uid.tests.test_models.AnimalTestCase.test_relationship() - Code Metrics - Inspection of ":boom: attempt to solve update issue - strong refa..." - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Pull Request — devel (#72)

by Paolo

created 2019-11-04 14:22 UTC

AnimalTestCase.test_relationship() A

↳ Parent: uid.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.helpers import get_deleted_objects
from common.tests import PersonMixinTestCase
from common.constants import (
    WAITING, LOADED, ERROR, READY, NEED_REVISION, SUBMITTED, COMPLETED)

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


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

    fixtures = [
        "uid/dictsex",
        "uid/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)

    def test_format_attribute_default(self):
        """Testing format attribute with no library_uri"""

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

        male = DictSex.objects.get(label=self.label)
        male.library_name = None
        test = male.format_attribute()

        self.assertEqual(reference, test)


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

    fixtures = [
        'uid/dictcountry',
        'uid/dictspecie',
        'uid/ontology',
        'uid/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_missing_taxon(self):
        """test no term returns no taxon"""

        sus = DictSpecie.objects.get(label=self.label)
        sus.term = None
        self.assertIsNone(sus.taxon_id)

    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)

    def test_get_specie_check_synonyms(self):
        """Get the same specie from latin or dictionary table"""

        # get a country object
        language = DictCountry.objects.get(label="Italy")

        sus = DictSpecie.get_specie_check_synonyms(
            species_label=self.label,
            language=language)

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

        sus = DictSpecie.get_specie_check_synonyms(
            species_label="Pig",
            language=language)

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


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

    fixtures = [
        "uid/dictcountry",
        "uid/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 = [
        "uid/dictbreed",
        "uid/dictcountry",
        "uid/dictspecie",
        "uid/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
        breed.mapped_breed_term = None
        self.assertEqual(
            str(breed), "Bunte Bentheimer (pig breed, Sus scrofa)")

    def test_default_mapped_breed(self):
        """Test mapped breed returns specie.label if no mapping occours"""

        breed = DictBreed.objects.get(pk=1)
        self.assertEqual(breed.mapped_breed, "Bentheim Black Pied")
        self.assertEqual(breed.mapped_breed_term, "LBO_0000347")

        # unset mapped_breed
        breed.mapped_breed = None
        breed.mapped_breed_term = None
        self.assertEqual(breed.mapped_breed, "pig breed")
        self.assertEqual(breed.mapped_breed_term, "LBO_0000003")

    def test_get_no_mapped_breed(self):
        """Test with a specie not defined in get_general_breed_by_species"""

        specie = DictSpecie(label='Anser anser', term="NCBITaxon_8843")
        breed = DictBreed(specie=specie, supplied_breed='Anser anser')

        self.assertIsNone(breed.mapped_breed)
        self.assertIsNone(breed.mapped_breed_term)
        self.assertIsNone(breed.format_attribute())


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

    fixtures = [
        'uid/dictcountry',
        'uid/dictrole',
        'uid/ontology',
        'uid/organization',
        'uid/submission',
        'uid/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 = [
        'uid/animal',
        'uid/dictbreed',
        'uid/dictcountry',
        'uid/dictrole',
        'uid/dictsex',
        'uid/dictspecie',
        'uid/ontology',
        'uid/organization',
        'uid/publication',
        'uid/submission',
        'uid/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.biosample_id = reference
        self.animal.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 = [
        'uid/animal',
        'uid/dictbreed',
        'uid/dictcountry',
        'uid/dictrole',
        'uid/dictsex',
        'uid/dictspecie',
        'uid/dictstage',
        'uid/dictuberon',
        'uid/ontology',
        'uid/organization',
        'uid/publication',
        'uid/sample',
        'uid/submission',
        'uid/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.biosample_id = animal_reference
        self.animal.save()

        sample_reference = "SAMEA4450075"
        self.sample.biosample_id = sample_reference
        self.sample.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_related_object(self):
        """Testing relationship using get_deleted_objects"""

        deletable_objects, model_count, protected = get_deleted_objects(
            [self.animal])

        self.assertEqual(model_count, {'animals': 2, 'samples': 1})

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

        reference = {
                'n_of_animals': 3,
                'n_of_samples': 1,
                'breeds_total': 1,
                'breeds_without_ontology': 0,
                'countries_total': 3,
                'countries_without_ontology': 0,
                'species_total': 1,
                'species_without_ontology': 0,
                'developmental_stages_total': 1,
                'developmental_stages_without_ontology': 0,
                'organism_parts_total': 1,
                'organism_parts_without_ontology': 0,
                'physiological_stages_total': 1,
                'physiological_stages_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 uid"""

