[ontodev#1017] Added check for empty labels into missing_label.rq.

Author: Petr Křemen

docs/report_queries/missing_label.md

@@ -1,10 +1,10 @@
-# Missing Label
-
-**Problem:** An entity does not have a label. This may cause confusion or misuse. Excludes deprecated entities.
-
-**OBO Foundry Principle:** [12 - Naming Conventions](http://www.obofoundry.org/principles/fp-012-naming-conventions.html)
-
-**Solution:** Add a label.
+# # Missing Label
+#
+# **Problem:** An entity does not have a label or the label is empty. This may cause confusion or misuse. Excludes deprecated entities.
+#
+# **OBO Foundry Principle:** [12 - Naming Conventions](http://www.obofoundry.org/principles/fp-012-naming-conventions.html)
+#
+# **Solution:** Add a label, or make it non-empty.
 
 ```sparql
 PREFIX owl: <http://www.w3.org/2002/07/owl#>
@@ -15,7 +15,10 @@ PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
 SELECT DISTINCT ?entity ?property ?value WHERE {
   VALUES ?property { rdfs:label }
   ?entity ?any ?o .
-  FILTER NOT EXISTS { ?entity ?property ?value }
+  FILTER NOT EXISTS {
+     ?entity ?property ?value .
+     FILTER(str(?value) != "")
+  }
   FILTER NOT EXISTS { ?entity a owl:Ontology }
   FILTER NOT EXISTS { ?entity owl:deprecated true }
   FILTER NOT EXISTS {

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

@@ -5,9 +5,13 @@
 import java.net.URL;
 import java.net.URLDecoder;
 import java.nio.charset.Charset;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.*;
 import java.util.jar.JarEntry;
 import java.util.jar.JarFile;
+import java.util.stream.Collectors;
 import org.apache.commons.io.FileUtils;
 import org.apache.jena.query.*;
 import org.apache.jena.tdb.TDBFactory;
@@ -695,20 +699,21 @@ private static Map<String, String> getDefaultQueryStrings(Set<String> rules)
     Map<String, String> queries = new HashMap<>();
     // Handle simple file path, probably accessed during testing
     if (dirURL != null && dirURL.getProtocol().equals("file")) {
-      String[] queryFilePaths = new File(dirURL.toURI()).list();
-      if (queryFilePaths == null || queryFilePaths.length == 0) {
+      final Set<Path> queryFilePaths =
+          Files.list(Paths.get(dirURL.toURI())).collect(Collectors.toSet());
+      if (queryFilePaths.size() == 0) {
         throw new IOException(
             "Cannot access report query files. There are no files in the directory.");
       }
       Set<String> defaultRuleNames = new HashSet<>();
-      for (String qPath : queryFilePaths) {
-        String ruleName = qPath.substring(qPath.lastIndexOf("/")).split(".")[0];
+      for (final Path qPath : queryFilePaths) {
+        final String ruleName = qPath.getFileName().toString().split("[.]")[0];
         defaultRuleNames.add(ruleName);
         // Only add it to the queries if the rule set contains that rule
         // If rules == null, include all rules
         if (rules == null || rules.contains(ruleName)) {
           queries.put(
-              ruleName, FileUtils.readFileToString(new File(qPath), Charset.defaultCharset()));
+              ruleName, FileUtils.readFileToString(qPath.toFile(), Charset.defaultCharset()));
         }
       }
       // Check that all the provided rule names are valid defaults
@@ -841,7 +846,7 @@ private static String getQueryResultOrNull(QuerySolution qs, String var) {
    * @return List of Violations
    * @throws IOException on issue parsing query
    */
-  private static List<Violation> getViolations(
+  public static List<Violation> getViolations(
       IOHelper ioHelper,
       Dataset dataset,
       String queryName,

robot-core/src/main/resources/report_queries/missing_label.rq

@@ -1,10 +1,10 @@
 # # Missing Label
 #
-# **Problem:** An entity does not have a label. This may cause confusion or misuse. Excludes deprecated entities.
