def test_prep_template_get_req_no_access(self):
obs = prep_template_get_req(1, '*****@*****.**')
exp = {
'status': 'error',
'message': 'User does not have access to study'
}
self.assertEqual(obs, exp)
def test_prep_template_get_req(self):
obs = prep_template_get_req(1, '*****@*****.**')
self.assertCountEqual(
list(obs.keys()), ['status', 'message', 'template'])
self.assertEqual(obs['status'], 'success')
self.assertEqual(obs['message'], '')
self.assertCountEqual(obs['template'].keys(), [
'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.assertEqual(obs['template']['1.SKD7.640191'], {
'experiment_center': 'ANL',
'center_name': 'ANL',
'run_center': 'ANL',
'run_prefix': 's_G1_L001_sequences',
'primer': 'GTGCCAGCMGCCGCGGTAA',
'target_gene': '16S rRNA',
'sequencing_meth': 'Sequencing by synthesis',
'run_date': '8/1/12',
'platform': 'Illumina',
'pcr_primers': 'FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT',
'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.',
'experiment_design_description':
'micro biome of soil and rhizosphere of cannabis plants '
'from CA',
'study_center': 'CCME',
'center_project_name': None,
'sample_center': 'ANL',
'samp_size': '.25,g',
'barcode': 'ACGCACATACAA',
'qiita_prep_id': '1',
'emp_status': 'EMP',
'illumina_technology': 'MiSeq',
'experiment_title': 'Cannabis Soil Microbiome',
'target_subfragment': 'V4',
'instrument_model': 'Illumina MiSeq'})
def test_prep_template_get_req(self):
obs = prep_template_get_req(1, '*****@*****.**')
self.assertItemsEqual(obs.keys(), ['status', 'message', 'template'])
self.assertEqual(obs['status'], 'success')
self.assertEqual(obs['message'], '')
self.assertEqual(obs['template'].keys(), [
'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.assertEqual(obs['template']['1.SKD7.640191'], {
'experiment_center': 'ANL',
'center_name': 'ANL',
'run_center': 'ANL',
'run_prefix': 's_G1_L001_sequences',
'primer': 'GTGCCAGCMGCCGCGGTAA',
'target_gene': '16S rRNA',
'sequencing_meth': 'Sequencing by synthesis',
'run_date': '8/1/12',
'platform': 'Illumina',
'pcr_primers': 'FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT',
'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.',
'experiment_design_description':
'micro biome of soil and rhizosphere of cannabis plants '
'from CA',
'study_center': 'CCME',
'center_project_name': None,
'sample_center': 'ANL',
'samp_size': '.25,g',
'barcode': 'ACGCACATACAA',
'qiita_prep_id': '1',
'emp_status': 'EMP',
'illumina_technology': 'MiSeq',
'experiment_title': 'Cannabis Soil Microbiome',
'target_subfragment': 'V4',
'instrument_model': 'Illumina MiSeq'})
def test_prep_template_get_req_no_exists(self):
obs = prep_template_get_req(3100, '*****@*****.**')
self.assertEqual(obs, {'status': 'error',
'message': 'Prep template 3100 does not exist'})
def test_prep_template_get_req_no_access(self):
obs = prep_template_get_req(1, '*****@*****.**')
exp = {'status': 'error',
'message': 'User does not have access to study'}
self.assertEqual(obs, exp)
def test_prep_template_get_req_no_exists(self):
obs = prep_template_get_req(3100, '*****@*****.**')
self.assertEqual(obs, {
'status': 'error',
'message': 'Prep template 3100 does not exist'
})
