biosample.tests.test_tasks.SubmitTestCase.test_submit_patch() - Code Metrics - Inspection of "git checkout master Merge branch 'issue-24'" - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Completed
Push — master ( 836b69...b5edd3 )

by Paolo
created 2019-06-11 09:02 UTC
SubmitTestCase.test_submit_patch() B

↳ Parent: biosample.tests.test_tasks
Complexity

Conditions
Size

Total Lines	61
Code Lines	37
Duplication

Lines	0
Ratio	0 %
Importance

Changes
Metric	Value
eloc	37
dl	0
loc	61
rs	8.9919
c	0
b	0
f	0
cc	2
nop	3
How to fix Long Method

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Oct  9 14:51:13 2018

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

import redis

from billiard.einfo import ExceptionInfo
from pytest import raises
from collections import Counter
from unittest.mock import patch, Mock, PropertyMock
from datetime import timedelta

from celery.exceptions import Retry

from django.test import TestCase
from django.conf import settings
from django.core import mail
from django.utils import timezone

from common.constants import (
    LOADED, ERROR, READY, NEED_REVISION, SUBMITTED, COMPLETED)
from image_app.models import Submission, Name

from ..tasks import SubmitTask, FetchStatusTask
from ..models import ManagedTeam

from .common import SubmitMixin, generate_token


class RedisMixin():
    """A class to setup a test token in redis database"""

    # this will be the token key in redis database
    submission_key = "token:submission:1:test"

    @classmethod
    def setUpClass(cls):
        # calling my base class setup
        super().setUpClass()

        cls.redis = redis.StrictRedis(
            host=settings.REDIS_HOST,
            port=settings.REDIS_PORT,
            db=settings.REDIS_DB)

        # generate a token
        token = generate_token(domains=['subs.test-team-1'])

        # write token to database
        cls.redis.set(cls.submission_key, token, ex=3600)

    @classmethod
    def tearDownClass(cls):
        if cls.redis.exists(cls.submission_key):
            cls.redis.delete(cls.submission_key)

        super().tearDownClass()


class SubmitTestCase(SubmitMixin, RedisMixin, TestCase):

    def setUp(self):
        # call Mixin method
        super().setUp()

        # setting tasks
        self.my_task = SubmitTask()

    @patch('biosample.tasks.send_message_to_websocket')
    @patch('asyncio.get_event_loop')
    def test_submit(self, asyncio_mock, send_message_to_websocket_mock):
        """Test submitting into biosample"""
        tmp = asyncio_mock.return_value
        tmp.run_until_complete = Mock()

        # NOTE that I'm calling the function directly, without delay
        # (AsyncResult). I've patched the time consuming task
        res = self.my_task.run(submission_id=self.submission_id)

        # assert a success with data uploading
        self.assertEqual(res, "success")

        # check submission status and message
        self.submission_obj.refresh_from_db()

        # check submission.state changed
        self.assertEqual(self.submission_obj.status, SUBMITTED)
        self.assertEqual(
            self.submission_obj.message,
            "Waiting for biosample validation")
        self.assertEqual(
            self.submission_obj.biosample_submission_id,
            "new-submission")

        # check name status changed
        qs = Name.objects.filter(status=SUBMITTED)
        self.assertEqual(len(qs), self.n_to_submit)

        # assert called mock objects
        self.assertTrue(self.mock_root.called)
        self.assertTrue(self.my_root.get_team_by_name.called)
        self.assertTrue(self.my_team.create_submission.called)
        self.assertFalse(self.my_root.get_submission_by_name.called)
        self.assertEqual(
            self.new_submission.create_sample.call_count, self.n_to_submit)
        self.assertFalse(self.new_submission.propertymock.called)

        self.assertEqual(asyncio_mock.call_count, 1)
        self.assertEqual(tmp.run_until_complete.call_count, 1)
        self.assertEqual(send_message_to_websocket_mock.call_count, 1)
        send_message_to_websocket_mock.assert_called_with(
            {
                'message': 'Submitted',
                'notification_message': 'Waiting for biosample validation'}, 1)

    # http://docs.celeryproject.org/en/latest/userguide/testing.html#tasks-and-unit-tests
    @patch("biosample.tasks.SubmitTask.retry")
    @patch("biosample.tasks.SubmitTask.submit_biosample")
    def test_submit_retry(self, my_submit, my_retry):
        """Test submissions with retry"""

        # Set a side effect on the patched methods
        # so that they raise the errors we want.
        my_retry.side_effect = Retry()
        my_submit.side_effect = Exception()

        with raises(Retry):
            self.my_task.run(submission_id=1)

        self.assertTrue(my_submit.called)
        self.assertTrue(my_retry.called)