+# **Problem:** An entity does not have a label or the label is empty. This may cause confusion or misuse. Excludes deprecated entities.
 #
 # **OBO Foundry Principle:** [12 - Naming Conventions](http://www.obofoundry.org/principles/fp-012-naming-conventions.html)
 #
-# **Solution:** Add a label.
+# **Solution:** Add a label, or make it non-empty.
 
 PREFIX owl: <http://www.w3.org/2002/07/owl#>
 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
@@ -14,7 +14,10 @@ PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
 SELECT DISTINCT ?entity ?property ?value WHERE {
   VALUES ?property { rdfs:label }
   ?entity ?any ?o .
-  FILTER NOT EXISTS { ?entity ?property ?value }
+  FILTER NOT EXISTS {
+     ?entity ?property ?value .
+     FILTER(str(?value) != "")
+  }
   FILTER NOT EXISTS { ?entity a owl:Ontology }
   FILTER NOT EXISTS { ?entity owl:deprecated true }
   FILTER NOT EXISTS {

robot-core/src/test/java/org/obolibrary/robot/ReportQueriesTest.java

@@ -0,0 +1,62 @@
+package org.obolibrary.robot;
+
+import java.io.InputStream;
+import java.util.*;
+import java.util.stream.Collectors;
+import org.apache.jena.query.Dataset;
+import org.junit.Assert;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.obolibrary.robot.checks.Violation;
+import org.semanticweb.owlapi.model.OWLOntology;
+
+@RunWith(Parameterized.class)
+public class ReportQueriesTest extends CoreTest {
+
+  @Parameterized.Parameters
+  public static Collection<Object[]> data() {
+    return Arrays.asList(
+        new Object[][] {
+          {
+            "missing_label",
+            "/1017-empty-label-input.owl",
+            new String[] {
+              "http://test.org/test#B", "http://test.org/test#C", "http://test.org/test#D"
+            }
+          }
+        });
+  }
+
+  private final String inputFile;
+  private final String queryName;
+  private final String[] failingEntities;
+
+  public ReportQueriesTest(
+      final String queryFile, final String inputFile, final String[] failingEntities) {
+    this.queryName = queryFile;
+    this.inputFile = inputFile;
+    this.failingEntities = failingEntities;
+  }
+
+  /** Test report queries */
+  @Test
+  public void testReportQuery() throws Exception {
+    final OWLOntology ontology = loadOntology(inputFile);
+    final Dataset dataset = QueryOperation.loadOntologyAsDataset(ontology, false);
+
+    final InputStream is = getClass().getResourceAsStream("/report_queries/" + queryName + ".rq");
+    assert is != null;
+    final String query =
+        new Scanner(is, "UTF-8").useDelimiter("" + Character.LINE_SEPARATOR).next();
+    final List<Violation> violations =
+        ReportOperation.getViolations(
+            new IOHelper(), dataset, queryName, query, Collections.emptyMap());
+
+    final Set<String> expected = new HashSet<>(Arrays.asList(failingEntities));
+    assert violations != null;
+    final Set<String> actual =
+        violations.stream().map(v -> v.entity.getIRI().toString()).collect(Collectors.toSet());
+    Assert.assertEquals(expected, actual);
+  }
+}

robot-core/src/test/resources/1017-empty-label-input.owl

@@ -0,0 +1,27 @@
+<rdf:RDF
+     xmlns:obo="http://purl.obolibrary.org/obo/"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:xml="http://www.w3.org/XML/1998/namespace">
+    <owl:Ontology rdf:about="http://test.org/test"/>
+
+    <owl:Class rdf:about="http://test.org/test#A"/>
+
+    <owl:Class rdf:about="http://test.org/test#B">
+      <obo:IAO_0000115>Sample definition</obo:IAO_0000115>
+    </owl:Class>
+
+    <owl:Class rdf:about="http://test.org/test#C">
+      <rdfs:label></rdfs:label>
+    </owl:Class>
+
+    <owl:Class rdf:about="http://test.org/test#D">
+      <rdfs:label xml:lang="en"></rdfs:label>
+    </owl:Class>
+
+    <owl:Class rdf:about="http://test.org/test#E">
+      <rdfs:label>E</rdfs:label>
+    </owl:Class>
+
+</rdf:RDF>