uid.tests.test_models.SubmissionTestCase.setUp() - Code Metrics - Inspection of ":twisted_rightwards_arrows: Merge pull request #68..." - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( 4f7ee6...646424 )

by Paolo

created 2019-11-07 14:18 UTC

uid.tests.test_models.SubmissionTestCase.setUp() A

↳ Parent: uid.tests.test_models

Complexity

Conditions

Size

Total Lines	2
Code Lines	2

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	2
dl	0
loc	2
rs	10
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 - United Kingdom (Bentheim Black Pied, "
             "Sus scrofa)"))

        # unset mapped_breed
        breed.mapped_breed = None
        breed.mapped_breed_term = None
        self.assertEqual(
            str(breed),
            "Bunte Bentheimer - United Kingdom (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': 'child of'},
            {'alias': 'IMAGEA000000002',
             'relationshipNature': 'child of'}
        ]

        # 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': 'child of'},
        ]

        # 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 - United Kingdom (Bentheim Black Pied, "
208		"Sus scrofa)"))
209
210		# unset mapped_breed
211		breed.mapped_breed = None
212		breed.mapped_breed_term = None
213		self.assertEqual(
214		str(breed),
215		"Bunte Bentheimer - United Kingdom (pig breed, Sus scrofa)")
216
217		def test_default_mapped_breed(self):
218		"""Test mapped breed returns specie.label if no mapping occours"""
219
220		breed = DictBreed.objects.get(pk=1)
221		self.assertEqual(breed.mapped_breed, "Bentheim Black Pied")
222		self.assertEqual(breed.mapped_breed_term, "LBO_0000347")
223
224		# unset mapped_breed
225		breed.mapped_breed = None
226		breed.mapped_breed_term = None
227		self.assertEqual(breed.mapped_breed, "pig breed")
228		self.assertEqual(breed.mapped_breed_term, "LBO_0000003")
229
230		def test_get_no_mapped_breed(self):
231		"""Test with a specie not defined in get_general_breed_by_species"""
232
233		specie = DictSpecie(label='Anser anser', term="NCBITaxon_8843")
234		breed = DictBreed(specie=specie, supplied_breed='Anser anser')
235
236		self.assertIsNone(breed.mapped_breed)
237		self.assertIsNone(breed.mapped_breed_term)
238		self.assertIsNone(breed.format_attribute())
239
240
241		class SubmissionTestCase(TestCase):
242		"""Testing Submission class"""
243
244		fixtures = [
245		'uid/dictcountry',
246		'uid/dictrole',
247		'uid/ontology',
248		'uid/organization',
249		'uid/submission',
250		'uid/user'
251		]
252
253		def setUp(self):
254		self.submission = Submission.objects.get(pk=1)
255
256		def test_str(self):
257		test = str(self.submission)
258		reference = "Cryoweb (United Kingdom, test)"
259
260		self.assertEqual(reference, test)
261
262		def test_waiting(self):
263		"""Test waiting status"""
264
265		# force submission status
266		self.submission.status = WAITING
267
268		# test my helper methods
269		self.assertFalse(self.submission.can_edit())
270		self.assertFalse(self.submission.can_validate())
271		self.assertFalse(self.submission.can_submit())
272
273		def test_loaded(self):
274		"""Test loaded status"""
275
276		# force submission status
277		self.submission.status = LOADED
278
279		# test my helper methods
280		self.assertTrue(self.submission.can_edit())
281		self.assertTrue(self.submission.can_validate())
282		self.assertFalse(self.submission.can_submit())
283
284		def test_submitted(self):
285		"""Test submitted status"""
286
287		# force submission status
288		self.submission.status = SUBMITTED
289
290		# test my helper methods
291		self.assertFalse(self.submission.can_edit())
292		self.assertFalse(self.submission.can_validate())
293		self.assertFalse(self.submission.can_submit())
294
295		def test_error(self):
296		"""Test error status"""
297
298		# force submission status
299		self.submission.status = ERROR
300
301		# test my helper methods
302		self.assertTrue(self.submission.can_edit())
303		self.assertFalse(self.submission.can_validate())
304		self.assertFalse(self.submission.can_submit())
305
306		def test_need_revision(self):
307		"""Test need_revision status"""
308
