def test_prep_template_post_req(self):
obs = prep_template_post_req(1, '*****@*****.**', 'update.txt',
'16S')
exp = {'status': 'warning',
'message': [
'Sample names were already prefixed with the study id.',
('Some columns required to generate a QIIME-compliant '
'mapping file are not present in the template. A '
'placeholder value (XXQIITAXX) has been used to populate '
'these columns. Missing columns: BarcodeSequence, '
'LinkerPrimerSequence'),
('Some functionality will be disabled due to missing '
'columns:'),
('\tDemultiplexing with multiple input files disabled.: '
'barcode, primer, run_prefix;'),
'\tDemultiplexing disabled.: barcode, primer;',
('\tEBI submission disabled: center_name, '
'experiment_design_description, instrument_model, '
'library_construction_protocol, platform, primer.'),
('See the Templates tutorial for a description of these '
'fields.')],
'file': 'update.txt',
'id': 'ignored in test'}
self.assertItemsEqual(obs['message'].split('\n'), exp['message'])
self.assertEqual(obs['status'], exp['status'])
self.assertEqual(obs['file'], exp['file'])
self.assertIsInstance(obs['id'], int)
# Make sure new prep template added
prep = PrepTemplate(obs['id'])
self.assertEqual(prep.data_type(), '16S')
self.assertEqual([x for x in prep.keys()], ['1.SKD6.640190'])
self.assertEqual([x._to_dict() for x in prep.values()],
[{'new_col': 'new_value'}])
def test_prep_template_post_req_errors(self):
# User doesn't have access
obs = prep_template_post_req(1, '*****@*****.**', 'filepath', '16S')
exp = {'status': 'error',
'message': 'User does not have access to study'}
self.assertEqual(obs, exp)
# The file does not exist
obs = prep_template_post_req(1, '*****@*****.**', 'badfilepath', '16S')
exp = {'status': 'error',
'message': 'file does not exist',
'file': 'badfilepath'}
self.assertEqual(obs, exp)
# Prep template does not exist
obs = prep_template_post_req(3100, '*****@*****.**', 'update.txt',
'16S')
self.assertEqual(obs, {'status': 'error',
'message': 'Study does not exist'})
def test_prep_template_post_req(self):
obs = prep_template_post_req(1,
'*****@*****.**',
'update.txt',
'16S',
name=" ")
exp = {
'status':
'warning',
'message': [
'Both a converter and dtype were specified for column '
'sample_name - only the converter will be used', 'Some '
'functionality will be disabled due to missing columns:',
'\tEBI submission disabled: center_name, '
'experiment_design_description, instrument_model, '
'library_construction_protocol, platform;',
'\tDemultiplexing disabled.: barcode;', '\tDemultiplexing '
'with multiple input files disabled.: barcode, primer, '
'run_prefix.', 'See the Templates tutorial for a '
'description of these fields.', 'Some columns required to '
'generate a QIIME-compliant mapping file are not present '
'in the template. A placeholder value (XXQIITAXX) '
'has been used to populate these columns. Missing columns: '
'BarcodeSequence, LinkerPrimerSequence'
],
'file':
'update.txt',
'id':
'ignored in test'
}
self.assertCountEqual(obs['message'].split('\n'), exp['message'])
self.assertEqual(obs['status'], exp['status'])
self.assertEqual(obs['file'], exp['file'])
self.assertIsInstance(obs['id'], int)
# Make sure new prep template added
prep = PrepTemplate(obs['id'])
self.assertEqual(prep.data_type(), '16S')
self.assertEqual([x for x in prep.keys()], ['1.SKD6.640190'])
self.assertEqual([x._to_dict() for x in prep.values()],
[{
'new_col': 'new_value'
}])
self.assertEqual(prep.name, "Prep information %s" % prep.id)
