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Fixes for handling negations in ShEx validation #433

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Nov 10, 2021
Merged

Fixes for handling negations in ShEx validation #433

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a452b1a
Correctly find superclasses for negated types during ShEx validation.…
balhoff Nov 10, 2021
b752e60
Add test file to git.
balhoff Nov 10, 2021
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24 changes: 18 additions & 6 deletions minerva-core/src/main/java/org/geneontology/minerva/validation/ShexValidator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -589,9 +589,15 @@ public Model enrichSuperClasses(Model model) throws IOException {
String getOntTerms =
"PREFIX owl: <http://www.w3.org/2002/07/owl#> "
+ "SELECT DISTINCT ?term " +
" WHERE { " +
" WHERE { " +
" { " +
" ?ind a owl:NamedIndividual . " +
" ?ind a ?term . " +
" ?ind a ?term . " +
" } " +
" UNION" +
" {" +
" ?term a owl:Class ." +
" }" +
" FILTER(?term != owl:NamedIndividual)" +
" FILTER(isIRI(?term)) ." +
" }";
Expand Down Expand Up @@ -672,9 +678,11 @@ public Set<String> getNodeTypes(Model model, String node_uri) throws IOException
String getOntTerms =
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> "
+ "PREFIX owl: <http://www.w3.org/2002/07/owl#> "
+ "SELECT DISTINCT ?type " +
" WHERE { " +
"<"+node_uri+"> rdf:type ?type . " +
+ "SELECT DISTINCT ?type ?is_negated " +
" WHERE { " +
"{ <"+node_uri+"> rdf:type ?type . FILTER(isIRI(?type)) VALUES ?is_negated { false } }" +
"UNION" +
"{ <"+node_uri+"> rdf:type ?blank . ?blank owl:complementOf ?type . FILTER(isBlank(?blank) && isIRI(?type)) VALUES ?is_negated { true } }" +
"FILTER(?type != owl:NamedIndividual)" +
" }";
Set<String> types = new HashSet<String>();
Expand All @@ -684,7 +692,11 @@ public Set<String> getNodeTypes(Model model, String node_uri) throws IOException
while (results.hasNext()) {
QuerySolution qs = results.next();
Resource type = qs.getResource("type");
types.add(getCurie(type.getURI()));
boolean isNegated = qs.getLiteral("is_negated").getBoolean();
String typeCurie = getCurie(type.getURI());
if (isNegated) {
types.add("NOT(" + typeCurie + ")");
} else types.add(typeCurie);
// OWLClass t = tbox_reasoner.getRootOntology().getOWLOntologyManager().getOWLDataFactory().getOWLClass(IRI.create(type.getURI()));
// for(OWLClass p : tbox_reasoner.getSuperClasses(t, false).getFlattened()) {
// String type_curie = getCurie(p.getIRI().toString());
Expand Down
39 changes: 24 additions & 15 deletions minerva-core/src/test/java/org/geneontology/minerva/validation/ShexValidatorTest.java
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Expand Up @@ -76,25 +76,34 @@ public void testShexMetadata() throws IOException {
boolean should_be_valid = true;
validate("src/test/resources/validation/should_pass/", shexMeta, should_be_valid);
}

@Test
public void testHandleNegatedTermInReport() throws Exception {
validate(new File("src/test/resources/validation/model_test/ZFIN_ZDB-GENE-030131-514.ttl"), shex, true);
}

public void validate(String dir, ShexValidator shex, boolean should_be_valid) throws IOException {
public void validate(String dir, ShexValidator shex, boolean shouldBeValid) throws IOException {
File directory = new File(dir);
if(directory.isDirectory()) {
for(File file : directory.listFiles()) {
if(file.getName().endsWith("ttl")) {
Model test_model = ModelFactory.createDefaultModel();
test_model.read(file.getAbsolutePath());
System.out.println("validating "+file.getAbsolutePath()+" size "+test_model.size());
//Note that in the live system, Arachne is executed on the model prior to this step, potentially adding inferred classes that are missed with this.
//this is faster and useful for debugging the shex though. See org.geneontology.minerva.server.validation.ValidationTest in the Test branch of Minerva server for a more complete test
test_model = shex.enrichSuperClasses(test_model);
ShexValidationReport report = shex.runShapeMapValidation(test_model);
if(should_be_valid) {
assertTrue(file+" not conformant "+report.getAsText()+"\n"+report.getAsTab(""), report.isConformant());
}else {
assertFalse(file+" is conformant (should not be)", report.isConformant());
}
}
validate(file, shex, shouldBeValid);
}
}
}

