def test_remove_dt_non_existent(self):
"""
Try to call remove on a dataType with no H5 file.
Should work.
"""
folder_path = self.files_helper.get_project_folder(self.test_project, "42")
datatype = MappedType()
datatype.storage_path = folder_path
assert not os.path.exists(datatype.get_storage_file_path())
self.files_helper.remove_datatype(datatype)
def test_remove_dt_non_existent(self):
"""
Try to call remove on a dataType with no H5 file.
Should throw an exception.
"""
folder_path = self.files_helper.get_project_folder(self.test_project, "42")
datatype = MappedType()
datatype.storage_path = folder_path
self.assertFalse(os.path.exists(datatype.get_storage_file_path()))
self.assertRaises(FileStructureException, self.files_helper.remove_datatype, datatype)
def test_remove_dt_non_existent(self):
"""
Try to call remove on a dataType with no H5 file.
Should work.
"""
folder_path = self.files_helper.get_project_folder(self.test_project, "42")
datatype = MappedType()
datatype.storage_path = folder_path
self.assertFalse(os.path.exists(datatype.get_storage_file_path()))
self.files_helper.remove_datatype(datatype)
def test_remove_dt_happy_flow(self):
"""
Happy flow for removing a file related to a DataType.
"""
folder_path = self.files_helper.get_project_folder(self.test_project, "42")
datatype = MappedType()
datatype.storage_path = folder_path
open(datatype.get_storage_file_path(), 'w')
self.assertTrue(os.path.exists(datatype.get_storage_file_path()), "Test file was not created!")
self.files_helper.remove_datatype(datatype)
self.assertFalse(os.path.exists(datatype.get_storage_file_path()), "Test file was not deleted!")
class ProjectionMatrixData(MappedType):
"""
Base DataType for representing a ProjectionMatrix.
The projection is between a source of type Connectivity regions or Surface and a set of Sensors.
"""
sources = MappedType(label = "surface or region",
default = None, required = True)
## We can not use base class sensors here due to polymorphic selection
sensors = MappedType(label = "Sensors", default = None, required = False,
doc = """ A set of sensors to compute projection matrix for them. """)
projection_data = arrays.FloatArray(label = "Projection Matrix Data",
default = None, required = True)
def setUp(self):
"""
Prepare data for tests
"""
storage_folder = os.path.join(config.TVB_STORAGE, "test_hdf5")
if os.path.exists(storage_folder):
shutil.rmtree(storage_folder)
os.makedirs(storage_folder)
# Create data type for which to store data
self.data_type = MappedType()
self.data_type.storage_path = storage_folder
self.test_2D_array = numpy.random.random((10, 10))
self.data_name = "vertex"
def accepted_filters():
filters = MappedType.accepted_filters()
filters.update({
'datatype_class._number_of_regions': {
'type': 'int',
'display': 'No of Regions',
'operations': ['==', '<', '>']
}
})
return filters
def test_move_datatype(self):
"""
Make sure associated H5 file is moved to a correct new location.
"""
folder_path = self.files_helper.get_project_folder(self.test_project, "42")
datatype = MappedType()
datatype.storage_path = folder_path
open(datatype.get_storage_file_path(), 'w')
self.assertTrue(os.path.exists(datatype.get_storage_file_path()), "Test file was not created!")
self.files_helper.move_datatype(datatype, self.PROJECT_NAME + '11', "43")
self.assertFalse(os.path.exists(datatype.get_storage_file_path()), "Test file was not moved!")
datatype.storage_path = self.files_helper.get_project_folder(self.PROJECT_NAME + '11', "43")
self.assertTrue(os.path.exists(datatype.get_storage_file_path()), "Test file was not created!")
def setUp(self):
"""
Prepare data for tests
"""
storage_folder = os.path.join(TvbProfile.current.TVB_STORAGE, "test_hdf5")
if os.path.exists(storage_folder):
shutil.rmtree(storage_folder)
os.makedirs(storage_folder)
# Create data type for which to store data
self.data_type = MappedType()
self.data_type.storage_path = storage_folder
self.test_2D_array = numpy.random.random((10, 10))
self.data_name = "vertex"
def test_move_datatype(self):
"""
Make sure associated H5 file is moved to a correct new location.
