image_app.tests.test_models.AnimalTestCase.test_relationship() - Code Metrics - Inspection of "modelling relationship between objects" - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Pull Request — master (#26)

by Paolo

created 2019-06-11 08:55 UTC

AnimalTestCase.test_relationship() A

↳ Parent: image_app.tests.test_models

Complexity

Conditions

Size

Total Lines	42
Code Lines	21

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	21
dl	0
loc	42
rs	9.376
c	0
b	0
f	0
cc	1
nop	1

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Apr  3 12:16:55 2018

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

import os
import json

from django.test import TestCase
from django.utils import timezone

from common.constants import OBO_URL
from common.tests import PersonMixinTestCase
from common.constants import (
    WAITING, LOADED, ERROR, READY, NEED_REVISION, SUBMITTED, COMPLETED)

from image_app.models import (Animal, Submission, DictBreed, DictCountry,
                              DictSex, DictSpecie, Sample, uid_report,
                              Person, User, db_has_data)


class DictSexTestCase(TestCase):
    """Testing DictSex class"""

    fixtures = [
        "image_app/dictsex",
        "image_app/ontology"
    ]

    def setUp(self):
        # my attributes
        self.label = 'male'
        self.term = 'PATO_0000384'

    def test_str(self):
        """Testing str representation"""

        male = DictSex.objects.get(label=self.label)
        self.assertEqual(
                str(male),
                "{label} ({term})".format(
                        label=self.label,
                        term=self.term))

    def test_format_attribute(self):
        """Testing format attribute"""

        reference = [{
            "value": "male",
            "terms": [{
                "url": "%s/PATO_0000384" % (OBO_URL)
             }]
        }]

        male = DictSex.objects.get(label=self.label)
        test = male.format_attribute()

        self.assertEqual(reference, test)


class DictSpecieTestCase(TestCase):
    """Testing DictSpecie class"""

    fixtures = [
        'image_app/dictcountry',
        'image_app/dictspecie',
        'image_app/ontology',
        'image_app/speciesynonym'
    ]

    def setUp(self):
        # my attributes
        self.label = 'Sus scrofa'
        self.term = 'NCBITaxon_9823'

    def test_str(self):
        """Testing str representation"""

        sus = DictSpecie.objects.get(label=self.label)
        self.assertEqual(
                str(sus),
                "{label} ({term})".format(
                        label=self.label,
                        term=self.term))

    def test_get_specie_by_synonym(self):
        """Getting specie using synonym"""

        sus = DictSpecie.get_by_synonym('Pig', 'United Kingdom')

        self.assertEqual(sus.label, self.label)
        self.assertEqual(sus.term, self.term)

        # assert a specie in a different language (synonym not defined)
        sus = DictSpecie.get_by_synonym('Pig', 'Italy')

        self.assertEqual(sus.label, self.label)
        self.assertEqual(sus.term, self.term)

        # using a word not registered returns no data
        with self.assertRaises(DictSpecie.DoesNotExist):
            DictSpecie.get_by_synonym('Foo', 'United Kingdom')

    def test_get_specie_by_synonym_nospaces(self):
        """Getting specie using synonym, no matters spaces"""

        # assert with spaces
        sus = DictSpecie.get_by_synonym('Pig (domestic)', 'United Kingdom')

        self.assertEqual(sus.label, self.label)
        self.assertEqual(sus.term, self.term)

        # assert without spaces
        sus = DictSpecie.get_by_synonym('Pig(domestic)', 'United Kingdom')

        self.assertEqual(sus.label, self.label)
        self.assertEqual(sus.term, self.term)


class DictCountryTestCase(TestCase):
    """Testing DictCountry class"""

    fixtures = [
        "image_app/dictcountry",
        "image_app/ontology"
    ]

    def setUp(self):
        # my attributes
        self.label = 'United Kingdom'
        self.term = 'NCIT_C17233'

    def test_str(self):
        """Testing str representation"""

        uk = DictCountry.objects.get(label=self.label)
        self.assertEqual(
                str(uk),
                "{label} ({term})".format(
                        label=self.label,
                        term=self.term))


class DictBreedTestCase(TestCase):
    """Testing DictBreed class"""

    fixtures = [
        "image_app/dictbreed",
        "image_app/dictcountry",
        "image_app/dictspecie",
        "image_app/ontology"
    ]

    def test_str(self):
        """Testing str representation (as mapped_breed, if present)"""

        breed = DictBreed.objects.get(pk=1)
        self.assertEqual(
            str(breed),
            "Bunte Bentheimer (Bentheim Black Pied, Sus scrofa)")

