ontodev · jamesaoverton · May 12, 2020 · May 11, 2020 · May 11, 2020 · May 11, 2020
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -22,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fix releasing dataset after exception when running [`report`] with `--tdb true` [#659]
 - Reduced time spent loading datasets for [`query`] in [#666]
 - Fix writing JSON format to use `OutputStream` with ['convert'] in [#671]
+- Fix IRI resolution for `template` in [#689]
 
 
 ## [1.6.0] - 2020-03-04
@@ -186,6 +187,7 @@ First official release of ROBOT!
 [`report`]: http://robot.obolibrary.org/report
 [`template`]: http://robot.obolibrary.org/template
 
+[#689]: https://github.com/ontodev/robot/pull/689
 [#685]: https://github.com/ontodev/robot/pull/685
 [#671]: https://github.com/ontodev/robot/pull/671
 [#666]: https://github.com/ontodev/robot/pull/666

diff --git a/docs/template.md b/docs/template.md
@@ -229,6 +229,9 @@ Annotation properties should not have any value in the `CHARACTERISTIC` column,
 ### Annotation Property Error
 
 The annotation property provided could not be resolved. Check your template to ensure the provided annotation property is in a correct IRI or CURIE format. For legibility, using CURIEs is recommended, but you must ensure that the prefix is defined.
+
+If you are using a label, make sure that the label is defined either in the template or input ontology.
+
 ```
 A rdfs:label
 A http://www.w3.org/2000/01/rdf-schema#label

diff --git a/robot-core/src/main/java/org/obolibrary/robot/IOHelper.java b/robot-core/src/main/java/org/obolibrary/robot/IOHelper.java
@@ -37,6 +37,7 @@
 import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.formats.*;
 import org.semanticweb.owlapi.model.*;
+import org.semanticweb.owlapi.rdf.rdfxml.renderer.IllegalElementNameException;
 import org.semanticweb.owlapi.rdf.rdfxml.renderer.XMLWriterPreferences;
 import org.semanticweb.owlapi.util.DefaultPrefixManager;
 import org.slf4j.Logger;
@@ -748,9 +749,22 @@ public Set<String> extractTerms(String input) {
    */
   @SuppressWarnings("unchecked")
   public IRI createIRI(String term) {
+    return createIRI(term, false);
+  }
+
+  /**
+   * Given a term string, use the current prefixes to create an IRI.
+   *
+   * @param term the term to convert to an IRI
+   * @param qName if true, check that the expanded IRI is a valid QName (if not, return null)
+   * @return the new IRI or null
+   */
+  @SuppressWarnings("unchecked")
+  public IRI createIRI(String term, boolean qName) {
     if (term == null) {
       return null;
     }
+    IRI iri;
 
     try {
       // This is stupid, because better methods aren't public.
@@ -764,15 +778,21 @@ public IRI createIRI(String term) {
       Object expanded = new JsonLdApi().expand(context, jsonMap);
       String result = ((Map<String, Object>) expanded).keySet().iterator().next();
       if (result != null) {
-        return IRI.create(result);
+        iri = IRI.create(result);
       } else {
-        return IRI.create(term);
+        iri = IRI.create(term);
       }
     } catch (Exception e) {
       logger.warn("Could not create IRI for {}", term);
       logger.warn(e.getMessage());
+      return null;
+    }
+
+    // Check that this is a valid QName
+    if (qName && !iri.getRemainder().isPresent()) {
+      return null;
     }
-    return null;
+    return iri;
   }
 
   /**
@@ -1434,6 +1454,8 @@ private void saveOntologyFile(
       // use native save functionality
       try {
         ontology.getOWLOntologyManager().saveOntology(ontology, format, ontologyIRI);
+      } catch (IllegalElementNameException e) {
+        throw new IOException("ELEMENT NAME EXCEPTION " + e.getCause().getMessage());
       } catch (OWLOntologyStorageException e) {
         // Determine if its caused by an OBO Format error
         if (format instanceof OBODocumentFormat

diff --git a/robot-core/src/main/java/org/obolibrary/robot/QuotedEntityChecker.java b/robot-core/src/main/java/org/obolibrary/robot/QuotedEntityChecker.java
@@ -293,7 +293,7 @@ private IRI getIRI(Map<String, IRI> map, String name) {
   public IRI getIRI(String name, boolean create) {
     IRI iri = iris.getOrDefault(name, null);
     if (iri == null && ioHelper != null && create) {
