コード例 #1
0
ファイル: test_job_db.py プロジェクト: NLeSC/MAGMa
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)
コード例 #2
0
ファイル: test_job_db.py プロジェクト: wangjs/MAGMa
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)
コード例 #3
0
ファイル: test_job_db.py プロジェクト: NLeSC/MAGMa
 def setUp(self):
     self.job = JobDb(initTestingDB(dataset="useallpeaks"))
コード例 #4
0
ファイル: test_job_db.py プロジェクト: NLeSC/MAGMa
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,
            },
        )
コード例 #5
0
ファイル: test_job_db.py プロジェクト: NLeSC/MAGMa
 def setUp(self):
     # mock job session
     self.session = initTestingDB(dataset=None)
     self.job = JobDb(self.session)
コード例 #6
0
ファイル: test_job_db.py プロジェクト: wangjs/MAGMa
 def setUp(self):
     # mock job session
     self.session = initTestingDB()
     self.job = JobDb(self.session)
コード例 #7
0
ファイル: test_job_db.py プロジェクト: wangjs/MAGMa
 def setUp(self):
     self.job = JobDb(initTestingDB(dataset='useallpeaks'))
コード例 #8
0
ファイル: test_job_db.py プロジェクト: wangjs/MAGMa
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
        })