biosample.tests.common.BaseMixin.setUp() - Code Metrics - Inspection of ":zap: Batch submission to Biosamples" - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Pull Request — master (#44)

by Paolo

created 2019-07-19 15:52 UTC

biosample.tests.common.BaseMixin.setUp() A

↳ Parent: biosample.tests.common

Complexity

Conditions

Size

Total Lines	55
Code Lines	25

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	25
dl	0
loc	55
rs	9.28
c	0
b	0
f	0
cc	1
nop	1

How to fix Long Method

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Jan 21 15:15:09 2019

@author: Paolo Cozzi <[email protected]>
"""

import redis
import python_jwt

from billiard.einfo import ExceptionInfo
from unittest.mock import patch, PropertyMock

from django.core import mail
from django.conf import settings
from django.db.models import Q
from django.utils import timezone

from common.constants import READY, ERROR, WAITING
from common.tests import PersonMixinTestCase, WebSocketMixin
from image_app.models import Submission, Person, Name


def generate_token(now=None, domains=['subs.test-team-1']):
    """A function to generate a 'fake' token"""

    if not now:
        now = int(timezone.now().timestamp())

    claims = {
        'iss': 'https://explore.aai.ebi.ac.uk/sp',
        'iat': now,
        'exp': now+3600,
        'sub': 'usr-f1801430-51e1-4718-8fca-778887087bad',
        'email': '[email protected]',
        'nickname': 'foo',
        'name': 'Foo Bar',
        'domains': domains
    }

    return python_jwt.generate_jwt(
        claims,
        algorithm='RS256')


class BaseMixin(PersonMixinTestCase):
    # an attribute for PersonMixinTestCase
    person = Person

    fixtures = [
        'biosample/account',
        'biosample/managedteam',
        'image_app/animal',
        'image_app/dictbreed',
        'image_app/dictcountry',
        'image_app/dictrole',
        'image_app/dictsex',
        'image_app/dictspecie',
        'image_app/dictstage',
        'image_app/dictuberon',
        'image_app/name',
        'image_app/ontology',
        'image_app/organization',
        'image_app/publication',
        'image_app/sample',
        'image_app/submission',
        'image_app/user'
    ]

    def setUp(self):
        # calling my base class setup
        super().setUp()

        # track submission ID
        self.submission_id = 1

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

        # set a status which I can submit (equal as calling submit by view)
        self.submission_obj.status = WAITING
        self.submission_obj.message = "Waiting for biosample submission"
        self.submission_obj.save()

        # get the names I want to submit
        self.name_qs = Name.objects.filter(
            Q(animal__isnull=False) | Q(sample__isnull=False),
            submission=self.submission_obj)

        # set status for names, like validation does. Update only animal
        # and sample names (excluding unkwnon animals)
        self.name_qs.update(status=READY)

        # count number of names in UID for such submission (exclude
        # unknown animals)
        self.n_to_submit = self.name_qs.count()

        # starting mocked objects
        self.mock_root_patcher = patch('pyUSIrest.client.Root')
        self.mock_root = self.mock_root_patcher.start()

        # start root object
        self.my_root = self.mock_root.return_value

        # mocking chain
        self.my_team = self.my_root.get_team_by_name.return_value
        self.my_team.name = "subs.test-team-1"

        # mocking a new submission
        self.new_submission = self.my_team.create_submission.return_value
        self.new_submission.name = "new-submission"

        # set status. Because of the way mock attributes are stored you can’t
        # directly attach a PropertyMock to a mock object. Instead you can
        # attach it to the mock type object:
        self.new_submission.propertymock = PropertyMock(return_value='Draft')
        type(self.new_submission).status = self.new_submission.propertymock

        # mocking get_submission_by_name
        self.my_submission = self.my_root.get_submission_by_name.return_value
        self.my_submission.name = "test-submission"

        self.my_submission.propertymock = PropertyMock(return_value='Draft')
        type(self.my_submission).status = self.my_submission.propertymock


class TaskFailureMixin(WebSocketMixin, BaseMixin):
    def test_on_failure(self):

