tests.test_root.RootTest.test_get_team_by_name() - Code Metrics - cnr-ibba/pyUSIrest - Measure and Improve Code Quality continuously with Scrutinizer

tests.test_root.RootTest.test_get_team_by_name() A
last analyzed 2020-01-27 09:04 UTC

↳ Parent: tests.test_root

Complexity

Conditions

Size

Total Lines	14
Code Lines	9

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	9
nop	1
dl	0
loc	14
rs	9.95
c	0
b	0
f	0

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jan 10 11:28:10 2020

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

import os
import json
import types

from collections import defaultdict
from unittest.mock import patch, Mock
from unittest import TestCase

from pyUSIrest.auth import Auth
from pyUSIrest.usi import Root, Team, Submission
from pyUSIrest.settings import ROOT_URL
from pyUSIrest.exceptions import USIConnectionError, USIDataError

from .common import DATA_PATH
from .test_auth import generate_token


class RootTest(TestCase):
    @classmethod
    def setup_class(cls):
        cls.mock_get_patcher = patch('requests.Session.get')
        cls.mock_get = cls.mock_get_patcher.start()

    @classmethod
    def teardown_class(cls):
        cls.mock_get_patcher.stop()

    def setUp(self):
        self.auth = Auth(token=generate_token())

        with open(os.path.join(DATA_PATH, "root.json")) as handle:
            data = json.load(handle)

        self.mock_get.return_value = Mock()
        self.mock_get.return_value.json.return_value = data
        self.mock_get.return_value.status_code = 200

        # get a root object
        self.root = Root(self.auth)

    def test_str(self):
        test = self.root.__str__()
        reference = "Biosample API root at %s" % (ROOT_URL + "/api/")

        self.assertIsInstance(test, str)
        self.assertEqual(reference, test)

    def read_userTeams(self, filename="userTeams.json"):
        with open(os.path.join(DATA_PATH, filename)) as handle:
            data = json.load(handle)

        self.mock_get.return_value = Mock()
        self.mock_get.return_value.json.return_value = data
        self.mock_get.return_value.status_code = 200

    def test_get_user_teams(self):
        # initialize
        self.read_userTeams()

        # get user teams
        teams = self.root.get_user_teams()

        # teams is now a generator
        self.assertIsInstance(teams, types.GeneratorType)
        teams = list(teams)

        self.assertEqual(len(teams), 1)

        team = teams[0]
        self.assertIsInstance(team, Team)

    def test_get_user_no_teams(self):
        """Test for a user having no teams"""

        # initialize
        self.read_userTeams(filename="userNoTeams.json")

        # get user teams (is an empty iterator)
        teams = self.root.get_user_teams()

        self.assertRaises(StopIteration, next, teams)

    def test_get_team_by_name(self):
        # initialize
        self.read_userTeams()

        # get a specific team
        team = self.root.get_team_by_name("subs.dev-team-1")
        self.assertIsInstance(team, Team)

        # get a team I dont't belong to
        self.assertRaisesRegex(
            NameError,
            "team: .* not found",
            self.root.get_team_by_name,
            "subs.dev-team-2")

    def mocked_get_submission(*args, **kwargs):
        class MockResponse:
            def __init__(self, json_data, status_code):
                self.json_data = json_data
                self.status_code = status_code
                self.text = "MockResponse not implemented: %s" % (args[0])

            def json(self):
                return self.json_data

        # this variable will collect all replies
        replies = defaultdict(lambda: MockResponse(None, 404))

        # a custom function to set up replies for link
        def set_reply(url, filename, status=200):

            # referring to the upper replies variable
            nonlocal replies


            # open data file
            with open(os.path.join(DATA_PATH, filename)) as handle:
                data = json.load(handle)

            # track reply to URL
            replies[url] = MockResponse(data, status)

        submission_prefix = "https://submission-test.ebi.ac.uk/api/submissions"
        status_suffix = "submissionStatus"

        status_link1 = "/".join([
            submission_prefix,
            "87e7abda-81a8-4b5e-a1c0-323f7f0a4e43",
            status_suffix])

        status_link2 = "/".join([
            submission_prefix,
            "8b05e7f2-92c1-4651-94cb-9101f351f000",
            status_suffix])

