cryoweb.tests.test_helpers.CryowebImport.test_cryoweb_import() - Code Metrics - Inspection of ":twisted_rightwards_arrows: Merge branch 'issue-15..." - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Branch — master (206998)

by Paolo

created 2019-06-27 15:05 UTC

CryowebImport.test_cryoweb_import() A

↳ Parent: cryoweb.tests.test_helpers

Complexity

Conditions

Size

Total Lines	45
Code Lines	32

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	32
dl	0
loc	45
rs	9.112
c	0
b	0
f	0
cc	1
nop	3

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Sep 20 16:01:04 2018

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

# --- import
from unittest.mock import patch

from django.conf import settings
from django.core.management import call_command
from django.test import TestCase

from common.constants import ERROR
from common.tests import WebSocketMixin
from language.models import SpecieSynonym
from image_app.models import (
    Submission, DictBreed, Name, Animal, Sample, DictSex,
    DictCountry, DictSpecie)
from common.tests import DataSourceMixinTestCase

from ..helpers import (
    upload_cryoweb, check_species, CryoWebImportError, cryoweb_import,
    check_UID)
from ..models import db_has_data, truncate_database, BreedsSpecies


class BaseMixin():
    # import this file and populate database once
    fixtures = [
        'cryoweb/dictbreed',
        'image_app/dictcountry',
        'image_app/dictrole',
        'image_app/dictsex',
        'image_app/organization',
        'image_app/submission',
        'image_app/user',
        'language/dictspecie',
        'language/speciesynonym'
    ]

    # By default, fixtures are only loaded into the default database. If you
    # are using multiple databases and set multi_db=True, fixtures will be
    # loaded into all databases. However, this will raise problems when
    # managing extended user models
    multi_db = False

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

        # track submission
        self.submission = Submission.objects.get(pk=1)


class CryoWebMixin(object):
    """Custom methods to upload cryoweb data into database for testing"""

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

        # this fixture have to be loaded in a secondary (test) database,
        # I can't upload it using names and fixture section, so it will
        # be added manually using loaddata
        call_command(
            'loaddata',
            'cryoweb/cryoweb.json',
            app='cryoweb',
            database='cryoweb',
            verbosity=0)

    @classmethod
    def tearDownClass(cls):
        # truncate cryoweb database after loading
        if db_has_data():
            truncate_database()

        # calling my base class teardown class
        super().tearDownClass()


class ImportMixin(WebSocketMixin, CryoWebMixin):
    """Mixing to test cryoweb_import method"""

    def test_cryoweb_import(self):
        """A method to test if data were imported from cryoweb or not"""

        self.assertTrue(cryoweb_import(self.submission))

        # check breed upload
        queryset = DictBreed.objects.all()

        breeds = [(dictbreed.supplied_breed, dictbreed.country.label)
                  for dictbreed in queryset]

        self.assertEqual(len(queryset), 4)
        self.assertListEqual(
            breeds, [
                ('Bunte Bentheimer', 'United Kingdom'),
                ('Ostfriesisches Milchschaf', 'Italy'),
                ('Aberdeen Angus', 'Germany'),
                ('Ostfriesisches Milchschaf', 'Germany')],
            msg="Check breeds loaded")

        # check name upload (5 animal, 1 sample)
        queryset = Name.objects.filter(submission=self.submission)
        self.assertEqual(len(queryset), 6, msg='check name load')

        # check animal name
        queryset = Animal.objects.all()
        self.assertEqual(len(queryset), 3, msg="check animal load")

        queryset = Sample.objects.all()
        self.assertEqual(len(queryset), 1, msg="check sample load")

        # check async message called
        message = 'Loaded'
        notification_message = (
            'Cryoweb import completed for submission: 1')
        validation_message = {
            'animals': 3, 'samples': 1,
            'animal_unkn': 3, 'sample_unkn': 1,
            'animal_issues': 0, 'sample_issues': 0}

        self.check_message(message, notification_message, validation_message)


class CheckSpecie(CryoWebMixin, BaseMixin, TestCase):
    def test_check_species(self):
        """Testing species and synonyms"""

        united_kingdom = DictCountry.objects.get(label="United Kingdom")

