[pagoda] Move project to Scala

This commit includes a few changes:
- The repository still uses Maven to manage dependency but it is now a
  Scala project.
- The code has been ported from OWLAPI 3.4.10 to 5.1.20
- A proof of concept program using both RSAComb and PAGOdA has been
  added.

1 files changed, 0 insertions, 259 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/util/PagodaProperties.java b/src/uk/ac/ox/cs/pagoda/util/PagodaProperties.java
deleted file mode 100644
index 2b52a89..0000000
--- a/src/uk/ac/ox/cs/pagoda/util/PagodaProperties.java
+++ /dev/null
@@ -1,259 +0,0 @@
-package uk.ac.ox.cs.pagoda.util;
-
-import org.apache.log4j.Logger;
-
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.Properties;
-
-public class PagodaProperties {
-
-    public enum SkolemUpperBoundOptions {DISABLED, BEFORE_SUMMARISATION, AFTER_SUMMARISATION}
-
-    public static final String DEFAULT_CONFIG_FILE = "_default_pagoda.properties";
-    public static final String CONFIG_FILE = "pagoda.properties";
-    public static final boolean DEFAULT_DEBUG = false;
-    private static final boolean DEFAULT_USE_ALWAYS_SIMPLE_UPPER_BOUND;
-    private static final SkolemUpperBoundOptions DEFAULT_SKOLEM_UPPER_BOUND;
-    private static final int DEFAULT_SKOLEM_DEPTH;
-    private static final boolean DEFAULT_TO_CALL_HERMIT;
-    private static final Path DEFAULT_STATISTICS_DIR;
-    private static final long DEFAULT_MAX_TRIPLES_IN_SKOLEM_STORE;
-
-    public static boolean shellModeDefault = false;
-    private static boolean debug = DEFAULT_DEBUG;
-
-    static {
-        Logger logger = Logger.getLogger("PagodaProperties");
-
-        boolean defaultUseAlwaysSimpleUpperBound = false;
-        SkolemUpperBoundOptions defaultSkolemUpperBound = SkolemUpperBoundOptions.DISABLED;
-        int defaultSkolemDepth = 1;
-        boolean toCallHermit = true;
-        Path defaultStatisticsDir = null;
-        long defaultMaxTriplesInSkolemStore = 1000000;
-
-        InputStream configStream = PagodaProperties.class.getClassLoader().getResourceAsStream(CONFIG_FILE);
-
-        if(configStream == null) {
-            logger.info("Unable to find user-defined configuration file (\"" + CONFIG_FILE + "\" in classpath)");
-            logger.info("Using default configuration");
-            configStream = PagodaProperties.class.getClassLoader().getResourceAsStream(DEFAULT_CONFIG_FILE);
-        }
-
-        try {
-            Properties config = new Properties();
-            config.load(configStream);
-            configStream.close();
-
-            if (config.containsKey("debug")) {
-                debug = Boolean.parseBoolean(config.getProperty("debug"));
-                logger.info("Debugging mode is enabled");
-
-                if (config.containsKey("statisticsDir")) {
-                    defaultStatisticsDir = Paths.get(config.getProperty("statisticsDir"));
-                    logger.info("The directory where statistics are saved is: \"" + defaultStatisticsDir + "\"");
-                }
-            }
-            if (config.containsKey("useAlwaysSimpleUpperBound")) {
-                defaultUseAlwaysSimpleUpperBound =
-                        Boolean.parseBoolean(config.getProperty("useAlwaysSimpleUpperBound"));
-                if (defaultUseAlwaysSimpleUpperBound)
-                    logger.debug("By default the simple upper bound is always used");
-            }
-            if (config.containsKey("skolemUpperBound")) {
-                defaultSkolemUpperBound = SkolemUpperBoundOptions.valueOf(config.getProperty("skolemUpperBound"));
-                switch (defaultSkolemUpperBound) {
-                    case AFTER_SUMMARISATION:
-                        logger.debug("By default the Skolem upper bound is applied AFTER Summarisation");
-                        break;
-                    case BEFORE_SUMMARISATION:
-                        logger.debug("By default the Skolem upper bound is applied BEFORE Summarisation");
-                        break;
-                    default:
-                        defaultSkolemUpperBound = SkolemUpperBoundOptions.DISABLED;
-                    case DISABLED:
-                        logger.debug("By default the Skolem upper bound is disabled");
-                }
-            }
-            if (config.containsKey("toCallHermit")) {
-                toCallHermit = Boolean.parseBoolean(config.getProperty("toCallHermit"));
-                if (toCallHermit)
-                    logger.debug("By default Hermit is enabled");
-                else
-                    logger.debug("By default Hermit is disabled");
-            }
-            if (config.containsKey("skolemDepth")) {
-                defaultSkolemDepth = Integer.parseInt(config.getProperty("skolemDepth"));
-                logger.debug("By default the max skolemisation depth is " + defaultSkolemDepth);
-            }
