excel.tests.test_helpers.ExcelTemplateReaderTestCase.test_check_columns() - Code Metrics - Inspection of ":recycle: Small changes, minor updates" - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Pull Request — devel (#76)

by Paolo

created 2019-11-14 15:03 UTC

ExcelTemplateReaderTestCase.test_check_columns() A

↳ Parent: excel.tests.test_helpers

Complexity

Conditions

Size

Total Lines	7
Code Lines	5

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	5
dl	0
loc	7
rs	10
c	0
b	0
f	0
cc	1
nop	1

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Jul  2 10:58:42 2019

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

import types
from collections import defaultdict, namedtuple
from unittest.mock import patch, Mock

from django.test import TestCase

from common.tests import (
    WebSocketMixin, DataSourceMixinTestCase as CommonDataSourceMixinTest)
from uid.models import Animal, Sample, Submission
from uid.tests.mixins import (
    DataSourceMixinTestCase, FileReaderMixinTestCase)

from ..helpers import (
    ExcelTemplateReader, upload_template, TEMPLATE_COLUMNS, ExcelImportError)
from .common import BaseExcelMixin


class ExcelTemplateReaderTestCase(
        FileReaderMixinTestCase, DataSourceMixinTestCase, BaseExcelMixin,
        TestCase):
    """Test excel class upload"""

    def setUp(self):
        # calling my base class setup
        super().setUp()

        self.maxDiff = None

        # crate a Excel Template object
        self.reader = ExcelTemplateReader()

        # get filenames for DataSourceMixinTestCase.dst_path
        self.reader.read_file(self.dst_path)

    def test_check_sheets(self):
        # test check sheets method
        status, not_found = self.reader.check_sheets()

        self.assertTrue(status)
        self.assertEqual(not_found, [])

        # override sheet names
        self.reader.sheet_names = []

        # check method
        status, not_found = self.reader.check_sheets()

        self.assertFalse(status)
        self.assertEqual(not_found, ['breed', 'animal', 'sample'])

    def test_check_columns(self):
        # test check sheets method
        status, not_found = self.reader.check_columns()

        self.assertTrue(status)
        self.assertIsInstance(not_found, defaultdict)
        self.assertEqual(len(not_found), 0)

    @patch('xlrd.open_workbook')
    def test_check_columns_issue(self, mock_open):
        """Test a file with columns issues"""

        # creating a mock excel book
        mock_book = Mock()

        # customizing the mock object
        mock_book.sheet_names.return_value = ['breed', 'animal', 'sample']

        # creating a mock sheet for breed
        breed_sheet = Mock()
        breed_sheet.nrows = 1

        # now setting rows to a fake sheet
        breed_sheet.row_values.return_value = []

        # creating a mock sheet for animal
        animal_sheet = Mock()
        animal_sheet.nrows = 1

        # now setting rows to a fake sheet
        animal_sheet.row_values.return_value = []

        # creating a mock sheet for sample
        sample_sheet = Mock()
        sample_sheet.nrows = 1

        # now setting rows to a fake sheet
        sample_sheet.row_values.return_value = []

        # finally setting sheet to the fabe excel object
        mock_book.sheet_by_name.side_effect = [
            breed_sheet, animal_sheet, sample_sheet]

        # returning the mock object when opening a workbook
        mock_open.return_value = mock_book

        # now calling methods
        reader = ExcelTemplateReader()
        reader.read_file("fake file")

        # create the reference error output
        reference = defaultdict(list)
        reference['breed'] += TEMPLATE_COLUMNS['breed']
        reference['animal'] += TEMPLATE_COLUMNS['animal']
        reference['sample'] += TEMPLATE_COLUMNS['sample']

        status, test = reader.check_columns()

        self.assertFalse(status)
        self.assertIsInstance(test, defaultdict)
        self.assertDictEqual(reference, test)

    def check_generator(self, records, length):
        self.assertIsInstance(records, types.GeneratorType)
        self.assertEqual(len(list(records)), length)

    def test_get_breed_records(self):
        """get_breed_records returns an iterator"""

        breeds = self.reader.get_breed_records()
        self.check_generator(breeds, 2)

    def test_get_animal_records(self):
        """get_animal_records returns an iterator"""

        animals = self.reader.get_animal_records()
        self.check_generator(animals, 3)

    def test_get_sample_records(self):
        """get_sample_records returns an iterator"""

        samples = self.reader.get_sample_records()
        self.check_generator(samples, 3)

    def test_check_accuracies(self):
        """Test check accuracies method"""

        check, not_found = self.reader.check_accuracies()

        self.assertTrue(check)
        self.assertEqual(len(not_found), 0)

