Merge branch 'master' into query_update

.github/workflows/java-ci.yml

@@ -11,6 +11,7 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
+    timeout-minutes: 10
     strategy:
       matrix:
         java: [11, 15, 17]

CHANGELOG.md

@@ -7,6 +7,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Added
+- Added option to input template strings from external file [#1152]
+
 ### Changed
 - Updated `duplicate_exact_syonym` [`report`] query to be case-insensitive and ignore synoyms annotated as abbreviation or acronym synonym types [#1179]
 
@@ -15,12 +18,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fix how Template adds entities to the QuotedEntityChecker [#1104]
 - [`merge`] and 'annotate' operations '--annotate-defined-by' excludes reserved OWL 2 vocabularies [#1171]
 - Handle IRIs that are not entities in export [#1168]
+- Fix integration tests [#1181]
 
 ## [1.9.5] - 2023-09-20
 
 ### Added
 - 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]
+- Add `--drop-axiom-annotations` option to drop axiom annotations in [`remove`] and [`filter`] [#1023]
 
 ### Changed
 - Migrate to OWL API 4.5.26 to deal with [broken turtle serialiser](https://github.com/ontodev/robot/issues/1129). [#1135]
@@ -384,10 +389,13 @@ First official release of ROBOT!
 [`report`]: http://robot.obolibrary.org/report
 [`template`]: http://robot.obolibrary.org/template
 [`validate`]: http://robot.obolibrary.org/validate
-
+;
+[#1181]: https://github.com/ontodev/robot/pull/1181
+[#1179]: https://github.com/ontodev/robot/pull/1179
 [#1171]: https://github.com/ontodev/robot/pull/1171
 [#1168]: https://github.com/ontodev/robot/pull/1168
 [#1160]: https://github.com/ontodev/robot/pull/1160
+[#1152]: https://github.com/ontodev/robot/issues/1152
 [#1148]: https://github.com/ontodev/robot/pull/1148
 [#1135]: https://github.com/ontodev/robot/pull/1135
 [#1119]: https://github.com/ontodev/robot/pull/1119
@@ -403,6 +411,7 @@ First official release of ROBOT!
 [#1061]: https://github.com/ontodev/robot/issues/1061
 [#1030]: https://github.com/ontodev/robot/issues/1030
 [#1026]: https://github.com/ontodev/robot/issues/1026
+[#1023]: https://github.com/ontodev/robot/pull/1023
 [#1017]: https://github.com/ontodev/robot/issues/1017
 [#1016]: https://github.com/ontodev/robot/issues/1016
 [#1009]: https://github.com/ontodev/robot/issues/1009

docs/examples/animals_ext_template.owl

@@ -0,0 +1,55 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://www.w3.org/2002/07/owl#"
+     xml:base="http://www.w3.org/2002/07/owl"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:xml="http://www.w3.org/XML/1998/namespace"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+    <Ontology/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/0000001 -->
+
+    <Class rdf:about="http://purl.obolibrary.org/obo/0000001">
+        <rdfs:comment>Any animal in the world.</rdfs:comment>
+        <rdfs:label>animal</rdfs:label>
+    </Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/0000002 -->
+
+    <Class rdf:about="http://purl.obolibrary.org/obo/0000002">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/0000001"/>
+        <rdfs:comment>A member of the genus Canis.</rdfs:comment>
+        <rdfs:label>canine</rdfs:label>
+    </Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/0000003 -->
+
+    <Class rdf:about="http://purl.obolibrary.org/obo/0000003">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/0000001"/>
+        <rdfs:comment>A member of the genus Felis.</rdfs:comment>
+        <rdfs:label>feline</rdfs:label>
+    </Class>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
+

docs/examples/animals_ext_template.tsv

@@ -0,0 +1,2 @@
+CURIE	Label	Parent	Comment
+ID	LABEL	SC %	A rdfs:comment

docs/examples/animals_template.tsv

@@ -0,0 +1,4 @@
+CURIE	Label	Parent	Comment
+obo:0000001	animal		Any animal in the world.
+obo:0000002	canine	animal	A member of the genus Canis.
+obo:0000003	feline	animal	A member of the genus Felis.

docs/examples/animals_template_error.tsv

@@ -0,0 +1,5 @@
+CURIE	Label	Parent	Comment
+ID	LABEL	SC %	A rdfs:comment
+obo:0000001	animal		Any animal in the world.
+0000002	canine	animal	A member of the genus Canis.
+obo:0000003	feline	animal	A member of the genus Felis.

docs/examples/template-drop-axiom-filter.owl

@@ -0,0 +1,130 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="https://github.com/ontodev/robot/examples/template.owl#"
+     xml:base="https://github.com/ontodev/robot/examples/template.owl"
+     xmlns:obo="http://purl.obolibrary.org/obo/"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:xml="http://www.w3.org/XML/1998/namespace"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:example="http://example.com/">
+    <owl:Ontology rdf:about="https://github.com/ontodev/robot/examples/template.owl"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Annotation properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000117 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Data properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://example.com/propery-1 -->
+
+    <owl:DatatypeProperty rdf:about="http://example.com/propery-1">
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weight of a mouse or rat in kilograms (kg).</obo:IAO_0000115>
+        <obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rebecca C Jackson</obo:IAO_0000117>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">weight in kilograms</rdfs:label>
+    </owl:DatatypeProperty>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://example.com/B6C3F1 -->
+
+    <owl:Class rdf:about="http://example.com/B6C3F1">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10090"/>
+        <owl:disjointWith rdf:resource="http://example.com/F344N"/>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An inbred strain of mouse used in many scientific investigations.</obo:IAO_0000115>
+        <obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James A. Overton</obo:IAO_0000117>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">B6C3F1</rdfs:label>
+        <rdfs:seeAlso rdf:resource="http://jaxmice.jax.org/strain/100010.html"/>
+    </owl:Class>
+
+
+
+    <!-- http://example.com/F344N -->
+
+    <owl:Class rdf:about="http://example.com/F344N">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10116"/>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An inbred strain of rat used in many scientific investigations.</obo:IAO_0000115>
+        <obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James A. Overton</obo:IAO_0000117>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">F 344/N</rdfs:label>
+        <rdfs:seeAlso rdf:resource="http://www.informatics.jax.org/external/festing/rat/docs/F344.shtml"/>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_10090 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10090"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_10116 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10116"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Individuals
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://example.com/rat-1234 -->
+
+    <owl:NamedIndividual rdf:about="http://example.com/rat-1234">
+        <rdf:type rdf:resource="http://example.com/F344N"/>
+        <example:propery-1 rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">0.2</example:propery-1>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">rat 1234</rdfs:label>
+    </owl:NamedIndividual>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
+