Merge pull request #1135 from ontodev/owlapi4526

Update OWL API to 4.5.26
ontodev · Sep 20, 2023 · 797cc73 · 797cc73
2 parents fa04ed6 + 1e05594
commit 797cc73
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Showing 5 changed files with 37 additions and 27 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - 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.
 - Add support for pluggable commands [#1119]
 
+### Changed
+- Migrate to OWL API 4.5.26 to deal with [broken turtle serialiser](https://github.com/ontodev/robot/issues/1129). [#1135]
+- Improvements to `export` and `report` for XLSX format [#1148]
+
 ## [1.9.4] - 2023-05-23
 
 ### Changed
@@ -369,6 +373,8 @@ First official release of ROBOT!
 [`template`]: http://robot.obolibrary.org/template
 [`validate`]: http://robot.obolibrary.org/validate
 
+[#1148]: https://github.com/ontodev/robot/pull/1148
+[#1135]: https://github.com/ontodev/robot/pull/1135
 [#1119]: https://github.com/ontodev/robot/pull/1119
 [#1100]: https://github.com/ontodev/robot/pull/1100
 [#1091]: https://github.com/ontodev/robot/issues/1091

diff --git a/docs/examples/subset_result.owl b/docs/examples/subset_result.owl
@@ -25,29 +25,31 @@
     <!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
 
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref">
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">database_cross_reference</rdfs:label>
+        <rdfs:label>database_cross_reference</rdfs:label>
     </owl:AnnotationProperty>
 
 
 
     <!-- http://www.geneontology.org/formats/oboInOwl#id -->
 
-    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/>
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id">
+        <rdfs:label>id</rdfs:label>
+    </owl:AnnotationProperty>
 
 
 
     <!-- http://www.geneontology.org/formats/oboInOwl#inSubset -->
 
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#inSubset">
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">in_subset</rdfs:label>
+        <rdfs:label>in_subset</rdfs:label>
     </owl:AnnotationProperty>
 
 
 
     <!-- http://www.geneontology.org/formats/oboInOwl#shorthand -->
 
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#shorthand">
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">shorthand</rdfs:label>
+        <rdfs:label>shorthand</rdfs:label>
     </owl:AnnotationProperty>
 
 
@@ -66,10 +68,10 @@
     <!-- http://purl.obolibrary.org/obo/BFO_0000050 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
-    	<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BFO:0000050</oboInOwl:hasDbXref>
-        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">part_of</oboInOwl:id>
-        <oboInOwl:shorthand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">part_of</oboInOwl:shorthand>
+        <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
+        <oboInOwl:hasDbXref>BFO:0000050</oboInOwl:hasDbXref>
+        <oboInOwl:id>part_of</oboInOwl:id>
+        <oboInOwl:shorthand>part_of</oboInOwl:shorthand>
     </owl:ObjectProperty>
 
 
@@ -88,7 +90,7 @@
     <!-- http://purl.obolibrary.org/obo/ONT_1 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/ONT_1">
-        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ONT:1</oboInOwl:id>
+        <oboInOwl:id>ONT:1</oboInOwl:id>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/test#foo"/>
     </owl:Class>
 
@@ -103,11 +105,12 @@
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ONT_1"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ONT:5</oboInOwl:id>
+        <oboInOwl:id>ONT:5</oboInOwl:id>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/test#foo"/>
     </owl:Class>
 </rdf:RDF>
 
 
 
