def setUp(self):
api.initialize(extra_jars=(os.environ[OVATION_TEST_JAR_PATH_KEY],os.environ[OVATION_TEST_JAR_PATH_KEY]))
if not CONNECTION_PATH_KEY in os.environ:
raise OvationTestException("OVATION_CONNECTION_FILE not defined in the test environment")
self.connection_file_path = os.environ[CONNECTION_PATH_KEY]
if not os.path.exists(self.connection_file_path):
if 'OVATION_LOCK_SERVER' in os.environ:
host = os.environ['OVATION_LOCK_SERVER']
else:
host = gethostname()
if host == 'localhost':
host = '127.0.0.1'
create_local_database(self.connection_file_path,
host=host,
federatedDatabaseID=os.environ.get(OVATION_FDID_KEY, None))
test = api.ovation_package().test
self.test_manager = test.TestManager(self.connection_file_path,
'Institution',
'Lab',
'crS9RjS6wJgmZkJZ1WRbdEtIIwynAVmqFwrooGgsM7ytyR+wCD3xpjJEENey+b0GVVEgib++HAKh94LuvLQXQ2lL2UCUo75xJwVLL3wmd21WbumQqKzZk9p6fkHCVoiSxgon+2RaGA75ckKNmUVTeIBn+QkalKCg9p1P7FbWqH3diXlAOKND2mwjI8V4unq7aaKEUuCgdU9V/BjFBkoytG8FzyBCNn+cBUNTByYy7RxYxH37xECZJ6/hG/vP4QjKpks9cu3yQL9QjXBQIizrzini0eQj62j+QzCSf0oQg8KdIeZHuU+ZSZZ1pUHLYiOiQWaOL9cVPxqMzh5Q/Zvu6Q==',
'TestUser',
'TestPassword')
self.dsc = self.test_manager.setupDatabase()
# Make sure we cleanup
self.addCleanup(clean_local_database, self.test_manager)
def create_local_database(connection_path, host=None, federatedDatabaseID=1):
if host is None:
host = gethostname()
ovation = api.ovation_package()
ovation.database.DatabaseManager.createLocalDatabase(connection_path,
host,
int(federatedDatabaseID))
# Retrieving each parameter may throw a DatabaseError, so we can't use a list comprehension
for k in xnatScan.attrs():
try:
if k.startswith(dtype + '/parameters/'):
parametersDict[k] = xnat_api(xnatScan.attrs.get, k)
except (DatabaseError, StopIteration):
_log.error("Unable to retrieve parameter " + k)
except DatabaseError, e:
_log.error("Unable to set parameters")
parametersDict = {}
parameters = dict2map(parametersDict)
scannerParameters = parameters
ovation = api.ovation_package()
BYTE_DATATYPE = ovation.NumericDataType(
ovation.NumericDataFormat.SignedFixedPointDataType, 1,
ovation.NumericByteOrder.ByteOrderNeutral)
for r in iterate_entity_collection(xnatScan.resources):
_log.info(" Resource " + xnat_api(r.label))
# Insert one epoch group per resource group
resourceGroup = g.insertEpochGroup(xnat_api(r.label), g.getStartTime())
for f in iterate_entity_collection(r.files):
# Import one epoch per resource file
e = resourceGroup.insertEpoch(
g.getStartTime(),
g.getEndTime(), #TODO
scanType,
# Retrieving each parameter may throw a DatabaseError, so we can't use a list comprehension
for k in xnatScan.attrs():
try:
if k.startswith(dtype + '/parameters/'):
parametersDict[k] = xnat_api(xnatScan.attrs.get, k)
except (DatabaseError,StopIteration):
_log.error("Unable to retrieve parameter " + k)
except DatabaseError, e:
_log.error("Unable to set parameters")
parametersDict = {}
parameters = dict2map(parametersDict)
scannerParameters = parameters
ovation = api.ovation_package()
BYTE_DATATYPE = ovation.NumericDataType(ovation.NumericDataFormat.SignedFixedPointDataType, 1, ovation.NumericByteOrder.ByteOrderNeutral)
for r in iterate_entity_collection(xnatScan.resources):
_log.info(" Resource " + xnat_api(r.label))
# Insert one epoch group per resource group
resourceGroup = g.insertEpochGroup(xnat_api(r.label),
g.getStartTime())
for f in iterate_entity_collection(r.files):
# Import one epoch per resource file
e = resourceGroup.insertEpoch(
g.getStartTime(),
g.getEndTime(), #TODO
scanType,
parameters
