Integrated fix (manually) from upper stream.

4 files changed, 9 insertions, 6 deletions

diff --git a/src/resources/pagoda.properties b/src/resources/pagoda.properties
index aa08593..8bcbca6 100644
--- a/src/resources/pagoda.properties
+++ b/src/resources/pagoda.properties
@@ -1,8 +1,8 @@
 debug=true
 useAlwaysSimpleUpperBound=false
-#skolemUpperBound=DISABLED
+skolemUpperBound=DISABLED
+#skolemUpperBound=BEFORE_SUMMARISATION
 #skolemUpperBound=BEFORE_SUMMARISATION
-skolemUpperBound=BEFORE_SUMMARISATION
 skolemDepth=10
 
 # seems ok for -Xmx6g
diff --git a/src/uk/ac/ox/cs/pagoda/query/rollup/QueryGraph.java b/src/uk/ac/ox/cs/pagoda/query/rollup/QueryGraph.java
index 02697b8..9b4ce01 100644
--- a/src/uk/ac/ox/cs/pagoda/query/rollup/QueryGraph.java
+++ b/src/uk/ac/ox/cs/pagoda/query/rollup/QueryGraph.java
@@ -184,7 +184,9 @@ public class QueryGraph {
 
         private void rollupEdge(Term u, OWLObjectPropertyExpression op, Term v, boolean inverse) {
                 if (existVars.contains(v)) {
-                        concepts.add(u, factory.getOWLObjectSomeValuesFrom(op, factory.getOWLObjectIntersectionOf(concepts.get(v))));
+                        Set<OWLClassExpression> exps = concepts.get(v);
+                        if (exps == null) exps = new HashSet<OWLClassExpression>();
+                        concepts.add(u, factory.getOWLObjectSomeValuesFrom(op, factory.getOWLObjectIntersectionOf(exps)));
                 }
                 else {
                         OWLIndividual obj = getOWLIndividual(v);
diff --git a/test/resources/ExistentialEvaluation.xml b/test/resources/ExistentialEvaluation.xml
index c0149e9..5356364 100644
--- a/test/resources/ExistentialEvaluation.xml
+++ b/test/resources/ExistentialEvaluation.xml
@@ -12,9 +12,9 @@
         </groups>
 
         <classes>
-            <class name="uk.ac.ox.cs.pagoda.global_tests.MadeUpCases" />
+            <!--<class name="uk.ac.ox.cs.pagoda.global_tests.MadeUpCases" />-->
             <!--<class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaUOBM" />-->
-            <!--<class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaReactome" />-->
+            <class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaReactome" />
         </classes>
 
     </test>
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
index a13b7f4..9263602 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
@@ -44,7 +44,8 @@ public class TestPagodaReactome {
         Pagoda.builder()
                 .ontology(Paths.get(ontoDir, "reactome/biopax-level3-processed.owl"))
                 .data(Paths.get(ontoDir, "reactome/data/sample_10.ttl"))
-                .query(Paths.get(ontoDir, "reactome/existential_queries.sparql"))
+//                .query(Paths.get(ontoDir, "reactome/existential_queries.sparql"))
+                .query(Paths.get(ontoDir, "reactome/Queries_by_Feier-et-al.sparql"))
                 .build()
                 .run();
     }