    @patch('biosample.tasks.send_message_to_websocket')
    @patch('asyncio.get_event_loop')
    @patch("biosample.tasks.SubmitTask.retry")
    @patch("biosample.tasks.SubmitTask.submit_biosample")
    def test_issues_with_api(self, my_submit, my_retry, asyncio_mock,
                             send_message_to_websocket_mock):
        """Test errors with submission API"""
        tmp = asyncio_mock.return_value
        tmp.run_until_complete = Mock()

        # Set a side effect on the patched methods
        # so that they raise the errors we want.
        my_retry.side_effect = Retry()
        my_submit.side_effect = ConnectionError()

        # call task. No retries with issues at EBI
        res = self.my_task.run(submission_id=1)

        # assert a success with validation taks
        self.assertEqual(res, "success")

        # check submission status and message
        self.submission_obj.refresh_from_db()

        # this is the message I want
        message = "Errors in EBI API endpoints. Please try again later"

        # check submission.status NOT changed
        self.assertEqual(self.submission_obj.status, READY)
        self.assertIn(
            message,
            self.submission_obj.message)

        # test email sent
        self.assertEqual(len(mail.outbox), 1)

        # read email
        email = mail.outbox[0]

        self.assertEqual(
            "Error in biosample submission 1",
            email.subject)

        self.assertTrue(my_submit.called)
        self.assertFalse(my_retry.called)

        self.assertEqual(asyncio_mock.call_count, 1)
        self.assertEqual(tmp.run_until_complete.call_count, 1)
        self.assertEqual(send_message_to_websocket_mock.call_count, 1)
        send_message_to_websocket_mock.assert_called_with(
            {
                'message': 'Ready',
                'notification_message': 'Errors in EBI API endpoints. '
                                        'Please try again later'}, 1)

    @patch('biosample.tasks.send_message_to_websocket')
    @patch('asyncio.get_event_loop')
    def test_submit_recover(
            self, asyncio_mock, send_message_to_websocket_mock):
        """Test submission recovering"""
        tmp = asyncio_mock.return_value
        tmp.run_until_complete = Mock()

        # update submission object
        self.submission_obj.biosample_submission_id = "test-submission"
        self.submission_obj.save()

        # set one name as uploaded
        name = Name.objects.get(name='ANIMAL:::ID:::132713')
        name.status = SUBMITTED
        name.save()

        # calling submit
        res = self.my_task.run(submission_id=self.submission_id)

        # assert a success with data uploading
        self.assertEqual(res, "success")

        # reload submission
        self.submission_obj.refresh_from_db()

        # check submission.state changed
        self.assertEqual(self.submission_obj.status, SUBMITTED)
        self.assertEqual(
            self.submission_obj.message,
            "Waiting for biosample validation")

        # check name status changed
        qs = Name.objects.filter(status=SUBMITTED)
        self.assertEqual(len(qs), self.n_to_submit)

        # assert called mock objects
        self.assertTrue(self.mock_root.called)
        self.assertFalse(self.my_root.get_team_by_name.called)
        self.assertFalse(self.my_team.create_submission.called)
        self.assertTrue(self.my_root.get_submission_by_name.called)
        # I'm testing submission recover with 1 sample already sent, so:
        self.assertEqual(
            self.my_submission.create_sample.call_count, self.n_to_submit-1)
        self.assertTrue(self.my_submission.propertymock.called)

        self.assertEqual(asyncio_mock.call_count, 1)
        self.assertEqual(tmp.run_until_complete.call_count, 1)
        self.assertEqual(send_message_to_websocket_mock.call_count, 1)
        send_message_to_websocket_mock.assert_called_with(
            {'message': 'Submitted',
             'notification_message': 'Waiting for biosample validation'}, 1)

    @patch('biosample.tasks.send_message_to_websocket')
    @patch('asyncio.get_event_loop')
    def test_submit_no_recover(self, asyncio_mock,
                               send_message_to_websocket_mock):
        """Test submission recovering with a closed submission"""
        tmp = asyncio_mock.return_value
        tmp.run_until_complete = Mock()

        # update submission status
        self.my_submission.propertymock = PropertyMock(
            return_value='Completed')
        type(self.my_submission).status = self.my_submission.propertymock

        # update submission object
        self.submission_obj.biosample_submission_id = "test-submission"
        self.submission_obj.save()

        # calling submit
        res = self.my_task.run(submission_id=self.submission_id)

        # assert a success with data uploading
        self.assertEqual(res, "success")

        # reload submission
        self.submission_obj.refresh_from_db()

        # check submission.state changed
        self.assertEqual(
            self.submission_obj.biosample_submission_id,
            "new-submission")
        self.assertEqual(self.submission_obj.status, SUBMITTED)
        self.assertEqual(
            self.submission_obj.message,
            "Waiting for biosample validation")

        self.assertEqual(asyncio_mock.call_count, 1)
        self.assertEqual(tmp.run_until_complete.call_count, 1)
        self.assertEqual(send_message_to_websocket_mock.call_count, 1)
        send_message_to_websocket_mock.assert_called_with(
            {'message': 'Submitted',
             'notification_message': 'Waiting for biosample validation'}, 1)