        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())


class PersonTestCase(PersonMixinTestCase, TestCase):
    """Testing Person Class"""

    # an attribute for PersonMixinTestCase
    person = Person

    fixtures = [
        'uid/dictcountry',
        'uid/dictrole',
        'uid/organization',
        'uid/user'
    ]

    def setUp(self):
        # get a person
        self.person = Person.objects.get(user__id=1)

    def test_str(self):
        """test a repr method"""

        test = str(self.person)
        self.assertEqual(
            test, "Foo Bar (Test organization (United Kingdom))")


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.helpers import get_deleted_objects
17		from common.tests import PersonMixinTestCase
18		from common.constants import (
19		WAITING, LOADED, ERROR, READY, NEED_REVISION, SUBMITTED, COMPLETED)
20
21		from uid.models import (
22		Animal, Submission, DictBreed, DictCountry,
23		DictSex, DictSpecie, Sample, uid_report, Person, User, db_has_data)
24
25
26		class DictSexTestCase(TestCase):
27		"""Testing DictSex class"""
28
29		fixtures = [
30		"uid/dictsex",
31		"uid/ontology"
32		]
33
34		def setUp(self):
35		# my attributes
36		self.label = 'male'
37		self.term = 'PATO_0000384'
38
39		def test_str(self):
40		"""Testing str representation"""
41
42		male = DictSex.objects.get(label=self.label)
43		self.assertEqual(
44		str(male),
45		"{label} ({term})".format(
46		label=self.label,
47		term=self.term))
48
49		def test_format_attribute(self):
50		"""Testing format attribute"""
51
52		reference = [{
53		"value": "male",
54		"terms": [{
55		"url": "%s/PATO_0000384" % (OBO_URL)
56		}]
57		}]
58
59		male = DictSex.objects.get(label=self.label)
60		test = male.format_attribute()
61
62		self.assertEqual(reference, test)
63
64		def test_format_attribute_default(self):
65		"""Testing format attribute with no library_uri"""
66
67		reference = [{
68		"value": "male",
69		"terms": [{
70		"url": "%s/PATO_0000384" % (OBO_URL)
71		}]
72		}]
73
74		male = DictSex.objects.get(label=self.label)
75		male.library_name = None
76		test = male.format_attribute()
77
78		self.assertEqual(reference, test)
79
80
81		class DictSpecieTestCase(TestCase):
82		"""Testing DictSpecie class"""
83
84		fixtures = [
85		'uid/dictcountry',
86		'uid/dictspecie',
87		'uid/ontology',
88		'uid/speciesynonym'
89		]
90
91		def setUp(self):
92		# my attributes
93		self.label = 'Sus scrofa'
94		self.term = 'NCBITaxon_9823'
95
96		def test_str(self):
97		"""Testing str representation"""
98
99		sus = DictSpecie.objects.get(label=self.label)
100		self.assertEqual(
101		str(sus),
102		"{label} ({term})".format(
103		label=self.label,
104		term=self.term))
105
106		def test_missing_taxon(self):
107		"""test no term returns no taxon"""
108
109		sus = DictSpecie.objects.get(label=self.label)
110		sus.term = None
111		self.assertIsNone(sus.taxon_id)
112
113		def test_get_specie_by_synonym(self):
114		"""Getting specie using synonym"""
115
116		sus = DictSpecie.get_by_synonym('Pig', 'United Kingdom')
117
118		self.assertEqual(sus.label, self.label)
119		self.assertEqual(sus.term, self.term)
120
121		# assert a specie in a different language (synonym not defined)
122		sus = DictSpecie.get_by_synonym('Pig', 'Italy')
123
124		self.assertEqual(sus.label, self.label)
125		self.assertEqual(sus.term, self.term)
126
127		# using a word not registered returns no data
128		with self.assertRaises(DictSpecie.DoesNotExist):
129		DictSpecie.get_by_synonym('Foo', 'United Kingdom')
130
131		def test_get_specie_by_synonym_nospaces(self):
132		"""Getting specie using synonym, no matters spaces"""
133
134		# assert with spaces
135		sus = DictSpecie.get_by_synonym('Pig (domestic)', 'United Kingdom')
136
137		self.assertEqual(sus.label, self.label)
138		self.assertEqual(sus.term, self.term)
139
140		# assert without spaces
141		sus = DictSpecie.get_by_synonym('Pig(domestic)', 'United Kingdom')
142
143		self.assertEqual(sus.label, self.label)
144		self.assertEqual(sus.term, self.term)
145
146		def test_get_specie_check_synonyms(self):
147		"""Get the same specie from latin or dictionary table"""
148
149		# get a country object
