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Merge pull request #1104 from ontodev/template-cycle-bug
Fix how Template adds entities to the QuotedEntityChecker
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‎CHANGELOG.md

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@@ -7,6 +7,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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## [Unreleased]
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### Fixed
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- Fix how Template adds entities to the QuotedEntityChecker [#1104]
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## [1.9.5] - 2023-09-20
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### Added
@@ -379,6 +384,7 @@ First official release of ROBOT!
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[#1148]: https://github.com/ontodev/robot/pull/1148
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[#1135]: https://github.com/ontodev/robot/pull/1135
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[#1119]: https://github.com/ontodev/robot/pull/1119
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[#1104]: https://github.com/ontodev/robot/pull/1104
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[#1100]: https://github.com/ontodev/robot/pull/1100
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[#1091]: https://github.com/ontodev/robot/issues/1091
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[#1089]: https://github.com/ontodev/robot/issues/1089

‎docs/extract.md

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@@ -79,12 +79,14 @@ For more details see the [MIREOT paper](http://dx.doi.org/10.3233/AO-2011-0087).
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The subset method extracts a sub-ontology that contains only the seed terms (that you specify with `--term` and `--term-file` options) and the relations between them. This method uses the [relation-graph](https://github.com/balhoff/relation-graph) to materialize the existential relations among the seed terms. Procedurally, the subset method materializes the input ontology and adds the inferred axioms to the input ontology. Then filters the ontology with the given seed terms. Finally, it reduces the filtered ontology to remove redundant subClassOf axioms.
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82-
robot extract --method subset \
83-
--input subset.obo \
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--term "obo:ONT_1" \
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--term "obo:ONT_5" \
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--term "BFO:0000050" \
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--output results/subset_result.owl
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```
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robot extract --method subset \
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--input subset.obo \
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--term "obo:ONT_1" \
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--term "obo:ONT_5" \
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--term "BFO:0000050" \
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--output results/subset_result.owl
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```
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ROBOT expects any `--term` or IRI in the `--term-file` to exist in the input ontology. If none of the input terms exist, the command will fail with an [empty terms error](errors#empty-terms-error). This can be overridden by including `--force true`.
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‎robot-core/src/main/java/org/obolibrary/robot/QuotedEntityChecker.java

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@@ -249,6 +249,9 @@ public void add(OWLEntity entity, String name) {
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if (entity == null) {
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return;
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}
252+
if (name == null) {
253+
return;
254+
}
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253256
Map<String, IRI> map = pickMap(entity);
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if (map == null) {

‎robot-core/src/main/java/org/obolibrary/robot/Template.java

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Original file line numberDiff line numberDiff line change
@@ -173,7 +173,7 @@ public Template(@Nonnull String name, @Nonnull List<List<String>> rows) throws E
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// Add the contents of the tableRows
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addTable(rows);
176-
addLabels();
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addEntities();
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createParser();
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}
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@@ -203,7 +203,7 @@ public Template(@Nonnull String name, @Nonnull List<List<String>> rows, IOHelper
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// Add the contents of the tableRows
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addTable(rows);
206-
addLabels();
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addEntities();
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createParser();
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}
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@@ -237,7 +237,7 @@ public Template(@Nonnull String name, @Nonnull List<List<String>> rows, OWLOntol
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// Add the contents of the tableRows
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addTable(rows);
240-
addLabels();
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addEntities();
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createParser();
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}
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@@ -276,7 +276,7 @@ public Template(
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// Add the contents of the tableRows
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addTable(rows);
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addLabels();
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addEntities();
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createParser();
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}
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@@ -320,7 +320,7 @@ public Template(
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// Add the contents of the tableRows
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addTable(rows);
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addLabels();
323+
addEntities();
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createParser();
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parser.setOWLEntityChecker(this.checker);
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}
@@ -557,102 +557,103 @@ private void addTable(List<List<String>> rows) throws Exception {
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}
558558
}
559559

560-
/** Add the labels from the rows of the template to the QuotedEntityChecker. */
561-
private void addLabels() {
562-
// If there's no label column, we can't add labels
563-
if (labelColumn == -1) {
560+
/** Add the entities from the rows of the template to the QuotedEntityChecker. */
561+
private void addEntities() {
562+
for (List<String> row : tableRows) {
563+
addEntity(row);
564+
}
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}
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567+
/** Add the entity from this row of the template to the QuotedEntityChecker. */
568+
private void addEntity(List<String> row) {
569+
String id = null;
570+
try {
571+
id = row.get(idColumn);
572+
} catch (IndexOutOfBoundsException e) {
573+
// ignore
574+
}
575+
576+
if (id == null) {
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return;
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}
566-
for (List<String> row : tableRows) {
567-
String id = null;
568-
if (idColumn != -1) {
569-
try {
570-
id = row.get(idColumn);
571-
} catch (IndexOutOfBoundsException e) {
572-
// ignore
573-
}
574-
}
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576-
String label = null;
580+
String label = null;
581+
try {
582+
label = row.get(labelColumn);
583+
} catch (IndexOutOfBoundsException e) {
584+
// ignore
585+
}
586+
587+
String type = null;
588+
if (typeColumn != -1) {
577589
try {
578-
label = row.get(labelColumn);
590+
type = row.get(typeColumn);
579591
} catch (IndexOutOfBoundsException e) {
580592
// ignore
581593
}
594+
}
595+
if (type == null || type.trim().isEmpty()) {
596+
type = "class";
597+
}
582598

