animals.tasks.BatchDeleteAnimals.run() - Code Metrics - Inspection of "Batch remove" - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Pull Request — master (#45)

by Paolo

created 2019-09-16 13:23 UTC

animals.tasks.BatchDeleteAnimals.run() B

↳ Parent: animals.tasks

Complexity

Conditions

Size

Total Lines	72
Code Lines	42

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	42
dl	0
loc	72
rs	7.472
c	0
b	0
f	0
cc	7
nop	3

How to fix Long Method

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Feb 27 16:38:37 2019
@author: Paolo Cozzi <[email protected]>
"""

from celery.utils.log import get_task_logger

from django.db import transaction

from common.constants import ERROR, NEED_REVISION
from image.celery import app as celery_app, MyTask
from image_app.models import Submission, Animal, Name
from submissions.helpers import send_message
from validation.helpers import construct_validation_message
from validation.models import ValidationSummary

# Get an instance of a logger
logger = get_task_logger(__name__)


class BatchDeleteAnimals(MyTask):
    name = "Batch delete animals"
    description = """Batch remove animals and associated samples"""

    # Ovverride default on failure method
    # This is not a failed validation for a wrong value, this is an
    # error in task that mean an error in coding
    def on_failure(self, exc, task_id, args, kwargs, einfo):

        logger.error('{0!r} failed: {1!r}'.format(task_id, exc))

        # get submission object
        submission_obj = Submission.objects.get(pk=kwargs['submission_id'])

        # mark submission with ERROR
        submission_obj.status = ERROR
        submission_obj.message = (
            "Error in animal batch delete: %s" % (str(exc)))
        submission_obj.save()

        send_message(submission_obj)

        # send a mail to the user with the stacktrace (einfo)
        submission_obj.owner.email_user(
            "Error in animal batch delete for submission: %s" % (
                submission_obj.id),
            ("Something goes wrong in batch delete for animals. Please report "
             "this to InjectTool team\n\n %s" % str(einfo)),
        )

        # TODO: submit mail to admin

    def run(self, submission_id, animal_ids):
        """Function for batch update attribute in animals
        Args:
            submission_id (int): id of submission
            animal_ids (list): set with ids to delete
        """

        # get a submisision object
        submission_obj = Submission.objects.get(pk=submission_id)

        logger.info("Start batch delete for animals")
        success_ids = list()
        failed_ids = list()

        for animal_id in animal_ids:
            try:
                name = Name.objects.get(
                    name=animal_id, submission=submission_obj)

                animal_object = Animal.objects.get(name=name)
                samples = animal_object.sample_set.all()

                with transaction.atomic():
                    for sample in samples:
                        sample_name = sample.name
                        sample.delete()
                        sample_name.delete()

                    logger.debug("Clearing all childs from this animal")
                    name.mother_of.clear()
                    name.father_of.clear()

                    # delete this animal object
                    logger.debug(
                        "Deleting animal:%s and name:%s" % (
                            animal_object, name))
                    animal_object.delete()
                    name.delete()

                success_ids.append(animal_id)

            except Name.DoesNotExist:
                failed_ids.append(animal_id)

            except Animal.DoesNotExist:
                failed_ids.append(animal_id)

        # Update submission
        submission_obj.refresh_from_db()
        submission_obj.status = NEED_REVISION

        if len(failed_ids) != 0:
            submission_obj.message = f"You've removed {len(success_ids)} " \
                f"animals. It wasn't possible to find records with these " \
                f"ids: {', '.join(failed_ids)}. Rerun validation please!"
        else:
            submission_obj.message = f"You've removed {len(success_ids)} " \
                f"animals. Rerun validation please!"

        submission_obj.save()

        summary_obj, created = ValidationSummary.objects.get_or_create(
            submission=submission_obj, type='animal')
        summary_obj.reset_all_count()

        send_message(
            submission_obj, construct_validation_message(submission_obj)
        )

        logger.info("batch delete for animals completed")

        return 'success'


# register explicitly tasks
# https://github.com/celery/celery/issues/3744#issuecomment-271366923
celery_app.tasks.register(BatchDeleteAnimals)


