Merge pull request #767 from ontodev/bnode-report

Workaround for blank nodes
ontodev · Nov 18, 2020 · f31323e · f31323e
2 parents 8a93134 + def1a22
commit f31323e
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Showing 4 changed files with 17 additions and 6 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fix reported row number in [`validate`] error tables in [#727]
 - Fix equivalent class rendering for [`template`] in [#728]
 - Fix ontology IRI rendering for [`report`] in [#739]
+- Fix blank node subjects in [`report`] in [#767]
 
 ## [1.7.0] - 2020-07-31
 

diff --git a/robot-core/src/main/java/org/obolibrary/robot/DiffOperation.java b/robot-core/src/main/java/org/obolibrary/robot/DiffOperation.java
@@ -153,9 +153,7 @@ public static boolean compare(
     return false;
   }
 
-  /**
-   * OWLOntologySetProvider for two (left and right) ontologies.
-   */
+  /** OWLOntologySetProvider for two (left and right) ontologies. */
   private static class DualOntologySetProvider implements OWLOntologySetProvider {
 
     private static final long serialVersionUID = -8942374248162307075L;

diff --git a/robot-core/src/main/java/org/obolibrary/robot/ReportOperation.java b/robot-core/src/main/java/org/obolibrary/robot/ReportOperation.java
@@ -565,7 +565,6 @@ public static boolean processReport(Report report, String outputPath, Map<String
 
         case "tsv":
         default:
-          System.out.print("tsv!");
           rows = reportTable.toList("");
           if (outputPath != null) {
             if (print > 0) {
@@ -906,7 +905,15 @@ private static List<Violation> getViolationsFromResults(
         continue;
       }
 
-      Violation violation = new Violation(dataFactory.getOWLClass(ioHelper.createIRI(entity)));
+      Violation violation;
+      try {
+        OWLClass cls = dataFactory.getOWLClass(ioHelper.createIRI(entity));
+        violation = new Violation(cls);
+      } catch (Exception e) {
+        // Blank node, use the string bnode ID
+        violation = new Violation("blank node");
+      }
+
       // try and get a property and value from the query
       String property = getQueryResultOrNull(qs, "property");
       String value = getQueryResultOrNull(qs, "value");

diff --git a/robot-core/src/main/java/org/obolibrary/robot/checks/Report.java b/robot-core/src/main/java/org/obolibrary/robot/checks/Report.java
@@ -352,7 +352,12 @@ private void addToTable(
       Cell ruleCell = new Cell(columns.get(1), ruleName);
       for (Violation v : vs.getValue()) {
         // Subject of the violation for the following rows
-        String subject = OntologyHelper.renderManchester(v.entity, provider, displayRenderer);
+        String subject;
+        if (v.entity != null) {
+          subject = OntologyHelper.renderManchester(v.entity, provider, displayRenderer);
+        } else {
+          subject = v.subject;
+        }
         Cell subjectCell = new Cell(columns.get(2), subject);
         for (Entry<OWLEntity, List<OWLObject>> statement : v.entityStatements.entrySet()) {
           // Property of the violation for the following rows