        # test for species synonoms for cryoweb
        self.assertTrue(check_species(united_kingdom))

        # now delete a synonym
        synonym = SpecieSynonym.objects.get(
            language__label='United Kingdom',
            word='Cattle')
        synonym.delete()

        self.assertFalse(check_species(united_kingdom))

    def test_no_species(self):
        """Test no species in cryoweb database"""

        queryset = BreedsSpecies.objects.all()
        queryset.delete()

        self.assertRaisesRegex(
            CryoWebImportError,
            "You have no species",
            check_species, "United Kingdom")


class CheckBreed(TestCase):
    # import this file and populate database once
    fixtures = [
        'image_app/dictbreed',
        'image_app/dictcountry',
        'image_app/dictrole',
        'image_app/dictsex',
        'image_app/dictspecie',
        'image_app/organization',
        'image_app/submission',
        'image_app/user',
    ]

    def test_add_breed(self):
        italy = DictCountry.objects.get(label="Italy")
        united_kingdom = DictCountry.objects.get(label="United Kingdom")

        sus = DictSpecie.objects.get(label="Sus scrofa")

        # inserting an already present breed get the object without creation
        breed, created = DictBreed.objects.get_or_create(
            supplied_breed="Bunte Bentheimer",
            specie=sus,
            country=united_kingdom)

        self.assertFalse(created)

        # inserting a breed in a different country add a record
        breed, created = DictBreed.objects.get_or_create(
            supplied_breed="Bunte Bentheimer",
            specie=sus,
            country=italy)

        self.assertTrue(created)


class CheckUIDTest(CryoWebMixin, BaseMixin, TestCase):
    def test_empty_dictsex(self):
        """Empty dictsex and check that I can't proceed"""

        queryset = DictSex.objects.all()
        queryset.delete()

        self.assertRaisesRegex(
            CryoWebImportError,
            "You have to upload DictSex data",
            check_UID, self.submission)

    def test_no_synonym(self):
        # now delete a synonym
        synonym = SpecieSynonym.objects.get(
            language__label='United Kingdom',
            word='Cattle')
        synonym.delete()

        self.assertRaisesRegex(
            CryoWebImportError,
            "Some species haven't a synonym!",
            check_UID, self.submission)

    def test_check_UID(self):
        """testing normal behaviour"""

        self.assertTrue(check_UID(self.submission))


class UploadCryoweb(
        WebSocketMixin, DataSourceMixinTestCase, BaseMixin, TestCase):
    """Test upload cryoweb dump into cryoweb database"""

    # define attribute in DataSourceMixinTestCase
    model = Submission

    # need to clean database after testing import. Can't use CryowebMixin
    # since i need to test cryoweb import
    def tearDown(self):
        """Clean test database after modifications"""

        # truncate cryoweb database after loading
        if db_has_data():
            truncate_database()

        # calling my base class teardown class
        super().tearDown()

    def test_database_name(self):
        self.assertEqual(
            settings.DATABASES['cryoweb']['NAME'], 'test_cryoweb')

    def test_upload_cryoweb(self):
        """Testing uploading and importing data from cryoweb to UID"""

        self.assertTrue(upload_cryoweb(self.submission.id))
        self.assertTrue(db_has_data())

        # if I try again to upload cryoweb, I will get a False object and
        # submission message
        self.assertRaises(
            CryoWebImportError,
            upload_cryoweb,
            self.submission.id)

        # reload submission
        self.submission = Submission.objects.get(pk=1)

        self.assertEqual(
            self.submission.status,
            ERROR)

        self.assertIn(
            "Cryoweb has data",
            self.submission.message)

        # check async message called
        message = 'Error'
        notification_message = 'Error in importing data: Cryoweb has data'

        self.check_message(message, notification_message)

    # mock subprocess.run and raise Exception. Read it and update submission
    # message using helpers.upload_cryoweb
    def test_upload_cryoweb_errors(self):
        """Testing errors in uploading cryoweb data"""

        with patch('subprocess.run') as runMock:
            runMock.side_effect = Exception("Test upload failed")
            self.assertFalse(upload_cryoweb(self.submission.id))