        # unset mapped_breed
        breed.mapped_breed = None
        self.assertEqual(
            str(breed), "Bunte Bentheimer (None, Sus scrofa)")


class SubmissionTestCase(TestCase):
    """Testing Submission class"""

    fixtures = [
        'image_app/dictcountry',
        'image_app/dictrole',
        'image_app/ontology',
        'image_app/organization',
        'image_app/submission',
        'image_app/user'
    ]

    def setUp(self):
        self.submission = Submission.objects.get(pk=1)

    def test_str(self):
        test = str(self.submission)
        reference = "Cryoweb (United Kingdom, test)"

        self.assertEqual(reference, test)

    def test_waiting(self):
        """Test waiting status"""

        # force submission status
        self.submission.status = WAITING

        # test my helper methods
        self.assertFalse(self.submission.can_edit())
        self.assertFalse(self.submission.can_validate())
        self.assertFalse(self.submission.can_submit())

    def test_loaded(self):
        """Test loaded status"""

        # force submission status
        self.submission.status = LOADED

        # test my helper methods
        self.assertTrue(self.submission.can_edit())
        self.assertTrue(self.submission.can_validate())
        self.assertFalse(self.submission.can_submit())

    def test_submitted(self):
        """Test submitted status"""

        # force submission status
        self.submission.status = SUBMITTED

        # test my helper methods
        self.assertFalse(self.submission.can_edit())
        self.assertFalse(self.submission.can_validate())
        self.assertFalse(self.submission.can_submit())

    def test_error(self):
        """Test error status"""

        # force submission status
        self.submission.status = ERROR

        # test my helper methods
        self.assertTrue(self.submission.can_edit())
        self.assertFalse(self.submission.can_validate())
        self.assertFalse(self.submission.can_submit())

    def test_need_revision(self):
        """Test need_revision status"""

        # force submission status
        self.submission.status = NEED_REVISION

        # test my helper methods
        self.assertTrue(self.submission.can_edit())
        self.assertTrue(self.submission.can_validate())
        self.assertFalse(self.submission.can_submit())

    def test_ready(self):
        """Test ready status"""

        # force submission status
        self.submission.status = READY

        # test my helper methods
        self.assertTrue(self.submission.can_edit())
        self.assertTrue(self.submission.can_validate())
        self.assertTrue(self.submission.can_submit())

    def test_completed(self):
        """Test completed status"""

        # force submission status
        self.submission.status = COMPLETED

        # test my helper methods
        self.assertTrue(self.submission.can_edit())
        self.assertFalse(self.submission.can_validate())
        self.assertFalse(self.submission.can_submit())


class AnimalTestCase(PersonMixinTestCase, TestCase):
    """Testing Animal Class"""

    # an attribute for PersonMixinTestCase
    person = Person

    fixtures = [
        'image_app/animal',
        'image_app/dictbreed',
        'image_app/dictcountry',
        'image_app/dictrole',
        'image_app/dictsex',
        'image_app/dictspecie',
        'image_app/name',
        'image_app/ontology',
        'image_app/organization',
        'image_app/publication',
        'image_app/submission',
        'image_app/user'
    ]

    def setUp(self):
        # create animal
        self.animal = Animal.objects.get(pk=1)
        self.submission = self.animal.submission

    def test_to_biosample(self):

        """Testing JSON conversion for biosample submission"""

        base_dir = os.path.dirname(os.path.abspath(__file__))
        file_path = os.path.join(base_dir, "biosample_animal.json")
        handle = open(file_path)
        reference = json.load(handle)

        # fix release date to today
        now = timezone.now()
        reference['releaseDate'] = str(now.date())

        test = self.animal.to_biosample()

        self.maxDiff = None
        self.assertEqual(reference, test)

    def test_to_biosample2(self):
        """testing json conversion with a biosample_id"""

        # assign a different biosample id
        reference = "SAMEA4450079"
        self.animal.name.biosample_id = reference
        self.animal.name.save()

        test = self.animal.to_biosample()

