import_annotate_batch.py

"""
NOTE: This needs to be run as the service account that runs the OMERO server.
This should be separate from the service account that owns the image data, for
safety.
"""
import argparse
import json
from jax_omeroutils.config import OMERO_USER, OMERO_PASS
from jax_omeroutils.config import OMERO_HOST, OMERO_PORT
from pathlib import Path
import subprocess
import sys


def main(import_md):

    # Load metadata to orchestrate import
    with open(import_md, 'r') as fp:
        batch_md = json.load(fp)

    import_user = batch_md['user']
    import_group = batch_md['group']
    # file_metadata = batch_md['import_targets']
    data_dir = Path(batch_md['server_path'])

    env_folder = Path(sys.executable).parent
    omero_path = "/opt/omero/server/server_venv/bin/omero"
    kube_ns = "omero-prod"
    kube_data_dir = str(data_dir).replace("/nfs/hyperfile", "/hyperfile")
    unpack = ["kubectl", "exec", "--namespace", kube_ns, "omero-server", "--", "bash", "-c", f"{omero_path} -s {OMERO_HOST} -p {str(OMERO_PORT)} -u {import_user} -w {OMERO_PASS} -g '{import_group}' --sudo {OMERO_USER} transfer unpack --ln_s --folder '{kube_data_dir}' --merge"]
    process = subprocess.Popen(unpack,
                               stdout=subprocess.PIPE,
                               stderr=subprocess.PIPE
                               )
    stdoutval, stderrval = process.communicate()
    stdoutval, stderrval = stdoutval.decode('UTF-8'), stderrval.decode('UTF-8')
    print("stdout unpack:", stdoutval)
    print("stderr unpack:", stderrval)

    # LEGACY CODE
    # Create user connection
    # suconn = BlitzGateway(OMERO_USER,
    #                       OMERO_PASS,
    #                       host=OMERO_HOST,
    #                       port=OMERO_PORT,
    #                       secure=True)
    # suconn.connect()
    # conn = suconn.suConn(import_user, import_group, 2160000000)
    # suconn.close()

    # # do I need a session key for conn? can I pass --sudo on transfer itself?
    # # you should be able to pass --sudo on transfer!

    # Import targets from import.json
    # for md in file_metadata:
    #     filename = md['filename']
    #     file_path = data_dir / filename
    #     print(f'Preparing to import {str(file_path)}')
    #     imp_ctl = Importer(conn, file_path, md)
    #     imp_ctl.import_ln_s(OMERO_HOST, OMERO_PORT)
    #     print("import done")
    #     if imp_ctl.screen:
    #         print("it's a screen")
    #         imp_ctl.get_plate_ids()
    #         print(f"plate ids get! {str(imp_ctl.plate_ids[0])}")
    #         imp_ctl.organize_plates()
    #         print("plate organized")
    #         imp_ctl.annotate_plates()
    #         print("plate annotated")
    #     else:
    #         imp_ctl.get_image_ids()
    #         imp_ctl.organize_images()
    #         imp_ctl.annotate_images()

    # conn.close()
    return


if __name__ == "__main__":
    description = 'Use import.json to orchestrate OMERO import'
    parser = argparse.ArgumentParser(description=description)
    parser.add_argument('import_json',
                        type=str,
                        help='Full path to import.json')
    args = parser.parse_args()

    main(Path(args.import_json))