        # --- to test get_submission_by_name
        byname_link = "/".join([
            submission_prefix, "c8c86558-8d3a-4ac5-8638-7aa354291d61"])

        status_link3 = "/".join([
            submission_prefix,
            "c8c86558-8d3a-4ac5-8638-7aa354291d61",
            status_suffix])

        # --- for each url, return a different response
        set_reply(
            'https://submission-test.ebi.ac.uk/api/user/submissions',
            "userSubmissionsPage1.json")

        set_reply(
            'https://submission-test.ebi.ac.uk/api/user/submissions'
            '?page=1&size=1',
            "userSubmissionsPage2.json")

        set_reply(status_link1, "submissionStatus1.json")

        set_reply(status_link2, "submissionStatus2.json")

        set_reply(byname_link, "newSubmission.json")

        set_reply(byname_link, "newSubmission.json")

        set_reply(status_link3, "submissionStatus2.json")

        return replies[args[0]]

    @patch('requests.Session.get', side_effect=mocked_get_submission)
    def test_get_user_submissions(self, mock_get):
        # get userSubmissions
        submissions = self.root.get_user_submissions()

        # submissions is now a generator
        self.assertIsInstance(submissions, types.GeneratorType)

        # convert it into a list
        submissions = list(submissions)
        self.assertEqual(len(submissions), 2)

        for submission in submissions:
            self.assertIsInstance(submission, Submission)

        # testing filtering
        draft = self.root.get_user_submissions(status="Draft")

        # submissions is now a generator
        self.assertIsInstance(draft, types.GeneratorType)

        # convert it into a list
        draft = list(draft)
        self.assertEqual(len(draft), 1)

        team1 = self.root.get_user_submissions(team="subs.test-team-1")

        # submissions is now a generator
        self.assertIsInstance(team1, types.GeneratorType)

        # convert it into a list
        team1 = list(team1)
        self.assertEqual(len(team1), 1)

        completed1 = self.root.get_user_submissions(
            team="subs.dev-team-1", status="Completed")

        # submissions is now a generator
        self.assertIsInstance(completed1, types.GeneratorType)

        # convert it into a list
        completed1 = list(completed1)
        self.assertEqual(len(completed1), 0)

    @patch('requests.Session.get', side_effect=mocked_get_submission)
    def test_get_submission_by_name(self, mock_get):
        submission = self.root.get_submission_by_name(
            submission_name='c8c86558-8d3a-4ac5-8638-7aa354291d61')

        self.assertIsInstance(submission, Submission)

    def test_get_submission_not_found(self):
        """Test get a submission with a wrong name"""

        self.mock_get.return_value = Mock()
        self.mock_get.return_value.json.return_value = ''
        self.mock_get.return_value.status_code = 404

        self.assertRaisesRegex(
            NameError,
            "submission: .* not found",
            self.root.get_submission_by_name,
            submission_name='c8c86558-8d3a-4ac5-8638-7aa354291d61')

        # a different 40x error type
        self.mock_get.return_value = Mock()
        self.mock_get.return_value.text = (
            "The request did not include an Authorization header")
        self.mock_get.return_value.status_code = 401

        self.assertRaisesRegex(
            USIDataError,
            "Error with request",
            self.root.get_submission_by_name,
            submission_name='c8c86558-8d3a-4ac5-8638-7aa354291d61')

        self.mock_get.return_value = Mock()
        self.mock_get.return_value.status_code = 500

        self.assertRaises(
            USIConnectionError,
            self.root.get_submission_by_name,
            submission_name='c8c86558-8d3a-4ac5-8638-7aa354291d61')