        # asserting biosample_.id in response
        self.assertEqual(test["accession"], reference)

    def test_relationship(self):
        """Testing an animal who has mother and father"""

        animal = Animal.objects.get(pk=3)

        test = animal.to_biosample()

        reference = [
            {'alias': 'IMAGEA000000001',
             'relationshipNature': 'derived from'},
            {'alias': 'IMAGEA000000002',
             'relationshipNature': 'derived from'}
        ]

        # asserting relationship
        self.assertEqual(test['sampleRelationships'], reference)

        # cleaning up relationship (by erasing fk - as crbanim data could be)
        # erase father relationship
        animal.father = None
        animal.save()

        test = animal.to_biosample()

        reference = [
            {'alias': 'IMAGEA000000002',
             'relationshipNature': 'derived from'},
        ]

        # asserting relationship
        self.assertEqual(test['sampleRelationships'], reference)

        # cleaning up last relationship
        animal.mother = None
        animal.save()

        test = animal.to_biosample()

        reference = []

        # asserting relationship
        self.assertEqual(test['sampleRelationships'], reference)

    # TODO: test None rendering

    def test_waiting(self):
        """Test waiting status"""

        # force submission status
        self.submission.status = WAITING
        self.submission.save()

        # test my helper methods
        self.assertFalse(self.animal.can_delete())
        self.assertFalse(self.animal.can_edit())

    def test_loaded(self):
        """Test loaded status"""

        # force submission status
        self.submission.status = LOADED
        self.submission.save()

        # test my helper methods
        self.assertTrue(self.animal.can_delete())
        self.assertTrue(self.animal.can_edit())

    def test_submitted(self):
        """Test submitted status"""

        # force submission status
        self.submission.status = SUBMITTED
        self.submission.save()

        # test my helper methods
        self.assertFalse(self.animal.can_delete())
        self.assertFalse(self.animal.can_edit())

    def test_error(self):
        """Test error status"""

        # force submission status
        self.submission.status = ERROR
        self.submission.save()

        # test my helper methods
        self.assertTrue(self.animal.can_delete())
        self.assertTrue(self.animal.can_edit())

    def test_need_revision(self):
        """Test need_revision status"""

        # force submission status
        self.submission.status = NEED_REVISION
        self.submission.save()

        # test my helper methods
        self.assertTrue(self.animal.can_delete())
        self.assertTrue(self.animal.can_edit())

    def test_ready(self):
        """Test ready status"""

        # force submission status
        self.submission.status = READY
        self.submission.save()

        # test my helper methods
        self.assertTrue(self.animal.can_delete())
        self.assertTrue(self.animal.can_edit())

    def test_completed(self):
        """Test completed status"""

        # force submission status
        self.submission.status = COMPLETED
        self.submission.save()

        # test my helper methods
        self.assertTrue(self.animal.can_delete())
        self.assertTrue(self.animal.can_edit())


class SampleTestCase(PersonMixinTestCase, TestCase):
    """testing sample class"""

    # an attribute for PersonMixinTestCase
    person = Person

    fixtures = [
        '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):
        # create animal
        self.animal = Animal.objects.get(pk=1)

        # now get a sample object
        self.sample = Sample.objects.get(pk=1)

        # set submission
        self.submission = self.sample.submission

    def test_to_biosample(self):

        """Testing JSON conversion for biosample submission"""

        base_dir = os.path.dirname(os.path.abspath(__file__))
        file_path = os.path.join(base_dir, "biosample_sample.json")
        handle = open(file_path)
        reference = json.load(handle)

        # fix release date to today
        now = timezone.now()
        reference['releaseDate'] = str(now.date())

        test = self.sample.to_biosample()

        self.maxDiff = None
        self.assertEqual(reference, test)

    def test_to_biosample2(self):
        """testing json conversion with a biosample_id"""

        # assign a different biosample id
        animal_reference = "SAMEA4450079"
        self.animal.name.biosample_id = animal_reference
        self.animal.name.save()

        sample_reference = "SAMEA4450075"
        self.sample.name.biosample_id = sample_reference
        self.sample.name.save()

        test = self.sample.to_biosample()

        # asserting biosample_.id in response
        self.assertEqual(test["accession"], sample_reference)

        # asserting animal biosample_id in relatioship
        reference = [{
            "accession": animal_reference,
            "relationshipNature": "derived from",
        }]
        self.assertEqual(test['sampleRelationships'], reference)

    def test_to_biosample_no_foreign(self):
        """Testing JSON conversion for biosample submission without
        foreign keys"""

        base_dir = os.path.dirname(os.path.abspath(__file__))
        file_path = os.path.join(base_dir, "biosample_sample.json")
        handle = open(file_path)
        reference = json.load(handle)

