def setUpClass(cls):
if os.path.isfile('ODKFiles/odkBCExportNew.csv'):
os.remove('ODKFiles/odkBCExportNew.csv')
if os.path.isfile('ODKFiles/odkBCExportPrev.csv'):
os.remove('ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/odkExport_phmrc-1.csv',
'ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/odkExport_phmrc-2.csv',
'ODKFiles/odkBCExportNew.csv')
if not os.path.isfile('smartva'):
downloadSmartVA()
if not os.path.isfile('Pipeline.db'):
createTransferDB('Pipeline.db', '.', 'enilepiP')
# pipelineRunDate = datetime.datetime.now()
pipelineRunDate = datetime.datetime(2018, 9, 1, 9, 0, 0). \
strftime('%Y_%m_%d_%H:%M:%S')
xferDB = TransferDB(dbFileName = 'copy_Pipeline.db',
dbDirectory = '.',
dbKey = 'enilepiP',
plRunDate = pipelineRunDate)
conn = xferDB.connectDB()
c = conn.cursor()
sql = 'UPDATE Pipeline_Conf SET algorithm = ?, algorithmMetadataCode = ?'
par = ('SmartVA', 'SmartVA|2.0.0_a8|PHMRCShort|1|PHMRCShort|1')
c.execute(sql, par)
settingsPipeline = xferDB.configPipeline(conn)
settingsODK = xferDB.configODK(conn)
settingsSmartVA = xferDB.configOpenVA(conn,
'SmartVA',
settingsPipeline.workingDirectory)
conn.rollback()
conn.close()
cls.staticRunDate = datetime.datetime(2018, 9, 1, 9, 0, 0). \
strftime('%Y_%m_%d_%H:%M:%S')
shutil.rmtree(
os.path.join('OpenVAFiles', cls.staticRunDate),
ignore_errors = True
)
cliSmartVA = OpenVA(vaArgs = settingsSmartVA,
pipelineArgs = settingsPipeline,
odkID = settingsODK.odkID,
runDate = cls.staticRunDate)
zeroRecords = cliSmartVA.copyVA()
cls.completed = cliSmartVA.getCOD()
cls.svaOut = os.path.join(
'OpenVAFiles',
cls.staticRunDate,
'1-individual-cause-of-death/individual-cause-of-death.csv'
)
def setUpClass(cls):
if os.path.isfile('ODKFiles/odkBCExportNew.csv'):
os.remove('ODKFiles/odkBCExportNew.csv')
if os.path.isfile('ODKFiles/odkBCExportPrev.csv'):
os.remove('ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/previous_bc_export.csv',
'ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/another_bc_export.csv',
'ODKFiles/odkBCExportNew.csv')
if os.path.isfile('Check_InSilicoVA_Pipeline.db'):
os.remove('Check_InSilicoVA_Pipeline.db')
createTransferDB('Check_InSilicoVA_Pipeline.db', '.', 'enilepiP')
# pipelineRunDate = datetime.datetime.now()
pipelineRunDate = datetime.datetime(2018, 9, 1, 9, 0, 0). \
strftime('%Y_%m_%d_%H:%M:%S')
xferDB = TransferDB(dbFileName = 'Check_InSilicoVA_Pipeline.db',
dbDirectory = '.',
dbKey = 'enilepiP',
plRunDate = pipelineRunDate)
conn = xferDB.connectDB()
c = conn.cursor()
sql = 'UPDATE Pipeline_Conf SET algorithm = ?, algorithmMetadataCode = ?'
par = ('InSilicoVA', 'InSilicoVA-2016|1.0.0|InterVA|5|2016 WHO Verbal Autopsy Form|v1_4_1')
c.execute(sql, par)
sql = 'UPDATE InSilicoVA_Conf SET data_type = ?'
