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Update owl_reader.py
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@mrnolte
mrnolte committed May 14, 2024
1 parent d594c24 commit cf5ba8a
Showing 1 changed file with 119 additions and 114 deletions.
233 changes: 119 additions & 114 deletions docs/vocab/owl_reader.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
'''
"""
This file parses the owl ontologies to get the comments, label and superclass of entities.
'''
"""

import owlready2 as owl
import sys
Expand All @@ -9,123 +9,128 @@


class OWLClassInfo(NamedTuple):
name: None
label: None
superclass: None
comment: None
name: None
label: None
superclass: None
comment: None


def split_comment_into_sentences(text):
# text = " " + text + " "
if not text.endswith("."):
text = text + "."
text = text.replace("\n", " ")
if "e.g." in text:
text = text.replace("e.g.", "e<prd>g<prd>")
if "i.e." in text:
text = text.replace("i.e.", "i<prd>e<prd>")
if "\"" in text:
text = text.replace(".\"", "\".")
if "!" in text:
text = text.replace("!\"", "\"!")
if "?" in text:
text = text.replace("?\"", "\"?")
text = text.replace(".", ".<stop>")
text = text.replace("?", "?<stop>")
text = text.replace("!", "!<stop>")
text = text.replace("<prd>", ".")

comments = text.split("<stop>")
comments = comments[:-1]
comments = [s.strip() for s in comments]
return comments


def _parse_string(string_val, split_param, desired_str_pos):
if split_param in string_val:
return string_val.split(split_param)[desired_str_pos]
else:
return string_val


def _get_string_list(object_list, prefix):
temp = []
for i in list(object_list):
if str(i).startswith(prefix):
temp.append(_parse_string(str(i), ".", 1))
return temp


def _printdict(class_obj):
for obj in class_obj:
if obj.comment:
print(r'\appendixstyle{{{}}} {{$\sqsubseteq$ }} \textit{{{}}} {{--}} {{{}}}\\'.format(
obj.label, str(obj.superclass), str(obj.comment)))
else:
print(r'\appendixstyle{{{}}} {{$\sqsubseteq$ }} \textit{{{}}}.\\'.format(
obj.label, str(obj.superclass)))


def _get_valid_string(temp_val):
if isinstance(temp_val, list):
final_val = []
for i in temp_val:
i = str(i)
final_val.append(_parse_string(i, ".", 1))
return final_val
else:
return _parse_string(str(temp_val), ".", 1)


class OWLReader:

def __init__(self, iri_list):
self.iri_list = iri_list
self.class_objects = []

def get_classes(self):
'''
Gets the classes defined in the ontology their corresponding
superclass, label and comment
'''
for iri in self.iri_list:
self._load_ontology(iri)
self.class_objects = self._create_class_objects() + self.class_objects
self.class_objects = sorted(self.class_objects, key=attrgetter('name'))
self._printdict(self.class_objects)
#return self.class_objects

def _print(self):
for obj in self.class_objects:
print(obj.label, str(obj.superclass), str(obj.comment))

def _load_ontology(self, iri):
self.ontology = owl.get_ontology(iri).load()
self.namespace = self.ontology.get_namespace(iri+"#")
self.prefix = self._parse_string(iri, "/", -1)[:-3]

def _create_class_objects(self):
objects = []
for class_name in list(self.ontology.classes()):
if str(class_name).startswith(self.prefix):
class_name = str(class_name).split(".")[1].replace("_", "\\_")
class_info = self.set_class_info(class_name)
objects.append(OWLClassInfo(name=class_name,
label=class_info[0][0] if class_info[0] else class_name,
superclass=class_info[1],
comment=class_info[2]))
return objects

def set_class_info(self, target_class):
comment = None
try:
def __init__(self, iri_list):
self.iri_list = iri_list
self.class_objects = []