            # reload submission
            self.submission = Submission.objects.get(pk=1)

            self.assertEqual(
                self.submission.status,
                ERROR)

            self.assertIn(
                "Test upload failed",
                self.submission.message)

            # check async message called
            message = 'Error'
            notification_message = ('Error in importing data: Test '
                                    'upload failed')

            self.check_message(message, notification_message)


class CryowebImport(ImportMixin, BaseMixin, TestCase):
    def test_database_name(self):
        self.assertEqual(
            settings.DATABASES['cryoweb']['NAME'], 'test_cryoweb')

    @patch("cryoweb.helpers.check_UID", side_effect=Exception("Test message"))
    def test_cryoweb_import_errors(self, my_check):
        """Testing importing with data into UID with errors"""

        self.assertFalse(cryoweb_import(self.submission))
        self.assertTrue(my_check.called)

        # reload submission
        self.submission = Submission.objects.get(pk=1)

        self.assertEqual(
            self.submission.status,
            ERROR)

        self.assertIn(
            "Test message",
            self.submission.message)

        # check async message called
        message = 'Error'
        notification_message = (
            'Error in importing data: Test message')

        self.check_message(message, notification_message)


class CryowebReload(ImportMixin, BaseMixin, TestCase):
    """Simulate a cryoweb reload case. Load data as in CryowebImport, then
    call test which reload the same data"""

    # override fixtures
    fixtures = [
        'cryoweb/auth',
        'cryoweb/dictbreed',
        'cryoweb/image_app',
        'language/dictspecie',
        'language/speciesynonym'
    ]