        # check name status changed
        qs = Name.objects.filter(status=SUBMITTED)
        self.assertEqual(len(qs), self.n_to_submit)

        # assert called mock objects
        self.assertTrue(self.mock_root.called)
        self.assertTrue(self.my_root.get_team_by_name.called)
        self.assertTrue(self.my_root.get_submission_by_name.called)
        self.assertTrue(self.my_team.create_submission.called)
        self.assertFalse(self.my_submission.create_sample.called)
        self.assertEqual(
            self.new_submission.create_sample.call_count, self.n_to_submit)
        self.assertTrue(self.my_submission.propertymock.called)
        self.assertFalse(self.new_submission.propertymock.called)

    @patch('biosample.tasks.send_message_to_websocket')
    @patch('asyncio.get_event_loop')
    def test_submit_patch(self, asyncio_mock, send_message_to_websocket_mock):
        """Test patching submission"""
        tmp = asyncio_mock.return_value
        tmp.run_until_complete = Mock()

        # creating mock samples
        my_samples = [
            Mock(**{'alias': 'IMAGEA000000001',
                    'title': 'a 4-year old pig organic fed'}),
            Mock(**{'alias': 'IMAGES000000001',
                    'title': 'semen collected when the animal turns to 4'}),
        ]

        # mocking set samples
        self.my_submission.get_samples.return_value = my_samples

        # update submission object
        self.submission_obj.biosample_submission_id = "test-submission"
        self.submission_obj.save()

        # calling submit
        res = self.my_task.run(submission_id=self.submission_id)

        # assert a success with data uploading
        self.assertEqual(res, "success")

        # reload submission
        self.submission_obj.refresh_from_db()

        # check submission.state changed
        self.assertEqual(self.submission_obj.status, SUBMITTED)
        self.assertEqual(
            self.submission_obj.message,
            "Waiting for biosample validation")

        self.assertEqual(asyncio_mock.call_count, 1)
        self.assertEqual(tmp.run_until_complete.call_count, 1)
        self.assertEqual(send_message_to_websocket_mock.call_count, 1)
        send_message_to_websocket_mock.assert_called_with(
            {'message': 'Submitted',
             'notification_message': 'Waiting for biosample validation'}, 1)

        # check name status changed
        qs = Name.objects.filter(status=SUBMITTED)
        self.assertEqual(len(qs), self.n_to_submit)

        # assert called mock objects
        self.assertTrue(self.mock_root.called)
        self.assertFalse(self.my_root.get_team_by_name.called)
        self.assertFalse(self.my_team.create_submission.called)
        self.assertTrue(self.my_root.get_submission_by_name.called)
        # I've patched 2 samples in this test, so:
        self.assertEqual(
            self.my_submission.create_sample.call_count, 2)
        self.assertTrue(self.my_submission.propertymock.called)

        # testing patch
        for sample in my_samples:
            self.assertTrue(sample.patch.called)

    @patch('biosample.tasks.send_message_to_websocket')

    @patch('asyncio.get_event_loop')
    def test_on_failure(self, asyncio_mock, send_message_to_websocket_mock):
        """Testing on failure methods"""
        tmp = asyncio_mock.return_value
        tmp.run_until_complete = Mock()

        exc = Exception("Test")
        task_id = "test_task_id"
        args = [self.submission_id]
        kwargs = {}
        einfo = ExceptionInfo

        # call on_failure method
        self.my_task.on_failure(exc, task_id, args, kwargs, einfo)

        # check submission status and message
        submission = Submission.objects.get(pk=self.submission_id)

        # check submission.state changed
        self.assertEqual(submission.status, ERROR)
        self.assertEqual(
            submission.message,
            "Error in biosample submission: Test")

        # test email sent
        self.assertEqual(len(mail.outbox), 1)

        # read email
        email = mail.outbox[0]

        self.assertEqual(
            "Error in biosample submission %s" % self.submission_id,
            email.subject)
        self.assertEqual(asyncio_mock.call_count, 1)
        self.assertEqual(tmp.run_until_complete.call_count, 1)
        self.assertEqual(send_message_to_websocket_mock.call_count, 1)
        send_message_to_websocket_mock.assert_called_with(
            {'message': 'Error',
             'notification_message': 'Error in biosample submission: Test'}, 1)

    @patch('biosample.tasks.send_message_to_websocket')
    @patch('asyncio.get_event_loop')
    def test_token_expired(self, asyncio_mock, send_message_to_websocket_mock):
        """Testing token expiring during a submission"""
        tmp = asyncio_mock.return_value
        tmp.run_until_complete = Mock()

