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

Passed

Pull Request — master (#41)

by Paolo

created 2019-09-18 13:18 UTC

animals.tasks.BatchDeleteAnimals.run() B

↳ Parent: animals.tasks

Complexity

Conditions

Size

Total Lines	82
Code Lines	45

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	45
dl	0
loc	82
rs	7.4
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 common.tasks import BatchUpdateMixin
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))

        submission_id, animal_ids = args[0], args[1]

        logger.error(
            ("BatchDeleteAnimals called with submission_id: %s and "
             "animal_ids: %s" % (submission_id, animal_ids))
        )

        # get submission object
        submission_obj = Submission.objects.get(pk=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()

        # after removing animal associated samples, we need to update also
        # sample all count
        summary_obj, created = ValidationSummary.objects.get_or_create(
            submission=submission_obj, type='sample')
        summary_obj.reset()

        # TODO: validation summary could be updated relying database, instead
        # doing validation. Define a method in validation.helpers to update
        # summary relying only on database

        send_message(
            submission_obj, construct_validation_message(submission_obj)
        )

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

        return 'success'


class BatchUpdateAnimals(MyTask, BatchUpdateMixin):

    name = "Batch update animals"
    description = """Batch update of field in animals"""

    item_cls = Animal
    submission_cls = Submission

    # 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=args[0])

        # mark submission with ERROR
        submission_obj.status = ERROR
        submission_obj.message = ("Error in batch update for animals: %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 batch update for animals: %s" % (args[0]),
            ("Something goes wrong  in batch update 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, attribute):
        """Function for batch update attribute in animals
        Args:
            submission_id (int): id of submission
            animal_ids (dict): dict with id and values to update
            attribute (str): attribute to update
        """

        logger.info("Start batch update for animals")
        super(BatchUpdateAnimals, self).batch_update(submission_id, animal_ids,
                                                     attribute)
        return 'success'