1			#!/usr/bin/env python3
2			# -- coding: utf-8 --
3			"""
4			Created on Thu Sep 20 16:01:04 2018
5
6			@author: Paolo Cozzi <[email protected]>
7			"""
8
9			# --- import
10			from unittest.mock import patch
11
12			from django.conf import settings
13			from django.core.management import call_command
14			from django.test import TestCase
15
16			from common.constants import ERROR
17			from common.tests import WebSocketMixin
18			from language.models import SpecieSynonym
19			from image_app.models import (
20			Submission, DictBreed, Name, Animal, Sample, DictSex,
21			DictCountry, DictSpecie)
22			from common.tests import DataSourceMixinTestCase
23
24			from ..helpers import (
25			upload_cryoweb, check_species, CryoWebImportError, cryoweb_import,
26			check_UID)
27			from ..models import db_has_data, truncate_database, BreedsSpecies
28
29
30			class BaseMixin():
31			# import this file and populate database once
32			fixtures = [
33			'cryoweb/dictbreed',
34			'image_app/dictcountry',
35			'image_app/dictrole',
36			'image_app/dictsex',
37			'image_app/organization',
38			'image_app/submission',
39			'image_app/user',
40			'language/dictspecie',
41			'language/speciesynonym'
42			]
43
44			# By default, fixtures are only loaded into the default database. If you
45			# are using multiple databases and set multi_db=True, fixtures will be
46			# loaded into all databases. However, this will raise problems when
47			# managing extended user models
48			multi_db = False
49
50			def setUp(self):
51			# calling my base class setup
52			super().setUp()
53
54			# track submission
55			self.submission = Submission.objects.get(pk=1)
56
57
58			class CryoWebMixin(object):
59			"""Custom methods to upload cryoweb data into database for testing"""
60
61			@classmethod
62			def setUpClass(cls):
63			# calling my base class setup
64			super().setUpClass()
65
66			# this fixture have to be loaded in a secondary (test) database,
67			# I can't upload it using names and fixture section, so it will
68			# be added manually using loaddata
69			call_command(
70			'loaddata',
71			'cryoweb/cryoweb.json',
72			app='cryoweb',
73			database='cryoweb',
74			verbosity=0)
75
76			@classmethod
77			def tearDownClass(cls):
78			# truncate cryoweb database after loading
79			if db_has_data():
80			truncate_database()
81
82			# calling my base class teardown class
83			super().tearDownClass()
84
85
86			class ImportMixin(WebSocketMixin, CryoWebMixin):
87			"""Mixing to test cryoweb_import method"""
88
89			def test_cryoweb_import(self):
90			"""A method to test if data were imported from cryoweb or not"""
91
92			self.assertTrue(cryoweb_import(self.submission))
93
94			# check breed upload
95			queryset = DictBreed.objects.all()
96
97			breeds = [(dictbreed.supplied_breed, dictbreed.country.label)
98			for dictbreed in queryset]
99
100			self.assertEqual(len(queryset), 4)
101			self.assertListEqual(
102			breeds, [
103			('Bunte Bentheimer', 'United Kingdom'),
104			('Ostfriesisches Milchschaf', 'Italy'),
105			('Aberdeen Angus', 'Germany'),
106			('Ostfriesisches Milchschaf', 'Germany')],
107			msg="Check breeds loaded")
108
109			# check name upload (5 animal, 1 sample)
110			queryset = Name.objects.filter(submission=self.submission)
111			self.assertEqual(len(queryset), 6, msg='check name load')
112
113			# check animal name
114			queryset = Animal.objects.all()
115			self.assertEqual(len(queryset), 3, msg="check animal load")
116
117			queryset = Sample.objects.all()
118			self.assertEqual(len(queryset), 1, msg="check sample load")
119
120			# check async message called
121			message = 'Loaded'
122			notification_message = (
123			'Cryoweb import completed for submission: 1')
124			validation_message = {
125			'animals': 3, 'samples': 1,
126			'animal_unkn': 3, 'sample_unkn': 1,
127			'animal_issues': 0, 'sample_issues': 0}
128
129			self.check_message(message, notification_message, validation_message)
130
131
132			class CheckSpecie(CryoWebMixin, BaseMixin, TestCase):
133			def test_check_species(self):
134			"""Testing species and synonyms"""
135
136			united_kingdom = DictCountry.objects.get(label="United Kingdom")
137
138			# test for species synonoms for cryoweb
139			self.assertTrue(check_species(united_kingdom))
140
141			# now delete a synonym
142			synonym = SpecieSynonym.objects.get(
143			language__label='United Kingdom',
144			word='Cattle')
145			synonym.delete()
146
147			self.assertFalse(check_species(united_kingdom))
148
149			def test_no_species(self):
150			"""Test no species in cryoweb database"""
151
152			queryset = BreedsSpecies.objects.all()
153			queryset.delete()
154
155			self.assertRaisesRegex(
156			CryoWebImportError,
157			"You have no species",
158			check_species, "United Kingdom")
159
160
161			class CheckBreed(TestCase):
162			# import this file and populate database once
163			fixtures = [
164			'image_app/dictbreed',
165			'image_app/dictcountry',
166			'image_app/dictrole',
167			'image_app/dictsex',
168			'image_app/dictspecie',
169			'image_app/organization',
170			'image_app/submission',
171			'image_app/user',
172			]
173
174			def test_add_breed(self):
175			italy = DictCountry.objects.get(label="Italy")
176			united_kingdom = DictCountry.objects.get(label="United Kingdom")