par = ('WHO2016',)
c.execute(sql, par)
settingsPipeline = xferDB.configPipeline(conn)
settingsODK = xferDB.configODK(conn)
settingsInSilicoVA = xferDB.configOpenVA(conn,
'InSilicoVA',
settingsPipeline.workingDirectory)
# conn.rollback()
conn.close()
cls.staticRunDate = datetime.datetime(2018, 9, 1, 9, 0, 0). \
strftime('%Y_%m_%d_%H:%M:%S')
cls.rScript = os.path.join('OpenVAFiles', cls.staticRunDate,
'Rscript_' + cls.staticRunDate + '.R')
cls.rOutFile = os.path.join('OpenVAFiles', cls.staticRunDate,
'Rscript_' + cls.staticRunDate + '.Rout')
rOpenVA = OpenVA(vaArgs = settingsInSilicoVA,
pipelineArgs = settingsPipeline,
odkID = settingsODK.odkID,
runDate = cls.staticRunDate)
zeroRecords = rOpenVA.copyVA()
rOpenVA.rScript()
cls.completed = rOpenVA.getCOD()
def test_3_getCOD_interva(self):
"""Check that getCOD() executes R script for interva"""
c = self.conn.cursor()
sql = "UPDATE Pipeline_Conf SET algorithm = ?, algorithmMetadataCode = ?"
par = ("InterVA",
"InterVA4|4.04|Custom|1|2016 WHO Verbal Autopsy Form|v1_4_1")
c.execute(sql, par)
settingsPipeline = self.xferDB.configPipeline(self.conn)
settingsODK = self.xferDB.configODK(self.conn)
settingsInterVA = self.xferDB.configOpenVA(
self.conn, "InterVA", settingsPipeline.workingDirectory)
self.conn.rollback()
dirOpenVA = os.path.join(settingsPipeline.workingDirectory,
"OpenVAFiles")
dirODK = os.path.join(settingsPipeline.workingDirectory, "ODKFiles")
staticRunDate = datetime.datetime(2018, 9, 1, 9, 0, 0). \
strftime("%Y_%m_%d_%H:%M:%S")
rOutFile = os.path.join(dirOpenVA, staticRunDate,
"Rscript_" + staticRunDate + ".Rout")
shutil.rmtree(os.path.join(dirOpenVA, staticRunDate),
ignore_errors=True)
rOpenVA = OpenVA(vaArgs=settingsInterVA,
pipelineArgs=settingsPipeline,
odkID=settingsODK.odkID,
runDate=staticRunDate)
if os.path.isfile(dirODK + "/odkBCExportNew.csv"):
os.remove(dirODK + "/odkBCExportNew.csv")
if os.path.isfile(dirODK + "/odkBCExportPrev.csv"):
os.remove(dirODK + "/odkBCExportPrev.csv")
shutil.copy(dirODK + "/previous_bc_export.csv",
dirODK + "/odkBCExportPrev.csv")
shutil.copy(dirODK + "/another_bc_export.csv",
dirODK + "/odkBCExportNew.csv")
zeroRecords = rOpenVA.copyVA()
rOpenVA.rScript()
rOpenVA.getCOD()
self.assertTrue(os.path.isfile(rOutFile))
shutil.rmtree(os.path.join(dirOpenVA, staticRunDate),
ignore_errors=True)
def test_3_getCOD_smartva_exception(self):
"""getCOD() should raise an exception with faulty args for smartva cli"""
c = self.conn.cursor()
sql = "UPDATE Pipeline_Conf SET algorithm = ?, algorithmMetadataCode = ?"
