# -----------------------------------------------------------------------------
# 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 copy import deepcopy
from json import loads
from qiita_pet.test.tornado_test_base import TestHandlerBase
class TestRedbiom(TestHandlerBase):
def test_get(self):
response = self.get('/redbiom/')
self.assertEqual(response.code, 200)
def test_post_metadata(self):
post_args = {
'search': 'Diesel',
'search_on': 'metadata'
}
response = self.post('/redbiom/', post_args)
self.assertEqual(response.code, 200)
exp_artifact_biom_ids = {
'5': ['1.SKD2.640178'],
'4': sorted(['1.SKD2.640178', '1.SKD8.640184'])}
response_body = loads(response.body)
obs_artifact_biom_ids = response_body['data'][0].pop(
'artifact_biom_ids')
# making sure they are in the same order
obs_artifact_biom_ids['4'] = sorted(obs_artifact_biom_ids['4'])
self.assertDictEqual(obs_artifact_biom_ids, exp_artifact_biom_ids)
exp = {'status': 'success', 'message': '', 'data': DATA}
self.assertEqual(response_body, exp)
post_args = {
'search': 'inf',
'search_on': 'metadata'
}
response = self.post('/redbiom/', post_args)
self.assertEqual(response.code, 200)
exp = {'status': 'success',
'message': 'No samples were found! Try again ...', 'data': []}
self.assertEqual(loads(response.body), exp)
post_args = {
'search': '4353076',
'search_on': 'metadata'
}
response = self.post('/redbiom/', post_args)
self.assertEqual(response.code, 200)
exp = {'status': 'success',
'message': ('The query ("4353076") did not work and may be '
'malformed. Please check the search help for more '
'information on the queries.'), 'data': []}
self.assertEqual(loads(response.body), exp)
def test_post_features(self):
post_args = {
'search': '4479944',
'search_on': 'feature'
}
response = self.post('/redbiom/', post_args)
data = deepcopy(DATA)
data[0]['artifact_biom_ids'] = {
'5': ['1.SKM3.640197'], '4': ['1.SKM3.640197']}
exp = {'status': 'success', 'message': '', 'data': data}
self.assertEqual(response.code, 200)
self.assertEqual(loads(response.body), exp)
post_args = {
'search': 'TT',
'search_on': 'feature'
}
response = self.post('/redbiom/', post_args)
exp = {'status': 'success',
'message': 'No samples were found! Try again ...', 'data': []}
self.assertEqual(response.code, 200)
self.assertEqual(loads(response.body), exp)
def test_post_taxon(self):
post_args = {
'search': 'o__0319-7L14',
'search_on': 'taxon'
}
data = deepcopy(DATA)
data[0]['artifact_biom_ids'] = {
'5': sorted(['1.SKD2.640178', '1.SKM3.640197']),
'4': sorted(['1.SKM3.640197', '1.SKD2.640178'])}
response = self.post('/redbiom/', post_args)
exp = {'status': 'success', 'message': '', 'data': data}
# making sure they are in the same order
obs = loads(response.body)
obs['data'][0]['artifact_biom_ids'] = {
'4': sorted(obs['data'][0]['artifact_biom_ids']['4']),
'5': sorted(obs['data'][0]['artifact_biom_ids']['5'])}
self.assertEqual(response.code, 200)
self.assertEqual(obs, exp)
post_args = {
'search': 'o_0319-7L14',
'search_on': 'taxon'
}
response = self.post('/redbiom/', post_args)
exp = {'status': 'success',
'message': 'No samples were found! Try again ...', 'data': []}
self.assertEqual(response.code, 200)
self.assertEqual(loads(response.body), exp)
def test_post_errors(self):
post_args = {
'search_on': 'metadata'
}
response = self.post('/redbiom/', post_args)
self.assertEqual(response.code, 400)
post_args = {
'search': 'infant',
'search_on': 'error'
}
response = self.post('/redbiom/', post_args)
self.assertEqual(response.code, 200)
exp = {'status': 'success',
'message': ('Incorrect search by: you can use metadata, '
'features or taxon and you passed: error'),
'data': []}
self.assertEqual(loads(response.body), exp)
DATA = [
{'study_title': 'Identification of the Microbiomes for Cannabis Soils',
'metadata_complete': True, 'publication_pid': ['123456', '7891011'],
'autoloaded': False,
'study_id': 1, 'ebi_study_accession': 'EBI123456-BB',
'study_abstract': ('This is a preliminary study to examine the '
'microbiota associated with the Cannabis plant. Soils '
'samples from the bulk soil, soil associated with the '
'roots, and the rhizosphere were extracted and the '
'DNA sequenced. Roots from three independent plants '
'of different strains were examined. These roots were '
'obtained November 11, 2011 from plants that had been '
'harvested in the summer. Future studies will attempt '
'to analyze the soils and rhizospheres from the same '
'location at different time points in the plant '
'lifecycle.'),
'pi': ['PI_dude@foo.bar', 'PIDude'],
'publication_doi': ['10.100/123456', '10.100/7891011'],
'study_alias': 'Cannabis Soils', 'number_samples_collected': 27}]
if __name__ == "__main__":
main()
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