    @patch.dict("excel.helpers.exceltemplate.TEMPLATE_COLUMNS",
                {'breed': ["a column"]})
    def test_column_not_found(self):
        """Test a column not found raise an informativa exception"""

        # get a generator object
        generator = self.reader.get_sheet_records('breed')

        self.assertRaisesRegex(
            ExcelImportError,
            "Column 'a column' not found in 'breed' sheet",
            list,
            generator)

    @patch('xlrd.open_workbook')
    def test_check_accuracies_issue(self, mock_open):
        """Checking issues with accuracy in excels data"""

        # creating a mock excel book
        mock_book = Mock()

        # customizing the mock object
        mock_book.sheet_names.return_value = ['breed', 'animal', 'sample']

        # creating a mock sheet for animal
        animal_sheet = Mock()
        animal_sheet.nrows = 2

        # creating a fake row of data
        fake_row = ["" for col in TEMPLATE_COLUMNS['animal']]

        # get birth location accuracy index
        accuracy_idx = TEMPLATE_COLUMNS['animal'].index(
            "Birth location accuracy")

        # set a fake accuracy item
        fake_row[accuracy_idx] = "Fake"

        # now setting rows to a fake sheet
        animal_sheet.row_values.side_effect = [
            TEMPLATE_COLUMNS['animal'],
            fake_row]

        # creating a mock sheet for sample
        sample_sheet = Mock()
        sample_sheet.nrows = 2

        # creating a fake row of data
        fake_row = ["" for col in TEMPLATE_COLUMNS['sample']]

        # get birth location accuracy index
        accuracy_idx = TEMPLATE_COLUMNS['sample'].index(
            "Collection place accuracy")

        # set a fake accuracy item
        fake_row[accuracy_idx] = "Fake"

        # now setting rows to a fake sheet
        sample_sheet.row_values.side_effect = [
            TEMPLATE_COLUMNS['sample'],
            fake_row]

        # finally setting sheet to the fabe excel object
        mock_book.sheet_by_name.side_effect = [animal_sheet, sample_sheet]

        # returning the mock object when opening a workbook
        mock_open.return_value = mock_book

        # now calling methods
        reader = ExcelTemplateReader()
        reader.read_file("fake file")

        # define the expected value
        reference = (False, set(["Fake"]))
        test = reader.check_accuracies()

        self.assertEqual(reference, test)

    @patch('excel.helpers.ExcelTemplateReader.get_animal_records')
    def test_species_in_animal_and_breeds_differ(self, my_animal):
        # creating a fake row of data
        fake_row = ["" for col in TEMPLATE_COLUMNS['animal']]

        # get birth location accuracy index
        specie_idx = TEMPLATE_COLUMNS['animal'].index(
            "Species")

        # set a fake specie item
        fake_row[specie_idx] = "Fake"

        # create a namedtuple object
        columns = [col.lower().replace(" ", "_")
                   for col in TEMPLATE_COLUMNS['animal']]
        Record = namedtuple("Animal", columns)
        record = Record._make(fake_row)
        my_animal.return_value = [record]

        # define the expected value
        reference = (False, ["Fake"])
        test = self.reader.check_species_in_animal_sheet()

        self.assertEqual(reference, test)


class ExcelMixin(DataSourceMixinTestCase, WebSocketMixin, BaseExcelMixin):
    """Common tests for Excel classes"""

    # define the method to upload data from. Since the function is now inside
    # a class it becomes a method, specifically a bound method and is supposed
    # to receive the self attribute by default. If we don't want to get the
    # self attribute, we have to declare function as a staticmetho
    # https://stackoverflow.com/a/35322635/4385116
    upload_method = staticmethod(upload_template)

    def test_upload_template(self):
        """Testing uploading and importing data from excel template to UID"""

