Summarisation before Skolemisation. Added Reactome testcase.

5 files changed, 34 insertions, 6 deletions

diff --git a/test/resources/LightTests.xml b/test/resources/LightTests.xml
index 69cb572..544833b 100644
--- a/test/resources/LightTests.xml
+++ b/test/resources/LightTests.xml
@@ -7,13 +7,15 @@
             <run>
                 <include name="light"/>
                 <!--<include name="justExecute"/>-->
+                <exclude name="nonOriginal"/>
             </run>
         </groups>
         <classes>
-            <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.TestPagodaUOBM"/>-->
             <!--<class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaLUBM"/>-->
             <!--Fly does not terminate: query-5 looks really hard-->
-            <!--<class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaFLY"/>-->
+            <class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaFLY"/>
         </classes>
     </test>
 </suite>
\ No newline at end of file
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
index caaad35..31d2eac 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
@@ -52,7 +52,7 @@ public class TestPagodaFLY {
         CheckAnswers.assertSameAnswers(answers, givenAnswers);
     }
 
-    @Test(groups = {"light", "justExecute"})
+    @Test(groups = {"light", "justExecute", "nonOriginal"})
     public void justExecute_newQueries() throws IOException {
         String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
 
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
new file mode 100644
index 0000000..5c05b94
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
@@ -0,0 +1,26 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.pagoda.Pagoda;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+import java.io.IOException;
+import java.nio.file.Paths;
+
+public class TestPagodaReactome {
+
+    @Test(groups = {"light"})
+    public void justExecute() throws IOException {
+        String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+
+        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/test.sparql"))
+              .classify(true)
+              .hermit(true)
+              .build()
+              .run();
+    }
+
+}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java
index d0f0b9a..9fb6cbe 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java
@@ -87,7 +87,8 @@ public class TestPagodaUOBM {
                           .query(Paths.get(ontoDir, "uobm/queries/uobm_sygenia_all-blanks.sparql"))
                           .classify(true)
                           .hermit(true)
-                          .build().run();
+                          .build()
+                          .run();
         }
 
         @Test(groups = {"justExecute"})
diff --git a/test/uk/ac/ox/cs/pagoda/query/CheckAnswers.java b/test/uk/ac/ox/cs/pagoda/query/CheckAnswers.java
index 97e3a57..71730c3 100644
--- a/test/uk/ac/ox/cs/pagoda/query/CheckAnswers.java
+++ b/test/uk/ac/ox/cs/pagoda/query/CheckAnswers.java
@@ -25,8 +25,7 @@ public class CheckAnswers {
 
         Gson gson = QueryRecord.GsonCreator.getInstance();
 
-        Type cqType = new TypeToken<Set<QueryRecord>>() {
-        }.getType();
+        Type cqType = new TypeToken<Set<QueryRecord>>() {}.getType();
         Set<QueryRecord> computedAnswersRecords = gson.fromJson(computedReader, cqType);
         Set<QueryRecord> givenAnswersRecords = gson.fromJson(givenReader, cqType);