def test_fillSpectrumException(self):
mzMLinstance = pymzml.run.Reader(
testFolder + 'mzml_test_file_1.mzML') # make a Reader instance
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = database.FillDatabase(sqlCon)
self.assertRaises(RuntimeError, fd.fillSpectrum, mzMLinstance)
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = database.FillDatabase(sqlCon)
self.assertRaises(RuntimeError, fd.fillSpectrum, mzMLinstance)
def test_fillMsrunException(self):
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = database.FillDatabase(sqlCon, 'test')
fd.fillMsrun(testFolder + 'mzml_test_file_1.mzML')
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = database.FillDatabase(sqlCon, 'test')
self.assertRaises(sqlite.IntegrityError, fd.fillMsrun,
testFolder + 'mzml_test_file_1.mzML')
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = database.FillDatabase(sqlCon)
self.assertRaises(RuntimeError, fd.fillMsrun,
testFolder + 'mzml_test_file_1.mzML')
def test_linkSpectrumToFeature(self):
expectedNumResult = 4
expectedResult = [(1, 2), (1, 2), (1, 4), (1, 4)]
mzMLinstance = pymzml.run.Reader(
testFolder + 'mzml_test_file_1.mzML') # make a Reader instance
featureXML = parseFeatureXML.Reader(
testFolder +
'featurexmlTestFile_1.featureXML') # make a Reader instance
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = database.FillDatabase(sqlCon, 'test')
fd.fillMsrun(testFolder + 'mzml_test_file_1.mzML')
fd.fillFeatures(featureXML)
fd.fillSpectrum(mzMLinstance)
fd.linkSpectrumToFeature()
actualResult = []
self.cursor.execute("SELECT * FROM feature_has_MSMS_precursor")
for result in self.cursor.fetchall():
actualResult.append(result)
actualResult.append(result)
self.assertEqual(expectedNumResult, len(actualResult))
self.assertListEqual(expectedResult, actualResult)
def test_fillFeaturesException(self):
featureXML = parseFeatureXML.Reader(
testFolder +
'featurexmlTestFile_1.featureXML') # make a Reader instance
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = database.FillDatabase(sqlCon)
self.assertRaises(RuntimeError, fd.fillFeatures, featureXML)
def sanitizeStringError(self):
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = FillDatabase(sqlCon)
self.assertRaises(
UnicodeEncodeError,
fd.sanitizeString("Fo\x00o!")) # raises UnicodeEncodeError
self.assertRaises(UnicodeEncodeError, fd.sanitizeString(
chr(0xD800))) # raises UnicodeEncodeError
def test_updateDescription(self):
# updating from within the same instance
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = database.FillDatabase(sqlCon, 'test')
fd.fillMsrun(testFolder + 'mzml_test_file_1.mzML')
fd.updateDescription('update from same instance')
self.cursor.execute(
"SELECT description FROM `msrun` WHERE msrun_name = 'test'")
self.assertEqual(str(self.cursor.fetchone()[0]),
'update from same instance')
with database.ConnectMySQL('gjb-mysql-1.cluster.lifesci.dundee.ac.uk',
'ndeklein', 'm31th3amh4', 'test') as sqlCon:
fd = database.FillDatabase(sqlCon, 'test')
fd.fillMsrun(testFolder + 'mzml_test_file_1.mzML')
fd.updateDescription('update from same instance')
self.mysql_cursor.execute(
"SELECT description FROM `msrun` WHERE msrun_name = 'test'")
self.assertEqual(str(self.mysql_cursor.fetchone()[0]),
'update from same instance')
# updating from within a different instance
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = database.FillDatabase(sqlCon, 'test')
fd.updateDescription('update from different instance')
self.cursor.execute(
"SELECT description FROM `msrun` WHERE msrun_name = 'test'")
self.assertEqual(str(self.cursor.fetchone()[0]),
