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Fix referencing properties by CURIE in export #722

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merged 3 commits into from
Aug 18, 2020
Merged

Fix referencing properties by CURIE in export #722

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f435dd5
Fix export with CURIEs as headers
Aug 17, 2020
51c27f5
Update CHANGELOG
Aug 17, 2020
c0aec45
Remove toString()
Aug 17, 2020
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Fixed
- Handle empty [`template`] property charactersitics in [#719]
- Fix referencing properties by CURIE in [`export`] in [#722]

## [1.7.0] - 2020-07-31

Expand Down Expand Up @@ -198,6 +199,7 @@ First official release of ROBOT!
[`template`]: http://robot.obolibrary.org/template
[`validate`]: http://robot.obolibrary.org/validate

[#722]: https://github.com/ontodev/robot/pull/722
[#719]: https://github.com/ontodev/robot/pull/716
[#715]: https://github.com/ontodev/robot/pull/715
[#710]: https://github.com/ontodev/robot/pull/710
Expand Down
104 changes: 65 additions & 39 deletions robot-core/src/main/java/org/obolibrary/robot/ExportOperation.java
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Expand Up @@ -217,20 +217,47 @@ public static Table createExportTable(
currentEntitySelect = "NAMED";
}

// Maybe get a property
OWLAnnotationProperty ap = checker.getOWLAnnotationProperty(colName, false);
OWLAnnotationProperty ap = null;

// Handle some defaults
IRI colIRI = ioHelper.createIRI(colName);
if (colIRI != null
&& colIRI.toString().equals(dataFactory.getRDFSLabel().getIRI().toString())) {
// Handle rdfs:label defaults
if (iri != null && iri.equals(dataFactory.getRDFSLabel().getIRI())) {
currentEntityFormat = "LABEL";
currentEntitySelect = "NAMED";
ap = dataFactory.getRDFSLabel();
}

OWLDataProperty dp = checker.getOWLDataProperty(colName);
OWLObjectProperty op = checker.getOWLObjectProperty(colName);
// checker only resolves labels, so try with IRI
if (ap == null && iri != null && ontology.containsAnnotationPropertyInSignature(iri)) {
ap = dataFactory.getOWLAnnotationProperty(iri);
} else {
// Try by label
ap = checker.getOWLAnnotationProperty(colName);
}

// Check for object/data properties if not an annotation property
OWLDataProperty dp = null;
OWLObjectProperty op = null;
if (ap == null) {
// annotation property not found
if (iri != null && ontology.containsDataPropertyInSignature(iri)) {
// Use IRI to create data property
dp = dataFactory.getOWLDataProperty(iri);
} else {
// Try by label
dp = checker.getOWLDataProperty(colName);
}

if (dp == null) {
// data property not found
if (iri != null && ontology.containsObjectPropertyInSignature(iri)) {
// Use IRI to create object property
op = dataFactory.getOWLObjectProperty(iri);
} else {
// Try by label
op = checker.getOWLObjectProperty(colName);
}
}
}

