add disk HDT indexing

hdt-java-cli/bin/hdtVerify.bat

@@ -0,0 +1,5 @@
+@echo off
+
+call "%~dp0\javaenv.bat"
+
+"%JAVACMD%" -XX:NewRatio=1 -XX:SurvivorRatio=9 %JAVAOPTIONS% -classpath %JAVACP% org.rdfhdt.hdt.tools.HDTVerify %*

hdt-java-core/src/main/java/org/rdfhdt/hdt/compact/bitmap/Bitmap375Disk.java

@@ -27,6 +27,7 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
+import java.nio.file.Path;
 import java.util.Arrays;
 
 /**
@@ -51,6 +52,14 @@ public Bitmap375Disk(String location, long nbits) {
         super(location, nbits);
     }
 
+    public Bitmap375Disk(Path location) {
+        super(location);
+    }
+
+    public Bitmap375Disk(Path location, long nbits) {
+        super(location, nbits);
+    }
+
     public void dump() {
         int count = (int) numWords(this.numbits);
         for(int i=0;i<count;i++) {

hdt-java-core/src/main/java/org/rdfhdt/hdt/compact/bitmap/Bitmap64Disk.java

@@ -34,6 +34,7 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
+import java.nio.file.Path;
 
 /**
  * Version of Bitmap64 which is backed up on disk
@@ -54,7 +55,16 @@ public Bitmap64Disk(String location) {
 
     public Bitmap64Disk(String location, long nbits) {
         this.numbits = 0;
-        this.words = new LongArrayDisk(location,numWords(nbits));
+        this.words = new LongArrayDisk(location, numWords(nbits));
+    }
+
+    public Bitmap64Disk(Path location) {
+        this(location, W);
+    }
+
+    public Bitmap64Disk(Path location, long nbits) {
+        this.numbits = 0;
+        this.words = new LongArrayDisk(location, numWords(nbits));
     }
 
     /**
@@ -79,8 +89,10 @@ protected static int lastWordNumBits(long numbits) {
         return (int) ((numbits-1) % W)+1;	// +1 To have output in the range 1-64, -1 to compensate.
     }
 
-    protected final void ensureSize(long wordsRequired) {
-        words.resize(Math.max(words.getSize()*2, wordsRequired));
+    protected final void ensureSize(long wordsRequired) throws IOException {
+        if (words.length() < wordsRequired) {
+            words.resize(Math.max(words.getSize() * 2, wordsRequired));
+        }
     }
 
     public void trim(long numbits) {
@@ -90,7 +102,11 @@ public void trim(long numbits) {
     public void trimToSize() {
         int wordNum = (int) numWords(numbits);
         if(wordNum!=words.length()) {
-            words.resize(wordNum);
+            try {
+                words.resize(wordNum);
+            } catch (IOException e) {
+                throw new RuntimeException(e);
+            }
         }
     }
 
@@ -177,7 +193,11 @@ public void set(long bitIndex, boolean value) {
             throw new IndexOutOfBoundsException("bitIndex < 0: " + bitIndex);
 
         long wordIndex = wordIndex(bitIndex);
-        ensureSize(wordIndex+1);
+        try {
+            ensureSize(wordIndex+1);
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
 
         if(value) {
             words.set(wordIndex, words.get(wordIndex) | (1L << bitIndex));

hdt-java-core/src/main/java/org/rdfhdt/hdt/compact/sequence/DynamicSequence.java

@@ -56,4 +56,6 @@ public interface DynamicSequence extends Sequence, LongArray {
 	default long length() {
 		return getNumberOfElements();
 	}
+
+	void resize(long size);
 }

hdt-java-core/src/main/java/org/rdfhdt/hdt/compact/sequence/SequenceInt32.java

@@ -61,7 +61,16 @@ public SequenceInt32(int capacity) {
 		data = new int[capacity];
 		numelements = 0;
 	}
-
+
+	@Override
+	public void resize(long numentries) {
+		if (numentries > (long) Integer.MAX_VALUE) {
+			throw new IllegalArgumentException("Can't resize to size bigger than int value");
+		}
+		resizeArray((int) numentries);
+		this.numelements = (int) numentries;
+	}
+
 	private void resizeArray(int size) {
 		int [] newData = new int[size];
 		System.arraycopy(data, 0, newData, 0, Math.min(newData.length, data.length));

hdt-java-core/src/main/java/org/rdfhdt/hdt/compact/sequence/SequenceInt64.java

@@ -62,7 +62,16 @@ public SequenceInt64(long capacity) {
 		data = new long[(int)capacity];
 		numelements = 0;
 	}
-
+
+	@Override
+	public void resize(long numentries) {
+		if (numentries > (long) Integer.MAX_VALUE) {
+			throw new IllegalArgumentException("Can't resize to size bigger than int value");
+		}
+		resizeArray((int) numentries);
+		this.numelements = numentries;
+	}
+
 	private void resizeArray(int size) {
 		long [] newData = new long[size];
 		System.arraycopy(data, 0, newData, 0, Math.min(newData.length, data.length));

hdt-java-core/src/main/java/org/rdfhdt/hdt/compact/sequence/SequenceLog64.java

@@ -281,7 +281,8 @@ public void aggressiveTrimToSize() {
     public void trimToSize() {
 		resizeArray((int)numWordsFor(numbits, numentries));
 	}
-
+
+	@Override
 	public void resize(long numentries) {
 		this.numentries = numentries;
 		resizeArray((int)numWordsFor(numbits, numentries));	

hdt-java-core/src/main/java/org/rdfhdt/hdt/compact/sequence/SequenceLog64Big.java