par = ("SmartVA", "SmartVA|2.0.0_a8|PHMRCShort|1|PHMRCShort|1")
c.execute(sql, par)
settingsPipeline = self.xferDB.configPipeline(self.conn)
settingsODK = self.xferDB.configODK(self.conn)
self.conn.rollback()
ntSmartVA = collections.namedtuple("ntSmartVA", [
"SmartVA_country", "SmartVA_hiv", "SmartVA_malaria", "SmartVA_hce",
"SmartVA_freetext", "SmartVA_figures", "SmartVA_language"
])
settingsSmartVA = ntSmartVA("Unknown", "Wrong", "Wrong", "Wrong",
"Wrong", "Wrong", "Wrong")
dirOpenVA = os.path.join(settingsPipeline.workingDirectory,
"OpenVAFiles")
dirODK = os.path.join(settingsPipeline.workingDirectory, "ODKFiles")
staticRunDate = datetime.datetime(2018, 9, 1, 9, 0, 0). \
strftime("%Y_%m_%d_%H:%M:%S")
shutil.rmtree(os.path.join(dirOpenVA, staticRunDate),
ignore_errors=True)
if os.path.isfile(dirODK + "/odkBCExportNew.csv"):
os.remove(dirODK + "/odkBCExportNew.csv")
if os.path.isfile(dirODK + "/odkBCExportPrev.csv"):
os.remove(dirODK + "/odkBCExportPrev.csv")
shutil.copy(dirODK + "/previous_bc_export.csv",
dirODK + "/odkBCExportPrev.csv")
shutil.copy(dirODK + "/another_bc_export.csv",
dirODK + "/odkBCExportNew.csv")
cliSmartVA = OpenVA(vaArgs=settingsSmartVA,
pipelineArgs=settingsPipeline,
odkID=settingsODK.odkID,
runDate=staticRunDate)
zeroRecords = cliSmartVA.copyVA()
self.assertRaises(SmartVAError, cliSmartVA.getCOD)
shutil.rmtree(os.path.join(dirOpenVA, staticRunDate),
ignore_errors=True)
def test_3_getCOD_smartva(self):
"""Check that getCOD() executes smartva cli"""
c = self.conn.cursor()
sql = "UPDATE Pipeline_Conf SET algorithm = ?, algorithmMetadataCode = ?"
par = ("SmartVA", "SmartVA|2.0.0_a8|PHMRCShort|1|PHMRCShort|1")
c.execute(sql, par)
settingsPipeline = self.xferDB.configPipeline(self.conn)
settingsODK = self.xferDB.configODK(self.conn)
settingsSmartVA = self.xferDB.configOpenVA(
self.conn, "SmartVA", settingsPipeline.workingDirectory)
self.conn.rollback()
dirOpenVA = os.path.join(settingsPipeline.workingDirectory,
"OpenVAFiles")
dirODK = os.path.join(settingsPipeline.workingDirectory, "ODKFiles")
staticRunDate = datetime.datetime(2018, 9, 1, 9, 0, 0). \
strftime("%Y_%m_%d_%H:%M:%S")
shutil.rmtree(os.path.join(dirOpenVA, staticRunDate),
ignore_errors=True)
if os.path.isfile(dirODK + "/odkBCExportNew.csv"):
os.remove(dirODK + "/odkBCExportNew.csv")
if os.path.isfile(dirODK + "/odkBCExportPrev.csv"):
os.remove(dirODK + "/odkBCExportPrev.csv")
shutil.copy(dirODK + "/odkExport_phmrc-1.csv",
dirODK + "/odkBCExportPrev.csv")
shutil.copy(dirODK + "/odkExport_phmrc-2.csv",
dirODK + "/odkBCExportNew.csv")
cliSmartVA = OpenVA(vaArgs=settingsSmartVA,
pipelineArgs=settingsPipeline,
odkID=settingsODK.odkID,
runDate=staticRunDate)
zeroRecords = cliSmartVA.copyVA()
completed = cliSmartVA.getCOD()
svaOut = os.path.join(
dirOpenVA, staticRunDate,
"1-individual-cause-of-death/individual-cause-of-death.csv")
self.assertTrue(os.path.isfile(svaOut))
shutil.rmtree(os.path.join(dirOpenVA, staticRunDate),
ignore_errors=True)
def setUpClass(cls):
if os.path.isfile('ODKFiles/odkBCExportNew.csv'):
os.remove('ODKFiles/odkBCExportNew.csv')
if os.path.isfile('ODKFiles/odkBCExportPrev.csv'):
os.remove('ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/zeroRecords_bc_export.csv',
'ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/zeroRecords_bc_export.csv',
'ODKFiles/odkBCExportNew.csv')
if os.path.isfile('OpenVAFiles/openVA_input.csv'):
