zooma.tests.test_helpers.TestZooma.test_organism_part() - Code Metrics - Inspection of ":sparkles: Structure ZOOMA calls into InjectTool" - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Pull Request — master (#51)

by Paolo

created 2019-09-26 15:16 UTC

TestZooma.test_organism_part() A

↳ Parent: zooma.tests.test_helpers

Complexity

Conditions

Size

Total Lines	20
Code Lines	15

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	15
dl	0
loc	20
rs	9.65
c	0
b	0
f	0
cc	1
nop	2

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon May  7 16:23:17 2018

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

from unittest.mock import patch

from django.test import TestCase

from image_app.models import (
    DictBreed, DictSpecie, DictCountry, DictUberon, DictDevelStage,
    DictPhysioStage)
from common.constants import OBO_URL, GOOD, HIGH

from ..helpers import (
    annotate_breed, annotate_specie, annotate_country, annotate_uberon,
    annotate_dictdevelstage, annotate_dictphysiostage)


class TestAnnotateBreed(TestCase):
    """A class to test annotate breeds"""

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

    def setUp(self):
        # get a breed object
        self.breed = DictBreed.objects.get(pk=1)

        # erase attributes
        self.breed.mapped_breed = None
        self.breed.mapped_breed_term = None
        self.breed.confidence = None
        self.breed.save()

    @patch("zooma.helpers.use_zooma")
    def test_annotate_breed(self, my_zooma):
        """Testing annotate breed"""

        my_zooma.return_value = {
            'type': 'breed',
            'confidence': 'Good',
            'text': 'Bentheim Black Pied',
            'ontologyTerms': '%s/LBO_0000347' % (OBO_URL)
        }

        # call my method
        annotate_breed(self.breed)

        self.assertTrue(my_zooma.called)

        # ensure annotation
        self.breed.refresh_from_db()

        self.assertEqual(self.breed.mapped_breed, "Bentheim Black Pied")
        self.assertEqual(self.breed.mapped_breed_term, "LBO_0000347")
        self.assertEqual(self.breed.confidence, GOOD)


class TestAnnotateCountry(TestCase):
    """A class to test annotate countries"""

    fixtures = [
        "image_app/dictcountry",
    ]

    def setUp(self):
        # get a country object
        self.country = DictCountry.objects.get(pk=1)

        # erase attributes
        self.country.term = None
        self.country.confidence = None
        self.country.save()

    @patch("zooma.helpers.use_zooma")
    def test_annotate_country(self, my_zooma):
        """Testing annotate country"""

        my_zooma.return_value = {
            'type': 'country',
            'confidence': 'Good',
            'text': 'United Kingdom',
            'ontologyTerms': '%s/NCIT_C17233' % (OBO_URL)}

        # call my method
        annotate_country(self.country)

        self.assertTrue(my_zooma.called)

        # ensure annotation
        self.country.refresh_from_db()

        self.assertEqual(self.country.label, "United Kingdom")
        self.assertEqual(self.country.term, "NCIT_C17233")
        self.assertEqual(self.country.confidence, GOOD)


class TestAnnotateSpecie(TestCase):
    """A class to test annotate species"""

    fixtures = [
        "image_app/dictspecie",
    ]

    def setUp(self):
        # get a specie object
        self.specie = DictSpecie.objects.get(pk=1)

        # erase attributes
        self.specie.term = None
        self.specie.confidence = None
        self.specie.save()

    @patch("zooma.helpers.use_zooma")
    def test_annotate_specie(self, my_zooma):
        """Testing annotate specie"""

        my_zooma.return_value = {
            'type': 'specie',
            'confidence': 'Good',
            'text': 'Sus scrofa',
            'ontologyTerms': '%s/NCBITaxon_9823' % (OBO_URL)
        }

        # call my method
        annotate_specie(self.specie)

        self.assertTrue(my_zooma.called)

        # ensure annotation
        self.specie.refresh_from_db()

        self.assertEqual(self.specie.label, "Sus scrofa")
        self.assertEqual(self.specie.term, "NCBITaxon_9823")
        self.assertEqual(self.specie.confidence, GOOD)


class TestAnnotateUberon(TestCase):
    """A class to test annotate uberon"""

    fixtures = [
        "image_app/dictuberon",
    ]

    def setUp(self):
        # get a specie object
        self.part = DictUberon.objects.get(pk=1)

        # erase attributes
        self.part.term = None
        self.part.confidence = None
        self.part.save()

    @patch("zooma.helpers.use_zooma")
    def test_annotate_uberon(self, my_zooma):
        """Testing annotate uberon"""

        my_zooma.return_value = {
            'type': 'organism part',
            'confidence': 'Good',
            'text': 'semen',
            'ontologyTerms': '%s/UBERON_0001968' % (OBO_URL)
        }

        # call my method
        annotate_uberon(self.part)

        self.assertTrue(my_zooma.called)