"""
folder_path = self.files_helper.get_project_folder(self.test_project, "42")
datatype = MappedType()
datatype.storage_path = folder_path
open(datatype.get_storage_file_path(), 'w')
self.assertTrue(os.path.exists(datatype.get_storage_file_path()), "Test file was not created!")
self.files_helper.move_datatype(datatype, self.PROJECT_NAME + '11', "43")
self.assertFalse(os.path.exists(datatype.get_storage_file_path()), "Test file was not moved!")
datatype.storage_path = self.files_helper.get_project_folder(self.PROJECT_NAME + '11', "43")
self.assertTrue(os.path.exists(datatype.get_storage_file_path()), "Test file was not created!")
def test_remove_dt_happy_flow(self):
"""
Happy flow for removing a file related to a DataType.
"""
folder_path = self.files_helper.get_project_folder(self.test_project, "42")
datatype = MappedType()
datatype.storage_path = folder_path
open(datatype.get_storage_file_path(), 'w')
self.assertTrue(os.path.exists(datatype.get_storage_file_path()), "Test file was not created!")
self.files_helper.remove_datatype(datatype)
self.assertFalse(os.path.exists(datatype.get_storage_file_path()), "Test file was not deleted!")
def accepted_filters():
filters = MappedType.accepted_filters()
filters.update({
'datatype_class._nr_dimensions': {
'type': 'int',
'display': 'Dimensionality',
'operations': ['==', '<', '>']
},
'datatype_class._length_1d': {
'type': 'int',
'display': 'Shape 1',
'operations': ['==', '<', '>']
},
'datatype_class._length_2d': {
'type': 'int',
'display': 'Shape 2',
'operations': ['==', '<', '>']
}
})
return filters
class MappedTypeStorageTests(unittest.TestCase):
"""
Test class for testing mapped type data storage into file.
Most of the storage functionality is tested in the test suite
of HDF5StorageManager
"""
def setUp(self):
"""
Prepare data for tests
"""
storage_folder = os.path.join(TvbProfile.current.TVB_STORAGE, "test_hdf5")
if os.path.exists(storage_folder):
shutil.rmtree(storage_folder)
os.makedirs(storage_folder)
# Create data type for which to store data
self.data_type = MappedType()
self.data_type.storage_path = storage_folder
self.test_2D_array = numpy.random.random((10, 10))
self.data_name = "vertex"
def tearDown(self):
"""
Clean up tests data
"""
if os.path.exists(self.data_type.storage_path):
shutil.rmtree(self.data_type.storage_path)
def test_store_data(self):
"""
Test data storage into file
"""
self.data_type.store_data(self.data_name, self.test_2D_array)
read_data = self.data_type.get_data(self.data_name)
numpy.testing.assert_array_equal(self.test_2D_array, read_data, "Did not get the expected data")
def test_store_chunked_data(self):
"""
Test data storage into file, but splitted in chunks
"""
self.data_type.store_data_chunk(self.data_name, self.test_2D_array)
read_data = self.data_type.get_data(self.data_name)
numpy.testing.assert_array_equal(self.test_2D_array, read_data, "Did not get the expected data")
def test_set_metadata(self):
"""
This test checks assignment of metadata to dataset or storage file
"""
# First create some data and check if it is stored
self.data_type.store_data(self.data_name, self.test_2D_array)
key = "meta_key"
value = "meva_val"
self.data_type.set_metadata({key: value}, self.data_name)
read_meta_data = self.data_type.get_metadata(self.data_name)
self.assertEqual(value, read_meta_data[key], "Meta value is not correct")
# Now we'll store metadata on file /root node
self.data_type.set_metadata({key: value})
read_meta_data = self.data_type.get_metadata()
self.assertEqual(value, read_meta_data[key], "Meta value is not correct")
def test_remove_metadata(self):
"""
This test checks removal of metadata from dataset
"""
# First create some data and check if it is stored
self.data_type.store_data(self.data_name, self.test_2D_array)
key = "meta_key"
value = "meva_val"
self.data_type.set_metadata({key: value}, self.data_name)
read_meta_data = self.data_type.get_metadata(self.data_name)
self.assertEqual(value, read_meta_data[key], "Meta value is not correct")
# Now delete metadata
self.data_type.remove_metadata(key, self.data_name)
read_meta_data = self.data_type.get_metadata(self.data_name)
self.assertEqual(0, len(read_meta_data), "There should be no metadata on node")
class MappedTypeStorageTests(unittest.TestCase):
"""
Test class for testing mapped type data storage into file.