583-
if (idColumn != -1 && id == null) {
584-
continue;
585-
}
586-
587-
if (id == null || label == null) {
588-
continue;
589-
}
590-
591-
String type = null;
592-
if (typeColumn != -1) {
593-
try {
594-
type = row.get(typeColumn);
595-
} catch (IndexOutOfBoundsException e) {
596-
// ignore
597-
}
598-
}
599-
if (type == null || type.trim().isEmpty()) {
600-
type = "class";
601-
}
599+
IRI iri = ioHelper.createIRI(id);
600+
if (iri == null) {
601+
iri = IRI.create(id);
602+
}
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603-
IRI iri = ioHelper.createIRI(id);
604-
if (iri == null) {
605-
iri = IRI.create(id);
606-
}
604+
// Try to resolve a CURIE
605+
IRI typeIRI = ioHelper.createIRI(type);
607606

608-
// Try to resolve a CURIE
609-
IRI typeIRI = ioHelper.createIRI(type);
607+
// Set to IRI string or to type string
608+
String typeOrIRI = type;
609+
if (typeIRI != null) {
610+
typeOrIRI = typeIRI.toString();
611+
}
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611-
// Set to IRI string or to type string
612-
String typeOrIRI = type;
613-
if (typeIRI != null) {
614-
typeOrIRI = typeIRI.toString();
615-
}
613+
// Check against builtin types (ignore case), otherwise treat as individual
614+
OWLEntity entity;
615+
String lowerCaseType = typeOrIRI.toLowerCase();
616+
switch (lowerCaseType) {
617+
case "":
618+
case "http://www.w3.org/2002/07/owl#class":
619+
case "class":
620+
entity = dataFactory.getOWLEntity(EntityType.CLASS, iri);
621+
break;
616622

617-
// Check against builtin types (ignore case), otherwise treat as individual
618-
OWLEntity entity;
619-
String lowerCaseType = typeOrIRI.toLowerCase();
620-
switch (lowerCaseType) {
621-
case "":
622-
case "http://www.w3.org/2002/07/owl#class":
623-
case "class":
624-
entity = dataFactory.getOWLEntity(EntityType.CLASS, iri);
625-
break;
623+
case "http://www.w3.org/2002/07/owl#objectproperty":
624+
case "object property":
625+
entity = dataFactory.getOWLEntity(EntityType.OBJECT_PROPERTY, iri);
626+
break;
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627-
case "http://www.w3.org/2002/07/owl#objectproperty":
628-
case "object property":
629-
entity = dataFactory.getOWLEntity(EntityType.OBJECT_PROPERTY, iri);
630-
break;
628+
case "http://www.w3.org/2002/07/owl#dataproperty":
629+
case "data property":
630+
entity = dataFactory.getOWLEntity(EntityType.DATA_PROPERTY, iri);
631+
break;
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632-
case "http://www.w3.org/2002/07/owl#dataproperty":
633-
case "data property":
634-
entity = dataFactory.getOWLEntity(EntityType.DATA_PROPERTY, iri);
635-
break;
633+
case "http://www.w3.org/2002/07/owl#annotationproperty":
634+
case "annotation property":
635+
entity = dataFactory.getOWLEntity(EntityType.ANNOTATION_PROPERTY, iri);
636+
break;
636637

637-
case "http://www.w3.org/2002/07/owl#annotationproperty":
638-
case "annotation property":
639-
entity = dataFactory.getOWLEntity(EntityType.ANNOTATION_PROPERTY, iri);
640-
break;
638+
case "http://www.w3.org/2002/07/owl#datatype":
639+
case "datatype":
640+
entity = dataFactory.getOWLEntity(EntityType.DATATYPE, iri);
641+
break;
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642-
case "http://www.w3.org/2002/07/owl#datatype":
643-
case "datatype":
644-
entity = dataFactory.getOWLEntity(EntityType.DATATYPE, iri);
645-
break;
643+
case "http://www.w3.org/2002/07/owl#individual":
644+
case "individual":
645+
case "http://www.w3.org/2002/07/owl#namedindividual":
646+
case "named individual":
647+
default:
648+
// Assume type is an individual (checked later)
649+
entity = dataFactory.getOWLEntity(EntityType.NAMED_INDIVIDUAL, iri);
650+
break;
651+
}
646652

