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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 Tue Jan 21 10:54:09 2020 |
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@author: Paolo Cozzi <[email protected]> |
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""" |
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import os |
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import json |
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import types |
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import asynctest |
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from aioresponses import aioresponses |
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from django.test import TestCase |
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from unittest.mock import patch, Mock |
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from common.constants import BIOSAMPLE_URL |
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from uid.models import Animal as UIDAnimal, Sample as UIDSample |
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from ..tasks.cleanup import check_samples, purge_orphan_samples |
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from ..models import OrphanSample, ManagedTeam |
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from .common import generate_token |
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# get my path |
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dir_path = os.path.dirname(os.path.realpath(__file__)) |
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# define data path |
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DATA_PATH = os.path.join(dir_path, "data") |
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with open(os.path.join(DATA_PATH, "page_0.json")) as handle: |
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page0 = handle.read() |
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with open(os.path.join(DATA_PATH, "page_1.json")) as handle: |
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page1 = handle.read() |
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with open(os.path.join(DATA_PATH, "issue_page1.json")) as handle: |
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issue_page1 = handle.read() |
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class AsyncBioSamplesTestCase(asynctest.TestCase, TestCase): |
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fixtures = [ |
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'biosample/managedteam', |
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'uid/animal', |
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'uid/dictbreed', |
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'uid/dictcountry', |
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'uid/dictrole', |
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'uid/dictsex', |
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'uid/dictspecie', |
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'uid/dictstage', |
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'uid/dictuberon', |
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'uid/ontology', |
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'uid/organization', |
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'uid/publication', |
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'uid/sample', |
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'uid/submission', |
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'uid/user' |
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] |
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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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cls.mock_auth_patcher = patch('pyUSIrest.auth.requests.get') |
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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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def setUp(self): |
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# calling my base setup |
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super().setUp() |
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# well, updating data and set two biosample ids. Those are not |
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# orphans |
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animal = UIDAnimal.objects.get(pk=1) |
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animal.biosample_id = "SAMEA6376980" |
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animal.save() |
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sample = UIDSample.objects.get(pk=1) |
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sample.biosample_id = "SAMEA6376982" |
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sample.save() |
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# generate tocken |
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self.mock_auth.return_value = Mock() |
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self.mock_auth.return_value.text = generate_token() |
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self.mock_auth.return_value.status_code = 200 |
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async def test_request(self) -> None: |
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with aioresponses() as mocked: |
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mocked.get( |
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'{url}?filter=attr:project:IMAGE&size=20'.format( |
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url=BIOSAMPLE_URL), |
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status=200, |
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body=page0) |
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mocked.get( |
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'{url}?filter=attr:project:IMAGE&page=1&size=20'.format( |
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url=BIOSAMPLE_URL), |
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status=200, |
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body=page1) |
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await check_samples() |
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# get accessions |
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reference = ['SAMEA6376991', 'SAMEA6376992'] |
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self.assertEqual(OrphanSample.objects.count(), 2) |
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# check objects into UID |
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for accession in reference: |
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qs = OrphanSample.objects.filter(biosample_id=accession) |
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self.assertTrue(qs.exists()) |
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async def test_request_with_issues(self) -> None: |
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"""Test a temporary issue with BioSamples reply""" |
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with aioresponses() as mocked: |
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mocked.get( |
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'{url}?filter=attr:project:IMAGE&size=20'.format( |
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url=BIOSAMPLE_URL), |
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status=200, |
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body=page0) |
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mocked.get( |
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'{url}?filter=attr:project:IMAGE&page=1&size=20'.format( |
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url=BIOSAMPLE_URL), |
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status=200, |
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body=issue_page1) |
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await check_samples() |
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# no objects where tracked since issue in response |
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self.assertEqual(OrphanSample.objects.count(), 0) |
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class PurgeOrphanSampleTestCase(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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@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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cls.mock_get_patcher = patch('requests.Session.get') |
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cls.mock_get = cls.mock_get_patcher.start() |
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@classmethod |
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def tearDownClass(cls): |
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cls.mock_get_patcher.stop() |
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# calling base method |
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super().tearDownClass() |
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def setUp(self): |
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# calling my base setup |
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super().setUp() |
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def test_purge_orphan_samples(self): |
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"""Test biosample data conversion""" |
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with open(os.path.join(DATA_PATH, "SAMEA6376982.json")) as handle: |
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data = json.load(handle) |
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self.mock_get.return_value = Mock() |
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self.mock_get.return_value.json.return_value = data |
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self.mock_get.return_value.status_code = 200 |
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# call my method |
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samples = purge_orphan_samples() |
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# teams is now a generator |
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self.assertIsInstance(samples, types.GeneratorType) |
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samples = list(samples) |
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self.assertEqual(len(samples), 1) |
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sample = samples[0] |
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self.assertIsInstance(sample, dict) |
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cnr-ibba /
IMAGE-InjectTool
