Making the output machine-readable (JSON).

4 files changed, 213 insertions, 125 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java b/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java
index 8d7e0b1..183cbe1 100644
--- a/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java
+++ b/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java
@@ -1,13 +1,10 @@
 package uk.ac.ox.cs.pagoda.query;
 
-import java.util.HashMap;
-import java.util.Map;
-
+import com.google.gson.*;
 import org.semanticweb.HermiT.model.Constant;
 import org.semanticweb.HermiT.model.Individual;
 import org.semanticweb.HermiT.model.Term;
 import org.semanticweb.HermiT.model.Variable;
-
 import uk.ac.ox.cs.JRDFox.JRDFStoreException;
 import uk.ac.ox.cs.JRDFox.model.Datatype;
 import uk.ac.ox.cs.JRDFox.model.GroundTerm;
@@ -15,6 +12,10 @@ import uk.ac.ox.cs.JRDFox.model.Literal;
 import uk.ac.ox.cs.JRDFox.store.TupleIterator;
 import uk.ac.ox.cs.pagoda.util.Namespace;
 
+import java.lang.reflect.Type;
+import java.util.HashMap;
+import java.util.Map;
+
 public class AnswerTuple {
         
         public static final String SEPARATOR = "\t";
@@ -40,17 +41,21 @@ public class AnswerTuple {
                 m_tuple = new GroundTerm[arity]; 
                 for (int i = 0; i < arity; ++i) m_tuple[i] = sup.m_tuple[i]; 
         }
+
+        private AnswerTuple(String m_str) {
+                this.m_str = m_str;
+        }
         
         public int getArity() {
                 return m_tuple.length; 
         }
 
         public int hashCode() {
-//              return toString().hashCode();
-                int code = 0; 
-                for (int i = 0; i < m_tuple.length; ++i)
-                        code = code * 1997 + m_tuple[i].hashCode();
-                return code; 
+                return toString().hashCode();
+//              int code = 0;
+//              for (int i = 0; i < m_tuple.length; ++i)
+//                      code = code * 1997 + m_tuple[i].hashCode();
+//              return code;
         }
         
         public boolean equals(Object obj) {
@@ -131,5 +136,21 @@ public class AnswerTuple {
                 if (length == extendedTuple.getArity()) return extendedTuple;
                 else return new AnswerTuple(extendedTuple, length); 
         }
-        
+
+
+        public static class AnswerTupleSerializer implements JsonSerializer<AnswerTuple> {
+
+                public JsonElement serialize(AnswerTuple src, Type typeOfSrc, JsonSerializationContext context) {
+                        return new JsonPrimitive(src.toString());
+                }
+
+        }
+
+        public class AnswerTupleDeserializer implements JsonDeserializer<AnswerTuple> {
+                public AnswerTuple deserialize(JsonElement json, Type typeOfT, JsonDeserializationContext context)
+                                throws JsonParseException {
+                        return new AnswerTuple(json.getAsJsonPrimitive().getAsString());
+                }
+        }
+
 }
diff --git a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java b/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
index ce92a67..4b55046 100644
--- a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
+++ b/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
@@ -1,37 +1,9 @@
 package uk.ac.ox.cs.pagoda.query;
 
-import java.io.BufferedWriter;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStreamWriter;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.Map;
-import java.util.Set;
-
-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.DLPredicate;
-import org.semanticweb.HermiT.model.Variable;
-import org.semanticweb.owlapi.model.OWLAxiom;
-import org.semanticweb.owlapi.model.OWLClass;
-import org.semanticweb.owlapi.model.OWLClassAssertionAxiom;
-import org.semanticweb.owlapi.model.OWLDataProperty;
-import org.semanticweb.owlapi.model.OWLDataPropertyAssertionAxiom;
-import org.semanticweb.owlapi.model.OWLIndividual;
-import org.semanticweb.owlapi.model.OWLLiteral;
-import org.semanticweb.owlapi.model.OWLObjectProperty;
-import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom;
-import org.semanticweb.owlapi.model.OWLOntology;
-import org.semanticweb.owlapi.model.OWLOntologyManager;
-import org.semanticweb.owlapi.model.OWLOntologyStorageException;
-
+import com.google.gson.*;
+import com.google.gson.reflect.TypeToken;
+import org.semanticweb.HermiT.model.*;
+import org.semanticweb.owlapi.model.*;
 import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
 import uk.ac.ox.cs.pagoda.reasoner.light.RDFoxAnswerTuples;
 import uk.ac.ox.cs.pagoda.rules.GeneralProgram;
@@ -39,6 +11,10 @@ import uk.ac.ox.cs.pagoda.util.ConjunctiveQueryHelper;
 import uk.ac.ox.cs.pagoda.util.Namespace;
 import uk.ac.ox.cs.pagoda.util.Utility;
 
