Merge pull request #513 from dice-group/drill-update

Drill bug fix

ontolearn/incomplete_kb.py

@@ -1,3 +1,26 @@
+# -----------------------------------------------------------------------------
+# MIT License
+#
+# Copyright (c) 2024 Ontolearn Team
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+# -----------------------------------------------------------------------------
 from owlready2 import *
 import random
 from typing import Set

ontolearn/learners/celoe.py

@@ -1,3 +1,27 @@
+# -----------------------------------------------------------------------------
+# MIT License
+#
+# Copyright (c) 2024 Ontolearn Team
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+# -----------------------------------------------------------------------------
+
 from ..base_concept_learner import RefinementBasedConceptLearner
 
 from ..abstracts import AbstractScorer, BaseRefinement, AbstractHeuristic, EncodedPosNegLPStandardKind, \

ontolearn/learners/drill.py

@@ -25,9 +25,11 @@
 
 import pandas as pd
 import json
-from owlapy.class_expression import OWLClassExpression
+from owlapy.class_expression import OWLClassExpression, OWLThing, OWLClass
+from owlapy.iri import IRI
 from owlapy.owl_individual import OWLNamedIndividual
 from owlapy import owl_expression_to_dl
+
 from ontolearn.base_concept_learner import RefinementBasedConceptLearner
 from ontolearn.refinement_operators import LengthBasedRefinement
 from ontolearn.abstracts import AbstractNode, AbstractKnowledgeBase
@@ -51,8 +53,8 @@
 from tqdm import tqdm
 from owlapy.converter import owl_expression_to_sparql_with_confusion_matrix
 
-from ..triple_store import TripleStore
-from ..utils.static_funcs import make_iterable_verbose
+from ontolearn.triple_store import TripleStore
+from ontolearn.utils.static_funcs import make_iterable_verbose
 from owlapy.utils import get_expression_length
 
 
@@ -438,17 +440,23 @@ def compute_quality_of_class_expression(self, state: RL_State) -> None:
         # (3) Increment the number of tested concepts attribute.
 
         """
-        if isinstance(self.kb,TripleStore):
-            sparql_query=owl_expression_to_sparql_with_confusion_matrix(expression=state.concept,
-                                                           positive_examples=self.pos,
-                                                           negative_examples=self.neg)
-            bindings=self.kb.query(sparql_query).json()["results"]["bindings"]
+        if isinstance(self.kb, TripleStore):
+            c = state.concept
+            if c is OWLThing:
+                tp = list(self.kb.reasoner.types(list(self.pos)[0], True))  # get types of a lp example
+                if OWLThing not in tp:  # if owl:Thing not explicitly specified check for owl:NamedIndividual
+                    named_individual = OWLClass(IRI('http://www.w3.org/2002/07/owl#', 'NamedIndividual'))
+                    if named_individual in tp:
+                        c = named_individual
+
+            sparql_query = owl_expression_to_sparql_with_confusion_matrix(expression=c, positive_examples=self.pos,
+                                                                          negative_examples=self.neg)
+            bindings = self.kb.query(sparql_query).json()["results"]["bindings"]
             assert len(bindings) == 1
-            bindings=bindings.pop()
-            confusion_matrix={k : v["value"]for k,v in bindings.items()}
+            bindings = bindings.pop()
+            confusion_matrix = {k: v["value"]for k, v in bindings.items()}
             quality = self.quality_func(confusion_matrix=confusion_matrix)
 
-
         else:
             individuals = frozenset([i for i in self.kb.individuals(state.concept)])
             quality = self.quality_func(individuals=individuals, pos=self.pos, neg=self.neg)

ontolearn/learners/ocel.py

@@ -1,3 +1,27 @@
+# -----------------------------------------------------------------------------
+# MIT License
+#
+# Copyright (c) 2024 Ontolearn Team
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+# -----------------------------------------------------------------------------
+
 from .celoe import CELOE
 from typing import Optional
 import owlapy

ontolearn/owl_neural_reasoner.py

@@ -1,3 +1,26 @@
+# -----------------------------------------------------------------------------
+# MIT License
+#
+# Copyright (c) 2024 Ontolearn Team
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+# -----------------------------------------------------------------------------
 from owlapy.owl_property import (
     OWLDataProperty,
     OWLObjectInverseOf,

ontolearn/scripts/litserve_neural_reasoner.py

@@ -1,3 +1,26 @@
+# -----------------------------------------------------------------------------
+# MIT License
+#
+# Copyright (c) 2024 Ontolearn Team
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+# -----------------------------------------------------------------------------
 import argparse
 import litserve as ls
 from ontolearn.owl_neural_reasoner import TripleStoreNeuralReasoner

ontolearn/scripts/run.py

@@ -1,7 +1,3 @@
-"""
-
-
-"""
 # -----------------------------------------------------------------------------
 # MIT License
 #

ontolearn/triple_store.py

@@ -565,11 +565,7 @@ def types(self, ind: OWLNamedIndividual, direct: bool = False) -> Iterable[OWLCl
             query = "SELECT ?x WHERE {" + f"<{ind.str}> a" + " ?x. }"
         else:
             query = rdfs_prefix + "SELECT DISTINCT ?x WHERE {" + f"<{ind.str}> a ?cls. " " ?cls rdfs:subClassOf* ?x}"
-        yield from [
-            i
-            for i in send_http_request_to_ts_and_fetch_results(self.url, query, OWLClass)
-            if i != OWLClass(IRI("http://www.w3.org/2002/07/owl#", "NamedIndividual"))
-        ]
+        yield from send_http_request_to_ts_and_fetch_results(self.url, query, OWLClass)
 
     def get_root_ontology(self) -> AbstractOWLOntology:
         return self.ontology