8 files changed, 252 insertions, 2 deletions

diff --git a/src/resources/fly.properties b/src/resources/fly.properties
new file mode 100644
index 0000000..88c85c3
--- /dev/null
+++ b/src/resources/fly.properties
@@ -0,0 +1,19 @@
+#ONTOLOGY variable points to the file that stores ontology of interest
+ONTOLOGY=data/fly/fly_anatomy_XP_with_GJ_FC_individuals.owl
+#ONTOLOGY=data/fly/fbbt_vfb_ind_pr_nr.owl
+
+#QUERY variable points to the file that stores all queries
+QUERY=data/fly/fly.sparql
+#QUERY=data/fly/test.sparql
+
+#ANSWER variable points to the file to output all answers 
+#ANSWER=data/fly/fly.ans
+
+#TO_CLASSIFY switch for the optimisation to specify if the ontology is first classified by HermiT
+TO_CLASSIFY=false
+
+#CALL_HERMIT variable to specify if HermiT is called or not
+CALL_HERMIT=true
+
+#SHELL_MODE to enable query execution from console input
+SHELL_MODE=false
\ No newline at end of file
diff --git a/src/resources/log4j.properties b/src/resources/log4j.properties
new file mode 100644
index 0000000..3bfd32e
--- /dev/null
+++ b/src/resources/log4j.properties
@@ -0,0 +1,25 @@
+log = .
+log4j.rootLogger=DEBUG, CONSOLE, FILE_LAST, FILE
+
+log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
+log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
+log4j.appender.CONSOLE.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %c - %m%n
+log4j.appender.CONSOLE.Target=System.out
+log4j.appender.CONSOLE.Threshold=INFO
+
+log4j.appender.FILE_LAST=org.apache.log4j.RollingFileAppender
+log4j.appender.FILE_LAST.File=${log}/pagoda_last_only.log
+log4j.appender.FILE_LAST.MaxFileSize=10MB
+log4j.appender.FILE_LAST.MaxBackupIndex=3
+log4j.appender.FILE_LAST.layout=org.apache.log4j.PatternLayout
+log4j.appender.FILE_LAST.layout.conversionPattern=[%5p] %d{yyyy-MM-dd HH:mm:ss} %c - %m%n
+log4j.appender.FILE_LAST.append=false
+log4j.appender.FILE_LAST.Threshold=DEBUG
+
+log4j.appender.FILE=org.apache.log4j.RollingFileAppender
+log4j.appender.FILE.File=${log}/pagoda.log
+log4j.appender.FILE.MaxFileSize=10MB
+log4j.appender.FILE.MaxBackupIndex=3
+log4j.appender.FILE.layout=org.apache.log4j.PatternLayout
+log4j.appender.FILE.layout.conversionPattern=[%5p] %d{yyyy-MM-dd HH:mm:ss} %c - %m%n
+log4j.appender.FILE.Threshold=DEBUG
\ No newline at end of file
diff --git a/src/resources/lubm.properties b/src/resources/lubm.properties
new file mode 100644
index 0000000..73ed470
--- /dev/null
+++ b/src/resources/lubm.properties
@@ -0,0 +1,20 @@
+#DATA variable points to the file that stores data
+DATA=data/lubm/lubm1.ttl
+
+#ONTOLOGY variable points to the file that stores ontology of interest
+ONTOLOGY=data/lubm/univ-bench.owl
+
+#QUERY variable points to the file that stores all queries
+QUERY=data/lubm/lubm.sparql
+
+#ANSWER variable points to the file to output all answers 
+#ANSWER=data/lubm/lubm.ans
+
+#TO_CLASSIFY switch for the optimisation to specify if the ontology is first classified by HermiT
+TO_CLASSIFY=true
+
+#CALL_HERMIT variable to specify if HermiT is called or not
+CALL_HERMIT=true
+
+#SHELL_MODE to enable query execution from console input
+SHELL_MODE=false
\ No newline at end of file
diff --git a/src/resources/uobm.properties b/src/resources/uobm.properties
new file mode 100644
index 0000000..acbe78e
--- /dev/null
+++ b/src/resources/uobm.properties
@@ -0,0 +1,20 @@
+#DATA variable points to the file that stores data
+DATA=data/uobm/uobm1.ttl
+
+#ONTOLOGY variable points to the file that stores ontology of interest
+ONTOLOGY=data/uobm/univ-bench-dl.owl
+
+#QUERY variable points to the file that stores all queries
+QUERY=data/uobm/uobm.sparql
+
+#ANSWER variable points to the file to output all answers 
+#ANSWER=data/uobm/uobm.ans
+
+#TO_CLASSIFY switch for the optimisation to specify if the ontology is first classified by HermiT
+TO_CLASSIFY=true
+
+#CALL_HERMIT variable to specify if HermiT is called or not
+CALL_HERMIT=true
+
+#SHELL_MODE to enable query execution from console input
+SHELL_MODE=false
\ No newline at end of file
diff --git a/src/uk/ac/ox/cs/pagoda/Pagoda.java b/src/uk/ac/ox/cs/pagoda/Pagoda.java
new file mode 100644
index 0000000..3263c03
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/Pagoda.java
@@ -0,0 +1,164 @@
+package uk.ac.ox.cs.pagoda;
+
+import org.apache.commons.cli.*;
+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;
+
+import java.nio.file.Path;
+
+/**
+ * The main class
+ */
+public class Pagoda implements Runnable {
+
+    private static final String OPTION_ONTOLOGY = "o";
+    private static final String OPTION_DATA = "d";
+    private static final String OPTION_QUERY = "q";
+    private static final String OPTION_ANSWER = "a";
+    private static final String OPTION_CLASSIFY = "c";
+    private static final String OPTION_HERMIT = "f";
+
+    public static void main(String... args) {
+
+        Options options = new Options();