+import java.io.*;
+import java.lang.reflect.Type;
+import java.util.*;
+
 public class QueryRecord {
         
         public static final String botQueryText = "SELECT ?X WHERE { ?X <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Nothing> }";
@@ -47,11 +23,12 @@ public class QueryRecord {
         
         private String queryText; 
         private int queryID = -1; 
-        private String[][] answerVariables = null; 
-        private Set<AnswerTuple> soundAnswerTuples = new HashSet<AnswerTuple>(); 
+
+        private String[][] answerVariables = null;
+        private Set<AnswerTuple> soundAnswerTuples = new HashSet<AnswerTuple>();
         private Set<AnswerTuple> gapAnswerTuples = null;
         
-        private QueryManager m_manager; 
+        private QueryManager m_manager;
         
         public QueryRecord(QueryManager manager, String text, int id, int subID) {
                 m_manager =manager; 
@@ -178,7 +155,7 @@ public class QueryRecord {
 //                              str.contains("internal:def"); 
 //      }
 
-        boolean processed = false; 
+        boolean processed = false;
 
         public void markAsProcessed() {
                 processed = true; 
@@ -205,7 +182,7 @@ public class QueryRecord {
                 return queryText; 
         }
         
-        String stringQueryID = null; 
+        String stringQueryID = null;
         
         public String getQueryID() {
                 return stringQueryID; 
@@ -233,27 +210,27 @@ public class QueryRecord {
                         writer.newLine();
                         writer.write(queryText);
                         writer.newLine();
-                        StringBuilder space = new StringBuilder(); 
-                        int arity = getArity(), varSpace = 0; 
+                        StringBuilder space = new StringBuilder();
+                        int arity = getArity(), varSpace = 0;
                         for (int i = 0; i < arity; ++i)
-                                varSpace += answerVariables[0][i].length(); 
+                                varSpace += answerVariables[0][i].length();
                         for (int i = 0; i < (SEPARATOR.length() - varSpace) / (arity + 1); ++i)
-                                space.append(" "); 
+                                space.append(" ");
                         for (int i = 0; i < getArity(); ++i) {
                                 writer.write(space.toString());
                                 writer.write(answerVariables[0][i]);
                         }
                         writer.newLine();
                         writer.write(SEPARATOR);
-                        writer.newLine(); 
+                        writer.newLine();
                         for (AnswerTuple tuple: soundAnswerTuples) {
-                                writer.write(tuple.toString()); 
+                                writer.write(tuple.toString());
                                 writer.newLine();
                         }
                         if (!processed())
                                 for (AnswerTuple tuple: gapAnswerTuples) {
                                         writer.write("*");
-                                        writer.write(tuple.toString()); 
+                                        writer.write(tuple.toString());
                                         writer.newLine();
                                 }
 //                      writer.write(SEPARATOR);
@@ -261,6 +238,38 @@ public class QueryRecord {
                 }
                 