177
178			sus = DictSpecie.objects.get(label="Sus scrofa")
179
180			# inserting an already present breed get the object without creation
181			breed, created = DictBreed.objects.get_or_create(
182			supplied_breed="Bunte Bentheimer",
183			specie=sus,
184			country=united_kingdom)
185
186			self.assertFalse(created)
187
188			# inserting a breed in a different country add a record
189			breed, created = DictBreed.objects.get_or_create(
190			supplied_breed="Bunte Bentheimer",
191			specie=sus,
192			country=italy)
193
194			self.assertTrue(created)
195
196
197			class CheckUIDTest(CryoWebMixin, BaseMixin, TestCase):
198			def test_empty_dictsex(self):
199			"""Empty dictsex and check that I can't proceed"""
200
201			queryset = DictSex.objects.all()
202			queryset.delete()
203
204			self.assertRaisesRegex(
205			CryoWebImportError,
206			"You have to upload DictSex data",
207			check_UID, self.submission)
208
209			def test_no_synonym(self):
210			# now delete a synonym
211			synonym = SpecieSynonym.objects.get(
212			language__label='United Kingdom',
213			word='Cattle')
214			synonym.delete()
215
216			self.assertRaisesRegex(
217			CryoWebImportError,
218			"Some species haven't a synonym!",
219			check_UID, self.submission)
220
221			def test_check_UID(self):
222			"""testing normal behaviour"""
223
224			self.assertTrue(check_UID(self.submission))
225
226
227			class UploadCryoweb(
228			WebSocketMixin, DataSourceMixinTestCase, BaseMixin, TestCase):
229			"""Test upload cryoweb dump into cryoweb database"""
230
231			# define attribute in DataSourceMixinTestCase
232			model = Submission
233
234			# need to clean database after testing import. Can't use CryowebMixin
235			# since i need to test cryoweb import
236			def tearDown(self):
237			"""Clean test database after modifications"""
238
239			# truncate cryoweb database after loading
240			if db_has_data():
241			truncate_database()
242
243			# calling my base class teardown class
244			super().tearDown()
245
246			def test_database_name(self):
247			self.assertEqual(
248			settings.DATABASES['cryoweb']['NAME'], 'test_cryoweb')
249
250			def test_upload_cryoweb(self):
251			"""Testing uploading and importing data from cryoweb to UID"""
252
253			self.assertTrue(upload_cryoweb(self.submission.id))
254			self.assertTrue(db_has_data())
255
256			# if I try again to upload cryoweb, I will get a False object and
257			# submission message
258			self.assertRaises(
259			CryoWebImportError,
260			upload_cryoweb,
261			self.submission.id)
262
263			# reload submission
264			self.submission = Submission.objects.get(pk=1)
265
266			self.assertEqual(
267			self.submission.status,
268			ERROR)
269
270			self.assertIn(
271			"Cryoweb has data",
272			self.submission.message)
273
274			# check async message called
275			message = 'Error'
276			notification_message = 'Error in importing data: Cryoweb has data'
277
278			self.check_message(message, notification_message)
279
280			# mock subprocess.run and raise Exception. Read it and update submission
281			# message using helpers.upload_cryoweb
282			def test_upload_cryoweb_errors(self):
283			"""Testing errors in uploading cryoweb data"""
284
285			with patch('subprocess.run') as runMock:
286			runMock.side_effect = Exception("Test upload failed")
287			self.assertFalse(upload_cryoweb(self.submission.id))
288
289			# reload submission
290			self.submission = Submission.objects.get(pk=1)
291
292			self.assertEqual(
293			self.submission.status,
294			ERROR)
295
296			self.assertIn(
297			"Test upload failed",
298			self.submission.message)
299
300			# check async message called
301			message = 'Error'
302			notification_message = ('Error in importing data: Test '
303			'upload failed')
304
305			self.check_message(message, notification_message)
306
307
308			class CryowebImport(ImportMixin, BaseMixin, TestCase):
309			def test_database_name(self):
310			self.assertEqual(
311			settings.DATABASES['cryoweb']['NAME'], 'test_cryoweb')
312
313			@patch("cryoweb.helpers.check_UID", side_effect=Exception("Test message"))
314			def test_cryoweb_import_errors(self, my_check):
315			"""Testing importing with data into UID with errors"""
316
317			self.assertFalse(cryoweb_import(self.submission))
318			self.assertTrue(my_check.called)
319
320			# reload submission
321			self.submission = Submission.objects.get(pk=1)
322
323			self.assertEqual(
324			self.submission.status,
325			ERROR)
326
327			self.assertIn(
328			"Test message",
329			self.submission.message)
330
331			# check async message called
332			message = 'Error'
333			notification_message = (
334			'Error in importing data: Test message')
335
336			self.check_message(message, notification_message)
337
338
339			class CryowebReload(ImportMixin, BaseMixin, TestCase):
340			"""Simulate a cryoweb reload case. Load data as in CryowebImport, then
341			call test which reload the same data"""
342
343			# override fixtures
344			fixtures = [
345			'cryoweb/auth',
346			'cryoweb/dictbreed',
347			'cryoweb/image_app',
348			'language/dictspecie',
349			'language/speciesynonym'
350			]
351

cnr-ibba / IMAGE-InjectTool

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CryowebImport.test_cryoweb_import() A

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