Unittest does not run properly

[tomraulet]

Hi there,

First, thank you for your package ;)

I'm unfortunately running on an issue. I've written unit tests, and trying to run them, I'm getting this error :

python -m unittest discover -s tests -p "*_tests.py"
usage: python -m unittest [-h] [--name NAME] [--log-level LOG_LEVEL]
                          [--log-format {json,pretty}] [--log-file LOG_FILE]
                          [--quiet]
                          [--metric-grouping-interval METRIC_GROUPING_INTERVAL]
                          [--debug] [--minimal]
                          {run} ...
python -m unittest: error: argument commands: invalid choice: 'discover' (choose from 'run')
E
======================================================================
ERROR: test_MY_SCRIPT_MY_FUNCTION (MY_SCRIPT_tests.MYSCRIPTSTests)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/miniconda/path/envs/bioinfo_sdk/lib/python3.7/argparse.py", line 1787, in parse_known_args
    namespace, args = self._parse_known_args(args, namespace)
  File "/miniconda/path/envs/bioinfo_sdk/lib/python3.7/argparse.py", line 1975, in _parse_known_args
    positionals_end_index = consume_positionals(start_index)
  File "/miniconda/path/envs/bioinfo_sdk/lib/python3.7/argparse.py", line 1952, in consume_positionals
    take_action(action, args)
  File "/miniconda/path/envs/bioinfo_sdk/lib/python3.7/argparse.py", line 1845, in take_action
    argument_values = self._get_values(action, argument_strings)
  File "/miniconda/path/envs/bioinfo_sdk/lib/python3.7/argparse.py", line 2386, in _get_values
    self._check_value(action, value[0])
  File "/miniconda/path/envs/bioinfo_sdk/lib/python3.7/argparse.py", line 2433, in _check_value
    raise ArgumentError(action, msg % args)
argparse.ArgumentError: argument commands: invalid choice: 'discover' (choose from 'run')

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/my/home/path/tests/MY_SCRIPT_tests.py", line 13, in test_MY_SCRIPT_MY_FUNCTION
    MY_SCRIPT = StatsGtMatrix()
  File "/my/home/path/scripts/MY_SCRIPT.py", line 84, in __init__
    super(StatsGtMatrix, self).__init__()
  File "/miniconda/path/envs/bioinfo_sdk/lib/python3.7/site-packages/basescript/basescript.py", line 29, in __init__
    self.args = self.parser.parse_args(args=args)
  File "/miniconda/path/envs/bioinfo_sdk/lib/python3.7/argparse.py", line 1755, in parse_args
    args, argv = self.parse_known_args(args, namespace)
  File "/miniconda/path/envs/bioinfo_sdk/lib/python3.7/argparse.py", line 1794, in parse_known_args
    self.error(str(err))
  File "/miniconda/path/envs/bioinfo_sdk/lib/python3.7/argparse.py", line 2508, in error
    self.exit(2, _('%(prog)s: error: %(message)s\n') % args)
  File "/miniconda/path/envs/bioinfo_sdk/lib/python3.7/argparse.py", line 2495, in exit
    _sys.exit(status)
SystemExit: 2

----------------------------------------------------------------------
Ran 1 test in 0.005s

FAILED (errors=1)

Here is a sample from my unittest file :

import unittest
from unittest.mock import MagicMock

from scripts.my_script import MyScript, ClassA, ClassB

class MyScriptTests(unittest.TestCase):

    _fake_A_classes = [ClassA('ped1'), ClassA('ped2')]

    _fake_B_class = ClassB('ped1','A','A', False, False)

    def test_my_script_my_function(self):
        my_script = MyScript()
        my_script.A_classes = \
        MagicMock(
            return_value=self._fake_A_classes
        )

        returned_ped = my_script.my_function(self._fake_B_class)

        self.assertEqual('ped1', returned_ped.name)

and from my script :

...
class MyScript(BaseScript):
    # The following specifies the script description so that it be used
    # as a part of the usage doc when --help option is used during running.
    DESC = """
    Usage
    """

    def __init__(self):
        #this set class attribute
        super(MyScript, self).__init__()
        self.custom_array = []

    def define_args(self, parser):
        parser.add_argument('arg_one', type=str, help='input file path')

    def my_function(self, class_a: ClassA):
    # function I'm trying to test
        return class_a
...

