I have a number of functions that I want to test using pytest.
Throughout my testing, I use several input files that I specify at the top of the script:
import pytest
from mymodule.mymodule import *
test_bam = 'bam/test/test_reads_pb.bwa.bam'
sample_mapping_file = 'tests/test_sample_mapping.txt'
pb_errors_file = 'tests/data/pb_test_out.json'
pb_stats = 'tests/data/pb_stats.json'
I am then running several tests using this input:
#pytest.fixture
def options():
o, a = get_args()
return o
#pytest.fixture
def samples_dict():
d = get_sample_mapping(sample_mapping_file)
return d
#pytest.fixture
def read_stats(options, samples_dict):
stats, bam = clean_reads(options, test_bam, samples_dict)
return stats
#pytest.fixture
def clean_bam(options, samples_dict):
stats, bam = clean_reads(options, test_bam, samples_dict)
return bam
def test_errors(options, samples_dict, clean_bam):
"""Test successful return from find_errors"""
sample, genome, chrom = set_genome(options, test_bam, samples_dict)
base_data = find_errors(options, chrom, sample, clean_bam)
assert base_data
I would like to be able to run the same tests on multiple different sets of input, where test_bam, sample_mapping_file, pb_errors_file and pb_stats will all be different.
What's the best way of running the same tests on different sets of input data?
I've played around with using marks to run input-specific functions:
#pytest.mark.pd
def get_pb_data():
"""Read in all pb-related files"""
#pytest.mark.ab
def get_ab_data():
"""Read in all ab-related files"""
But this doesn't work with the fixtures that I have set up (unless I'm missing something).
Any advice would be great!
use pytest parametrize wrapper.
test_bam = 'bam/test/test_reads_pb.bwa.bam'
sample_mapping_file = 'tests/test_sample_mapping.txt'
pb_errors_file = 'tests/data/pb_test_out.json'
pb_stats = 'tests/data/pb_stats.json'
#pytest.mark.parametrize("config", [test_bam, sample_mapping_file, pb_errors_file, pb_stats])
def do_something(config):
#
It will create multiple test on every config test input and assign to config variable.
#pytest.mark.pd doesn't specify an input type, it adds pd marker to the test which can be used when running the tests, for example running all the tests marked with pd
pytest TestsFolder -m pd
If you want to run the tests on different sets of files you can store the files names in a csv for example and read the sets from there in the test parametrized marker
def data_source():
for files in read_files_groups_from_csv():
yield files
#pytest.mark.parametrize('files', data_source())
def test_errors(options, samples_dict, clean_bam, files):
"""for example, files parameter will be ['bam/test/test_reads_pb.bwa.bam', 'tests/test_sample_mapping.txt', 'tests/data/pb_test_out.json', 'tests/data/pb_stats.json']"""
mark.parametrize will run before the fixtures, so you can send files as a parameter to them as well
#pytest.fixture
def options(files):
d = samples_dict(files[1])
return d
If you don't want to rely on index create a class with files names as attributes and return it from data_source().
Related
I have function that looks like this:
def file1_exists(directory):
file1_path = os.path.join(directory, 'file1.json')
return os.path.exists(file1_path)
def file2_exists(directory):
log_path = os.path.join(directory, 'file2.log')
return os.path.exists(file2_path)
def create_file1(directory):
if file1_exists(directory):
return
if not file2_exists(directory):
return
mod_time = os.stat(os.path.join(directory, 'file2.log')).st_mtime
timestamp = {
"creation_timestamp": datetime.datetime.fromtimestamp(mod_time).isoformat()
}
with open(os.path.join(directory, "file1.json"), "w") as f:
json.dump(timestamp, f)
And I need to create a unittest that uses mock files.
The 3 Unittests that I need are:
A mock myfile.json file where I will assert that the function will return None (based on the 1st if statement, since the file exists)
A way to mock-hide the data.txt item in order to assert that the function will return None (based on the second if statement)
A mock myfile.json file where I write the required data and then assert that the return matches the expected outcome.
So far I've tried tests 1. and 2. with variations of this but I've been unsuccessful:
class TestAdminJsonCreation(unittest.TestCase):
#patch('os.path.exists', return_value=True)
def test_existing_admin_json(self):
self.assertNone(postprocess_results.create_json_file())
I've also read about other solutions such as:
Python testing: using a fake file with mock & io.StringIO
But I haven't found a way to successfully do what I need...
