samples.tasks.BatchDeleteSamples.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 2019-09-17 13:45 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
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(MyTask):
    name = "Batch delete samples"
    description = """Batch remove 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, sample_ids = args[0], args[1]

        logger.error(
            ("BatchDeleteAnimals called with submission_id: %s and "
             "sample_ids: %s" % (submission_id, sample_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 sample 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 sample batch delete for submission: %s" % (
                submission_obj.id),
            ("Something goes wrong in batch delete for samples. Please report "
             "this to InjectTool team\n\n %s" % str(einfo)),
        )

        # TODO: submit mail to admin

    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(MyTask, BatchUpdateMixin):

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

    item_cls = Sample
    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 samples: %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 samples: %s" % (args[0]),
            ("Something goes wrong in batch update for samples. Please report "
             "this to InjectTool team\n\n %s" % str(einfo)),
        )

        # TODO: submit mail to admin

    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")
        super(BatchUpdateSamples, 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
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(MyTask):
26		name = "Batch delete samples"
27		description = """Batch remove 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, sample_ids = args[0], args[1]
36
37		logger.error(
38		("BatchDeleteAnimals called with submission_id: %s and "
39		"sample_ids: %s" % (submission_id, sample_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 sample 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 sample batch delete for submission: %s" % (
56		submission_obj.id),
57		("Something goes wrong in batch delete for samples. 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, sample_ids):
64		"""Function for batch update attribute in animals
65		Args:
66		submission_id (int): id of submission
67		sample_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 samples")
74		success_ids = list()
75		failed_ids = list()
76
77		for sample_id in sample_ids:
78		try:
79		name = Name.objects.get(
80		name=sample_id, submission=submission_obj)
81
82		sample_obj = Sample.objects.get(name=name)
83
84		with transaction.atomic():
85		sample_obj.delete()
86		name.delete()
87		success_ids.append(sample_id)
88
89		except Name.DoesNotExist:
90		failed_ids.append(sample_id)
91
92		except Sample.DoesNotExist:
93		failed_ids.append(sample_id)
94
95		# Update submission
96		submission_obj.refresh_from_db()
97		submission_obj.status = NEED_REVISION
98
99		if len(failed_ids) != 0:
100		submission_obj.message = f"You've removed {len(success_ids)} " \
101		f"samples. It wasn't possible to find records with these " \
102		f"ids: {', '.join(failed_ids)}. Rerun validation please!"
103		else:
104		submission_obj.message = f"You've removed {len(success_ids)} " \
105		f"samples. Rerun validation please!"
106
107		submission_obj.save()
108
109		summary_obj, created = ValidationSummary.objects.get_or_create(
110		submission=submission_obj, type='sample')
111		summary_obj.reset_all_count()
112
113		send_message(
114		submission_obj, construct_validation_message(submission_obj)
115		)
116
117		logger.info("batch delete for samples completed")
118
119		return 'success'
120
121
122	View Code Duplication	class BatchUpdateSamples(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...
123		name = "Batch update samples"
124		description = """Batch update of field in samples"""
125
126		item_cls = Sample
127		submission_cls = Submission
128
129		# Ovverride default on failure method
130		# This is not a failed validation for a wrong value, this is an
131		# error in task that mean an error in coding
132		def on_failure(self, exc, task_id, args, kwargs, einfo):
133		logger.error('{0!r} failed: {1!r}'.format(task_id, exc))
134
135		# get submission object
136		submission_obj = Submission.objects.get(pk=args[0])
137
138		# mark submission with ERROR
139		submission_obj.status = ERROR
140		submission_obj.message = ("Error in batch update for samples: %s"
141		% (str(exc)))
142		submission_obj.save()
143
144		send_message(submission_obj)
145
146		# send a mail to the user with the stacktrace (einfo)
147		submission_obj.owner.email_user(
148		"Error in batch update for samples: %s" % (args[0]),
149		("Something goes wrong in batch update for samples. Please report "
150		"this to InjectTool team\n\n %s" % str(einfo)),
151		)
152
153		# TODO: submit mail to admin
154
155		def run(self, submission_id, sample_ids, attribute):
156		"""Function for batch update attribute in samples
157		Args:
158		submission_id (int): id of submission
159		sample_ids (dict): dict with id and values to update
160		attribute (str): attribute to update
161		"""
162
163		logger.info("Start batch update for samples")
164		super(BatchUpdateSamples, self).batch_update(submission_id, sample_ids,
165		attribute)
166		return 'success'
167
168
169		# register explicitly tasks
170		# https://github.com/celery/celery/issues/3744#issuecomment-271366923
171		celery_app.tasks.register(BatchDeleteSamples)
172		celery_app.tasks.register(BatchUpdateSamples)
173

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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