309		# force submission status
310		self.submission.status = NEED_REVISION
311
312		# test my helper methods
313		self.assertTrue(self.submission.can_edit())
314		self.assertTrue(self.submission.can_validate())
315		self.assertFalse(self.submission.can_submit())
316
317		def test_ready(self):
318		"""Test ready status"""
319
320		# force submission status
321		self.submission.status = READY
322
323		# test my helper methods
324		self.assertTrue(self.submission.can_edit())
325		self.assertTrue(self.submission.can_validate())
326		self.assertTrue(self.submission.can_submit())
327
328		def test_completed(self):
329		"""Test completed status"""
330
331		# force submission status
332		self.submission.status = COMPLETED
333
334		# test my helper methods
335		self.assertTrue(self.submission.can_edit())
336		self.assertFalse(self.submission.can_validate())
337		self.assertFalse(self.submission.can_submit())
338
339
340		class AnimalTestCase(PersonMixinTestCase, TestCase):
341		"""Testing Animal Class"""
342
343		# an attribute for PersonMixinTestCase
344		person = Person
345
346		fixtures = [
347		'uid/animal',
348		'uid/dictbreed',
349		'uid/dictcountry',
350		'uid/dictrole',
351		'uid/dictsex',
352		'uid/dictspecie',
353		'uid/ontology',
354		'uid/organization',
355		'uid/publication',
356		'uid/submission',
357		'uid/user'
358		]
359
360		def setUp(self):
361		# create animal
362		self.animal = Animal.objects.get(pk=1)
363		self.submission = self.animal.submission
364
365	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...
366		"""Testing JSON conversion for biosample submission"""
367
368		base_dir = os.path.dirname(os.path.abspath(__file__))
369		file_path = os.path.join(base_dir, "biosample_animal.json")
370		handle = open(file_path)
371		reference = json.load(handle)
372
373		# fix release date to today
374		now = timezone.now()
375		reference['releaseDate'] = str(now.date())
376
377		test = self.animal.to_biosample()
378
379		self.maxDiff = None
380		self.assertEqual(reference, test)
381
382		def test_to_biosample2(self):
383		"""testing json conversion with a biosample_id"""
384
385		# assign a different biosample id
386		reference = "SAMEA4450079"
387		self.animal.biosample_id = reference
388		self.animal.save()
389
390		test = self.animal.to_biosample()
391
392		# asserting biosample_.id in response
393		self.assertEqual(test["accession"], reference)
394
395		def test_relationship(self):
396		"""Testing an animal who has mother and father"""
397
398		animal = Animal.objects.get(pk=3)
399
400		test = animal.to_biosample()
401
402		reference = [
403		{'alias': 'IMAGEA000000001',
404		'relationshipNature': 'child of'},
405		{'alias': 'IMAGEA000000002',
406		'relationshipNature': 'child of'}
407		]
408
409		# asserting relationship
410		self.assertEqual(test['sampleRelationships'], reference)
411
412		# cleaning up relationship (by erasing fk - as crbanim data could be)
413		# erase father relationship
414		animal.father = None
415		animal.save()
416
417		test = animal.to_biosample()
418
419		reference = [
420		{'alias': 'IMAGEA000000002',
421		'relationshipNature': 'child of'},
422		]
423
424		# asserting relationship
425		self.assertEqual(test['sampleRelationships'], reference)
426
427		# cleaning up last relationship
428		animal.mother = None
429		animal.save()
430
431		test = animal.to_biosample()
432
433		reference = []
434
435		# asserting relationship
436		self.assertEqual(test['sampleRelationships'], reference)
437
438		# TODO: test None rendering
439
440		def test_waiting(self):
441		"""Test waiting status"""
442
443		# force submission status
444		self.submission.status = WAITING
445		self.submission.save()
446
447		# test my helper methods
448		self.assertFalse(self.animal.can_delete())
449		self.assertFalse(self.animal.can_edit())
450
451		def test_loaded(self):
452		"""Test loaded status"""
453
454		# force submission status
455		self.submission.status = LOADED
456		self.submission.save()
457
458		# test my helper methods
459		self.assertTrue(self.animal.can_delete())
460		self.assertTrue(self.animal.can_edit())
461
462		def test_submitted(self):
463		"""Test submitted status"""