1		#!/usr/bin/env python3
2		# -- coding: utf-8 --
3		"""
4		Created on Wed Feb 27 16:38:37 2019
5		@author: Paolo Cozzi <[email protected]>
6		"""
7
8		from celery.utils.log import get_task_logger
9
10		from django.db import transaction
11
12		from common.constants import ERROR, NEED_REVISION
13		from image.celery import app as celery_app, MyTask
14		from image_app.models import Submission, Animal, Name
15		from submissions.helpers import send_message
16		from validation.helpers import construct_validation_message
17		from validation.models import ValidationSummary
18
19		# Get an instance of a logger
20		logger = get_task_logger(__name__)
21
22
23		class BatchDeleteAnimals(MyTask):
24		name = "Batch delete animals"
25		description = """Batch remove animals and associated samples"""
26
27		# Ovverride default on failure method
28		# This is not a failed validation for a wrong value, this is an
29		# error in task that mean an error in coding
30	View Code Duplication	def on_failure(self, exc, task_id, args, kwargs, einfo):
		0 ignored issues – show Duplication introduced 2019-06-07 17:57 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
31		logger.error('{0!r} failed: {1!r}'.format(task_id, exc))
32
33		# get submission object
34		submission_obj = Submission.objects.get(pk=kwargs['submission_id'])
35
36		# mark submission with ERROR
37		submission_obj.status = ERROR
38		submission_obj.message = (
39		"Error in animal batch delete: %s" % (str(exc)))
40		submission_obj.save()
41
42		send_message(submission_obj)
43
44		# send a mail to the user with the stacktrace (einfo)
45		submission_obj.owner.email_user(
46		"Error in animal batch delete for submission: %s" % (
47		submission_obj.id),
48		("Something goes wrong in batch delete for animals. Please report "
49		"this to InjectTool team\n\n %s" % str(einfo)),
50		)
51
52		# TODO: submit mail to admin
53
54		def run(self, submission_id, animal_ids):
55		"""Function for batch update attribute in animals
56		Args:
57		submission_id (int): id of submission
58		animal_ids (list): set with ids to delete
59		"""
60
61		# get a submisision object
62		submission_obj = Submission.objects.get(pk=submission_id)
63
64		logger.info("Start batch delete for animals")
65		success_ids = list()
66		failed_ids = list()
67
68		for animal_id in animal_ids:
69		try:
70		name = Name.objects.get(
71		name=animal_id, submission=submission_obj)
72
73		animal_object = Animal.objects.get(name=name)
74		samples = animal_object.sample_set.all()
75
76		with transaction.atomic():
77		for sample in samples:
78		sample_name = sample.name
79		sample.delete()
80		sample_name.delete()
81
82		logger.debug("Clearing all childs from this animal")
83		name.mother_of.clear()
84		name.father_of.clear()
85
86		# delete this animal object
87		logger.debug(
88		"Deleting animal:%s and name:%s" % (
89		animal_object, name))
90		animal_object.delete()
91		name.delete()
92
93		success_ids.append(animal_id)
94
95		except Name.DoesNotExist:
96		failed_ids.append(animal_id)
97
98		except Animal.DoesNotExist:
99		failed_ids.append(animal_id)
100
101		# Update submission
102		submission_obj.refresh_from_db()
103		submission_obj.status = NEED_REVISION
104
105		if len(failed_ids) != 0:
106		submission_obj.message = f"You've removed {len(success_ids)} " \
107		f"animals. It wasn't possible to find records with these " \
108		f"ids: {', '.join(failed_ids)}. Rerun validation please!"
109		else:
110		submission_obj.message = f"You've removed {len(success_ids)} " \
111		f"animals. Rerun validation please!"
112
113		submission_obj.save()
114
115		summary_obj, created = ValidationSummary.objects.get_or_create(
116		submission=submission_obj, type='animal')
117		summary_obj.reset_all_count()
118
119		send_message(
120		submission_obj, construct_validation_message(submission_obj)
121		)
122
123		logger.info("batch delete for animals completed")
124
125		return 'success'
126
127
128		# register explicitly tasks
129		# https://github.com/celery/celery/issues/3744#issuecomment-271366923
130		celery_app.tasks.register(BatchDeleteAnimals)
131

cnr-ibba / IMAGE-InjectTool

Pull Request — master (#45)

animals.tasks.BatchDeleteAnimals.run() B

Complexity

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Duplication

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How to fix Long Method

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