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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 May 28 16:06:56 2020 |
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@author: Paolo Cozzi <[email protected]> |
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Fetch the Orphan submissions and track BioSamples removal |
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""" |
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import json |
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import logging |
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import pyUSIrest.usi |
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from django.core.management import BaseCommand |
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from django.utils import timezone |
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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.retrieval import FetchStatusHelper |
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from common.constants import SUBMITTED, NEED_REVISION, COMPLETED |
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# Get an instance of a logger |
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logger = logging.getLogger(__name__) |
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class SubmissionHelper(FetchStatusHelper): |
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def __init__(self, root, usi_submission, can_finalize=False): |
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self.root = root |
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self.usi_submission = usi_submission |
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self.can_finalize = can_finalize |
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self.submission_name = usi_submission.usi_submission_name |
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logger.info( |
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"Getting info for usi submission '%s'" % (self.submission_name)) |
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self.submission = root.get_submission_by_name( |
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submission_name=self.submission_name) |
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# override finalize method |
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def finalize(self): |
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"""Finalize a submission by closing document and send it to |
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biosample""" |
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if not self.can_finalize: |
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# skip finalizing a submission |
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logger.warning( |
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"Ignoring finalization: please call with '--finalize'" |
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" argument") |
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return |
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logger.info("Finalizing submission '%s'" % ( |
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self.submission_name)) |
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# get errors for a submission |
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errors = self.submission.has_errors() |
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# collect all error messages in a list |
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messages = [] |
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if True in errors: |
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# get sample with errors then update database |
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samples = self.submission.get_samples(has_errors=True) |
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for sample in samples: |
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if sample.has_errors(): |
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logger.error("%s has errors!!!" % sample) |
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# mark this sample since has problems |
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errorMessages = self.sample_has_errors(sample) |
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# append this into error messages list |
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messages.append(errorMessages) |
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# if a sample has no errors, status will be the same |
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logger.error( |
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"Errors for submission: '%s'" % (self.submission_name)) |
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logger.error("Fix them, then finalize") |
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# report error |
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message = json.dumps(messages, indent=2) |
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# Update status for biosample.models.Submission |
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self.usi_submission.status = NEED_REVISION |
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self.usi_submission.message = message |
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self.usi_submission.save() |
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else: |
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# TODO: model and test exception in finalization |
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self.submission.finalize() |
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# override complete method |
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def complete(self): |
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"""Complete a submission and fetch biosample names""" |
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logger.info("Completing submission '%s'" % ( |
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self.submission_name)) |
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for sample in self.submission.get_samples(): |
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# if no accession, return without doing anything |
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if sample.accession is None: |
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logger.error("No accession found for sample '%s'" % (sample)) |
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logger.error("Ignoring submission '%s'" % (self.submission)) |
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return |
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orphan_sample = self.usi_submission.submission_data.get( |
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biosample_id=sample.accession) |
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orphan_sample.status = COMPLETED |
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orphan_sample.removed = True |
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orphan_sample.removed_at = timezone.now() |
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orphan_sample.save() |
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# update submission |
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self.usi_submission.status = COMPLETED |
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self.usi_submission.message = "Successful removal from biosample" |
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self.usi_submission.save() |
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logger.info( |
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"Submission %s is now completed and its samples " |
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"removed from BioSamples" % (self.submission_name) |
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) |
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# custom implementation: here I don't have a record in UID and I |
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# can't use the base method of this class |
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def sample_has_errors(self, sample): |
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""" |
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Get USI error for sample |
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Args: |
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sample (pyUSIrest.usi.sample): a USI sample object |
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""" |
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# track status in db like FetchStatusHelper |
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orphan_sample = self.usi_submission.submission_data.get( |
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biosample_id=sample.accession) |
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orphan_sample.status = NEED_REVISION |
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orphan_sample.save() |
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# get a USI validation result |
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validation_result = sample.get_validation_result() |
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# track errors in validation tables |
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errorMessages = validation_result.errorMessages |
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# return an error for each object |
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return {str(sample): errorMessages} |
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class Command(BaseCommand): |
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help = 'Fetch the Orphan submissions and track BioSamples removal' |
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def add_arguments(self, parser): |
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parser.add_argument( |
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'--finalize', |
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default=False, |
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action='store_true', |
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) |
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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 fetch_orphan_biosamples") |
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# Ok get all Orphaned BioSample submission in SUBMITTED status |
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qs = OrphanSubmission.objects.filter(status=SUBMITTED) |
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if qs.count() > 0: |
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# ok do stuff |
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auth = get_manager_auth() |
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root = pyUSIrest.usi.Root(auth) |
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for orphan_submission in qs: |
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submission_helper = SubmissionHelper( |
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root, |
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orphan_submission, |
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options['finalize']) |
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submission_helper.check_submission_status() |
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# call commands and fill tables. |
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logger.info("fetch_orphan_biosamples finished") |
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cnr-ibba /
IMAGE-InjectTool
