Merge pull request #1093 from ontodev/owlapi4525

Migrate to OWL API 4.5.25 (not released yet)

Author: jamesaoverton

CHANGELOG.md

@@ -6,6 +6,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+- Upgrade OWLAPI to 4.5.25 [#1093]
+- Fixing OBO Serialiser erroneous logging [#1088]
+- Fixing OBO Serialiser bug where built in vocabulary was introduced as annotation properties [#1089]
 
 ### Added
 - Subset method added to [`extract`] [#1000]
@@ -14,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Restore logging details for CLI [#1091]
 
 ## [1.9.2] - 2023-02-09
+- Upgrade OWLAPI to 4.5.24 [#1086]
 
 ### Changed
 - Upgrade OWLAPI to 4.5.24 [#1086]

pom.xml

@@ -165,7 +165,7 @@
     <dependency>
       <groupId>net.sourceforge.owlapi</groupId>
       <artifactId>owlapi-api</artifactId>
-      <version>4.5.24</version>
+      <version>4.5.25</version>
       <exclusions>
         <exclusion>
           <groupId>com.google.code.findbugs</groupId>
@@ -176,7 +176,7 @@
     <dependency>
       <groupId>net.sourceforge.owlapi</groupId>
       <artifactId>owlapi-apibinding</artifactId>
-      <version>4.5.24</version>
+      <version>4.5.25</version>
       <exclusions>
         <exclusion>
           <groupId>com.google.code.findbugs</groupId>
@@ -187,7 +187,7 @@
     <dependency>
       <groupId>net.sourceforge.owlapi</groupId>
       <artifactId>owlapi-rio</artifactId>
-      <version>4.5.24</version>
+      <version>4.5.25</version>
       <exclusions>
         <exclusion>
           <groupId>com.google.code.findbugs</groupId>

robot-command/src/test/java/org/obolibrary/robot/CommandLineIT.java

@@ -231,9 +231,18 @@ public void testExecute() throws Exception {
       }
       runCommand(command);
     }
-    // Regression test for dropped axiom:
+
+    // Regression test for dropped axiom should fail:
     // https://github.com/ontodev/robot/issues/98
-    runCommand("robot convert -i dropped_axiom.owl -o " + "results/dropped_axiom.owl");
+    boolean passed = true;
+    try {
+      runCommand("robot convert -i dropped_axiom.owl -o " + "results/dropped_axiom.owl");
+    } catch (Exception e) {
+      passed = false;
+    }
+    if (passed) {
+      throw new Exception("dropped_axiom.owl test should fail but it passed");
+    }
 
     compareResults();
   }

robot-core/pom.xml

@@ -59,7 +59,7 @@
             <excludes></excludes>
             -->
             <ignoreMissingClassesByRegularExpressions>
-            	<!-- To handle sesame-rio-api-2.7.16.jar -> rdf4j-rio-api-2.4.2.jar lib change on owlapi 4.5.24 upgrade:  -->
+            	<!-- To handle sesame-rio-api-2.7.16.jar -> rdf4j-rio-api-2.4.2.jar lib change on owlapi 4.5.25 upgrade:  -->
             	<!-- This ignore can be removed in consecutive releases -->
             	<ignoreMissingClassesByRegularExpression>org.openrdf.rio.*</ignoreMissingClassesByRegularExpression>
             </ignoreMissingClassesByRegularExpressions>
@@ -86,7 +86,7 @@
     <dependency>
       <groupId>net.sourceforge.owlapi</groupId>
       <artifactId>owlapi-api</artifactId>
-      <version>4.5.24</version>
+      <version>4.5.25</version>
       <exclusions>
         <exclusion>
           <groupId>com.google.code.findbugs</groupId>
@@ -97,7 +97,7 @@
     <dependency>
       <groupId>net.sourceforge.owlapi</groupId>
       <artifactId>owlapi-apibinding</artifactId>
-      <version>4.5.24</version>
+      <version>4.5.25</version>
       <exclusions>
         <exclusion>
           <groupId>com.google.code.findbugs</groupId>
@@ -108,7 +108,7 @@
     <dependency>
       <groupId>net.sourceforge.owlapi</groupId>
       <artifactId>owlapi-rio</artifactId>
-      <version>4.5.24</version>
+      <version>4.5.25</version>
       <exclusions>
         <exclusion>
           <groupId>com.google.code.findbugs</groupId>