-            if (config.containsKey("maxTriplesInSkolemStore")) {
-                defaultMaxTriplesInSkolemStore = Long.parseLong(config.getProperty("maxTriplesInSkolemStore"));
-                logger.debug("By default the maximum number of triples in the Skolem store is " + defaultMaxTriplesInSkolemStore);
-            }
-
-        } catch (IOException e) {
-            e.printStackTrace();
-        }
-        DEFAULT_USE_ALWAYS_SIMPLE_UPPER_BOUND = defaultUseAlwaysSimpleUpperBound;
-        DEFAULT_SKOLEM_UPPER_BOUND = defaultSkolemUpperBound;
-        DEFAULT_TO_CALL_HERMIT = toCallHermit;
-        DEFAULT_STATISTICS_DIR = defaultStatisticsDir;
-        DEFAULT_SKOLEM_DEPTH = defaultSkolemDepth;
-        DEFAULT_MAX_TRIPLES_IN_SKOLEM_STORE = defaultMaxTriplesInSkolemStore;
-    }
-
-    String dataPath = null;
-    String ontologyPath;
-    String queryPath = null;
-    String answerPath = null;
-    boolean toClassify = true;
-    boolean toCallHermiT = DEFAULT_TO_CALL_HERMIT;
-
-    public int getSkolemDepth() {
-        return skolemDepth;
-    }
-
-    public void setSkolemDepth(int skolemDepth) {
-        this.skolemDepth = skolemDepth;
-    }
-
-    int skolemDepth = DEFAULT_SKOLEM_DEPTH;
-    boolean shellMode = shellModeDefault;
-    private boolean useAlwaysSimpleUpperBound = DEFAULT_USE_ALWAYS_SIMPLE_UPPER_BOUND;
-    private SkolemUpperBoundOptions skolemUpperBound = DEFAULT_SKOLEM_UPPER_BOUND;
-    private Path statisticsDir = DEFAULT_STATISTICS_DIR;
-    private long maxTriplesInSkolemStore = DEFAULT_MAX_TRIPLES_IN_SKOLEM_STORE;
-
-    public PagodaProperties(String path) {
-        java.util.Properties m_properties = new java.util.Properties();
-        InputStream inputStream = null;
-        try {
-            inputStream = new FileInputStream(path);
-            m_properties.load(inputStream);
-
-            setOntologyPath(m_properties.getProperty("ONTOLOGY"));
-            setDataPath(m_properties.getProperty("DATA"));
-            setQueryPath(m_properties.getProperty("QUERY"));
-            setAnswerPath(m_properties.getProperty("ANSWER"));
-            setToClassify(Boolean.parseBoolean(m_properties.getProperty("TO_CLASSIFY")));
-            setToCallHermiT(Boolean.parseBoolean(m_properties.getProperty("CALL_HERMIT")));
-
-        } catch (IOException e) {
-            e.printStackTrace();
-        } finally {
-            if (inputStream != null)
-                try {
-                    inputStream.close();
-                } catch (IOException e) {
-                    e.printStackTrace();
-                }
-        }
-    }
-
-    public PagodaProperties() {
-    }
-
-    public static boolean isDebuggingMode() {
-        return debug;
-    }
-
-    public static boolean getDefaultUseAlwaysSimpleUpperBound() {
-        return DEFAULT_USE_ALWAYS_SIMPLE_UPPER_BOUND;
-    }
-
-    public static Path getDefaultStatisticsDir() {
-        return DEFAULT_STATISTICS_DIR;
-    }
-
-    public static SkolemUpperBoundOptions getDefaultSkolemUpperBound() {
-        return DEFAULT_SKOLEM_UPPER_BOUND;
-    }
-
-    public String getDataPath() {
-        return dataPath;
-    }
-
-    public void setDataPath(String path) {
-        dataPath = path;
-    }
-
-    public String getOntologyPath() {
-        return ontologyPath;
-    }
-
-    public void setOntologyPath(String path) {
-        ontologyPath = path;
-    }
-
-    public String getQueryPath() {
-        return queryPath;
-    }
-
-    public void setQueryPath(String path) {
-        queryPath = path;
-    }
-
-    public String getAnswerPath() {
-        return answerPath;
-    }
-
-    public void setAnswerPath(String path) {
-        answerPath = path;
-    }
-
-    public boolean getToClassify() {
-        return toClassify;
-    }
-
-    public void setToClassify(boolean flag) {
-        toClassify = flag;
-    }
-
-    public boolean getToCallHermiT() {
-        return toCallHermiT;
-    }
-
-    public void setToCallHermiT(boolean flag) {
-        toCallHermiT = flag;
-    }
-
-    public boolean getShellMode() {
-        return shellMode;
-    }
-
-    public void setShellMode(boolean flag) {
-        shellMode = flag;
-    }
-
-    public boolean getUseAlwaysSimpleUpperBound() {
-        return useAlwaysSimpleUpperBound;
-    }
-
-    public void setUseAlwaysSimpleUpperBound(boolean flag) {
-        useAlwaysSimpleUpperBound = flag;
-    }
-
-    public SkolemUpperBoundOptions getSkolemUpperBound() {
-        return skolemUpperBound;
-    }
-
-    public void setSkolemUpperBound(SkolemUpperBoundOptions flag) {
-        skolemUpperBound = flag;
-    }
-
-    public Path getStatisticsDir() {
-        return statisticsDir;
-    }
-
-    public void setStatisticsDir(Path statisticsDir) {
-        this.statisticsDir = statisticsDir;
-    }
-
-    public long getMaxTriplesInSkolemStore() {
-        return maxTriplesInSkolemStore;
-    }
-}