You want to be able to provide different return values for each call to os.path.exists. Since you know the order of the calls, you can use side_effects to supply a list of values to be used in order.
class TestAdminJsonCreation(unittest.TestCase):
# No JSON file
#patch('os.path.exists', return_value=True)
def test_existing_admin_json(self):
self.assertNone(postprocess_results.create_json_file())
# JSON file, log file
#patch('os.path.exists', side_effects=[True, False])
def test_existing_admin_json(self):
self.assertNone(postprocess_results.create_json_file())
# JSON file, no log file
#patch('os.path.exists', side_effects=[True, True])
def test_existing_admin_json(self):
...
The third test requires an actual file system, or for you to mock open.
So, I ended up breaking my original function into 3 different functions for easier testing.
The tests are performed by checking what the result of the 'def create_file1' would be when we feed it different return_values from the other 2 functions and when we add valid data.
class TestFile1JsonCreation(unittest.TestCase):
#patch('builtins.open', new_callable=mock_open())
#patch('os.stat')
#patch('file1_exists', return_value=True)
#patch('file2_exists', return_value=False)
def test_existing_file1_json(self, file2_exists, file1_existsmock, stat, mopen):
create_file1('.')
# file1.json should not have been written
mopen.assert_not_called()
#patch('builtins.open', new_callable=mock_open())
#patch('os.stat')
#patch('file1_exists', return_value=False)
#patch('file2_exists', return_value=False)
def test_missing_file2(self, file2_exists, file1_existsmock, stat, mopen):
create_file1('.')
# file1.json should not have been written
mopen.assert_not_called()
#patch('builtins.open', new_callable=mock_open())
#patch('os.stat')
#patch('file1_exists', return_value=False)
#patch('file2_exists', return_value=True)
def test_write_data(self, file2_exists, file1_existsmock, stat, mopen):
class FakeStat:
st_mtime = 1641992788
stat.return_value = FakeStat()
create_file1('.')
# file1.json should have been written
mopen.assert_called_once_with('./file1.json', 'w')
written_data = ''.join(
c[1][0]
for c in mopen().__enter__().write.mock_calls
)
expected_data = {"creation_timestamp": "2022-01-12T13:06:28"}
written_dict_data = json.loads(written_data)
self.assertEqual(written_dict_data, expected_data)
I have following test case:
#pytest.mark.parametrize('env_a, env_b', [(env_a, env_b)], indirect=True) #its existing fixture, cannot modify it
#pytest.mark.parametrize('platform_a, platform_b', [(platform_a, platform_b)])
#pytest.mark.parametrize('resource', [resource1, resource2, resource3, resource4])
def test_compare_items_lists(env_a, env_b, platform_a, platform_b, resource):
path_a = env_a / platform_a / resource / file.txt #move to fixture
path_b = env_b / platform_b / resource / file.txt #move to fixture
list_of_items_in_a = path_a.read() #move to fixture
list_of_items_in_b = path_b.read() #move to fixture
extras_in_a = get_extras(list_of_items_in_a, list_of_items_in_b)
extras_in_b = get_extras(list_of_items_in_b, list_of_items_in_a)
assert not extras_in_a and not extras_in_b
This parameterized test do:
path preparation
data read
data compare
but it's test, so should only compare data.
So I guess fixture(s?) should be created to prepare paths and read files. Then it should be passed to test which should only compare data. But how to do it?
pytest fixtures can be parametrized by setting the params option.
You can extract each marker to a separate fixture.
#pytest.fixture(params=[(platform_a, platform_b)], ids=['platform_a,platform_b'])
def platform(request):
yield request.param
#pytest.fixture(params=[(env_a, env_b)], ids=['env_a,env_b'])
def env(request):
yield request.param
#pytest.fixture(params=[resource1, resource2, resource3, resource4])
def resource(request):
yield request.param
Then use them in another fixture that builds the resource path and returns the contents from it.
