Backup before changes in MyQueryReasoner.

1 files changed, 291 insertions, 19 deletions

diff --git a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
index 7d9b49c..274946d 100644
--- a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
+++ b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
@@ -1,46 +1,318 @@
 package uk.ac.ox.cs.pagoda.tester;
 
+import uk.ac.ox.cs.pagoda.query.AnswerTuple;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
 import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
 import uk.ac.ox.cs.pagoda.util.Properties;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
 
-// TODO clean it, or code another one
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.Scanner;
+
+@Deprecated
 public class PagodaTester {
 
+        //      public static final String onto_dir = "/media/RDFData/yzhou/";
+//      public static final String onto_dir = "/users/yzhou/ontologies/";
+//      public static final String onto_dir = "/home/scratch/yzhou/ontologies/";
+        public static final String onto_dir = "/home/alessandro/Big_files/Ontologies/";
+
+        public static final String fly = onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl";
+        public static final String fly_query = onto_dir + "fly/queries/fly.sparql";
+
+        public static final String test_tbox = onto_dir + "smallExampleFromAna/dummy.owl";
+        public static final String test_abox = onto_dir + "smallExampleFromAna/initialABox.ttl";
+        public static final String test_query = onto_dir + "smallExampleFromAna/queries.dlog";
+
+        public static final int lubm_number = 1;
+        public static final String lubm_tbox = onto_dir + "lubm/univ-bench.owl";
+        public static final String lubm_abox = onto_dir + "lubm/data/lubm" + lubm_number + ".ttl";
+        public static final String lubm_abox_copy = onto_dir + "lubm/data/lubm" + lubm_number + " (copy).ttl";
+        public static final String lubm_query = onto_dir + "lubm/queries/test.sparql";
+        public static final String lubm_query6 = onto_dir + "lubm/queries/test_q6.sparql";
+        public static final String lubm_query20 = onto_dir + "lubm/queries/test_q16.sparql";
+
+        public static final int uobm_number = 1;
+        public static final String uobm_tbox = onto_dir + "uobm/univ-bench-dl.owl";
+        public static final String uobm_abox = onto_dir + "uobm/data/uobm" + uobm_number + ".ttl";
+        public static final String uobm_query = onto_dir + "uobm/queries/test.sparql";
+        public static final String uobm_query_temp = onto_dir + "uobm/queries/temp.sparql";
+        public static final String uobm_query2 = onto_dir + "uobm/queries/standard_q2.sparql";
+        public static final String uobm_query9 = onto_dir + "uobm/queries/standard_q9.sparql";
+        public static final String uobm_query11 = onto_dir + "uobm/queries/standard_q11.sparql";
+        public static final String uobm_query12 = onto_dir + "uobm/queries/standard_q12.sparql";
+        public static final String uobm_query14 = onto_dir + "uobm/queries/standard_q14.sparql";
+        public static final String uobm_query15 = onto_dir + "uobm/queries/standard_q15.sparql";
+        public static final String uobm_query_multi = onto_dir + "uobm/queries/standard_multi.sparql";
+        public static final String uobm_generated_query1 = onto_dir + "uobm/queries/generated_q1.sparql";
+        public static final String uobm_query_group3 = onto_dir + "uobm/queries/standard_group3.sparql";
+
+        public static final String npd_tbox = onto_dir + "npd/npd-all-minus-datatype.owl";
+        // "npd/npd-all.owl";
+        // "npd-all-minus-datatype.owl";
+        public static final String npd_abox = onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl";
+        // "npd/data/npd-data-dump-processed.ttl";
+        // "npd-data-dump-minus-datatype-old.ttl";
+        public static final String npd_query = onto_dir + "npd/queries/atomic.sparql";
+
+        public static final String npd_bench_tbox = onto_dir + "npd-benchmark/npd-v2-ql_a.owl";
+                        // npd-all-minus-datatype.owl";
+        public static final String npd_bench_abox = onto_dir + "npd-benchmark/npd-v2-ql_a.ttl";
+                        // npd-data-dump-minus-datatype-old.ttl";
+        public static final String npd_bench_query = onto_dir + "npd-benchmark/queries/all.sparql";
+
+        public static final String dbpedia_tbox = onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl";
+        public static final String dbpedia_abox = onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl";
+        public static final String dbpedia_query = onto_dir + "dbpedia/queries/atomic_ground.sparql";
+        public static final String dbpedia_query274 = onto_dir + "dbpedia/atomic_q274.sparql";
+
+        public static final String dbpedia_latest_tbox = onto_dir + "dbpedia/dbpedia_2014.owl";
+        public static final String travel_tbox = onto_dir + "dbpedia/travel.owl";
+        public static final String dbpedia_tbox_simple = onto_dir + "dbpedia/dbpedia_simple.owl";
+
+        public static final String bioModels_tbox = onto_dir + "biomodels/biomodels-21.owl";
+        public static final String bioModels_abox = onto_dir + "biomodels/data_processed_1.ttl";
+        public static final String bioModels_queries = onto_dir + "biomodels/queries/queries.sparql";
+
+        public static final String chembl_tbox = onto_dir + "bio2rdf/chembl/cco-processed-noDPR-noDPD.ttl";