        # simulating a token expiring during a submission
        self.new_submission.create_sample.side_effect = RuntimeError(
                "Your token is expired")

        # calling task
        res = self.my_task.run(submission_id=self.submission_id)

        # assert a success with data uploading
        self.assertEqual(res, "success")

        # check submission status and message
        self.submission_obj.refresh_from_db()

        # check submission.state return to ready (if it was valid before,
        # should be valid again, if rules are the same)
        self.assertEqual(self.submission_obj.status, READY)
        self.assertEqual(
            self.submission_obj.message,
            "Your token is expired: please submit again to resume submission")
        self.assertEqual(
            self.submission_obj.biosample_submission_id,
            "new-submission")
        self.assertEqual(asyncio_mock.call_count, 1)
        self.assertEqual(tmp.run_until_complete.call_count, 1)
        self.assertEqual(send_message_to_websocket_mock.call_count, 1)
        send_message_to_websocket_mock.assert_called_with(
            {'message': 'Ready',
             'notification_message': 'Your token is expired: please submit '
                                     'again to resume submission'}, 1)

        # check name status unchanged (counts are equal to setUp name queryset)
        qs = Name.objects.filter(status=READY)
        self.assertEqual(len(qs), self.name_qs.count())

        # test email sent
        self.assertEqual(len(mail.outbox), 1)

        # read email
        email = mail.outbox[0]

        self.assertEqual(
            "Error in biosample submission 1",
            email.subject)

        # assert called mock objects
        self.assertTrue(self.mock_root.called)
        self.assertTrue(self.my_root.get_team_by_name.called)
        self.assertTrue(self.my_team.create_submission.called)
        self.assertFalse(self.my_root.get_submission_by_name.called)

        # is called once. With the first call, I got an exception and I
        # dont't do the second request
        self.assertEqual(self.new_submission.create_sample.call_count, 1)
        self.assertFalse(self.new_submission.propertymock.called)


class UpdateSubmissionTestCase(SubmitMixin, RedisMixin, TestCase):
    """Test a submission for an already completed submission which
    receives one update, is valid and need to be updated in biosample"""

    def setUp(self):
        # call Mixin method
        super().setUp()

        # get all name objects and set status to completed
        self.name_qs.update(status=COMPLETED)

        # Now get first animal and set status to ready. Take also its sample
        # and assign a fake biosample id
        self.animal_name = Name.objects.get(pk=3)
        self.sample_name = Name.objects.get(pk=4)

        # update name objects. In this case, animal was modified
        self.animal_name.status = READY
        self.animal_name.save()

        # sample is supposed to be submitted with success
        self.sample_name.status = COMPLETED
        self.sample_name.biosample_id = "FAKES123456"
        self.sample_name.save()

        # setting tasks
        self.my_task = SubmitTask()

    @patch('biosample.tasks.send_message_to_websocket')
    @patch('asyncio.get_event_loop')
    def test_submit(self, asyncio_mock, send_message_to_websocket_mock):
        """Test submitting into biosample"""
        tmp = asyncio_mock.return_value
        tmp.run_until_complete = Mock()

        res = self.my_task.run(submission_id=self.submission_id)

        # assert a success with data uploading
        self.assertEqual(res, "success")

        # check submission status and message
        self.submission_obj.refresh_from_db()

        # check submission.state changed
        self.assertEqual(self.submission_obj.status, SUBMITTED)
        self.assertEqual(
            self.submission_obj.message,
            "Waiting for biosample validation")
        self.assertEqual(
            self.submission_obj.biosample_submission_id,
            "new-submission")
        self.assertEqual(asyncio_mock.call_count, 1)
        self.assertEqual(tmp.run_until_complete.call_count, 1)
        self.assertEqual(send_message_to_websocket_mock.call_count, 1)
        send_message_to_websocket_mock.assert_called_with(
            {'message': 'Submitted',
             'notification_message': 'Waiting for biosample validation'}, 1)

        # check name status changed for animal
        self.animal_name.refresh_from_db()
        self.assertEqual(self.animal_name.status, SUBMITTED)

        # check that sample status is unchanged
        self.sample_name.refresh_from_db()
        self.assertEqual(self.sample_name.status, COMPLETED)

        # assert that all statuses (except one) remain unchanged
        qs = Name.objects.filter(status=COMPLETED)
        self.assertEqual(qs.count(), self.name_qs.count()-1)

