Fix OBO renderer stuck with untranslatable axioms on concurrent managers

protegeproject/protege#501

OBO renderers serialise untranslatable axioms as a functional syntax
string, but the FS renderer needs an ontology to work on. Using the
manager that hosts the ontology to save to create the new ontology
causes a deadlock - the read lock has already been acquired, the
creation of a new ontology tries to engage the write lock -> deadlock.

Fix is to use an injector to get a new manager to create the ontology. A
manager provider would be a better solution but there are static methods
and interface changes involved.

contract/src/test/java/org/obolibrary/obo2owl/OBOWithUntranslatableAxiomTest.java

@@ -0,0 +1,27 @@
+package org.obolibrary.obo2owl;
+
+import org.junit.Test;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.formats.OBODocumentFormat;
+import org.semanticweb.owlapi.io.OWLOntologyDocumentTarget;
+import org.semanticweb.owlapi.io.StringDocumentTarget;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyStorageException;
+
+@SuppressWarnings({"javadoc", "null"})
+public class OBOWithUntranslatableAxiomTest {
+
+    @Test
+    public void testNoDeadlock() throws OWLOntologyStorageException, OWLOntologyCreationException {
+        OWLDataFactory df = OWLManager.getOWLDataFactory();
+        OWLOntology o = OWLManager.createConcurrentOWLOntologyManager()
+            .createOntology(IRI.create("urn:test:ontology"));
+        o.getOWLOntologyManager().addAxiom(o,
+            df.getOWLSubClassOfAxiom(df.getOWLNothing(), df.getOWLThing()));
+        OWLOntologyDocumentTarget target = new StringDocumentTarget();
+        o.saveOntology(new OBODocumentFormat(), target);
+    }
+}

oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIOwl2Obo.java

@@ -83,6 +83,7 @@
 import org.semanticweb.owlapi.model.OWLTransitiveObjectPropertyAxiom;
 import org.semanticweb.owlapi.vocab.Namespaces;
 import org.semanticweb.owlapi.vocab.OWL2Datatype;
+import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -123,7 +124,7 @@ public class OWLAPIOwl2Obo {
     /**
      * The fac.
      */
-    protected OWLDataFactory fac;
+    protected final OWLDataFactory fac;
     /**
      * The obodoc.
      */
@@ -167,7 +168,6 @@ protected final void init() {
         // legacy:
         idSpaceMap.put("http://www.obofoundry.org/ro/ro.owl#", "OBO_REL");
         untranslatableAxioms = new HashSet<>();
-        fac = manager.getOWLDataFactory();
         apToDeclare = new HashSet<>();
     }
 
@@ -178,6 +178,7 @@ protected final void init() {
      */
     public OWLAPIOwl2Obo(@Nonnull OWLOntologyManager translationManager) {
         manager = translationManager;
+        fac = manager.getOWLDataFactory();
         init();
     }
 
@@ -314,8 +315,7 @@ protected OBODoc tr() {
         axioms.sort(null);
         axioms.forEach(this::consume);
         AxiomType.skipDeclarations().flatMap(t -> getOWLOntology().getAxioms(t).stream())
-        .map(x->(OWLAxiom)x)
-            .forEach(this::consume);
+            .map(x -> (OWLAxiom) x).forEach(this::consume);
         if (!untranslatableAxioms.isEmpty() && !discardUntranslatable) {
             try {
                 String axiomString = OwlStringTools.translate(untranslatableAxioms, manager);
@@ -432,8 +432,8 @@ protected void preProcess() {
                     LOG.error("ECA did not fit expected pattern: {}", eca);
                 }
             }
-            manager.removeAxioms(getOWLOntology(), rmAxioms);
-            manager.addAxioms(getOWLOntology(), newAxioms);
+            getOWLOntology().getOWLOntologyManager().removeAxioms(getOWLOntology(), rmAxioms);
+            getOWLOntology().getOWLOntologyManager().addAxioms(getOWLOntology(), newAxioms);
         }
     }
 