        # test data loaded
        message = "Template import completed for submission"
        self.upload_datasource(message)

        # check async message called
        notification_message = (
            'Template import completed for submission: 1')
        validation_message = {
            'animals': 3, 'samples': 3,
            'animal_unkn': 3, 'sample_unkn': 3,
            'animal_issues': 0, 'sample_issues': 0}

        # check async message called using WebSocketMixin.check_message
        self.check_message('Loaded', notification_message, validation_message)

    def check_errors(self, my_check, message, notification_message):
        """Common stuff for error in excel template loading"""

        super().check_errors(my_check, message)

        # check async message called using WebSocketMixin.check_message
        self.check_message('Error', notification_message)


class UploadTemplateTestCase(ExcelMixin, TestCase):
    """Test uploading data for Template excel path"""

    @patch("excel.helpers.ExcelTemplateReader.check_species",
           return_value=[False, 'Rainbow trout'])
    def test_upload_template_errors_with_species(self, my_check):
        """Testing importing with data into UID with errors in species"""

        message = "species are not loaded into database"
        notification_message = (
            "Error in importing data: Some species "
            "are not loaded into database: check "
            "for 'Rainbow trout' in your dataset")

        # check template import fails
        self.check_errors(my_check, message, notification_message)

    @patch("excel.helpers.ExcelTemplateReader.check_species_in_animal_sheet",
           return_value=[False, 'Rainbow trout'])
    def test_upload_template_errors_with_species_in_animal(self, my_check):
        """Testing importing with data into UID with errors animal"""

        message = "Some species are not defined in breed sheet"
        notification_message = (
            "Error in importing data: %s: check for 'Rainbow trout' "
            "in your dataset" % message)

        # check template import fails
        self.check_errors(my_check, message, notification_message)

    @patch("excel.helpers.ExcelTemplateReader.check_sex",
           return_value=[False, 'unknown'])
    def test_upload_template_errors_with_sex(self, my_check):
        """Testing importing with data into UID with errors"""

        message = "Not all Sex terms are loaded into database"
        notification_message = (
            "Error in importing data: Not all Sex "
            "terms are loaded into database: check "
            "for 'unknown' in your dataset")

        # check template import fails
        self.check_errors(my_check, message, notification_message)

    @patch("excel.helpers.ExcelTemplateReader.check_accuracies",
           return_value=(False, set(["Fake"])))
    def test_upload_template_errors_with_accuracies(self, my_check):
        """Testing importing with data into UID with errors"""

        message = "Not all accuracy levels are defined in database"
        notification_message = (
            "Error in importing data: Not all accuracy "
            "levels are defined in database: check "
            "for '{'Fake'}' in your dataset")

        # check template import fails
        self.check_errors(my_check, message, notification_message)

    @patch("excel.helpers.ExcelTemplateReader.check_countries",
           return_value=(False, set(["Fake"])))
    def test_upload_template_errors_with_countries(self, my_check):
        """Testing importing with data into UID with errors"""

        message = "Those countries are not loaded in database"
        notification_message = (
            "Error in importing data: %s: check for '{'Fake'}' "
            "in your dataset" % message)

        # check template import fails
        self.check_errors(my_check, message, notification_message)

    @patch("excel.helpers.fill_uid.image_timedelta",
           side_effect=ValueError("message"))
    def test_issue_animal_age_at_collection(self, my_check):
        """Test an issue in animal_age_at_collection column"""

        message = "message"

        notification_message = (
            "Error in importing data: Error for Sample '%s' at "
            "animal_age_at_collection column: %s" % (
                "CS05_1999_IBBACNR_PTP_02.06.1999", message))

        # check template import fails, calling a parent method since
        # database is filled and the base ExcelMixin doesn't work
        CommonDataSourceMixinTest.check_errors(
            self, my_check, message)

        # check async message called using WebSocketMixin.check_message
        self.check_message('Error', notification_message)

    @patch("excel.helpers.fill_uid.parse_image_timedelta",
           side_effect=[[None, None], ValueError("message")])
    def test_issue_sampling_to_preparation_interval(self, my_check):
        """Test an issue in animal_age_at_collection column"""

        message = "message"

        notification_message = (
            "Error in importing data: Error for Sample '%s' at sampling_to_"
            "preparation_interval column: %s" % (
                "VERCH1539971_2010_RegLomBank_PTPLodi_03.09.2011", message))