150		language = DictCountry.objects.get(label="Italy")
151
152		sus = DictSpecie.get_specie_check_synonyms(
153		species_label=self.label,
154		language=language)
155
156		self.assertEqual(sus.label, self.label)
157		self.assertEqual(sus.term, self.term)
158
159		sus = DictSpecie.get_specie_check_synonyms(
160		species_label="Pig",
161		language=language)
162
163		self.assertEqual(sus.label, self.label)
164		self.assertEqual(sus.term, self.term)
165
166
167		class DictCountryTestCase(TestCase):
168		"""Testing DictCountry class"""
169
170		fixtures = [
171		"uid/dictcountry",
172		"uid/ontology"
173		]
174
175		def setUp(self):
176		# my attributes
177		self.label = 'United Kingdom'
178		self.term = 'NCIT_C17233'
179
180		def test_str(self):
181		"""Testing str representation"""
182
183		uk = DictCountry.objects.get(label=self.label)
184		self.assertEqual(
185		str(uk),
186		"{label} ({term})".format(
187		label=self.label,
188		term=self.term))
189
190
191		class DictBreedTestCase(TestCase):
192		"""Testing DictBreed class"""
193
194		fixtures = [
195		"uid/dictbreed",
196		"uid/dictcountry",
197		"uid/dictspecie",
198		"uid/ontology"
199		]
200
201		def test_str(self):
202		"""Testing str representation (as mapped_breed, if present)"""
203
204		breed = DictBreed.objects.get(pk=1)
205		self.assertEqual(
206		str(breed),
207		"Bunte Bentheimer (Bentheim Black Pied, Sus scrofa)")
208
209		# unset mapped_breed
210		breed.mapped_breed = None
211		breed.mapped_breed_term = None
212		self.assertEqual(
213		str(breed), "Bunte Bentheimer (pig breed, Sus scrofa)")
214
215		def test_default_mapped_breed(self):
216		"""Test mapped breed returns specie.label if no mapping occours"""
217
218		breed = DictBreed.objects.get(pk=1)
219		self.assertEqual(breed.mapped_breed, "Bentheim Black Pied")
220		self.assertEqual(breed.mapped_breed_term, "LBO_0000347")
221
222		# unset mapped_breed
223		breed.mapped_breed = None
224		breed.mapped_breed_term = None
225		self.assertEqual(breed.mapped_breed, "pig breed")
226		self.assertEqual(breed.mapped_breed_term, "LBO_0000003")
227
228		def test_get_no_mapped_breed(self):
229		"""Test with a specie not defined in get_general_breed_by_species"""
230
231		specie = DictSpecie(label='Anser anser', term="NCBITaxon_8843")
232		breed = DictBreed(specie=specie, supplied_breed='Anser anser')
233
234		self.assertIsNone(breed.mapped_breed)
235		self.assertIsNone(breed.mapped_breed_term)
236		self.assertIsNone(breed.format_attribute())
237
238
239		class SubmissionTestCase(TestCase):
240		"""Testing Submission class"""
241
242		fixtures = [
243		'uid/dictcountry',
244		'uid/dictrole',
245		'uid/ontology',
246		'uid/organization',
247		'uid/submission',
248		'uid/user'
249		]
250
251		def setUp(self):
252		self.submission = Submission.objects.get(pk=1)
253
254		def test_str(self):
255		test = str(self.submission)
256		reference = "Cryoweb (United Kingdom, test)"
257
258		self.assertEqual(reference, test)
259
260		def test_waiting(self):
261		"""Test waiting status"""
262
263		# force submission status
264		self.submission.status = WAITING
265
266		# test my helper methods
267		self.assertFalse(self.submission.can_edit())
268		self.assertFalse(self.submission.can_validate())
269		self.assertFalse(self.submission.can_submit())
270
271		def test_loaded(self):
272		"""Test loaded status"""
273
274		# force submission status
275		self.submission.status = LOADED
276
277		# test my helper methods
278		self.assertTrue(self.submission.can_edit())
279		self.assertTrue(self.submission.can_validate())
280		self.assertFalse(self.submission.can_submit())
281
282		def test_submitted(self):
283		"""Test submitted status"""
284
285		# force submission status
286		self.submission.status = SUBMITTED
287
288		# test my helper methods
289		self.assertFalse(self.submission.can_edit())
290		self.assertFalse(self.submission.can_validate())
291		self.assertFalse(self.submission.can_submit())
292
293		def test_error(self):
294		"""Test error status"""
295
296		# force submission status
297		self.submission.status = ERROR
298
299		# test my helper methods
300		self.assertTrue(self.submission.can_edit())
301		self.assertFalse(self.submission.can_validate())
