image_app.tests.test_models.SampleTestCase.test_uid_report() - Code Metrics - Inspection of ":twisted_rightwards_arrows: Merge pull request #69..." - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — devel ( 3eb06e...2ff9b7 )

by Paolo

created 2019-10-29 14:31 UTC

SampleTestCase.test_uid_report() A

↳ Parent: image_app.tests.test_models

Complexity

Conditions

Size

Total Lines	25
Code Lines	19

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	19
dl	0
loc	25
rs	9.45
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 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)

    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 = [
        '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_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 = [
        "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
        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 = [
        '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_related_object(self):
        """Testing relationship using get_deleted_objects"""

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

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


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

    # an attribute for PersonMixinTestCase
    person = Person

    fixtures = [
        'image_app/dictcountry',
        'image_app/dictrole',
        'image_app/organization',
        'image_app/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 image_app.models import (Animal, Submission, DictBreed, DictCountry,
22		DictSex, DictSpecie, Sample, uid_report,
23		Person, User, db_has_data)
24
25
26		class DictSexTestCase(TestCase):
27		"""Testing DictSex class"""
28
29		fixtures = [
30		"image_app/dictsex",
31		"image_app/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		'image_app/dictcountry',
86		'image_app/dictspecie',
87		'image_app/ontology',
88		'image_app/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		"image_app/dictcountry",
172		"image_app/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		"image_app/dictbreed",
196		"image_app/dictcountry",
197		"image_app/dictspecie",
198		"image_app/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		'image_app/dictcountry',
244		'image_app/dictrole',
245		'image_app/ontology',
246		'image_app/organization',
247		'image_app/submission',
248		'image_app/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		'image_app/animal',
346		'image_app/dictbreed',
347		'image_app/dictcountry',
348		'image_app/dictrole',
349		'image_app/dictsex',
350		'image_app/dictspecie',
351		'image_app/name',
352		'image_app/ontology',
353		'image_app/organization',
354		'image_app/publication',
355		'image_app/submission',
356		'image_app/user'
357		]
358
359		def setUp(self):
360		# create animal
361		self.animal = Animal.objects.get(pk=1)
362		self.submission = self.animal.submission
363
364	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...
365		"""Testing JSON conversion for biosample submission"""
366
367		base_dir = os.path.dirname(os.path.abspath(__file__))
368		file_path = os.path.join(base_dir, "biosample_animal.json")
369		handle = open(file_path)
370		reference = json.load(handle)
371
372		# fix release date to today
373		now = timezone.now()
374		reference['releaseDate'] = str(now.date())
375
376		test = self.animal.to_biosample()
377
378		self.maxDiff = None
379		self.assertEqual(reference, test)
380
381		def test_to_biosample2(self):
382		"""testing json conversion with a biosample_id"""
383
384		# assign a different biosample id
385		reference = "SAMEA4450079"
386		self.animal.name.biosample_id = reference
387		self.animal.name.save()
388
389		test = self.animal.to_biosample()
390
391		# asserting biosample_.id in response
392		self.assertEqual(test["accession"], reference)
393
394		def test_relationship(self):
395		"""Testing an animal who has mother and father"""
396
397		animal = Animal.objects.get(pk=3)
398
399		test = animal.to_biosample()
400
401		reference = [
402		{'alias': 'IMAGEA000000001',
403		'relationshipNature': 'derived from'},
404		{'alias': 'IMAGEA000000002',
405		'relationshipNature': 'derived from'}
406		]
407
408		# asserting relationship
409		self.assertEqual(test['sampleRelationships'], reference)
410
411		# cleaning up relationship (by erasing fk - as crbanim data could be)
412		# erase father relationship
413		animal.father = None
414		animal.save()
415
416		test = animal.to_biosample()
417
418		reference = [
419		{'alias': 'IMAGEA000000002',
420		'relationshipNature': 'derived from'},
421		]
422
423		# asserting relationship
424		self.assertEqual(test['sampleRelationships'], reference)
425
426		# cleaning up last relationship
427		animal.mother = None
428		animal.save()
429
430		test = animal.to_biosample()
431
432		reference = []
433
434		# asserting relationship
435		self.assertEqual(test['sampleRelationships'], reference)
436
437		# TODO: test None rendering
438
439		def test_waiting(self):
440		"""Test waiting status"""
441
442		# force submission status
443		self.submission.status = WAITING
444		self.submission.save()
445
446		# test my helper methods
447		self.assertFalse(self.animal.can_delete())
448		self.assertFalse(self.animal.can_edit())
449
450		def test_loaded(self):
451		"""Test loaded status"""
452
453		# force submission status
454		self.submission.status = LOADED
455		self.submission.save()
456
457		# test my helper methods
458		self.assertTrue(self.animal.can_delete())
459		self.assertTrue(self.animal.can_edit())
460
461		def test_submitted(self):
462		"""Test submitted status"""
463
464		# force submission status
465		self.submission.status = SUBMITTED
466		self.submission.save()
467
468		# test my helper methods
469		self.assertFalse(self.animal.can_delete())
470		self.assertFalse(self.animal.can_edit())
471
472		def test_error(self):
473		"""Test error status"""
474
475		# force submission status
476		self.submission.status = ERROR
477		self.submission.save()
478
479		# test my helper methods
480		self.assertTrue(self.animal.can_delete())
481		self.assertTrue(self.animal.can_edit())
482
483		def test_need_revision(self):
484		"""Test need_revision status"""
485
486		# force submission status
487		self.submission.status = NEED_REVISION
488		self.submission.save()
489
490		# test my helper methods
491		self.assertTrue(self.animal.can_delete())
492		self.assertTrue(self.animal.can_edit())
493
494		def test_ready(self):
495		"""Test ready status"""
496
497		# force submission status
498		self.submission.status = READY
499		self.submission.save()
500
501		# test my helper methods
502		self.assertTrue(self.animal.can_delete())
503		self.assertTrue(self.animal.can_edit())
504
505		def test_completed(self):
506		"""Test completed status"""
507
508		# force submission status
509		self.submission.status = COMPLETED
510		self.submission.save()
511
512		# test my helper methods
513		self.assertTrue(self.animal.can_delete())
514		self.assertTrue(self.animal.can_edit())
515
516
517		class SampleTestCase(PersonMixinTestCase, TestCase):
518		"""testing sample class"""
519
520		# an attribute for PersonMixinTestCase
521		person = Person
522
523		fixtures = [
524		'image_app/animal',
525		'image_app/dictbreed',
526		'image_app/dictcountry',
527		'image_app/dictrole',
528		'image_app/dictsex',
529		'image_app/dictspecie',
530		'image_app/dictstage',
531		'image_app/dictuberon',
532		'image_app/name',
533		'image_app/ontology',
534		'image_app/organization',
535		'image_app/publication',
536		'image_app/sample',
537		'image_app/submission',
538		'image_app/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.name.biosample_id = animal_reference
574		self.animal.name.save()
575
576		sample_reference = "SAMEA4450075"
577		self.sample.name.biosample_id = sample_reference
578		self.sample.name.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': 1, '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 image_app"""
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		'image_app/dictcountry',
747		'image_app/dictrole',
748		'image_app/organization',
749		'image_app/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

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SampleTestCase.test_uid_report() A

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