class TestExamples(unittest.TestCase):
def __init__(self, *args, **kwargs):
super(TestExamples, self).__init__(*args, **kwargs)
namespaces_def = os.path.join(RELPATH, "terms", "templates", 'Namespaces.txt')
fid = open(namespaces_def, "r")
namespaces = fid.read()
fid.close()
self.term_examples = glob.glob(os.path.join(RELPATH, "terms", "examples", '*.txt'))
self.example_files = example_filenames.union(self.term_examples)
self.examples = dict()
self.owl_files = dict()
for example_file in self.example_files:
ttl_file = os.path.join(os.path.dirname(os.path.dirname(
os.path.abspath(__file__))), example_file)
# ttl_file_url = get_turtle(provn_file)
# ttl_file = provn_file.replace(".provn", ".ttl")
# Read turtle
self.examples[example_file] = Graph()
if example_file in self.term_examples:
fid = open(ttl_file, "r")
ttl_txt = fid.read()
fid.close()
self.examples[example_file].parse(data=namespaces+ttl_txt, format='turtle')
else:
self.examples[example_file].parse(ttl_file, format='turtle')
term_dir = os.path.join(os.path.dirname(ttl_file), os.pardir, 'terms')
if not os.path.isdir(term_dir):
term_dir = os.path.join(os.path.dirname(ttl_file), os.pardir, os.pardir, 'terms')
# Retreive owl file for minimal examples
if not os.path.isdir(term_dir):
term_dir = os.path.join(
os.path.dirname(ttl_file), os.pardir, os.pardir,
os.pardir, 'terms')
owl_files = glob.glob(os.path.join(term_dir, '*.owl'))
self.owl_files[example_file] = owl_files[0]
self.owl_readers = dict()
def _load_owl(self, owl_file):
if owl_file in self.owl_readers:
self.owl = self.owl_readers[owl_file]
else:
# Retreive owl file for NIDM-Results
# owl_file = os.path.join(RELPATH, 'terms', 'nidm-results.owl')
# check the file exists
assert os.path.exists(owl_file)
# Read owl (turtle) file
owl_path = os.path.dirname(owl_file)
if not "extension" in os.path.dirname(owl_file):
import_files = glob.glob(os.path.join(owl_path, \
os.pardir, os.pardir, "imports", '*.ttl'))
else:
import_files = glob.glob(os.path.join(owl_path, \
os.pardir, os.pardir, os.pardir, os.pardir, "imports", '*.ttl'))
# Main ontology file
import_files += glob.glob(os.path.join(owl_path, \
os.pardir, os.pardir, os.pardir, "terms", '*.owl'))
self.owl = OwlReader(owl_file, import_files)
self.owl_readers[owl_file] = self.owl
def test_check_classes(self):
logger.info("TestExamples: test_check_classes")
my_exception = dict()
for example_file in self.example_files:
example_name = example_file
example_graph = self.examples[example_file]
owl = self.owl_files[example_file]
self._load_owl(owl)
# Check that all entity, activity, agent are defined in the data model
exception_msg = self.owl.check_class_names(example_graph, example_name)
my_exception = merge_exception_dict(my_exception, exception_msg)
# Aggredate errors over examples for conciseness
if my_exception:
error_msg = ""
for unrecognised_class_name, examples in my_exception.items():
error_msg += unrecognised_class_name+" (from "+', '.join(examples)+")"
raise Exception(error_msg)
def test_check_attributes(self):
logger.info("TestExamples: test_check_attributes")
my_exception = dict()
my_range_exception = dict()
my_restriction_exception = dict()
for example_file in self.example_files:
example_name = example_file
example_graph = self.examples[example_file]
owl = self.owl_files[example_file]
self._load_owl(owl)
exception_msg = self.owl.check_attributes(example_graph, example_name)
my_exception = merge_exception_dict(my_exception, exception_msg[0])
if not example_file in self.term_examples:
my_range_exception = merge_exception_dict(my_range_exception, exception_msg[1])
else:
# Ignore range exceptions for test examples (as for object
# properties the linked object will be missing)
my_range_exception = dict()
my_restriction_exception = merge_exception_dict(my_restriction_exception, exception_msg[2])
# Aggregate errors over examples for conciseness
error_msg = ""
for found_exception in list([my_exception, my_range_exception, my_restriction_exception]):
if found_exception:
for unrecognised_attribute, example_names in found_exception.items():
error_msg += unrecognised_attribute+" (from "+', '.join(example_names)+")"
# if my_range_exception:
# for unrecognised_range, example_names in my_range_exception.items():
# error_msg += unrecognised_range+" (from "+', '.join(example_names)+")"
if error_msg:
raise Exception(error_msg)