-<!-- Generated by the OWL API (version 4.5.9) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
+
diff --git a/pom.xml b/pom.xml
@@ -166,7 +166,7 @@
     <dependency>
       <groupId>net.sourceforge.owlapi</groupId>
       <artifactId>owlapi-api</artifactId>
-      <version>4.5.25</version>
+      <version>4.5.26</version>
       <exclusions>
         <exclusion>
           <groupId>com.google.code.findbugs</groupId>
@@ -177,7 +177,7 @@
     <dependency>
       <groupId>net.sourceforge.owlapi</groupId>
       <artifactId>owlapi-apibinding</artifactId>
-      <version>4.5.25</version>
+      <version>4.5.26</version>
       <exclusions>
         <exclusion>
           <groupId>com.google.code.findbugs</groupId>
@@ -188,7 +188,7 @@
     <dependency>
       <groupId>net.sourceforge.owlapi</groupId>
       <artifactId>owlapi-rio</artifactId>
-      <version>4.5.25</version>
+      <version>4.5.26</version>
       <exclusions>
         <exclusion>
           <groupId>com.google.code.findbugs</groupId>

diff --git a/robot-core/pom.xml b/robot-core/pom.xml
@@ -86,7 +86,7 @@
     <dependency>
       <groupId>net.sourceforge.owlapi</groupId>
       <artifactId>owlapi-api</artifactId>
-      <version>4.5.25</version>
+      <version>4.5.26</version>
       <exclusions>
         <exclusion>
           <groupId>com.google.code.findbugs</groupId>
@@ -97,7 +97,7 @@
     <dependency>
       <groupId>net.sourceforge.owlapi</groupId>
       <artifactId>owlapi-apibinding</artifactId>
-      <version>4.5.25</version>
+      <version>4.5.26</version>
       <exclusions>
         <exclusion>
           <groupId>com.google.code.findbugs</groupId>
@@ -108,7 +108,7 @@
     <dependency>
       <groupId>net.sourceforge.owlapi</groupId>
       <artifactId>owlapi-rio</artifactId>
-      <version>4.5.25</version>
+      <version>4.5.26</version>
       <exclusions>
         <exclusion>
           <groupId>com.google.code.findbugs</groupId>

diff --git a/robot-core/src/test/resources/subset_result.owl b/robot-core/src/test/resources/subset_result.owl
@@ -25,29 +25,30 @@
     <!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
 
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref">
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">database_cross_reference</rdfs:label>
+        <rdfs:label>database_cross_reference</rdfs:label>
     </owl:AnnotationProperty>
 
 
 
     <!-- http://www.geneontology.org/formats/oboInOwl#id -->
 
-    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/>
-
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id">
+        <rdfs:label>id</rdfs:label>
+    </owl:AnnotationProperty>
 
 
     <!-- http://www.geneontology.org/formats/oboInOwl#inSubset -->
 
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#inSubset">
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">in_subset</rdfs:label>
+        <rdfs:label>in_subset</rdfs:label>
     </owl:AnnotationProperty>
 
 
 
     <!-- http://www.geneontology.org/formats/oboInOwl#shorthand -->
 
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#shorthand">
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">shorthand</rdfs:label>
+        <rdfs:label>shorthand</rdfs:label>
     </owl:AnnotationProperty>
 
 
@@ -67,9 +68,9 @@
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BFO:0000050</oboInOwl:hasDbXref>
-        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">part_of</oboInOwl:id>
-        <oboInOwl:shorthand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">part_of</oboInOwl:shorthand>
+        <oboInOwl:hasDbXref>BFO:0000050</oboInOwl:hasDbXref>
+        <oboInOwl:id>part_of</oboInOwl:id>
+        <oboInOwl:shorthand>part_of</oboInOwl:shorthand>
     </owl:ObjectProperty>
 
 
@@ -88,7 +89,7 @@
     <!-- http://purl.obolibrary.org/obo/ONT_1 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/ONT_1">
-        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ONT:1</oboInOwl:id>
+        <oboInOwl:id>ONT:1</oboInOwl:id>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/test#foo"/>
     </owl:Class>
 
@@ -103,7 +104,7 @@
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ONT_1"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ONT:5</oboInOwl:id>
+        <oboInOwl:id>ONT:5</oboInOwl:id>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/test#foo"/>
     </owl:Class>
 </rdf:RDF>