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#!/usr/bin/env python3 |
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# -*- coding: utf-8 -*- |
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""" |
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Created on Tue May 26 17:21:28 2020 |
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@author: Paolo Cozzi <[email protected]> |
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""" |
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import logging |
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from pyUSIrest.usi import Root |
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from pyUSIrest.exceptions import USIDataError |
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from django.core.management import BaseCommand |
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from biosample.helpers import get_manager_auth |
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from biosample.models import OrphanSubmission |
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from biosample.tasks.cleanup import get_orphan_samples |
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from common.constants import SUBMITTED |
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# Get an instance of a logger |
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logger = logging.getLogger(__name__) |
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def create_biosample_submission(root, team): |
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logger.debug("Creating a new submission") |
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usi_team = root.get_team_by_name(team.name) |
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usi_submission = usi_team.create_submission() |
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submission = OrphanSubmission( |
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usi_submission_name=usi_submission.name) |
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submission.save() |
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logger.debug("Created submission %s" % submission) |
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return usi_submission, submission |
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def update_submission_status(submission): |
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"""Set SUBMITTED status to submission""" |
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# update submission status |
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if submission: |
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submission.status = SUBMITTED |
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submission.save() |
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class Command(BaseCommand): |
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help = 'Get a JSON for biosample submission' |
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def handle(self, *args, **options): |
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# call commands and fill tables. |
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logger.info("Called patch_orphan_samples") |
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# get a new auth object |
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auth = get_manager_auth() |
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# get a new root object |
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root = Root(auth) |
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# some variables |
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count = 1 |
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old_team = None |
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usi_submission = None |
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submission = None |
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# iterate among orphan sample, create a BioSample submission |
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# and then add biosample for patch |
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for orphan_sample in get_orphan_samples(): |
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data, team = orphan_sample['data'], orphan_sample['team'] |
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if count % 100 == 0 or old_team != team: |
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update_submission_status(submission) |
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# create a new Biosample submission |
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usi_submission, submission = create_biosample_submission( |
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root, team) |
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# reset count and old_team |
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count = 1 |
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old_team = team |
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# add sample to submission |
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try: |
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usi_submission.create_sample(data) |
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except USIDataError: |
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logger.error("Can't remove %s" % data) |
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continue |
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# update submission count |
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submission.samples_count = count |
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submission.save() |
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# new element |
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count += 1 |
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# update the last submission status |
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update_submission_status(submission) |
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# end the script |
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logger.info("patch_orphan_samples ended") |
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cnr-ibba /
IMAGE-InjectTool