+        public static final String chembl_abox = onto_dir + "bio2rdf/chembl/graph sampling old/sample_100.nt";
+        public static final String chembl_queries = onto_dir + "bio2rdf/chembl/queries/problematic.sparql";
+                        //"bio2rdf/chembl/queries/atomic_one_filtered.sparql"; //
+
+        public static final String reactome_tbox = onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl";
+        public static final String reactome_abox = onto_dir + "bio2rdf/reactome/graph sampling old/sample.ttl";
+                        //data/data.ttl"; //graph sampling old/reactome_sample_10.ttl"; //
+        public static final String reactome_queries = onto_dir + "bio2rdf/reactome/queries/atomic.sparql";
+
+        public static final String uniprot_tbox = onto_dir + "bio2rdf/uniprot/core-processed.owl";
+        public static final String uniprot_abox = onto_dir + "bio2rdf/uniprot/graph sampling/sample_1.nt";
+        public static final String uniprot_queries = onto_dir + "bio2rdf/uniprot/queries/atomic_one.sparql";
+
+        public static final String atlas_tbox = onto_dir + "bio2rdf/atlas/gxaterms.owl";
+        public static final String atlas_abox = onto_dir + "bio2rdf/atlas/graph sampling/sample_1.nt";
+        public static final String atlas_queries = onto_dir + "bio2rdf/atlas/queries/atomic_one.sparql";
+        QueryReasoner pagoda;
+
+        //      private void printPredicatesWithGap() {
+//              for (String p: ((MyQueryReasoner) pagoda).getPredicatesWithGap()) {
+//                      System.out.println(p); 
+//              }
+//      }
+        Timer timer = new Timer();
+
+        public PagodaTester(QueryReasoner reasoner) {
+                pagoda = reasoner;
+        }
+
         public static void main(String... args) {
-//              Properties properties = new Properties(PagodaTester.class.
-//                              getClassLoader().getResource("uobm.properties").getPath());
-                Properties properties = new Properties();
-
-                int index = 0; 
-                if (args.length > index) properties.setOntologyPath(args[index++]);   
-                if (args.length > index && (args[index].endsWith(".ttl") || args[index].endsWith(".nt"))) properties.setDataPath(args[index++]);   
-                if (args.length > index && args[index].endsWith(".sparql")) properties.setQueryPath(args[index++]);   
-                if (args.length > index && !args[index].startsWith("-")) properties.setAnswerPath(args[index++]);   
-                if (args.length > index) properties.setToClassify(Boolean.parseBoolean(args[index++].substring(1)));   
-                if (args.length > index) properties.setToCallHermiT(Boolean.parseBoolean(args[index++].substring(1)));   
-        
+                if(args.length == 0) {
+//                      args = new String[] {test_tbox, test_abox, test_query};
+//                      args = new String[] {lubm_tbox, lubm_abox, lubm_query};
+//                      args = new String[] {uobm_tbox, uobm_abox, uobm_query};
+//                      args = new String[] {fly, "null", fly_query};
+//                      args = new String[] {dbpedia_tbox, dbpedia_abox, dbpedia_query};
+//                      args = new String[] {travel_tbox, null, dbpedia_query274};
+                        args = new String[]{fly, fly_query};
+//                      args = new String[] {npd_tbox, npd_abox, npd_query};
+//                      args = new String[] {npd_bench_tbox, npd_bench_abox, npd_bench_query};
+//                      args = new String[] {"../SemFacet/WebContent/WEB-INF/data/dbpedia.owl", "../SemFacet/WebContent/WEB-INF/data/dbpediaA.nt", null};
+//                      args = new String[] {"../core/WebContent/WEB-INF/data/fly.owl", "../core/WebContent/WEB-INF/data/fly-data.nt", null};
+//                      args = new String[] {"data/lubm/univ-bench.owl", "data/lubm/lubm1.ttl", "data/lubm/lubm.sparql", "lubm.ans"};
+//                      args = new String[] {"data/uobm/univ-bench-dl.owl", "data/uobm/uobm1.ttl", "data/uobm/uobm.sparql", "uobm.ans"};
+//                      args = new String[] {"data/fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", "data/fly/fly.sparql", "fly.ans"};
+//                      args = new String[] {bioModels_tbox, bioModels_abox, bioModels_queries};
+//                      args = new String[] {chembl_tbox, chembl_abox, chembl_queries};
+//                      args = new String[] {reactome_tbox, reactome_abox, reactome_queries};
+//                      args = new String[] {reactome_tbox, "/users/yzhou/temp/reactome_debug.ttl", onto_dir +"bio2rdf/reactome/queries/atomic_one_q65.sparql"};
+//                      args = new String[] {uniprot_tbox.replace(".owl", "-noDis.owl"), "/users/yzhou/temp/uniprot_debug/sample_1_string.nt", uniprot_queries};
+//                      args = new String[] {uniprot_tbox.replace(".owl", "-noDis.owl"), uniprot_abox, uniprot_queries};
+//                      args = new String[] {atlas_tbox, atlas_abox, atlas_queries};
+//                      args = new String[] {onto_dir + "test/unsatisfiable.owl", null, onto_dir + "test/unsatisfiable_queries.sparql"};
+//                      args = new String[] {onto_dir + "test/jair-example.owl", null, onto_dir + "test/jair-example_query.sparql"};
+//                      args[2] = args[2].replace(".sparql", "_all_pagoda.sparql");