302		self.assertFalse(self.submission.can_submit())
303
304		def test_need_revision(self):
305		"""Test need_revision status"""
306
307		# force submission status
308		self.submission.status = NEED_REVISION
309
310		# test my helper methods
311		self.assertTrue(self.submission.can_edit())
312		self.assertTrue(self.submission.can_validate())
313		self.assertFalse(self.submission.can_submit())
314
315		def test_ready(self):
316		"""Test ready status"""
317
318		# force submission status
319		self.submission.status = READY
320
321		# test my helper methods
322		self.assertTrue(self.submission.can_edit())
323		self.assertTrue(self.submission.can_validate())
324		self.assertTrue(self.submission.can_submit())
325
326		def test_completed(self):
327		"""Test completed status"""
328
329		# force submission status
330		self.submission.status = COMPLETED
331
332		# test my helper methods
333		self.assertTrue(self.submission.can_edit())
334		self.assertFalse(self.submission.can_validate())
335		self.assertFalse(self.submission.can_submit())
336
337
338		class AnimalTestCase(PersonMixinTestCase, TestCase):
339		"""Testing Animal Class"""
340
341		# an attribute for PersonMixinTestCase
342		person = Person
343
344		fixtures = [
345		'uid/animal',
346		'uid/dictbreed',
347		'uid/dictcountry',
348		'uid/dictrole',
349		'uid/dictsex',
350		'uid/dictspecie',
351		'uid/ontology',
352		'uid/organization',
353		'uid/publication',
354		'uid/submission',
355		'uid/user'
356		]
357
358		def setUp(self):
359		# create animal
360		self.animal = Animal.objects.get(pk=1)
361		self.submission = self.animal.submission
362
363	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...
364		"""Testing JSON conversion for biosample submission"""
365
366		base_dir = os.path.dirname(os.path.abspath(__file__))
367		file_path = os.path.join(base_dir, "biosample_animal.json")
368		handle = open(file_path)
369		reference = json.load(handle)
370
371		# fix release date to today
372		now = timezone.now()
373		reference['releaseDate'] = str(now.date())
374
375		test = self.animal.to_biosample()
376
377		self.maxDiff = None
378		self.assertEqual(reference, test)
379
380		def test_to_biosample2(self):
381		"""testing json conversion with a biosample_id"""
382
383		# assign a different biosample id
384		reference = "SAMEA4450079"
385		self.animal.biosample_id = reference
386		self.animal.save()
387
388		test = self.animal.to_biosample()
389
390		# asserting biosample_.id in response
391		self.assertEqual(test["accession"], reference)
392
393		def test_relationship(self):
394		"""Testing an animal who has mother and father"""
395
396		animal = Animal.objects.get(pk=3)
397
398		test = animal.to_biosample()
399
400		reference = [
401		{'alias': 'IMAGEA000000001',
402		'relationshipNature': 'derived from'},
403		{'alias': 'IMAGEA000000002',
404		'relationshipNature': 'derived from'}
405		]
406
407		# asserting relationship
408		self.assertEqual(test['sampleRelationships'], reference)
409
410		# cleaning up relationship (by erasing fk - as crbanim data could be)
411		# erase father relationship
412		animal.father = None
413		animal.save()
414
415		test = animal.to_biosample()
416
417		reference = [
418		{'alias': 'IMAGEA000000002',
419		'relationshipNature': 'derived from'},
420		]
421
422		# asserting relationship
423		self.assertEqual(test['sampleRelationships'], reference)
424
425		# cleaning up last relationship
426		animal.mother = None
427		animal.save()
428
429		test = animal.to_biosample()
430
431		reference = []
432
433		# asserting relationship
434		self.assertEqual(test['sampleRelationships'], reference)
435
436		# TODO: test None rendering
437
438		def test_waiting(self):
439		"""Test waiting status"""
440
441		# force submission status
442		self.submission.status = WAITING
443		self.submission.save()
444
445		# test my helper methods
446		self.assertFalse(self.animal.can_delete())
447		self.assertFalse(self.animal.can_edit())
448
449		def test_loaded(self):
450		"""Test loaded status"""
451
452		# force submission status
453		self.submission.status = LOADED
454		self.submission.save()
455
456		# test my helper methods
