add time tag to the temporary output

fixed a bug about equality in the tracking datalog encoding

3 files changed, 16 insertions, 5 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java b/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java
index 5abb2fe..f40ae31 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java
@@ -76,7 +76,9 @@ public abstract class Pick4NegativeConcept implements Treatment {
                         String negativeQuery; 
                         String[] subVars; 
                         for (Atom headAtom: orderedAtoms) {
-                                negativeQuery = SparqlHelper.getSPARQLQuery(new Atom[] { MultiStageUpperProgram.getNegativeAtom(headAtom) }, 
+                                Atom negativeAtom = MultiStageUpperProgram.getNegativeAtom(headAtom); 
+                                if (negativeAtom == null) continue; 
+                                negativeQuery = SparqlHelper.getSPARQLQuery(new Atom[] { negativeAtom }, 
                                                 subVars = MultiStageUpperProgram.getVarSubset(violation.getVariables(), headAtom));
                                 negTuples.clear();
                                 Atom gapHeadAtom = addGap ? getGapAtom(headAtom) : null; 
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java b/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
index e7bd188..67d07a8 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
+++ b/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
@@ -3,10 +3,12 @@ package uk.ac.ox.cs.pagoda.tracking;
 import java.util.Collection;
 import java.util.LinkedList;
 
+import org.semanticweb.HermiT.model.AnnotatedEquality;
 import org.semanticweb.HermiT.model.Atom;
 import org.semanticweb.HermiT.model.AtomicConcept;
 import org.semanticweb.HermiT.model.AtomicRole;
 import org.semanticweb.HermiT.model.DLClause;
+import org.semanticweb.HermiT.model.Equality;
 import org.semanticweb.HermiT.model.Variable;
 import org.semanticweb.owlapi.model.OWLClass;
 import org.semanticweb.owlapi.model.OWLObjectProperty;
@@ -83,11 +85,12 @@ public class TrackingRuleEncoderWithGap extends TrackingRuleEncoder {
                 }
 
                 DLClause newClause;
+                headAtom = clause.getHeadAtom(0);
                 
-                int offset = (clause.getBodyLength() == 1 && clause.getBodyAtom(0).getDLPredicate().toString().contains("owl:Nothing")) ? 1 : 2; 
+                boolean equalityHead = headAtom.getDLPredicate() instanceof Equality || headAtom.getDLPredicate() instanceof AnnotatedEquality; 
+                int offset = (equalityHead || (clause.getBodyLength() == 1 && clause.getBodyAtom(0).getDLPredicate().toString().contains("owl:Nothing"))) ? 1 : 2;
                 
                 Atom[] newBodyAtoms = new Atom[clause.getBodyLength() + offset];
-                headAtom = clause.getHeadAtom(0);
                 newBodyAtoms[0] = Atom.create(
                                 getTrackingDLPredicate(headAtom.getDLPredicate()), 
                                 DLClauseHelper.getArguments(headAtom));
diff --git a/src/uk/ac/ox/cs/pagoda/util/Utility.java b/src/uk/ac/ox/cs/pagoda/util/Utility.java
index 120d463..6982bb1 100644
--- a/src/uk/ac/ox/cs/pagoda/util/Utility.java
+++ b/src/uk/ac/ox/cs/pagoda/util/Utility.java
@@ -11,6 +11,8 @@ import java.io.InputStreamReader;
 import java.io.OutputStreamWriter;

 import java.io.PrintStream;

 import java.text.SimpleDateFormat;

+import java.time.LocalDateTime;

+import java.time.format.DateTimeFormatter;

 import java.util.Collection;

 import java.util.Date;

 import java.util.HashSet;

@@ -30,7 +32,7 @@ public class Utility {
         public static final String FILE_SEPARATOR = System.getProperty("file.separator");

         public static final String LINE_SEPARATOR = System.getProperty("line.separator");

         

-        public static final String TempDirectory = (new File("tmp")).getAbsolutePath() + FILE_SEPARATOR;

+        public static final String TempDirectory = (new File("tmp" + DateTimeFormatter.ISO_LOCAL_DATE_TIME.format(LocalDateTime.now()))).getAbsolutePath() + FILE_SEPARATOR;

         

         public static final int TEST = -1; 

         public static final int FLY = 0;

@@ -235,7 +237,11 @@ public class Utility {
 

         public static void cleanup() {

                 File tmp = new File(TempDirectory);

-                if (tmp.exists()) tmp.delete(); 

+                if (tmp.exists()) {

+                        for (File file: tmp.listFiles())

+                                file.delete(); 

+                        tmp.delete();

+                }

         }

 

         public static String toFileIRI(String path) {