Remove use of ModelWriterHelper to eliminate unneccessary Tbox axioms…

… in model graphs. Related to #185.
geneontology · May 13, 2018 · 843e5d6 · 843e5d6
1 parent 508663f
commit 843e5d6
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Showing 4 changed files with 9 additions and 291 deletions.
diff --git a/minerva-server/src/main/java/org/geneontology/minerva/ModelReaderHelper.java b/minerva-server/src/main/java/org/geneontology/minerva/ModelReaderHelper.java
@@ -19,9 +19,16 @@
 import org.semanticweb.owlapi.model.RemoveAxiom;
 import org.semanticweb.owlapi.model.RemoveOntologyAnnotation;
 
+/**
+ * The axioms tagged with the lego:derived property are removed upon reading in the model.
+ * This system is not really used anymore, but this class should still be active while
+ * some models still contain these annotated axioms.
+ */
 public class ModelReaderHelper implements PostLoadOntologyFilter {
 
 	public static final ModelReaderHelper INSTANCE = new ModelReaderHelper();
+	public static final IRI DERIVED_IRI = IRI.create("http://geneontology.org/lego/derived");
+	public static final String DERIVED_VALUE = "true";
 
 	private ModelReaderHelper() {
 		// no public constructor, use instance
@@ -31,7 +38,7 @@ private ModelReaderHelper() {
 	public OWLOntology filter(OWLOntology model) {
 		final OWLOntologyManager m = model.getOWLOntologyManager();
 		final OWLDataFactory f = m.getOWLDataFactory();
-		final OWLAnnotationProperty derivedProperty = f.getOWLAnnotationProperty(ModelWriterHelper.DERIVED_IRI);
+		final OWLAnnotationProperty derivedProperty = f.getOWLAnnotationProperty(DERIVED_IRI);
 
 		List<OWLOntologyChange> allChanges = new ArrayList<OWLOntologyChange>();
 
@@ -81,7 +88,7 @@ public String visit(OWLLiteral literal) {
 							return literal.getLiteral();
 						}
 					});
-					if (value != null && ModelWriterHelper.DERIVED_VALUE.equalsIgnoreCase(value)) {
+					if (value != null && DERIVED_VALUE.equalsIgnoreCase(value)) {
 						return true;
 					}
 				}

diff --git a/minerva-server/src/main/java/org/geneontology/minerva/ModelWriterHelper.java b/minerva-server/src/main/java/org/geneontology/minerva/ModelWriterHelper.java
diff --git a/minerva-server/src/main/java/org/geneontology/minerva/server/StartUpTool.java b/minerva-server/src/main/java/org/geneontology/minerva/server/StartUpTool.java
@@ -12,7 +12,6 @@
 import org.eclipse.jetty.servlet.ServletContextHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
 import org.geneontology.minerva.ModelReaderHelper;
-import org.geneontology.minerva.ModelWriterHelper;
 import org.geneontology.minerva.UndoAwareMolecularModelManager;
 import org.geneontology.minerva.curie.CurieHandler;
 import org.geneontology.minerva.curie.CurieMappings;
@@ -331,7 +330,6 @@ public static Server startUp(final MinervaStartUpConfig conf)
 				conf.curieHandler, conf.modelIdPrefix, conf.journalFile, conf.exportFolder);
 		// set pre and post file handlers
 		models.addPostLoadOntologyFilter(ModelReaderHelper.INSTANCE);
-		models.addPreFileSaveHandler(new ModelWriterHelper(conf.curieHandler, conf.lookupService));
 
 		// start server
 		Server server = startUp(models, conf);

diff --git a/minerva-server/src/test/java/org/geneontology/minerva/ModelDecorationTest.java b/minerva-server/src/test/java/org/geneontology/minerva/ModelDecorationTest.java