        # check template import fails, calling a parent method since
        # database is filled and the base ExcelMixin doesn't work
        CommonDataSourceMixinTest.check_errors(
            self, my_check, message)

        # check async message called using WebSocketMixin.check_message
        self.check_message('Error', notification_message)

    @patch('excel.helpers.ExcelTemplateReader.get_animal_records')
    def test_issue_with_relationship(self, my_check):
        """Test a relationship that don't exists"""

        # create a fake record with wrong relationship for testing
        fake_data = [
            'ANIMAL:::ID:::CS05_1999',
            None,
            855,
            "fake father",
            "fake mother",
            'Cinta Senese',
            'Pig',
            'male',
            None,
            None,
            None,
            None,
            'missing geographic information']

        Animal = namedtuple(
            'Animal',
            [column.lower().replace(" ", "_")
             for column in TEMPLATE_COLUMNS['animal']]
        )

        record = Animal._make(fake_data)

        my_check.return_value = [record]

        # ok now test method
        message = "Unknown parent '%s'" % (fake_data[3])
        notification_message = (
            "Error in importing data: %s: check animal '%s' "
            "in your dataset" % (message, fake_data[0]))

        # check template import fails
        self.check_errors(my_check, message, notification_message)


class ReloadTemplateTestCase(ExcelMixin, TestCase):
    """Simulate a template reload case. Load data as in
    UploadTemplateTestCase, then call test which reload the same data"""

    # override used fixtures
    fixtures = [
        'crbanim/auth',
        'excel/dictspecie',
        'excel/uid',
        'excel/submission',
        'excel/speciesynonym'
    ]


class UpdateTemplateTestCase(ExcelMixin, TestCase):

    """Simulate an excel update with the same dataset. Data already
    present will be ignored."""

    # override used fixtures
    fixtures = [
        'crbanim/auth',
        'excel/dictspecie',
        'excel/uid',
        'excel/submission',
        'excel/speciesynonym'
    ]

    def setUp(self):
        # calling my base class setup
        super().setUp()

        # track old submission
        self.old_submission = Submission.objects.get(pk=1)

        # generate a new submission from old submission object
        submission = self.submission
        submission.pk = None
        submission.title = "Updated database"
        submission.datasource_version = "Updated database"
        submission.save()

        # track the new submission
        self.submission = submission

        # remove items from database
        sample = Sample.objects.get(pk=6)
        animal = sample.animal
        animal.delete()

    def test_upload_template(self):
        """Testing uploading and importing data from excel template to UID"""

        # test data loaded
        message = "Template import completed for submission"
        self.upload_datasource(message)

        # check animal and sample
        queryset = Animal.objects.all()
        self.assertEqual(len(queryset), 3, msg="check animal load")

        queryset = Sample.objects.all()
        self.assertEqual(len(queryset), 3, msg="check sample load")

        # assert data are in the proper submission
        self.assertEqual(self.old_submission.animal_set.count(), 2)
        self.assertEqual(self.old_submission.sample_set.count(), 2)

        self.assertEqual(self.submission.animal_set.count(), 1)
        self.assertEqual(self.submission.sample_set.count(), 1)

        # check async message called
        notification_message = (
            'Template import completed for submission: 2')
        validation_message = {
            'animals': 1, 'samples': 1,
            'animal_unkn': 1, 'sample_unkn': 1,
            'animal_issues': 0, 'sample_issues': 0}

        # check async message called using WebSocketMixin.check_message
        self.check_message(
            'Loaded',
            notification_message,
            validation_message,
            pk=self.submission.id)