1		#!/usr/bin/env python3
2		# -- coding: utf-8 --
3		"""
4		Created on Fri Jan 10 11:28:10 2020
5
6		@author: Paolo Cozzi <[email protected]>
7		"""
8
9		import os
10		import json
11		import types
12
13		from collections import defaultdict
14		from unittest.mock import patch, Mock
15		from unittest import TestCase
16
17		from pyUSIrest.auth import Auth
18		from pyUSIrest.usi import Root, Team, Submission
19		from pyUSIrest.settings import ROOT_URL
20		from pyUSIrest.exceptions import USIConnectionError, USIDataError
21
22		from .common import DATA_PATH
23		from .test_auth import generate_token
24
25
26		class RootTest(TestCase):
27		@classmethod
28		def setup_class(cls):
29		cls.mock_get_patcher = patch('requests.Session.get')
30		cls.mock_get = cls.mock_get_patcher.start()
31
32		@classmethod
33		def teardown_class(cls):
34		cls.mock_get_patcher.stop()
35
36		def setUp(self):
37		self.auth = Auth(token=generate_token())
38
39		with open(os.path.join(DATA_PATH, "root.json")) as handle:
40		data = json.load(handle)
41
42		self.mock_get.return_value = Mock()
43		self.mock_get.return_value.json.return_value = data
44		self.mock_get.return_value.status_code = 200
45
46		# get a root object
47		self.root = Root(self.auth)
48
49		def test_str(self):
50		test = self.root.__str__()
51		reference = "Biosample API root at %s" % (ROOT_URL + "/api/")
52
53		self.assertIsInstance(test, str)
54		self.assertEqual(reference, test)
55
56		def read_userTeams(self, filename="userTeams.json"):
57		with open(os.path.join(DATA_PATH, filename)) as handle:
58		data = json.load(handle)
59
60		self.mock_get.return_value = Mock()
61		self.mock_get.return_value.json.return_value = data
62		self.mock_get.return_value.status_code = 200
63
64		def test_get_user_teams(self):
65		# initialize
66		self.read_userTeams()
67
68		# get user teams
69		teams = self.root.get_user_teams()
70
71		# teams is now a generator
72		self.assertIsInstance(teams, types.GeneratorType)
73		teams = list(teams)
74
75		self.assertEqual(len(teams), 1)
76
77		team = teams[0]
78		self.assertIsInstance(team, Team)
79
80		def test_get_user_no_teams(self):
81		"""Test for a user having no teams"""
82
83		# initialize
84		self.read_userTeams(filename="userNoTeams.json")
85
86		# get user teams (is an empty iterator)
87		teams = self.root.get_user_teams()
88
89		self.assertRaises(StopIteration, next, teams)
90
91		def test_get_team_by_name(self):
92		# initialize
93		self.read_userTeams()
94
95		# get a specific team
96		team = self.root.get_team_by_name("subs.dev-team-1")
97		self.assertIsInstance(team, Team)
98
99		# get a team I dont't belong to
100		self.assertRaisesRegex(
101		NameError,
102		"team: .* not found",
103		self.root.get_team_by_name,
104		"subs.dev-team-2")
105
106		def mocked_get_submission(args, *kwargs):
107		class MockResponse:
108		def __init__(self, json_data, status_code):
109		self.json_data = json_data
110		self.status_code = status_code
111		self.text = "MockResponse not implemented: %s" % (args[0])
112
113		def json(self):
114		return self.json_data
115
116		# this variable will collect all replies
117		replies = defaultdict(lambda: MockResponse(None, 404))
118
119		# a custom function to set up replies for link
120	View Code Duplication	def set_reply(url, filename, status=200):
		0 ignored issues – show Duplication introduced 2020-01-10 10:39 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
121		# referring to the upper replies variable
122		nonlocal replies
		0 ignored issues – show Comprehensibility Best Practice introduced 2020-01-10 10:39 UTC by Report Bug Copy Issue Report The variable `replies` does not seem to be defined. Loading history...
123
124		# open data file
125		with open(os.path.join(DATA_PATH, filename)) as handle:
126		data = json.load(handle)
127
128		# track reply to URL
129		replies[url] = MockResponse(data, status)
130
131		submission_prefix = "https://submission-test.ebi.ac.uk/api/submissions"
132		status_suffix = "submissionStatus"
133
134		status_link1 = "/".join([
135		submission_prefix,