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


1		#!/usr/bin/env python3
2		# -- coding: utf-8 --
3		"""
4		Created on Wed Feb 27 16:38:37 2019
5
6		@author: Paolo Cozzi <[email protected]>
7		"""
8
9		from celery.utils.log import get_task_logger
10
11		from django.db import transaction
12
13		from common.constants import ERROR, NEED_REVISION
14		from common.tasks import BatchUpdateMixin
15		from image.celery import app as celery_app, MyTask
16		from image_app.models import Submission, Animal, Name
17		from submissions.helpers import send_message
18		from validation.helpers import construct_validation_message
19		from validation.models import ValidationSummary
20
21		# Get an instance of a logger
22		logger = get_task_logger(__name__)
23
24
25		class BatchDeleteAnimals(MyTask):
26		name = "Batch delete animals"
27		description = """Batch remove animals and associated samples"""
28
29		# Ovverride default on failure method
30		# This is not a failed validation for a wrong value, this is an
31		# error in task that mean an error in coding
32		def on_failure(self, exc, task_id, args, kwargs, einfo):
33		logger.error('{0!r} failed: {1!r}'.format(task_id, exc))
34
35		submission_id, animal_ids = args[0], args[1]
36
37		logger.error(
38		("BatchDeleteAnimals called with submission_id: %s and "
39		"animal_ids: %s" % (submission_id, animal_ids))
40		)
41
42		# get submission object
43		submission_obj = Submission.objects.get(pk=submission_id)
44
45		# mark submission with ERROR
46		submission_obj.status = ERROR
47		submission_obj.message = (
48		"Error in animal batch delete: %s" % (str(exc)))
49		submission_obj.save()
50
51		send_message(submission_obj)
52
53		# send a mail to the user with the stacktrace (einfo)
54		submission_obj.owner.email_user(
55		"Error in animal batch delete for submission: %s" % (
56		submission_obj.id),
57		("Something goes wrong in batch delete for animals. Please report "
58		"this to InjectTool team\n\n %s" % str(einfo)),
59		)
60
61		# TODO: submit mail to admin
62
63		def run(self, submission_id, animal_ids):
64		"""Function for batch update attribute in animals
65		Args:
66		submission_id (int): id of submission
67		animal_ids (list): set with ids to delete
68		"""
69
70		# get a submisision object
71		submission_obj = Submission.objects.get(pk=submission_id)
72
73		logger.info("Start batch delete for animals")
74		success_ids = list()
75		failed_ids = list()
76
77		for animal_id in animal_ids:
78		try:
79		name = Name.objects.get(
80		name=animal_id, submission=submission_obj)
81
82		animal_object = Animal.objects.get(name=name)
83		samples = animal_object.sample_set.all()
84
85		with transaction.atomic():
86		for sample in samples:
87		sample_name = sample.name
88		sample.delete()
89		sample_name.delete()
90
91		logger.debug("Clearing all childs from this animal")
92		name.mother_of.clear()
93		name.father_of.clear()
94
95		# delete this animal object
96		logger.debug(
97		"Deleting animal:%s and name:%s" % (
98		animal_object, name))
99		animal_object.delete()
100		name.delete()
101
102		success_ids.append(animal_id)
103
104		except Name.DoesNotExist:
105		failed_ids.append(animal_id)
106
107		except Animal.DoesNotExist:
108		failed_ids.append(animal_id)
109
110		# Update submission
111		submission_obj.refresh_from_db()
112		submission_obj.status = NEED_REVISION
113
114		if len(failed_ids) != 0:
115		submission_obj.message = f"You've removed {len(success_ids)} " \
116		f"animals. It wasn't possible to find records with these " \
117		f"ids: {', '.join(failed_ids)}. Rerun validation please!"
118		else:
119		submission_obj.message = f"You've removed {len(success_ids)} " \
120		f"animals. Rerun validation please!"
121
122		submission_obj.save()
123
124		summary_obj, created = ValidationSummary.objects.get_or_create(
125		submission=submission_obj, type='animal')
126		summary_obj.reset()
127
128		# after removing animal associated samples, we need to update also
129		# sample all count
130		summary_obj, created = ValidationSummary.objects.get_or_create(
131		submission=submission_obj, type='sample')
132		summary_obj.reset()
133
134		# TODO: validation summary could be updated relying database, instead
135		# doing validation. Define a method in validation.helpers to update
136		# summary relying only on database
137
138		send_message(
139		submission_obj, construct_validation_message(submission_obj)
140		)
141
142		logger.info("batch delete for animals completed")
143
144		return 'success'
145
146
147	View Code Duplication	class BatchUpdateAnimals(MyTask, BatchUpdateMixin):
		0 ignored issues – show Duplication introduced 2019-07-17 15:38 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
148		name = "Batch update animals"
149		description = """Batch update of field in animals"""
150
151		item_cls = Animal
152		submission_cls = Submission
153
154		# Ovverride default on failure method
155		# This is not a failed validation for a wrong value, this is an
156		# error in task that mean an error in coding
157		def on_failure(self, exc, task_id, args, kwargs, einfo):
158		logger.error('{0!r} failed: {1!r}'.format(task_id, exc))
159
160		# get submission object
161		submission_obj = Submission.objects.get(pk=args[0])
162
163		# mark submission with ERROR
164		submission_obj.status = ERROR
165		submission_obj.message = ("Error in batch update for animals: %s"
166		% (str(exc)))
167		submission_obj.save()
168
169		send_message(submission_obj)
170
171		# send a mail to the user with the stacktrace (einfo)
172		submission_obj.owner.email_user(
173		"Error in batch update for animals: %s" % (args[0]),
174		("Something goes wrong in batch update for animals. Please "
175		"report this to InjectTool team\n\n %s" % str(einfo)),
176		)
177
178		# TODO: submit mail to admin
179
180		def run(self, submission_id, animal_ids, attribute):
181		"""Function for batch update attribute in animals
182		Args:
183		submission_id (int): id of submission
184		animal_ids (dict): dict with id and values to update
185		attribute (str): attribute to update
186		"""
187
188		logger.info("Start batch update for animals")
189		super(BatchUpdateAnimals, self).batch_update(submission_id, animal_ids,
190		attribute)
191		return 'success'
192
193
194		# register explicitly tasks
195		# https://github.com/celery/celery/issues/3744#issuecomment-271366923
196		celery_app.tasks.register(BatchDeleteAnimals)
197		celery_app.tasks.register(BatchUpdateAnimals)
198

cnr-ibba / IMAGE-InjectTool

Pull Request — master (#41)

animals.tasks.BatchDeleteAnimals.run() B

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Duplication

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How to fix Long Method

Long Method

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