// Maybe get a short form provider
ShortFormProvider provider;
Expand Down Expand Up @@ -342,8 +369,8 @@ public static void saveTable(Table table, String exportPath, Map<String, String>
* @param rt RendererType to use to render Manchester
* @param provider ShortFormProvider to resolve entities
* @param classes Set of class expressions to convert to string
* @param includeNamed
* @param includeAnonymous
* @param includeNamed if true, include named classes in output
* @param includeAnonymous if true, include anonymous classes in output
* @return String of class expressions or null
*/
private static List<String> classExpressionsToString(
Expand Down Expand Up @@ -374,8 +401,8 @@ private static List<String> classExpressionsToString(
* @param displayRendererType RendererType for display value
* @param sortRendererType RendererType for sort value
* @param provider ShortFormProvider to resolve entities
* @param includeNamed
* @param includeAnonymous
* @param includeNamed if true, include named classes in output
* @param includeAnonymous if true, include anonymous classes in output
* @return Cell for this Column containing class expressions
*/
private static Cell getClassCell(
Expand Down Expand Up @@ -502,8 +529,8 @@ private static Cell getEntityTypeCell(EntityType type, Column column) {
* @param displayRendererType RendererType for display value
* @param sortRendererType RendererType for sort value
* @param provider ShortFormProvider to resolve entities
* @param includeNamed
* @param includeAnonymous
* @param includeNamed if true, include named classes in output
* @param includeAnonymous if true, include anonymous classes in output
* @return Cell for this Column containing property expressions
*/
private static Cell getPropertyCell(
Expand Down Expand Up @@ -548,7 +575,7 @@ private static List<String> getPropertyValues(
List<String> values = new ArrayList<>();
for (OWLAnnotationAssertionAxiom a :
EntitySearcher.getAnnotationAssertionAxioms(entity, ontology)) {
if (a.getProperty().getIRI() == ap.getIRI()) {
if (a.getProperty().getIRI().equals(ap.getIRI())) {
if (a.getValue().isIRI()) {
IRI iri = a.getValue().asIRI().orNull();
if (iri != null) {
Expand All @@ -575,8 +602,8 @@ private static List<String> getPropertyValues(
* @param provider ShortFormProvider to resolve entities
* @param entity OWLEntity to get relations of
* @param dp OWLDataProperty to get the value(s) of
* @param includeNamed
* @param includeAnonymous
* @param includeNamed if true, include named classes in output
* @param includeAnonymous if true, include anonymous classes in output
* @return String of values or null
*/
private static List<String> getPropertyValues(
Expand Down Expand Up @@ -631,8 +658,8 @@ private static List<String> getPropertyValues(
* @param provider ShortFormProvider to resolve entities
* @param entity OWLEntity to get annotations on
* @param op OWLObjectProperty to get the value(s) of
* @param includeNamed
* @param includeAnonymous
* @param includeNamed if true, include named classes in output
* @param includeAnonymous if true, include anonymous classes in output
* @return String of values or null
*/
private static List<String> getPropertyValues(
Expand Down Expand Up @@ -691,8 +718,8 @@ private static List<String> getPropertyValues(
* @param dp OWLDataProperty to look for
* @param rt RendererType to use to render Manchester
* @param provider ShortFormProvider to resolve entities
* @param includeNamed
* @param includeAnonymous
* @param includeNamed if true, include named classes in output
* @param includeAnonymous if true, include anonymous classes in output
* @return set of fillers that are 'values' of the data property
*/
private static Set<String> getRestrictionFillers(
Expand All @@ -716,7 +743,7 @@ private static Set<String> getRestrictionFillers(
pe = avf.getProperty();
if (!pe.isAnonymous()) {
OWLDataProperty prop = pe.asOWLDataProperty();
if (prop.getIRI() == dp.getIRI()) {
if (prop.getIRI().equals(dp.getIRI())) {
if ((!f.isAnonymous() && includeNamed) || (f.isAnonymous() && includeAnonymous)) {
fillers.add(renderRestrictionString(rt, provider, f, null));
}
Expand All @@ -729,7 +756,7 @@ private static Set<String> getRestrictionFillers(
pe = svf.getProperty();
if (!pe.isAnonymous()) {
OWLDataProperty prop = pe.asOWLDataProperty();
if (prop.getIRI() == dp.getIRI()) {
if (prop.getIRI().equals(dp.getIRI())) {
if ((!f.isAnonymous() && includeNamed) || (f.isAnonymous() && includeAnonymous)) {
fillers.add(renderRestrictionString(rt, provider, f, null));
}
Expand All @@ -743,7 +770,7 @@ private static Set<String> getRestrictionFillers(
n = ec.getCardinality();
if (!pe.isAnonymous()) {
OWLDataProperty prop = pe.asOWLDataProperty();
if (prop.getIRI() == dp.getIRI()) {
if (prop.getIRI().equals(dp.getIRI())) {
if ((!f.isAnonymous() && includeNamed) || (f.isAnonymous() && includeAnonymous)) {
fillers.add(renderRestrictionString(rt, provider, f, n));
}
Expand All @@ -757,7 +784,7 @@ private static Set<String> getRestrictionFillers(
n = minc.getCardinality();
if (!pe.isAnonymous()) {
OWLDataProperty prop = pe.asOWLDataProperty();
if (prop.getIRI() == dp.getIRI()) {
if (prop.getIRI().equals(dp.getIRI())) {
if ((!f.isAnonymous() && includeNamed) || (f.isAnonymous() && includeAnonymous)) {
fillers.add(renderRestrictionString(rt, provider, f, n));
}
Expand All @@ -771,7 +798,7 @@ private static Set<String> getRestrictionFillers(
n = maxc.getCardinality();
if (!pe.isAnonymous()) {
OWLDataProperty prop = pe.asOWLDataProperty();
if (prop.getIRI() == dp.getIRI()) {
if (prop.getIRI().equals(dp.getIRI())) {
if ((!f.isAnonymous() && includeNamed) || (f.isAnonymous() && includeAnonymous)) {
fillers.add(renderRestrictionString(rt, provider, f, n));
}
Expand All @@ -793,8 +820,8 @@ private static Set<String> getRestrictionFillers(
* @param op OWLObjectProperty to look for
* @param rt RendererType to use to render Manchester
* @param provider ShortFormProvider to resolve entities
* @param includeNamed
* @param includeAnonymous
* @param includeNamed if true, include named classes in output
* @param includeAnonymous if true, include anonymous classes in output
* @return set of fillers that are 'values' of the object property
*/
private static Set<String> getRestrictionFillers(
Expand All @@ -819,7 +846,7 @@ private static Set<String> getRestrictionFillers(
f = avf.getFiller();
if (!pe.isAnonymous()) {
OWLObjectProperty prop = pe.asOWLObjectProperty();
if (prop.getIRI() == op.getIRI()) {
if (prop.getIRI().equals(op.getIRI())) {
if ((f.isAnonymous() && includeAnonymous) || (!f.isAnonymous() && includeNamed)) {
fillers.add(renderRestrictionString(rt, provider, f, null));
}
Expand All @@ -833,7 +860,7 @@ private static Set<String> getRestrictionFillers(
f = svf.getFiller();
if (!pe.isAnonymous()) {
OWLObjectProperty prop = pe.asOWLObjectProperty();
if (prop.getIRI() == op.getIRI()) {
if (prop.getIRI().equals(op.getIRI())) {
if ((f.isAnonymous() && includeAnonymous) || (!f.isAnonymous() && includeNamed)) {
fillers.add(renderRestrictionString(rt, provider, f, null));
}
Expand All @@ -848,7 +875,7 @@ private static Set<String> getRestrictionFillers(
n = ec.getCardinality();
if (!pe.isAnonymous()) {
OWLObjectProperty prop = pe.asOWLObjectProperty();
if (prop.getIRI() == op.getIRI()) {
if (prop.getIRI().equals(op.getIRI())) {
if ((f.isAnonymous() && includeAnonymous) || (!f.isAnonymous() && includeNamed)) {
fillers.add(renderRestrictionString(rt, provider, f, n));
}
Expand All @@ -863,7 +890,7 @@ private static Set<String> getRestrictionFillers(
n = minc.getCardinality();
if (!pe.isAnonymous()) {
OWLObjectProperty prop = pe.asOWLObjectProperty();
if (prop.getIRI() == op.getIRI()) {
if (prop.getIRI().equals(op.getIRI())) {
if ((f.isAnonymous() && includeAnonymous) || (!f.isAnonymous() && includeNamed)) {
fillers.add(renderRestrictionString(rt, provider, f, n));
}
Expand All @@ -878,7 +905,7 @@ private static Set<String> getRestrictionFillers(
n = maxc.getCardinality();
if (!pe.isAnonymous()) {
OWLObjectProperty prop = pe.asOWLObjectProperty();
if (prop.getIRI() == op.getIRI()) {
if (prop.getIRI().equals(op.getIRI())) {
if ((f.isAnonymous() && includeAnonymous) || (!f.isAnonymous() && includeNamed)) {
fillers.add(renderRestrictionString(rt, provider, f, n));
}
Expand Down Expand Up @@ -927,9 +954,9 @@ private static Row getRow(OWLOntology ontology, Table table, OWLEntity entity) t
boolean includeAnonymous = col.getIncludeAnonymous();