@@ -1937,7 +1937,7 @@ protected void tr(@Nonnull OWLClassAssertionAxiom ax) {
             return;
         }
         String clsIRI = ((OWLClass) cls).getIRI().toString();
-        OWLAnnotationProperty labelProperty = manager.getOWLDataFactory().getRDFSLabel();
+        IRI labelPropertyIRI = OWLRDFVocabulary.RDFS_LABEL.getIRI();
         if (IRI_CLASS_SYNONYMTYPEDEF.equals(clsIRI)) {
             Frame f = getObodoc().getHeaderFrame();
             Clause c = new Clause(OboFormatTag.TAG_SYNONYMTYPEDEF.getTag());
@@ -1956,7 +1956,7 @@ protected void tr(@Nonnull OWLClassAssertionAxiom ax) {
             String scopeValue = null;
             for (OWLAnnotation ann : getAnnotationObjects(indv, getOWLOntology(), null)) {
                 String value = ((OWLLiteral) ann.getValue()).getLiteral();
-                if (ann.getProperty().equals(labelProperty)) {
+                if (ann.getProperty().getIRI().equals(labelPropertyIRI)) {
                     nameValue = '"' + value + '"';
                 } else {
                     scopeValue = value;
@@ -1983,7 +1983,7 @@ protected void tr(@Nonnull OWLClassAssertionAxiom ax) {
             String nameValue = "";
             for (OWLAnnotation ann : getAnnotationObjects(indv, getOWLOntology(), null)) {
                 String value = ((OWLLiteral) ann.getValue()).getLiteral();
-                if (ann.getProperty().equals(labelProperty)) {
+                if (ann.getProperty().getIRI().equals(labelPropertyIRI)) {
                     nameValue = '"' + value + '"';
                 }
             }

oboformat/src/main/java/org/obolibrary/obo2owl/OwlStringTools.java

@@ -1,71 +1,79 @@
 package org.obolibrary.obo2owl;
 
-import java.io.IOException;
 import java.io.StringWriter;
 import java.io.Writer;
+import java.util.HashSet;
 import java.util.Set;
+import java.util.concurrent.locks.ReadWriteLock;
+import java.util.concurrent.locks.ReentrantReadWriteLock;
 
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
 
-import org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser;
+import org.semanticweb.owlapi.formats.FunctionalSyntaxDocumentFormat;
 import org.semanticweb.owlapi.functional.renderer.OWLFunctionalSyntaxRenderer;
 import org.semanticweb.owlapi.io.OWLOntologyDocumentSource;
 import org.semanticweb.owlapi.io.OWLParserException;
 import org.semanticweb.owlapi.io.OWLRendererException;
 import org.semanticweb.owlapi.io.StringDocumentSource;
+import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLAxiom;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyFactory;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
 import org.semanticweb.owlapi.model.UnloadableImportException;
+import org.semanticweb.owlapi.utilities.Injector;
 
 /**
- * Tools to read and write a set of owl axioms to/from a string. Used to
- * preserve untranslatable axioms in an owl2obo conversion.
+ * Tools to read and write a set of owl axioms to/from a string. Used to preserve untranslatable
+ * axioms in an owl2obo conversion.
  */
 public class OwlStringTools {
 
     /**
-     * Exception indicating an un-recoverable error during the handling of axiom
-     * strings.
+     * Exception indicating an un-recoverable error during the handling of axiom strings.
      */
     public static class OwlStringException extends Exception {
 
         // generated
         private static final long serialVersionUID = 40000L;
 
         /**
-         * @param cause
-         *        cause
+         * @param cause cause
          */
         protected OwlStringException(Throwable cause) {
             super(cause);
         }
     }
 
