Fix entity rendering in report when value is an entity

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

@@ -785,7 +785,7 @@ private static Map<String, String> getProfile(String path) throws IOException {
     if (path == null) {
       is = ReportOperation.class.getResourceAsStream("/report_profile.txt");
     } else {
-      is = new FileInputStream(new File(path));
+      is = new FileInputStream(path);
     }
     try (BufferedReader br = new BufferedReader(new InputStreamReader(is))) {
       String line;
@@ -944,13 +944,14 @@ private static List<Violation> getViolationsFromResults(
         OWLEntity e = dataFactory.getOWLClass(ioHelper.createIRI(property));
         if (value != null) {
           IRI valIRI = ioHelper.createIRI(value);
-          if (valIRI != null) {
-            violation.addStatement(e, valIRI);
+          if (valIRI != null && !valIRI.toString().contains(" ")) {
+            OWLEntity v = dataFactory.getOWLClass(valIRI);
+            violation.addStatement(e, v);
           } else {
-            violation.addStatement(e, dataFactory.getOWLLiteral(value));
+            violation.addStatement(e, value);
           }
         } else {
-          violation.addStatement(e, null);
+          violation.addStatement(e, "");
         }
       }
       violations.add(violation);

robot-core/src/main/java/org/obolibrary/robot/checks/Report.java

@@ -57,7 +57,7 @@ public class Report {
   private Integer errorCount = 0;
 
   /** IOHelper to use. */
-  private IOHelper ioHelper;
+  private final IOHelper ioHelper;
 
   /** Manager to use. */
   private OWLOntologyManager manager;
@@ -270,20 +270,7 @@ public Integer getViolationCount(String ruleName) throws Exception {
    * @return export Table object
    */
   public Table toTable(String format) {
-    CURIEShortFormProvider curieProvider = new CURIEShortFormProvider(ioHelper.getPrefixes());
-    QuotedAnnotationValueShortFormProvider nameProvider =
-        new QuotedAnnotationValueShortFormProvider(
-            manager,
-            curieProvider,
-            ioHelper.getPrefixManager(),
-            Collections.singletonList(OWLManager.getOWLDataFactory().getRDFSLabel()),
-            Collections.emptyMap());
-    ShortFormProvider provider;
-    if (useLabels) {
-      provider = nameProvider;
-    } else {
-      provider = curieProvider;
-    }
+    ShortFormProvider provider = getProvider();
 
     Table table = new Table(format);
     for (String h : header) {
@@ -316,20 +303,7 @@ public String toJSON() throws IOException {
    * @return YAML string
    */
   public String toYAML() {
-    CURIEShortFormProvider curieProvider = new CURIEShortFormProvider(ioHelper.getPrefixes());
-    QuotedAnnotationValueShortFormProvider nameProvider =
-        new QuotedAnnotationValueShortFormProvider(
-            manager,
-            curieProvider,
-            ioHelper.getPrefixManager(),
-            Collections.singletonList(OWLManager.getOWLDataFactory().getRDFSLabel()),
-            Collections.emptyMap());
-    ShortFormProvider provider;
-    if (useLabels) {
-      provider = nameProvider;
-    } else {
-      provider = curieProvider;
-    }
+    ShortFormProvider provider = getProvider();
     return yamlHelper(provider, ERROR, error)
         + yamlHelper(provider, WARN, warn)
         + yamlHelper(provider, INFO, info);
@@ -372,7 +346,7 @@ private void addToTable(
           }
         }
         Cell subjectCell = new Cell(columns.get(2), subject);
-        for (Entry<OWLEntity, List<OWLObject>> statement : v.entityStatements.entrySet()) {
+        for (Entry<OWLEntity, List<OWLEntity>> statement : v.entityStatements.entrySet()) {
           // Property of the violation for the following rows
           String property = "";
           if (statement.getKey() != null) {
@@ -382,33 +356,43 @@ private void addToTable(
           Cell propertyCell = new Cell(columns.get(3), property);
 
           if (statement.getValue().isEmpty()) {
-            Row row = new Row(level);
             Cell valueCell = new Cell(columns.get(4), "");
-            row.add(levelCell);
-            row.add(ruleCell);
-            row.add(subjectCell);
-            row.add(propertyCell);
-            row.add(valueCell);
-            table.addRow(row);
+            addRowToTable(table, level, levelCell, ruleCell, subjectCell, propertyCell, valueCell);
           } else {
-            for (OWLObject o : statement.getValue()) {
-              Row row = new Row(level);
+            for (OWLEntity e : statement.getValue()) {
+              String value = OntologyHelper.renderManchester(e, provider, displayRenderer);
+              Cell valueCell = new Cell(columns.get(4), value);
+              addRowToTable(
+                  table, level, levelCell, ruleCell, subjectCell, propertyCell, valueCell);
+            }
+          }
+        }
 