+//                      args[2] = args[2].replace(".sparql", "_pellet.sparql");
+                }
+
+                Properties properties = new Properties("config/uobm.properties");
+
+                int index = 0;
+                if(args.length > index) properties.setOntologyPath(args[index++]);
+                if(args.length > index && (args[index].endsWith(".ttl") || args[index].endsWith(".nt")))
+                        properties.setDataPath(args[index++]);
+                if(args.length > index && args[index].endsWith(".sparql")) properties.setQueryPath(args[index++]);
+                if(args.length > index && !args[index].startsWith("-")) properties.setAnswerPath(args[index++]);
+                if(args.length > index) properties.setToClassify(Boolean.parseBoolean(args[index++].substring(1)));
+                if(args.length > index) properties.setToCallHermiT(Boolean.parseBoolean(args[index++].substring(1)));
+
                 Utility.logInfo("Ontology file: " + properties.getOntologyPath());
                 Utility.logInfo("Data files: " + properties.getDataPath());
                 Utility.logInfo("Query files: " + properties.getQueryPath());
                 Utility.logInfo("Answer file: " + properties.getAnswerPath());
-                
-                QueryReasoner pagoda = null; 
-                
+
+                QueryReasoner pagoda = null;
+
                 try {
                         Timer t = new Timer();
-                        pagoda = QueryReasoner.getInstance(properties); 
+                        pagoda = QueryReasoner.getInstance(properties);
                         if (pagoda == null) return;
-                        
+
                         Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds.");
-                        
+
                         if (properties.getQueryPath() != null)
                                 for (String queryFile: properties.getQueryPath().split(";"))
                                         pagoda.evaluate(pagoda.getQueryManager().collectQueryRecords(queryFile));
+
+                        if(properties.getShellMode())
+                                try {
+                                        evaluateConsoleQuery(pagoda);
+                                } catch(IOException e) {
+                                        e.printStackTrace();
+                                }
                 } finally {
                         if (pagoda != null) pagoda.dispose();
                 }
+
+//              Utility.closeCurrentOut();
+
+                if(properties.getShellMode()) System.exit(0);
+        }
+
+        private static void evaluateConsoleQuery(QueryReasoner pagoda) throws IOException {
+                int ending = (int) '$', symbol;
+                while(true) {
+                        Utility.logInfo("Input your query ending with $");
+                        StringBuilder queryBuilder = new StringBuilder();
+                        while((symbol = System.in.read()) != ending) {
+                                queryBuilder.append((char) symbol);
+                        }
+                        System.in.read();
+                        if(queryBuilder.length() == 0) return;
+                        pagoda.evaluate_shell(queryBuilder.toString());
+                }
+        }
+
+        void testReactomeQueries() {
+                evaluate("select ?x where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.biopax.org/release/biopax-level3.owl#DnaReference> . }");
+                evaluate("select ?y ?z where { <http://identifiers.org/ensembl/ENSG00000157557> ?y ?z . }");
+                evaluate("select ?y where { <http://identifiers.org/ensembl/ENSG00000157557> <http://www.biopax.org/release/biopax-level3.owl#name> ?y . }", true);
+
+        }
+
+        void testSemFacetQueries() {
+//              try {
+//                      BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream("query.line")));
+//                      for (String line; (line = reader.readLine()) != null && !line.isEmpty(); )
+//                              evaluate(line, true);
+//                      reader.close();
+//              } catch (FileNotFoundException e) {
+//                      e.printStackTrace();
+//              } catch (IOException e) {
+//                      e.printStackTrace();
+//              }
+                evaluate("select ?x ?z where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z }", true);
+                evaluate("select distinct ?y where { ?x ?y ?z }", true);
+                evaluate("select distinct ?z where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z }", true);
+                evaluate("select ?y ?z where { <http://www.reactome.org/biopax/46/49633#Protein3885> ?y ?z .}", true);
+        }
+
+        void testISGQueries() {
+                evaluate("select ?z where {<http://cs.ox.ac.uk/Evgeny_Kharlamov> <http://cs.ox.ac.uk/lat> ?z .}", false);
+                evaluate("select ?x where {?x <http://cs.ox.ac.uk/type> <http://cs.ox.ac.uk/person> .}", false);
+        }
+
+        void testSomeTravelQueries() {
+                evaluate("select ?y ?z where {<http://www.owl-ontologies.com/travel.owl#BlueMountains> ?y ?z. }", true);
+                evaluate("select ?x where {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.owl-ontologies.com/travel.owl#RetireeDestination>. }");
+                evaluate("select ?x where {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.owl-ontologies.com/travel.owl#BackpackersDestination>. }");