        # ensure annotation
        self.part.refresh_from_db()

        self.assertEqual(self.part.label, "semen")
        self.assertEqual(self.part.term, "UBERON_0001968")
        self.assertEqual(self.part.confidence, GOOD)


class TestAnnotateDevelStage(TestCase):
    """A class to test developmental stage"""

    fixtures = [
        "image_app/dictstage",
    ]

    def setUp(self):
        # get a specie object
        self.stage = DictDevelStage.objects.get(pk=1)

        # erase attributes
        self.stage.term = None
        self.stage.confidence = None
        self.stage.save()

    @patch("zooma.helpers.use_zooma")
    def test_annotate_dictdevelstage(self, my_zooma):
        """Testing annotate dictdevelstage"""

        my_zooma.return_value = {
            'confidence': 'High',
            'ontologyTerms': 'http://www.ebi.ac.uk/efo/EFO_0001272',
            'text': 'adult',
            'type': 'developmental stage'
        }

        # call my method
        annotate_dictdevelstage(self.stage)

        self.assertTrue(my_zooma.called)

        # ensure annotation
        self.stage.refresh_from_db()

        self.assertEqual(self.stage.label, "adult")
        self.assertEqual(self.stage.term, "EFO_0001272")
        self.assertEqual(self.stage.confidence, HIGH)


class TestAnnotatePhysioStage(TestCase):
    """A class to test developmental stage"""

    fixtures = [
        "image_app/dictstage",
    ]

    def setUp(self):
        # get a specie object
        self.stage = DictPhysioStage.objects.get(pk=1)

        # erase attributes
        self.stage.term = None
        self.stage.confidence = None
        self.stage.save()

    @patch("zooma.helpers.use_zooma")
    def test_annotate_dictphysiostage(self, my_zooma):
        """Testing annotate dictphysiostage"""

        my_zooma.return_value = {
            'confidence': 'High',
            'ontologyTerms': 'http://purl.obolibrary.org/obo/PATO_0001701',
            'text': 'mature',
            'type': 'developmental stage'
        }

        # call my method
        annotate_dictphysiostage(self.stage)

        self.assertTrue(my_zooma.called)

        # ensure annotation
        self.stage.refresh_from_db()

        self.assertEqual(self.stage.label, "mature")
        self.assertEqual(self.stage.term, "PATO_0001701")
        self.assertEqual(self.stage.confidence, HIGH)