Most of the storage functionality is tested in the test suite
of HDF5StorageManager
"""
def setUp(self):
"""
Prepare data for tests
"""
storage_folder = os.path.join(TvbProfile.current.TVB_STORAGE,
"test_hdf5")
if os.path.exists(storage_folder):
shutil.rmtree(storage_folder)
os.makedirs(storage_folder)
# Create data type for which to store data
self.data_type = MappedType()
self.data_type.storage_path = storage_folder
self.test_2D_array = numpy.random.random((10, 10))
self.data_name = "vertex"
def tearDown(self):
"""
Clean up tests data
"""
if os.path.exists(self.data_type.storage_path):
shutil.rmtree(self.data_type.storage_path)
def test_store_data(self):
"""
Test data storage into file
"""
self.data_type.store_data(self.data_name, self.test_2D_array)
read_data = self.data_type.get_data(self.data_name)
numpy.testing.assert_array_equal(self.test_2D_array, read_data,
"Did not get the expected data")
def test_store_chunked_data(self):
"""
Test data storage into file, but splitted in chunks
"""
self.data_type.store_data_chunk(self.data_name, self.test_2D_array)
read_data = self.data_type.get_data(self.data_name)
numpy.testing.assert_array_equal(self.test_2D_array, read_data,
"Did not get the expected data")
def test_set_metadata(self):
"""
This test checks assignment of metadata to dataset or storage file
"""
# First create some data and check if it is stored
self.data_type.store_data(self.data_name, self.test_2D_array)
key = "meta_key"
value = "meva_val"
self.data_type.set_metadata({key: value}, self.data_name)
read_meta_data = self.data_type.get_metadata(self.data_name)
self.assertEqual(value, read_meta_data[key],
"Meta value is not correct")
# Now we'll store metadata on file /root node
self.data_type.set_metadata({key: value})
read_meta_data = self.data_type.get_metadata()
self.assertEqual(value, read_meta_data[key],
"Meta value is not correct")
def test_remove_metadata(self):
"""
This test checks removal of metadata from dataset
"""
# First create some data and check if it is stored
self.data_type.store_data(self.data_name, self.test_2D_array)
key = "meta_key"
value = "meva_val"
self.data_type.set_metadata({key: value}, self.data_name)
read_meta_data = self.data_type.get_metadata(self.data_name)
self.assertEqual(value, read_meta_data[key],
"Meta value is not correct")
# Now delete metadata
self.data_type.remove_metadata(key, self.data_name)
read_meta_data = self.data_type.get_metadata(self.data_name)
self.assertEqual(0, len(read_meta_data),
"There should be no metadata on node")
def __init__(self, row1="test", row2="test"):
MappedType.__init__(self)
self.row1 = row1
self.row2 = row2
def __init__(self, row1="test", row2="test"):
MappedType.__init__(self)
self.row1 = row1
self.row2 = row2