1		#!/usr/bin/env python3
2		# -- coding: utf-8 --
3		"""
4		Created on Tue Jul 2 10:58:42 2019
5
6		@author: Paolo Cozzi <[email protected]>
7		"""
8
9		import types
10		from collections import defaultdict, namedtuple
11		from unittest.mock import patch, Mock
12
13		from django.test import TestCase
14
15		from common.tests import (
16		WebSocketMixin, DataSourceMixinTestCase as CommonDataSourceMixinTest)
17		from uid.models import Animal, Sample, Submission
18		from uid.tests.mixins import (
19		DataSourceMixinTestCase, FileReaderMixinTestCase)
20
21		from ..helpers import (
22		ExcelTemplateReader, upload_template, TEMPLATE_COLUMNS, ExcelImportError)
23		from .common import BaseExcelMixin
24
25
26		class ExcelTemplateReaderTestCase(
27		FileReaderMixinTestCase, DataSourceMixinTestCase, BaseExcelMixin,
28		TestCase):
29		"""Test excel class upload"""
30
31		def setUp(self):
32		# calling my base class setup
33		super().setUp()
34
35		self.maxDiff = None
36
37		# crate a Excel Template object
38		self.reader = ExcelTemplateReader()
39
40		# get filenames for DataSourceMixinTestCase.dst_path
41		self.reader.read_file(self.dst_path)
42
43		def test_check_sheets(self):
44		# test check sheets method
45		status, not_found = self.reader.check_sheets()
46
47		self.assertTrue(status)
48		self.assertEqual(not_found, [])
49
50		# override sheet names
51		self.reader.sheet_names = []
52
53		# check method
54		status, not_found = self.reader.check_sheets()
55
56		self.assertFalse(status)
57		self.assertEqual(not_found, ['breed', 'animal', 'sample'])
58
59		def test_check_columns(self):
60		# test check sheets method
61		status, not_found = self.reader.check_columns()
62
63		self.assertTrue(status)
64		self.assertIsInstance(not_found, defaultdict)
65		self.assertEqual(len(not_found), 0)
66
67		@patch('xlrd.open_workbook')
68		def test_check_columns_issue(self, mock_open):
69		"""Test a file with columns issues"""
70
71		# creating a mock excel book
72		mock_book = Mock()
73
74		# customizing the mock object
75		mock_book.sheet_names.return_value = ['breed', 'animal', 'sample']
76
77		# creating a mock sheet for breed
78		breed_sheet = Mock()
79		breed_sheet.nrows = 1
80
81		# now setting rows to a fake sheet
82		breed_sheet.row_values.return_value = []
83
84		# creating a mock sheet for animal
85		animal_sheet = Mock()
86		animal_sheet.nrows = 1
87
88		# now setting rows to a fake sheet
89		animal_sheet.row_values.return_value = []
90
91		# creating a mock sheet for sample
92		sample_sheet = Mock()
93		sample_sheet.nrows = 1
94
95		# now setting rows to a fake sheet
96		sample_sheet.row_values.return_value = []
97
98		# finally setting sheet to the fabe excel object
99		mock_book.sheet_by_name.side_effect = [
100		breed_sheet, animal_sheet, sample_sheet]
101
102		# returning the mock object when opening a workbook
103		mock_open.return_value = mock_book
104
105		# now calling methods
106		reader = ExcelTemplateReader()
107		reader.read_file("fake file")
108
109		# create the reference error output
110		reference = defaultdict(list)
111		reference['breed'] += TEMPLATE_COLUMNS['breed']
112		reference['animal'] += TEMPLATE_COLUMNS['animal']
113		reference['sample'] += TEMPLATE_COLUMNS['sample']
114
115		status, test = reader.check_columns()
116
117		self.assertFalse(status)
118		self.assertIsInstance(test, defaultdict)
119		self.assertDictEqual(reference, test)
120
121		def check_generator(self, records, length):
122		self.assertIsInstance(records, types.GeneratorType)
123		self.assertEqual(len(list(records)), length)
124
125		def test_get_breed_records(self):
126		"""get_breed_records returns an iterator"""
127
128		breeds = self.reader.get_breed_records()
129		self.check_generator(breeds, 2)
130
131		def test_get_animal_records(self):
132		"""get_animal_records returns an iterator"""
133
134		animals = self.reader.get_animal_records()
135		self.check_generator(animals, 3)
136
137		def test_get_sample_records(self):
138		"""get_sample_records returns an iterator"""
139
140		samples = self.reader.get_sample_records()
141		self.check_generator(samples, 3)
142
143		def test_check_accuracies(self):
144		"""Test check accuracies method"""
145
146		check, not_found = self.reader.check_accuracies()
147
148		self.assertTrue(check)
149		self.assertEqual(len(not_found), 0)
150