@@ -156,9 +156,11 @@ private static void setField(LongLargeArray data, int bitsField, long index, lon
 	private void resizeArray(long size) {
 		//data = Arrays.copyOf(data, size);
 		if(size > 0) {
-			LongLargeArray a = new LongLargeArray(size);
-			LargeArrayUtils.arraycopy(data, 0, a, 0, Math.min(size, data.length()));
-			data = a;
+			if (data.length() != size) {
+				LongLargeArray a = new LongLargeArray(size);
+				LargeArrayUtils.arraycopy(data, 0, a, 0, Math.min(size, data.length()));
+				data = a;
+			}
 		}else{
 			this.numentries = 0;
 		}
@@ -295,7 +297,8 @@ public void aggressiveTrimToSize() {
     public void trimToSize() {
 		resizeArray(numWordsFor(numbits, numentries));
 	}
-
+
+	@Override
 	public void resize(long numentries) {
 		this.numentries = numentries;
 		resizeArray(numWordsFor(numbits, numentries));

hdt-java-core/src/main/java/org/rdfhdt/hdt/compact/sequence/SequenceLog64BigDisk.java

@@ -32,6 +32,7 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Iterator;
 
@@ -53,16 +54,31 @@ public SequenceLog64BigDisk(String location, int numbits) {
     }
 
     public SequenceLog64BigDisk(String location, int numbits, long capacity) {
+        this(location, numbits, capacity, false);
+    }
+
+    public SequenceLog64BigDisk(String location, int numbits, long capacity, boolean initialize) {
+        this(Path.of(location), numbits, capacity, initialize);
+    }
+    public SequenceLog64BigDisk(Path location) {
+        this(location, W);
+    }
+
+    public SequenceLog64BigDisk(Path location, int numbits) {
+        this(location, numbits, 0);
+    }
+
+    public SequenceLog64BigDisk(Path location, int numbits, long capacity) {
+        this(location, numbits, capacity, false);
+    }
+
+    public SequenceLog64BigDisk(Path location, int numbits, long capacity, boolean initialize) {
         this.numentries = 0;
         this.numbits = numbits;
         this.maxvalue = BitUtil.maxVal(numbits);
         long size = numWordsFor(numbits, capacity);
         data = new LongArrayDisk(location, Math.max(size,1));
-    }
-
-    public SequenceLog64BigDisk(String location, int numbits, long capacity, boolean initialize) {
-        this(location, numbits, capacity);
-        if(initialize) {
+        if (initialize) {
             numentries = capacity;
         }
     }
@@ -132,7 +148,7 @@ private static void setField(LongArrayDisk data, int bitsField, long index, long
         }
     }
 
-    private void resizeArray(long size) {
+    private void resizeArray(long size) throws IOException {
         data.resize(size);
     }
 
@@ -179,7 +195,11 @@ public void append(long value) {
 
         long neededSize = numWordsFor(numbits, numentries+1);
         if(data.length()<neededSize) {
-            resizeArray(data.length()*2);
+            try {
+                resizeArray(data.length()*2);
+            } catch (IOException e) {
+                throw new RuntimeException(e);
+            }
         }
         this.set(numentries, value);
         numentries++;
@@ -208,20 +228,32 @@ public void aggressiveTrimToSize() {
             long totalSize = numWordsFor(numbits, numentries);
 
             if (totalSize!=data.length()){
-                resizeArray(totalSize);
+                try {
+                    resizeArray(totalSize);
+                } catch (IOException e) {
+                    throw new RuntimeException(e);
+                }
             }
         }
 
     }
 
     @Override
     public void trimToSize() {
-        resizeArray(numWordsFor(numbits, numentries));
+        try {
+            resizeArray(numWordsFor(numbits, numentries));
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
     }
 
     public void resize(long numentries) {
         this.numentries = numentries;
-        resizeArray(numWordsFor(numbits, numentries));
+        try {
+            resizeArray(numWordsFor(numbits, numentries));
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
     }
 
     /* (non-Javadoc)

hdt-java-core/src/main/java/org/rdfhdt/hdt/hdt/HDTFactory.java

@@ -33,6 +33,8 @@
 import org.rdfhdt.hdt.options.HDTOptions;
 import org.rdfhdt.hdt.options.HDTSpecification;
 
