class JobDbEmptyDatasetTestCase(unittest.TestCase):
def setUp(self):
# mock job session
self.session = initTestingDB(dataset=None)
self.job = JobDb(self.session)
def test_runInfo(self):
runInfo = self.job.runInfo()
self.assertIsNone(runInfo)
def test_maxMSLevel(self):
maxmslevel = self.job.maxMSLevel()
self.assertEqual(maxmslevel, 0)
def test_chromatogram(self):
expected_chromatogram = {"scans": [], "cutoff": None}
self.assertEqual(self.job.chromatogram(), expected_chromatogram)
def test_moleculesTotalCount(self):
self.assertEqual(self.job.moleculesTotalCount(), 0)
class JobDbEmptyDatasetTestCase(unittest.TestCase):
def setUp(self):
# mock job session
self.session = initTestingDB(dataset=None)
self.job = JobDb(self.session)
def test_runInfo(self):
runInfo = self.job.runInfo()
self.assertIsNone(runInfo)
def test_maxMSLevel(self):
maxmslevel = self.job.maxMSLevel()
self.assertEqual(maxmslevel, 0)
def test_chromatogram(self):
expected_chromatogram = {'scans': [], 'cutoff': None}
self.assertEqual(self.job.chromatogram(), expected_chromatogram)
def test_moleculesTotalCount(self):
self.assertEqual(self.job.moleculesTotalCount(), 0)
def setUp(self):
self.job = JobDb(initTestingDB(dataset="useallpeaks"))
class JobWithAllPeaksTestCase(unittest.TestCase):
def setUp(self):
self.job = JobDb(initTestingDB(dataset="useallpeaks"))
def test_default(self):
response = self.job.molecules()
self.assertEquals(
response,
{
"total": 1,
"page": 1,
"molid": None,
"rows": [
{
"molid": 12,
"predicted": True,
"mol": u"Molfile",
"formula": u"C11H12O7S",
"nhits": 1,
"name": u"5-(3,4)-dihydroxyphenyl-g-valerolactone (F)",
"refscore": 0.119004,
"reactionsequence": [u"sulfation_(aromatic_hydroxyl)"],
"smiles": u"Oc1ccc(CC2OC(=O)CC2)cc1OS(O)(=O)=O",
"inchikey14": u"YAXFVDUJDAQPTJ",
"mim": 288.0303734299,
"logp": 1.9027,
"assigned": False,
"reference": u"",
}
],
},
)
def test_lvl1fragments(self):
response = self.job.fragments(molid=12, scanid=1, node="root")
self.assertEqual(
response,
{
"children": [
{
"atoms": u"0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18",
"children": [],
"deltah": -1.0,
"deltappm": -7.046696487857745e-09,
"expanded": True,
"fragid": 17,
"leaf": True,
"mass": 288.0303734299,
"molid": 12,
"mol": u"Molfile",
"mslevel": 1,
"mz": 287.015686035156,
"scanid": 1,
"score": 0.0,
"isAssigned": False,
"formula": "C4H6O2",
},
{
"atoms": u"0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18",
"deltah": -1.0,
"deltappm": -7.020570507205176e-09,
"expanded": True,
"fragid": 18,
"leaf": False,
"mz": 287.023132324219,
"molid": 12,
"mol": u"Molfile",
"mslevel": 1,
"mass": 288.0303734299,
"scanid": 1,
"score": 0.5,
"isAssigned": False,
"formula": "C4H6O2",
"children": [
{
"fragid": 19,
"molid": 12,
"scanid": 2,
"mz": 207.066223144531,
"mass": 207.0657338415,
"score": 0.5,
"mol": u"Molfile",
"atoms": u"0,1,2,3,4,5,6,7,8,9,10,11,12,13,14",
"expanded": True,
"leaf": True,
"mslevel": 2,
"deltah": 0.0,
"deltappm": 2.3630267823129625e-12,
"formula": "C4H6O2",
},
{
"fragid": 20,
"molid": 12,
"scanid": 2,
"mz": 287.022827148438,
"mass": 288.0303734299,
"score": 0.0,
"mol": u"Molfile",
"atoms": u"0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18",
"expanded": True,
"leaf": True,
"mslevel": 2,
"deltah": -1.0,
"deltappm": -7.021641217476223e-09,
"formula": "C4H6O2",
},
],
},
],
"expanded": True,
},
)
def setUp(self):
# mock job session
self.session = initTestingDB(dataset=None)
self.job = JobDb(self.session)
def setUp(self):
# mock job session
self.session = initTestingDB()
self.job = JobDb(self.session)
def setUp(self):
self.job = JobDb(initTestingDB(dataset='useallpeaks'))
class JobWithAllPeaksTestCase(unittest.TestCase):
def setUp(self):
self.job = JobDb(initTestingDB(dataset='useallpeaks'))
def test_default(self):
response = self.job.molecules()
self.assertEquals(
response,
{
'total': 1,
'page': 1,
'molid': None,
'rows': [{
'molid': 12,
'predicted': True,
'mol': u'Molfile',
'formula': u'C11H12O7S',
'nhits': 1,
'name': u'5-(3,4)-dihydroxyphenyl-g-valerolactone (F)',
'refscore': 0.119004,
'reactionsequence': [u'sulfation_(aromatic_hydroxyl)'],
'smiles': u'Oc1ccc(CC2OC(=O)CC2)cc1OS(O)(=O)=O',
'inchikey14': u'YAXFVDUJDAQPTJ',
'mim': 288.0303734299, 'logp':1.9027,
'assigned': False,
'reference': u''
}]
}
)
def test_lvl1fragments(self):
response = self.job.fragments(molid=12, scanid=1, node='root')
self.assertEqual(response, {
'children': [{
'atoms': u'0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18',
'children': [],
'deltah': -1.0,
'deltappm': -7.046696487857745e-09,
'expanded': True,
'fragid': 17,
'leaf': True,
'mass': 288.0303734299,
'molid': 12,
'mol': u'Molfile',
'mslevel': 1,
'mz': 287.015686035156,
'scanid': 1,
'score': 0.0,
'isAssigned': False,
'formula': "C4H6O2",
}, {
'atoms': u'0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18',
'deltah': -1.0,
'deltappm': -7.020570507205176e-09,
'expanded': True,
'fragid': 18,
'leaf': False,
'mz': 287.023132324219,
'molid': 12,
'mol': u'Molfile',
'mslevel': 1,
'mass': 288.0303734299,
'scanid': 1,
'score': 0.5,
'isAssigned': False,
'formula': "C4H6O2",
'children': [{
'fragid': 19,
'molid': 12,
'scanid': 2,
'mz': 207.066223144531,
'mass': 207.0657338415,
'score': 0.5,
'mol': u'Molfile',
'atoms': u'0,1,2,3,4,5,6,7,8,9,10,11,12,13,14',
'expanded': True,
'leaf': True,
'mslevel': 2,
'deltah': 0.0,
'deltappm': 2.3630267823129625e-12,
'formula': "C4H6O2",
}, {
'fragid': 20,
'molid': 12,
'scanid': 2,
'mz': 287.022827148438,
'mass': 288.0303734299,
'score': 0.0,
'mol': u'Molfile',
'atoms': u'0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18',
'expanded': True,
'leaf': True,
'mslevel': 2,
'deltah': -1.0,
'deltappm': -7.021641217476223e-09,
'formula': "C4H6O2",
}]
}], 'expanded': True
})