464
465		# force submission status
466		self.submission.status = SUBMITTED
467		self.submission.save()
468
469		# test my helper methods
470		self.assertFalse(self.animal.can_delete())
471		self.assertFalse(self.animal.can_edit())
472
473		def test_error(self):
474		"""Test error status"""
475
476		# force submission status
477		self.submission.status = ERROR
478		self.submission.save()
479
480		# test my helper methods
481		self.assertTrue(self.animal.can_delete())
482		self.assertTrue(self.animal.can_edit())
483
484		def test_need_revision(self):
485		"""Test need_revision status"""
486
487		# force submission status
488		self.submission.status = NEED_REVISION
489		self.submission.save()
490
491		# test my helper methods
492		self.assertTrue(self.animal.can_delete())
493		self.assertTrue(self.animal.can_edit())
494
495		def test_ready(self):
496		"""Test ready status"""
497
498		# force submission status
499		self.submission.status = READY
500		self.submission.save()
501
502		# test my helper methods
503		self.assertTrue(self.animal.can_delete())
504		self.assertTrue(self.animal.can_edit())
505
506		def test_completed(self):
507		"""Test completed status"""
508
509		# force submission status
510		self.submission.status = COMPLETED
511		self.submission.save()
512
513		# test my helper methods
514		self.assertTrue(self.animal.can_delete())
515		self.assertTrue(self.animal.can_edit())
516
517
518		class SampleTestCase(PersonMixinTestCase, TestCase):
519		"""testing sample class"""
520
521		# an attribute for PersonMixinTestCase
522		person = Person
523
524		fixtures = [
525		'uid/animal',
526		'uid/dictbreed',
527		'uid/dictcountry',
528		'uid/dictrole',
529		'uid/dictsex',
530		'uid/dictspecie',
531		'uid/dictstage',
532		'uid/dictuberon',
533		'uid/ontology',
534		'uid/organization',
535		'uid/publication',
536		'uid/sample',
537		'uid/submission',
538		'uid/user'
539		]
540
541		def setUp(self):
542		# create animal
543		self.animal = Animal.objects.get(pk=1)
544
545		# now get a sample object
546		self.sample = Sample.objects.get(pk=1)
547
548		# set submission
549		self.submission = self.sample.submission
550
551	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...
552		"""Testing JSON conversion for biosample submission"""
553
554		base_dir = os.path.dirname(os.path.abspath(__file__))
555		file_path = os.path.join(base_dir, "biosample_sample.json")
556		handle = open(file_path)
557		reference = json.load(handle)
558
559		# fix release date to today
560		now = timezone.now()
561		reference['releaseDate'] = str(now.date())
562
563		test = self.sample.to_biosample()
564
565		self.maxDiff = None
566		self.assertEqual(reference, test)
567
568		def test_to_biosample2(self):
569		"""testing json conversion with a biosample_id"""
570
571		# assign a different biosample id
572		animal_reference = "SAMEA4450079"
573		self.animal.biosample_id = animal_reference
574		self.animal.save()
575
576		sample_reference = "SAMEA4450075"
577		self.sample.biosample_id = sample_reference
578		self.sample.save()
579
580		test = self.sample.to_biosample()
581
582		# asserting biosample_.id in response
583		self.assertEqual(test["accession"], sample_reference)
584
585		# asserting animal biosample_id in relatioship
586		reference = [{
587		"accession": animal_reference,
588		"relationshipNature": "derived from",
589		}]
590		self.assertEqual(test['sampleRelationships'], reference)
591
592		def test_to_biosample_no_foreign(self):
593		"""Testing JSON conversion for biosample submission without
594		foreign keys"""
595
596		base_dir = os.path.dirname(os.path.abspath(__file__))
597		file_path = os.path.join(base_dir, "biosample_sample.json")
598		handle = open(file_path)
599		reference = json.load(handle)
600
601		# fix release date to today
602		now = timezone.now()
603		reference['releaseDate'] = str(now.date())
604
605		# remove foreign keys from reference
606		for key in ["Organism part", "Developmental stage"]:
607		if key in reference["attributes"]:
608		del(reference["attributes"][key])
609
610		# remove foreing keys from sample object
611		self.sample.organism_part = None