+    private static final Injector injector = injector();
+
     /**
-     * Create a string for the given set of axioms. Return null for empty sets
-     * or if the set is null.
+     * Create a string for the given set of axioms. Return null for empty sets or if the set is
+     * null.
      * 
-     * @param axioms
-     *        axioms
-     * @param translationManager
-     *        translationManager
+     * @param axioms axioms
+     * @param translationManager translationManager
      * @return string or null
-     * @throws OwlStringException
-     *         OwlStringException
+     * @throws OwlStringException OwlStringException
      * @see #translate(String, OWLOntologyManager)
      */
     @Nullable
-    public static String translate(@Nullable Set<OWLAxiom> axioms, @Nonnull OWLOntologyManager translationManager)
-        throws OwlStringException {
+    public static String translate(@Nullable Set<OWLAxiom> axioms,
+        @Nonnull OWLOntologyManager translationManager) throws OwlStringException {
         if (axioms == null || axioms.isEmpty()) {
             return null;
         }
         try {
-            OWLOntology ontology = translationManager.createOntology();
-            translationManager.addAxioms(ontology, axioms);
+
+            OWLOntologyManager m =
+                injector.inject(injector.getImplementation(OWLOntologyManager.class));
+            Set<OWLOntologyFactory> set = new HashSet<>();
+            translationManager.getOntologyFactories().forEach(set::add);
+            m.setOntologyFactories(set);
+            OWLOntology ontology = m.createOntology();
+            ontology.getOWLOntologyManager().addAxioms(ontology, axioms);
             OWLFunctionalSyntaxRenderer r = new OWLFunctionalSyntaxRenderer();
             Writer writer = new StringWriter();
             r.render(ontology, writer);
@@ -77,39 +85,42 @@ public static String translate(@Nullable Set<OWLAxiom> axioms, @Nonnull OWLOntol
         }
     }
 
+    private static Injector injector() {
+        Injector i = new Injector();
+        i.bindToOne(() -> new ReentrantReadWriteLock(), ReadWriteLock.class);
+        return i;
+    }
+
     /**
-     * Parse the axioms from the given axiom string. Returns null for empty and
-     * null strings.
+     * Parse the axioms from the given axiom string. Returns null for empty and null strings.
      * 
-     * @param axioms
-     *        axioms
-     * @param translationManager
-     *        translationManager
+     * @param axioms axioms
+     * @param translationManager translationManager
      * @return set of axioms or null
-     * @throws OwlStringException
-     *         OwlStringException
+     * @throws OwlStringException OwlStringException
      * @see #translate(Set,OWLOntologyManager)
      */
     @Nullable
-    public static Set<OWLAxiom> translate(@Nullable String axioms, @Nonnull OWLOntologyManager translationManager)
-        throws OwlStringException {
+    public static Set<OWLAxiom> translate(@Nullable String axioms,
+        @Nonnull OWLOntologyManager translationManager) throws OwlStringException {
         if (axioms == null || axioms.isEmpty()) {
             return null;
         }
         try {
-            OWLFunctionalSyntaxOWLParser p = new OWLFunctionalSyntaxOWLParser();
-            OWLOntologyDocumentSource documentSource = new StringDocumentSource(axioms);
-            OWLOntology ontology = translationManager.createOntology();
-            p.parse(documentSource, ontology, translationManager.getOntologyLoaderConfiguration());
-            return ontology.getAxioms();
+            OWLOntologyDocumentSource documentSource = new StringDocumentSource(axioms,
+                IRI.generateDocumentIRI(), new FunctionalSyntaxDocumentFormat(), null);
+            OWLOntologyManager m =
+                injector.inject(injector.getImplementation(OWLOntologyManager.class));
+            Set<OWLOntologyFactory> set = new HashSet<>();
+            translationManager.getOntologyFactories().forEach(set::add);
+            m.setOntologyFactories(set);
+            return m.loadOntologyFromOntologyDocument(documentSource).getAxioms();
         } catch (UnloadableImportException e) {
             throw new OwlStringException(e);
         } catch (OWLOntologyCreationException e) {
             throw new OwlStringException(e);
         } catch (OWLParserException e) {
             throw new OwlStringException(e);
-        } catch (IOException e) {
-            throw new OwlStringException(e);
         }
     }
 }