# -----------------------------------------------------------------------------
# Copyright (c) 2014--, The Qiita Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# -----------------------------------------------------------------------------
from unittest import main, TestCase
from tornado.escape import json_decode
import qiita_db
from qiita_pet.test.rest.test_base import RESTHandlerTestCase
from qiita_pet.handlers.rest.study_samples import _sample_details
class SupportTests(TestCase):
def test_samples_detail(self):
exp = [{'sample_id': '1.SKD7.640191',
'sample_found': True,
'ebi_sample_accession': 'ERS000021',
'preparation_id': 1,
'ebi_experiment_accession': 'ERX0000021',
'preparation_visibility': 'private',
'preparation_type': '18S'},
{'sample_id': '1.SKD7.640191',
'sample_found': True,
'ebi_sample_accession': 'ERS000021',
'preparation_id': 2,
'ebi_experiment_accession': 'ERX0000021',
'preparation_visibility': 'private',
'preparation_type': '18S'},
{'sample_id': 'doesnotexist',
'sample_found': False,
'ebi_sample_accession': None,
'preparation_id': None,
'ebi_experiment_accession': None,
'preparation_visibility': None,
'preparation_type': None}]
obs = _sample_details(qiita_db.study.Study(1),
['1.SKD7.640191', 'doesnotexist'])
self.assertEqual(len(obs), len(exp))
self.assertCountEqual(obs, exp)
class SampleDetailHandlerTests(RESTHandlerTestCase):
def test_get_missing_sample(self):
exp = [{'sample_id': 'doesnotexist',
'sample_found': False,
'ebi_sample_accession': None,
'preparation_id': None,
'ebi_experiment_accession': None,
'preparation_visibility': None,
'preparation_type': None}, ]
response = self.get('/api/v1/study/1/sample/doesnotexist/status',
headers=self.headers)
self.assertEqual(response.code, 200)
obs = json_decode(response.body)
self.assertEqual(obs, exp)
def test_get_valid_sample(self):
exp = [{'sample_id': '1.SKD7.640191',
'sample_found': True,
'ebi_sample_accession': 'ERS000021',
'preparation_id': 1,
'ebi_experiment_accession': 'ERX0000021',
'preparation_visibility': 'private',
'preparation_type': '18S'},
{'sample_id': '1.SKD7.640191',
'sample_found': True,
'ebi_sample_accession': 'ERS000021',
'preparation_id': 2,
'ebi_experiment_accession': 'ERX0000021',
'preparation_visibility': 'private',
'preparation_type': '18S'}]
response = self.get('/api/v1/study/1/sample/1.SKD7.640191/status',
headers=self.headers)
self.assertEqual(response.code, 200)
obs = json_decode(response.body)
self.assertCountEqual(obs, exp)
def test_post_samples_status_bad_request(self):
body = {'malformed': 'with garbage'}
response = self.post('/api/v1/study/1/samples/status',
headers=self.headers,
data=body, asjson=True)
self.assertEqual(response.code, 400)
def test_post_samples_status(self):
exp = [{'sample_id': '1.SKD7.640191',
'sample_found': True,
'ebi_sample_accession': 'ERS000021',
'preparation_id': 1,
'ebi_experiment_accession': 'ERX0000021',
'preparation_visibility': 'private',
'preparation_type': '18S'},
{'sample_id': '1.SKD7.640191',
'sample_found': True,
'ebi_sample_accession': 'ERS000021',
'preparation_id': 2,
'ebi_experiment_accession': 'ERX0000021',
'preparation_visibility': 'private',
'preparation_type': '18S'},
{'sample_id': 'doesnotexist',
'sample_found': False,
'ebi_sample_accession': None,
'preparation_id': None,
'ebi_experiment_accession': None,
'preparation_visibility': None,
'preparation_type': None},
{'sample_id': '1.SKM5.640177',
'sample_found': True,
'ebi_sample_accession': 'ERS000005',
'preparation_id': 1,
'ebi_experiment_accession': 'ERX0000005',
'preparation_visibility': 'private',
'preparation_type': '18S'},
{'sample_id': '1.SKM5.640177',
'sample_found': True,
'ebi_sample_accession': 'ERS000005',
'preparation_id': 2,
'ebi_experiment_accession': 'ERX0000005',
'preparation_visibility': 'private',
'preparation_type': '18S'}]
body = {'sample_ids': ['1.SKD7.640191', 'doesnotexist',
'1.SKM5.640177']}
response = self.post('/api/v1/study/1/samples/status',
headers=self.headers,
data=body, asjson=True)
self.assertEqual(response.code, 200)
obs = json_decode(response.body)
self.assertCountEqual(obs, exp)
if __name__ == '__main__':
main()
Datasets
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