+        options.addOption(Option.builder(OPTION_ONTOLOGY).argName(OPTION_ONTOLOGY).required().hasArg().desc("The ontology path").build());
+        options.addOption(Option.builder(OPTION_DATA).argName(OPTION_DATA).hasArg().desc("The data path").build());
+        options.addOption(Option.builder(OPTION_QUERY).argName(OPTION_QUERY).required().hasArg().desc("The query path").build());
+        options.addOption(Option.builder(OPTION_ANSWER).argName(OPTION_ANSWER).hasArg().desc("The answer path").build());
+        options.addOption(Option.builder(OPTION_CLASSIFY).argName(OPTION_CLASSIFY).desc("Tell whether to classify").type(Boolean.class).build());
+        options.addOption(Option.builder(OPTION_HERMIT).argName(OPTION_HERMIT).desc("Tell whether to call Hermit").type(Boolean.class).build());
+
+        CommandLineParser parser = new DefaultParser();
+        try {
+            CommandLine cmd = parser.parse( options, args );
+            PagodaBuilder pagodaBuilder = Pagoda.builder()
+                                                .ontology(cmd.getOptionValue(OPTION_ONTOLOGY))
+                                                .query(cmd.getOptionValue(OPTION_QUERY));
+            if(cmd.hasOption(OPTION_DATA)) pagodaBuilder.data(cmd.getOptionValue(OPTION_DATA));
+            if(cmd.hasOption(OPTION_ANSWER))  pagodaBuilder.answer(cmd.getOptionValue(OPTION_ANSWER));
+            if(cmd.hasOption(OPTION_CLASSIFY)) pagodaBuilder.classify(Boolean.parseBoolean(cmd.getOptionValue(OPTION_CLASSIFY)));
+            if(cmd.hasOption(OPTION_HERMIT)) pagodaBuilder.hermit(Boolean.parseBoolean(cmd.getOptionValue(OPTION_HERMIT)));
+
+            pagodaBuilder.build().run();
+        }
+        catch( ParseException exp ) {
+            HelpFormatter formatter = new HelpFormatter();
+            formatter.printHelp("PAGOdA", options);
+            Utility.logError("Parsing failed.  Reason: " + exp.getMessage());
+            System.exit(0);
+        }
+    }
+
+    /**
+     * Do not use it
+     * */
+    private Pagoda() {
+        properties = new Properties();
+    }
+
+    private final Properties properties;
+
+    /**
+     * Get a builder.
+     * */
+    public static PagodaBuilder builder() {
+        return new PagodaBuilder();
+    }
+
+    @Override
+    public void run() {
+        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;
+
+        try {
+            Timer t = new Timer();
+            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));
+        } finally {
+            if (pagoda != null) pagoda.dispose();
+        }
+    }
+
+    /**
+     * Allows to set the parameters before creating a Pagoda instance.
+     * */
+    public static class PagodaBuilder {
+
+        private Pagoda instance;
+
+        private PagodaBuilder() {
+            instance = new Pagoda();
+        }
+
+        public PagodaBuilder ontology(String ontologyPath) {
+            if(instance == null) return null;
+            instance.properties.setOntologyPath(ontologyPath);
+            return this;
+        }
+
+        public PagodaBuilder ontology(Path ontologyPath) {
+            return ontology(ontologyPath.toString());
+        }
+
+        public PagodaBuilder data(String dataPath) {
+            if(instance == null) return null;
+            instance.properties.setDataPath(dataPath);
+            return this;
+        }
+
+        public PagodaBuilder data(Path dataPath) {
+            return data(dataPath.toString());
+        }
+
+        public PagodaBuilder query(String queryPath) {
+            if(instance == null) return null;
+            instance.properties.setQueryPath(queryPath);
+            return this;
+        }
+
+        public PagodaBuilder query(Path queryPath) {
+            return query(queryPath.toString());
+        }
+
+        public PagodaBuilder answer(String answerPath) {
+            if(instance == null) return null;
+            instance.properties.setAnswerPath(answerPath);
+            return this;
+        }
+
+        public PagodaBuilder answer(Path answerPath) {
+            return answer(answerPath.toString());
+        }
+
+        public PagodaBuilder classify(Boolean toClassify) {
+            if(instance == null) return null;
+            instance.properties.setToClassify(toClassify);
+            return this;
+        }
+
+        public PagodaBuilder hermit(Boolean callHermit) {
+            if(instance == null) return null;
+            instance.properties.setToCallHermiT(callHermit);
+            return this;
+        }
+
+        public Pagoda build() {
+            Pagoda builtInstance = instance;
+            instance = null;
+            return builtInstance;
+        }
+
+    }
+}
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
index 97bab50..dfe0c5f 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
@@ -17,6 +17,7 @@ import java.nio.file.Files;
 import java.nio.file.Paths;
 import java.util.Collection;
 