151		@patch.dict("excel.helpers.exceltemplate.TEMPLATE_COLUMNS",
152		{'breed': ["a column"]})
153		def test_column_not_found(self):
154		"""Test a column not found raise an informativa exception"""
155
156		# get a generator object
157		generator = self.reader.get_sheet_records('breed')
158
159		self.assertRaisesRegex(
160		ExcelImportError,
161		"Column 'a column' not found in 'breed' sheet",
162		list,
163		generator)
164
165		@patch('xlrd.open_workbook')
166		def test_check_accuracies_issue(self, mock_open):
167		"""Checking issues with accuracy in excels data"""
168
169		# creating a mock excel book
170		mock_book = Mock()
171
172		# customizing the mock object
173		mock_book.sheet_names.return_value = ['breed', 'animal', 'sample']
174
175		# creating a mock sheet for animal
176		animal_sheet = Mock()
177		animal_sheet.nrows = 2
178
179		# creating a fake row of data
180		fake_row = ["" for col in TEMPLATE_COLUMNS['animal']]
181
182		# get birth location accuracy index
183		accuracy_idx = TEMPLATE_COLUMNS['animal'].index(
184		"Birth location accuracy")
185
186		# set a fake accuracy item
187		fake_row[accuracy_idx] = "Fake"
188
189		# now setting rows to a fake sheet
190		animal_sheet.row_values.side_effect = [
191		TEMPLATE_COLUMNS['animal'],
192		fake_row]
193
194		# creating a mock sheet for sample
195		sample_sheet = Mock()
196		sample_sheet.nrows = 2
197
198		# creating a fake row of data
199		fake_row = ["" for col in TEMPLATE_COLUMNS['sample']]
200
201		# get birth location accuracy index
202		accuracy_idx = TEMPLATE_COLUMNS['sample'].index(
203		"Collection place accuracy")
204
205		# set a fake accuracy item
206		fake_row[accuracy_idx] = "Fake"
207
208		# now setting rows to a fake sheet
209		sample_sheet.row_values.side_effect = [
210		TEMPLATE_COLUMNS['sample'],
211		fake_row]
212
213		# finally setting sheet to the fabe excel object
214		mock_book.sheet_by_name.side_effect = [animal_sheet, sample_sheet]
215
216		# returning the mock object when opening a workbook
217		mock_open.return_value = mock_book
218
219		# now calling methods
220		reader = ExcelTemplateReader()
221		reader.read_file("fake file")
222
223		# define the expected value
224		reference = (False, set(["Fake"]))
225		test = reader.check_accuracies()
226
227		self.assertEqual(reference, test)
228
229		@patch('excel.helpers.ExcelTemplateReader.get_animal_records')
230		def test_species_in_animal_and_breeds_differ(self, my_animal):
231		# creating a fake row of data
232		fake_row = ["" for col in TEMPLATE_COLUMNS['animal']]
233
234		# get birth location accuracy index
235		specie_idx = TEMPLATE_COLUMNS['animal'].index(
236		"Species")
237
238		# set a fake specie item
239		fake_row[specie_idx] = "Fake"
240
241		# create a namedtuple object
242		columns = [col.lower().replace(" ", "_")
243		for col in TEMPLATE_COLUMNS['animal']]
244		Record = namedtuple("Animal", columns)
245		record = Record._make(fake_row)
246		my_animal.return_value = [record]
247
248		# define the expected value
249		reference = (False, ["Fake"])
250		test = self.reader.check_species_in_animal_sheet()
251
252		self.assertEqual(reference, test)
253
254
255		class ExcelMixin(DataSourceMixinTestCase, WebSocketMixin, BaseExcelMixin):
256		"""Common tests for Excel classes"""
257
258		# define the method to upload data from. Since the function is now inside
259		# a class it becomes a method, specifically a bound method and is supposed
260		# to receive the self attribute by default. If we don't want to get the
261		# self attribute, we have to declare function as a staticmetho
262		# https://stackoverflow.com/a/35322635/4385116
263		upload_method = staticmethod(upload_template)
264
265		def test_upload_template(self):
266		"""Testing uploading and importing data from excel template to UID"""
267
268		# test data loaded
269		message = "Template import completed for submission"
270		self.upload_datasource(message)
271
272		# check async message called
273		notification_message = (
274		'Template import completed for submission: 1')
275		validation_message = {
276		'animals': 3, 'samples': 3,
277		'animal_unkn': 3, 'sample_unkn': 3,
278		'animal_issues': 0, 'sample_issues': 0}
279
280		# check async message called using WebSocketMixin.check_message
281		self.check_message('Loaded', notification_message, validation_message)
282