#pytest.fixture
def diffable_resources(request, env, platform, resource):
env_a, env_b = env
platform_a, platform_b = platform
resource = resource
path_a = env_a / platform_a / resource / 'file.txt'
path_b = env_b / platform_b / resource / 'file.txt'
yield (path_a.read(), path_b.read())
That way your test can be like:
def test_foo(diffable_resources):
list_of_items_in_a, list_of_items_in_b = diffable_resources
extras_in_a = get_extras(list_of_items_in_a, list_of_items_in_b)
extras_in_b = get_extras(list_of_items_in_b, list_of_items_in_a)
assert not extras_in_a and not extras_in_b
I'd like to add metadata to individual tests in a TestCase that I've written to use Python's unittest framework. The metadata (a string, really) needs to be carried through the testing process and output to an XML file.
Other than remaining with the test the data isn't going to be used by unittest, nor my test code. (I've got a program that will run afterwards, open the XML file, and go looking for the metadata/string).
I've previously used NUnit which allows one to use C# attribute to do this. Specifically, you can put this above a class:
[Property("SmartArrayAOD", -3)]
and then later find that in the XML output.
Is it possible to attach metadata to a test in Python's unittest?
Simple way for just dumping XML
If all you want to do is write stuff to an XML file after every unit test, just add a tearDown method to your test class (e.g. if you have , give it a).
class MyTest(unittest.TestCase):
def tearDown(self):
dump_xml_however_you_do()
def test_whatever(self):
pass
General method
If you want a general way to collect and track metadata from all your tests and return it at the end, try creating an astropy table in your test class's __init__() and adding rows to it during tearDown(), then extracting a reference to your initialized instances of your test class from unittest, like this:
Step 1: set up a re-usable subclass of unittest.TestCase so we don't have to duplicate the table handling
(put all the example code in the same file or copy the imports)
"""
Demonstration of adding and retrieving meta data from python unittest tests
"""
import sys
import warnings
import unittest
import copy
import time
import astropy
import astropy.table
if sys.version_info < (3, 0):
from StringIO import StringIO
else:
from io import StringIO
class DemoTest(unittest.TestCase):
"""
Demonstrates setup of an astropy table in __init__, adding data to the table in tearDown
"""
def __init__(self, *args, **kwargs):
super(DemoTest, self).__init__(*args, **kwargs)
# Storing results in a list made it convenient to aggregate them later
self.results_tables = [astropy.table.Table(
names=('Name', 'Result', 'Time', 'Notes'),
dtype=('S50', 'S30', 'f8', 'S50'),
)]
self.results_tables[0]['Time'].unit = 'ms'
self.results_tables[0]['Time'].format = '0.3e'
self.test_timing_t0 = 0
self.test_timing_t1 = 0
def setUp(self):
self.test_timing_t0 = time.time()
def tearDown(self):
test_name = '.'.join(self.id().split('.')[-2:])
self.test_timing_t1 = time.time()
dt = self.test_timing_t1 - self.test_timing_t0
# Check for errors/failures in order to get state & description. https://stackoverflow.com/a/39606065/6605826
if hasattr(self, '_outcome'): # Python 3.4+
result = self.defaultTestResult() # these 2 methods have no side effects
self._feedErrorsToResult(result, self._outcome.errors)
problem = result.errors or result.failures
state = not problem
if result.errors:
exc_note = result.errors[0][1].split('\n')[-2]
elif result.failures:
exc_note = result.failures[0][1].split('\n')[-2]
else:
exc_note = ''