        # assert called mock objects
        self.assertTrue(self.mock_root.called)
        self.assertTrue(self.my_root.get_team_by_name.called)
        self.assertTrue(self.my_team.create_submission.called)
        self.assertFalse(self.my_root.get_submission_by_name.called)
        self.assertEqual(self.new_submission.create_sample.call_count, 1)
        self.assertFalse(self.new_submission.propertymock.called)


class FetchMixin():
    """Mixin for fetching status"""

    fixtures = [
        'biosample/account',
        'biosample/managedteam',
        'image_app/dictcountry',
        'image_app/dictrole',
        'image_app/organization',
        'image_app/submission',
        'image_app/user'
    ]

    @classmethod
    def setUpClass(cls):
        # calling my base class setup
        super().setUpClass()

        unmanaged = ManagedTeam.objects.get(pk=2)
        unmanaged.delete()

        # starting mocked objects
        cls.mock_root_patcher = patch('pyUSIrest.client.Root')
        cls.mock_root = cls.mock_root_patcher.start()

        cls.mock_auth_patcher = patch('biosample.helpers.Auth')
        cls.mock_auth = cls.mock_auth_patcher.start()

    @classmethod
    def tearDownClass(cls):
        cls.mock_root_patcher.stop()
        cls.mock_auth_patcher.stop()

        # calling base method
        super().tearDownClass()

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

        # get a submission object
        self.submission_obj = Submission.objects.get(pk=1)

        # set a status which I can fetch_status
        self.submission_obj.status = SUBMITTED
        self.submission_obj.biosample_submission_id = "test-fetch"
        self.submission_obj.save()

        # set status for names, like submittask does. Only sample not unknown
        # are submitted
        self.name_qs = Name.objects.exclude(name__contains="unknown")
        self.name_qs.update(status=SUBMITTED)

        # count number of names in UID for such submission (exclude
        # unknown animals)
        self.n_to_submit = self.name_qs.count()

        # track submission ID
        self.submission_obj_id = self.submission_obj.id

        # start root object
        self.my_root = self.mock_root.return_value

        # define my task
        self.my_task = FetchStatusTask()

        # change lock_id (useful when running test during cron)
        self.my_task.lock_id = "test-FetchStatusTask"

    def common_tests(self, my_submission):
        # passing submission to Mocked Root
        self.my_root.get_submission_by_name.return_value = my_submission

        # NOTE that I'm calling the function directly, without delay
        # (AsyncResult). I've patched the time consuming task
        res = self.my_task.run()

        # assert a success with data uploading
        self.assertEqual(res, "success")

        self.assertTrue(self.mock_auth.called)
        self.assertTrue(self.mock_root.called)
        self.assertTrue(self.my_root.get_submission_by_name.called)


class FetchCompletedTestCase(FetchMixin, TestCase):
    """a completed submission with two samples"""

    fixtures = [
        'biosample/account',
        'biosample/managedteam',
        'image_app/animal',
        'image_app/dictbreed',
        'image_app/dictcountry',
        'image_app/dictrole',
        'image_app/dictsex',
        'image_app/dictspecie',
        'image_app/dictstage',
        'image_app/dictuberon',
        'image_app/name',
        'image_app/organization',
        'image_app/publication',
        'image_app/sample',
        'image_app/submission',
        'image_app/user'
    ]

    @patch('biosample.tasks.send_message_to_websocket')
    @patch('asyncio.get_event_loop')
    def test_fetch_status(self, asyncio_mock, send_message_to_websocket_mock):
        # a completed submission with two samples
        tmp = asyncio_mock.return_value
        tmp.run_until_complete = Mock()
        my_submission = Mock()
        my_submission.name = "test-fetch"
        my_submission.status = 'Completed'

        # Add samples
        my_sample1 = Mock()
        my_sample1.name = "test-animal"
        my_sample1.alias = "IMAGEA000000001"
        my_sample1.accession = "SAMEA0000001"
        my_sample2 = Mock()
        my_sample2.name = "test-sample"
        my_sample2.alias = "IMAGES000000001"
        my_sample2.accession = "SAMEA0000002"
        my_submission.get_samples.return_value = [my_sample1, my_sample2]

        # assert task and mock methods called
        self.common_tests(my_submission)

        # assert status for submissions
        self.submission_obj.refresh_from_db()
        self.assertEqual(self.submission_obj.status, COMPLETED)

        self.assertEqual(asyncio_mock.call_count, 1)
        self.assertEqual(tmp.run_until_complete.call_count, 1)
        self.assertEqual(send_message_to_websocket_mock.call_count, 1)
        send_message_to_websocket_mock.assert_called_with(
            {'message': 'Completed',
             'notification_message': 'Successful submission into biosample'},
            1)

        # check name status changed
        qs = Name.objects.filter(status=COMPLETED)
        self.assertEqual(len(qs), 2)

        # fetch two name objects
        name = Name.objects.get(name='ANIMAL:::ID:::132713')
        self.assertEqual(name.biosample_id, "SAMEA0000001")

        name = Name.objects.get(name='Siems_0722_393449')
        self.assertEqual(name.biosample_id, "SAMEA0000002")

    def test_fetch_status_no_accession(self):
        # a completed submission with two samples
        my_submission = Mock()
        my_submission.name = "test-fetch"
        my_submission.status = 'Submitted'