647-
case "http://www.w3.org/2002/07/owl#individual":
648-
case "individual":
649-
case "http://www.w3.org/2002/07/owl#namedindividual":
650-
case "named individual":
651-
default:
652-
// Assume type is an individual (checked later)
653-
entity = dataFactory.getOWLEntity(EntityType.NAMED_INDIVIDUAL, iri);
654-
break;
655-
}
653+
if (id != null) {
654+
checker.add(entity, id);
655+
}
656+
if (label != null) {
656657
checker.add(entity, label);
657658
}
658659
}
@@ -795,6 +796,8 @@ private void processRow(List<String> row) throws Exception {
795796
case "http://www.w3.org/2002/07/owl#namedindividual":
796797
case "named individual":
797798
default:
799+
// This is a bit unsafe imo, for example in the case of where the datatype turns out to be
800+
// http://www.w3.org/2002/07/owl#DatatypeProperty""
798801
addIndividualAxioms(iri, row);
799802
break;
800803
}

‎robot-core/src/test/java/org/obolibrary/robot/TemplateTest.java

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@@ -49,6 +49,35 @@ public void testLegacyTemplateCSV() throws Exception {
4949
assertIdentical("/template.owl", template);
5050
}
5151

52+
/**
53+
* Test a strange case where a sequence .
54+
*
55+
* @throws Exception if entities cannot be found
56+
*/
57+
@Test
58+
public void testNoLabelsNoTypes() throws Exception {
59+
String path = "/sequence-template.csv";
60+
List<List<String>> rows = TemplateHelper.readCSV(this.getClass().getResourceAsStream(path));
61+
Template t = new Template(path, rows);
62+
t.generateOutputOntology("http://test.com/template.owl", false, null);
63+
}
64+
65+
/**
66+
* Test a strange case where a sequence .
67+
*
68+
* @throws Exception if entities cannot be found
69+
*/
70+
@Test
71+
public void testNoLabels() throws Exception {
72+
String path = "/workflow-template.csv";
73+
List<List<String>> rows = TemplateHelper.readCSV(this.getClass().getResourceAsStream(path));
74+
IOHelper ioHelper = new IOHelper();
75+
ioHelper.addPrefix("ex", "http://example.com/");
76+
Template t = new Template(path, rows, ioHelper);
77+
OWLOntology template = t.generateOutputOntology("http://test.com/template.owl", false, null);
78+
assertIdentical("/workflow-template.ttl", template);
79+
}
80+
5281
/**
5382
* Test multiple templates.
5483
*

‎robot-core/src/test/resources/sequence-template.csv

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1+
ID,isa
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ID,SC %
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CL:4030028,CL:0000561
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CL:0000561,CL:0000099

‎robot-core/src/test/resources/workflow-template.csv

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1+
Identifier,Type,Class Restriction Lower,Class Restriction Upper,Domain,Range
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ID,TYPE,SC %,SC %,DOMAIN,RANGE
3+
ex:consists_of,owl:ObjectProperty,,,ex:Workflow,ex:Task
4+
ex:Workflow,class,(ex:consists_of min 1 ex:Task),(ex:consists_of max 7 ex:Task),,
5+
ex:Task,class,,,,

‎robot-core/src/test/resources/workflow-template.ttl

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1+
@prefix owl: <http://www.w3.org/2002/07/owl#> .
2+
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
3+
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
4+
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
5+
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
6+
@base <http://www.w3.org/2002/07/owl#> .
7+
8+
<http://test.com/template.owl> rdf:type owl:Ontology .
9+
10+
#################################################################
11+
# Object Properties
12+
#################################################################
13+
14+
### http://example.com/consists_of
15+
<http://example.com/consists_of> rdf:type owl:ObjectProperty ;
16+
rdfs:domain <http://example.com/Workflow> ;
17+
rdfs:range <http://example.com/Task> .
18+
19+
20+
#################################################################
21+
# Classes
22+
#################################################################
23+
24+
### http://example.com/Task
25+
<http://example.com/Task> rdf:type owl:Class .
26+
27+
28+
### http://example.com/Workflow
29+
<http://example.com/Workflow> rdf:type owl:Class ;
30+
rdfs:subClassOf [ rdf:type owl:Restriction ;
31+
owl:onProperty <http://example.com/consists_of> ;
32+
owl:minQualifiedCardinality "1"^^xsd:nonNegativeInteger ;
33+
owl:onClass <http://example.com/Task>
34+
] ,
35+
[ rdf:type owl:Restriction ;
36+
owl:onProperty <http://example.com/consists_of> ;
37+
owl:maxQualifiedCardinality "7"^^xsd:nonNegativeInteger ;
38+
owl:onClass <http://example.com/Task>
39+
] .
40+
41+
42+
### Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi

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