-      iri = ioHelper.createIRI(name);
+      iri = ioHelper.createIRI(name, true);
     }
     return iri;
   }
@@ -337,7 +337,7 @@ public OWLAnnotationProperty getOWLAnnotationProperty(@Nonnull String name, bool
       return dataFactory.getOWLAnnotationProperty(iri);
     }
     if (create && ioHelper != null) {
-      iri = ioHelper.createIRI(name);
+      iri = ioHelper.createIRI(name, true);
       if (iri != null) {
         return dataFactory.getOWLAnnotationProperty(iri);
       }
@@ -358,7 +358,7 @@ public OWLClass getOWLClass(@Nonnull String name) {
       return dataFactory.getOWLClass(iri);
     }
     if (ioHelper != null) {
-      iri = ioHelper.createIRI(name);
+      iri = ioHelper.createIRI(name, true);
       if (iri != null) {
         return dataFactory.getOWLClass(iri);
       }
@@ -379,7 +379,7 @@ public OWLDataProperty getOWLDataProperty(@Nonnull String name) {
       return dataFactory.getOWLDataProperty(iri);
     }
     if (ioHelper != null) {
-      iri = ioHelper.createIRI(name);
+      iri = ioHelper.createIRI(name, true);
       if (iri != null) {
         return dataFactory.getOWLDataProperty(iri);
       }
@@ -413,7 +413,7 @@ public OWLDatatype getOWLDatatype(@Nonnull String name, boolean create) {
       return dataFactory.getOWLDatatype(iri);
     }
     if (create && ioHelper != null) {
-      iri = ioHelper.createIRI(name);
+      iri = ioHelper.createIRI(name, true);
       if (iri != null) {
         return dataFactory.getOWLDatatype(iri);
       }
@@ -434,7 +434,7 @@ public OWLNamedIndividual getOWLIndividual(@Nonnull String name) {
       return dataFactory.getOWLNamedIndividual(iri);
     }
     if (ioHelper != null) {
-      iri = ioHelper.createIRI(name);
+      iri = ioHelper.createIRI(name, true);
       if (iri != null) {
         return dataFactory.getOWLNamedIndividual(iri);
       }
@@ -455,7 +455,7 @@ public OWLObjectProperty getOWLObjectProperty(@Nonnull String name) {
       return dataFactory.getOWLObjectProperty(iri);
     }
     if (ioHelper != null) {
-      iri = ioHelper.createIRI(name);
+      iri = ioHelper.createIRI(name, true);
       if (iri != null) {
         return dataFactory.getOWLObjectProperty(iri);
       }

diff --git a/robot-core/src/main/java/org/obolibrary/robot/Template.java b/robot-core/src/main/java/org/obolibrary/robot/Template.java
@@ -143,6 +143,10 @@ public class Template {
       NS
           + "UNKNOWN TEMPLATE ERROR could not interpret template string \"%4$s\" for column %2$d (\"%3$s\") in table \"%1$s\".";
 
+  private static final String unknownEntityError =
+      NS
+          + "UNKNOWN ENTITY ERROR could not interpret '%1$s' in row %2$d, column %3$d (\"%4$s\") in table \"%5$s\".";
+
   private static final List<String> validClassTypes =
       new ArrayList<>(Arrays.asList("subclass", "disjoint", "equivalent"));
 
@@ -549,13 +553,13 @@ private void addLabels() {
         type = "class";
       }
 
-      IRI iri = ioHelper.createIRI(id);
+      IRI iri = ioHelper.createIRI(id, true);
       if (iri == null) {
         iri = IRI.create(id);
       }
 
       // Try to resolve a CURIE
-      IRI typeIRI = ioHelper.createIRI(type);
+      IRI typeIRI = ioHelper.createIRI(type, true);
 
       // Set to IRI string or to type string
       String typeOrIRI = type;
@@ -626,18 +630,27 @@ private void processRow(List<String> row) throws Exception {
     String id = null;
     try {
       id = row.get(idColumn);
+      if (id.trim().isEmpty()) {
+        id = null;
+      }
     } catch (IndexOutOfBoundsException e) {
       // ignore
     }
     String label = null;
     try {
       label = row.get(labelColumn);
+      if (label.trim().isEmpty()) {
+        label = null;
+      }
     } catch (IndexOutOfBoundsException e) {
       // ignore
     }
     String type = null;
     try {
       type = row.get(typeColumn);
+      if (type.trim().isEmpty()) {
+        type = null;
+      }
     } catch (IndexOutOfBoundsException e) {
       // ignore
     }
@@ -647,7 +660,7 @@ private void processRow(List<String> row) throws Exception {
       return;
     }
 
-    if (type == null || type.trim().isEmpty()) {
+    if (type == null) {
