def test_defaults(self):
expected = dict(scenario=[
{'type': 'phase1', 'steps': '2'},
{'type': 'phase2', 'steps': '1'}
],
ionisation_mode=1,
ms_data_format='mzxml',
ms_data_area='',
ms_intensity_cutoff=0.0,
msms_intensity_cutoff=5,
mz_precision=5.0,
mz_precision_abs=0.001,
abs_peak_cutoff=5000,
max_ms_level=10,
precursor_mz_precision=0.005,
max_broken_bonds=3,
max_water_losses=1,
)
self.assertDictEqual(expected, JobQuery.defaults())
def test_defaults_example(self):
example_tree = [
'353.087494: 69989984 (',
' 191.055756: 54674544 (',
' 85.029587: 2596121,',
' 93.034615: 1720164,',
' 109.029442: 917026,',
' 111.045067: 1104891 (',
' 81.034691: 28070,',
' 83.014069: 7618,',
' 83.050339: 25471,',
' 93.034599: 36300,',
' 96.021790: 8453',
' ),',
' 127.039917: 2890439 (',
' 57.034718: 16911,',
' 81.034706: 41459,',
' 83.050301: 35131,',
' 85.029533: 236887,',
' 99.045074: 73742,',
' 109.029404: 78094',
' ),',
' 171.029587: 905226,',
' 173.045212: 2285841 (',
' 71.013992: 27805,',
' 93.034569: 393710,',
' 111.008629: 26219,',
' 111.045029: 339595,',
' 137.024292: 27668,',
' 155.034653: 145773',
' ),',
' 191.055725: 17000514',
' ),',
' 353.087097: 4146696',
' )'
]
expected = dict(ms_data="\n".join(example_tree),
ms_data_format='mass_tree',
ionisation_mode=-1,
)
self.assertDictEqual(expected, JobQuery.defaults('example'))
def test_defaults_example2(self):
example_tree = [
'C16H17O9: 69989984 (',
' C7H11O6: 54674544 (',
' C4H5O2: 2596121,',
' C6H5O: 1720164,',
' C6H5O2: 917026,',
' C6H7O2: 1104891 (',
' C5H5O: 28070,',
' C4H3O2: 7618,',
' C5H7O: 25471,',
' C6H5O: 36300,',
' C5H4O2: 8453',
' ),',
' C6H7O3: 2890439 (',
' C3H5O: 16911,',
' C5H5O: 41459,',
' C5H7O: 35131,',
' C4H5O2: 236887,',
' C5H7O2: 73742,',
' C6H5O2: 78094',
' ),',
' C7H7O5: 905226,',
' C7H9O5: 2285841 (',
' C3H3O2: 27805,',
' C6H5O: 393710,',
' C5H3O3: 26219,',
' C6H7O2: 339595,',
' C7H5O3: 27668,',
' C7H7O4: 145773',
' ),',
' C7H11O6: 17000514',
' ),',
' C16H17O9: 4146696',
' )',
]
expected = dict(ms_data="\n".join(example_tree),
ms_data_format='form_tree',
ionisation_mode=-1,
)
self.assertDictEqual(expected, JobQuery.defaults('example2'))
def defaults(self):
"""Returns defaults settings to run a job"""
selection = self.request.params.get('selection')
return {'success': True, 'data': JobQuery.defaults(selection)}
def defaults(self):
"""Returns defaults settings to run a job"""
selection = self.request.params.get('selection')
return {'success': True,
'data': JobQuery.defaults(selection)}