        """Testing on failure methods"""

        exc = Exception("Test")
        task_id = "test_task_id"
        args = [self.submission_id]
        kwargs = {}
        einfo = ExceptionInfo

        # call on_failure method
        self.my_task.on_failure(exc, task_id, args, kwargs, einfo)

        # check submission status and message
        submission = Submission.objects.get(pk=self.submission_id)

        # check submission.state changed
        self.assertEqual(submission.status, ERROR)
        self.assertEqual(
            submission.message,
            "Error in biosample submission: Test")

        # test email sent
        self.assertEqual(len(mail.outbox), 1)

        # read email
        email = mail.outbox[0]

        self.assertEqual(
            "Error in biosample submission %s" % self.submission_id,
            email.subject)

        message = 'Error'
        notification_message = 'Error in biosample submission: Test'

        # calling a WebSocketMixin method
        self.check_message(message, notification_message)


class RedisMixin():

    """A class to setup a test token in redis database"""

    # this will be the token key in redis database
    submission_key = "token:submission:1:test"

    @classmethod
    def setUpClass(cls):
        # calling my base class setup
        super().setUpClass()

        cls.redis = redis.StrictRedis(
            host=settings.REDIS_HOST,
            port=settings.REDIS_PORT,
            db=settings.REDIS_DB)

        # generate a token
        cls.token = generate_token(domains=['subs.test-team-1'])

        # write token to database
        cls.redis.set(cls.submission_key, cls.token, ex=3600)

    @classmethod
    def tearDownClass(cls):
        if cls.redis.exists(cls.submission_key):
            cls.redis.delete(cls.submission_key)

        super().tearDownClass()