1			#!/usr/bin/env python3
2			# -- coding: utf-8 --
3			"""
4			Created on Mon May 7 16:23:17 2018
5
6			@author: Paolo Cozzi <[email protected]>
7			"""
8
9			from unittest.mock import patch
10
11			from django.test import TestCase
12
13			from image_app.models import (
14			DictBreed, DictSpecie, DictCountry, DictUberon, DictDevelStage,
15			DictPhysioStage)
16			from common.constants import OBO_URL, GOOD, HIGH
17
18			from ..helpers import (
19			annotate_breed, annotate_specie, annotate_country, annotate_uberon,
20			annotate_dictdevelstage, annotate_dictphysiostage)
21
22
23			class TestAnnotateBreed(TestCase):
24			"""A class to test annotate breeds"""
25
26			fixtures = [
27			"image_app/dictbreed",
28			"image_app/dictcountry",
29			"image_app/dictspecie"
30			]
31
32			def setUp(self):
33			# get a breed object
34			self.breed = DictBreed.objects.get(pk=1)
35
36			# erase attributes
37			self.breed.mapped_breed = None
38			self.breed.mapped_breed_term = None
39			self.breed.confidence = None
40			self.breed.save()
41
42			@patch("zooma.helpers.use_zooma")
43			def test_annotate_breed(self, my_zooma):
44			"""Testing annotate breed"""
45
46			my_zooma.return_value = {
47			'type': 'breed',
48			'confidence': 'Good',
49			'text': 'Bentheim Black Pied',
50			'ontologyTerms': '%s/LBO_0000347' % (OBO_URL)
51			}
52
53			# call my method
54			annotate_breed(self.breed)
55
56			self.assertTrue(my_zooma.called)
57
58			# ensure annotation
59			self.breed.refresh_from_db()
60
61			self.assertEqual(self.breed.mapped_breed, "Bentheim Black Pied")
62			self.assertEqual(self.breed.mapped_breed_term, "LBO_0000347")
63			self.assertEqual(self.breed.confidence, GOOD)
64
65
66			class TestAnnotateCountry(TestCase):
67			"""A class to test annotate countries"""
68
69			fixtures = [
70			"image_app/dictcountry",
71			]
72
73			def setUp(self):
74			# get a country object
75			self.country = DictCountry.objects.get(pk=1)
76
77			# erase attributes
78			self.country.term = None
79			self.country.confidence = None
80			self.country.save()
81
82			@patch("zooma.helpers.use_zooma")
83			def test_annotate_country(self, my_zooma):
84			"""Testing annotate country"""
85
86			my_zooma.return_value = {
87			'type': 'country',
88			'confidence': 'Good',
89			'text': 'United Kingdom',
90			'ontologyTerms': '%s/NCIT_C17233' % (OBO_URL)}
91
92			# call my method
93			annotate_country(self.country)
94
95			self.assertTrue(my_zooma.called)
96
97			# ensure annotation
98			self.country.refresh_from_db()
99
100			self.assertEqual(self.country.label, "United Kingdom")
101			self.assertEqual(self.country.term, "NCIT_C17233")
102			self.assertEqual(self.country.confidence, GOOD)
103
104
105			class TestAnnotateSpecie(TestCase):
106			"""A class to test annotate species"""
107
108			fixtures = [
109			"image_app/dictspecie",
110			]
111
112			def setUp(self):
113			# get a specie object
114			self.specie = DictSpecie.objects.get(pk=1)
115
116			# erase attributes
117			self.specie.term = None
118			self.specie.confidence = None
119			self.specie.save()
120
121			@patch("zooma.helpers.use_zooma")
122			def test_annotate_specie(self, my_zooma):
123			"""Testing annotate specie"""
124
125			my_zooma.return_value = {
126			'type': 'specie',
127			'confidence': 'Good',
128			'text': 'Sus scrofa',
129			'ontologyTerms': '%s/NCBITaxon_9823' % (OBO_URL)
130			}
131
132			# call my method
133			annotate_specie(self.specie)
134
135			self.assertTrue(my_zooma.called)
136
137			# ensure annotation
138			self.specie.refresh_from_db()
139
140			self.assertEqual(self.specie.label, "Sus scrofa")
141			self.assertEqual(self.specie.term, "NCBITaxon_9823")
142			self.assertEqual(self.specie.confidence, GOOD)
143
144
145			class TestAnnotateUberon(TestCase):
146			"""A class to test annotate uberon"""
147
148			fixtures = [
149			"image_app/dictuberon",
150			]
151
152			def setUp(self):
153			# get a specie object
154			self.part = DictUberon.objects.get(pk=1)
155
156			# erase attributes
157			self.part.term = None
158			self.part.confidence = None
159			self.part.save()
160
161			@patch("zooma.helpers.use_zooma")
162			def test_annotate_uberon(self, my_zooma):
163			"""Testing annotate uberon"""
164
165			my_zooma.return_value = {
166			'type': 'organism part',
167			'confidence': 'Good',
168			'text': 'semen',
169			'ontologyTerms': '%s/UBERON_0001968' % (OBO_URL)
170			}
171
172			# call my method
173			annotate_uberon(self.part)
174
175			self.assertTrue(my_zooma.called)
176
177			# ensure annotation
178			self.part.refresh_from_db()
179
180			self.assertEqual(self.part.label, "semen")
181			self.assertEqual(self.part.term, "UBERON_0001968")
182			self.assertEqual(self.part.confidence, GOOD)
183
184
185			class TestAnnotateDevelStage(TestCase):
186			"""A class to test developmental stage"""
187
188			fixtures = [
189			"image_app/dictstage",
190			]
191
192			def setUp(self):
193			# get a specie object
194			self.stage = DictDevelStage.objects.get(pk=1)
195
196			# erase attributes
197			self.stage.term = None
198			self.stage.confidence = None
199			self.stage.save()
200
201			@patch("zooma.helpers.use_zooma")
202			def test_annotate_dictdevelstage(self, my_zooma):
203			"""Testing annotate dictdevelstage"""
204
205			my_zooma.return_value = {
206			'confidence': 'High',
207			'ontologyTerms': 'http://www.ebi.ac.uk/efo/EFO_0001272',
208			'text': 'adult',
209			'type': 'developmental stage'
210			}
211
212			# call my method
213			annotate_dictdevelstage(self.stage)
214
215			self.assertTrue(my_zooma.called)
216
217			# ensure annotation
218			self.stage.refresh_from_db()
219
220			self.assertEqual(self.stage.label, "adult")
221			self.assertEqual(self.stage.term, "EFO_0001272")
222			self.assertEqual(self.stage.confidence, HIGH)
223
224
225			class TestAnnotatePhysioStage(TestCase):
226			"""A class to test developmental stage"""
227
228			fixtures = [
229			"image_app/dictstage",
230			]
231
232			def setUp(self):
233			# get a specie object
234			self.stage = DictPhysioStage.objects.get(pk=1)
235
236			# erase attributes
237			self.stage.term = None
238			self.stage.confidence = None
239			self.stage.save()
240
241			@patch("zooma.helpers.use_zooma")
242			def test_annotate_dictphysiostage(self, my_zooma):
243			"""Testing annotate dictphysiostage"""
244
245			my_zooma.return_value = {
246			'confidence': 'High',
247			'ontologyTerms': 'http://purl.obolibrary.org/obo/PATO_0001701',
248			'text': 'mature',
249			'type': 'developmental stage'
250			}
251
252			# call my method
253			annotate_dictphysiostage(self.stage)
254
255			self.assertTrue(my_zooma.called)
256
257			# ensure annotation
258			self.stage.refresh_from_db()
259
260			self.assertEqual(self.stage.label, "mature")
261			self.assertEqual(self.stage.term, "PATO_0001701")
262			self.assertEqual(self.stage.confidence, HIGH)
263

cnr-ibba / IMAGE-InjectTool

Pull Request — master (#51)

TestZooma.test_organism_part() A

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