String colName = col.getName();
OWLProperty maybeAnnotation = col.getProperty();
if (maybeAnnotation instanceof OWLAnnotationProperty) {
OWLAnnotationProperty maybeLabel = (OWLAnnotationProperty) maybeAnnotation;
OWLProperty colProperty = col.getProperty();
if (colProperty instanceof OWLAnnotationProperty) {
OWLAnnotationProperty maybeLabel = (OWLAnnotationProperty) colProperty;
if (maybeLabel.isLabel()) {
// Handle like we do default LABEL columns
colName = "LABEL";
Expand Down Expand Up @@ -982,7 +1009,6 @@ private static Row getRow(OWLOntology ontology, Table table, OWLEntity entity) t
}

// If a property exists, use this property to get values
OWLProperty colProperty = col.getProperty();
if (colProperty != null) {
if (colProperty instanceof OWLAnnotationProperty) {
OWLAnnotationProperty ap = (OWLAnnotationProperty) colProperty;
Expand Down Expand Up @@ -1306,8 +1332,8 @@ private static List<String> getSynonyms(OWLOntology ontology, OWLEntity entity)
* @param rt RendererType to use to render Manchester
* @param provider ShortFormProvider to resolve entities
* @param props Set of property expressions to convert to string
* @param includeNamed
* @param includeAnonymous
* @param includeNamed if true, include named classes in output
* @param includeAnonymous if true, include anonymous classes in output
* @return String of property expressions or null
*/
private static List<String> propertyExpressionsToString(
Expand Down