# -----------------------------------------------------------------------------
# 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
from tornado.escape import json_decode
from qiita_db.study import Study
from qiita_pet.test.rest.test_base import RESTHandlerTestCase
class StudyHandlerTests(RESTHandlerTestCase):
def test_get_valid(self):
exp = {u'title': u'Identification of the Microbiomes for Cannabis '
u'Soils',
u'contacts': {'principal_investigator': [u'PIDude',
u'Wash U',
u'PI_dude@foo.bar'],
'lab_person': [u'LabDude',
u'knight lab',
u'lab_dude@foo.bar']},
u'study_abstract':
(u'This is a preliminary study to examine the '
u'microbiota associated with the Cannabis plant. '
u'Soils samples from the bulk soil, soil '
u'associated with the roots, and the rhizosphere '
u'were extracted and the DNA sequenced. Roots '
u'from three independent plants of different '
u'strains were examined. These roots were '
u'obtained November 11, 2011 from plants that '
u'had been harvested in the summer. Future '
u'studies will attempt to analyze the soils and '
u'rhizospheres from the same location at '
u'different time points in the plant lifecycle.'),
u'study_description': (u'Analysis of the Cannabis Plant '
u'Microbiome'),
u'study_alias': 'Cannabis Soils'}
response = self.get('/api/v1/study/1', headers=self.headers)
self.assertEqual(response.code, 200)
obs = json_decode(response.body)
self.assertEqual(obs, exp)
def test_get_invalid(self):
response = self.get('/api/v1/study/0', headers=self.headers)
self.assertEqual(response.code, 404)
self.assertEqual(json_decode(response.body),
{'message': 'Study not found'})
def test_get_invalid_negative(self):
response = self.get('/api/v1/study/-1', headers=self.headers)
self.assertEqual(response.code, 404)
# not asserting the body content as this is not a valid URI according
# to the regex associating the handler to the webserver
def test_get_invalid_namespace(self):
response = self.get('/api/v1/study/1.11111', headers=self.headers)
self.assertEqual(response.code, 404)
# not asserting the body content as this is not a valid URI according
# to the regex associating the handler to the webserver
class StudyCreatorTests(RESTHandlerTestCase):
def test_post_malformed_study(self):
response = self.post('/api/v1/study', data={'foo': 'bar'},
headers=self.headers, asjson=True)
self.assertEqual(response.code, 400)
def test_post_already_exists(self):
payload = {'title': 'Identification of the Microbiomes for Cannabis '
'Soils',
'study_abstract': 'stuff',
'study_description': 'asdasd',
'owner': 'admin@foo.bar',
'study_alias': 'blah',
'notes': '',
'contacts': {'principal_investigator': [u'PIDude',
u'PI_dude@foo.bar'],
'lab_person': [u'LabDude',
u'lab_dude@foo.bar']}}
response = self.post('/api/v1/study', data=payload, asjson=True,
headers=self.headers)
self.assertEqual(response.code, 409)
obs = json_decode(response.body)
self.assertEqual(obs,
{'message': 'Study title already exists'})
def test_post_valid(self):
payload = {'title': 'foo',
'study_abstract': 'stuff',
'study_description': 'asdasd',
'owner': 'admin@foo.bar',
'study_alias': 'blah',
'notes': '',
'contacts': {'principal_investigator': [u'PIDude',
u'Wash U'],
'lab_person': [u'LabDude',
u'knight lab']}}
response = self.post('/api/v1/study', data=payload,
headers=self.headers, asjson=True)
self.assertEqual(response.code, 201)
study_id = json_decode(response.body)['id']
study = Study(int(study_id))
self.assertEqual(study.title, payload['title'])
self.assertEqual(study.info['study_abstract'],
payload['study_abstract'])
self.assertEqual(study.info['study_description'],
payload['study_description'])
self.assertEqual(study.info['study_alias'], payload['study_alias'])
self.assertEqual(study.owner.email, payload['owner'])
self.assertEqual(study.info['principal_investigator'].name,
payload['contacts']['principal_investigator'][0])
self.assertEqual(study.info['principal_investigator'].affiliation,
payload['contacts']['principal_investigator'][1])
self.assertEqual(study.info['lab_person'].name,
payload['contacts']['lab_person'][0])
self.assertEqual(study.info['lab_person'].affiliation,
payload['contacts']['lab_person'][1])
def test_post_invalid_user(self):
payload = {'title': 'foo',
'study_abstract': 'stuff',
'study_description': 'asdasd',
'owner': 'doesnotexist@foo.bar',
'study_alias': 'blah',
'notes': '',
'contacts': {'principal_investigator': [u'PIDude',
u'Wash U'],
'lab_person': [u'LabDude',
u'knight lab']}}
response = self.post('/api/v1/study', data=payload,
headers=self.headers, asjson=True)
self.assertEqual(response.code, 403)
obs = json_decode(response.body)
self.assertEqual(obs, {'message': 'Unknown user'})
class StudyStatusHandlerTests(RESTHandlerTestCase):
def test_get_no_study(self):
response = self.get('/api/v1/study/0/status', headers=self.headers)
self.assertEqual(response.code, 404)
obs = json_decode(response.body)
exp = {'message': 'Study not found'}
self.assertEqual(obs, exp)
def test_get_valid(self):
response = self.get('/api/v1/study/1/status', headers=self.headers)
self.assertEqual(response.code, 200)
exp = {'is_public': False,
'has_sample_information': True,
'sample_information_has_warnings': False,
'preparations': [{'id': 1, 'has_artifact': True},
{'id': 2, 'has_artifact': True}]
}
obs = json_decode(response.body)
self.assertEqual(obs, exp)
if __name__ == '__main__':
main()
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