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import unittest
import os
import pymzml.obo
class TestObo(unittest.TestCase):
def test_valid_obo(self):
# Test features of the OBO that differ for each version
obos = {
version: pymzml.obo.oboTranslator(version)
for version in ('1.18.2', '2.0.0', '2.01.0')
}
# Changes from 1.18.2 to 2.0.0
self.assertEqual(
obos['1.18.2']['MS:0000000'],
'Proteomics Standards Initiative Mass Spectrometry Ontology'
)
self.assertEqual(
obos['2.0.0']['MS:0000000'],
'Proteomics Standards Initiative Mass Spectrometry Vocabularies'
)
self.assertEqual(
obos['2.0.0']['MS:0000000'],
obos['2.01.0']['MS:0000000'],
)
# Changes from 2.0.0 to 2.01.0
self.assertEqual(obos['1.18.2']['MS:1000854'], None)
self.assertEqual(obos['2.0.0']['MS:1000854'], None)
self.assertEqual(obos['2.01.0']['MS:1000854'], 'LTQ XL')
def test_most_recent_obo(self):
obo = pymzml.obo.oboTranslator()
self.assertEqual(obo.version, None)
# Changes only implemented in 3.78.0
self.assertEqual(
obo[obo['MS:1000130']]['is_a'],
'MS:1000808 ! chromatogram attribute',
)
def test_invalid_obo(self):
with self.assertRaises(Exception):
obo = pymzml.obo.oboTranslator('1.1.1')
parsing_on_demand = obo['MS:1002569']
def test_getitem(self):
obo = pymzml.obo.oboTranslator('3.78.0')
data = {
'id': 'MS:1002569',
'name': 'ProteomeDiscoverer:Number of Spectra Processed At Once',
'def': '"Number of spectra processed at once in a ProteomeDiscoverer search." [PSI:PI]',
'xref': 'value-type:xsd\:int "The allowed value-type for this CV term."',
'is_a': 'MS:1002101 ! ProteomeDiscoverer input parameter',
}
# Lookup by ID and get name
self.assertEqual(obo[data['id']], data['name'])
# Lookup by name and get a dict
self.assertEqual(obo[data['name']], data)
# Nested lookup
self.assertEqual(obo[obo[data['id']]], data)
# Lookup by definition and get a name
self.assertEqual(obo[data['def']], data)
if __name__ == '__main__':
unittest.main()
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