        # fix release date to today
        now = timezone.now()
        reference['releaseDate'] = str(now.date())

        # remove foreign keys from reference
        for key in ["Organism part", "Developmental stage"]:
            if key in reference["attributes"]:
                del(reference["attributes"][key])

        # remove foreing keys from sample object
        self.sample.organism_part = None
        self.sample.developmental_stage = None
        self.sample.save()

        test = self.sample.to_biosample()

        self.maxDiff = None
        self.assertEqual(reference, test)

    # TODO: test biosample with None rendering

    def test_uid_report(self):
        """testing uid report after a Sample and Animal insert"""

        reference = {
                'n_of_animals': 3,
                'n_of_samples': 1,
                'breeds_without_ontology': 0,
                'countries_without_ontology': 0,
                'species_without_ontology': 0,
                }

        user = User.objects.get(pk=1)

        test = uid_report(user)

        self.assertEqual(reference, test)

    def test_uid_has_data(self):
        """testing db_has_data for image_app"""

        self.assertTrue(db_has_data())

    def test_waiting(self):
        """Test waiting status"""

        # force submission status
        self.submission.status = WAITING
        self.submission.save()

        # test my helper methods
        self.assertFalse(self.sample.can_delete())
        self.assertFalse(self.sample.can_edit())

    def test_loaded(self):
        """Test loaded status"""

        # force submission status
        self.submission.status = LOADED
        self.submission.save()

        # test my helper methods
        self.assertTrue(self.sample.can_delete())
        self.assertTrue(self.sample.can_edit())

    def test_submitted(self):
        """Test submitted status"""

        # force submission status
        self.submission.status = SUBMITTED
        self.submission.save()

        # test my helper methods
        self.assertFalse(self.sample.can_delete())
        self.assertFalse(self.sample.can_edit())

    def test_error(self):
        """Test error status"""

        # force submission status
        self.submission.status = ERROR
        self.submission.save()

        # test my helper methods
        self.assertTrue(self.sample.can_delete())
        self.assertTrue(self.sample.can_edit())

    def test_need_revision(self):
        """Test need_revision status"""

        # force submission status
        self.submission.status = NEED_REVISION
        self.submission.save()

        # test my helper methods
        self.assertTrue(self.sample.can_delete())
        self.assertTrue(self.sample.can_edit())

    def test_ready(self):
        """Test ready status"""

        # force submission status
        self.submission.status = READY
        self.submission.save()

        # test my helper methods
        self.assertTrue(self.sample.can_delete())
        self.assertTrue(self.sample.can_edit())

    def test_completed(self):
        """Test completed status"""

        # force submission status
        self.submission.status = COMPLETED
        self.submission.save()

        # test my helper methods
        self.assertTrue(self.sample.can_delete())
        self.assertTrue(self.sample.can_edit())


