Merge pull request #505 from geneontology/issue-502

Dump model on each save.

minerva-core/src/main/java/org/geneontology/minerva/BlazegraphMolecularModelManager.java

@@ -30,6 +30,7 @@
 import org.semanticweb.owlapi.rio.RioMemoryTripleSource;
 import org.semanticweb.owlapi.rio.RioRenderer;
 
+import javax.annotation.Nonnull;
 import java.io.*;
 import java.util.*;
 import java.util.Map.Entry;
@@ -63,7 +64,7 @@ public class BlazegraphMolecularModelManager<METADATA> extends CoreMolecularMode
      * @throws OWLOntologyCreationException
      * @throws IOException
      */
-    public BlazegraphMolecularModelManager(OWLOntology tbox, CurieHandler curieHandler, String modelIdPrefix, String pathToJournal, String pathToExportFolder, String pathToOntologyJournal, boolean downloadOntologyJournal)
+    public BlazegraphMolecularModelManager(OWLOntology tbox, CurieHandler curieHandler, String modelIdPrefix, @Nonnull String pathToJournal, String pathToExportFolder, String pathToOntologyJournal, boolean downloadOntologyJournal)
             throws OWLOntologyCreationException, IOException {
         super(tbox, pathToOntologyJournal, downloadOntologyJournal);
         if (curieHandler == null) {
@@ -198,6 +199,11 @@ public void saveModel(ModelContainer m)
                 this.writeModelToDatabase(ont, modelId);
                 // reset modified flag for abox after successful save
                 m.setAboxModified(false);
+                // dump stored model to export file
+                if (this.pathToExportFolder != null) {
+                    File folder = new File(this.pathToExportFolder);
+                    dumpStoredModel(modelId, folder);
+                }
             } finally {
                 if (changes != null) {
                     List<OWLOntologyChange> invertedChanges = ReverseChangeGenerator
@@ -210,7 +216,6 @@ public void saveModel(ModelContainer m)
         }
     }
 
-
     private void writeModelToDatabase(OWLOntology model, IRI modelId) throws RepositoryException, IOException {
         // Only one thread at a time can use the unisolated connection.
         synchronized (repo) {

minerva-core/src/test/java/org/geneontology/minerva/BlazegraphMolecularModelManagerTest.java

@@ -47,12 +47,11 @@ public void testImportDump() throws Exception {
         BlazegraphMolecularModelManager<Void> m3 = createBlazegraphMolecularModelManager();
 
         /* Import the test turtle file */
-        m3.importModelToDatabase(new File(sourceModelPath), false);
+        String modelId = m3.importModelToDatabase(new File(sourceModelPath), false);
         /* Dump back triples in the model to temporary files */
-        for (IRI modelId : m3.getStoredModelIds())
-            m3.dumpStoredModel(modelId, folder.getRoot());
-
-        compareDumpUsingJena(new File(sourceModelPath), folder.getRoot(), null);
+        m3.dumpStoredModel(IRI.create(modelId), folder.getRoot());
+        File dumpedModel = folder.getRoot().toPath().resolve(modelId.toString().replace("http://model.geneontology.org/", "") + ".ttl").toFile();
+        compareDumpUsingJena(new File(sourceModelPath), dumpedModel, null);
         m3.dispose();
     }
 
@@ -253,7 +252,7 @@ private void testModelAddRemove(BlazegraphMolecularModelManager<Void> m3, ModelC
     }
 
     /**
-     * Dump stored model and and read back the dumped ttl files; check whether the model is properly reconstructed
+     * Dump stored model and read back the dumped ttl files; check whether the model is properly reconstructed
      * from ttl files. Double-check whether the model is properly dumped using Jena.
      *
      * @param m3
@@ -285,7 +284,8 @@ private void testModelImport(BlazegraphMolecularModelManager<Void> m3, ModelCont
         }
 
         /* Compare the model constructed from dump files with the model constructed using pre-dumped files */
-        compareDumpUsingJena(new File("src/test/resources/mmg/basic-fullcycle-dump.ttl"), folder.getRoot(), modelId.toString());
+        File dumpedModel = folder.getRoot().toPath().resolve(modelId.toString().replace("http://model.geneontology.org/", "") + ".ttl").toFile();
+        compareDumpUsingJena(new File("src/test/resources/mmg/basic-fullcycle-dump.ttl"), dumpedModel, modelId.toString());
         m3.dispose();
     }
 
@@ -330,9 +330,7 @@ private void compareDumpUsingJena(File sourceFile, File targetFile, String targe
         String[] extensions = new String[]{"ttl"};
         Model targetModel = ModelFactory.createDefaultModel();
         extensions = new String[]{"ttl"};
-        List<File> files = (List<File>) FileUtils.listFiles(targetFile, extensions, true);
-        for (File file : files)
-            targetModel.read(file.getCanonicalPath());
+        targetModel.read(targetFile.getCanonicalPath());
 
         /*
          * The modelId is randomly generated for every time we create a new model and the modelId

minerva-core/src/test/java/org/geneontology/minerva/MolecularModelManagerTest.java

@@ -33,7 +33,7 @@ public class MolecularModelManagerTest {
     }
 
     private MolecularModelManager<Void> createM3(OWLOntology tbox, File journal) throws OWLOntologyCreationException, IOException {
-        return new MolecularModelManager<Void>(tbox, curieHandler, "http://testmodel.geneontology.org/", journal.getAbsolutePath(), null, go_lego_journal_file, true);
+        return new MolecularModelManager<Void>(tbox, curieHandler, "http://testmodel.geneontology.org/", journal.getAbsolutePath(), folder.getRoot().getAbsolutePath(), go_lego_journal_file, true);
     }
 
     @Test