os.remove('OpenVAFiles/openVA_input.csv')
if not os.path.isfile('Pipeline.db'):
createTransferDB('Pipeline.db', '.', 'enilepiP')
# pipelineRunDate = datetime.datetime.now()
pipelineRunDate = datetime.datetime(2018, 9, 1, 9, 0, 0). \
strftime('%Y_%m_%d_%H:%M:%S')
xferDB = TransferDB(dbFileName = 'Pipeline.db',
dbDirectory = '.',
dbKey = 'enilepiP',
plRunDate = pipelineRunDate)
conn = xferDB.connectDB()
settingsPipeline = xferDB.configPipeline(conn)
settingsODK = xferDB.configODK(conn)
settingsInterVA = xferDB.configOpenVA(conn,
'InterVA',
settingsPipeline.workingDirectory)
cls.staticRunDate = datetime.datetime(2018, 9, 1, 9, 0, 0). \
strftime('%Y_%m_%d_%H:%M:%S')
shutil.rmtree(
os.path.join('OpenVAFiles', cls.staticRunDate),
ignore_errors = True
)
rOpenVA = OpenVA(vaArgs = settingsInterVA,
pipelineArgs = settingsPipeline,
odkID = settingsODK.odkID,
runDate = cls.staticRunDate)
cls.zeroRecords = rOpenVA.copyVA()
class Check_Exceptions(unittest.TestCase):
def setUp(self):
if os.path.isfile('ODKFiles/odkBCExportNew.csv'):
os.remove('ODKFiles/odkBCExportNew.csv')
if os.path.isfile('ODKFiles/odkBCExportPrev.csv'):
os.remove('ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/odkExport_phmrc-1.csv',
'ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/odkExport_phmrc-2.csv',
'ODKFiles/odkBCExportNew.csv')
if not os.path.isfile('smartva'):
downloadSmartVA()
self.staticRunDate = datetime.datetime(2018, 9, 1, 9, 0, 0). \
strftime('%Y_%m_%d_%H:%M:%S')
xferDB = TransferDB(dbFileName = 'copy_Pipeline.db',
dbDirectory = '.',
dbKey = 'enilepiP',
plRunDate = self.staticRunDate)
conn = xferDB.connectDB()
c = conn.cursor()
if self.id() == 'test_openVA.Check_Exceptions.test_insilico_exception':
algorithm = 'InSilicoVA'
sql = 'UPDATE Pipeline_Conf SET algorithm = ?, algorithmMetadataCode = ?'
par = ('InSilicoVA', 'InSilicoVA|1.1.4|Custom|1|2016 WHO Verbal Autopsy Form|v1_4_1')
c.execute(sql, par)
sql = 'UPDATE InSilicoVA_Conf SET data_type = ?'
par = ('WHO2016',)
c.execute(sql, par)
elif self.id() == 'test_openVA.Check_Exceptions.test_interva_exception':
algorithm = 'InterVA'
sql = 'UPDATE Pipeline_Conf SET algorithm = ?, algorithmMetadataCode = ?'
par = ('InterVA', 'InterVA4|4.04|Custom|1|2016 WHO Verbal Autopsy Form|v1_4_1')
c.execute(sql, par)
sql = 'UPDATE InterVA_Conf SET version = ?'
par = ('5',)
c.execute(sql, par)
else:
algorithm = 'SmartVA'
sql = 'UPDATE Pipeline_Conf SET algorithm = ?, algorithmMetadataCode = ?'
par = ('SmartVA', 'SmartVA|2.0.0_a8|PHMRCShort|1|PHMRCShort|1')
c.execute(sql, par)
settingsPipeline = xferDB.configPipeline(conn)
settingsODK = xferDB.configODK(conn)
settingsAlgorithm = xferDB.configOpenVA(conn,
algorithm,
settingsPipeline.workingDirectory)
if self.id() == 'test_openVA.Check_Exceptions.test_smartva_exception':
ntSmartVA = collections.namedtuple("ntSmartVA",
["SmartVA_country",
"SmartVA_hiv",
"SmartVA_malaria",
"SmartVA_hce",
"SmartVA_freetext",
"SmartVA_figures",
"SmartVA_language"]
)
settingsAlgorithm = ntSmartVA("Unknown",
"Wrong",
"Wrong",
"Wrong",
"Wrong",
"Wrong",
"Wrong")
conn.rollback()
conn.close()
self.rOpenVA = OpenVA(vaArgs = settingsAlgorithm,
pipelineArgs = settingsPipeline,
odkID = '',
runDate = self.staticRunDate)
zeroRecords = self.rOpenVA.copyVA()
self.rOpenVA.rScript()
def test_insilico_exception(self):
"""getCOD() raises exception with faulty R script for InSilicoVA."""