1		#!/usr/bin/env python3
2		# -- coding: utf-8 --
3		"""
4		Created on Tue Apr 3 12:16:55 2018
5
6		@author: Paolo Cozzi <[email protected]>
7		"""
8
9		import os
10		import json
11
12		from django.test import TestCase
13		from django.utils import timezone
14
15		from common.constants import OBO_URL
16		from common.tests import PersonMixinTestCase
17		from common.constants import (
18		WAITING, LOADED, ERROR, READY, NEED_REVISION, SUBMITTED, COMPLETED)
19
20		from image_app.models import (Animal, Submission, DictBreed, DictCountry,
21		DictSex, DictSpecie, Sample, uid_report,
22		Person, User, db_has_data)
23
24
25		class DictSexTestCase(TestCase):
26		"""Testing DictSex class"""
27
28		fixtures = [
29		"image_app/dictsex",
30		"image_app/ontology"
31		]
32
33		def setUp(self):
34		# my attributes
35		self.label = 'male'
36		self.term = 'PATO_0000384'
37
38		def test_str(self):
39		"""Testing str representation"""
40
41		male = DictSex.objects.get(label=self.label)
42		self.assertEqual(
43		str(male),
44		"{label} ({term})".format(
45		label=self.label,
46		term=self.term))
47
48		def test_format_attribute(self):
49		"""Testing format attribute"""
50
51		reference = [{
52		"value": "male",
53		"terms": [{
54		"url": "%s/PATO_0000384" % (OBO_URL)
55		}]
56		}]
57
58		male = DictSex.objects.get(label=self.label)
59		test = male.format_attribute()
60
61		self.assertEqual(reference, test)
62
63
64		class DictSpecieTestCase(TestCase):
65		"""Testing DictSpecie class"""
66
67		fixtures = [
68		'image_app/dictcountry',
69		'image_app/dictspecie',
70		'image_app/ontology',
71		'image_app/speciesynonym'
72		]
73
74		def setUp(self):
75		# my attributes
76		self.label = 'Sus scrofa'
77		self.term = 'NCBITaxon_9823'
78
79		def test_str(self):
80		"""Testing str representation"""
81
82		sus = DictSpecie.objects.get(label=self.label)
83		self.assertEqual(
84		str(sus),
85		"{label} ({term})".format(
86		label=self.label,
87		term=self.term))
88
89		def test_get_specie_by_synonym(self):
90		"""Getting specie using synonym"""
91
92		sus = DictSpecie.get_by_synonym('Pig', 'United Kingdom')
93
94		self.assertEqual(sus.label, self.label)
95		self.assertEqual(sus.term, self.term)
96
97		# assert a specie in a different language (synonym not defined)
98		sus = DictSpecie.get_by_synonym('Pig', 'Italy')
99
100		self.assertEqual(sus.label, self.label)
101		self.assertEqual(sus.term, self.term)
102
103		# using a word not registered returns no data
104		with self.assertRaises(DictSpecie.DoesNotExist):
105		DictSpecie.get_by_synonym('Foo', 'United Kingdom')
106
107		def test_get_specie_by_synonym_nospaces(self):
108		"""Getting specie using synonym, no matters spaces"""
109
110		# assert with spaces
111		sus = DictSpecie.get_by_synonym('Pig (domestic)', 'United Kingdom')
112
113		self.assertEqual(sus.label, self.label)
114		self.assertEqual(sus.term, self.term)
115
116		# assert without spaces
117		sus = DictSpecie.get_by_synonym('Pig(domestic)', 'United Kingdom')
118
119		self.assertEqual(sus.label, self.label)
120		self.assertEqual(sus.term, self.term)
121
122
123		class DictCountryTestCase(TestCase):
124		"""Testing DictCountry class"""
125
126		fixtures = [
127		"image_app/dictcountry",
128		"image_app/ontology"
129		]
130
131		def setUp(self):
132		# my attributes
133		self.label = 'United Kingdom'
134		self.term = 'NCIT_C17233'
135
136		def test_str(self):
137		"""Testing str representation"""
138
139		uk = DictCountry.objects.get(label=self.label)
140		self.assertEqual(
141		str(uk),
142		"{label} ({term})".format(
143		label=self.label,
144		term=self.term))
145
146
147		class DictBreedTestCase(TestCase):
148		"""Testing DictBreed class"""
149
150		fixtures = [
151		"image_app/dictbreed",
152		"image_app/dictcountry",
153		"image_app/dictspecie",
154		"image_app/ontology"
155		]
156
157		def test_str(self):
158		"""Testing str representation (as mapped_breed, if present)"""
159
160		breed = DictBreed.objects.get(pk=1)
161		self.assertEqual(
162		str(breed),
163		"Bunte Bentheimer (Bentheim Black Pied, Sus scrofa)")
164
165		# unset mapped_breed
166		breed.mapped_breed = None
167		self.assertEqual(
168		str(breed), "Bunte Bentheimer (None, Sus scrofa)")
169
170
171		class SubmissionTestCase(TestCase):
172		"""Testing Submission class"""
173
174		fixtures = [
175		'image_app/dictcountry',
176		'image_app/dictrole',
177		'image_app/ontology',
178		'image_app/organization',
179		'image_app/submission',
