def test_gen_orig_params_per_with_a_single_sra(self):
# mock a series and sample
series = Series('GSE123456', 'GSE123456_family.soft.subset')
sample = Sample('GSM1', series)
sample.outdir = 'some_outdir/GSE123456/some_species/GSM1'
series.add_passed_sample(sample)
with mock.patch('rsempipeline.utils.download.open',
mock.mock_open(read_data=SRA_INFO_YAML_SINGLE_SRA)):
vals = download.gen_orig_params_per(sample)
self.assertEqual(vals, [
[None, ['some_outdir/GSE123456/some_species/GSM1/SRX685892/SRR1557065/SRR1557065.sra',
'some_outdir/GSE123456/some_species/GSM1/SRR1557065.sra.download.COMPLETE'], sample]])
def test_gen_orig_params_per_with_a_single_sra(self):
# mock a series and sample
series = Series('GSE123456', 'GSE123456_family.soft.subset')
sample = Sample('GSM1', series)
sample.outdir = 'some_outdir/GSE123456/some_species/GSM1'
series.add_passed_sample(sample)
with mock.patch('rsempipeline.utils.download.open',
mock.mock_open(read_data=SRA_INFO_YAML_SINGLE_SRA)):
vals = download.gen_orig_params_per(sample)
self.assertEqual(vals, [[
None,
[
'some_outdir/GSE123456/some_species/GSM1/SRX685892/SRR1557065/SRR1557065.sra',
'some_outdir/GSE123456/some_species/GSM1/SRR1557065.sra.download.COMPLETE'
], sample
]])
def test_gen_orig_params_per_with_multiple_sras(self):
# mock a series and sample
series = Series('GSE123456', 'GSE123456_family.soft.subset')
sample = Sample('GSM1', series)
sample.outdir = 'some_outdir/GSE123456/some_species/GSM1'
series.add_passed_sample(sample)
with mock.patch('rsempipeline.utils.download.open',
mock.mock_open(read_data=SRA_INFO_YAML_MULTIPLE_SRAS)):
vals = download.gen_orig_params_per(sample)
self.assertEqual(vals, [
# in the format of input, outputs, other params
[None, ['some_outdir/GSE123456/some_species/GSM1/SRX135160/SRR453140/SRR453140.sra', 'some_outdir/GSE123456/some_species/GSM1/SRR453140.sra.download.COMPLETE'], sample],
[None, ['some_outdir/GSE123456/some_species/GSM1/SRX135160/SRR453141/SRR453141.sra', 'some_outdir/GSE123456/some_species/GSM1/SRR453141.sra.download.COMPLETE'], sample],
[None, ['some_outdir/GSE123456/some_species/GSM1/SRX135160/SRR453142/SRR453142.sra', 'some_outdir/GSE123456/some_species/GSM1/SRR453142.sra.download.COMPLETE'], sample],
[None, ['some_outdir/GSE123456/some_species/GSM1/SRX135160/SRR453143/SRR453143.sra', 'some_outdir/GSE123456/some_species/GSM1/SRR453143.sra.download.COMPLETE'], sample]
])
def test_gen_orig_params_per_with_multiple_sras(self):
# mock a series and sample
series = Series('GSE123456', 'GSE123456_family.soft.subset')
sample = Sample('GSM1', series)
sample.outdir = 'some_outdir/GSE123456/some_species/GSM1'
series.add_passed_sample(sample)
with mock.patch('rsempipeline.utils.download.open',
mock.mock_open(read_data=SRA_INFO_YAML_MULTIPLE_SRAS)):
vals = download.gen_orig_params_per(sample)
self.assertEqual(
vals,
[
# in the format of input, outputs, other params
[
None,
[
'some_outdir/GSE123456/some_species/GSM1/SRX135160/SRR453140/SRR453140.sra',
'some_outdir/GSE123456/some_species/GSM1/SRR453140.sra.download.COMPLETE'
], sample
],
[
None,
[
'some_outdir/GSE123456/some_species/GSM1/SRX135160/SRR453141/SRR453141.sra',
'some_outdir/GSE123456/some_species/GSM1/SRR453141.sra.download.COMPLETE'
], sample
],
[
None,
[
'some_outdir/GSE123456/some_species/GSM1/SRX135160/SRR453142/SRR453142.sra',
'some_outdir/GSE123456/some_species/GSM1/SRR453142.sra.download.COMPLETE'
], sample
],
[
None,
[
'some_outdir/GSE123456/some_species/GSM1/SRX135160/SRR453143/SRR453143.sra',
'some_outdir/GSE123456/some_species/GSM1/SRR453143.sra.download.COMPLETE'
], sample
]
])