         }
+
+        public void outputAnswerStatistics() {
+
+                int answerCounter = soundAnswerTuples.size();
+                if (!processed()) answerCounter += gapAnswerTuples.size();
+
+                Utility.logInfo("The number of answer tuples: " + answerCounter);
+//              if (jsonAnswers != null) {
+//                      JSONObject jsonAnswer = new JSONObject();
+//
+//                      jsonAnswer.put("queryID", queryID);
+//                      jsonAnswer.put("queryText", queryText);
+//
+//                      JSONArray answerVars = new JSONArray();
+//                      int arity = getArity(), varSpace = 0;
+//                      for (int i = 0; i < getArity(); i++)
+//                              answerVars.add(answerVariables[0][i]);
+//                      jsonAnswer.put("answerVars", answerVars);
+//
+//                      JSONArray answerTuples = new JSONArray();
+//                      soundAnswerTuples.stream().forEach(t -> answerTuples.add(t));
+//                      jsonAnswer.put("answerTuples", answerTuples);
+//
+//                      if (!processed) {
+//                              JSONArray gapAnswerTuples = new JSONArray();
+//                              gapAnswerTuples.stream().forEach(t -> gapAnswerTuples.add(t));
+//                      }
+//                      jsonAnswer.put("gapAnswerTuples", gapAnswerTuples);
+//
+//                      jsonAnswers.put(Integer.toString(queryID), jsonAnswer);
+//              }
+        }
         
         public void outputTimes() {
                 for (Step step: Step.values()) {
@@ -290,8 +299,8 @@ public class QueryRecord {
                 return diffculty; 
         }
 
-        OWLOntology relevantOntology = null; 
-        Set<DLClause> relevantClauses = new HashSet<DLClause>(); 
+        OWLOntology relevantOntology = null;
+        Set<DLClause> relevantClauses = new HashSet<DLClause>();
 
         public void setRelevantOntology(OWLOntology knowledgebase) {
                 relevantOntology = knowledgebase; 
@@ -355,7 +364,7 @@ public class QueryRecord {
         public enum Step {LowerBound, UpperBound, ELLowerBound, 
                 Fragment, FragmentRefinement, Summarisation, Dependency, FullReasoning};  
         
-        double[] timer; 
+        double[] timer;
 
         public void addProcessingTime(Step step, double time) {
                 timer[step.ordinal()] += time; 
@@ -431,14 +440,14 @@ public class QueryRecord {
                 }
         }
 
-        int subID; 
+        int subID;
         
         public void updateSubID() {
                 ++subID; 
                 stringQueryID = String.valueOf(queryID) + "_" + subID;
         }
         
-        DLClause queryClause = null; 
+        DLClause queryClause = null;
 
         public DLClause getClause() {
                 if (queryClause != null)
@@ -557,6 +566,88 @@ public class QueryRecord {
         public boolean hasNonAnsDistinguishedVariables() {
                 return answerVariables[1].length > answerVariables[0].length;
         }
-        
 
