Beispiel #1
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 def test_get_mz(self):
     m1 = Molecule(name='test', sum_formula="C1H2O3")
     m1.save()
     a1 = Adduct(nM=1, delta_formula='-H', charge=-1)
     a1.save()
     s1 = Standard(molecule=m1)
     s1.save()
     self.assertEqual(Standard.objects.all().count(), 1)
     self.assertAlmostEqual(s1.molecule.get_mz(a1), 60.99311, places=4)
Beispiel #2
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    def test_xic_and_standard_and_adduct(self):
        # create some datasets
        d1 = Dataset(name='Dataset1')
        d1.save()
        a1 = Adduct(nM=1, delta_formula='-H', charge=-1)
        a1.save()
        m1 = Molecule(name='TestMolecule1', sum_formula="C1H2O3")
        m1.save()
        s1 = Standard(molecule=m1, inventory_id="0")
        s1.save()
        # create some xics
        x1 = Xic(mz=60.993, dataset=d1)
        xic = [1.0, 2.0, 3.0, 4.0, 5.0]
        x1.set_xic(xic)
        x1.standard = s1
        x1.adduct = a1
        x1.save()
        self.assertEqual(Xic.objects.all().count(), 1)
        self.assertEqual(Dataset.objects.all().count(), 1)
        self.assertEqual(Standard.objects.all().count(), 1)
        # mass check
        with self.assertRaises(ValueError):
            x1.mz = 123.993
            x1.save()
            x1.check_mass()

        def test_xic_mass_filter(self):
            d1 = Dataset(name='dataset')
            d1.save()
            mz = 60.993
            # three larger
            Xic(mz=mz + 5., dataset=d1).save()
            Xic(mz=mz + 10., dataset=d1).save()
            Xic(mz=mz + 15., dataset=d1).save()
            # three approx equal
            Xic(mz=mz + 0.005, dataset=d1).save()
            Xic(mz=mz + 0.0, dataset=d1).save()
            Xic(mz=mz - 0.0015, dataset=d1).save()
            # three smaller
            Xic(mz=mz - 5., dataset=d1).save()
            Xic(mz=mz - 10., dataset=d1).save()
            Xic(mz=mz - 15., dataset=d1).save()
            # three approx equal from another dataset
            d2 = Dataset(name='dataset2')
            d2.save()
            Xic(mz=mz + 0.005, dataset=d2).save()
            Xic(mz=mz + 0.0, dataset=d2).save()
            Xic(mz=mz - 0.0015, dataset=d2).save()
            self.assertEqual(Xic.objects.all().count(), 12)
            xics = Xic.objects.all().filter(dataset=d1).filter(mz__gte=mz + 0.01).filter(mz__lte=mz - 0.01)
            self.assertEqual(xics.objects.all().count(), 3)
Beispiel #3
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 def test_add_xic(self):
     m1 = Molecule(name='TestMolecule1', sum_formula="C1H2O3")
     m1.save()
     s1 = Standard(molecule=m1, inventory_id="0")
     s1.save()
     a1 = Adduct(nM=1, delta_formula='+H+K', charge=-2)
     a1.save()
     d1 = Dataset(name='Dataset1')
     d1.save()
     d1.standards_present.add(s1)
     d1.adducts_present.add(a1)
     x1 = Xic(mz='0.0', dataset=d1)
     xic = [1.0, 2.0, 3.0, 4.0, 5.0]
     x1.set_xic(xic)
     x1.save()
     self.assertEqual(Xic.objects.all().count(), 1)
     np.testing.assert_array_almost_equal(xic, x1.xic)
Beispiel #4
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 def test_add_dataset(self):
     # create standards
     m1 = Molecule(name='TestMolecule1', sum_formula="C1H2O3")
     m1.save()
     m2 = Molecule(name='TestMolecule1', sum_formula="C2H2O3")
     m2.save()
     s1 = Standard(molecule=m1, inventory_id="0")
     s1.save()
     s2 = Standard(molecule=m2, inventory_id="1")
     s2.save()
     # create adduct
     a1 = Adduct(nM=1, delta_formula='+H+K', charge=-2)
     a1.save()
     # create a dataset
     d1 = Dataset(name='Dataset1')
     d1.save()
     d1.standards_present.add(s1)
     d1.standards_present.add(s2)
     d1.adducts_present.add(a1)
     self.assertEqual(Dataset.objects.all().count(), 1)
     self.assertEqual(Dataset.objects.all()[0].standards_present.count(), 2)