Merge pull request #722 from ontodev/721-fix

Fix referencing properties by CURIE in export
ontodev · Aug 18, 2020 · 298a2a3 · 298a2a3
2 parents 2fc3ac5 + c0aec45
commit 298a2a3
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -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
 
@@ -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

diff --git a/robot-core/src/main/java/org/obolibrary/robot/ExportOperation.java b/robot-core/src/main/java/org/obolibrary/robot/ExportOperation.java
@@ -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;
@@ -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(
@@ -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(
@@ -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(
@@ -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) {
@@ -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(
@@ -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(
@@ -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(
@@ -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));
               }
@@ -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));
               }
@@ -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));
               }
@@ -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));
               }
@@ -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));
               }
@@ -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(
@@ -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));
               }
@@ -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));
               }
@@ -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));
               }
@@ -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));
               }
@@ -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));
               }
@@ -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";
@@ -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;
@@ -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(