283		def check_errors(self, my_check, message, notification_message):
284		"""Common stuff for error in excel template loading"""
285
286		super().check_errors(my_check, message)
287
288		# check async message called using WebSocketMixin.check_message
289		self.check_message('Error', notification_message)
290
291
292		class UploadTemplateTestCase(ExcelMixin, TestCase):
293		"""Test uploading data for Template excel path"""
294
295		@patch("excel.helpers.ExcelTemplateReader.check_species",
296		return_value=[False, 'Rainbow trout'])
297		def test_upload_template_errors_with_species(self, my_check):
298		"""Testing importing with data into UID with errors in species"""
299
300		message = "species are not loaded into database"
301		notification_message = (
302		"Error in importing data: Some species "
303		"are not loaded into database: check "
304		"for 'Rainbow trout' in your dataset")
305
306		# check template import fails
307		self.check_errors(my_check, message, notification_message)
308
309		@patch("excel.helpers.ExcelTemplateReader.check_species_in_animal_sheet",
310		return_value=[False, 'Rainbow trout'])
311		def test_upload_template_errors_with_species_in_animal(self, my_check):
312		"""Testing importing with data into UID with errors animal"""
313
314		message = "Some species are not defined in breed sheet"
315		notification_message = (
316		"Error in importing data: %s: check for 'Rainbow trout' "
317		"in your dataset" % message)
318
319		# check template import fails
320		self.check_errors(my_check, message, notification_message)
321
322		@patch("excel.helpers.ExcelTemplateReader.check_sex",
323		return_value=[False, 'unknown'])
324		def test_upload_template_errors_with_sex(self, my_check):
325		"""Testing importing with data into UID with errors"""
326
327		message = "Not all Sex terms are loaded into database"
328		notification_message = (
329		"Error in importing data: Not all Sex "
330		"terms are loaded into database: check "
331		"for 'unknown' in your dataset")
332
333		# check template import fails
334		self.check_errors(my_check, message, notification_message)
335
336		@patch("excel.helpers.ExcelTemplateReader.check_accuracies",
337		return_value=(False, set(["Fake"])))
338		def test_upload_template_errors_with_accuracies(self, my_check):
339		"""Testing importing with data into UID with errors"""
340
341		message = "Not all accuracy levels are defined in database"
342		notification_message = (
343		"Error in importing data: Not all accuracy "
344		"levels are defined in database: check "
345		"for '{'Fake'}' in your dataset")
346
347		# check template import fails
348		self.check_errors(my_check, message, notification_message)
349
350		@patch("excel.helpers.ExcelTemplateReader.check_countries",
351		return_value=(False, set(["Fake"])))
352		def test_upload_template_errors_with_countries(self, my_check):
353		"""Testing importing with data into UID with errors"""
354
355		message = "Those countries are not loaded in database"
356		notification_message = (
357		"Error in importing data: %s: check for '{'Fake'}' "
358		"in your dataset" % message)
359
360		# check template import fails
361		self.check_errors(my_check, message, notification_message)
362
363		@patch("excel.helpers.fill_uid.image_timedelta",
364		side_effect=ValueError("message"))
365		def test_issue_animal_age_at_collection(self, my_check):
366		"""Test an issue in animal_age_at_collection column"""
367
368		message = "message"
369
370		notification_message = (
371		"Error in importing data: Error for Sample '%s' at "
372		"animal_age_at_collection column: %s" % (
373		"CS05_1999_IBBACNR_PTP_02.06.1999", message))
374
375		# check template import fails, calling a parent method since
376		# database is filled and the base ExcelMixin doesn't work
377		CommonDataSourceMixinTest.check_errors(
378		self, my_check, message)
379
380		# check async message called using WebSocketMixin.check_message
381		self.check_message('Error', notification_message)
382
383		@patch("excel.helpers.fill_uid.parse_image_timedelta",
384		side_effect=[[None, None], ValueError("message")])
385		def test_issue_sampling_to_preparation_interval(self, my_check):
386		"""Test an issue in animal_age_at_collection column"""
387
388		message = "message"
389
390		notification_message = (
391		"Error in importing data: Error for Sample '%s' at sampling_to_"