        # Add samples
        my_sample1 = Mock()
        my_sample1.name = "test-animal"
        my_sample1.alias = "IMAGEA000000001"
        my_sample1.accession = None
        my_sample2 = Mock()
        my_sample2.name = "test-sample"
        my_sample2.alias = "IMAGES000000001"
        my_sample2.accession = None
        my_submission.get_samples.return_value = [my_sample1, my_sample2]

        # assert task and mock methods called
        self.common_tests(my_submission)

        # assert status for submissions
        self.submission_obj.refresh_from_db()
        self.assertEqual(self.submission_obj.status, SUBMITTED)

        # check name status changed
        qs = Name.objects.filter(status=SUBMITTED)
        self.assertEqual(len(qs), self.n_to_submit)

    # http://docs.celeryproject.org/en/latest/userguide/testing.html#tasks-and-unit-tests
    @patch("biosample.tasks.FetchStatusTask.retry")
    @patch("biosample.tasks.FetchStatusTask.fetch_queryset")
    def test_fetch_status_retry(self, my_fetch, my_retry):
        """Test fetch status with retry"""

        # Set a side effect on the patched methods
        # so that they raise the errors we want.
        my_retry.side_effect = Retry()
        my_fetch.side_effect = ConnectionError()

        with raises(Retry):
            self.my_task.run()

        self.assertTrue(my_fetch.called)
        self.assertTrue(my_retry.called)

    # Test a non blocking instance
    @patch("biosample.tasks.FetchStatusTask.fetch_queryset")
    @patch("redis.lock.Lock.acquire", return_value=False)
    def test_fetch_status_nb(self, my_lock, my_fetch):
        """Test FetchSTatus while a lock is present"""

        res = self.my_task.run()

        # assert database is locked
        self.assertEqual(res, "%s already running!" % (self.my_task.name))
        self.assertFalse(my_fetch.called)


class FetchNotInDBTestCase(FetchMixin, TestCase):
    """A submission not in db"""

    def test_fetch_status(self):
        # mocking submissions. A submission not in db
        my_submission = Mock()
        my_submission.name = "not-present-in-db"

        # assert task and mock methods called
        self.common_tests(my_submission)


class FetchWithErrorsTestCase(FetchMixin, TestCase):
    """Test a submission with errors for biosample"""

    fixtures = [
        'biosample/account',
        'biosample/managedteam',
        'image_app/animal',
        'image_app/dictbreed',
        'image_app/dictcountry',
        'image_app/dictrole',
        'image_app/dictsex',
        'image_app/dictspecie',
        'image_app/dictstage',
        'image_app/dictuberon',
        'image_app/name',
        'image_app/organization',
        'image_app/publication',
        'image_app/sample',
        'image_app/submission',
        'image_app/user'
    ]

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

        # a draft submission with errors
        my_submission = Mock()
        my_submission.name = "test-fetch"
        my_submission.status = 'Draft'
        my_submission.has_errors.return_value = Counter({True: 1, False: 1})
        my_submission.get_status.return_value = Counter({'Complete': 2})

        # Add samples. Suppose that first failed, second is ok
        my_validation_result1 = Mock()
        my_validation_result1.errorMessages = {
            'Ena': [
                'a sample message',
            ]
        }

        my_sample1 = Mock()
        my_sample1.name = "test-animal"
        my_sample1.alias = "IMAGEA000000001"
        my_sample1.has_errors.return_value = True
        my_sample1.get_validation_result.return_value = my_validation_result1

        # sample2 is ok
        my_validation_result2 = Mock()
        my_validation_result2.errorMessages = None

        my_sample2 = Mock()
        my_sample2.name = "test-sample"
        my_sample2.alias = "IMAGES000000001"
        my_sample2.has_errors.return_value = False
        my_sample2.get_validation_result.return_value = my_validation_result2

        # simulate that IMAGEA000000001 has errors
        my_submission.get_samples.return_value = [my_sample1, my_sample2]

        # track objects
        self.my_submission = my_submission
        self.my_validation_result1 = my_validation_result1
        self.my_validation_result2 = my_validation_result2
        self.my_sample1 = my_sample1
        self.my_sample2 = my_sample2

        # track names
        self.animal_name = Name.objects.get(pk=3)
        self.sample_name = Name.objects.get(pk=4)

    def common_tests(self):
        # assert task and mock methods called
        super().common_tests(self.my_submission)

        # assert custom mock attributes called
        self.assertTrue(self.my_sample1.has_errors.called)
        self.assertTrue(self.my_sample1.get_validation_result.called)