class TestExamples(unittest.TestCase):
def __init__(self, *args, **kwargs):
super(TestExamples, self).__init__(*args, **kwargs)
namespaces_def = os.path.join(RELPATH, "terms", "templates",
'Namespaces.txt')
fid = open(namespaces_def, "r")
namespaces = fid.read()
fid.close()
self.term_examples = glob.glob(
os.path.join(RELPATH, "terms", "examples", '*.txt'))
self.example_files = example_filenames.union(self.term_examples)
self.examples = dict()
self.owl_files = dict()
for example_file in self.example_files:
ttl_file = os.path.join(
os.path.dirname(os.path.dirname(os.path.abspath(__file__))),
example_file)
# ttl_file_url = get_turtle(provn_file)
# ttl_file = provn_file.replace(".provn", ".ttl")
# Read turtle
self.examples[example_file] = Graph()
if example_file in self.term_examples:
fid = open(ttl_file, "r")
ttl_txt = fid.read()
fid.close()
self.examples[example_file].parse(data=namespaces + ttl_txt,
format='turtle')
else:
self.examples[example_file].parse(ttl_file, format='turtle')
term_dir = os.path.join(os.path.dirname(ttl_file), os.pardir,
'terms')
if not os.path.isdir(term_dir):
term_dir = os.path.join(os.path.dirname(ttl_file), os.pardir,
os.pardir, 'terms')
# Retreive owl file for minimal examples
if not os.path.isdir(term_dir):
term_dir = os.path.join(os.path.dirname(ttl_file), os.pardir,
os.pardir, os.pardir, 'terms')
owl_files = glob.glob(os.path.join(term_dir, '*.owl'))
self.owl_files[example_file] = owl_files[0]
self.owl_readers = dict()
def _load_owl(self, owl_file):
if owl_file in self.owl_readers:
self.owl = self.owl_readers[owl_file]
else:
# Retreive owl file for NIDM-Results
# owl_file = os.path.join(RELPATH, 'terms', 'nidm-results.owl')
# check the file exists
assert os.path.exists(owl_file)
# Read owl (turtle) file
owl_path = os.path.dirname(owl_file)
if not "extension" in os.path.dirname(owl_file):
import_files = glob.glob(os.path.join(owl_path, \
os.pardir, os.pardir, "imports", '*.ttl'))
else:
import_files = glob.glob(os.path.join(owl_path, \
os.pardir, os.pardir, os.pardir, os.pardir, "imports", '*.ttl'))
# Main ontology file
import_files += glob.glob(os.path.join(owl_path, \
os.pardir, os.pardir, os.pardir, "terms", '*.owl'))
self.owl = OwlReader(owl_file, import_files)
self.owl_readers[owl_file] = self.owl
def test_check_classes(self):
logger.info("TestExamples: test_check_classes")
my_exception = dict()
for example_file in self.example_files:
example_name = example_file
example_graph = self.examples[example_file]
owl = self.owl_files[example_file]
self._load_owl(owl)
# Check that all entity, activity, agent are defined in the data model
exception_msg = self.owl.check_class_names(example_graph,
example_name)
my_exception = merge_exception_dict(my_exception, exception_msg)
# Aggredate errors over examples for conciseness
if my_exception:
error_msg = ""
for unrecognised_class_name, examples in my_exception.items():
error_msg += unrecognised_class_name + " (from " + ', '.join(
examples) + ")"
raise Exception(error_msg)
def test_check_attributes(self):
logger.info("TestExamples: test_check_attributes")
my_exception = dict()
my_range_exception = dict()
my_restriction_exception = dict()
for example_file in self.example_files:
example_name = example_file
example_graph = self.examples[example_file]
owl = self.owl_files[example_file]
self._load_owl(owl)
exception_msg = self.owl.check_attributes(example_graph,
example_name)
my_exception = merge_exception_dict(my_exception, exception_msg[0])
if not example_file in self.term_examples:
my_range_exception = merge_exception_dict(
my_range_exception, exception_msg[1])
else:
# Ignore range exceptions for test examples (as for object
# properties the linked object will be missing)
my_range_exception = dict()
my_restriction_exception = merge_exception_dict(
my_restriction_exception, exception_msg[2])
# Aggregate errors over examples for conciseness
error_msg = ""
for found_exception in list(
[my_exception, my_range_exception, my_restriction_exception]):
if found_exception:
for unrecognised_attribute, example_names in found_exception.items(
):
error_msg += unrecognised_attribute + " (from " + ', '.join(
example_names) + ")"
# if my_range_exception:
# for unrecognised_range, example_names in my_range_exception.items():
# error_msg += unrecognised_range+" (from "+', '.join(example_names)+")"
if error_msg:
raise Exception(error_msg)