self.assertRaises(OpenVAError, self.rOpenVA.getCOD)
def test_interva_exception(self):
"""getCOD() should raise an exception with problematic interva R script."""
self.assertRaises(OpenVAError, self.rOpenVA.getCOD)
def test_smartva_exception(self):
"""getCOD() should raise an exception with faulty args for smartva cli"""
self.assertRaises(SmartVAError, self.rOpenVA.getCOD)
def tearDown(self):
shutil.rmtree(
os.path.join('OpenVAFiles', self.staticRunDate),
ignore_errors = True
)
if os.path.isfile('ODKFiles/odkBCExportNew.csv'):
os.remove('ODKFiles/odkBCExportNew.csv')
if os.path.isfile('ODKFiles/odkBCExportPrev.csv'):
os.remove('ODKFiles/odkBCExportPrev.csv')
if os.path.isfile('OpenVAFiles/openVA_input.csv'):
os.remove('OpenVAFiles/openVA_input.csv')
if os.path.isfile("OpenVAFiles/recordStorage.csv"):
os.remove("OpenVAFiles/recordStorage.csv")
if os.path.isfile("OpenVAFiles/entityAttributeValue.csv"):
os.remove("OpenVAFiles/entityAttributeValue.csv")
class Check_Exceptions_SmartVA(unittest.TestCase):
@classmethod
def setUpClass(cls):
if os.path.isfile('ODKFiles/odkBCExportNew.csv'):
os.remove('ODKFiles/odkBCExportNew.csv')
if os.path.isfile('ODKFiles/odkBCExportPrev.csv'):
os.remove('ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/odkExport_phmrc-1.csv',
'ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/odkExport_phmrc-2.csv',
'ODKFiles/odkBCExportNew.csv')
if not os.path.isfile('smartva'):
downloadSmartVA()
def setUp(self):
staticRunDate = datetime.datetime(
2018, 9, 1, 9, 0, 0).strftime('%Y_%m_%d_%H:%M:%S')
xferDB = TransferDB(dbFileName='copy_Pipeline.db',
dbDirectory='.',
dbKey='enilepiP',
plRunDate=staticRunDate)
conn = xferDB.connectDB()
c = conn.cursor()
algorithm = 'SmartVA'
sql = 'UPDATE Pipeline_Conf SET algorithm = ?, algorithmMetadataCode = ?'