612		self.sample.developmental_stage = None
613		self.sample.save()
614
615		test = self.sample.to_biosample()
616
617		self.maxDiff = None
618		self.assertEqual(reference, test)
619
620		# TODO: test biosample with None rendering
621
622		def test_related_object(self):
623		"""Testing relationship using get_deleted_objects"""
624
625		deletable_objects, model_count, protected = get_deleted_objects(
626		[self.animal])
627
628		self.assertEqual(model_count, {'animals': 2, 'samples': 1})
629
630		def test_uid_report(self):
631		"""testing uid report after a Sample and Animal insert"""
632
633		reference = {
634		'n_of_animals': 3,
635		'n_of_samples': 1,
636		'breeds_total': 1,
637		'breeds_without_ontology': 0,
638		'countries_total': 3,
639		'countries_without_ontology': 0,
640		'species_total': 1,
641		'species_without_ontology': 0,
642		'developmental_stages_total': 1,
643		'developmental_stages_without_ontology': 0,
644		'organism_parts_total': 1,
645		'organism_parts_without_ontology': 0,
646		'physiological_stages_total': 1,
647		'physiological_stages_without_ontology': 0,
648		}
649
650		user = User.objects.get(pk=1)
651
652		test = uid_report(user)
653
654		self.assertEqual(reference, test)
655
656		def test_uid_has_data(self):
657		"""testing db_has_data for uid"""
658
659		self.assertTrue(db_has_data())
660
661		def test_waiting(self):
662		"""Test waiting status"""
663
664		# force submission status
665		self.submission.status = WAITING
666		self.submission.save()
667
668		# test my helper methods
669		self.assertFalse(self.sample.can_delete())
670		self.assertFalse(self.sample.can_edit())
671
672		def test_loaded(self):
673		"""Test loaded status"""
674
675		# force submission status
676		self.submission.status = LOADED
677		self.submission.save()
678
679		# test my helper methods
680		self.assertTrue(self.sample.can_delete())
681		self.assertTrue(self.sample.can_edit())
682
683		def test_submitted(self):
684		"""Test submitted status"""
685
686		# force submission status
687		self.submission.status = SUBMITTED
688		self.submission.save()
689
690		# test my helper methods
691		self.assertFalse(self.sample.can_delete())
692		self.assertFalse(self.sample.can_edit())
693
694		def test_error(self):
695		"""Test error status"""
696
697		# force submission status
698		self.submission.status = ERROR
699		self.submission.save()
700
701		# test my helper methods
702		self.assertTrue(self.sample.can_delete())
703		self.assertTrue(self.sample.can_edit())
704
705		def test_need_revision(self):
706		"""Test need_revision status"""
707
708		# force submission status
709		self.submission.status = NEED_REVISION
710		self.submission.save()
711
712		# test my helper methods
713		self.assertTrue(self.sample.can_delete())
714		self.assertTrue(self.sample.can_edit())
715
716		def test_ready(self):
717		"""Test ready status"""
718
719		# force submission status
720		self.submission.status = READY
721		self.submission.save()
722
723		# test my helper methods
724		self.assertTrue(self.sample.can_delete())
725		self.assertTrue(self.sample.can_edit())
726
727		def test_completed(self):
728		"""Test completed status"""
729
730		# force submission status
731		self.submission.status = COMPLETED
732		self.submission.save()
733
734		# test my helper methods
735		self.assertTrue(self.sample.can_delete())
736		self.assertTrue(self.sample.can_edit())
737
738
739		class PersonTestCase(PersonMixinTestCase, TestCase):
740		"""Testing Person Class"""
741
742		# an attribute for PersonMixinTestCase
743		person = Person
744
745		fixtures = [
746		'uid/dictcountry',
747		'uid/dictrole',
748		'uid/organization',
749		'uid/user'
750		]
751
752		def setUp(self):
753		# get a person
754		self.person = Person.objects.get(user__id=1)
755
756		def test_str(self):
757		"""test a repr method"""
758
759		test = str(self.person)
760		self.assertEqual(
761		test, "Foo Bar (Test organization (United Kingdom))")
762

cnr-ibba / IMAGE-InjectTool

Push — master ( 4f7ee6...646424 )

uid.tests.test_models.SubmissionTestCase.setUp() A

Complexity

Size

Duplication

Importance

Duplication Side-by-Side

Filter issues like