1 files changed, 85 insertions, 0 deletions

diff --git a/test/uk/ac/ox/cs/pagoda/junit/JAIR_Scalability.java b/test/uk/ac/ox/cs/pagoda/junit/JAIR_Scalability.java
new file mode 100644
index 0000000..5bd3134
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/junit/JAIR_Scalability.java
@@ -0,0 +1,85 @@
+package uk.ac.ox.cs.pagoda.junit;
+
+import org.junit.Test;
+
+import uk.ac.ox.cs.pagoda.tester.PagodaTester;
+
+public class JAIR_Scalability {
+        
+        private static final String date = "_0123"; 
+
+        @Test
+        public void reactome() {
+                testReactome(10, false);
+        }
+        
+        @Test
+        public void chembl() {
+                testChEMBL(1, false);
+        }
+
+        @Test
+        public void uniprot() {
+                testUniProt(1, false);
+        }
+
+        public void testReactome(int percentage, boolean save) {
+                String[] args = new String[] {
+                                PagodaTester.onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl", 
+                                PagodaTester.onto_dir + "bio2rdf/reactome/graph sampling/simplifed_sample_" + percentage + ".ttl", 
+                                PagodaTester.onto_dir + "bio2rdf/reactome/queries/test.sparql"
+                                , "reactome.ans"
+                }; 
+                if (percentage == 10)
+                        args[1] = args[1].replace("simplifed", "reactome");
+                
+                PagodaTester.main(args); 
+                if (save)
+                        AllTests.copy("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/reactome/pagoda_" + percentage + "p" + date); 
+        }
+        
+        public void testChEMBL(int percentage, boolean save) {
+                String[] args = new String[] {
+                                PagodaTester.onto_dir + "bio2rdf/chembl/cco-noDPR.ttl", 
+                                PagodaTester.onto_dir + "bio2rdf/chembl/sample_" + percentage + ".nt",
+//                              PagodaTester.onto_dir + "bio2rdf/chembl/queries/atomic_ground.sparql"
+                                PagodaTester.onto_dir + "bio2rdf/chembl/queries/test.sparql"
+                                , "chembl.ans"
+                }; 
+                if (percentage == 1 || percentage == 10 || percentage == 50)
+                        args[1] = args[1].replace("chembl", "chembl/graph sampling");
+                else 
+                        if (percentage == 100)
+                                args[1] = "/home/yzhou/RDFData/ChEMBL/facts/ChEMBL.ttl"; 
+                
+                PagodaTester.main(args);
+                if (save)
+                AllTests.copy("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/chembl/pagoda_" + percentage + "p" + date); 
+        }
+        
+        public void testUniProt(int percentage, boolean save) {
+                String[] args = new String[] {
+                                PagodaTester.onto_dir + "bio2rdf/uniprot/core-sat-processed.owl", 
+                                PagodaTester.onto_dir + "bio2rdf/uniprot/sample_" + percentage + ".nt",
+//                              PagodaTester.onto_dir + "bio2rdf/uniprot/queries/atomic_ground.sparql"
+                                PagodaTester.onto_dir + "bio2rdf/uniprot/queries/test.sparql"
+                                , "uniprot.ans"
+                }; 
+                
+                if (percentage == 1 || percentage == 10 || percentage == 50)
+                        args[1] = args[1].replace("uniprot", "uniprot/graph sampling");
+                else 
+                        if (percentage == 100)
+                                args[1] = "/home/yzhou/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/data/uniprot_cleaned.nt"; 
+                
+                PagodaTester.main(args); 
+                if (save)
+                        AllTests.copy("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uniprot/pagoda_" + percentage + "p" + date); 
+        }
+        
+        public static void main(String... args) {
+                PagodaTester.ShellMode = true; 
+                new JAIR_Scalability().testUniProt(50, false);
+        }
+
+}