-              String value = "";
-              if (o != null) {
-                value = OntologyHelper.renderManchester(o, provider, displayRenderer);
-              }
+        for (Entry<OWLEntity, List<String>> statement : v.literalStatements.entrySet()) {
+          // Property of the violation for the following rows
+          String property = "";
+          if (statement.getKey() != null) {
+            property =
+                OntologyHelper.renderManchester(statement.getKey(), provider, displayRenderer);
+          }
+          Cell propertyCell = new Cell(columns.get(3), property);
 
+          if (statement.getValue().isEmpty()) {
+            Cell valueCell = new Cell(columns.get(4), "");
+            addRowToTable(table, level, levelCell, ruleCell, subjectCell, propertyCell, valueCell);
+          } else {
+            for (String value : statement.getValue()) {
+              if (value == null) {
+                value = "";
+              }
               Cell valueCell = new Cell(columns.get(4), value);
-              row.add(levelCell);
-              row.add(ruleCell);
-              row.add(subjectCell);
-              row.add(propertyCell);
-              row.add(valueCell);
-              table.addRow(row);
+              addRowToTable(
+                  table, level, levelCell, ruleCell, subjectCell, propertyCell, valueCell);
             }
           }
         }
+
+        // Support for old statements method
         for (Entry<String, List<String>> statement : v.statements.entrySet()) {
           String property = statement.getKey();
           if (property == null) {
@@ -417,34 +401,71 @@ private void addToTable(
           Cell propertyCell = new Cell(columns.get(3), property);
 
           if (statement.getValue().isEmpty()) {
-            Row row = new Row(level);
             Cell valueCell = new Cell(columns.get(4), "");
-            row.add(levelCell);
-            row.add(ruleCell);
-            row.add(subjectCell);
-            row.add(propertyCell);
-            row.add(valueCell);
-            table.addRow(row);
+            addRowToTable(table, level, levelCell, ruleCell, subjectCell, propertyCell, valueCell);
           } else {
             for (String value : statement.getValue()) {
               if (value == null) {
                 continue;
               }
-              Row row = new Row(level);
               Cell valueCell = new Cell(columns.get(4), value);
-              row.add(levelCell);
-              row.add(ruleCell);
-              row.add(subjectCell);
-              row.add(propertyCell);
-              row.add(valueCell);
-              table.addRow(row);
+              addRowToTable(
+                  table, level, levelCell, ruleCell, subjectCell, propertyCell, valueCell);
             }
           }
         }
       }
     }
   }
 
+  /**
+   * Add a row to a table.
+   *
+   * @param table Table to add row to
+   * @param level String violation level
+   * @param levelCell Cell for level
+   * @param ruleCell Cell for rule
+   * @param subjectCell Cell for subject
+   * @param propertyCell Cell for property
+   * @param valueCell Cell for value
+   */
+  private void addRowToTable(
+      Table table,
+      String level,
+      Cell levelCell,
+      Cell ruleCell,
+      Cell subjectCell,
+      Cell propertyCell,
+      Cell valueCell) {
+    Row row = new Row(level);
+    row.add(levelCell);
+    row.add(ruleCell);
+    row.add(subjectCell);
+    row.add(propertyCell);
+    row.add(valueCell);
+    table.addRow(row);
+  }
+
+  /**
+   * Get a ShortFormProvider to render entities based on if we are rendering labels or not.
+   *
+   * @return ShortFormProvider that either uses names (labels or CURIEs) or CURIEs
+   */
+  private ShortFormProvider getProvider() {
+    CURIEShortFormProvider curieProvider = new CURIEShortFormProvider(ioHelper.getPrefixes());
+    QuotedAnnotationValueShortFormProvider nameProvider =
+        new QuotedAnnotationValueShortFormProvider(
+            manager,
+            curieProvider,
+            ioHelper.getPrefixManager(),
+            Collections.singletonList(OWLManager.getOWLDataFactory().getRDFSLabel()),
+            Collections.emptyMap());
+    if (useLabels) {
+      return nameProvider;
+    }
+    return curieProvider;
+  }
+
   /**
    * Given a rule name, return a rule name. If the string starts with "file", the name is the path
    * and should be stripped to just the name. Otherwise, the input is returned.
@@ -493,7 +514,7 @@ private String yamlHelper(
             OntologyHelper.renderManchester(v.entity, provider, RendererType.OBJECT_RENDERER);
         sb.append("    - subject: \"").append(subject).append("\"");
         sb.append("\n");
-        for (Entry<OWLEntity, List<OWLObject>> statement : v.entityStatements.entrySet()) {
+        for (Entry<OWLEntity, List<OWLEntity>> statement : v.entityStatements.entrySet()) {
           String property =
               OntologyHelper.renderManchester(
                   statement.getKey(), provider, RendererType.OBJECT_RENDERER);
@@ -504,7 +525,7 @@ private String yamlHelper(
           }
           sb.append("      values:");
           sb.append("\n");
-          for (OWLObject value : statement.getValue()) {
+          for (OWLEntity value : statement.getValue()) {
             String display = "";
             if (value != null) {
               display =
@@ -566,16 +587,10 @@ public Set<String> getIRIs(Map<String, List<Violation>> violationSets) {
     for (Entry<String, List<Violation>> vs : violationSets.entrySet()) {
       for (Violation v : vs.getValue()) {
         iris.add(v.entity.getIRI().toString());
-        for (Entry<OWLEntity, List<OWLObject>> statement : v.entityStatements.entrySet()) {
+        for (Entry<OWLEntity, List<OWLEntity>> statement : v.entityStatements.entrySet()) {
           iris.add(statement.getKey().getIRI().toString());
-          for (OWLObject value : statement.getValue()) {
-            if (value instanceof OWLEntity) {
-              OWLEntity e = (OWLEntity) value;
-              iris.add(e.getIRI().toString());
-            } else if (value instanceof IRI) {
-              IRI iri = (IRI) value;
-              iris.add(iri.toString());
-            }
+          for (OWLEntity value : statement.getValue()) {
+            iris.add(value.getIRI().toString());
           }
         }
       }