+        public static class QueryRecordSerializer implements JsonSerializer<QueryRecord> {
+
+                public JsonElement serialize(QueryRecord src, Type typeOfSrc, JsonSerializationContext context) {
+                        Gson gson = new GsonBuilder().setPrettyPrinting().create();
+                        JsonObject object = new JsonObject();
+                        object.addProperty("queryID", src.queryID);
+                        object.addProperty("queryText", src.queryText);
+                        object.addProperty("difficulty", src.diffculty.toString());
+
+                        object.add("answerVariables", context.serialize(src.getAnswerVariables()));
+                        object.add("answers", context.serialize(src.soundAnswerTuples));
+                        object.add("gapAnswers", context.serialize(src.gapAnswerTuples));
+
+                        return object;
+                }
+        }
+
+        private QueryRecord() { }
+
+        public class QueryRecordDeserializer implements JsonDeserializer<QueryRecord> {
+
+                public QueryRecord deserialize(JsonElement json, Type typeOfT, JsonDeserializationContext context)
+                                throws JsonParseException {
+
+                        QueryRecord record = new QueryRecord();
+                        JsonObject object = json.getAsJsonObject();
+                        record.queryID = object.getAsJsonPrimitive("queryID").getAsInt();
+                        record.queryText = object.getAsJsonPrimitive("queryText").getAsString();
+
+                        JsonArray answerVariablesJson = object.getAsJsonArray("answerVariables");
+                        record.answerVariables = new String[2][];
+                        record.answerVariables[0] = new String[answerVariablesJson.size()];
+                        for(int i = 0; i < answerVariablesJson.size(); i++)
+                                record.answerVariables[0][i] = answerVariablesJson.get(i).getAsString();
+
+                        record.soundAnswerTuples = context.deserialize(object.getAsJsonObject("answers"),
+                                                                                                                   new TypeToken<Set<AnswerTuple>>() {}.getType());
+
+                        record.gapAnswerTuples = context.deserialize(object.getAsJsonObject("gapAnswers"),
+                                                                                                                 new TypeToken<Set<AnswerTuple>>() {}.getType());
+                        return null;
+                }
+        }
+
+        /*
+         * Two QueryRecords are equal iff
+         * they have the same queryText and
+         * their AnswerTuples have the same string representation
+         * */
+        @Override
+        public boolean equals(Object o) {
+                if(!o.getClass().equals(getClass())) return false;
+                QueryRecord that = (QueryRecord) o;
+
+                if(!this.queryText.equals(that.queryText)) return false;
+
+                if(soundAnswerTuples.size() != that.soundAnswerTuples.size()) return false;
+                if(gapAnswerTuples.size() != that.gapAnswerTuples.size()) return false;
+
+                ArrayList<AnswerTuple> thisSoundAnswers = new ArrayList<>(soundAnswerTuples);
+                Collections.sort(thisSoundAnswers, (AnswerTuple t1, AnswerTuple t2) -> t1.m_str.compareTo(t2.m_str));
+
+                ArrayList<AnswerTuple> thatSoundAnswers = new ArrayList<>(that.soundAnswerTuples);
+                Collections.sort(thatSoundAnswers, (AnswerTuple t1, AnswerTuple t2) -> t1.m_str.compareTo(t2.m_str));
+
+                Iterator<AnswerTuple> soundIt1 = this.soundAnswerTuples.iterator();
+                Iterator<AnswerTuple> soundIt2 = that.soundAnswerTuples.iterator();
+                while(soundIt1.hasNext() && soundIt2.hasNext())
+                        if(!soundIt1.next().m_str.equals(soundIt2.next().m_str)) return false;
+
+                ArrayList<AnswerTuple> thisGapAnswers = new ArrayList<>(gapAnswerTuples);
+                Collections.sort(thisGapAnswers, (AnswerTuple t1, AnswerTuple t2) -> t1.m_str.compareTo(t2.m_str));
+
+                ArrayList<AnswerTuple> thatGapAnswers = new ArrayList<>(that.gapAnswerTuples);
+                Collections.sort(thatGapAnswers, (AnswerTuple t1, AnswerTuple t2) -> t1.m_str.compareTo(t2.m_str));
+
+                Iterator<AnswerTuple> gapIt1 = this.gapAnswerTuples.iterator();
+                Iterator<AnswerTuple> gapIt2 = that.gapAnswerTuples.iterator();
+                while(gapIt1.hasNext() && gapIt2.hasNext())
+                        if(!gapIt1.next().m_str.equals(gapIt2.next().m_str)) return false;
+
+                return true;
+        }
 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
index f2b7251..1f08fdf 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
@@ -1,16 +1,10 @@
 package uk.ac.ox.cs.pagoda.reasoner;
 
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStreamWriter;
-import java.util.Collection;
-
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
 import org.semanticweb.owlapi.model.OWLOntology;
-
 import uk.ac.ox.cs.pagoda.owl.OWLHelper;
+import uk.ac.ox.cs.pagoda.query.AnswerTuple;
 import uk.ac.ox.cs.pagoda.query.AnswerTuples;
 import uk.ac.ox.cs.pagoda.query.QueryManager;
 import uk.ac.ox.cs.pagoda.query.QueryRecord;
@@ -18,6 +12,13 @@ import uk.ac.ox.cs.pagoda.util.Properties;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
 
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.util.Collection;
+
 public abstract class QueryReasoner {
         
 //      protected boolean forSemFacet = false;
@@ -179,28 +180,33 @@ public abstract class QueryReasoner {
   
