From 0c8e7a221c6a088d71a20a3c3b3ca14693cc9610 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 7 May 2022 08:47:27 +0300 Subject: [PATCH 1/7] Update pom.xml --- pom.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index c011bc11b..c1f3e8938 100644 --- a/pom.xml +++ b/pom.xml @@ -207,8 +207,8 @@ org.semanticweb.elk - elk-owlapi - 0.4.3 + elk-owlapi4 + 0.5.0-SNAPSHOT log4j From 2582313cde69a33d197da31e8b93c91aa4285106 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 7 May 2022 08:51:34 +0300 Subject: [PATCH 2/7] Update pom.xml --- pom.xml | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/pom.xml b/pom.xml index c1f3e8938..8d35db245 100644 --- a/pom.xml +++ b/pom.xml @@ -156,6 +156,19 @@ + + + sonatype-nexus-snapshots + https://oss.sonatype.org/content/repositories/snapshots/ + + false + + + true + + + + net.sourceforge.owlapi From 542775905f721111329b181ac49549a181c5f0ec Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sat, 5 Aug 2023 20:55:22 +0300 Subject: [PATCH 3/7] Update ReasonerHelperTest.java --- .../test/java/org/obolibrary/robot/ReasonerHelperTest.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/robot-core/src/test/java/org/obolibrary/robot/ReasonerHelperTest.java b/robot-core/src/test/java/org/obolibrary/robot/ReasonerHelperTest.java index aaee02de0..dd20f0b54 100644 --- a/robot-core/src/test/java/org/obolibrary/robot/ReasonerHelperTest.java +++ b/robot-core/src/test/java/org/obolibrary/robot/ReasonerHelperTest.java @@ -49,7 +49,9 @@ public void testIncoherentRBox() } catch (IncoherentRBoxException e) { isCaughtException = true; } - assertTrue(isCaughtException); + // To our great disappointment, ELK does not recognise this incoherent R Box + // https://github.com/ontodev/robot/pull/999#issuecomment-1666567017 + // assertTrue(isCaughtException); } } From a805341511b8345e62cb47b01324d632e82828a8 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Mon, 7 Aug 2023 14:34:41 +0300 Subject: [PATCH 4/7] Fix ELK 0.5 test --- pom.xml | 19 +++---------------- .../org/obolibrary/robot/ReasonerHelper.java | 5 ++--- .../obolibrary/robot/ReasonerHelperTest.java | 2 +- 3 files changed, 6 insertions(+), 20 deletions(-) diff --git a/pom.xml b/pom.xml index 1903099a7..dd4908801 100644 --- a/pom.xml +++ b/pom.xml @@ -156,19 +156,6 @@ - - - sonatype-nexus-snapshots - https://oss.sonatype.org/content/repositories/snapshots/ - - false - - - true - - - - com.google.guava @@ -224,9 +211,9 @@ 1.7.32 - org.semanticweb.elk - elk-owlapi4 - 0.5.0-SNAPSHOT + au.csiro + elk-owlapi4 + 0.5.0 log4j diff --git a/robot-core/src/main/java/org/obolibrary/robot/ReasonerHelper.java b/robot-core/src/main/java/org/obolibrary/robot/ReasonerHelper.java index aba706401..9acdbcebd 100644 --- a/robot-core/src/main/java/org/obolibrary/robot/ReasonerHelper.java +++ b/robot-core/src/main/java/org/obolibrary/robot/ReasonerHelper.java @@ -46,9 +46,8 @@ public class ReasonerHelper { public static Set getUnsatisfiableObjectProperties(OWLReasoner reasoner) { Set unsatObjectProps = new HashSet<>(); - if (reasoner - .getPrecomputableInferenceTypes() - .contains(InferenceType.OBJECT_PROPERTY_HIERARCHY)) { + if (reasoner.getPrecomputableInferenceTypes().contains(InferenceType.OBJECT_PROPERTY_HIERARCHY) + && !reasoner.getClass().getName().equals("org.semanticweb.elk.owlapi.ElkReasoner")) { // Fast object-unsat check logger.info( "Object-property precomputation is supported; using that to find unsatisfiable object properties..."); diff --git a/robot-core/src/test/java/org/obolibrary/robot/ReasonerHelperTest.java b/robot-core/src/test/java/org/obolibrary/robot/ReasonerHelperTest.java index dd20f0b54..0eed596ec 100644 --- a/robot-core/src/test/java/org/obolibrary/robot/ReasonerHelperTest.java +++ b/robot-core/src/test/java/org/obolibrary/robot/ReasonerHelperTest.java @@ -51,7 +51,7 @@ public void testIncoherentRBox() } // To our great disappointment, ELK does not recognise this incoherent R Box // https://github.com/ontodev/robot/pull/999#issuecomment-1666567017 - // assertTrue(isCaughtException); + assertTrue(isCaughtException); } } From 49a569e8fedecb04433e0369fd0bc65130214d0a Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Mon, 7 Aug 2023 14:56:48 +0300 Subject: [PATCH 5/7] Update ReasonerHelperTest.java --- .../src/test/java/org/obolibrary/robot/ReasonerHelperTest.java | 2 -- 1 file changed, 2 deletions(-) diff --git a/robot-core/src/test/java/org/obolibrary/robot/ReasonerHelperTest.java b/robot-core/src/test/java/org/obolibrary/robot/ReasonerHelperTest.java index 0eed596ec..aaee02de0 100644 --- a/robot-core/src/test/java/org/obolibrary/robot/ReasonerHelperTest.java +++ b/robot-core/src/test/java/org/obolibrary/robot/ReasonerHelperTest.java @@ -49,8 +49,6 @@ public void testIncoherentRBox() } catch (IncoherentRBoxException e) { isCaughtException = true; } - // To our great disappointment, ELK does not recognise this incoherent R Box - // https://github.com/ontodev/robot/pull/999#issuecomment-1666567017 assertTrue(isCaughtException); } } From 514365675eefed1168d1f8d66c5edebc9d4de767 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Mon, 7 Aug 2023 14:57:12 +0300 Subject: [PATCH 6/7] Update pom.xml --- pom.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pom.xml b/pom.xml index dd4908801..5272cf580 100644 --- a/pom.xml +++ b/pom.xml @@ -211,9 +211,9 @@ 1.7.32 - au.csiro - elk-owlapi4 - 0.5.0 + au.csiro + elk-owlapi4 + 0.5.0 log4j From 8e375d53ab819e06289ff25dfd05e7f76092d669 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Mon, 7 Aug 2023 15:05:54 +0300 Subject: [PATCH 7/7] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fc76d039b..ec6c958a4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] +- Updated ELK from 0.4.3 to 0.5.0. [#999]. This is an important change as ELK 0.5.0 is more complete than 0.4.3, which means that it will potentially uncover inferences, in particular unsatisfiable classes, which were not recognised by ELK 0.4.3. + ## [1.9.4] - 2023-05-23 ### Changed