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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 Wed Feb 27 16:38:37 2019 |
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@author: Paolo Cozzi <[email protected]> |
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""" |
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from celery.utils.log import get_task_logger |
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from django.db import transaction |
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from common.constants import NEED_REVISION |
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from common.tasks import BatchUpdateMixin, BatchFailurelMixin |
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from image.celery import app as celery_app, MyTask |
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from image_app.models import Submission, Animal, Name |
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from submissions.helpers import send_message |
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from validation.helpers import construct_validation_message |
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from validation.models import ValidationSummary |
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# Get an instance of a logger |
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logger = get_task_logger(__name__) |
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class BatchDeleteAnimals(BatchFailurelMixin, MyTask): |
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name = "Batch delete animals" |
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description = """Batch remove animals and associated samples""" |
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batch_type = "delete" |
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model_type = "animal" |
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submission_cls = Submission |
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def run(self, submission_id, animal_ids): |
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"""Function for batch update attribute in animals |
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Args: |
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submission_id (int): id of submission |
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animal_ids (list): set with ids to delete |
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""" |
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# get a submisision object |
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submission_obj = Submission.objects.get(pk=submission_id) |
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logger.info("Start batch delete for animals") |
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success_ids = list() |
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failed_ids = list() |
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for animal_id in animal_ids: |
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try: |
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name = Name.objects.get( |
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name=animal_id, submission=submission_obj) |
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animal_object = Animal.objects.get(name=name) |
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samples = animal_object.sample_set.all() |
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with transaction.atomic(): |
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for sample in samples: |
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sample_name = sample.name |
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sample.delete() |
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sample_name.delete() |
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logger.debug("Clearing all childs from this animal") |
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name.mother_of.clear() |
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name.father_of.clear() |
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# delete this animal object |
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logger.debug( |
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"Deleting animal:%s and name:%s" % ( |
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animal_object, name)) |
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animal_object.delete() |
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name.delete() |
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success_ids.append(animal_id) |
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except Name.DoesNotExist: |
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failed_ids.append(animal_id) |
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except Animal.DoesNotExist: |
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failed_ids.append(animal_id) |
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# Update submission |
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submission_obj.refresh_from_db() |
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submission_obj.status = NEED_REVISION |
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if len(failed_ids) != 0: |
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submission_obj.message = f"You've removed {len(success_ids)} " \ |
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f"animals. It wasn't possible to find records with these " \ |
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f"ids: {', '.join(failed_ids)}. Rerun validation please!" |
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else: |
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submission_obj.message = f"You've removed {len(success_ids)} " \ |
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f"animals. Rerun validation please!" |
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submission_obj.save() |
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summary_obj, created = ValidationSummary.objects.get_or_create( |
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submission=submission_obj, type='animal') |
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summary_obj.reset() |
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# after removing animal associated samples, we need to update also |
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# sample all count |
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summary_obj, created = ValidationSummary.objects.get_or_create( |
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submission=submission_obj, type='sample') |
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summary_obj.reset() |
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# TODO: validation summary could be updated relying database, instead |
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# doing validation. Define a method in validation.helpers to update |
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# summary relying only on database |
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send_message( |
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submission_obj, construct_validation_message(submission_obj) |
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) |
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logger.info("batch delete for animals completed") |
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return 'success' |
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class BatchUpdateAnimals(BatchFailurelMixin, BatchUpdateMixin, MyTask): |
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name = "Batch update animals" |
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description = """Batch update of field in animals""" |
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batch_type = "update" |
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model_type = "animal" |
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# defined in common.tasks.BatchUpdateMixin |
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item_cls = Animal |
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submission_cls = Submission |
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def run(self, submission_id, animal_ids, attribute): |
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"""Function for batch update attribute in animals |
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Args: |
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submission_id (int): id of submission |
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animal_ids (dict): dict with id and values to update |
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attribute (str): attribute to update |
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""" |
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logger.info("Start batch update for animals") |
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self.batch_update(submission_id, animal_ids, attribute) |
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return 'success' |
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# register explicitly tasks |
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# https://github.com/celery/celery/issues/3744#issuecomment-271366923 |
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celery_app.tasks.register(BatchDeleteAnimals) |
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celery_app.tasks.register(BatchUpdateAnimals) |
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cnr-ibba /
IMAGE-InjectTool
