Merge pull request #659 from ontodev/658-fix

Ignore TDBFactory.release Exceptions
ontodev · Apr 6, 2020 · d176933 · d176933
2 parents e292856 + 6dbf27b
commit d176933
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Showing 2 changed files with 25 additions and 12 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 - Fix filtering axioms with multiple axiom selectors [#644]
 - Fix comparator method for sorting empty strings with [`export`] in [#654]
+- Fix releasing dataset after exception when running [`report`] with `--tdb true` [#659]
 
 ## [1.6.0] - 2020-03-04
 
@@ -181,6 +182,7 @@ First official release of ROBOT!
 [`report`]: http://robot.obolibrary.org/report
 [`template`]: http://robot.obolibrary.org/template
 
+[#659]: https://github.com/ontodev/robot/issues/659
 [#657]: https://github.com/ontodev/robot/pull/657
 [#654]: https://github.com/ontodev/robot/issues/654
 [#646]: https://github.com/ontodev/robot/issues/646

diff --git a/robot-core/src/main/java/org/obolibrary/robot/ReportOperation.java b/robot-core/src/main/java/org/obolibrary/robot/ReportOperation.java
@@ -24,6 +24,7 @@
 import org.apache.commons.io.FileUtils;
 import org.apache.jena.query.*;
 import org.apache.jena.tdb.TDBFactory;
+import org.apache.jena.tdb.transaction.TDBTransactionException;
 import org.obolibrary.robot.checks.Report;
 import org.obolibrary.robot.checks.Violation;
 import org.semanticweb.owlapi.model.IRI;
@@ -338,7 +339,12 @@ public static Report getTDBReport(String inputPath, Map<String, String> options)
     } finally {
       // Close and release
       dataset.close();
-      TDBFactory.release(dataset);
+      try {
+        TDBFactory.release(dataset);
+      } catch (TDBTransactionException e) {
+        // Do nothing - already released
+      }
+
       if (!keepMappings) {
         // Maybe delete
         boolean success = IOHelper.cleanTDB(tdbDir);
@@ -371,27 +377,32 @@ public static Report getTDBReport(Dataset dataset, Map<String, String> options)
 
     String profilePath = OptionsHelper.getOption(options, "profile", null);
 
+    // The profile is a map of rule name and reporting level
+    Map<String, String> profile = getProfile(profilePath);
+    // The queries is a map of rule name and query string
+    Map<String, String> queries = getQueryStrings(profile.keySet());
+
     boolean useLabels = OptionsHelper.optionIsTrue(options, "labels");
     Map<IRI, String> labelMap = null;
     if (useLabels) {
       labelMap = new HashMap<>();
       // Run query over dataset to retrive all labels
       String query =
           "SELECT ?s ?label WHERE { ?s <http://www.w3.org/2000/01/rdf-schema#label> ?label }";
-      ResultSet labelResults = QueryOperation.execQuery(dataset, query);
-      while (labelResults.hasNext()) {
-        QuerySolution qs = labelResults.next();
-        IRI iri = IRI.create(qs.getResource("s").getURI());
-        String label = qs.getLiteral("label").getString();
-        labelMap.put(iri, label);
+      dataset.begin(ReadWrite.READ);
+      try {
+        ResultSet labelResults = QueryOperation.execQuery(dataset, query);
+        while (labelResults.hasNext()) {
+          QuerySolution qs = labelResults.next();
+          IRI iri = IRI.create(qs.getResource("s").getURI());
+          String label = qs.getLiteral("label").getString();
+          labelMap.put(iri, label);
+        }
+      } finally {
+        dataset.end();
       }
     }
 
-    // The profile is a map of rule name and reporting level
-    Map<String, String> profile = getProfile(profilePath);
-    // The queries is a map of rule name and query string
-    Map<String, String> queries = getQueryStrings(profile.keySet());
-
     // Create the report object (maybe using labels)
     Report report = new Report(labelMap);