From 5a8b62e383afc479c5ecf7294f29b1872dbc1e89 Mon Sep 17 00:00:00 2001
From: Bugra Altug <baltug@genetec.com>
Date: Sat, 27 Jul 2024 18:09:59 +0200
Subject: [PATCH] extract equivalence correction
---
dbrepo-somapper/matching/read_inputs.py | 23 ++++++-----------------
1 file changed, 6 insertions(+), 17 deletions(-)
diff --git a/dbrepo-somapper/matching/read_inputs.py b/dbrepo-somapper/matching/read_inputs.py
index b63640c67a..8a132ae3ee 100644
--- a/dbrepo-somapper/matching/read_inputs.py
+++ b/dbrepo-somapper/matching/read_inputs.py
@@ -283,7 +283,7 @@ class OntologyParser:
# Direct/Indirect imports need to be deleted from ontologies (or imported as seperate. see Owlready2 documentation). Protege can be used for this.
# OWL 2.0 ontologies in NTriples, RDF/XML or OWL/XML format are supported. (OWL/XML is recommended.)
# Relation (A is a B, B is a C, C is a A) is not supported: http://owlready.306.s1.nabble.com/TypeError-metaclass-conflict-td2889.html
- def parse(self, _loc:str, _include_only:OntologyClassTypes=None, _use_reasoner=True, _only_local:bool=True) -> OntologyData:
+ def parse(self, _loc:str, _include_only:[OntologyClassTypes]=None, _use_reasoner=True, _only_local:bool=True) -> OntologyData:
self._data = OntologyData()
try:
Loggers.info(LoggerTypes.LOAD_SERVICE, "Parsing ontology "+str(_loc))
@@ -400,13 +400,9 @@ class OntologyParser:
def _fill_indirect_class_datatype(self, subject, property, value):
if isinstance(property, or2.DataPropertyClass): # Datatype
- if isinstance(value, or2.LogicalClassConstruct):
- logical_values = self._extract_class_construct_information(value)
- logical_values = [self._get_iri(v) for _, v in logical_values]
- self._data.safe_append_class_indirectdatatypes(self._get_iri(subject), logical_values)
- elif isinstance(value, type):
- self._data.safe_append_class_indirectdatatypes(self._get_iri(subject), [self._get_iri(value)])
- elif type(value)==subject: # Individuals will use their parent data types.
+ values = self._extract_range_construct_information(value)
+ self._data.safe_append_class_indirectdatatypes(self._get_iri(subject), values)
+ elif type(value)==subject: # Individuals will use their parent data types. This is done in the "get_individual_datatypes"
self._data.safe_append_class_indirectdatatypes(self._get_iri(subject), [])
def _fill_indirectly_defined_object_property_class(self, property, value):
@@ -424,11 +420,9 @@ class OntologyParser:
Loggers.info(LoggerTypes.LOAD_SERVICE, "Extracting class construct information.")
if isinstance(class_construct, or2.Restriction):
Loggers.info(LoggerTypes.LOAD_SERVICE, "("+str(class_construct.value)+") Extracting restriction.")
- if isinstance(class_construct.value, or2.Restriction):
+ if isinstance(class_construct.value, or2.Restriction): # property chain (op some (dp exactly 1 int))
#return [(class_construct.property, class_construct.value.property)] + self._extract_class_construct_information(class_construct.value) # Gets all chained relations
return self._extract_class_construct_information(class_construct.value) # Gets only chain end.
- elif isinstance(class_construct.value, or2.ConstrainedDatatype):
- return [(class_construct.property, class_construct.value.base_datatype)]
else:
return [(class_construct.property, class_construct.value)]
elif isinstance(class_construct, or2.LogicalClassConstruct): # Complex construction with logical operators
@@ -455,11 +449,6 @@ class OntologyParser:
Loggers.info(LoggerTypes.LOAD_SERVICE, "("+str(class_construct.property)+") Extracting inverse.")
# [(type(class_construct) , class_construct.property)]
return []
- elif isinstance(class_construct, type):
- Loggers.info(LoggerTypes.LOAD_SERVICE, "("+str(class_construct)+") Extracting python type.")
- return [(str(type(class_construct)), class_construct)]
- elif hasattr(class_construct, 'value') and isinstance(class_construct.value, or2.ConstrainedDatatype):
- return [(class_construct.property, class_construct.value.base_datatype)]
else:
Loggers.error(LoggerTypes.LOAD_SERVICE, "In class_construct_information unknown type:"+str(type(class_construct)))
return []
@@ -505,7 +494,7 @@ class OntologyParser:
tmp += self._extract_range_construct_information(cls)
return tmp
else:
- Loggers.error(LoggerTypes.LOAD_SERVICE, "In range_construct_information unknown type:"+str(type(_construct)))
+ Loggers.error(LoggerTypes.LOAD_SERVICE, "In range_construct_information unknown: \"" + str(_construct) + "\" type: \""+str(type(_construct)) + "\".")
return []
def _get_name(self, _entity:or2) -> str:
--
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