def get_classes(self):
"""
Gets the classes defined in the ontology their corresponding
superclass, label and comment
"""
for iri in self.iri_list:
self._load_ontology(iri)
self.class_objects = self._create_class_objects() + self.class_objects
self.class_objects = sorted(self.class_objects, key=attrgetter('name'))
_printdict(self.class_objects)
# return self.class_objects

def _print(self):
for obj in self.class_objects:
print(obj.label, str(obj.superclass), str(obj.comment))

def _load_ontology(self, iri):
self.ontology = owl.get_ontology(iri).load()
self.namespace = self.ontology.get_namespace(iri + "#")
self.prefix = _parse_string(iri, "/", -1)[:-3]

def _create_class_objects(self):
objects = []
for class_name in list(self.ontology.classes()):
if str(class_name).startswith(self.prefix):
class_name = str(class_name).split(".")[1].replace("_", "\\_")
class_info = self.set_class_info(class_name)
objects.append(OWLClassInfo(name=class_name,
label=class_info[0][0] if class_info[0] else class_name,
superclass=class_info[1],
comment=class_info[2]))
return objects

def set_class_info(self, target_class):
comment = None
try:
target_class_instance = getattr(self.namespace, target_class)
comment = getattr(target_class_instance, "comment")
except AttributeError as e:
raise AttributeError(
"Error accessing 'comment' attribute. The target class '{}' might be incorrect or missing.".format(target_class)
"Error accessing 'comment' attribute. The target class '{}' might be incorrect or missing.".format(
target_class)
) from e
if(comment):
comment = self.split_comment_into_sentences(comment[0])[0]
label = getattr(
getattr(getattr(self.namespace, target_class), "label"), "en")
superclass = self._get_valid_string(
getattr(getattr(self.namespace, target_class), "is_a")[0])

return (label, superclass, comment)

def split_comment_into_sentences(self, text):
#text = " " + text + " "
if not text.endswith("."):
text = text + "."
text = text.replace("\n", " ")
if "e.g." in text:
text = text.replace("e.g.", "e<prd>g<prd>")
if "i.e." in text:
text = text.replace("i.e.", "i<prd>e<prd>")
if "\"" in text:
text = text.replace(".\"", "\".")
if "!" in text:
text = text.replace("!\"", "\"!")
if "?" in text:
text = text.replace("?\"", "\"?")
text = text.replace(".", ".<stop>")
text = text.replace("?", "?<stop>")
text = text.replace("!", "!<stop>")
text = text.replace("<prd>", ".")

comments = text.split("<stop>")
comments = comments[:-1]
comments = [s.strip() for s in comments]
return comments

def _get_valid_string(self, temp_val):
if(isinstance(temp_val, list)):
final_val = []
for i in temp_val:
i = str(i)
final_val.append(self._parse_string(i, ".", 1))
return final_val
else:
return self._parse_string(str(temp_val), ".", 1)

def _get_string_list(self, object_list, prefix):
temp = []
for i in list(object_list):
if str(i).startswith(prefix):
temp.append(self._parse_string(str(i), ".", 1))
return temp

def _parse_string(self, string_val, split_param, desired_str_pos):
if split_param in string_val:
return string_val.split(split_param)[desired_str_pos]
else:
return string_val

def _printdict(self, class_obj):
for obj in class_obj:
if (obj.comment):
print(r'\appendixstyle{{{}}} {{$\sqsubseteq$ }} \textit{{{}}} {{--}} {{{}}}\\'.format(
obj.label, str(obj.superclass), str(obj.comment)))
else:
print(r'\appendixstyle{{{}}} {{$\sqsubseteq$ }} \textit{{{}}}.\\'.format(
obj.label, str(obj.superclass)))


if comment:
comment = split_comment_into_sentences(comment[0])[0]
label = getattr(
getattr(getattr(self.namespace, target_class), "label"), "en")
superclass = _get_valid_string(
getattr(getattr(self.namespace, target_class), "is_a")[0])

return label, superclass, comment

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