else: # Python 3.2 - 3.3 or 3.0 - 3.1 and 2.7
# result = getattr(self, '_outcomeForDoCleanups', self._resultForDoCleanups) # DOESN'T WORK RELIABLY
# This is probably only good for python 2.x, meaning python 3.0, 3.1, 3.2, 3.3 are not supported.
exc_type, exc_value, exc_traceback = sys.exc_info()
state = exc_type is None
exc_note = '' if exc_value is None else '{}: {}'.format(exc_type.__name__, exc_value)
# Add a row to the results table
self.results_tables[0].add_row()
self.results_tables[0][-1]['Time'] = dt*1000 # Convert to ms
self.results_tables[0][-1]['Result'] = 'pass' if state else 'FAIL'
with warnings.catch_warnings():
warnings.filterwarnings('ignore', category=astropy.table.StringTruncateWarning)
self.results_tables[0][-1]['Name'] = test_name
self.results_tables[0][-1]['Notes'] = exc_note
Step 2: set up a test manager that extracts metadata
def manage_tests(tests):
"""
Function for running tests and extracting meta data
:param tests: list of classes sub-classed from DemoTest
:return: (TextTestResult, Table, string)
result returned by unittest
astropy table
string: formatted version of the table
"""
table_sorting_columns = ['Result', 'Time']
# Build test suite
suite_list = []
for test in tests:
suite_list.append(unittest.TestLoader().loadTestsFromTestCase(test))
combo_suite = unittest.TestSuite(suite_list)
# Run tests
results = [unittest.TextTestRunner(verbosity=1, stream=StringIO(), failfast=False).run(combo_suite)]
# Catch test classes
suite_tests = []
for suite in suite_list:
suite_tests += suite._tests
# Collect results tables
results_tables = []
for suite_test in suite_tests:
if getattr(suite_test, 'results_tables', [None])[0] is not None:
results_tables += copy.copy(suite_test.results_tables)
# Process tables, if any
if len(results_tables):
a = []
while (len(a) == 0) and len(results_tables):
a = results_tables.pop(0) # Skip empty tables, if any
results_table = a
for rt in results_tables:
if len(rt):
with warnings.catch_warnings():
warnings.filterwarnings('ignore', category=DeprecationWarning)
results_table = astropy.table.join(results_table, rt, join_type='outer')
try:
results_table = results_table.group_by(table_sorting_columns)
except Exception:
print('Error sorting test results table. Columns may not be in the preferred order.')
column_names = list(results_table.columns.keys())
alignments = ['<' if cn == 'Notes' else '>' for cn in column_names]
if len(results_table):
rtf = '\n'.join(results_table.pformat(align=alignments, max_width=-1))
exp_res = sum([result.testsRun - len(result.skipped) for result in results])
if len(results_table) != exp_res:
print('ERROR forming results table. Expected {} results, but table length is {}.'.format(
exp_res, len(results_table),
))
else:
rtf = None
else:
results_table = rtf = None
return results, results_table, rtf
Step 3: Example usage
class FunTest1(DemoTest):
#staticmethod
def test_pass_1():
pass
#staticmethod
def test_fail_1():
assert False, 'Meant to fail for demo 1'
class FunTest2(DemoTest):
#staticmethod
def test_pass_2():
pass
#staticmethod
def test_fail_2():
assert False, 'Meant to fail for demo 2'
res, tab, form = manage_tests([FunTest1, FunTest2])
print(form)
print('')
for r in res:
print(r)
for error in r.errors:
print(error[0])
print(error[1])
Sample results:
$ python unittest_metadata.py
Name Result Time Notes
ms
-------------------- ------ --------- ----------------------------------------
FunTest2.test_fail_2 FAIL 5.412e-02 AssertionError: Meant to fail for demo 2
FunTest1.test_fail_1 FAIL 1.118e-01 AssertionError: Meant to fail for demo 1
FunTest2.test_pass_2 pass 6.199e-03
FunTest1.test_pass_1 pass 6.914e-03
<unittest.runner.TextTestResult run=4 errors=0 failures=2>
Should work with python 2.7 or 3.7. You can add whatever columns you want to the table. You can add parameters and stuff to the table in setUp, tearDown, or even during the tests.
Warnings:
This solution accesses a protected attribute _tests of unittest.suite.TestSuite, which can have unexpected results. This specific implementation works as expected for me in python2.7 and python3.7, but slight variations on how the suite is built and interrogated can easily lead to strange things happening. I couldn't figure out a different way to extract references to the instances of my classes that unittest uses, though.
I'm looking for a pythonic way to compare two files file1 and file2 obtain the differences in form of a patch file and merge their differences into file2. The code should do something like this:
diff file1 file2 > diff.patch
apply the patch diff.patch to file2 // this must be doing something like git apply.
I have seen the following post Implementing Google's DiffMatchPatch API for Python 2/3 on google's python API dif_match_patch to find the differences but I'm looking for a solution to create and apply patch.
First you need to install diff_match_patch.