457		self.assertTrue(self.animal.can_delete())
458		self.assertTrue(self.animal.can_edit())
459
460		def test_submitted(self):
461		"""Test submitted status"""
462
463		# force submission status
464		self.submission.status = SUBMITTED
465		self.submission.save()
466
467		# test my helper methods
468		self.assertFalse(self.animal.can_delete())
469		self.assertFalse(self.animal.can_edit())
470
471		def test_error(self):
472		"""Test error status"""
473
474		# force submission status
475		self.submission.status = ERROR
476		self.submission.save()
477
478		# test my helper methods
479		self.assertTrue(self.animal.can_delete())
480		self.assertTrue(self.animal.can_edit())
481
482		def test_need_revision(self):
483		"""Test need_revision status"""
484
485		# force submission status
486		self.submission.status = NEED_REVISION
487		self.submission.save()
488
489		# test my helper methods
490		self.assertTrue(self.animal.can_delete())
491		self.assertTrue(self.animal.can_edit())
492
493		def test_ready(self):
494		"""Test ready status"""
495
496		# force submission status
497		self.submission.status = READY
498		self.submission.save()
499
500		# test my helper methods
501		self.assertTrue(self.animal.can_delete())
502		self.assertTrue(self.animal.can_edit())
503
504		def test_completed(self):
505		"""Test completed status"""
506
507		# force submission status
508		self.submission.status = COMPLETED
509		self.submission.save()
510
511		# test my helper methods
512		self.assertTrue(self.animal.can_delete())
513		self.assertTrue(self.animal.can_edit())
514
515
516		class SampleTestCase(PersonMixinTestCase, TestCase):
517		"""testing sample class"""
518
519		# an attribute for PersonMixinTestCase
520		person = Person
521
522		fixtures = [
523		'uid/animal',
524		'uid/dictbreed',
525		'uid/dictcountry',
526		'uid/dictrole',
527		'uid/dictsex',
528		'uid/dictspecie',
529		'uid/dictstage',
530		'uid/dictuberon',
531		'uid/ontology',
532		'uid/organization',
533		'uid/publication',
534		'uid/sample',
535		'uid/submission',
536		'uid/user'
537		]
538
539		def setUp(self):
540		# create animal
541		self.animal = Animal.objects.get(pk=1)
542
543		# now get a sample object
544		self.sample = Sample.objects.get(pk=1)
545
546		# set submission
547		self.submission = self.sample.submission
548
549	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...
550		"""Testing JSON conversion for biosample submission"""
551
552		base_dir = os.path.dirname(os.path.abspath(__file__))
553		file_path = os.path.join(base_dir, "biosample_sample.json")
554		handle = open(file_path)
555		reference = json.load(handle)
556
557		# fix release date to today
558		now = timezone.now()
559		reference['releaseDate'] = str(now.date())
560
561		test = self.sample.to_biosample()
562
563		self.maxDiff = None
564		self.assertEqual(reference, test)
565
566		def test_to_biosample2(self):
567		"""testing json conversion with a biosample_id"""
568
569		# assign a different biosample id
570		animal_reference = "SAMEA4450079"
571		self.animal.biosample_id = animal_reference
572		self.animal.save()
573
574		sample_reference = "SAMEA4450075"
575		self.sample.biosample_id = sample_reference
576		self.sample.save()
577
578		test = self.sample.to_biosample()
579
580		# asserting biosample_.id in response
581		self.assertEqual(test["accession"], sample_reference)
582
583		# asserting animal biosample_id in relatioship
584		reference = [{
585		"accession": animal_reference,
586		"relationshipNature": "derived from",
587		}]
588		self.assertEqual(test['sampleRelationships'], reference)
589
590		def test_to_biosample_no_foreign(self):
591		"""Testing JSON conversion for biosample submission without
592		foreign keys"""
593
594		base_dir = os.path.dirname(os.path.abspath(__file__))
595		file_path = os.path.join(base_dir, "biosample_sample.json")
596		handle = open(file_path)
597		reference = json.load(handle)
598
599		# fix release date to today
600		now = timezone.now()
601		reference['releaseDate'] = str(now.date())
602
603		# remove foreign keys from reference
604		for key in ["Organism part", "Developmental stage"]:
605		if key in reference["attributes"]:
606		del(reference["attributes"][key])
