# -----------------------------------------------------------------------------
# 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 json import loads, dumps
from os.path import join
from functools import partial
from tornado.web import HTTPError
from qiita_db.handlers.tests.oauthbase import OauthTestingBase
import qiita_db as qdb
from qiita_db.handlers.prep_template import _get_prep_template
class UtilTests(TestCase):
def test_get_prep_template(self):
obs = _get_prep_template(1)
exp = qdb.metadata_template.prep_template.PrepTemplate(1)
self.assertEqual(obs, exp)
# It does not exist
with self.assertRaises(HTTPError):
_get_prep_template(100)
class PrepTemplateHandlerTests(OauthTestingBase):
def test_get_does_not_exist(self):
obs = self.get('/qiita_db/prep_template/100/', headers=self.header)
self.assertEqual(obs.code, 404)
def test_get_no_header(self):
obs = self.get('/qiita_db/prep_template/1/')
self.assertEqual(obs.code, 400)
def test_get(self):
obs = self.get('/qiita_db/prep_template/1/', headers=self.header)
self.assertEqual(obs.code, 200)
db_test_template_dir = qdb.util.get_mountpoint('templates')[0][1]
path_builder = partial(join, db_test_template_dir)
obs = loads(obs.body)
# have to check per key because since patch 51 we are updating the
# test info files
self.assertEqual(obs['data_type'], '18S')
self.assertEqual(obs['artifact'], 1)
self.assertEqual(obs['investigation_type'], 'Metagenomics')
self.assertEqual(obs['study'], 1)
self.assertEqual(obs['status'], 'private')
self.assertTrue(obs['sample-file'].startswith(
path_builder('1_')))
self.assertTrue(obs['prep-file'].startswith(
path_builder('1_prep_1_')))
class PrepTemplateDataHandlerTests(OauthTestingBase):
def test_get_does_not_exist(self):
obs = self.get('/qiita_db/prep_template/100/data/',
headers=self.header)
self.assertEqual(obs.code, 404)
def test_get_no_header(self):
obs = self.get('/qiita_db/prep_template/100/data/')
self.assertEqual(obs.code, 400)
def test_get(self):
obs = self.get('/qiita_db/prep_template/1/data/', headers=self.header)
self.assertEqual(obs.code, 200)
obs = loads(obs.body)
self.assertCountEqual(obs.keys(), ['data'])
obs = obs['data']
exp = ['1.SKB2.640194', '1.SKM4.640180', '1.SKB3.640195',
'1.SKB6.640176', '1.SKD6.640190', '1.SKM6.640187',
'1.SKD9.640182', '1.SKM8.640201', '1.SKM2.640199',
'1.SKD2.640178', '1.SKB7.640196', '1.SKD4.640185',
'1.SKB8.640193', '1.SKM3.640197', '1.SKD5.640186',
'1.SKB1.640202', '1.SKM1.640183', '1.SKD1.640179',
'1.SKD3.640198', '1.SKB5.640181', '1.SKB4.640189',
'1.SKB9.640200', '1.SKM9.640192', '1.SKD8.640184',
'1.SKM5.640177', '1.SKM7.640188', '1.SKD7.640191']
self.assertCountEqual(list(obs.keys()), exp)
obs = obs['1.SKB1.640202']
exp = {
'barcode': 'GTCCGCAAGTTA',
'center_name': 'ANL',
'center_project_name': None,
'emp_status': 'EMP',
'experiment_center': 'ANL',
'experiment_design_description':
'micro biome of soil and rhizosphere of cannabis plants '
'from CA',
'experiment_title': 'Cannabis Soil Microbiome',
'illumina_technology': 'MiSeq',
'instrument_model': 'Illumina MiSeq',
'library_construction_protocol':
'This analysis was done as in Caporaso et al 2011 Genome '
'research. The PCR primers (F515/R806) were developed against '
'the V4 region of the 16S rRNA (both bacteria and archaea), '
'which we determined would yield optimal community clustering '
'with reads of this length using a procedure similar to that '
'of ref. 15. [For reference, this primer pair amplifies the '
'region 533_786 in the Escherichia coli strain 83972 sequence '
'(greengenes accession no. prokMSA_id:470367).] The reverse '
'PCR primer is barcoded with a 12-base error-correcting Golay '
'code to facilitate multiplexing of up to 1,500 samples per '