180		'image_app/user'
181		]
182
183		def setUp(self):
184		self.submission = Submission.objects.get(pk=1)
185
186		def test_str(self):
187		test = str(self.submission)
188		reference = "Cryoweb (United Kingdom, test)"
189
190		self.assertEqual(reference, test)
191
192		def test_waiting(self):
193		"""Test waiting status"""
194
195		# force submission status
196		self.submission.status = WAITING
197
198		# test my helper methods
199		self.assertFalse(self.submission.can_edit())
200		self.assertFalse(self.submission.can_validate())
201		self.assertFalse(self.submission.can_submit())
202
203		def test_loaded(self):
204		"""Test loaded status"""
205
206		# force submission status
207		self.submission.status = LOADED
208
209		# test my helper methods
210		self.assertTrue(self.submission.can_edit())
211		self.assertTrue(self.submission.can_validate())
212		self.assertFalse(self.submission.can_submit())
213
214		def test_submitted(self):
215		"""Test submitted status"""
216
217		# force submission status
218		self.submission.status = SUBMITTED
219
220		# test my helper methods
221		self.assertFalse(self.submission.can_edit())
222		self.assertFalse(self.submission.can_validate())
223		self.assertFalse(self.submission.can_submit())
224
225		def test_error(self):
226		"""Test error status"""
227
228		# force submission status
229		self.submission.status = ERROR
230
231		# test my helper methods
232		self.assertTrue(self.submission.can_edit())
233		self.assertFalse(self.submission.can_validate())
234		self.assertFalse(self.submission.can_submit())
235
236		def test_need_revision(self):
237		"""Test need_revision status"""
238
239		# force submission status
240		self.submission.status = NEED_REVISION
241
242		# test my helper methods
243		self.assertTrue(self.submission.can_edit())
244		self.assertTrue(self.submission.can_validate())
245		self.assertFalse(self.submission.can_submit())
246
247		def test_ready(self):
248		"""Test ready status"""
249
250		# force submission status
251		self.submission.status = READY
252
253		# test my helper methods
254		self.assertTrue(self.submission.can_edit())
255		self.assertTrue(self.submission.can_validate())
256		self.assertTrue(self.submission.can_submit())
257
258		def test_completed(self):
259		"""Test completed status"""
260
261		# force submission status
262		self.submission.status = COMPLETED
263
264		# test my helper methods
265		self.assertTrue(self.submission.can_edit())
266		self.assertFalse(self.submission.can_validate())
267		self.assertFalse(self.submission.can_submit())
268
269
270		class AnimalTestCase(PersonMixinTestCase, TestCase):
271		"""Testing Animal Class"""
272
273		# an attribute for PersonMixinTestCase
274		person = Person
275
276		fixtures = [
277		'image_app/animal',
278		'image_app/dictbreed',
279		'image_app/dictcountry',
280		'image_app/dictrole',
281		'image_app/dictsex',
282		'image_app/dictspecie',
283		'image_app/name',
284		'image_app/ontology',
285		'image_app/organization',
286		'image_app/publication',
287		'image_app/submission',
288		'image_app/user'
289		]
290
291		def setUp(self):
292		# create animal
293		self.animal = Animal.objects.get(pk=1)
294		self.submission = self.animal.submission
295
296	View Code Duplication	def test_to_biosample(self):
		0 ignored issues – show Duplication introduced 2019-06-07 17:57 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
297		"""Testing JSON conversion for biosample submission"""
298
299		base_dir = os.path.dirname(os.path.abspath(__file__))
300		file_path = os.path.join(base_dir, "biosample_animal.json")
301		handle = open(file_path)
302		reference = json.load(handle)
303
304		# fix release date to today
305		now = timezone.now()
306		reference['releaseDate'] = str(now.date())
307
308		test = self.animal.to_biosample()
309
310		self.maxDiff = None
311		self.assertEqual(reference, test)
312
313		def test_to_biosample2(self):
314		"""testing json conversion with a biosample_id"""
315
316		# assign a different biosample id
317		reference = "SAMEA4450079"
318		self.animal.name.biosample_id = reference
319		self.animal.name.save()
320
321		test = self.animal.to_biosample()
322
323		# asserting biosample_.id in response
324		self.assertEqual(test["accession"], reference)
325
326		def test_relationship(self):
327		"""Testing an animal who has mother and father"""
328
329		animal = Animal.objects.get(pk=3)
330
331		test = animal.to_biosample()
332
333		reference = [
