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

Completed

Pull Request — master (#41)

by Paolo

created 2019-09-18 15:16 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 NEED_REVISION
from common.tasks import BatchUpdateMixin, BatchFailurelMixin
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(BatchFailurelMixin, MyTask):
    name = "Batch delete animals"
    description = """Batch remove animals and associated samples"""
    batch_type = "delete"
    model_type = "animal"
    submission_cls = Submission

    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(BatchFailurelMixin, BatchUpdateMixin, MyTask):
    name = "Batch update animals"
    description = """Batch update of field in animals"""
    batch_type = "update"
    model_type = "animal"

    # defined in common.tasks.BatchUpdateMixin
    item_cls = Animal
    submission_cls = Submission

    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")
        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 NEED_REVISION
14			from common.tasks import BatchUpdateMixin, BatchFailurelMixin
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(BatchFailurelMixin, MyTask):
26			name = "Batch delete animals"
27			description = """Batch remove animals and associated samples"""
28			batch_type = "delete"
29			model_type = "animal"
30			submission_cls = Submission
31
32			def run(self, submission_id, animal_ids):
33			"""Function for batch update attribute in animals
34			Args:
35			submission_id (int): id of submission
36			animal_ids (list): set with ids to delete
37			"""
38
39			# get a submisision object
40			submission_obj = Submission.objects.get(pk=submission_id)
41
42			logger.info("Start batch delete for animals")
43			success_ids = list()
44			failed_ids = list()
45
46			for animal_id in animal_ids:
47			try:
48			name = Name.objects.get(
49			name=animal_id, submission=submission_obj)
50
51			animal_object = Animal.objects.get(name=name)
52			samples = animal_object.sample_set.all()
53
54			with transaction.atomic():
55			for sample in samples:
56			sample_name = sample.name
57			sample.delete()
58			sample_name.delete()
59
60			logger.debug("Clearing all childs from this animal")
61			name.mother_of.clear()
62			name.father_of.clear()
63
64			# delete this animal object
65			logger.debug(
66			"Deleting animal:%s and name:%s" % (
67			animal_object, name))
68			animal_object.delete()
69			name.delete()
70
71			success_ids.append(animal_id)
72
73			except Name.DoesNotExist:
74			failed_ids.append(animal_id)
75
76			except Animal.DoesNotExist:
77			failed_ids.append(animal_id)
78
79			# Update submission
80			submission_obj.refresh_from_db()
81			submission_obj.status = NEED_REVISION
82
83			if len(failed_ids) != 0:
84			submission_obj.message = f"You've removed {len(success_ids)} " \
85			f"animals. It wasn't possible to find records with these " \
86			f"ids: {', '.join(failed_ids)}. Rerun validation please!"
87			else:
88			submission_obj.message = f"You've removed {len(success_ids)} " \
89			f"animals. Rerun validation please!"
90
91			submission_obj.save()
92
93			summary_obj, created = ValidationSummary.objects.get_or_create(
94			submission=submission_obj, type='animal')
95			summary_obj.reset()
96
97			# after removing animal associated samples, we need to update also
98			# sample all count
99			summary_obj, created = ValidationSummary.objects.get_or_create(
100			submission=submission_obj, type='sample')
101			summary_obj.reset()
102
103			# TODO: validation summary could be updated relying database, instead
104			# doing validation. Define a method in validation.helpers to update
105			# summary relying only on database
106
107			send_message(
108			submission_obj, construct_validation_message(submission_obj)
109			)
110
111			logger.info("batch delete for animals completed")
112
113			return 'success'
114
115
116			class BatchUpdateAnimals(BatchFailurelMixin, BatchUpdateMixin, MyTask):
117			name = "Batch update animals"
118			description = """Batch update of field in animals"""
119			batch_type = "update"
120			model_type = "animal"
121
122			# defined in common.tasks.BatchUpdateMixin
123			item_cls = Animal
124			submission_cls = Submission
125
126			def run(self, submission_id, animal_ids, attribute):
127			"""Function for batch update attribute in animals
128			Args:
129			submission_id (int): id of submission
130			animal_ids (dict): dict with id and values to update
131			attribute (str): attribute to update
132			"""
133
134			logger.info("Start batch update for animals")
135			self.batch_update(submission_id, animal_ids, attribute)
136			return 'success'
137
138
139			# register explicitly tasks
140			# https://github.com/celery/celery/issues/3744#issuecomment-271366923
141			celery_app.tasks.register(BatchDeleteAnimals)
142			celery_app.tasks.register(BatchUpdateAnimals)
143

cnr-ibba / IMAGE-InjectTool

Pull Request — master (#41)

animals.tasks.BatchDeleteAnimals.run() B

Complexity

Size

Duplication

Importance

How to fix Long Method

Long Method

Duplication Side-by-Side

Filter issues like