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Fix filtering axioms with multiple axiom selectors #644

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Mar 4, 2020
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Fix filtering axioms with multiple axiom selectors #644

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3d77fa9
Fix filtering axioms with mutliple axiom selectors
Mar 4, 2020
a5aa934
Update docs on axioms
Mar 4, 2020
fc8fe40
Update CHANGELOG.md
jamesaoverton Mar 4, 2020
27d26b5
Add integration tests
Mar 4, 2020
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## [Unreleased]

### Fixed
- Fix filtering axioms with multiple axiom selectors [#644]

## [1.6.0] - 2020-03-04

### Added
Expand Down Expand Up @@ -168,6 +171,7 @@ First official release of ROBOT!
[`report`]: http://robot.obolibrary.org/report
[`template`]: http://robot.obolibrary.org/template

[#644]: https://github.com/ontodev/robot/issues/644
[#630]: https://github.com/ontodev/robot/issues/630
[#625]: https://github.com/ontodev/robot/issues/625
[#619]: https://github.com/ontodev/robot/issues/619
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161 changes: 161 additions & 0 deletions docs/examples/no-class-logic.owl
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@@ -0,0 +1,161 @@
<?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"/>



<!-- http://purl.obolibrary.org/obo/IAO_0000119 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000119"/>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Data properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->




<!-- http://example.com/propery-1 -->

<owl:DatatypeProperty rdf:about="http://example.com/propery-1">
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://example.com/B6C3F1"/>
<rdf:Description rdf:about="http://example.com/F344N"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#decimal"/>
<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>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://example.com/propery-1"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weight of a mouse or rat in kilograms (kg).</owl:annotatedTarget>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rebecca C Jackson</obo:IAO_0000119>
</owl:Axiom>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->




<!-- http://example.com/B6C3F1 -->

<owl:Class rdf:about="http://example.com/B6C3F1">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10090"/>
<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>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://example.com/B6C3F1"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An inbred strain of mouse used in many scientific investigations.</owl:annotatedTarget>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James A. Overton</obo:IAO_0000119>
</owl:Axiom>



<!-- 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>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://example.com/F344N"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An inbred strain of rat used in many scientific investigations.</owl:annotatedTarget>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James A. Overton</obo:IAO_0000119>
</owl:Axiom>



<!-- 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">
<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 -->

6 changes: 6 additions & 0 deletions docs/remove.md
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Expand Up @@ -201,6 +201,12 @@ Remove structural tautologies (e.g., `owl:Nothing`):
--axioms structural-tautologies \
--output results/no-tautologies.owl

Remove disjoint classes and class assertions:

robot remove --input template.owl \
--axioms "DisjointClasses ClassAssertion" \
--output results/no-class-logic.owl

Create a "base" subset by removing external axioms (alternatively, use `filter --axioms internal`):

robot remove --input template.owl \
Expand Down
21 changes: 12 additions & 9 deletions robot-core/src/main/java/org/obolibrary/robot/RelatedObjectsHelper.java
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Expand Up @@ -89,7 +89,7 @@ public static Set<OWLAxiom> getAnnotationAxioms(OWLOntology ontology, Set<OWLObj
/**
* Filter a set of OWLAxioms based on the provided arguments.
*
* @param axioms Set of OWLAxioms to filter
* @param inputAxioms Set of OWLAxioms to filter
* @param objects Set of OWLObjects to get axioms for
* @param axiomSelectors List of string selectors for types of axioms
* @param baseNamespaces List of string base namespaces used for internal/external selections
Expand All @@ -99,7 +99,7 @@ public static Set<OWLAxiom> getAnnotationAxioms(OWLOntology ontology, Set<OWLObj
* @throws OWLOntologyCreationException on issue creating empty ontology for tautology checker
*/
public static Set<OWLAxiom> filterAxioms(
Set<OWLAxiom> axioms,
Set<OWLAxiom> inputAxioms,
Set<OWLObject> objects,
List<String> axiomSelectors,
List<String> baseNamespaces,
Expand All @@ -110,34 +110,37 @@ public static Set<OWLAxiom> filterAxioms(
// Go through the axiom selectors in order and process selections
boolean internal = false;
boolean external = false;
Set<OWLAxiom> filteredAxioms = new HashSet<>();
for (String axiomSelector : axiomSelectors) {
if (axiomSelector.equalsIgnoreCase("internal")) {
if (external) {
logger.error(
"ignoring 'internal' axiom selector - 'internal' and 'external' together will remove all axioms");
}
axioms = RelatedObjectsHelper.filterInternalAxioms(axioms, baseNamespaces);
filteredAxioms.addAll(
RelatedObjectsHelper.filterInternalAxioms(inputAxioms, baseNamespaces));
internal = true;
} else if (axiomSelector.equalsIgnoreCase("external")) {
if (internal) {
logger.error(
"ignoring 'external' axiom selector - 'internal' and 'external' together will remove all axioms");
}
axioms = RelatedObjectsHelper.filterExternalAxioms(axioms, baseNamespaces);
filteredAxioms.addAll(
RelatedObjectsHelper.filterExternalAxioms(inputAxioms, baseNamespaces));
external = true;
} else if (axiomSelector.equalsIgnoreCase("tautologies")) {
axioms = RelatedObjectsHelper.filterTautologicalAxioms(axioms, false);
filteredAxioms.addAll(RelatedObjectsHelper.filterTautologicalAxioms(inputAxioms, false));
} else if (axiomSelector.equalsIgnoreCase("structural-tautologies")) {
axioms = RelatedObjectsHelper.filterTautologicalAxioms(axioms, true);
filteredAxioms.addAll(RelatedObjectsHelper.filterTautologicalAxioms(inputAxioms, true));
} else {
// Assume this is a normal OWLAxiom type
Set<Class<? extends OWLAxiom>> axiomTypes =
RelatedObjectsHelper.getAxiomValues(axiomSelector);
axioms = filterAxiomsByAxiomType(axioms, objects, axiomTypes, partial, namedOnly);
filteredAxioms.addAll(
filterAxiomsByAxiomType(inputAxioms, objects, axiomTypes, partial, namedOnly));
}
}

return axioms;
return filteredAxioms;
}

/**
Expand Down