334		{'alias': 'IMAGEA000000001',
335		'relationshipNature': 'derived from'},
336		{'alias': 'IMAGEA000000002',
337		'relationshipNature': 'derived from'}
338		]
339
340		# asserting relationship
341		self.assertEqual(test['sampleRelationships'], reference)
342
343		# cleaning up relationship (by erasing fk - as crbanim data could be)
344		# erase father relationship
345		animal.father = None
346		animal.save()
347
348		test = animal.to_biosample()
349
350		reference = [
351		{'alias': 'IMAGEA000000002',
352		'relationshipNature': 'derived from'},
353		]
354
355		# asserting relationship
356		self.assertEqual(test['sampleRelationships'], reference)
357
358		# cleaning up last relationship
359		animal.mother = None
360		animal.save()
361
362		test = animal.to_biosample()
363
364		reference = []
365
366		# asserting relationship
367		self.assertEqual(test['sampleRelationships'], reference)
368
369		# TODO: test None rendering
370
371		def test_waiting(self):
372		"""Test waiting status"""
373
374		# force submission status
375		self.submission.status = WAITING
376		self.submission.save()
377
378		# test my helper methods
379		self.assertFalse(self.animal.can_delete())
380		self.assertFalse(self.animal.can_edit())
381
382		def test_loaded(self):
383		"""Test loaded status"""
384
385		# force submission status
386		self.submission.status = LOADED
387		self.submission.save()
388
389		# test my helper methods
390		self.assertTrue(self.animal.can_delete())
391		self.assertTrue(self.animal.can_edit())
392
393		def test_submitted(self):
394		"""Test submitted status"""
395
396		# force submission status
397		self.submission.status = SUBMITTED
398		self.submission.save()
399
400		# test my helper methods
401		self.assertFalse(self.animal.can_delete())
402		self.assertFalse(self.animal.can_edit())
403
404		def test_error(self):
405		"""Test error status"""
406
407		# force submission status
408		self.submission.status = ERROR
409		self.submission.save()
410
411		# test my helper methods
412		self.assertTrue(self.animal.can_delete())
413		self.assertTrue(self.animal.can_edit())
414
415		def test_need_revision(self):
416		"""Test need_revision status"""
417
418		# force submission status
419		self.submission.status = NEED_REVISION
420		self.submission.save()
421
422		# test my helper methods
423		self.assertTrue(self.animal.can_delete())
424		self.assertTrue(self.animal.can_edit())
425
426		def test_ready(self):
427		"""Test ready status"""
428
429		# force submission status
430		self.submission.status = READY
431		self.submission.save()
432
433		# test my helper methods
434		self.assertTrue(self.animal.can_delete())
435		self.assertTrue(self.animal.can_edit())
436
437		def test_completed(self):
438		"""Test completed status"""
439
440		# force submission status
441		self.submission.status = COMPLETED
442		self.submission.save()
443
444		# test my helper methods
445		self.assertTrue(self.animal.can_delete())
446		self.assertTrue(self.animal.can_edit())
447
448
449		class SampleTestCase(PersonMixinTestCase, TestCase):
450		"""testing sample class"""
451
452		# an attribute for PersonMixinTestCase
453		person = Person
454
455		fixtures = [
456		'image_app/animal',
457		'image_app/dictbreed',
458		'image_app/dictcountry',
459		'image_app/dictrole',
460		'image_app/dictsex',
461		'image_app/dictspecie',
462		'image_app/dictstage',
463		'image_app/dictuberon',
464		'image_app/name',
465		'image_app/ontology',
466		'image_app/organization',
467		'image_app/publication',
468		'image_app/sample',
469		'image_app/submission',
470		'image_app/user'
471		]
472
473		def setUp(self):
474		# create animal
475		self.animal = Animal.objects.get(pk=1)
476
477		# now get a sample object
478		self.sample = Sample.objects.get(pk=1)
479
480		# set submission
481		self.submission = self.sample.submission
482
483	View Code Duplication	def test_to_biosample(self):
		0 ignored issues – show Duplication introduced 2019-06-07 17:57 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
484		"""Testing JSON conversion for biosample submission"""
485
486		base_dir = os.path.dirname(os.path.abspath(__file__))
487		file_path = os.path.join(base_dir, "biosample_sample.json")
488		handle = open(file_path)
489		reference = json.load(handle)
490
491		# fix release date to today
492		now = timezone.now()
493		reference['releaseDate'] = str(now.date())
494
495		test = self.sample.to_biosample()
496
497		self.maxDiff = None
