def check_ontology_path(ontology_path):
'''
Check that ontology_path is a valid path
Argument:
ontology_path Path to serialized ontology file or directory of turtle files
Return:
Error message string
Empty string if there are no errors
'''
# If ontology_path is a file, it should be one of the Toolkit's serialized ontology files
if os.path.isfile(ontology_path):
try:
if serializer.get_identifier(ontology_path) != serializer.ONTOLOGY:
return '{} is not a serialized ontology file'.format(
ontology_path)
except serializer.DeserializeError:
return '{} is not a serialized ontology file'.format(ontology_path)
else:
return ''
# If ontology_path is a directory, it should contain at least one .ttl file
if os.path.isdir(ontology_path):
filenames = os.listdir(ontology_path)
for filename in filenames:
if filename.endswith('.ttl'):
return ''
return '{} is a directory that does not contain any turtle files'.format(
ontology_path)
# If it's something else, punt
return '{} is not a file or a directory'.format(ontology_path)
def check_data_paths(data_paths):
'''
Check that all the data_paths are a valid data path
Argument:
data_paths List of zero or more paths to json files or serialized casedata objects
Return:
List of error message strings
Empty list if there are no errors
'''
# Start with empty list of bad files
bad_files = []
# Do for each data_path
for path in data_paths:
# If path is a file, it should be
# one of the Toolkit's serialized json files or a valid json file
if os.path.isfile(path):
# If it's a Toolkit serialized json file, cool.
try:
if serializer.get_identifier(path) == serializer.CASEDATA:
continue
except serializer.DeserializeError:
pass
# If it's a valid json file, cool.
try:
json.load(open(path))
continue
except (json.decoder.JSONDecodeError, UnicodeDecodeError):
pass
# If it's neither, add to list of bad files
bad_files.append(path)
# If it's not a file, add to list of bad files
else:
bad_files.append(path)
# If there are any bad files, construct and return error message
if len(bad_files) == 0:
return ''
if len(bad_files) == 1:
return '{} is neither a serialized casedata object nor a valid json file.'.format(
bad_files[0])
return 'These are neither a serialized casedata objects nor a valid json files: {}.'.format(
bad_files)
def get_ontology(path, verbose=True, **kwargs):
'''
If path is a serialized ongology file, deserialize it and return it.
If path is a directory that contains turtle files, build Ontology object from scratch.
If path is something else, raise exception.
Arguments:
path Full path to a serialized ontology file or a directory containing turtle files
verbose If true and using Ontospy, Ontospy library runs verbosely
kwargs Additional arguments passed on to Ontospy
Return:
An Ontology object
Raise:
Exception if path is not a serialized ontology file or a directory containing turtle files
'''
# Start with empty Ontology object
ontology = Ontology()
# If path is a serialized ontology file, deserialize it and set context for error messages
if os.path.isfile(path) and serializer.get_identifier(
path) == serializer.ONTOLOGY:
_identifer, metadata, ontology.__dict__ = serializer.deserialize(path)
if metadata['version'] != VERSION:
print(
'{} was serialized with a different version of the toolkit. Use this command to reserialize:'
.format(path))
print()
print(' serialize {}'.format(metadata['path']))
print()
sys.exit(1)
# If path is a directory containing turtle files, build Ontology
# Note that _read_turtle_files sets the context for error messages
elif os.path.isdir(path) and [
filename
for filename in os.listdir(path) if filename.endswith('.ttl')
]:
ontology.__dict__ = _read_turtle_files(path, verbose, **kwargs)
# If path is something else, raise
else:
raise Exception(
'{} is neither a serialized ontology file nor a directory containing turtle files'
.format(path))
# Return the ontology object
return ontology
def get_ontology(path, verbose=True, **kwargs):
'''
If path is a serialized ongology file, deserialize it and return it.
If path is a directory that contains turtle files, build Ontology object from scratch.
If path is something else, raise exception.
Arguments:
path Full path to a serialized ontology file or a directory containing turtle files
verbose If true and using Ontospy, Ontospy library runs verbosely
kwargs Additional arguments passed on to Ontospy
Return:
An Ontology object
Side effect:
This function populates namespace_manager.namespace_manager
Raise:
Exception if path is not a serialized ontology file or a directory containing turtle files
'''
# Start with empty Ontology object
ontology = Ontology()
# If path is a serialized ontology file, deserialize it and populate namespace_manager
if os.path.isfile(path) and serializer.get_identifier(
path) == serializer.ONTOLOGY:
_identifer, _metadata, ontology.__dict__ = serializer.deserialize(path)
namespace_manager.populate(ontology.constraints.keys())
# If path is a directory containing turtle files, build Ontology object AND populate namespace_manager
# Note: _read_turtle_files() populates the namespace_manager so the ontology errors can use it
elif os.path.isdir(path) and [
filename
for filename in os.listdir(path) if filename.endswith('.ttl')
]:
ontology.__dict__ = _read_turtle_files(path, verbose, **kwargs)
# If path is something else, raise
else:
raise Exception(
'{} is neither a serialized ontology file nor a directory containing turtle files'
.format(path))
# Populate the namespace from the ontology classes
# Return the ontology object
return ontology