        # if sample has no errors, no all methods will be called
        self.assertTrue(self.my_sample2.has_errors.called)
        self.assertFalse(self.my_sample2.get_validation_result.called)

    @patch('biosample.tasks.send_message_to_websocket')
    @patch('asyncio.get_event_loop')
    def test_fetch_status(self, asyncio_mock, send_message_to_websocket_mock):
        tmp = asyncio_mock.return_value
        tmp.run_until_complete = Mock()
        # assert task and mock methods called
        self.common_tests()

        # assert submission status
        self.submission_obj.refresh_from_db()
        self.assertEqual(self.submission_obj.status, NEED_REVISION)

        # check name status changed only for animal (not sample)
        self.animal_name.refresh_from_db()
        self.assertEqual(self.animal_name.status, NEED_REVISION)

        self.sample_name.refresh_from_db()
        self.assertEqual(self.sample_name.status, SUBMITTED)

        self.assertEqual(asyncio_mock.call_count, 1)
        self.assertEqual(tmp.run_until_complete.call_count, 1)
        self.assertEqual(send_message_to_websocket_mock.call_count, 1)
        send_message_to_websocket_mock.assert_called_with(
            {'message': 'Need Revision',
             'notification_message': 'Error in biosample submission'}, 1)

    @patch('biosample.tasks.send_message_to_websocket')
    @patch('asyncio.get_event_loop')
    def test_email_sent(self, asyncio_mock, send_message_to_websocket_mock):
        tmp = asyncio_mock.return_value
        tmp.run_until_complete = Mock()
        # assert task and mock methods called
        self.common_tests()

        # test email sent
        self.assertEqual(len(mail.outbox), 1)

        # read email
        email = mail.outbox[0]

        self.assertEqual(
            "Error in biosample submission %s" % self.submission_obj_id,
            email.subject)

        # check for error messages in object
        self.assertIn("a sample message", email.body)
        self.assertEqual(asyncio_mock.call_count, 1)

        self.assertEqual(asyncio_mock.call_count, 1)
        self.assertEqual(tmp.run_until_complete.call_count, 1)
        self.assertEqual(send_message_to_websocket_mock.call_count, 1)
        send_message_to_websocket_mock.assert_called_with(
            {'message': 'Need Revision',
             'notification_message': 'Error in biosample submission'}, 1)


class FetchDraftTestCase(FetchMixin, TestCase):
    """a draft submission without errors"""

    def test_fetch_status(self):
        # a draft submission without errors
        my_submission = Mock()
        my_submission.name = "test-fetch"
        my_submission.status = 'Draft'
        my_submission.has_errors.return_value = Counter({False: 1})
        my_submission.get_status.return_value = Counter({'Complete': 1})

        # assert task and mock methods called
        self.common_tests(my_submission)

        # assert status for submissions
        self.submission_obj.refresh_from_db()
        self.assertEqual(self.submission_obj.status, SUBMITTED)

        # testing a finalized biosample condition
        self.assertTrue(my_submission.finalize.called)

    def test_fetch_status_pending(self):
        """Testing status with pending validation"""

        # a draft submission without errors
        my_submission = Mock()
        my_submission.name = "test-fetch"
        my_submission.status = 'Draft'
        my_submission.has_errors.return_value = Counter({False: 1})
        my_submission.get_status.return_value = Counter({'Pending': 1})

        # assert task and mock methods called
        self.common_tests(my_submission)

        # assert status for submissions
        self.submission_obj.refresh_from_db()
        self.assertEqual(self.submission_obj.status, SUBMITTED)

        # testing a not finalized biosample condition
        self.assertFalse(my_submission.finalize.called)

    def test_fetch_status_submitted(self):
        """Testing status during biosample submission"""

        # a draft submission without errors
        my_submission = Mock()
        my_submission.name = "test-fetch"
        my_submission.status = 'Submitted'
        my_submission.has_errors.return_value = Counter({False: 1})
        my_submission.get_status.return_value = Counter({'Complete': 1})

        # assert task and mock methods called
        self.common_tests(my_submission)

        # assert status for submissions
        self.submission_obj.refresh_from_db()
        self.assertEqual(self.submission_obj.status, SUBMITTED)

        # testing a not finalized biosample condition
        self.assertFalse(my_submission.finalize.called)


class FetchLongTaskTestCase(FetchMixin, TestCase):
    """A submission wich remain in the same status for a long time"""

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

        # make "now" 2 months ago
        testtime = timezone.now() - timedelta(days=60)

        # https://devblog.kogan.com/blog/testing-auto-now-datetime-fields-in-django
        with patch('django.utils.timezone.now') as mock_now:
            mock_now.return_value = testtime

            # update submission updated time with an older date than now
            self.submission_obj.updated_at = testtime
            self.submission_obj.save()