498		self.assertEqual(reference, test)
499
500		def test_to_biosample2(self):
501		"""testing json conversion with a biosample_id"""
502
503		# assign a different biosample id
504		animal_reference = "SAMEA4450079"
505		self.animal.name.biosample_id = animal_reference
506		self.animal.name.save()
507
508		sample_reference = "SAMEA4450075"
509		self.sample.name.biosample_id = sample_reference
510		self.sample.name.save()
511
512		test = self.sample.to_biosample()
513
514		# asserting biosample_.id in response
515		self.assertEqual(test["accession"], sample_reference)
516
517		# asserting animal biosample_id in relatioship
518		reference = [{
519		"accession": animal_reference,
520		"relationshipNature": "derived from",
521		}]
522		self.assertEqual(test['sampleRelationships'], reference)
523
524		def test_to_biosample_no_foreign(self):
525		"""Testing JSON conversion for biosample submission without
526		foreign keys"""
527
528		base_dir = os.path.dirname(os.path.abspath(__file__))
529		file_path = os.path.join(base_dir, "biosample_sample.json")
530		handle = open(file_path)
531		reference = json.load(handle)
532
533		# fix release date to today
534		now = timezone.now()
535		reference['releaseDate'] = str(now.date())
536
537		# remove foreign keys from reference
538		for key in ["Organism part", "Developmental stage"]:
539		if key in reference["attributes"]:
540		del(reference["attributes"][key])
541
542		# remove foreing keys from sample object
543		self.sample.organism_part = None
544		self.sample.developmental_stage = None
545		self.sample.save()
546
547		test = self.sample.to_biosample()
548
549		self.maxDiff = None
550		self.assertEqual(reference, test)
551
552		# TODO: test biosample with None rendering
553
554		def test_uid_report(self):
555		"""testing uid report after a Sample and Animal insert"""
556
557		reference = {
558		'n_of_animals': 3,
559		'n_of_samples': 1,
560		'breeds_without_ontology': 0,
561		'countries_without_ontology': 0,
562		'species_without_ontology': 0,
563		}
564
565		user = User.objects.get(pk=1)
566
567		test = uid_report(user)
568
569		self.assertEqual(reference, test)
570
571		def test_uid_has_data(self):
572		"""testing db_has_data for image_app"""
573
574		self.assertTrue(db_has_data())
575
576		def test_waiting(self):
577		"""Test waiting status"""
578
579		# force submission status
580		self.submission.status = WAITING
581		self.submission.save()
582
583		# test my helper methods
584		self.assertFalse(self.sample.can_delete())
585		self.assertFalse(self.sample.can_edit())
586
587		def test_loaded(self):
588		"""Test loaded status"""
589
590		# force submission status
591		self.submission.status = LOADED
592		self.submission.save()
593
594		# test my helper methods
595		self.assertTrue(self.sample.can_delete())
596		self.assertTrue(self.sample.can_edit())
597
598		def test_submitted(self):
599		"""Test submitted status"""
600
601		# force submission status
602		self.submission.status = SUBMITTED
603		self.submission.save()
604
605		# test my helper methods
606		self.assertFalse(self.sample.can_delete())
607		self.assertFalse(self.sample.can_edit())
608
609		def test_error(self):
610		"""Test error status"""
611
612		# force submission status
613		self.submission.status = ERROR
614		self.submission.save()
615
616		# test my helper methods
617		self.assertTrue(self.sample.can_delete())
618		self.assertTrue(self.sample.can_edit())
619
620		def test_need_revision(self):
621		"""Test need_revision status"""
622
623		# force submission status
624		self.submission.status = NEED_REVISION
625		self.submission.save()
626
627		# test my helper methods
628		self.assertTrue(self.sample.can_delete())
629		self.assertTrue(self.sample.can_edit())
630
631		def test_ready(self):
632		"""Test ready status"""
633
634		# force submission status
635		self.submission.status = READY
636		self.submission.save()
637
638		# test my helper methods
639		self.assertTrue(self.sample.can_delete())
640		self.assertTrue(self.sample.can_edit())
641
642		def test_completed(self):
643		"""Test completed status"""
644
645		# force submission status
646		self.submission.status = COMPLETED
647		self.submission.save()
648
649		# test my helper methods
650		self.assertTrue(self.sample.can_delete())
651		self.assertTrue(self.sample.can_edit())
652

cnr-ibba / IMAGE-InjectTool

Pull Request — master (#26)

AnimalTestCase.test_relationship() A

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