par = ('SmartVA', 'SmartVA|2.0.0_a8|PHMRCShort|1|PHMRCShort|1')
c.execute(sql, par)
ntSmartVA = collections.namedtuple("ntSmartVA",
["SmartVA_country",
"SmartVA_hiv",
"SmartVA_malaria",
"SmartVA_hce",
"SmartVA_freetext",
"SmartVA_figures",
"SmartVA_language"])
settingsAlgorithm = ntSmartVA("Unknown",
"Wrong",
"Wrong",
"Wrong",
"Wrong",
"Wrong",
"Wrong")
settingsPipeline = xferDB.configPipeline(conn)
self.rOpenVA = OpenVA(vaArgs=settingsAlgorithm,
pipelineArgs=settingsPipeline,
odkID=None,
runDate=staticRunDate)
zeroRecords = self.rOpenVA.copyVA()
conn.rollback()
conn.close()
def test_smartva_exception(self):
"""getCOD() should raise an exception with faulty args for smartva cli"""
self.assertRaises(SmartVAError, self.rOpenVA.getCOD)
def tearDown(self):
staticRunDate = datetime.datetime(
2018, 9, 1, 9, 0, 0).strftime('%Y_%m_%d_%H:%M:%S')
shutil.rmtree(
os.path.join('OpenVAFiles', staticRunDate),
ignore_errors=True
)
@classmethod
def tearDownClass(cls):
if os.path.isfile('ODKFiles/odkBCExportNew.csv'):
os.remove('ODKFiles/odkBCExportNew.csv')
if os.path.isfile('ODKFiles/odkBCExportPrev.csv'):
os.remove('ODKFiles/odkBCExportPrev.csv')
if os.path.isfile('OpenVAFiles/openVA_input.csv'):
os.remove('OpenVAFiles/openVA_input.csv')
if os.path.isfile("OpenVAFiles/recordStorage.csv"):
os.remove("OpenVAFiles/recordStorage.csv")
if os.path.isfile("OpenVAFiles/entityAttributeValue.csv"):
os.remove("OpenVAFiles/entityAttributeValue.csv")
class Check_Exceptions_InterVA(unittest.TestCase):
@classmethod
def setUpClass(cls):
if os.path.isfile('ODKFiles/odkBCExportNew.csv'):
os.remove('ODKFiles/odkBCExportNew.csv')
if os.path.isfile('ODKFiles/odkBCExportPrev.csv'):
os.remove('ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/odkExport_phmrc-1.csv',
'ODKFiles/odkBCExportPrev.csv')
shutil.copy('ODKFiles/odkExport_phmrc-2.csv',
'ODKFiles/odkBCExportNew.csv')
def setUp(self):
staticRunDate = datetime.datetime(
2018, 9, 1, 9, 0, 0).strftime('%Y_%m_%d_%H:%M:%S')
xferDB = TransferDB(dbFileName='copy_Pipeline.db',
dbDirectory='.',
dbKey='enilepiP',
plRunDate=staticRunDate)
conn = xferDB.connectDB()
c = conn.cursor()
algorithm = 'InterVA'
sql = 'UPDATE Pipeline_Conf SET algorithm = ?, algorithmMetadataCode = ?'
par = ('InterVA', 'InterVA4|4.04|Custom|1|2016 WHO Verbal Autopsy Form|v1_4_1')
c.execute(sql, par)
sql = 'UPDATE InterVA_Conf SET version = ?'
par = ('4',)
c.execute(sql, par)
settingsPipeline = xferDB.configPipeline(conn)
settingsAlgorithm = xferDB.configOpenVA(conn,
algorithm,
settingsPipeline.workingDirectory)
self.rOpenVA = OpenVA(vaArgs=settingsAlgorithm,
pipelineArgs=settingsPipeline,
odkID=None,
runDate=staticRunDate)
zeroRecords = self.rOpenVA.copyVA()
self.rOpenVA.rScript()
conn.rollback()
conn.close()
def test_interva_exception(self):
"""getCOD() should raise an exception with problematic Interva R script."""
self.assertRaises(OpenVAError, self.rOpenVA.getCOD)
def tearDown(self):
staticRunDate = datetime.datetime(
2018, 9, 1, 9, 0, 0).strftime('%Y_%m_%d_%H:%M:%S')
shutil.rmtree(
os.path.join('OpenVAFiles', staticRunDate),
ignore_errors=True
)
@classmethod
def tearDownClass(cls):
if os.path.isfile('ODKFiles/odkBCExportNew.csv'):
os.remove('ODKFiles/odkBCExportNew.csv')
if os.path.isfile('ODKFiles/odkBCExportPrev.csv'):
os.remove('ODKFiles/odkBCExportPrev.csv')
if os.path.isfile('OpenVAFiles/openVA_input.csv'):
os.remove('OpenVAFiles/openVA_input.csv')
if os.path.isfile("OpenVAFiles/recordStorage.csv"):
os.remove("OpenVAFiles/recordStorage.csv")
if os.path.isfile("OpenVAFiles/entityAttributeValue.csv"):
os.remove("OpenVAFiles/entityAttributeValue.csv")