       // Try to guess the type from already existing entities
       if (label != null) {
         OWLEntity e = checker.getOWLEntity(label);
@@ -668,13 +681,28 @@ private void processRow(List<String> row) throws Exception {
       }
     }
 
+    // Create an IRI for the subject of this row
     IRI iri = getIRI(id, label);
     if (iri == null) {
-      return;
+      // Unable to create an IRI from the entity
+      if (idColumn != -1) {
+        if (id != null) {
+          // Has an ID column with contents that could not be resolved
+          throw new RowParseException(
+              String.format(unknownEntityError, id, rowNum, idColumn, "ID", name));
+        } else {
+          // Has an ID column, but it's empty
+          return;
+        }
+      } else {
+        // No ID column and label could not be resolved
+        throw new RowParseException(
+            String.format(unknownEntityError, label, rowNum, labelColumn, "LABEL", name));
+      }
     }
 
     // Try to resolve a CURIE
-    IRI typeIRI = ioHelper.createIRI(type);
+    IRI typeIRI = ioHelper.createIRI(type, true);
 
     // Set to IRI string or to type string
     String typeOrIRI = type;
@@ -1734,7 +1762,7 @@ private void addIndividualAxioms(IRI iri, List<String> row) throws Exception {
       type = type.trim();
 
       // Try to resolve a CURIE
-      IRI typeIRI = ioHelper.createIRI(type);
+      IRI typeIRI = ioHelper.createIRI(type, true);
 
       // Set to IRI string or to type string
       String typeOrIRI = type;
@@ -2122,7 +2150,7 @@ private IRI getIRI(String id, String label) throws Exception {
       throw new Exception("You must specify either an ID or a label");
     }
     if (id != null) {
-      return ioHelper.createIRI(id);
+      return ioHelper.createIRI(id, true);
     }
     return checker.getIRI(label, true);
   }

diff --git a/robot-core/src/main/java/org/obolibrary/robot/TemplateHelper.java b/robot-core/src/main/java/org/obolibrary/robot/TemplateHelper.java
@@ -328,10 +328,10 @@ public static Set<OWLAnnotation> getAnnotations(
       if (split != null) {
         String[] values = value.split(Pattern.quote(split));
         for (String v : values) {
-          annotations.add(maybeGetIRIAnnotation(tableName, checker, template, v, rowNum, column));
+          annotations.add(maybeGetIRIAnnotation(checker, template, v));
         }
       } else {
-        annotations.add(maybeGetIRIAnnotation(tableName, checker, template, value, rowNum, column));
+        annotations.add(maybeGetIRIAnnotation(checker, template, value));
       }
       return annotations;
     } else if (template.equals("LABEL")) {
@@ -640,7 +640,7 @@ public static List<IRI> getIRIs(String tableName, List<List<String>> rows, IOHel
       if (id == null || id.trim().isEmpty()) {
         continue;
       }
-      IRI iri = ioHelper.createIRI(id);
+      IRI iri = ioHelper.createIRI(id, true);
       if (iri == null) {
         continue;
       }
@@ -1225,29 +1225,19 @@ private static String getTemplate(String template) {
   /**
    * Given a checker, a template string, and a value for the template, return an IRI annotation.
    *
-   * @param tableName name of table
    * @param checker QuotedEntityChecker to resolve entities
    * @param template template string
    * @param value value to use with the template string
-   * @param rowNum the row number for logging
-   * @param column the column number for logging
    * @return OWLAnnotation created from template and value
    * @throws RowParseException if entities cannot be resolved
    */
   private static OWLAnnotation maybeGetIRIAnnotation(
-      String tableName,
-      QuotedEntityChecker checker,
-      String template,
-      String value,
-      int rowNum,
-      int column)
-      throws Exception {
+      QuotedEntityChecker checker, String template, String value) throws Exception {
     IRI iri = checker.getIRI(value, true);
-    if (iri != null) {
-      return getIRIAnnotation(checker, template, iri);
-    } else {
-      throw new RowParseException(String.format(iriError, rowNum, column + 1, tableName, value));
+    if (iri == null) {
+      iri = IRI.create(value);
     }
+    return getIRIAnnotation(checker, template, iri);
   }
 
   /**