biosample.management.commands.patch_orphan_biosamples

Complexity

Total Complexity

9

Size/Duplication

Total Lines	123
Duplicated Lines	0 %

Importance

Changes

0

2 Functions

Rating	Name	Duplication	Size	Complexity
A	create_biosample_submission()	0	12	1
A	update_submission_status()	0	7	2

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue May 26 17:21:28 2020

@author: Paolo Cozzi <paolo.cozzi@ibba.cnr.it>
"""

import logging

import pyUSIrest.usi
import pyUSIrest.exceptions

from django.core.management import BaseCommand

from biosample.helpers import get_manager_auth
from biosample.models import OrphanSubmission
from biosample.tasks.cleanup import get_orphan_samples
from common.constants import SUBMITTED, ERROR

# Get an instance of a logger
logger = logging.getLogger(__name__)


def create_biosample_submission(root, team):
    logger.debug("Creating a new submission")

    usi_team = root.get_team_by_name(team.name)
    usi_submission = usi_team.create_submission()

    submission = OrphanSubmission(
        usi_submission_name=usi_submission.name)
    submission.save()

    logger.debug("Created submission '%s' for '%s'" % (submission, team.name))
    return usi_submission, submission


def update_submission_status(submission):
    """Set SUBMITTED status to submission"""

    # update submission status
    if submission:
        submission.status = SUBMITTED
        submission.save()


class Command(BaseCommand):
    help = 'Get a JSON for biosample submission'

    def add_arguments(self, parser):

        parser.add_argument(
            '--limit',
            required=False,
            help="Limit to LIMIT items",
            default=None,
            type=int)

    def handle(self, *args, **options):
        # call commands and fill tables.
        logger.info("Called patch_orphan_samples")

        # get a new auth object
        auth = get_manager_auth()

        # get a new root object
        root = pyUSIrest.usi.Root(auth)

        # some variables
        count = 1
        old_team = None
        usi_submission = None
        submission = None

        # iterate among orphan sample, create a BioSample submission
        # and then add biosample for patch
        for record in get_orphan_samples(limit=options['limit']):
            (data, team, sample) = (
                record['data'], record['team'], record['sample'])

            if count % 100 == 0 or old_team != team:
                update_submission_status(submission)

                # create a new Biosample submission
                usi_submission, submission = create_biosample_submission(
                    root, team)

                # reset count and old_team
                count = 1
                old_team = team

            # add sample to submission
            try:
                logger.info("Submitting '%s'" % data['accession'])
                usi_submission.create_sample(data)

            except pyUSIrest.exceptions.USIDataError as error:
                logger.error(
                    "Can't remove '%s': Error was '%s'" % (
                        data['accession'], str(error)))
                sample.status = ERROR
                sample.save()
                continue

            # update sample status and track submission
            sample.status = SUBMITTED
            sample.submission = submission
            sample.save()

            # update submission count
            submission.samples_count = count
            submission.save()

            # new element
            count += 1

        # update the last submission status
        update_submission_status(submission)

        # end the script
        logger.info("patch_orphan_samples ended")