'update from different instance')
with database.ConnectMySQL('gjb-mysql-1.cluster.lifesci.dundee.ac.uk',
'ndeklein', 'm31th3amh4', 'test') as sqlCon:
fd = database.FillDatabase(sqlCon, 'test')
fd.updateDescription('update from different instance')
self.mysql_cursor.execute(
"SELECT description FROM `msrun` WHERE msrun_name = 'test'")
self.assertEqual(str(self.mysql_cursor.fetchone()[0]),
'update from different instance')
def test_fillFeatureMappingException(self):
featureXML = parseFeatureXML.Reader(testFolder +
'featurexmlTestFile_1.featureXML')
featureXML_2 = parseFeatureXML.Reader(
testFolder + 'featurexmlTestFile_2.featureXML')
trafoXML = testFolder + 'featurexmlTestFile_2.trafoXML'
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = database.FillDatabase(sqlCon)
self.assertRaises(KeyError, fd.fillFeatureMapping, featureXML,
featureXML_2, trafoXML)
def test_fillFeatureMapping(self):
featureXML_1 = parseFeatureXML.Reader(
testFolder + 'featurexmlTestFile_1.featureXML')
featureXML_2 = parseFeatureXML.Reader(
testFolder + 'featurexmlTestFile_2.featureXML')
trafoXML = testFolder + 'featurexmlTestFile_2.trafoXML'
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = database.FillDatabase(sqlCon, 'test')
fd.fillMsrun(testFolder + 'mzml_test_file_1.mzML')
fd.fillFeatures(featureXML_1)
fd.fillFeatures(featureXML_2)
fd.fillFeatureMapping(featureXML_1, featureXML_2, trafoXML)
def test_updatedDescriptionException(self):
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = database.FillDatabase(sqlCon, 'test')
# msrun_name test doesn't exist, should give RuntimeError
self.assertRaises(RuntimeError, fd.updateDescription, 'test')
# for next test, fill msrun
fd.fillMsrun(testFolder + 'mzml_test_file_1.mzML')
veryLongDescription = 'a' * 501
# description can be only 500 chars max
self.assertRaises(TypeError,
database.FillDatabase.updateDescription, 'test',
veryLongDescription)
self.connection.commit()
def test_fillMsrun(self):
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = database.FillDatabase(sqlCon, 'test')
fd.fillMsrun(testFolder + 'mzml_test_file_1.mzML')
self.cursor.execute("SELECT msrun_name FROM `msrun`")
self.assertEqual(self.cursor.fetchone()[0], 'test')
with database.ConnectMySQL('gjb-mysql-1.cluster.lifesci.dundee.ac.uk',
'ndeklein', 'm31th3amh4', 'test') as sqlCon:
fd = database.FillDatabase(sqlCon, 'test')
fd.fillMsrun(testFolder + 'mzml_test_file_1.mzML')
self.mysql_cursor.execute("SELECT msrun_name FROM `msrun`")
self.assertEqual(self.mysql_cursor.fetchone()[0], 'test')
def test_fillSpectrum(self):
expectedNumResult = 10
mzMLinstance = pymzml.run.Reader(
testFolder + 'mzml_test_file_1.mzML',
'MS:1000527') # make a Reader instance
actualResult = []
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = database.FillDatabase(sqlCon, 'None')
fd.fillMsrun(testFolder + 'mzml_test_file_1.mzML')
fd.fillSpectrum(mzMLinstance)
self.cursor.execute("SELECT * FROM `spectrum`")
for result in self.cursor.fetchall():
actualResult.append(result)
self.assertEqual(expectedNumResult, len(actualResult))
def sanitizeString(self):
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = FillDatabase(sqlCon)
replace = fd.sanitizeString("Fo\x00o!", "replace") # "Fo?o!"
ignore = fd.sanitizeString("Fo\x00o!", "ignore") # "Foo!"
self.assertEqual(replace="Fo?o!")
self.assertEqual(ignore="Foo!")
with database.ConnectMySQL('gjb-mysql-1.cluster.lifesci.dundee.ac.uk',
'ndeklein', 'm31th3amh4', 'test') as sqlCon:
fd = FillDatabase(sqlCon)
replace = fd.sanitizeString("Fo\x00o!", "replace") # "Fo?o!"
