samples.tasks.BatchDeleteSamples.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 2019-09-19 12:04 UTC

samples.tasks.BatchDeleteSamples.run() B

↳ Parent: samples.tasks

Complexity

Conditions

Size

Total Lines	57
Code Lines	31

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	31
dl	0
loc	57
rs	8.2026
c	0
b	0
f	0
cc	6
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, BatchFailurelMixin
from image.celery import app as celery_app, MyTask
from image_app.models import Submission, Sample, 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 BatchDeleteSamples(BatchFailurelMixin, MyTask):
    name = "Batch delete samples"
    description = """Batch remove samples"""
    batch_type = "delete"
    model_type = "sample"
    submission_cls = Submission

    def run(self, submission_id, sample_ids):
        """Function for batch update attribute in animals
        Args:
            submission_id (int): id of submission
            sample_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 samples")
        success_ids = list()
        failed_ids = list()

        for sample_id in sample_ids:
            try:
                name = Name.objects.get(
                    name=sample_id, submission=submission_obj)

                sample_obj = Sample.objects.get(name=name)

                with transaction.atomic():
                    sample_obj.delete()
                    name.delete()
                success_ids.append(sample_id)

            except Name.DoesNotExist:
                failed_ids.append(sample_id)

            except Sample.DoesNotExist:
                failed_ids.append(sample_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"samples. 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"samples. Rerun validation please!"

        submission_obj.save()

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

        send_message(
            submission_obj, construct_validation_message(submission_obj)
        )

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

        return 'success'


class BatchUpdateSamples(BatchFailurelMixin, BatchUpdateMixin, MyTask):
    name = "Batch update samples"
    description = """Batch update of field in samples"""
    batch_type = "update"
    model_type = "sample"

    item_cls = Sample
    submission_cls = Submission

    def run(self, submission_id, sample_ids, attribute):
        """Function for batch update attribute in samples
        Args:
            submission_id (int): id of submission
            sample_ids (dict): dict with id and values to update
            attribute (str): attribute to update
        """

        logger.info("Start batch update for samples")
        self.batch_update(submission_id, sample_ids, attribute)

        return 'success'


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


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, BatchFailurelMixin
15			from image.celery import app as celery_app, MyTask
16			from image_app.models import Submission, Sample, 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 BatchDeleteSamples(BatchFailurelMixin, MyTask):
26			name = "Batch delete samples"
27			description = """Batch remove samples"""
28			batch_type = "delete"
29			model_type = "sample"
30			submission_cls = Submission
31
32			def run(self, submission_id, sample_ids):
33			"""Function for batch update attribute in animals
34			Args:
35			submission_id (int): id of submission
36			sample_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 samples")
43			success_ids = list()
44			failed_ids = list()
45
46			for sample_id in sample_ids:
47			try:
48			name = Name.objects.get(
49			name=sample_id, submission=submission_obj)
50
51			sample_obj = Sample.objects.get(name=name)
52
53			with transaction.atomic():
54			sample_obj.delete()
55			name.delete()
56			success_ids.append(sample_id)
57
58			except Name.DoesNotExist:
59			failed_ids.append(sample_id)
60
61			except Sample.DoesNotExist:
62			failed_ids.append(sample_id)
63
64			# Update submission
65			submission_obj.refresh_from_db()
66			submission_obj.status = NEED_REVISION
67
68			if len(failed_ids) != 0:
69			submission_obj.message = f"You've removed {len(success_ids)} " \
70			f"samples. It wasn't possible to find records with these " \
71			f"ids: {', '.join(failed_ids)}. Rerun validation please!"
72			else:
73			submission_obj.message = f"You've removed {len(success_ids)} " \
74			f"samples. Rerun validation please!"
75
76			submission_obj.save()
77
78			summary_obj, created = ValidationSummary.objects.get_or_create(
79			submission=submission_obj, type='sample')
80			summary_obj.reset_all_count()
81
82			send_message(
83			submission_obj, construct_validation_message(submission_obj)
84			)
85
86			logger.info("batch delete for samples completed")
87
88			return 'success'
89
90
91			class BatchUpdateSamples(BatchFailurelMixin, BatchUpdateMixin, MyTask):
92			name = "Batch update samples"
93			description = """Batch update of field in samples"""
94			batch_type = "update"
95			model_type = "sample"
96
97			item_cls = Sample
98			submission_cls = Submission
99
100			def run(self, submission_id, sample_ids, attribute):
101			"""Function for batch update attribute in samples
102			Args:
103			submission_id (int): id of submission
104			sample_ids (dict): dict with id and values to update
105			attribute (str): attribute to update
106			"""
107
108			logger.info("Start batch update for samples")
109			self.batch_update(submission_id, sample_ids, attribute)
110
111			return 'success'
112
113
114			# register explicitly tasks
115			# https://github.com/celery/celery/issues/3744#issuecomment-271366923
116			celery_app.tasks.register(BatchDeleteSamples)
117			celery_app.tasks.register(BatchUpdateSamples)
118

cnr-ibba / IMAGE-InjectTool

Pull Request — master (#41)

samples.tasks.BatchDeleteSamples.run() B

Complexity

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Duplication

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How to fix Long Method

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