Here is my code:
import sys
import time
import diff_match_patch as dmp_module
def readFileToText(filePath):
file = open(filePath,"r")
s = ''
for line in file:
s = s + line
return s
dmp = dmp_module.diff_match_patch()
origin = sys.argv[1];
lastest = sys.argv[2];
originText = readFileToText(origin)
lastestText = readFileToText(lastest)
patch = dmp.patch_make(originText, lastestText)
patchText = dmp.patch_toText(patch)
# floder = sys.argv[1]
floder = '/Users/test/Documents/patch'
print(floder)
patchFilePath = floder
patchFile = open(patchFilePath,"w")
patchFile.write(patchText)
print(patchText)
Running webui automated tests with pytest and selenium; having an issue where it appears that my tests are actually running during the collection phase. During this phase, I would expect pytest to be collecting tests - not running them. The end result is I end up with 6 test results where I would expect 2. Now the interesting piece, the 6 results only appear in the HTML report; on the command line I only get the expected 2 lines of output (but it 300 seconds to run those two tests because the tests are literally running multiple times).
tests/test_datadriven.py
#!/usr/bin/env python
from unittestzero import Assert
from pages.home import Home
from pages.administration import RolesTab
from api.api import ApiTasks
import time
import pytest
from data.datadrv import *
class TestRolesDataDriven(object):
scenarios = [scenario1,scenario2]
#pytest.mark.challenge
def test_datadriven_rbac(self, mozwebqa, org, perm_name, resource, verbs, allowed, disallowed):
"""
Perform a data driven test related to role based access controls.
All parameters are fullfilled by the data.
:param org: Organization Name
:param perm_name: Permission name
:param resource: Resource
:param verbs: A tuple of verbs
:returns: Pass or Fail for the test
"""
sysapi = ApiTasks(mozwebqa)
home_page = Home(mozwebqa)
rolestab = RolesTab(mozwebqa)
role_name = "role_%s" % (home_page.random_string())
perm_name = "perm_%s" % (home_page.random_string())
username = "user%s" % home_page.random_string()
email = username + "#example.com"
password = "redhat%s" % (home_page.random_string())
sysapi.create_org(org)
sysapi.create_user(username, password, email)
home_page.login()
home_page.tabs.click_tab("administration_tab")
home_page.tabs.click_tab("roles_administration")
home_page.click_new()
rolestab.create_new_role(role_name)
rolestab.click_role_permissions()
rolestab.role_org(org).click()
rolestab.click_add_permission()
rolestab.select_resource_type(resource)
home_page.click_next()
for v in verbs:
home_page.select('verbs', v)
home_page.click_next()
rolestab.enter_permission_name(perm_name)
rolestab.enter_permission_desc('Added by QE test.')
rolestab.click_permission_done()
rolestab.click_root_roles()
rolestab.click_role_users()
rolestab.role_user(username).add_user()
home_page.header.click_logout()
home_page.login(username, password)
for t in allowed:
Assert.true(t(home_page))
for t in disallowed:
Assert.false(t(home_page))
data/data.py
###
# DO NOT EDIT HERE
###
def pytest_generate_tests(metafunc):
"""
Parse the data provided in scenarios.
"""
idlist = []
argvalues = []
for scenario in metafunc.cls.scenarios:
idlist.append(scenario[0])
items = scenario[1].items()
argnames = [x[0] for x in items]
argvalues.append(([x[1] for x in items]))
metafunc.parametrize(argnames, argvalues, ids=idlist)
###
# EDIT BELOW
# ADD NEW SCENARIOS
###
scenario1 = ('ACME_Manage_Keys', { 'org': 'ACME_Corporation',
'perm_name': 'ManageAcmeCorp',
'resource': 'activation_keys',
'verbs': ('manage_all',),
'allowed': (Base.is_system_tab_visible,
Base.is_new_key_visible,
Base.is_activation_key_name_editable),
'disallowed': (Base.is_dashboard_subs_visible,)})
scenario2 = ('Global_Read_Only', { 'org': 'Global Permissions',
'perm_name': 'ReadOnlyGlobal',
'resource': 'organizations',
'verbs': ('read','create'),
'allowed': (Base.is_organizations_tab_visible,
Base.is_new_organization_visible,
Base.is_new_organization_name_field_editable),
'disallowed': (Base.is_system_tab_visible,
Base.is_new_key_visible)})
Full source is available at github; https://github.com/eanxgeek/katello_challenge
Anyone have any idea what might be going on here? I am using the pytest-mozwebqa plugin, pytests, and selenium.
Thanks!
Check the version of pytest-mozwebqa you have installed. If your installed version is < 0.10 then you must update.
pip-python install --upgrade pytest-mozwebqa
Due to the number of changes in pytest-mozwebqa I strongly encourage you to test first in a python virtualenv.