.ini", section="mlwh_ro"
)

engine = sqlalchemy.create_engine(dbconfig.url, pool_pre_ping=True, pool_recycle=3600)

with session_context(engine) as session:
    sample = find_sample_by_sample_id(session, "10132480")
    study = find_study_by_study_id(session, "6496")
    study_avus = make_study_metadata(study)
    sample_avus = make_sample_metadata(sample)

    # implement a to_json on partisan.irods.AVU instead?
    # print(study_avus, sample_avus)

    # Probably need to check `default namespace` when converting to json things
    meta = [{study_thing.attribute: study_thing.value, study_thing.units} for study_thing in study_avus]

    meta.extend(
        [{sample_thing.attribute: sample_thing.value, sample_thing.units} for sample_thing in sample_avus]
    )
    print(json.dumps(meta))