1		#!/usr/bin/env python3
2		# -- coding: utf-8 --
3		"""
4		Created on Mon Jan 21 15:15:09 2019
5
6		@author: Paolo Cozzi <[email protected]>
7		"""
8
9		import redis
10		import python_jwt
11
12		from billiard.einfo import ExceptionInfo
13		from unittest.mock import patch, PropertyMock
14
15		from django.core import mail
16		from django.conf import settings
17		from django.db.models import Q
18		from django.utils import timezone
19
20		from common.constants import READY, ERROR, WAITING
21		from common.tests import PersonMixinTestCase, WebSocketMixin
22		from image_app.models import Submission, Person, Name
23
24
25		def generate_token(now=None, domains=['subs.test-team-1']):
26		"""A function to generate a 'fake' token"""
27
28		if not now:
29		now = int(timezone.now().timestamp())
30
31		claims = {
32		'iss': 'https://explore.aai.ebi.ac.uk/sp',
33		'iat': now,
34		'exp': now+3600,
35		'sub': 'usr-f1801430-51e1-4718-8fca-778887087bad',
36		'email': '[email protected]',
37		'nickname': 'foo',
38		'name': 'Foo Bar',
39		'domains': domains
40		}
41
42		return python_jwt.generate_jwt(
43		claims,
44		algorithm='RS256')
45
46
47		class BaseMixin(PersonMixinTestCase):
48		# an attribute for PersonMixinTestCase
49		person = Person
50
51		fixtures = [
52		'biosample/account',
53		'biosample/managedteam',
54		'image_app/animal',
55		'image_app/dictbreed',
56		'image_app/dictcountry',
57		'image_app/dictrole',
58		'image_app/dictsex',
59		'image_app/dictspecie',
60		'image_app/dictstage',
61		'image_app/dictuberon',
62		'image_app/name',
63		'image_app/ontology',
64		'image_app/organization',
65		'image_app/publication',
66		'image_app/sample',
67		'image_app/submission',
68		'image_app/user'
69		]
70
71		def setUp(self):
72		# calling my base class setup
73		super().setUp()
74
75		# track submission ID
76		self.submission_id = 1
77
78		# get a submission object
79		self.submission_obj = Submission.objects.get(pk=self.submission_id)
80
81		# set a status which I can submit (equal as calling submit by view)
82		self.submission_obj.status = WAITING
83		self.submission_obj.message = "Waiting for biosample submission"
84		self.submission_obj.save()
85
86		# get the names I want to submit
87		self.name_qs = Name.objects.filter(
88		Q(animal__isnull=False) \| Q(sample__isnull=False),
89		submission=self.submission_obj)
90
91		# set status for names, like validation does. Update only animal
92		# and sample names (excluding unkwnon animals)
93		self.name_qs.update(status=READY)
94
95		# count number of names in UID for such submission (exclude
96		# unknown animals)
97		self.n_to_submit = self.name_qs.count()
98
99		# starting mocked objects
100		self.mock_root_patcher = patch('pyUSIrest.client.Root')
101		self.mock_root = self.mock_root_patcher.start()
102
103		# start root object
104		self.my_root = self.mock_root.return_value
105
106		# mocking chain
107		self.my_team = self.my_root.get_team_by_name.return_value
108		self.my_team.name = "subs.test-team-1"
109
110		# mocking a new submission
111		self.new_submission = self.my_team.create_submission.return_value
112		self.new_submission.name = "new-submission"
113
114		# set status. Because of the way mock attributes are stored you can’t
115		# directly attach a PropertyMock to a mock object. Instead you can
116		# attach it to the mock type object:
117		self.new_submission.propertymock = PropertyMock(return_value='Draft')
118		type(self.new_submission).status = self.new_submission.propertymock
119
120		# mocking get_submission_by_name
121		self.my_submission = self.my_root.get_submission_by_name.return_value
122		self.my_submission.name = "test-submission"
123
124		self.my_submission.propertymock = PropertyMock(return_value='Draft')
125		type(self.my_submission).status = self.my_submission.propertymock
126
127
128		class TaskFailureMixin(WebSocketMixin, BaseMixin):
129	View Code Duplication	def test_on_failure(self):
		0 ignored issues – show Duplication introduced 2019-07-19 15:58 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
130		"""Testing on failure methods"""
131
132		exc = Exception("Test")
133		task_id = "test_task_id"
134		args = [self.submission_id]
135		kwargs = {}
136		einfo = ExceptionInfo
137
138		# call on_failure method
139		self.my_task.on_failure(exc, task_id, args, kwargs, einfo)
140
141		# check submission status and message
142		submission = Submission.objects.get(pk=self.submission_id)
143
144		# check submission.state changed
145		self.assertEqual(submission.status, ERROR)
146		self.assertEqual(
147		submission.message,
148		"Error in biosample submission: Test")
149
150		# test email sent
151		self.assertEqual(len(mail.outbox), 1)
152
153		# read email
154		email = mail.outbox[0]
155
156		self.assertEqual(
157		"Error in biosample submission %s" % self.submission_id,
158		email.subject)
159
160		message = 'Error'
161		notification_message = 'Error in biosample submission: Test'
162
163		# calling a WebSocketMixin method
164		self.check_message(message, notification_message)
165
166
167	View Code Duplication	class RedisMixin():
		0 ignored issues – show Duplication introduced 2019-07-19 15:58 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
168		"""A class to setup a test token in redis database"""
169
170		# this will be the token key in redis database
171		submission_key = "token:submission:1:test"
172
173		@classmethod
174		def setUpClass(cls):
175		# calling my base class setup
176		super().setUpClass()
177
178		cls.redis = redis.StrictRedis(
179		host=settings.REDIS_HOST,
180		port=settings.REDIS_PORT,
181		db=settings.REDIS_DB)
182
183		# generate a token
184		cls.token = generate_token(domains=['subs.test-team-1'])
185
186		# write token to database
187		cls.redis.set(cls.submission_key, cls.token, ex=3600)
188
189		@classmethod
190		def tearDownClass(cls):
191		if cls.redis.exists(cls.submission_key):
192		cls.redis.delete(cls.submission_key)
193
194		super().tearDownClass()
195

cnr-ibba / IMAGE-InjectTool

Pull Request — master (#44)

biosample.tests.common.BaseMixin.setUp() A

Complexity

Size

Duplication

Importance

How to fix Long Method

Long Method

Duplication Side-by-Side

Filter issues like