+// TODO clean APIs
 public abstract class QueryReasoner {
         
 //      protected boolean forSemFacet = false;
diff --git a/src/uk/ac/ox/cs/pagoda/rules/approximators/SkolemTermsManager.java b/src/uk/ac/ox/cs/pagoda/rules/approximators/SkolemTermsManager.java
index 0413e65..0c12a27 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/approximators/SkolemTermsManager.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/approximators/SkolemTermsManager.java
@@ -22,6 +22,7 @@ public class SkolemTermsManager {
     private int dependenciesCounter = 0;
 
     // replace with hashcode. in case of collision you get only a different upper bound model.
+    // or, better, use perfect hashing (i.e. devise an ad-hoc hash function without collisions)
     private Map<Tuple<Individual>, Integer> mapDependencyToId = new HashMap<>();
 
     /**
diff --git a/src/uk/ac/ox/cs/pagoda/util/Properties.java b/src/uk/ac/ox/cs/pagoda/util/Properties.java
index b687b53..9ebebb6 100644
--- a/src/uk/ac/ox/cs/pagoda/util/Properties.java
+++ b/src/uk/ac/ox/cs/pagoda/util/Properties.java
@@ -30,9 +30,9 @@ public class Properties {
         public boolean getToCallHermiT() { return toCallHermiT; }
         public void setToCallHermiT(boolean flag) { toCallHermiT = flag; }
         
-        public static boolean ShellModeDefault = false;
+        public static boolean shellModeDefault = false;
         
-        boolean shellMode = ShellModeDefault; 
+        boolean shellMode = shellModeDefault;
         public boolean getShellMode() { return shellMode; }
         public void setShellMode(boolean flag) { shellMode = flag; }