run.py

from pathlib import Path
import sys
from datetime import datetime
import logging

import flywheel
import flywheel_gear_toolkit as gt

from utils import acquire_ROIs as ar

log = logging.getLogger(__name__)

def main(context):
    
    #fw = flywheel.Client()
    config = context.config
    for inp in context.config_json["inputs"].values():
        if inp["base"] == "api-key" and inp["key"]:
            api_key = inp["key"]

    fw = flywheel.Client(api_key)
    
    # Setup basic logging and log the configuration for this job
    if config["gear_log_level"] == "INFO":
        context.init_logging("info")
    else:
        context.init_logging("debug")
    context.log_config()
    
    
    dry_run = config.get('dry-run', False)
    log.debug(f"dry_run is {dry_run}")
    
    try:
    
        destination_id = context.destination.get('id')
        dest_container = fw.get(destination_id)
        project_id = dest_container.parents.project
        project = fw.get_project(project_id)

        output_dict = ar.acquire_rois(fw, project)
        
        output_path = Path(context.output_dir)/f"{project.label}_ROI-Export_{datetime.now().strftime('%d-%m-%Y_%H-%M-%S')}.csv"
        ar.save_csv(output_dict, output_path)


    
    except Exception as e:
        log.exception(e)
        return 1
     
    return 0
    


if __name__ == "__main__":
    
    result = main(gt.GearToolkitContext())
    sys.exit(result)