         }
         
+//      public void evaluate(Collection<QueryRecord> queryRecords) {
+//              evaluate(queryRecords);
+//      }
+
+        BufferedWriter answerWriter = null;
+
         public void evaluate(Collection<QueryRecord> queryRecords) {
-                evaluate(queryRecords, null); 
-        }
-        
-        BufferedWriter answerWriter = null; 
-        
-        public void evaluate(Collection<QueryRecord> queryRecords, String answerFile) {
                 if (!isConsistent()) {
                         Utility.logDebug("The ontology and dataset is inconsistent."); 
                         return ; 
                 }
-                
-                if (answerWriter == null && answerFile != null) {
+
+                if(properties.getAnswerPath() != null && answerWriter == null) {
                         try {
-                                answerWriter = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(answerFile)));
-                        } catch (FileNotFoundException e) {
-                                Utility.logInfo("The answer file not found! " + answerFile);
-                                return ; 
-                        } 
+                                answerWriter = Files.newBufferedWriter(Paths.get(properties.getAnswerPath()));
+                        } catch (IOException e) {
+                                Utility.logError("The answer path is not valid!");
+                                e.printStackTrace();
+                        }
                 }
                 
-                Timer t = new Timer(); 
+                Timer t = new Timer();
+                Gson gson = new GsonBuilder()
+                                .registerTypeAdapter(AnswerTuple.class, new AnswerTuple.AnswerTupleSerializer())
+                                .registerTypeAdapter(QueryRecord.class, new QueryRecord.QueryRecordSerializer())
+                                .setPrettyPrinting()
+                                .create();
                 for (QueryRecord record: queryRecords) {
 //                      if (Integer.parseInt(record.getQueryID()) != 218) continue; 
                         Utility.logInfo("---------- start evaluating Query " + record.getQueryID() + " ----------", 
@@ -215,24 +221,23 @@ public abstract class QueryReasoner {
                                         continue; 
                                 }
                         }
-                        // FIXME: change the argument below
-                        try {
-                                record.outputAnswers(answerWriter);
-                        } catch (IOException e) {
-                                Utility.logInfo("Error in outputing answers " + answerFile);
-                        }
+                        record.outputAnswerStatistics();
                         record.outputTimes();
-                        record.dispose();
                 }
+                // TODO it can handle one call only
+                // if you call twice, you will end up with a json file with multiple roots
+                gson.toJson(queryRecords, answerWriter);
+                queryRecords.stream().forEach(record -> record.dispose());
         }
         
         public void dispose() {
-                if (answerWriter != null)
+                if (answerWriter != null) {
                         try {
                                 answerWriter.close();
                         } catch (IOException e) {
                                 e.printStackTrace();
                         }
+                }
                 Utility.cleanup();
         }  
 
diff --git a/src/uk/ac/ox/cs/pagoda/util/Utility.java b/src/uk/ac/ox/cs/pagoda/util/Utility.java
index 7138ca9..6d50ee0 100644
--- a/src/uk/ac/ox/cs/pagoda/util/Utility.java
+++ b/src/uk/ac/ox/cs/pagoda/util/Utility.java
@@ -1,32 +1,13 @@
 package uk.ac.ox.cs.pagoda.util;

 

-import java.io.BufferedReader;

-import java.io.BufferedWriter;

-import java.io.File;

-import java.io.FileInputStream;

-import java.io.FileNotFoundException;

-import java.io.FileOutputStream;

-import java.io.IOException;

-import java.io.InputStreamReader;

-import java.io.OutputStreamWriter;

-import java.io.PrintStream;

-import java.nio.file.Files;

-import java.nio.file.Paths;

-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;

-import java.util.LinkedList;

-import java.util.Scanner;

-import java.util.Set;

-import java.util.Stack;

-

 import org.apache.log4j.Logger;

 import org.semanticweb.HermiT.model.Atom;

 

-import static java.nio.file.StandardCopyOption.REPLACE_EXISTING;

+import java.io.*;

+import java.text.SimpleDateFormat;

+import java.time.LocalDateTime;

+import java.time.format.DateTimeFormatter;

+import java.util.*;

 

 public class Utility {

         

@@ -259,14 +240,4 @@ public class Utility {
                 return iri.replace(FILE_SEPARATOR, JAVA_FILE_SEPARATOR).replace(" ", "%20");

         }

 

-        public static String combinePaths(String path1, String path2) {

-                File file1 = new File(path1);

-                File file2 = new File(file1, path2);

-                return file2.getPath();

-        }

-

-        public static void copyFile(String src, String dst) throws IOException {

-                Files.copy(Paths.get(src), Paths.get(dst), REPLACE_EXISTING);

-        }

-

 }