    @patch('biosample.tasks.send_message_to_websocket')

    @patch('asyncio.get_event_loop')
    def test_error_in_submitted_status(self, asyncio_mock,
                                       send_message_to_websocket_mock):
        tmp = asyncio_mock.return_value
        tmp.run_until_complete = Mock()
        # a still running submission
        self.my_submission = Mock()
        self.my_submission.name = "test-fetch"
        self.my_submission.status = 'Submitted'

        # assert task and mock methods called
        self.common_tests(self.my_submission)

        # test email sent
        self.assertEqual(len(mail.outbox), 1)

        # read email
        email = mail.outbox[0]

        self.assertEqual(
            "Error in biosample submission %s" % self.submission_obj_id,
            email.subject)

        # check submission.state changed
        self.submission_obj.refresh_from_db()

        self.assertEqual(self.submission_obj.status, ERROR)
        self.assertIn(
            "Biosample subission {} remained with the same status".format(
                    self.submission_obj),
            self.submission_obj.message
            )

        self.assertEqual(asyncio_mock.call_count, 1)
        self.assertEqual(tmp.run_until_complete.call_count, 1)
        self.assertEqual(send_message_to_websocket_mock.call_count, 1)
        send_message_to_websocket_mock.assert_called_with(
            {'message': 'Error',
             'notification_message': (
                     'Biosample subission Cryoweb '
                     '(United Kingdom, test) remained with the '
                     'same status for more than 5 days. Please '
                     'report it to InjectTool team')
             }, 1)

    @patch('biosample.tasks.send_message_to_websocket')

    @patch('asyncio.get_event_loop')
    def test_error_in_draft_status(self, asyncio_mock,
                                   send_message_to_websocket_mock):
        tmp = asyncio_mock.return_value
        tmp.run_until_complete = Mock()
        # a still running submission
        self.my_submission = Mock()
        self.my_submission.name = "test-fetch"
        self.my_submission.status = 'Draft'

        # assert task and mock methods called
        self.common_tests(self.my_submission)

        # test email sent
        self.assertEqual(len(mail.outbox), 1)

        # read email
        email = mail.outbox[0]

        self.assertEqual(
            "Error in biosample submission %s" % self.submission_obj_id,
            email.subject)

        # check submission.state changed
        self.submission_obj.refresh_from_db()

        self.assertEqual(self.submission_obj.status, ERROR)
        self.assertIn(
            "Biosample subission {} remained with the same status".format(
                    self.submission_obj),
            self.submission_obj.message
            )

        self.assertEqual(asyncio_mock.call_count, 1)
        self.assertEqual(tmp.run_until_complete.call_count, 1)
        self.assertEqual(send_message_to_websocket_mock.call_count, 1)
        send_message_to_websocket_mock.assert_called_with(
            {'message': 'Error',
             'notification_message': (
                     'Biosample subission Cryoweb '
                     '(United Kingdom, test) remained with the '
                     'same status for more than 5 days. Please '
                     'report it to InjectTool team')
             }, 1)


class FetchUnsupportedStatusTestCase(FetchMixin, TestCase):
    """A submission object with a status I can ignore"""

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

        # a still running submission
        self.my_submission = Mock()
        self.my_submission.name = "test-fetch"

        # passing submission to Mocked Root
        self.my_root.get_submission_by_name.return_value = self.my_submission

    def update_status(self, status):
        # change status
        self.submission_obj.status = status
        self.submission_obj.save()

    # override FetchMixing methods
    def common_tests(self, status):
        # update submission status
        self.update_status(status)

        # NOTE that I'm calling the function directly, without delay
        # (AsyncResult). I've patched the time consuming task
        res = self.my_task.run()

        # assert a success with data uploading
        self.assertEqual(res, "success")

        self.assertFalse(self.mock_auth.called)
        self.assertFalse(self.mock_root.called)
        self.assertFalse(self.my_root.get_submission_by_name.called)
        self.assertFalse(self.my_submission.follow_url.called)

        # assert status for submissions
        self.submission_obj.refresh_from_db()
        self.assertEqual(self.submission_obj.status, status)

    def test_loaded(self):
        """Test fecth_status with a loaded submission"""

        # assert task and mock methods called
        self.common_tests(LOADED)

    def test_need_revision(self):
        """Test fecth_status with a need_revision submission"""

        # assert task and mock methods called
        self.common_tests(NEED_REVISION)

    def test_ready(self):
        """Test fecth_status with a ready submission"""

        # assert task and mock methods called
        self.common_tests(READY)

    def test_completed(self):
        """Test fecth_status with a completed submission"""

        # assert task and mock methods called
        self.common_tests(COMPLETED)

cnr-ibba / IMAGE-InjectTool

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SubmitTestCase.test_submit_patch() B

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