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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 Thu Jun 14 15:30:47 2018 |
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@author: Paolo Cozzi <[email protected]> |
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Send a submission as biosample manager user |
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""" |
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import logging |
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from django.core.management import BaseCommand |
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import pyUSIrest |
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from common.constants import SUBMITTED |
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from image_app.models import Submission |
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from biosample.helpers import get_manager_auth |
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from biosample.models import Submission as USISubmission |
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from biosample.tasks.submission import SplitSubmissionHelper, SubmissionHelper |
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# Get an instance of a logger |
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logger = logging.getLogger(__name__) |
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# change the default level for pyUSIrest logging |
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logging.getLogger('pyUSIrest.auth').setLevel(logging.INFO) |
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logging.getLogger('pyUSIrest.client').setLevel(logging.INFO) |
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class Command(BaseCommand): |
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help = 'Submit to biosample a specific submission' |
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def add_arguments(self, parser): |
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parser.add_argument( |
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'--submission', |
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required=True, |
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type=int) |
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def handle(self, *args, **options): |
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# call commands and fill tables. |
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logger.info("Starting biosample_submission...") |
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# get a submission from submission id |
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submission_id = options['submission'] |
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submission_obj = Submission.objects.get(pk=submission_id) |
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# split data in submission objects like biosample.tasks does |
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submission_data_helper = SplitSubmissionHelper(submission_obj) |
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# iterate over animal and samples |
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submission_data_helper.process_data() |
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# get an auth object |
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auth = get_manager_auth() |
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# get root object |
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logger.debug("getting biosample root") |
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root = pyUSIrest.client.Root(auth=auth) |
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usi_submissions = USISubmission.objects.filter( |
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pk__in=submission_data_helper.submission_ids) |
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# ok get all biosample.model.Submission and iterate over them |
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for usi_submission in usi_submissions: |
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# define a submission helper object |
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submission_helper = SubmissionHelper( |
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submission_id=usi_submission.id) |
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# assign class attributes |
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submission_helper.auth = auth |
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submission_helper.root = root |
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# then call methods |
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submission_helper.start_submission() |
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submission_helper.add_samples() |
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submission_helper.mark_success() |
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# update submission status |
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# TODO: use a biosample.tasks or helper method to do this |
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submission_obj.status = SUBMITTED |
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submission_obj.message = "Waiting for biosample validation" |
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submission_obj.save() |
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logger.info("Submission completed!") |
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cnr-ibba /
IMAGE-InjectTool
