Source code for users_api.management.commands.datasets_export

import logging
import sys

from django.core.management.base import BaseCommand

from .dataset_mixin import DatasetBaseMixin

logger = logging.getLogger(__name__)




class Command(BaseCommand, DatasetBaseMixin):
    help = "Export all existing datasets"

    def __init__(self, **kwargs):
        gpf_instance = kwargs.pop("gpf_instance", None)
        DatasetBaseMixin.__init__(self, gpf_instance=gpf_instance)
        BaseCommand.__init__(self, **kwargs)



    def add_arguments(self, parser):
        parser.add_argument("--file", type=str)




    def handle(self, *args, **options):

        if options["file"]:
            outfile = open(options["file"], "w")
        else:
            outfile = sys.stdout

        print("dataset,groups", file=outfile)
        for genotype_data_id in self.gpf_instance.get_genotype_data_ids():
            try:
                dataset = self.get_dataset(genotype_data_id)
                authorized = ";".join([
                    group.name for group in dataset.groups.all()
                ])
                print(f"{genotype_data_id},{authorized}", file=outfile)
            except Exception as ex:
                logger.warning(f"dataset {genotype_data_id} not found")
                logger.exception(ex)