607
608		# remove foreing keys from sample object
609		self.sample.organism_part = None
610		self.sample.developmental_stage = None
611		self.sample.save()
612
613		test = self.sample.to_biosample()
614
615		self.maxDiff = None
616		self.assertEqual(reference, test)
617
618		# TODO: test biosample with None rendering
619
620		def test_related_object(self):
621		"""Testing relationship using get_deleted_objects"""
622
623		deletable_objects, model_count, protected = get_deleted_objects(
624		[self.animal])
625
626		self.assertEqual(model_count, {'animals': 2, 'samples': 1})
627
628		def test_uid_report(self):
629		"""testing uid report after a Sample and Animal insert"""
630
631		reference = {
632		'n_of_animals': 3,
633		'n_of_samples': 1,
634		'breeds_total': 1,
635		'breeds_without_ontology': 0,
636		'countries_total': 3,
637		'countries_without_ontology': 0,
638		'species_total': 1,
639		'species_without_ontology': 0,
640		'developmental_stages_total': 1,
641		'developmental_stages_without_ontology': 0,
642		'organism_parts_total': 1,
643		'organism_parts_without_ontology': 0,
644		'physiological_stages_total': 1,
645		'physiological_stages_without_ontology': 0,
646		}
647
648		user = User.objects.get(pk=1)
649
650		test = uid_report(user)
651
652		self.assertEqual(reference, test)
653
654		def test_uid_has_data(self):
655		"""testing db_has_data for uid"""
656
657		self.assertTrue(db_has_data())
658
659		def test_waiting(self):
660		"""Test waiting status"""
661
662		# force submission status
663		self.submission.status = WAITING
664		self.submission.save()
665
666		# test my helper methods
667		self.assertFalse(self.sample.can_delete())
668		self.assertFalse(self.sample.can_edit())
669
670		def test_loaded(self):
671		"""Test loaded status"""
672
673		# force submission status
674		self.submission.status = LOADED
675		self.submission.save()
676
677		# test my helper methods
678		self.assertTrue(self.sample.can_delete())
679		self.assertTrue(self.sample.can_edit())
680
681		def test_submitted(self):
682		"""Test submitted status"""
683
684		# force submission status
685		self.submission.status = SUBMITTED
686		self.submission.save()
687
688		# test my helper methods
689		self.assertFalse(self.sample.can_delete())
690		self.assertFalse(self.sample.can_edit())
691
692		def test_error(self):
693		"""Test error status"""
694
695		# force submission status
696		self.submission.status = ERROR
697		self.submission.save()
698
699		# test my helper methods
700		self.assertTrue(self.sample.can_delete())
701		self.assertTrue(self.sample.can_edit())
702
703		def test_need_revision(self):
704		"""Test need_revision status"""
705
706		# force submission status
707		self.submission.status = NEED_REVISION
708		self.submission.save()
709
710		# test my helper methods
711		self.assertTrue(self.sample.can_delete())
712		self.assertTrue(self.sample.can_edit())
713
714		def test_ready(self):
715		"""Test ready status"""
716
717		# force submission status
718		self.submission.status = READY
719		self.submission.save()
720
721		# test my helper methods
722		self.assertTrue(self.sample.can_delete())
723		self.assertTrue(self.sample.can_edit())
724
725		def test_completed(self):
726		"""Test completed status"""
727
728		# force submission status
729		self.submission.status = COMPLETED
730		self.submission.save()
731
732		# test my helper methods
733		self.assertTrue(self.sample.can_delete())
734		self.assertTrue(self.sample.can_edit())
735
736
737		class PersonTestCase(PersonMixinTestCase, TestCase):
738		"""Testing Person Class"""
739
740		# an attribute for PersonMixinTestCase
741		person = Person
742
743		fixtures = [
744		'uid/dictcountry',
745		'uid/dictrole',
746		'uid/organization',
747		'uid/user'
748		]
749
750		def setUp(self):
751		# get a person
752		self.person = Person.objects.get(user__id=1)
753
754		def test_str(self):
755		"""test a repr method"""
756
757		test = str(self.person)
758		self.assertEqual(
759		test, "Foo Bar (Test organization (United Kingdom))")
760

cnr-ibba / IMAGE-InjectTool

Pull Request — devel (#72)

AnimalTestCase.test_relationship() A

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