'lane, and both PCR primers contain sequencer adapter '
'regions.',
'pcr_primers': 'FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT',
'platform': 'Illumina',
'primer': 'GTGCCAGCMGCCGCGGTAA',
'run_center': 'ANL',
'run_date': '8/1/12',
'run_prefix': 's_G1_L001_sequences',
'samp_size': '.25,g',
'sample_center': 'ANL',
'sequencing_meth': 'Sequencing by synthesis',
'study_center': 'CCME',
'target_gene': '16S rRNA',
'target_subfragment': 'V4',
'qiita_prep_id': '1'}
self.assertEqual(obs, exp)
def test_get_sample_information(self):
obs = self.get(
'/qiita_db/prep_template/1/data/?sample_information=true',
headers=self.header)
self.assertEqual(obs.code, 200)
obs = loads(obs.body)
self.assertCountEqual(obs.keys(), ['data'])
# let's just check that the samples and the keys from the first element
# match - this assures us that is the sample_info, the rest is
# basically the same as the regular prep_info
obs = obs['data']
exp = ['1.SKB2.640194', '1.SKM4.640180', '1.SKB3.640195',
'1.SKB6.640176', '1.SKD6.640190', '1.SKM6.640187',
'1.SKD9.640182', '1.SKM8.640201', '1.SKM2.640199',
'1.SKD2.640178', '1.SKB7.640196', '1.SKD4.640185',
'1.SKB8.640193', '1.SKM3.640197', '1.SKD5.640186',
'1.SKB1.640202', '1.SKM1.640183', '1.SKD1.640179',
'1.SKD3.640198', '1.SKB5.640181', '1.SKB4.640189',
'1.SKB9.640200', '1.SKM9.640192', '1.SKD8.640184',
'1.SKM5.640177', '1.SKM7.640188', '1.SKD7.640191']
self.assertCountEqual(list(obs.keys()), exp)
exp = ['ph', 'temp', 'depth', 'country', 'texture', 'altitude',
'latitude', 'taxon_id', 'elevation', 'env_biome', 'longitude',
'tot_nitro', 'host_taxid', 'common_name', 'description',
'env_feature', 'env_package', 'sample_type', 'tot_org_carb',
'dna_extracted', 'samp_salinity', 'anonymized_name',
'host_subject_id', 'scientific_name', 'assigned_from_geo',
'season_environment', 'water_content_soil',
'collection_timestamp', 'description_duplicate',
'physical_specimen_location', 'physical_specimen_remaining',
'qiita_study_id']
self.assertCountEqual(obs['1.SKB2.640194'].keys(), exp)
class PrepTemplateAPItestHandlerTests(OauthTestingBase):
def test_post(self):
metadata_dict = {
'SKB8.640193': {'primer': 'GTGCCAGCMGCCGCGGTAA',
'barcode': 'GTCCGCAAGTTA',
'platform': 'Illumina',
'instrument_model': 'Illumina MiSeq'},
'SKD8.640184': {'primer': 'GTGCCAGCMGCCGCGGTAA',
'barcode': 'GTCCGCAAGTTA',
'platform': 'Illumina',
'instrument_model': 'Illumina MiSeq'}}
data = {'prep_info': dumps(metadata_dict),
'study': 1,
'data_type': '16S'}
obs = self.post('/apitest/prep_template/', headers=self.header,
data=data)
self.assertEqual(obs.code, 200)
obs = loads(obs.body)
self.assertCountEqual(obs.keys(), ['prep'])
pt = qdb.metadata_template.prep_template.PrepTemplate(obs['prep'])
# default name, and creation_job_id
self.assertTrue(pt.name.startswith('Prep information'))
self.assertIsNone(pt.creation_job_id)
self.assertCountEqual(pt.keys(), ['1.SKB8.640193', '1.SKD8.640184'])
# testing that a new prep doesn't break the call due to empty artifact
obs = self.get('/qiita_db/prep_template/%d/' % pt.id,
headers=self.header)
self.assertEqual(obs.code, 200)
# testing that using a non default value actually works
data['name'] = 'my long and informative name'
data['job-id'] = 'aaaaaaaa-aaaa-aaaa-aaaa-aaaaaaaaaaaa'
obs = self.post('/apitest/prep_template/', headers=self.header,
data=data)
obs = loads(obs.body)
pt = qdb.metadata_template.prep_template.PrepTemplate(obs['prep'])
self.assertEqual(pt.name, data['name'])
self.assertEqual(pt.creation_job_id, data['job-id'])
# testing setter
jid = 'aaaaaaaa-aaaa-bbbb-aaaa-aaaaaaaaaaaa'
pt.creation_job_id = jid
self.assertEqual(pt.creation_job_id, jid)
if __name__ == '__main__':
main()
Datasets
Models