It's not my real Classes, path, functions name.

I'm wondering how to run unittest for a basescript script ?

Any help would be appreciated.

Best regards

[jaswanth098]

@foxpowa In your in your test cases you need to pass the subcommand that you need to run by default it would be run, Please check the below snippet

import unittest
from unittest.mock import MagicMock

from scripts.my_script import MyScript, ClassA, ClassB

class MyScriptTests(unittest.TestCase):

    _fake_A_classes = [ClassA('ped1'), ClassA('ped2')]

    _fake_B_class = ClassB('ped1','A','A', False, False)

    def test_my_script_my_function(self):
        my_script = MyScript(["run"]).start() # changed here
        my_script.A_classes = \
        MagicMock(
            return_value=self._fake_A_classes
        )

        returned_ped = my_script.my_function(self._fake_B_class)

        self.assertEqual('ped1', returned_ped.name)

if there is a necessary for passing any other command line arguments you need to take the string and split it using shlex

import shlex

arguments = shlex.split("run --arg_one /root/file")
# Now the arguments variabel should be given to your class intialization
# MyScript(arguments).start()

[tomraulet]

Hi @jaswanth098,
thank you for your reply !

I've tested your snippet like this :

import unittest
from unittest.mock import MagicMock
import shlex

from scripts.my_script import MyScript, ClassA, ClassB

class MyScriptTests(unittest.TestCase):

    _fake_A_classes = [ClassA('ped1'), ClassA('ped2')]

    _fake_B_class = ClassB('ped1','A','A', False, False)

   def get_script_arg(self, args_string: str): # <---------------------------------
        return shlex.split(args_string)

    def test_my_script_my_function(self):
        args = self.get_script_arg("run my_file.txt") # <---------------------------------
        my_script = MyScript(args).start() # <---------------------------------
        my_script.A_classes = \
        MagicMock(
            return_value=self._fake_A_classes
        )

        returned_ped = my_script.my_function(self._fake_B_class)

        self.assertEqual('ped1', returned_ped.name)

and experienced this issue :

python -m unittest discover -s tests -p "*_tests.py"
...
Traceback (most recent call last):
  File "/path/to/repo/tests/my_script_tests.py", line 18, in test_my_script_my_function
    my_script = MyScript(args).start()
TypeError: __init__() takes 1 positional argument but 2 were given

Which seems legit to me, as __init__ function from MyScript take only self as arg.
Or am I missing something else ?

Best regards,

[jaswanth098]

@foxpowa, In that case, you can try something like below

class MyScript:
    def __init__(self, *args, **kwargs):
        # custom code
        super().__init__(*args, **kwargs)

Even custom arguments can be passed to your class
Eg:

class MyScript:
    def __init__(self, custom_args, *args, **kwargs):
        # custom code
        # you can do anything with custom_args but donot pass them to super
        super().__init__(*args, **kwargs)

BaseScript init function has to
NOTE: By the way above is python3 code

[jaswanth098]

@foxpowa And one more thing in the above code after your run function execution is completed if you want to run my_function you need to change as below

import unittest
from unittest.mock import MagicMock
import shlex

from scripts.my_script import MyScript, ClassA, ClassB

class MyScriptTests(unittest.TestCase):

    _fake_A_classes = [ClassA('ped1'), ClassA('ped2')]

    _fake_B_class = ClassB('ped1','A','A', False, False)

   def get_script_arg(self, args_string: str): 
        return shlex.split(args_string)

    def test_my_script_my_function(self):
        args = self.get_script_arg("run my_file.txt")
        my_script = MyScript(args) # <---------------------------------
        my_script.start() # <---------------------------------
        my_script.A_classes = \
        MagicMock(
            return_value=self._fake_A_classes
        )

        returned_ped = my_script.my_function(self._fake_B_class)

        self.assertEqual('ped1', returned_ped.name)

[tomraulet]

Thank you @jaswanth098

Your advice about

class MyScript:
    def __init__(self, *args, **kwargs):
        # custom code
        super().__init__(*args, **kwargs)

worked ;)

For unit test purposes, I don't even need to exec .start() to be able to unittest other function.

Thank you again !