+        }
+
+        void testSomeFlyQueries() {
+                evaluate("select ?x where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00005106> . }", false);
+
+                evaluate("select DISTINCT ?z where { ?x <http://purl.obolibrary.org/obo/FBbt#develops_from> ?any . ?any <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z .  ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00067123> . } ", true);
+
+                evaluate("Select ?x where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
+                                                 + "<http://purl.obolibrary.org/obo/FBbt_00067123>. ?x "
+                                                 + "<http://purl.obolibrary.org/obo/RO_0002131> ?any . ?any "
+                                                 + "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
+                                                 + "<http://purl.obolibrary.org/obo/FBbt_00005140> . }", true);
+
+                evaluate("Select ?x where {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
+                                                 + "<http://purl.obolibrary.org/obo/FBbt_00067363> . ?x "
+                                                 + "<http://purl.obolibrary.org/obo/RO_0002131> ?any . ?any "
+                                                 + "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
+                                                 + "<http://purl.obolibrary.org/obo/FBbt_00005140> . }", true);
+
+//              evaluate("Select ?x where { "
+//                              + "?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00003660>. "
+//                              + "?x <http://purl.obolibrary.org/obo/FBbt#develops_from> ?any . "
+//                              + "?any <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00001446> . }", true);
+
+                evaluate("select DISTINCT ?z where { ?x <http://purl.obolibrary.org/obo/RO_0002110> ?any . "
+                                                 + "?any <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z . "
+                                                 + "?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00007016>  . } ", true);
+
+                evaluate("Select * where {"
+                                                 + "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100607> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00007364>. "
+                                                 + "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100607> <http://www.w3.org/2002/07/owl#sameAs> ?z }", true);
+
+                evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://www.w3.org/2002/07/owl#sameAs> ?z}", true);
+                evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://purl.obolibrary.org/obo/BFO_0000051> ?z}", true);
+
+                evaluate("select DISTINCT ?y where { ?x ?y ?z . "
+                                                 + "?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00007364>  }", true);
+
+                evaluateQueriesFromFile("/users/yzhou/Downloads/logs(1).log");
+                evaluateQueriesFromFile("/users/yzhou/Downloads/logs.log");
+
+                evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z}", true);
+                evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://xmlns.com/foaf/0.1/depicts> ?z}", true);
+
+                evaluate("select ?x ?z where { ?x <http://www.w3.org/2002/07/owl#sameAs> ?z } ", true);
+                evaluate("select ?x ?z where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z } ", true);
+        }
+
+        public void evaluateQueriesFromFile(String fileName) {
+                Scanner scanner = null;
+                try {
+                        scanner = new Scanner(new File(fileName));
+                        String line;
+                        while(scanner.hasNextLine()) {
+                                line = scanner.nextLine();
+                                if(line.startsWith("select"))
+                                        evaluate(line, true);
+                        }
+                } catch(FileNotFoundException e) {
+                        e.printStackTrace();
+                } finally {
+                        if(scanner != null)
+                                scanner.close();
+                }
+        }
+
+        private void evaluate(String query) {
+                evaluate(query, false);
+        }
+
+        private void evaluate(String query, boolean tag) {
+                timer.reset();
+                AnswerTuples tuples = pagoda.evaluate(query, tag);
+                int arity = tuples.getArity();
+                int count = 0;
+                for(AnswerTuple tuple; tuples.isValid(); tuples.moveNext()) {
+                        tuple = tuples.getTuple();
+                        for(int i = 0; i < arity; ++i)
+                                tuple.getGroundTerm(i).toString();
+//                              System.out.print(tuple.getGroundTerm(i).toString() + "\t");
+//                      System.out.println();
+                        ++count;
+                }
+                tuples.dispose();
+                Utility.logInfo("The number of answers for this SemFacet query: " + count);
+                Utility.logInfo("Total time for this SemFacet query: " + timer.duration());
         }
 
 }