ignore = fd.sanitizeString("Fo\x00o!", "ignore") # "Foo!"
self.assertEqual(replace="Fo?o!")
self.assertEqual(ignore="Foo!")
def test_fillFeatures(self):
expectedNumResult = 4
featureXML = parseFeatureXML.Reader(
testFolder +
'featurexmlTestFile_1.featureXML') # make a Reader instance
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = database.FillDatabase(sqlCon, 'test')
fd.fillMsrun(testFolder + 'mzml_test_file_1.mzML')
fd.fillFeatures(featureXML)
actualResult = []
for feature in featureXML.getSimpleFeatureInfo():
self.cursor.execute("SELECT * FROM `feature` WHERE feature_id = ?",
(str(featureXML['id']), ))
actualResult.append(self.cursor.fetchone())
self.connection.commit()
self.assertEqual(len(actualResult), expectedNumResult)
def test_fillMascot(self):
expectedPeptideNumResult = 2
expectedPeptideResult = [(1,462.24009999999998,922.46569999999997, 2,923.45010000000002,-0.98440000000000005,1,20.309999999999999,75.0\
,u'K',u'CDVDIRK',u'D',u'Label:13C(6)15N(2) (K); Label:13C(6)15N(4) (R)',u'0.0000065.0',None,u'462.240142822266_751.5624'\
,3),(2,335.22239999999999,668.43029999999999,2,668.35339999999997,0.076899999999999996,0,12.720000000000001,400.0\
, None,u'FLDFK',None,None,None,None,u'335.222412109375_2270.0684',4)]
expectedProtNumResult = 2
expectedProtResult = [(1, 462.24009999999998, 922.46569999999997, 2, 923.45010000000002, -0.98440000000000005, 1, 20.309999999999999, 75.0, u'K'\
, u'CDVDIRK', u'D', u'Label:13C(6)15N(2) (K); Label:13C(6)15N(4) (R)', u'0.0000065.0', None, u'462.240142822266_751.5624', 3)
,(2, 335.22239999999999, 668.43029999999999, 2, 668.35339999999997, 0.076899999999999996, 0, 12.720000000000001, 400.0, None\
, u'FLDFK', None, None, None, None, u'335.222412109375_2270.0684', 4)]
mzMLinstance = pymzml.run.Reader(
testFolder + 'mzml_test_file_1.mzML',
'MS:1000527') # make a Reader instance
mascot = parseMascot.Reader(testFolder + 'test_mascot.xml')
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = database.FillDatabase(sqlCon, 'test')
fd.fillMsrun(testFolder + 'mzml_test_file_1.mzML')
fd.fillSpectrum(mzMLinstance)
fd.fillMascot(mascot)
actualPeptideResult = []
self.cursor.execute("SELECT * FROM `MASCOT_peptide`")
for result in self.cursor.fetchall():
actualPeptideResult.append(result)
actualProteinResult = []
self.cursor.execute("SELECT * FROM `MASCOT_protein`")
for result in self.cursor.fetchall():
actualProteinResult.append(result)
self.assertEqual(expectedPeptideNumResult, len(actualPeptideResult))
self.assertListEqual(expectedPeptideResult, actualPeptideResult)
self.assertEqual(expectedProtNumResult, len(actualPeptideResult))
self.assertListEqual(expectedProtResult, actualPeptideResult)
def test_linkSpectrumToFeatureException(self):
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = database.FillDatabase(sqlCon)
self.assertRaises(RuntimeError, fd.linkSpectrumToFeature)
def test_fillMascotException(self):
mascot = parseMascot.Reader(testFolder + 'test_mascot.xml')
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
fd = database.FillDatabase(sqlCon)
self.assertRaises(RuntimeError, fd.fillMascot, mascot)
def test_ConnectSqlite(self):
# no exception means succes
with database.ConnectSqlite(testDatabasePath +
'test_pyMSA_database.db') as sqlCon:
pass