private void validate(File file, ShexValidator shex, boolean shouldBeValid) throws IOException {
if(file.getName().endsWith("ttl")) {
Model test_model = ModelFactory.createDefaultModel();
test_model.read(file.getAbsolutePath());
System.out.println("validating "+file.getAbsolutePath()+" size "+test_model.size());
//Note that in the live system, Arachne is executed on the model prior to this step, potentially adding inferred classes that are missed with this.
//this is faster and useful for debugging the shex though. See org.geneontology.minerva.server.validation.ValidationTest in the Test branch of Minerva server for a more complete test
test_model = shex.enrichSuperClasses(test_model);
ShexValidationReport report = shex.runShapeMapValidation(test_model);
if(shouldBeValid) {
assertTrue(file+" not conformant "+report.getAsText()+"\n"+report.getAsTab(""), report.isConformant());
}else {
assertFalse(file+" is conformant (should not be)", report.isConformant());
}
}
}
Expand Down
166 changes: 166 additions & 0 deletions minerva-core/src/test/resources/validation/model_test/ZFIN_ZDB-GENE-030131-514.ttl
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Original file line number Diff line number Diff line change
@@ -0,0 +1,166 @@
@prefix : <http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@base <http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514> .

<http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514> rdf:type owl:Ontology ;
owl:versionIRI <http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514> ;
<http://geneontology.org/lego/modelstate> "production"^^xsd:string ;
<http://purl.org/dc/elements/1.1/contributor> "GOC:zfin_curators" ;
<http://purl.org/dc/elements/1.1/date> "2021-07-26"^^xsd:string ;
<http://purl.org/dc/elements/1.1/title> "fkbp4 (ZFIN:ZDB-GENE-030131-514)" ;
<http://purl.org/pav/providedBy> "http://zfin.org"^^xsd:string ;
<https://w3id.org/biolink/vocab/in_taxon> <http://purl.obolibrary.org/obo/NCBITaxon_7955> .

#################################################################
# Annotation properties
#################################################################

### http://geneontology.org/lego/evidence
<http://geneontology.org/lego/evidence> rdf:type owl:AnnotationProperty .


### http://geneontology.org/lego/modelstate
<http://geneontology.org/lego/modelstate> rdf:type owl:AnnotationProperty .


### http://geneontology.org/lego/hint/layout/x
<http://geneontology.org/lego/hint/layout/x> rdf:type owl:AnnotationProperty .


### http://geneontology.org/lego/hint/layout/y
<http://geneontology.org/lego/hint/layout/y> rdf:type owl:AnnotationProperty .


### http://purl.org/dc/elements/1.1/contributor
<http://purl.org/dc/elements/1.1/contributor> rdf:type owl:AnnotationProperty .


### http://purl.org/dc/elements/1.1/date
<http://purl.org/dc/elements/1.1/date> rdf:type owl:AnnotationProperty .


### http://purl.org/dc/elements/1.1/source
<http://purl.org/dc/elements/1.1/source> rdf:type owl:AnnotationProperty .


### http://purl.org/dc/elements/1.1/title
<http://purl.org/dc/elements/1.1/title> rdf:type owl:AnnotationProperty .


### http://purl.org/pav/providedBy
<http://purl.org/pav/providedBy> rdf:type owl:AnnotationProperty .


### https://w3id.org/biolink/vocab/in_taxon
<https://w3id.org/biolink/vocab/in_taxon> rdf:type owl:AnnotationProperty .


#################################################################
# Object Properties
#################################################################

### http://purl.obolibrary.org/obo/RO_0002333
<http://purl.obolibrary.org/obo/RO_0002333> rdf:type owl:ObjectProperty .


### http://purl.obolibrary.org/obo/RO_0002418
<http://purl.obolibrary.org/obo/RO_0002418> rdf:type owl:ObjectProperty .


#################################################################
# Classes
#################################################################

### http://identifiers.org/zfin/ZDB-GENE-030131-514
<http://identifiers.org/zfin/ZDB-GENE-030131-514> rdf:type owl:Class .


### http://purl.obolibrary.org/obo/ECO_0000314
<http://purl.obolibrary.org/obo/ECO_0000314> rdf:type owl:Class .


### http://purl.obolibrary.org/obo/GO_0003674
<http://purl.obolibrary.org/obo/GO_0003674> rdf:type owl:Class .


### http://purl.obolibrary.org/obo/GO_0060765
<http://purl.obolibrary.org/obo/GO_0060765> rdf:type owl:Class .


#################################################################
# Individuals
#################################################################

### http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514/f2a1f833-510d-4ec6-8fac-f378b60295fb
<http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514/f2a1f833-510d-4ec6-8fac-f378b60295fb> rdf:type owl:NamedIndividual ,
<http://purl.obolibrary.org/obo/ECO_0000314> ;
<http://purl.org/dc/elements/1.1/contributor> "GOC:zfin_curators" ;
<http://purl.org/dc/elements/1.1/date> "2020-08-31" ;
<http://purl.org/dc/elements/1.1/source> "PMID:31661769" ;
<http://purl.org/pav/providedBy> "http://zfin.org" .