robot-core/src/main/java/org/obolibrary/robot/checks/Violation.java

@@ -13,8 +13,11 @@ public class Violation {
   public String subject;
 
   // Statements about OWLEntity subject
-  public Map<OWLEntity, List<OWLObject>> entityStatements = new HashMap<>();
+  public Map<OWLEntity, List<OWLEntity>> entityStatements = new HashMap<>();
   // Statements about String subject
+  public Map<OWLEntity, List<String>> literalStatements = new HashMap<>();
+
+  // Deprecated statements with string properties
   public Map<String, List<String>> statements = new HashMap<>();
 
   /**
@@ -27,13 +30,22 @@ public Violation(OWLEntity subject) {
   }
 
   /**
-   * Add a statement to the Violation about the subject.
+   * Create a new Violation object about a String. This is used for blank nodes.
+   *
+   * @param subject String subject
+   */
+  public Violation(String subject) {
+    this.subject = subject;
+  }
+
+  /**
+   * Add a statement with an OWLEntity value to the Violation about the subject.
    *
    * @param property OWLEntity property
-   * @param value OWLObject value
+   * @param value OWLEntity value
    */
-  public void addStatement(OWLEntity property, OWLObject value) {
-    List<OWLObject> values;
+  public void addStatement(OWLEntity property, OWLEntity value) {
+    List<OWLEntity> values;
     if (entityStatements.get(property) != null) {
       // This property already has one value in the map
       // Add this value to the existing list
@@ -51,19 +63,38 @@ public void addStatement(OWLEntity property, OWLObject value) {
     entityStatements.put(property, values);
   }
 
-  /** @param subject String subject */
-  public Violation(String subject) {
-    this.subject = subject;
+  /**
+   * Add a literal statement to the Violation about the subject.
+   *
+   * @param property OWLEntity property
+   * @param value String literal value
+   */
+  public void addStatement(OWLEntity property, String value) {
+    List<String> values;
+    if (literalStatements.get(property) != null) {
+      values = new ArrayList<>(literalStatements.get(property));
+      values.add(value);
+    } else {
+      if (value != null) {
+        values = Collections.singletonList(value);
+      } else {
+        values = Collections.emptyList();
+      }
+    }
+    literalStatements.put(property, values);
   }
 
   /**
    * @param property String property
    * @param value String value
+   * @deprecated String properties are no longer recommended; create an OWLEntity for the property
+   *     instead
    */
+  @Deprecated
   public void addStatement(String property, String value) {
     List<String> values;
     if (statements.get(property) != null) {
-      values = new ArrayList<String>(statements.get(property));
+      values = new ArrayList<>(statements.get(property));
       values.add(value);
     } else {
       if (value != null) {
@@ -74,4 +105,18 @@ public void addStatement(String property, String value) {
     }
     statements.put(property, values);
   }
+
+  /**
+   * @param property String property
+   * @param object OWLObject value
+   * @deprecated OWLObjects are no longer supported; use OWLEntity or String literal instead
+   */
+  @Deprecated
+  public void addStatement(OWLEntity property, OWLObject object) {
+    // Do nothing
+    logger.error(
+        String.format(
+            "Cannot add OWLObject '%s'; use an OWLEntity or String literal instead.",
+            object.toString()));
+  }
 }