392		"preparation_interval column: %s" % (
393		"VERCH1539971_2010_RegLomBank_PTPLodi_03.09.2011", message))
394
395		# check template import fails, calling a parent method since
396		# database is filled and the base ExcelMixin doesn't work
397		CommonDataSourceMixinTest.check_errors(
398		self, my_check, message)
399
400		# check async message called using WebSocketMixin.check_message
401		self.check_message('Error', notification_message)
402
403		@patch('excel.helpers.ExcelTemplateReader.get_animal_records')
404		def test_issue_with_relationship(self, my_check):
405		"""Test a relationship that don't exists"""
406
407		# create a fake record with wrong relationship for testing
408		fake_data = [
409		'ANIMAL:::ID:::CS05_1999',
410		None,
411		855,
412		"fake father",
413		"fake mother",
414		'Cinta Senese',
415		'Pig',
416		'male',
417		None,
418		None,
419		None,
420		None,
421		'missing geographic information']
422
423		Animal = namedtuple(
424		'Animal',
425		[column.lower().replace(" ", "_")
426		for column in TEMPLATE_COLUMNS['animal']]
427		)
428
429		record = Animal._make(fake_data)
430
431		my_check.return_value = [record]
432
433		# ok now test method
434		message = "Unknown parent '%s'" % (fake_data[3])
435		notification_message = (
436		"Error in importing data: %s: check animal '%s' "
437		"in your dataset" % (message, fake_data[0]))
438
439		# check template import fails
440		self.check_errors(my_check, message, notification_message)
441
442
443		class ReloadTemplateTestCase(ExcelMixin, TestCase):
444		"""Simulate a template reload case. Load data as in
445		UploadTemplateTestCase, then call test which reload the same data"""
446
447		# override used fixtures
448		fixtures = [
449		'crbanim/auth',
450		'excel/dictspecie',
451		'excel/uid',
452		'excel/submission',
453		'excel/speciesynonym'
454		]
455
456
457	View Code Duplication	class UpdateTemplateTestCase(ExcelMixin, TestCase):
		0 ignored issues – show Duplication introduced 2019-11-04 18:34 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
458		"""Simulate an excel update with the same dataset. Data already
459		present will be ignored."""
460
461		# override used fixtures
462		fixtures = [
463		'crbanim/auth',
464		'excel/dictspecie',
465		'excel/uid',
466		'excel/submission',
467		'excel/speciesynonym'
468		]
469
470		def setUp(self):
471		# calling my base class setup
472		super().setUp()
473
474		# track old submission
475		self.old_submission = Submission.objects.get(pk=1)
476
477		# generate a new submission from old submission object
478		submission = self.submission
479		submission.pk = None
480		submission.title = "Updated database"
481		submission.datasource_version = "Updated database"
482		submission.save()
483
484		# track the new submission
485		self.submission = submission
486
487		# remove items from database
488		sample = Sample.objects.get(pk=6)
489		animal = sample.animal
490		animal.delete()
491
492		def test_upload_template(self):
493		"""Testing uploading and importing data from excel template to UID"""
494
495		# test data loaded
496		message = "Template import completed for submission"
497		self.upload_datasource(message)
498
499		# check animal and sample
500		queryset = Animal.objects.all()
501		self.assertEqual(len(queryset), 3, msg="check animal load")
502
503		queryset = Sample.objects.all()
504		self.assertEqual(len(queryset), 3, msg="check sample load")
505
506		# assert data are in the proper submission
507		self.assertEqual(self.old_submission.animal_set.count(), 2)
508		self.assertEqual(self.old_submission.sample_set.count(), 2)
509
510		self.assertEqual(self.submission.animal_set.count(), 1)
511		self.assertEqual(self.submission.sample_set.count(), 1)
512
513		# check async message called
514		notification_message = (
515		'Template import completed for submission: 2')
516		validation_message = {
517		'animals': 1, 'samples': 1,
518		'animal_unkn': 1, 'sample_unkn': 1,
519		'animal_issues': 0, 'sample_issues': 0}
520
521		# check async message called using WebSocketMixin.check_message
522		self.check_message(
523		'Loaded',
524		notification_message,
525		validation_message,
526		pk=self.submission.id)
527

cnr-ibba / IMAGE-InjectTool

Pull Request — devel (#76)

ExcelTemplateReaderTestCase.test_check_columns() A

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