def test_document_update_simple(self):
d1 = ProvDocument()
d1.set_default_namespace(EX_URI)
d1.entity('e')
b1 = d1.bundle('b1')
b1.entity('e')
d2 = ProvDocument()
d2.set_default_namespace(EX_URI)
d2.entity('e')
b1 = d2.bundle('b1')
b1.entity('e')
b2 = d2.bundle('b2')
b2.entity('e')
self.assertRaises(ProvException, lambda: d1.update(1))
d1.update(d2)
self.assertEqual(len(d1.get_records()), 2)
self.assertEqual(len(d1.bundles), 2)
def test_document_update_simple(self):
d1 = ProvDocument()
d1.set_default_namespace(EX_URI)
d1.entity('e')
b1 = d1.bundle('b1')
b1.entity('e')
d2 = ProvDocument()
d2.set_default_namespace(EX_URI)
d2.entity('e')
b1 = d2.bundle('b1')
b1.entity('e')
b2 = d2.bundle('b2')
b2.entity('e')
self.assertRaises(ProvException, lambda: d1.update(1))
d1.update(d2)
self.assertEqual(len(d1.get_records()), 2)
self.assertEqual(len(d1.bundles), 2)
class NIDMObjectsUnitTesting(unittest.TestCase):
"""
Unit testing of NIDM objects (compared to examples provided in
nidm-results.owl)
"""
def setUp(self):
self.export_dir = os.path.join(TEST_FOLDER, 'nidm')
if not os.path.isdir(self.export_dir):
os.mkdir(self.export_dir)
# Retreive owl file for NIDM-Results
owl_file = os.path.join(TERM_RESULTS_DIR, 'nidm-results.owl')
assert owl_file
self.owl = OwlReader(owl_file)
self.doc = ProvDocument()
# self.bundle = ProvBundle(identifier=NIIRI[software_lc+'_results_id'])
self.provn_file = os.path.join(self.export_dir, 'unit_test.provn')
namespaces_file = os.path.join(TERM_RESULTS_DIR, "templates", \
"Namespaces.txt")
namespaces_fid = open(namespaces_file)
self.prefixes = namespaces_fid.read()
namespaces_fid.close()
self.to_delete_files = [self.provn_file]
self.gt_ttl_files = list()
def test_design_matrix(self):
mat = np.matrix('1 2; 3 4')
mat_image = os.path.join(os.path.dirname(TEST_FOLDER), "data", \
"fmri.feat", "design.png")
design_matrix = DesignMatrix(mat, mat_image, self.export_dir)
self.doc.update(design_matrix.export())
# In the FSL export the design matrix contains both the Design Matrix
# entity and the Image entity representing the design matrix
# visualisation.
self.to_delete_files.append(os.path.join(self.export_dir, \
"DesignMatrix.csv"))
self.to_delete_files.append(os.path.join(self.export_dir, \
"DesignMatrix.png"))
gt_file = self.owl.get_example(NIDM['DesignMatrix'])
self.gt_ttl_files = [os.path.join(TERM_RESULTS_DIR, \
gt_file.replace("file://./", "")),
os.path.join(TERM_RESULTS_DIR, "examples", "Image-DesignMatrix.txt")]
self._create_gt_and_compare("Design Matrix")
def test_data(self):
data = Data(grand_mean_scaling=True, target=100.0)
self.doc.update(data.export())
gt_file = self.owl.get_example(NIDM['Data'])
self.gt_ttl_files.append(os.path.join(TERM_RESULTS_DIR, \
gt_file.replace("file://./", "")))
self._create_gt_and_compare("Data")
# INDEPEDENT_CORR = NIDM['IndependentError']
# SERIALLY_CORR = NIDM['SeriallyCorrelatedError']
# COMPOUND_SYMMETRY_CORR = NIDM['CompoundSymmetricError']
# ARBITRARILY_CORR = NIDM['ArbitriralyCorrelatedError']
# def test_error_model_indepdt_global(self):
# error_distribution = GAUSSIAN_DISTRIBUTION
# variance_homo = True
# variance_spatial = SPATIALLY_GLOBAL
# dependance = INDEPEDENT_CORR
# dependance_spatial = SPATIALLY_GLOBAL
# error_model = ErrorModel(error_distribution, variance_homo,
# variance_spatial, dependance, dependance_spatial)
# self.doc.update(error_model.export())
# nidm_classes = {
# "ErrorModel": dict(
# error_model_id="niiri:error_model_id",
# noise_distribution="nidm:GaussianDistribution",
# variance_homo="true",
# variance_spatial="nidm:SpatiallyGlobal",
# dependence="nidm:IndependentError",
# dependence_spatial="nidm:SpatiallyLocal"
# )
# }
# self._create_gt_and_compare(nidm_classes, "Data")
def _create_gt_and_compare(self, class_name):
# Write-out current example in a provn file and convert to turtle
provn_fid = open(self.provn_file, 'w')
provn_fid.write(self.doc.get_provn())
provn_fid.close()
ttl_file = self.provn_file.replace(".provn", ".ttl")
call("provconvert -infile "+self.provn_file+" -outfile "+ttl_file, \
shell=True)
self.to_delete_files.append(ttl_file)
# Load current example graph
ex_graph = Graph()
ex_graph.parse(source=ttl_file, format='turtle')
# Read and concatenate ground truth files
gt = ""
for gt_ttl_file in self.gt_ttl_files:
gt_fid = open(gt_ttl_file)
# What is described in the examples to be at any path is relative
# in export
gt = gt.replace("/path/to/", "./")
gt = gt+gt_fid.read()
gt_fid.close()
gt_graph = Graph()
gt = self.prefixes+gt
gt_graph.parse(data=gt, format='turtle')
# Compare graphs
found_diff = compare_graphs(ex_graph, gt_graph)
if found_diff:
raise Exception("Difference in "+class_name+".")
def tearDown(self):
# Delete files created for testing
for to_delete_file in self.to_delete_files:
if os.path.isfile(to_delete_file):
os.remove(to_delete_file)
os.rmdir(self.export_dir)