+import java.io.IOException;
+
 /**
  * Factory that creates HDT objects
  * 
@@ -45,7 +47,7 @@ private HDTFactory() {}
 	 * 
 	 * @return HDT
 	 */
-	public static HDT createHDT() {
+	public static HDT createHDT() throws IOException {
 		return new HDTImpl(new HDTSpecification());
 	}
 
@@ -54,7 +56,7 @@ public static HDT createHDT() {
 	 * 
 	 * @return HDT
 	 */
-	public static HDT createHDT(HDTOptions spec) {
+	public static HDT createHDT(HDTOptions spec) throws IOException {
 		return new HDTImpl(spec);
 	}
 

hdt-java-core/src/main/java/org/rdfhdt/hdt/hdt/HDTManagerImpl.java

@@ -93,7 +93,7 @@ public HDT doLoadHDT(InputStream hdtFile, ProgressListener listener, HDTOptions
 	public HDT doLoadIndexedHDT(String hdtFileName, ProgressListener listener, HDTOptions spec) throws IOException {
 		HDTPrivate hdt = new HDTImpl(spec);
 		hdt.loadFromHDT(hdtFileName, listener);
-		hdt.loadOrCreateIndex(listener);
+		hdt.loadOrCreateIndex(listener, spec);
 		return hdt;
 	}
 
@@ -102,21 +102,21 @@ public HDT doLoadIndexedHDT(String hdtFileName, ProgressListener listener, HDTOp
 	public HDT doMapIndexedHDT(String hdtFileName, ProgressListener listener, HDTOptions spec) throws IOException {
 		HDTPrivate hdt = new HDTImpl(spec);
 		hdt.mapFromHDT(new File(hdtFileName), 0, listener);
-		hdt.loadOrCreateIndex(listener);
+		hdt.loadOrCreateIndex(listener, spec);
 		return hdt;
 	}
 
 	@Override
 	public HDT doLoadIndexedHDT(InputStream hdtFile, ProgressListener listener, HDTOptions spec) throws IOException {
 		HDTPrivate hdt = new HDTImpl(spec);
 		hdt.loadFromHDT(hdtFile, listener);
-		hdt.loadOrCreateIndex(listener);
+		hdt.loadOrCreateIndex(listener, spec);
 		return hdt;
 	}
 
 	@Override
 	public HDT doIndexedHDT(HDT hdt, ProgressListener listener) throws IOException {
-		((HDTPrivate) hdt).loadOrCreateIndex(listener);
+		((HDTPrivate)hdt).loadOrCreateIndex(listener, new HDTSpecification());
 		return hdt;
 	}
 

hdt-java-core/src/main/java/org/rdfhdt/hdt/hdt/HDTPrivate.java

@@ -5,6 +5,7 @@
 import java.io.InputStream;
 
 import org.rdfhdt.hdt.listener.ProgressListener;
+import org.rdfhdt.hdt.options.HDTOptions;
 
 /**
  * HDT Operations that are using internally from the implementation.
@@ -36,7 +37,7 @@ public interface HDTPrivate extends HDT {
 	 * 
 	 * @param listener A listener to be notified of the progress.
 	 */
-	void loadOrCreateIndex(ProgressListener listener) throws IOException;
+	void loadOrCreateIndex(ProgressListener listener, HDTOptions disk) throws IOException;
 
 	void populateHeaderStructure(String baseUri);
 }

hdt-java-core/src/main/java/org/rdfhdt/hdt/hdt/impl/HDTImpl.java

@@ -111,7 +111,7 @@ public class HDTImpl extends HDTBase<HeaderPrivate, DictionaryPrivate, TriplesPr
 	private boolean isMapped;
 	private boolean isClosed=false;
 
-	public HDTImpl(HDTOptions spec) {
+	public HDTImpl(HDTOptions spec) throws IOException {
 		super(spec);
 
 		header = HeaderFactory.createHeader(this.spec);
@@ -369,7 +369,7 @@ public void loadFromModifiableHDT(TempHDT modHdt, ProgressListener listener) {
 	 * @see hdt.hdt.HDT#generateIndex(hdt.listener.ProgressListener)
 	 */
 	@Override
-	public void loadOrCreateIndex(ProgressListener listener) throws IOException {
+	public void loadOrCreateIndex(ProgressListener listener, HDTOptions spec) throws IOException {
 		if(triples.getNumberOfElements()==0) {
 			// We need no index.
 			return;
@@ -402,7 +402,7 @@ public void loadOrCreateIndex(ProgressListener listener) throws IOException {
 
 			// GENERATE
 			StopWatch st = new StopWatch();
-			triples.generateIndex(listener);
+			triples.generateIndex(listener, spec);
 
 			// SAVE
 			if(this.hdtFileName!=null) {

hdt-java-core/src/main/java/org/rdfhdt/hdt/hdt/impl/WriteHDTImpl.java

@@ -67,7 +67,7 @@ public void mapFromHDT(File f, long offset, ProgressListener listener) {
 	}
 
 	@Override
-	public void loadOrCreateIndex(ProgressListener listener) {
+	public void loadOrCreateIndex(ProgressListener listener, HDTOptions disk) {
 		throw new NotImplementedException();
 	}