136		"87e7abda-81a8-4b5e-a1c0-323f7f0a4e43",
137		status_suffix])
138
139		status_link2 = "/".join([
140		submission_prefix,
141		"8b05e7f2-92c1-4651-94cb-9101f351f000",
142		status_suffix])
143
144		# --- to test get_submission_by_name
145		byname_link = "/".join([
146		submission_prefix, "c8c86558-8d3a-4ac5-8638-7aa354291d61"])
147
148		status_link3 = "/".join([
149		submission_prefix,
150		"c8c86558-8d3a-4ac5-8638-7aa354291d61",
151		status_suffix])
152
153		# --- for each url, return a different response
154		set_reply(
155		'https://submission-test.ebi.ac.uk/api/user/submissions',
156		"userSubmissionsPage1.json")
157
158		set_reply(
159		'https://submission-test.ebi.ac.uk/api/user/submissions'
160		'?page=1&size=1',
161		"userSubmissionsPage2.json")
162
163		set_reply(status_link1, "submissionStatus1.json")
164
165		set_reply(status_link2, "submissionStatus2.json")
166
167		set_reply(byname_link, "newSubmission.json")
168
169		set_reply(byname_link, "newSubmission.json")
170
171		set_reply(status_link3, "submissionStatus2.json")
172
173		return replies[args[0]]
174
175		@patch('requests.Session.get', side_effect=mocked_get_submission)
176		def test_get_user_submissions(self, mock_get):
177		# get userSubmissions
178		submissions = self.root.get_user_submissions()
179
180		# submissions is now a generator
181		self.assertIsInstance(submissions, types.GeneratorType)
182
183		# convert it into a list
184		submissions = list(submissions)
185		self.assertEqual(len(submissions), 2)
186
187		for submission in submissions:
188		self.assertIsInstance(submission, Submission)
189
190		# testing filtering
191		draft = self.root.get_user_submissions(status="Draft")
192
193		# submissions is now a generator
194		self.assertIsInstance(draft, types.GeneratorType)
195
196		# convert it into a list
197		draft = list(draft)
198		self.assertEqual(len(draft), 1)
199
200		team1 = self.root.get_user_submissions(team="subs.test-team-1")
201
202		# submissions is now a generator
203		self.assertIsInstance(team1, types.GeneratorType)
204
205		# convert it into a list
206		team1 = list(team1)
207		self.assertEqual(len(team1), 1)
208
209		completed1 = self.root.get_user_submissions(
210		team="subs.dev-team-1", status="Completed")
211
212		# submissions is now a generator
213		self.assertIsInstance(completed1, types.GeneratorType)
214
215		# convert it into a list
216		completed1 = list(completed1)
217		self.assertEqual(len(completed1), 0)
218
219		@patch('requests.Session.get', side_effect=mocked_get_submission)
220		def test_get_submission_by_name(self, mock_get):
221		submission = self.root.get_submission_by_name(
222		submission_name='c8c86558-8d3a-4ac5-8638-7aa354291d61')
223
224		self.assertIsInstance(submission, Submission)
225
226		def test_get_submission_not_found(self):
227		"""Test get a submission with a wrong name"""
228
229		self.mock_get.return_value = Mock()
230		self.mock_get.return_value.json.return_value = ''
231		self.mock_get.return_value.status_code = 404
232
233		self.assertRaisesRegex(
234		NameError,
235		"submission: .* not found",
236		self.root.get_submission_by_name,
237		submission_name='c8c86558-8d3a-4ac5-8638-7aa354291d61')
238
239		# a different 40x error type
240		self.mock_get.return_value = Mock()
241		self.mock_get.return_value.text = (
242		"The request did not include an Authorization header")
243		self.mock_get.return_value.status_code = 401
244
245		self.assertRaisesRegex(
246		USIDataError,
247		"Error with request",
248		self.root.get_submission_by_name,
249		submission_name='c8c86558-8d3a-4ac5-8638-7aa354291d61')
250
251		self.mock_get.return_value = Mock()
252		self.mock_get.return_value.status_code = 500
253
254		self.assertRaises(
255		USIConnectionError,
256		self.root.get_submission_by_name,
257		submission_name='c8c86558-8d3a-4ac5-8638-7aa354291d61')
258

cnr-ibba / pyUSIrest

tests.test_root.RootTest.test_get_team_by_name() A last analyzed 2020-01-27 09:04 UTC

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tests.test_root.RootTest.test_get_team_by_name() A
last analyzed 2020-01-27 09:04 UTC