### http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514/f8df1fb9-8e8e-4308-b005-d1177bb42178
<http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514/f8df1fb9-8e8e-4308-b005-d1177bb42178> rdf:type owl:NamedIndividual ,
[ rdf:type owl:Class ;
owl:complementOf <http://purl.obolibrary.org/obo/GO_0060765>
] ;
<http://purl.org/dc/elements/1.1/contributor> "GOC:zfin_curators" ;
<http://purl.org/dc/elements/1.1/date> "2020-08-31" ;
<http://purl.org/pav/providedBy> "http://zfin.org" .


### http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514/7a68dea6-060e-46ea-afe7-4b4611cd3a9d
<http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514/7a68dea6-060e-46ea-afe7-4b4611cd3a9d> rdf:type owl:NamedIndividual ,
<http://purl.obolibrary.org/obo/ECO_0000314> ;
<http://purl.org/dc/elements/1.1/contributor> "GOC:zfin_curators" ;
<http://purl.org/dc/elements/1.1/date> "2020-08-31" ;
<http://purl.org/dc/elements/1.1/source> "PMID:31661769" ;
<http://purl.org/pav/providedBy> "http://zfin.org" .


### http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514/712db525-58a3-4d65-994e-7cdab1fa451f
<http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514/712db525-58a3-4d65-994e-7cdab1fa451f> rdf:type owl:NamedIndividual ,
<http://identifiers.org/zfin/ZDB-GENE-030131-514> ;
<http://purl.org/dc/elements/1.1/contributor> "GOC:zfin_curators" ;
<http://purl.org/dc/elements/1.1/date> "2020-08-31" ;
<http://purl.org/pav/providedBy> "http://zfin.org" .


### http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514/73729ebd-5c25-4827-bccd-fad00f800e26
<http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514/73729ebd-5c25-4827-bccd-fad00f800e26> rdf:type owl:NamedIndividual ,
<http://purl.obolibrary.org/obo/GO_0003674> ;
<http://purl.obolibrary.org/obo/RO_0002333> <http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514/712db525-58a3-4d65-994e-7cdab1fa451f> ;
<http://purl.obolibrary.org/obo/RO_0002418> <http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514/f8df1fb9-8e8e-4308-b005-d1177bb42178> ;
<http://purl.org/dc/elements/1.1/contributor> "GOC:zfin_curators" ;
<http://purl.org/dc/elements/1.1/date> "2020-08-31" ;
<http://purl.org/pav/providedBy> "http://zfin.org"^^xsd:string .

[ rdf:type owl:Axiom ;
owl:annotatedSource <http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514/73729ebd-5c25-4827-bccd-fad00f800e26> ;
owl:annotatedProperty <http://purl.obolibrary.org/obo/RO_0002333> ;
owl:annotatedTarget <http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514/712db525-58a3-4d65-994e-7cdab1fa451f> ;
<http://geneontology.org/lego/evidence> <http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514/7a68dea6-060e-46ea-afe7-4b4611cd3a9d> ;
<http://purl.org/dc/elements/1.1/contributor> "GOC:zfin_curators" ;
<http://purl.org/dc/elements/1.1/date> "2020-08-31" ;
<http://purl.org/pav/providedBy> "http://zfin.org"^^xsd:string ;
rdfs:comment "ZFIN:ZDB-GENE-030131-514 NOT RO:0002264 GO:0060765 ZFIN:ZDB-PUB-191031-1|PMID:31661769 ECO:0000314 2020-08-31 ZFIN contributor-id=GOC:zfin_curators"
] .

[ rdf:type owl:Axiom ;
owl:annotatedSource <http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514/73729ebd-5c25-4827-bccd-fad00f800e26> ;
owl:annotatedProperty <http://purl.obolibrary.org/obo/RO_0002418> ;
owl:annotatedTarget <http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514/f8df1fb9-8e8e-4308-b005-d1177bb42178> ;
<http://geneontology.org/lego/evidence> <http://model.geneontology.org/ZFIN_ZDB-GENE-030131-514/f2a1f833-510d-4ec6-8fac-f378b60295fb> ;
<http://purl.org/dc/elements/1.1/contributor> "GOC:zfin_curators" ;
<http://purl.org/dc/elements/1.1/date> "2020-08-31" ;
<http://purl.org/pav/providedBy> "http://zfin.org"^^xsd:string ;
rdfs:comment "ZFIN:ZDB-GENE-030131-514 NOT RO:0002264 GO:0060765 ZFIN:ZDB-PUB-191031-1|PMID:31661769 ECO:0000314 2020-08-31 ZFIN contributor-id=GOC:zfin_curators"
] .


### Generated by the OWL API (version 4.5.15) https://github.com/owlcs/owlapi