def test_prep_template_summary_get_req_no_access(self):
obs = prep_template_summary_get_req(1, '*****@*****.**')
exp = {
'status': 'error',
'message': 'User does not have access to study'
}
self.assertEqual(obs, exp)
def test_prep_template_summary_get_req(self):
obs = prep_template_summary_get_req(1, '*****@*****.**')
exp = {
'summary': {
'experiment_center': [('ANL', 27)],
'center_name': [('ANL', 27)],
'run_center': [('ANL', 27)],
'run_prefix': [('s_G1_L001_sequences', 27)],
'primer': [('GTGCCAGCMGCCGCGGTAA', 27)],
'target_gene': [('16S rRNA', 27)],
'sequencing_meth': [('Sequencing by synthesis', 27)],
'run_date': [('8/1/12', 27)],
'platform': [('Illumina', 27)],
'pcr_primers': [('FWD:GTGCCAGCMGCCGCGGTAA; '
'REV:GGACTACHVGGGTWTCTAAT', 27)],
'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.', 27)],
'experiment_design_description':
[('micro biome of soil and rhizosphere of cannabis plants from '
'CA', 27)],
'study_center': [('CCME', 27)],
'center_project_name': [],
'sample_center': [('ANL', 27)],
'samp_size': [('.25,g', 27)],
'barcode': [('AACTCCTGTGGA', 1), ('ACCTCAGTCAAG', 1),
('ACGCACATACAA', 1), ('AGCAGGCACGAA', 1),
('AGCGCTCACATC', 1), ('ATATCGCGATGA', 1),
('ATGGCCTGACTA', 1), ('CATACACGCACC', 1),
('CCACCCAGTAAC', 1), ('CCGATGCCTTGA', 1),
('CCTCGATGCAGT', 1), ('CCTCTGAGAGCT', 1),
('CGAGGTTCTGAT', 1), ('CGCCGGTAATCT', 1),
('CGGCCTAAGTTC', 1), ('CGTAGAGCTCTC', 1),
('CGTGCACAATTG', 1), ('GATAGCACTCGT', 1),
('GCGGACTATTCA', 1), ('GTCCGCAAGTTA', 1),
('TAATGGTCGTAG', 1), ('TAGCGCGAACTT', 1),
('TCGACCAAACAC', 1), ('TGAGTGGTCTGT', 1),
('TGCTACAGACGT', 1), ('TGGTTATGGCAC', 1),
('TTGCACCGTCGA', 1)],
'emp_status': [('EMP', 27)],
'illumina_technology': [('MiSeq', 27)],
'experiment_title': [('Cannabis Soil Microbiome', 27)],
'target_subfragment': [('V4', 27)],
'instrument_model': [('Illumina MiSeq', 27)]
},
'num_samples': 27,
'status': 'success',
'message': ''
}
self.assertEqual(obs, exp)
def test_prep_template_summary_get_req(self):
obs = prep_template_summary_get_req(1, '*****@*****.**')
exp = {'summary': {
'experiment_center': [('ANL', 27)],
'center_name': [('ANL', 27)],
'run_center': [('ANL', 27)],
'run_prefix': [('s_G1_L001_sequences', 27)],
'primer': [('GTGCCAGCMGCCGCGGTAA', 27)],
'target_gene': [('16S rRNA', 27)],
'sequencing_meth': [('Sequencing by synthesis', 27)],
'run_date': [('8/1/12', 27)],
'platform': [('Illumina', 27)],
'pcr_primers': [('FWD:GTGCCAGCMGCCGCGGTAA; '
'REV:GGACTACHVGGGTWTCTAAT', 27)],
'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.', 27)],
'experiment_design_description': [(
'micro biome of soil and rhizosphere of cannabis plants from '
'CA', 27)],
'study_center': [('CCME', 27)],
'center_project_name': [],
'sample_center': [('ANL', 27)],
'samp_size': [('.25,g', 27)],
'qiita_prep_id': [('1', 27)],
'barcode': [
('AACTCCTGTGGA', 1), ('ACCTCAGTCAAG', 1), ('ACGCACATACAA', 1),
('AGCAGGCACGAA', 1), ('AGCGCTCACATC', 1), ('ATATCGCGATGA', 1),
('ATGGCCTGACTA', 1), ('CATACACGCACC', 1), ('CCACCCAGTAAC', 1),
('CCGATGCCTTGA', 1), ('CCTCGATGCAGT', 1), ('CCTCTGAGAGCT', 1),
('CGAGGTTCTGAT', 1), ('CGCCGGTAATCT', 1), ('CGGCCTAAGTTC', 1),
('CGTAGAGCTCTC', 1), ('CGTGCACAATTG', 1), ('GATAGCACTCGT', 1),
('GCGGACTATTCA', 1), ('GTCCGCAAGTTA', 1), ('TAATGGTCGTAG', 1),
('TAGCGCGAACTT', 1), ('TCGACCAAACAC', 1), ('TGAGTGGTCTGT', 1),
('TGCTACAGACGT', 1), ('TGGTTATGGCAC', 1), ('TTGCACCGTCGA', 1)],
'emp_status': [('EMP', 27)],
'illumina_technology': [('MiSeq', 27)],
'experiment_title': [('Cannabis Soil Microbiome', 27)],
'target_subfragment': [('V4', 27)],
'instrument_model': [('Illumina MiSeq', 27)]},
'num_samples': 27,
'status': 'success',
'message': ''}
self.assertEqual(obs, exp)
def test_prep_template_summary_get_req_no_exists(self):
obs = prep_template_summary_get_req(3100, '*****@*****.**')
self.assertEqual(obs, {'status': 'error',
'message': 'Prep template 3100 does not exist'})
def test_prep_template_summary_get_req_no_access(self):
obs = prep_template_summary_get_req(1, '*****@*****.**')
exp = {'status': 'error',
'message': 'User does not have access to study'}
self.assertEqual(obs, exp)
def test_prep_template_summary_get_req_no_exists(self):
obs = prep_template_summary_get_req(3100, '*****@*****.**')
self.assertEqual(obs, {
'status': 'error',
'message': 'Prep template 3100 does not exist'
})
