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#!/usr/bin/env python3 |
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# -*- coding: utf-8 -*- |
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""" |
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Created on Mon Jan 21 14:30:04 2019 |
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@author: Paolo Cozzi <[email protected]> |
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""" |
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import io |
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import json |
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from pyUSIrest.auth import Auth |
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from pyUSIrest.usi import Sample |
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from pyUSIrest.exceptions import USIDataError |
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from unittest.mock import patch, PropertyMock |
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from django.core.management import call_command |
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from django.test import TestCase |
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from common.constants import SUBMITTED |
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from ..models import ManagedTeam, OrphanSubmission |
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from .common import BaseMixin, generate_token, BioSamplesMixin |
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class CommandsMixin(): |
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@classmethod |
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def setUpClass(cls): |
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# calling my base class setup |
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super().setUpClass() |
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# starting mocked objects |
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cls.mock_auth_patcher = patch('biosample.helpers.get_manager_auth') |
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cls.mock_auth = cls.mock_auth_patcher.start() |
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@classmethod |
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def tearDownClass(cls): |
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cls.mock_auth_patcher.stop() |
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# calling base method |
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super().tearDownClass() |
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class CommandsTestCase(CommandsMixin, BaseMixin, TestCase): |
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@patch('biosample.helpers.get_manager_auth') |
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def test_fill_managed(self, my_auth): |
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"""test fill_managed command""" |
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# remove a managed team |
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managed = ManagedTeam.objects.get(pk=2) |
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managed.delete() |
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# patch get_manager_auth value |
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my_auth.return_value = Auth( |
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token=generate_token( |
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domains=[ |
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'subs.test-team-1', |
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'subs.test-team-2', |
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'subs.test-team-3'] |
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) |
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) |
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# calling commands |
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call_command('fill_managed') |
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# get all managedteams object |
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self.assertEqual(ManagedTeam.objects.count(), 3) |
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self.assertTrue(my_auth.called) |
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def test_get_json_for_biosample(self): |
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args = ["--submission", 1] |
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# https://stackoverflow.com/questions/4219717/how-to-assert-output-with-nosetest-unittest-in-python |
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with patch('sys.stdout', new_callable=io.StringIO) as handle: |
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call_command('get_json_for_biosample', *args) |
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handle.seek(0) |
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data = json.load(handle) |
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self.assertIsInstance(data, dict) |
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class BioSampleRemovalTestCase(CommandsMixin, BioSamplesMixin, TestCase): |
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fixtures = [ |
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'biosample/managedteam', |
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'biosample/orphansample', |
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'uid/dictspecie', |
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] |
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def setUp(self): |
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# calling my base class setup |
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super().setUp() |
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# starting mocked objects |
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self.mock_root_patcher = patch('pyUSIrest.usi.Root') |
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self.mock_root = self.mock_root_patcher.start() |
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# start root object |
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self.my_root = self.mock_root.return_value |
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# mocking chain |
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self.my_team = self.my_root.get_team_by_name.return_value |
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self.my_team.name = "subs.test-team-1" |
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# mocking a new submission |
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self.new_submission = self.my_team.create_submission.return_value |
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self.new_submission.name = "new-submission" |
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# set status. Because of the way mock attributes are stored you can’t |
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# directly attach a PropertyMock to a mock object. Instead you can |
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# attach it to the mock type object: |
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self.new_submission.propertymock = PropertyMock(return_value='Draft') |
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type(self.new_submission).status = self.new_submission.propertymock |
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def tearDown(self): |
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self.mock_root_patcher.stop() |
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super().tearDown() |
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@patch('biosample.helpers.get_manager_auth') |
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def test_patch_orphan_biosamples(self, my_auth): |
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"""test patch_orphan_biosamples command""" |
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# patch get_manager_auth value |
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my_auth.return_value = Auth( |
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token=generate_token() |
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) |
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# mocking sample creation: two objects: one submitted, one not |
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self.new_submission.create_sample.side_effect = [ |
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Sample(auth=generate_token()), |
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USIDataError("test") |
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] |
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# calling commands |
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call_command('patch_orphan_biosamples') |
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# assert a submission created |
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self.assertTrue(my_auth.called) |
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self.assertTrue(self.my_team.create_submission.called) |
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self.assertTrue(self.new_submission.create_sample.called) |
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# check for an object into database |
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submissions = OrphanSubmission.objects.all() |
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self.assertEqual(len(submissions), 1) |
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# test submission attributes |
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submission = submissions[0] |
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self.assertEqual(submission.usi_submission_name, "new-submission") |
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self.assertEqual(submission.samples_count, 1) |
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self.assertEqual(submission.status, SUBMITTED) |
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cnr-ibba /
IMAGE-InjectTool
